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Ain Nazir NU, Shaukat MH, Luo R, Abbas SR. Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS. PLoS One 2023; 18:e0287465. [PMID: 37967076 PMCID: PMC10651033 DOI: 10.1371/journal.pone.0287465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 06/06/2023] [Indexed: 11/17/2023] Open
Abstract
According to WHO 2019, Hepatocellular carcinoma (HCC) is the fourth highest cause of cancer death worldwide. More precise diagnostic models are needed to enhance early HCC and cirrhosis quick diagnosis, treatment, and survival. Breath biomarkers known as volatile organic compounds (VOCs) in exhaled air can be used to make rapid, precise, and painless diagnoses. Gas chromatography and mass spectrometry (GCMS) are utilized to diagnose HCC and cirrhosis VOCs. In this investigation, metabolically generated VOCs in breath samples (n = 35) of HCC, (n = 35) cirrhotic, and (n = 30) controls were detected via GCMS and SPME. Moreover, this study also aims to identify diagnostic VOCs for distinction among HCC and cirrhosis liver conditions, which are most closely related, and cause misleading during diagnosis. However, using gas chromatography-mass spectrometry (GC-MS) to quantify volatile organic compounds (VOCs) is time-consuming and error-prone since it requires an expert. To verify GC-MS data analysis, we present an in-house R-based array of machine learning models that applies deep learning pattern recognition to automatically discover VOCs from raw data, without human intervention. All-machine learning diagnostic model offers 80% sensitivity, 90% specificity, and 95% accuracy, with an AUC of 0.9586. Our results demonstrated the validity and utility of GCMS-SMPE in combination with innovative ML models for early detection of HCC and cirrhosis-specific VOCs considered as potential diagnostic breath biomarkers and showed differentiation among HCC and cirrhosis. With these useful insights, we can build handheld e-nose sensors to detect HCC and cirrhosis through breath analysis and this unique approach can help in diagnosis by reducing integration time and costs without compromising accuracy or consistency.
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Affiliation(s)
- Noor ul Ain Nazir
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Electrical Engineering and Computer Science, The Henry Samueli School of Engineering, University of California, Irvine, Irvine, CA, United States of America
| | | | - Ray Luo
- Departments of Chemical and Biomolecular Engineering, Materials Science and Engineering and Biomedical Engineering, the University of California, Irvine, Irvine, CA, United States of America
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America
| | - Shah Rukh Abbas
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
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Autoantibodies to PAX5, PTCH1, and GNA11 as Serological Biomarkers in the Detection of Hepatocellular Carcinoma in Hispanic Americans. Int J Mol Sci 2023; 24:ijms24043721. [PMID: 36835134 PMCID: PMC9959316 DOI: 10.3390/ijms24043721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Studies have demonstrated that autoantibodies to tumor-associated antigens (TAAs) may be used as efficient biomarkers with low-cost and highly sensitive characteristics. In this study, an enzyme-linked immunosorbent assay (ELISA) was conducted to analyze autoantibodies to paired box protein Pax-5 (PAX5), protein patched homolog 1 (PTCH1), and guanine nucleotide-binding protein subunit alpha-11 (GNA11) in sera from Hispanic Americans including hepatocellular carcinoma (HCC) patients, patients with liver cirrhosis (LC), patients with chronic hepatitis (CH), as well as normal controls. Meanwhile, 33 serial sera from eight HCC patients before and after diagnosis were used to explore the potential of these three autoantibodies as early biomarkers. In addition, an independent non-Hispanic cohort was used to evaluate the specificity of these three autoantibodies. In the Hispanic cohort, at the 95.0% specificity for healthy controls, 52.0%, 44.0%, and 44.0% of HCC patients showed significantly elevated levels of autoantibodies to PAX5, PTCH1, and GNA11, respectively. Among patients with LC, the frequencies for autoantibodies to PAX5, PTCH1, and GNA11 were 32.1%, 35.7%, and 25.0%, respectively. The area under the ROC curves (AUCs) of autoantibodies to PAX5, PTCH1, and GNA11 for identifying HCC from healthy controls were 0.908, 0.924, and 0.913, respectively. When these three autoantibodies were combined as a panel, the sensitivity could be improved to 68%. The prevalence of PAX5, PTCH1, and GNA11 autoantibodies has already occurred in 62.5%, 62.5%, or 75.0% of patients before clinical diagnosis, respectively. In the non-Hispanic cohort, autoantibodies to PTCH1 showed no significant difference; however, autoantibodies to PAX5, PTCH1, and GNA11 showed potential value as biomarkers for early detection of HCC in the Hispanic population and they may monitor the transition of patients with high-risk (LC, CH) to HCC. Using a panel of the three anti-TAA autoantibodies may enhance the detection of HCC.
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Xie D, Zhang G, Ma Y, Wu D, Jiang S, Zhou S, Jiang X. Circulating Metabolic Markers Related to the Diagnosis of Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:7840606. [PMID: 36532884 PMCID: PMC9757943 DOI: 10.1155/2022/7840606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 01/04/2025]
Abstract
Primary liver carcinoma is the sixth most common cancer worldwide, while hepatocellular carcinoma (HCC) is the most dominant cancer type. Chronic hepatitis B and C virus infections and aflatoxin exposure are the main risk factors, while nonalcoholic fatty liver disease caused by obesity, diabetes, and metabolic syndrome are the more common risk factors for HCC. Metabolic disorders caused by these high-risk factors are closely related to the tumor microenvironment of HCC, revealing a possible cause-and-effect relationship between the two. These metabolic disorders involve many complex metabolic pathways, such as carbohydrate, lipid, lipid derivative, amino acid, and amino acid derivative metabolic processes. The resulting metabolites with significant abnormal changes in the concentration level in circulating blood may be used as biomarkers to guide the diagnosis, treatment, or prognosis of HCC. At present, there are high-throughput technologies that can quickly detect small molecular metabolites in many samples. Compared to tissue biopsy, blood samples are easier to obtain, and patients' willingness to participate is higher, which makes it possible to study blood HCC biomarkers. Over the past few years, a substantial body of research has been performed worldwide, and other potential biomarkers have been identified. Unfortunately, due to the limitations of each study, only a few markers have been widely verified and are suitable for clinical use. This review briefly summarizes the potential blood metabolic markers related to the diagnosis of HCC, mainly focusing on amino acids and their derivative metabolism, lipids and their derivative metabolism, and other possible related metabolisms.
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Affiliation(s)
- Da Xie
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
| | - Guangcong Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200030, China
| | - Yanan Ma
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
| | - Dongyu Wu
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
| | - Shuang Jiang
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
| | - Songke Zhou
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
| | - Xuemei Jiang
- Department of Gastroenterology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou 570100, China
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Schlichtemeier SM, Nahm CB, Xue A, Gill AJ, Smith RC, Hugh TJ. SELDI-TOF MS Analysis of Hepatocellular Carcinoma in an Australian Cohort. J Surg Res 2019; 238:127-136. [PMID: 30771682 DOI: 10.1016/j.jss.2019.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 11/05/2018] [Accepted: 01/04/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a common cause of cancer death worldwide. Resection offers the best chance of long-term survival, but a consistent adverse prognostic factor is the presence of microvascular invasion (MVI). In this study, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), a high throughput method of analyzing complex samples, was used to explore differentially expressed proteins between HCC and adjacent nontumour liver tissue (ANLT). These findings were correlated with clinical outcomes. MATERIALS AND METHODS From 2002 to 2011, tumor and ANLT were collected from patients who underwent liver resection and these samples were later prepared for SELDI-TOF MS. Output data were then used to identify proteins capable of discriminating HCC from ANLT. Proteins from the multivariate analysis were then analyzed to determine prognostic factors and the m/z ratios of these proteins were entered into the ExPASy database to infer potential candidates. RESULTS During the study period, 30 patients had SELDI-TOF MS performed on their HCC and ANLT samples. On multivariate analysis, a panel of four proteins-m/z 5840, m/z 8921, m/z 9961, and m/z 25,872-discriminated HCC from ANLT with an area under the ROC curve of 0.954 (P < 0.001). On prognostic factor assessment, decreased m/z 9961 was significantly associated with the presence of MVI (P = 0.025) and shorter disease-free survival (P = 0.045) in our patients. A potential candidate for this protein was coxsackievirus and adenovirus receptor, isoform 3 (CAR 3/7), which helps maintain tight junction integrity. CONCLUSIONS Using SELDI TOF-MS, we identified a panel of four proteins with excellent discriminative capacity between HCC and ANLT. Of these, m/z 9961 was the only protein significantly associated with a known poor prognostic factor (presence of MVI) and survival (shorter disease-free survival). While loss of CAR 3/7 could lead to MVI, further research is warranted to validate the identity of protein m/z 9961.
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Affiliation(s)
- Steven M Schlichtemeier
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia.
| | - Christopher B Nahm
- Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
| | - Aiqun Xue
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Anthony J Gill
- Department of Anatomical Pathology, Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, University of Sydney, Sydney NSW and NSW Health Pathology, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Ross C Smith
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
| | - Thomas J Hugh
- Cancer Surgery and Metabolism Research Group, University of Sydney, Kolling Institute of Medical Research, St Leonards, NSW, Australia; Upper GI Surgical Unit, Royal North Shore Hospital and North Shore Private Hospital, St Leonards, NSW, Australia; Discipline of Surgery, The University of Sydney, Camperdown, NSW, Australia
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Fan ZJ, Liu S, Zhang L, Tian YQ, Liu SY. Value of combined detection of serum vitronectin, alpha-1-B glycoprotein, antithrombin-Ⅲ, and alpha fetoprotein for diagnosis of early hepatocellular carcinoma. Shijie Huaren Xiaohua Zazhi 2018; 26:842-848. [DOI: 10.11569/wcjd.v26.i14.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To evaluate the value of combined detection of serum vitronectin (VTN), alpha-1-B glycoprotein (A1BG), antithrombin-Ⅲ (AT-Ⅲ), and alpha fetoprotein (AFP) for early diagnosis of hepatocellular carcinoma (HCC).
METHODS ELISA was used to detect the concentrations of serum VTN, A1BG, and AT-Ⅲ in 160 patients with HCC, 70 patients with chronic hepatitis B (CHB), 70 patients with liver cirrhosis (LC), and 50 healthy controls (HC), and electrochemical luminescence was used to detect serum concentration of AFP. The changes of VTN, A1BG, AT-Ⅲ, histidine-rich glycoprotein (HRG), and AFP in different groups of subjects were compared. The sensitivity and specificity of HRG, A1BG, AFP, and AT-Ⅲ, alone or in different combinations, in the diagnosis of HCC were determined by receiver operating characteristic (ROC) curve analysis. Serum AFP, A1BG, and AT-Ⅲ were then used as independent variables to establish a comprehensive prediction model for HCC.
RESULTS The levels of serum AFP, VTN, A1BG, and AT-Ⅲ were significantly different in the four groups (F = 1498.93, 51.68, 84.00, 115.34, P < 0.05). There was no significant difference in the level of VTN between the HCC group and other groups (F = 1.31), and its performance as a screening index was poor. The areas under the ROC curves (AUCs) of AFP, HRG, A1BG, and AT-Ⅲ were 0.878, 0.579, 0.712, and 0.801, respectively. The AUC of VTN was the lowest, suggesting that it has no diagnostic value. The AUC of the comprehensive prediction model was 0.923, which was significantly higher than those of A1BG and AT-Ⅲ (P < 0.05). The sensitivities of AFP, A1BG, and AT-Ⅲ for the diagnosis of HCC were 70.00%, 64.37%, and 61.25%, respectively, the specificities were 91.05%, 74.74%, and 83.68%, respectively, and the AUCs were 0.878, 0.712 and 0.801, respectively. The sensitivity and specificity of the integrated prediction model were 85.00% and 88.42%, respectively. The AUC was 0.923, which was significantly different from the single diagnosis (P < 0.05). The predictive equation was P = 1/[1+exp (0.152-0.035 AFP-0.006 A1BG + 0.021 AT-Ⅲ)], which had a good diagnostic performance.
CONCLUSION Combined detection of serum AFP, A1BG, and AT-Ⅲ can improve the early diagnosis of HCC.
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Affiliation(s)
- Zhi-Juan Fan
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
| | - Shuang Liu
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
| | - Lei Zhang
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
| | - Ya-Qiong Tian
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
| | - Shu-Ye Liu
- Department of Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
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Del Ben M, Overi D, Polimeni L, Carpino G, Labbadia G, Baratta F, Pastori D, Noce V, Gaudio E, Angelico F, Mancone C. Overexpression of the Vitronectin V10 Subunit in Patients with Nonalcoholic Steatohepatitis: Implications for Noninvasive Diagnosis of NASH. Int J Mol Sci 2018; 19:ijms19020603. [PMID: 29463024 PMCID: PMC5855825 DOI: 10.3390/ijms19020603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/13/2018] [Accepted: 02/16/2018] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic steatohepatitis (NASH) is the critical stage of nonalcoholic fatty liver disease (NAFLD). The persistence of necroinflammatory lesions and fibrogenesis in NASH is the leading cause of liver cirrhosis and, ultimately, hepatocellular carcinoma. To date, the histological examination of liver biopsies, albeit invasive, remains the means to distinguish NASH from simple steatosis (NAFL). Therefore, a noninvasive diagnosis by serum biomarkers is eagerly needed. Here, by a proteomic approach, we analysed the soluble low-molecular-weight protein fragments flushed out from the liver tissue of NAFL and NASH patients. On the basis of the assumption that steatohepatitis leads to the remodelling of the liver extracellular matrix (ECM), NASH-specific fragments were in silico analysed for their involvement in the ECM molecular composition. The 10 kDa C-terminal fragment of the ECM protein vitronectin (VTN) was then selected as a promising circulating biomarker in discriminating NASH. The analysis of sera of patients provided these major findings: the circulating VTN fragment (i) is overexpressed in NASH patients and positively correlates with the NASH activity score (NAS); (ii) originates from the disulfide bond reduction between the V10 and the V65 subunits. In conclusion, V10 determination in the serum could represent a reliable tool for the noninvasive discrimination of NASH from simple steatosis.
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Affiliation(s)
- Maria Del Ben
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Diletta Overi
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Licia Polimeni
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Guido Carpino
- Department of Movement, Human and Health Sciences, Division of Health Sciences, University of Rome "Foro Italico", Piazza Lauro De Bosis 6, 00135 Rome, Italy.
| | - Giancarlo Labbadia
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Francesco Baratta
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Daniele Pastori
- Department of Internal Medicine and Medical Specialties, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Valeria Noce
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Eugenio Gaudio
- Department of Anatomical, Histological, Forensic Medicine and Orthopedics Sciences, Sapienza University of Rome, Via Borelli 50, 00161 Rome, Italy.
| | - Francesco Angelico
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
| | - Carmine Mancone
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Viale del Policlinico 155, 00161 Rome, Italy.
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Sheng X, Huang T, Qin J, Yang L, Sa ZQ, Li Q. Identification of the Differential Expression Profiles of Serum and Tissue Proteins During Rat Hepatocarcinogenesis. Technol Cancer Res Treat 2018; 17:1533034618756785. [PMID: 29478368 PMCID: PMC5833169 DOI: 10.1177/1533034618756785] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The pathogenesis of hepatocellular carcinoma is complex and not fully known yet. This study aims to screen and identify the differentially expressed proteins in peripheral blood and liver tissue samples from rat hepatocellular carcinoma and to further clarify the pathogenesis and discover the specific tumor markers and molecular targets of hepatocellular carcinoma. The hepatocellular carcinoma model of Wistar rats were induced by chemical carcinogen. The serum and liver tissue samples were obtained after induction for 2, 4, 8, 14, 18, and 21 weeks. The results showed that the clusterin (IPI00198667), heat shock protein a8 (IPI00208205), and N-myc downstream-regulated gene-2 (IPI00382069) being closely related to hepatocarcinogenesis were eventually identified from the 30 different proteins. As the time progressed, the serum levels of clusterin and heat shock protein a8 increased gradually during induced liver cancer in rats. However, the serum N-myc downstream-regulated gene 2 level in induced liver cancer in rats underwent biphasic changes, and the serum N-myc downstream-regulated gene 2 level decreased at the 8th week, increased at the 14th week, and then decreased significantly. Statistical difference occurred in protein expression of clusterin and heat shock protein a8 in liver tissues at the different time points. In the liver tissues, the N-myc downstream-regulated gene 2 level decreased gradually at the 8th week, increased gradually at the 14th week, and then decreased significantly after 14 weeks. The study demonstrated that heat shock protein a8, clusterin, and N-myc downstream-regulated gene 2 participated in the process of abnormal cell division, proliferation, and carcinogenesis of liver cells during hepatocarcinogenesis.
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MESH Headings
- Animals
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Hepatocellular/blood
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Immunohistochemistry
- Liver/metabolism
- Liver/pathology
- Liver Neoplasms/blood
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Male
- Proteome
- Proteomics/methods
- Rats
- Transcriptome
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Affiliation(s)
- Xia Sheng
- 1 Department of pathology, Affiliated to the Third Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Tao Huang
- 2 Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Jianmin Qin
- 2 Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
- 3 Department of general surgery, Affiliated to the Third Hospital, Second Military Medical University, Shanghai, P.R. China
| | - Lin Yang
- 2 Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Zhong-Qiu Sa
- 2 Department of General Surgery, Putuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Qi Li
- 4 Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
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In-depth proteomic analysis of tissue interstitial fluid for hepatocellular carcinoma serum biomarker discovery. Br J Cancer 2017; 117:1676-1684. [PMID: 29024941 PMCID: PMC5729441 DOI: 10.1038/bjc.2017.344] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/25/2017] [Accepted: 09/01/2017] [Indexed: 12/12/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a primary malignancy of the liver. New serum biomarkers for HCC screening are needed, especially for alpha-fetoprotein (AFP) negative patients. As a proximal fluid between body fluids and intracellular fluid, tissue interstitial fluid (TIF) is a suitable source for serum biomarker discovery. Methods: Sixteen paired TIF samples from HCC tumour and adjacent non-tumour tissues were analysed by isobaric tags for relative and absolute quantitation (iTRAQ) method. Two proteins were selected for ELISA validation in serum samples. Results: Totally, 3629 proteins were identified and 3357 proteins were quantified in TIF samples. Among them, 232 proteins were significantly upregulated in HCC-TIF and 257 proteins down-regulated. Two overexpressed extracellular matrix proteins, SPARC and thrombospondin-2 (THBS2) were selected for further validation. ELISA result showed that the serum levels of SPARC and THBS2 in HCC patients were both significantly higher than those in healthy controls. The combination of serum SPARC and THBS2 could distinguish HCC (AUC=0.97, sensitivity=86%, specificity=100%) or AFP-negative HCC (AUC=0.95, sensitivity=91%, specificity=93%) from healthy controls. And the combination of serum SPARC and THBS2 could also distinguish HCC patients from benign liver disease patients (AUC=0.93, sensitivity=80%, specificity=94%). In addition, serum THBS2 was found to be a novel independent indicator for poor prognosis of HCC. Conclusions: Novel HCC candidate serum markers were found through in-depth proteomic analysis of TIF, which demonstrated the successful utility of TIF in cancer serum biomarker discovery.
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Garrisi VM, Sgherza N, Breccia M, Iacobazzi A, De Tullio G, Nardelli G, Negri A, Divella R, Daniele A, Micelli G, Tufaro A, Cascavilla N, Savino E, Abbate I, Guarini A. Association between proteomic profile and molecular response in chronic myeloid leukemia patients. Leuk Lymphoma 2017; 59:1016-1018. [PMID: 28695760 DOI: 10.1080/10428194.2017.1344841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Vito Michele Garrisi
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Nicola Sgherza
- b Hematology and Stem Cell Transplantation Unit , "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo , Italy
| | - Massimo Breccia
- c Department of Cellular Biotechnologies and Hematology , Sapienza University , Rome , Italy
| | - Angela Iacobazzi
- d Hematology Unit , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Giacoma De Tullio
- d Hematology Unit , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Giovanni Nardelli
- d Hematology Unit , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Antonio Negri
- d Hematology Unit , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Rosa Divella
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Antonella Daniele
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Giuseppina Micelli
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Antonio Tufaro
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Nicola Cascavilla
- b Hematology and Stem Cell Transplantation Unit , "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo , Italy
| | - Eufemia Savino
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Ines Abbate
- a Clinical and Experimental Pathology Laboratory , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
| | - Attilio Guarini
- d Hematology Unit , National Cancer Research Centre Istituto Tumori "Giovanni Paolo II" , Bari , Italy
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10
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Lavine BK, White CG, DeNoyer L, Mechref Y. Multivariate classification of disease phenotypes of esophageal adenocarcinoma by pattern recognition analysis of MALDI-TOF mass spectra of serum N-linked glycans. Microchem J 2017. [DOI: 10.1016/j.microc.2016.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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You N, Li J, Huang X, Wu K, Tang Y, Wang L, Li H, Mi N, Zheng L. COMMD7 promotes hepatocellular carcinoma through regulating CXCL10. Biomed Pharmacother 2017; 88:653-657. [PMID: 28142122 DOI: 10.1016/j.biopha.2017.01.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/28/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is still a heavy threat to public health. However, novel therapeutic and diagnostic method for HCC is still urgently needed thus far. Based on sequence analysis and homology comparison, we previously reported a novel gene termed COMMD7, which is mapped to 20q11.22 and promotes cell proliferation in HCC cells. But the molecular mechanisms underlying the pro-tumor property of COMMD7 are not fully addressed yet. In this study, we demonstrate that the conditional medium derived from COMMD7-overexpressed HCC cell promotes proliferation of naïve HCC cells. The over-expression of COMMD7 significantly induced the migratory and invasive in HCC cells. Mechanistic study found that over-expression of COMMD7 induces C-X-C motif chemokine 10 (CXCL10) expression. Blocking CXCL10 signal transduction by neutralizing antibody abolished COMMD7-mediated cell proliferation and migration. In conclusion, COMMD7 promotes hepatocellular carcinoma through regulating CXCL10. The present data suggests a potential role of CXCL10 in the oncogenic function of COMMD7, and will lead to a better understanding of the development of HCC.
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Affiliation(s)
- Nan You
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Jing Li
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Xiaobing Huang
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Ke Wu
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Yichen Tang
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Liang Wang
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Hongyan Li
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Na Mi
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China
| | - Lu Zheng
- Department of Hepatobiliary Surgery, Xinqiao Hospital of Third Military Medical University, Chongqing 400037, China.
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12
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Chen R, Zou H, Figeys D. Detergent-Assisted Glycoprotein Capture: A Versatile Tool for In-Depth N-Glycoproteome Analysis. J Proteome Res 2016; 15:2080-6. [PMID: 27147131 DOI: 10.1021/acs.jproteome.6b00056] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large-scale N-glycoproteome studies have been hindered by poor solubility of hydrophobic membrane proteins and the complexity of proteome samples. Herein, we developed a detergent-assisted glycoprotein capture method to reduce these issues by conducting hydrazide chemistry-based glycoprotein capture in the presence of strong detergents such as sodium dodecyl sulfate and Triton X-100. The strong detergents helped to solubilize hydrophobic membrane proteins and then increased the access of hydrazide groups to oxidized glycoproteins, thus increasing the coverage of the N-glycoproteome. Compared with the conventional glycopeptide capture method, the detergent-assisted glycoprotein capture approach nearly doubled the number of N-glycosylation sites identified from HEK 293T cells with improved specificity. Application of this approach in the larger scale N-glycoproteomics analysis of the HEK 293T cell membrane led to the identification of 2253 unique N-glycosites from 953 proteins. Furthermore, the application of this approach to human serum resulted in the identification of 850 N-glycosylation sites without any immunodepletion or fractionation. Overall, the detergent-assisted glycoprotein capture method simplified the capture process, and it increased the number of sites observed on both hydrophobic membrane proteins and hydrophilic secreted proteins.
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Affiliation(s)
- Rui Chen
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Hanfa Zou
- Key Lab of Separation Science for Analytical Chemistry, National Chromatography R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Science , Dalian 116023, China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology and Department of Chemistry and Biomolecular Sciences, University of Ottawa , 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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13
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Tracing the voyage of SELDI-TOF MS in cancer biomarker discovery and its current depreciation trend – need for resurrection? Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Wong RJ, Ahmed A, Gish RG. Elevated alpha-fetoprotein: differential diagnosis - hepatocellular carcinoma and other disorders. Clin Liver Dis 2015; 19:309-23. [PMID: 25921665 DOI: 10.1016/j.cld.2015.01.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The incidence of cirrhosis-related hepatocellular carcinoma (HCC) is rising. Curative surgical options are available; outcomes are acceptable with early diagnosis. Lens culinaris agglutinin-reactive fraction of alpha-fetoprotein (AFP-L3) and des-gamma-carboxy prothrombin (DCP) are HCC risk markers. A high or increasing serum biomarker level can be predictive of the eventual development of HCC, large tumor size, advanced stage, extrahepatic metastases, portal vein thrombosis, and postoperative HCC recurrence. Based on FDA guidelines for HCC risk assessment, clinicians can consider using either the combination of AFP-L3 with DCP, or the combination of AFP-L3 with AFP and DCP.
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Affiliation(s)
- Robert J Wong
- Division of Gastroenterology and Hepatology, Alameda Health System-Highland Hospital, Highland Care Pavilion, 5th floor, 1411 East 31st Street, Oakland, CA 94602, USA
| | - Aijaz Ahmed
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, 750 Welch Road, Suite# 210, Palo Alto, CA 94304, USA; Liver Transplant Program, Stanford University Medical Center, 750 Welch Road, Suite# 210, Palo Alto, CA 94304, USA
| | - Robert G Gish
- Liver Transplant Program, Stanford University Medical Center, 750 Welch Road, Suite# 210, Palo Alto, CA 94304, USA; Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902, USA.
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15
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Abstract
The increasing incidence of hepatocellular carcinoma (HCC) has led to the need to identify patients at risk for HCC so that a program of screening can be undertaken. Screening for HCC has led to earlier diagnosis of tumors and thus has aided in initiating optimal medical treatment earlier in the disease course. Advances in radiological techniques and the identification of more accurate serum tests to diagnose HCC continue to be important areas of study and exploration. In particular, there have been efforts to develop new tumor markers to aid in the diagnosis of HCC and guide therapy of tumors.
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Affiliation(s)
- Heather N Simpson
- The University of Alabama School of Medicine, Department of Medicine, Division of Gastroenterology & Hepatology, Boshell Diabetes Building, 1808 7th Avenue South, Birmingham, AL 35233, USA
| | - Brendan M McGuire
- The University of Alabama School of Medicine, Department of Medicine, Division of Gastroenterology & Hepatology, Boshell Diabetes Building, 1808 7th Avenue South, Birmingham, AL 35233, USA.
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16
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Tsai TH, Song E, Zhu R, Di Poto C, Wang M, Luo Y, Varghese RS, Tadesse MG, Ziada DH, Desai CS, Shetty K, Mechref Y, Ressom HW. LC-MS/MS-based serum proteomics for identification of candidate biomarkers for hepatocellular carcinoma. Proteomics 2015; 15:2369-81. [PMID: 25778709 DOI: 10.1002/pmic.201400364] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 01/28/2015] [Accepted: 03/11/2015] [Indexed: 12/21/2022]
Abstract
Associating changes in protein levels with the onset of cancer has been widely investigated to identify clinically relevant diagnostic biomarkers. In the present study, we analyzed sera from 205 patients recruited in the United States and Egypt for biomarker discovery using label-free proteomic analysis by LC-MS/MS. We performed untargeted proteomic analysis of sera to identify candidate proteins with statistically significant differences between hepatocellular carcinoma (HCC) and patients with liver cirrhosis. We further evaluated the significance of 101 proteins in sera from the same 205 patients through targeted quantitation by MRM on a triple quadrupole mass spectrometer. This led to the identification of 21 candidate protein biomarkers that were significantly altered in both the United States and Egyptian cohorts. Among the 21 candidates, ten were previously reported as HCC-associated proteins (eight exhibiting consistent trends with our observation), whereas 11 are new candidates discovered by this study. Pathway analysis based on the significant proteins reveals upregulation of the complement and coagulation cascades pathway and downregulation of the antigen processing and presentation pathway in HCC cases versus patients with liver cirrhosis. The results of this study demonstrate the power of combining untargeted and targeted quantitation methods for a comprehensive serum proteomic analysis, to evaluate changes in protein levels and discover novel diagnostic biomarkers. All MS data have been deposited in the ProteomeXchange with identifier PXD001171 (http://proteomecentral.proteomexchange.org/dataset/PXD001171).
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Affiliation(s)
- Tsung-Heng Tsai
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Cristina Di Poto
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Minkun Wang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Yue Luo
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rency S Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Dina Hazem Ziada
- Department of Tropical Medicine and Infectious Diseases, Tanta University, Tanta, Egypt
| | - Chirag S Desai
- MedStar Georgetown University Hospital and Georgetown University Medical Center, Washington, DC, USA
| | - Kirti Shetty
- Johns Hopkins University, Gastroenterology & Hepatology at Sibley, Washington, DC, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Habtom W Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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17
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Proteomic and metabonomic biomarkers for hepatocellular carcinoma: a comprehensive review. Br J Cancer 2015; 112:1141-56. [PMID: 25826224 PMCID: PMC4385954 DOI: 10.1038/bjc.2015.38] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 11/04/2014] [Accepted: 12/20/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) ranks third in overall global cancer-related mortality. Symptomatic presentation often means advanced disease where potentially curative treatment options become very limited. Numerous international guidelines propose the routine monitoring of those with the highest risk factors for the condition in order to diagnose potential tumourigenesis early. To aid this, the fields of metabonomic- and proteomic-based biomarker discovery have applied advanced tools to identify early changes in protein and metabolite expression in HCC patients vs controls. With robust validation, it is anticipated that from these candidates will rise a high-performance non-invasive test able to diagnose early HCC and related conditions. This review gathers the numerous markers proposed by studies using mass spectrometry and proton nuclear magnetic resonance spectroscopy and evaluates areas of consistency as well as discordance.
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18
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Montaldo C, Mattei S, Baiocchini A, Rotiroti N, Del Nonno F, Pucillo LP, Cozzolino AM, Battistelli C, Amicone L, Ippolito G, van Noort V, Conigliaro A, Alonzi T, Tripodi M, Mancone C. Spike-in SILAC proteomic approach reveals the vitronectin as an early molecular signature of liver fibrosis in hepatitis C infections with hepatic iron overload. Proteomics 2014; 14:1107-15. [PMID: 24616218 DOI: 10.1002/pmic.201300422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 01/06/2023]
Abstract
Hepatitis C virus (HCV)-induced iron overload has been shown to promote liver fibrosis, steatosis, and hepatocellular carcinoma. The zonal-restricted histological distribution of pathological iron deposits has hampered the attempt to perform large-scale in vivo molecular investigations on the comorbidity between iron and HCV. Diagnostic and prognostic markers are not yet available to assess iron overload-induced liver fibrogenesis and progression in HCV infections. Here, by means of Spike-in SILAC proteomic approach, we first unveiled a specific membrane protein expression signature of HCV cell cultures in the presence of iron overload. Computational analysis of proteomic dataset highlighted the hepatocytic vitronectin expression as the most promising specific biomarker for iron-associated fibrogenesis in HCV infections. Next, the robustness of our in vitro findings was challenged in human liver biopsies by immunohistochemistry and yielded two major results: (i) hepatocytic vitronectin expression is associated to liver fibrogenesis in HCV-infected patients with iron overload; (ii) hepatic vitronectin expression was found to discriminate also the transition between mild to moderate fibrosis in HCV-infected patients without iron overload.
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Affiliation(s)
- Claudia Montaldo
- Department of Cellular Biotechnologies and Haematology, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Italy; "L. Spallanzani" National Institute for Infectious Diseases, IRCCS, Rome, Italy
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Yang J, Zhu J, He K, Zhao LY, Liu LY, Song TS, Huang C. Proteomic Profiling of Invasive Ductal Carcinoma (IDC) using Magnetic Beads-based Serum Fractionation and MALDI-TOF MS. J Clin Lab Anal 2014; 29:321-7. [PMID: 25130542 DOI: 10.1002/jcla.21773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/03/2014] [Indexed: 11/11/2022] Open
Abstract
AIM To reveal the serum proteomic profiling of intraductal carcinoma (IDC) patients in China, establish a serum proteome fractionation technique for choosing magnetic beads for proteomic analysis in breast cancer research; and identify differentially expressed peptides (m/z; P < 0.0001) as potential biomarkers of early IDCs. METHODS We used two different kinds of magnetic beads (magnetic bead-based weak cation exchange chromatography (MB-WCX) and immobilized metal ion affinity chromatography (MB-IMAC-Cu)) to analyze 32 patients with early stage (stages I-II) IDC and 32 healthy control serum samples for proteomic profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The mass spectra, analyzed using ClinProTools software, distinguished between IDC patients and healthy individuals based on k-nearest neighbor genetic algorithm. RESULTS The serum samples purified in the MB-WCX group provided better proteomic patterns than the MB-IMAC-Cu group. The samples purified by MB-WCX had better average peak numbers, higher peak intensities, and better capturing ability of low abundance proteins or peptides in serum samples. In addition, the MB-WCX and MB-IMAC-Cu purification methods, followed MALDI-TOF MS identification and use of ClinProTools software accurately distinguished patients with early stage IDC from healthy individuals. CONCLUSION Serum proteomic profiling by MALDI-TOF MS is a novel potential tool for the clinical diagnosis of patients with IDC in China.
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Affiliation(s)
- Juan Yang
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
| | - Jiang Zhu
- Department of Mastopathy, Shaanxi Provincial Tumor Hospital, Xi'an, China
| | - Kang He
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
| | - Ling-Yu Zhao
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
| | - Li-Ying Liu
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
| | - Tu-Sheng Song
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
| | - Chen Huang
- Department of Genetics and Molecular Biology, Medical School of Xi'an Jiaotong University / Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Xi'an, China
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20
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Wang N, Cao Y, Song W, He K, Li T, Wang J, Xu B, Si HY, Hu CJ, Li AL. Serum peptide pattern that differentially diagnoses hepatitis B virus-related hepatocellular carcinoma from liver cirrhosis. J Gastroenterol Hepatol 2014; 29:1544-50. [PMID: 24612022 DOI: 10.1111/jgh.12545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2014] [Indexed: 01/22/2023]
Abstract
BACKGROUND Although alpha-fetoprotein (AFP) is a useful serologic marker of hepatocellular carcinoma (HCC), it is not sufficiently sensitive to differentiate HCC and liver cirrhosis (LC) caused by hepatitis B virus (HBV) infection. AIMS The aim is to discover novel noninvasive specific serum biomarkers for the differential diagnosis of HBV-related HCC and LC. METHODS With a highly optimized peptide extraction and matrix-assisted laser desorption/ionization time of flight/time of flight mass spectrometric approach, we investigated serum peptide profiles of 80 HCC and 67 LC patients. Three supervised machine learning methods were employed to construct classifiers. Receiver operator curves were plotted to evaluate the performance of classifiers. RESULTS With a support vector machine-based strategy, we picked nine peaks with m/z ratios of 819.49, 1076.14, 1341.72, 2551.44, 3156.44, 3812.88, 4184.26, 4465.92, and 4776.41 to construct the classifier. We proposed a novel method for distinguishing HCC from cirrhosis, based on a multilayer perceptron (MLP) method. We obtained a sensitivity of 90.0%, specificity of 79.4%, and overall accuracy of 85.1% on an independent test set. The combination of the MLP model and serum AFP level outperformed serum AFP marker alone in distinguishing HCC patients from LC patients. In this experience, sensitivity increased from 62.5% to 87.5%, and specificity increased from 79.4% to 88.2%. CONCLUSIONS Our results indicate that the MLP model is a novel and useful serum peptide pattern for distinguishing HCC and LC. The peptidome signature alone or together with serum AFP determination may be a more effective method for early diagnosis of HCC in patients with HBV-related LC.
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Affiliation(s)
- Na Wang
- Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China
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21
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Le Faouder J, Laouirem S, Alexandrov T, Ben-Harzallah S, Léger T, Albuquerque M, Bedossa P, Paradis V. Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry. Proteomics 2014; 14:965-72. [DOI: 10.1002/pmic.201300463] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/24/2014] [Accepted: 01/27/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Julie Le Faouder
- Claude Bernard Institute; Paris-Diderot University; Paris France
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
| | - Samira Laouirem
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
| | - Theodore Alexandrov
- Center for Industrial Mathematics; University of Bremen; Bremen Germany
- Steinbeis Innovation Center SCiLS Research; Bremen Germany
- SCiLS GmbH; Bremen Germany
- Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California San Diego; La Jolla CA USA
| | | | - Thibaut Léger
- Mass Spectrometry Facility; Jacques Monod Institute; UMR7592-CNRS; University Paris-Diderot; Paris France
| | - Miguel Albuquerque
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
| | - Pierre Bedossa
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
| | - Valérie Paradis
- INSERM U773; Biomedical Research Center; Paris-Diderot University; Paris France
- Pathology Department; Beaujon Hospital; Assistance Publique-Hôpitaux de Paris; Clichy France
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22
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Ferrín G, Ranchal I, Llamoza C, Rodríguez-Perálvarez ML, Romero-Ruiz A, Aguilar-Melero P, López-Cillero P, Briceño J, Muntané J, Montero-Álvarez JL, De la Mata M. Identification of candidate biomarkers for hepatocellular carcinoma in plasma of HCV-infected cirrhotic patients by 2-D DIGE. Liver Int 2014; 34:438-46. [PMID: 23944848 DOI: 10.1111/liv.12277] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 06/23/2013] [Indexed: 12/22/2022]
Abstract
BACKGROUND The current methods available for screening and detecting hepatocellular carcinoma (HCC) have insufficient sensitivity and specificity, and only a low percentage of diagnosis of small tumours is based on these assays. Because HCC is usually asymptomatic at potentially curative stages, identification of biomarkers for the early detection of HCC is essential to improve patient survival. AIM The aim of this study was to identify candidate markers for HCC development in the plasma from hepatitis C virus (HCV)-infected cirrhotic patients. METHODS We compared protein expression profiles of plasma samples from HCV-infected cirrhotic patients with and without HCC, using two-dimensional fluorescence difference gel electrophoresis (2-D DIGE) coupled with MALDI-TOF/TOF mass spectrometry. The 2-D DIGE results were analysed statistically using Decyder™ software, and verified by western blot and enzyme-linked immunosorbent assay (ELISA). RESULTS In the plasma of HCV-infected HCC patients, we observed decreased expression of complement component 9, ficolin-3 (FCN3), serum amyloid P component (SAP), fibrinogen-gamma and immunoglobulin gamma-1 chain, and increased expression of vitronectin (VTN) and galectin-3 binding protein (G3BP) by DIGE analysis. ELISA confirmed DIGE results for VTN and G3BP but not for SAP or FCN3 in a larger patient population. CONCLUSIONS The proteins VTN and SAP are candidate biomarkers for HCC development in HCV-infected cirrhotic patients.
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Affiliation(s)
- Gustavo Ferrín
- Maimónides Institute for Biomedical Research in Córdoba (IMBIC), Reina Sofía University Hospital, University of Córdoba, Córdoba, Spain; Networked Biomedical Research Center, Hepatic and Digestive Diseases (CIBERehd), Barcelona, Spain
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Tammen H, Peck A, Budde P, Zucht HD. Peptidomics analysis of human blood specimens for biomarker discovery. Expert Rev Mol Diagn 2014; 7:605-13. [PMID: 17892366 DOI: 10.1586/14737159.7.5.605] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review addresses the concepts, limitations and perspectives for the application of peptidomics science and technologies to discover putative biomarkers in blood specimens. Peptidomics can be defined as the comprehensive multiplex analysis of endogenous peptides contained within a biological sample under defined conditions to describe the multitude of native peptides in a biological compartment. In addition to the discovery of disease associated biomarkers, an emerging field in peptidomics is the analysis of peptides to describe in vivo effects of protease inhibitors. The development and application of peptidomics technologies represent an arena of biomarker research that has the potential for adding significant clinical value.
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Affiliation(s)
- Harald Tammen
- Digilab BioVisioN GmbH, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
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Abstract
In the past several years, proteomics and its subdiscipline clinical proteomics have been engaged in the discovery of the next generation protein of biomarkers. As the effort and the intensive debate it has sparked continue, it is becoming apparent that a paradigm shift is needed in proteomics in order to truly comprehend the complexity of the human proteome and assess its subtle variations among individuals. This review introduces the concept of population proteomics as a future direction in proteomics research. Population proteomics is the study of protein diversity in human populations. High-throughput, top-down mass spectrometric approaches are employed to investigate, define and understand protein diversity and modulations across and within populations. Population proteomics is a discovery-oriented endeavor with a goal of establishing the incidence of protein structural variations and quantitative regulation of these modifications. Assessing human protein variations among and within populations is viewed as a paramount undertaking that can facilitate clinical proteomics' effort in discovery and validation of protein features that can be used as markers for early diagnosis of disease, monitoring of disease progression and assessment of therapy. This review outlines the growing need for analyzing individuals' proteomes and describes the approaches that are likely to be applied in such a population proteomics endeavor.
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Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes, Inc., 625 S. Smith Rd, Suite 22, Tempe, AZ 85281, USA.
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25
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Abstract
Liver diseases remain among the most important causes of morbidity and mortality worldwide. Although the diagnostic tools (e.g., blood studies, imaging, genetic and molecular tests) available to clinicians have greatly expanded in number and increased in sensitivity, the examination of liver tissue by a pathologist skilled and experienced in hepatopathology remains vitally important in the evaluation and care of the patient with liver abnormalities. In some disorders, such as autoimmune hepatitis, liver biopsy is considered mandatory. The indications for performing liver biopsies have changed over the years (e.g., large duct obstruction was a common diagnostic problem 50 years ago and is only uncommonly so currently). Liver samples come to the pathologist as aspiration biopsies for cytologic examination, tissue biopsies (fine needle, core, transjugular, and wedge), resections, and explants. Each demands slightly different approaches for optimal handling and evaluation.
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Liu Y, Sogawa K, Sunaga M, Umemura H, Satoh M, Kazami T, Yoshikawa M, Tomonaga T, Yokosuka O, Nomura F. Increased concentrations of apo A-I and apo A-II fragments in the serum of patients with hepatocellular carcinoma by magnetic beads-assisted MALDI-TOF mass spectrometry. Am J Clin Pathol 2014; 141:52-61. [PMID: 24343737 DOI: 10.1309/ajcpblfbnap6n2un] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Recent advances in sophisticated technologies in proteomics should provide promising ways to discover novel markers for hepatocellular carcinoma (HCC) in the early diagnosis. METHODS Serum peptide and protein profiling was conducted by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Profiling was carried out in a training set of 16 patients with HCC and a testing set of 15 patients with cirrhosis without HCC. All the patients were hepatitis C virus positive. Candidate peaks were processed to partial purification, followed by protein identification by amino acid sequence analysis. Immunoprecipitation was conducted to confirm the protein identity. RESULTS Partial purification and protein identification revealed that one peak that was up-regulated in HCC sera both in the training and the testing sets was a fragment of apolipoprotein A-I (apo A-I). Immunoprecipitation confirmed this result. CONCLUSIONS MALDI-TOF MS analysis revealed that apo A-I is a potential novel serum marker of HCC. Combination of these pretreatments and the current magnet bead-assisted MALDI-TOF MS will further enhance the efficiency of biomarker discovery for HCC.
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Affiliation(s)
- Yang Liu
- Departments of Medicine and Clinical Oncology, Chiba University, Chiba, Japan
- Basic Medicine College, Beihua University, Jilin City, China
| | - Kazuyuki Sogawa
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Clinical Proteomics Center, Chiba University Hospital, Chiba
| | - Masahiko Sunaga
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroshi Umemura
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Mamoru Satoh
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Clinical Proteomics Center, Chiba University Hospital, Chiba
| | - Takahiro Kazami
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaharu Yoshikawa
- Departments of Medicine and Clinical Oncology, Chiba University, Chiba, Japan
| | - Takeshi Tomonaga
- Clinical Proteomics Center, Chiba University Hospital, Chiba
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Osaka, Japan
| | - Osamu Yokosuka
- Departments of Medicine and Clinical Oncology, Chiba University, Chiba, Japan
| | - Fumio Nomura
- Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
- Clinical Proteomics Center, Chiba University Hospital, Chiba
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Proteins related to early changes in carcinogenesis of hepatic oval cells after treatment with methylnitronitrosoguanidine. ACTA ACUST UNITED AC 2013; 66:139-46. [PMID: 24360059 DOI: 10.1016/j.etp.2013.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 06/19/2013] [Accepted: 11/25/2013] [Indexed: 12/26/2022]
Abstract
Hepatic oval cells are considered as facultative progenitor/stem cells of liver and able to differentiate into either hepatocytes or biliary epithelial cells. The transformed oval cells by carcinogen possess potential to develop carcinomas in animal models. In order to better understand the molecular mechanism in carcinogenetic process, we used a proteomic approach to assess the early changes in protein expression of oval cells (OC3W3-15) initiated by methylnitronitrosoguanidine (MNNG). Meanwhile, we compared cell biologic characteristics of the MNNG treated OC3W3-15 cells and control oval cells by electron microscopy, flow cytometry, karyotype and soft agar assay. The mRNA levels of GGT and GSTP1 determined by real-time PCR were also detected in both cell lines. Our results showed that MNNG-treated OC3W3-15 cells exhibited characteristics of malignant transformation, including growth rate, chromosomal aberrations, abnormal DNA content, and the ability to form colonies. The cells expressed higher levels of the tumor marker AFP, GGT and GSTP1 mRNA than that of control cells. Significant changes of several proteins involved in the malignant transformation process, including cell cycle related proteins, proteins involved in organism development and cell differentiation, are found in OC3W3-15 cells. The proteins may provide early affection in malignant transformation of hepatic oval cells, and yield further insight into mechanism of carcinogenesis of hepatocellular carcinoma.
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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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Profiling serologic biomarkers in cirrhotic patients via high-throughput Fourier transform infrared spectroscopy: toward a new diagnostic tool of hepatocellular carcinoma. Transl Res 2013; 162:279-86. [PMID: 23920432 DOI: 10.1016/j.trsl.2013.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 12/14/2022]
Abstract
Identification of novel serum biomarkers of hepatocellular carcinoma (HCC) is needed for early-stage disease detection and to improve patients' survival. The aim of this study was to evaluate the potential of serum Fourier transform infrared (FTIR) spectroscopy for differentiating sera from cirrhotic patients with and without HCC. Serum samples were collected from 2 sets of patients: cirrhotic patients with HCC (n = 39) and without HCC (n = 40). The FTIR spectra (10 per sample) were acquired in the transmission mode, and data homogeneity was tested by cluster analysis to exclude outliers. After data preprocessing by extended multiplicative signal correction and principal component analysis, the Support Vector Machine (SVM) method was applied using a leave-one-out cross-validation algorithm to classify the spectra into 2 classes of cirrhotic patients with and without HCC. When SVM was applied to all spectra (n = 790), the sensitivity and the specificity for the diagnosis of HCC were, respectively, 82.02% and 82.5%. When applied to the subset of spectra excluding the outliers (n = 739), SVM classification led to a sensitivity and specificity of 87.18% and 85%, respectively. Using median spectra for each patient instead of all replicates, the sensitivity and specificity were 84.62% and 82.50%, respectively. The overall accuracy rate was 82%-86%. In conclusion, this study suggests that FTIR spectroscopy combined with advanced methods of pattern analysis shows potential for differentiating sera from cirrhotic patients with and without HCC.
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Simsek C, Sonmez O, Yurdakul AS, Ozmen F, Zengin N, Keyf AI, Kubilay D, GUlbahar O, Karatayli SC, Bozdayi M, Ozturk C. Importance of Serum SELDI-TOF-MS Analysis in the Diagnosis of Early Lung Cancer. Asian Pac J Cancer Prev 2013; 14:2037-42. [DOI: 10.7314/apjcp.2013.14.3.2037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Li Y, Wu J, Zhang W, Zhang N, Guo H. Identification of serum CCL15 in hepatocellular carcinoma. Br J Cancer 2013; 108:99-106. [PMID: 23321514 PMCID: PMC3553511 DOI: 10.1038/bjc.2012.494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Background: Early serum detection is of critical importance to improve the therapy for hepatocellular carcinoma (HCC), one of the most deadly cancers. Hepatitis infection is a leading cause of HCC. Methods: In the present study, we collected total serum samples with informed consent from 80 HCC patients with HBV (+)/cirrhosis (+), 80 patients with benign diseases (50 liver cirrhosis patients and 30 HBV-infected patients) and 60 healthy controls. Analysis was by using surface-enhanced laser desorption/ionisation-time-of-flight mass spectroscopy (SELDI-TOF-MS) to find new serum markers of HCC. SELDI peaks were isolated by SDS–PAGE, identified by LC-MS/MS and validated by immunohistochemistry (IHC) in liver tissues. Migration and invasion assay were performed to test the ability of cell migration and invasion in vitro. Results: SELDI-TOF-MS revealed a band at 7777 M/Z in the serum samples from HCC patients but not from healthy controls or patients with benign diseases. The protein (7777.27 M/Z) in the proteomic signature was identified as C-C motif chemokine 15 (CCL15) by peptide mass fingerprinting. A significant increase in serum CCL15 was detected in HCC patients. Functional analysis showed that HCC cell expressed CCL15, which in turn promoted HCC cell migration and invasion. Conclusion: CCL15 may be a specific proteomic biomarker of HCC, which has an important role in tumorigenesis and tumour invasion.
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Affiliation(s)
- Y Li
- Clinical laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
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Serum biomarkers identification by mass spectrometry in high-mortality tumors. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:125858. [PMID: 23401773 PMCID: PMC3562576 DOI: 10.1155/2013/125858] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/16/2012] [Accepted: 12/11/2012] [Indexed: 02/08/2023]
Abstract
Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Several validated biomarkers are currently used to diagnose and monitor the progression of cancer, but none of them shows adequate specificity, sensitivity, and predictive value for population screening. So, there is an urgent need to isolate novel sensitive, specific biomarkers to detect the disease early and improve prognosis, especially in high-mortality tumors. Proteomic techniques are powerful tools to help in diagnosis and monitoring of treatment and progression of the disease. During the last decade, mass spectrometry has assumed a key role in most of the proteomic analyses that are focused on identifying cancer biomarkers in human serum, making it possible to identify and characterize at the molecular level many proteins or peptides differentially expressed. In this paper we summarize the results of mass spectrometry serum profiling and biomarker identification in high mortality tumors, such as ovarian, liver, lung, and pancreatic cancer.
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Alexandrov T, Becker M, Guntinas-Lichius O, Ernst G, von Eggeling F. MALDI-imaging segmentation is a powerful tool for spatial functional proteomic analysis of human larynx carcinoma. J Cancer Res Clin Oncol 2013; 139:85-95. [PMID: 22955295 DOI: 10.1007/s00432-012-1303-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/21/2012] [Indexed: 12/28/2022]
Abstract
PURPOSE For several decades, conventional histological staining and immunohistochemistry (IHC) have been the main tools to visualize and understand tissue morphology and structure. IHC visualizes the spatial distribution of individual protein species directly in tissue. However, a specific antibody is required for each protein, and multiplexing capabilities are extremely limited, rarely visualizing more than two proteins simultaneously. With the recent emergence of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-imaging), it is becoming possible to study more complex proteomic patterns directly in tissue. However, the analysis and interpretation of large and complex MALDI-imaging data requires advanced computational methods. In this paper, we show how the recently introduced method of spatial segmentation can be applied to analysis and interpretation of a larynx carcinoma section and compare the spatial segmentation with the histological annotation of the same tissue section. METHODS Matrix-assisted laser desorption/ionization imaging is a label-free spatially resolved analytical technique, which allows detection and visualization of hundreds of proteins at once. Spatial segmentation of the MALDI-imaging data by clustering of spectra by their similarity was performed, automatically generating a spatial segmentation map of the tissue section, where regions of similar proteomic patterns were highlighted. The tissue was stained with the hematoxylin and eosin (H&E), histopathologically analyzed and annotated. The segmentation map was interpreted after its overlay with the H&E microscopy image. RESULTS The automatically generated segmentation map exhibits high correspondence to the detailed histological annotation of the larynx carcinoma tissue section. By superimposing, the segmentation map based on the proteomic profiles with H&E-stained microscopic images, we demonstrate precise localization of complex and histopathologically relevant tissue features in an automated way. CONCLUSIONS The combination of MALDI-imaging and automatic spatial segmentation is a useful approach in analyzing carcinoma tissue and provides a deeper insight into the functional proteomic organization of the respective tissue.
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Affiliation(s)
- Theodore Alexandrov
- Center for Industrial Mathematics (ZeTeM), University of Bremen, Bibliothekstr. 1, 28359 Bremen, Germany.
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Abstract
The only hope for a cure from hepatocellular carcinoma (HCC) rests on early diagnosis as it can be attained through semiannual surveillance with abdominal ultrasound (US) of patients at risk. While the strategy of semiannual screening rests on the growth rate of the tumor that in cirrhotic patients takes 6 months to double its volume, on average, the noninvasive radiological diagnosis of HCC is possible in cirrhotic patients with a de novo HCC and patients with chronic hepatitis B. More recently, metabolic diseases related to insulin resistance, including diabetes and obesity, have been recognized to be causally related to HCC as well, in most patients bridging HCC to the histopathological diagnosis of non-alcoholic steatohepatitis (NASH). While the endpoint of an early diagnosis is achieved quite easily in most patients with >1 cm HCC by computed tomography (CT) or magnetic resonance imaging (MRI) demonstrating the specific pattern of an intense contrast uptake during the arterial phase (wash-in) and contrast wash-out during the venous/delayed phase, nodules <1 cm in size are more difficult to diagnose, almost invariably requiring an enhanced follow up with three monthly examinations with US until they grow in size or change their echo pattern. Owing to the lack of robust controlled evidence demonstrating a clinical benefit of surveillance, the real support for screening for liver cancer comes from the striking differences in response to therapy between screened populations in whom HCC is diagnosed and treated at early stages and patients with more advanced, incidentally detected tumors. This notwithstanding, numerous barriers work against screening effectiveness, including limited or outdated knowledge, lack of financial incentives, and limited access to appropriate testing and treatment. Though strengthening prediction in individual patients is expected to improve the cost-effectiveness ratio of screening, the benefits of approaches like pretreatment patient stratification by clinical, histologic, and genetic scores remain uncertain, while the worthiness of excluding patients with severe comorbidities and aged individuals is still debated.
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Affiliation(s)
- Cristina Della Corte
- Department of Medicine, First Division of Gastroenterology, Centro AM e A Migliavacca for the Study of Liver Disease, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico and Università degli Studi di Milano, Milan, Italy
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Mossuz P, Bouamrani A, Brugière S, Arlotto M, Hermouet S, Lippert E, Laporte F, Girodon F, Dobo I, Vincent P, Garin J, Cahn JY, Berger F. Apolipoprotein A1: A new serum marker correlated to JAK2 V617F proportion at diagnosis in patients with polycythemia vera. Proteomics Clin Appl 2012; 1:1605-12. [PMID: 21136658 DOI: 10.1002/prca.200601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Polycythemia vera (PV) is a myeloproliferative disorder (MPD) characterized by an acquired gain-of-function mutation of the JAK2 protein (JAK2 V617F). Allele-specific quantitative PCR has showed a JAK2 V617F dosage effect on haematological and clinical parameters of PV at diagnosis, but it is unknown whether the level of certain serum proteins might correlate with the proportion of mutated JAK2. Taking into account that such proteins could represent useful prognostic marker, we investigated the serum protein profile of PV patients by SELDI-TOF MS. We identified apolipoprotein A1 (Apo-A1) as a serum marker correlated to the percentage of JAK2 V617F alleles; Apo-A1 expression being the highest for PV patients with more than 75% of mutated alleles. Immuno-assay on an automated random immuno-analyser confirmed the correlation between Apo-A1 concentrations and JAK2 V617F percentages, and showed that serum Apo-A1 assay allowed the specific discrimination of PV patients with high levels of mutated alleles (≥75%). These data suggest that Apo-A1 assay could be a useful assay for the stratification of PV patients at diagnosis.
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Affiliation(s)
- Pascal Mossuz
- Laboratoire d'hématologie cellulaire et moléculaire, DBPC, CHU Grenoble, France.
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The application of a three-step serum proteome analysis for the discovery and identification of novel biomarkers of hepatocellular carcinoma. INTERNATIONAL JOURNAL OF PROTEOMICS 2012; 2012:623190. [PMID: 22957256 PMCID: PMC3431084 DOI: 10.1155/2012/623190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 06/05/2012] [Indexed: 02/07/2023]
Abstract
The representative tumor markers for HCC, AFP, and PIVKA-II are not satisfactory in terms of sensitivity and specificity in the early diagnosis of HCC. In search for novel markers for HCC, three-step proteome analyses were carried out in serum samples obtained from 12 patients with HCC and 10 with LC. As a first step, serum samples were subjected to antibody-based immunoaffinity column system that simultaneously removes twelve of abundant serum proteins. The concentrated flow-through was then fractionated using reversed-phase HPLC. Proteins obtained in each fraction were separated by SDS-PAGE. Serum samples obtained from patient with HCC and with LC were analyzed in parallel and their protein expression patterns were compared. A total of 83 protein bands were found to be upregulated in HCC serum. All the protein bands, the intensity of which was different between HCC and LC groups, were identified. Among them, clusterin was most significantly overexpressed (P = 0.023). The overexpression of serum clusterin was confirmed by ELISA using another validation set of HCC samples. Furthermore, serum clusterin was elevated in 40% of HCC cases in which both AFP and PIVKA-II were within their cut-off values. These results suggested that clusterin is a potential novel serum marker for HCC.
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Hu YB, Lin HL, Hao MZ, Ye YB, Chen HJ, Chen QZ, Chen Q. Application of surface-enhanced laser desorption ionization time-of-flight mass spectrometry to the diagnosis and evaluation of interventional effect in patients with hepatocellular carcinoma. Shijie Huaren Xiaohua Zazhi 2012; 20:1107-1111. [DOI: 10.11569/wcjd.v20.i13.1107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To establish a serum protein pattern model for diagnosing hepatocellular carcinoma (HCC) by using the surface-enhanced laser desorption ionization time-of-fligh mass spectrometry (SELDI-TOF-MS), and to evaluate the value of this model in predicting the effect of interventional treatment for HCC.
METHODS: Serum samples collected from patients with HCC (n = 60) and healthy people (n = 60) were used for SELDI-TOF-MS on CM10 chips. The proteomic spectra were analyzed by using the Biomarker Wizard software. The diagnosis model was established by using the Biomarker Pattern software.
RESULTS: Three significantly different protein peaks were found in serum samples between HCC patients and healthy controls. A protein peak at 6 992 Da showed higher expression and the other two protein peaks (4 182 Da, 5 710 Da) showed lower expression in HCC patients than in healthy people. The diagnostic model containing these three candidate biomarkers could distinguish patients with HCC from healthy controls with a sensitivity of 93.3% (28/30), a specificity of 90.0% (27/30), an accuracy of 91.7% (55/60), and a Youden index value of 0.833. The protein peak at 4 182 Da was significantly decreased one month after interventional treatment in HCC patients (P < 0.05).
CONCLUSION: The diagnostic model developed by using SELDI-TOF-MS allows efficiently identifying patients with HCC and may play a valuable role in the diagnosis of HCC. The protein peak at 4 182 Da is helpful for the evaluation of interventional curative effect in HCC patients.
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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: 2.9] [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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A classification method based on principal components of SELDI spectra to diagnose of lung adenocarcinoma. PLoS One 2012; 7:e34457. [PMID: 22461913 PMCID: PMC3312904 DOI: 10.1371/journal.pone.0034457] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 03/01/2012] [Indexed: 12/20/2022] Open
Abstract
Purpose Lung cancer is the leading cause of cancer death worldwide, but techniques for effective early diagnosis are still lacking. Proteomics technology has been applied extensively to the study of the proteins involved in carcinogenesis. In this paper, a classification method was developed based on principal components of surface-enhanced laser desorption/ionization (SELDI) spectral data. This method was applied to SELDI spectral data from 71 lung adenocarcinoma patients and 24 healthy individuals. Unlike other peak-selection-based methods, this method takes each spectrum as a unity. The aim of this paper was to demonstrate that this unity-based classification method is more robust and powerful as a method of diagnosis than peak-selection-based methods. Results The results showed that this classification method, which is based on principal components, has outstanding performance with respect to distinguishing lung adenocarcinoma patients from normal individuals. Through leaving-one-out, 19-fold, 5-fold and 2-fold cross-validation studies, we found that this classification method based on principal components completely outperforms peak-selection-based methods, such as decision tree, classification and regression tree, support vector machine, and linear discriminant analysis. Conclusions and Clinical Relevance The classification method based on principal components of SELDI spectral data is a robust and powerful means of diagnosing lung adenocarcinoma. We assert that the high efficiency of this classification method renders it feasible for large-scale clinical use.
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Proteomic assessment of markers for malignancy in the mucus of intraductal papillary mucinous neoplasms of the pancreas. Pancreas 2012; 41:169-74. [PMID: 22076567 DOI: 10.1097/mpa.0b013e3182289356] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Intraductal papillary mucinous neoplasms (IPMN) of the pancreas evolve from dysplasia to invasive adenocarcinoma. The aims of this study were to look for candidate protein profiles in IPMN mucus according to histological grade, using a differential proteomic technique, and to highlight protein peaks associated with malignant transformation. METHODS Forty-three mucus samples obtained from surgically resected IPMN and categorized as benign (low/moderate dysplasia) or malignant (severe dysplasia/invasive adenocarcinoma) in 21 and 22 patients, respectively. A surface-enhanced laser desorption ionization time-of-flight mass spectrometry was used to determine candidate protein expression profiles. Protein peaks that significantly differed between benign/malignant IPMN (area under curve > 0.88; P < 10; high intensity) were identified using adapted software. RESULTS Among 952 protein peaks, 31 were differentially expressed in benign/malignant IPMN (P < 0.001). Among them, 5 candidate proteins of interest (mass-to-charge ratio [m/z]: 5217, 6326, 6719, 10,453, and 10,849 d) were selected by their high diagnostic accuracy and ability to distinguish between malignant and benign tumors. No correlation was found between peak profiles and duct involvement. CONCLUSIONS Carcinogenic process in IPMN is associated with changes in mucus proteome with characteristic peaks that could be potential candidate biomarkers of malignancy. ABBREVIATIONS IPMN - intraductal papillary mucinous neoplasm, EPC - extrapancreatic cancer, MRI - magnetic resonance imaging, ERCP - endoscopic retrograde cholangiopancreatography.
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Henkel C, Schwamborn K, Zimmermann HW, Tacke F, Kühnen E, Odenthal M, Groseclose MR, Caprioli RM, Weiskirchen R. From proteomic multimarker profiling to interesting proteins: thymosin-β(4) and kininogen-1 as new potential biomarkers for inflammatory hepatic lesions. J Cell Mol Med 2012; 15:2176-88. [PMID: 21496200 PMCID: PMC4394227 DOI: 10.1111/j.1582-4934.2010.01204.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Despite tremendous efforts in disclosing the pathophysiological and epidemiological factors associated with liver fibrogenesis, non-invasive diagnostic measures to estimate the clinical outcome and progression of liver fibrogenesis are presently limited. Therefore, there is a mandatory need for methodologies allowing the reasonable and reliable assessment of the severity and/or progression of hepatic fibrogenesis. We here performed proteomic serum profiling by matrix-assisted laser desorption ionization time-of-flight mass spectrometry in 179 samples of patients chronically infected with hepatitis C virus and 195 control sera. Multidimensional analysis of spectra allowed the definition of algorithms capable to distinguish class-specific protein expression profiles in serum samples. Overall about 100 peaks could be detected per single spectrum. Different algorithms including protein peaks in the range of 2000 and 10,000 Da were generated after pre-fractionation on a weak cation exchange surface. A specificity of 93% with a sensitivity of 86% as mean of the test set results was found, respectively. The nature of three of these protein peaks that belonged to kininogen-1 and thymosin-β4 was further analysed by tandem mass spectrometry (MS)/MS. We further found that kininogen-1 mRNA was significantly down-regulated in cirrhotic livers. We have identified kininogen-1 and thymosin-β4 as potential new biomarkers for human chronic hepatitis C and conclude that serum profiling is a reliable technique to identify hepatitis-associated expression patterns. Based on the high throughput capability, the identified differential protein panel may serve as a diagnostic marker and warrants further validation in larger cohorts.
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Affiliation(s)
- Corinna Henkel
- Institute of Pathology, RWTH University Hospital Aachen, Aachen, Germany
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Circulating tumor cells measurements in hepatocellular carcinoma. Int J Hepatol 2012; 2012:684802. [PMID: 22690340 PMCID: PMC3368319 DOI: 10.1155/2012/684802] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/24/2012] [Indexed: 02/06/2023] Open
Abstract
Liver cancer is the fifth most common cancer in men and the seventh in women. During the past 20 years, the incidence of HCC has tripled while the 5-year survival rate has remained below 12%. The presence of circulating tumor cells (CTC) reflects the aggressiveness nature of a tumor. Many attempts have been made to develop assays that reliably detect and enumerate the CTC during the development of the HCC. In this case, the challenges are (1) there are few markers specific to the HCC (tumor cells versus nontumor cells) and (2) they can be used to quantify the number of CTC in the bloodstream. Another technical challenge consists of finding few CTC mixed with million leukocytes and billion erythrocytes. CTC detection and identification can be used to estimate prognosis and may serve as an early marker to assess antitumor activity of treatment. CTC can also be used to predict progression-free survival and overall survival. CTC are an interesting source of biological information in order to understand dissemination, drug resistance, and treatment-induced cell death. Our aim is to review and analyze the different new methods existing to detect, enumerate, and characterize the CTC in the peripheral circulation of patients with HCC.
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Identification of Regional Lymph Node Involvement of Colorectal Cancer by Serum SELDI Proteomic Patterns. Gastroenterol Res Pract 2011; 2011:784967. [PMID: 22253617 PMCID: PMC3255105 DOI: 10.1155/2011/784967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 09/29/2011] [Indexed: 12/18/2022] Open
Abstract
Background. To explore the application of serum proteomic patterns for the preoperative detection of regional lymph node involvement of colorectal cancer (CRC). Methods. Serum samples were applied to immobilized metal affinity capture ProteinChip to generate mass spectra by Surface-Enhanced Laser Desorption/ionization Time-of-Flight Mass Spectrometry (SELDI-TOF-MS). Proteomic spectra of serum samples from 70 node-positive CRC patients and 75 age- and gender-matched node-negative CRC patients were employed as a training set, and a classification tree was generated by using Biomarker Pattern Software package. The validity of the classification tree was then challenged with a blind test set including another 65 CRC patients. Results. The software identified an average of 46 mass peaks/spectrum and 5 of the identified peaks at m/z 3,104, 3,781, 5,867, 7,970, and 9,290 were used to construct the classification tree. The classification tree separated effectively node-positive CRC patients from node-negative CRC patients, achieving a sensitivity of 94.29% and a specificity of 100.00%. The blind test challenged the model independently with a sensitivity of 91.43% a specificity of 96.67%. Conclusions. The results indicate that SELDI-TOF-MS can correctly distinguish node-positive CRC patients from node-negative ones and show great potential for preoperative screening for regional lymph node involvement of CRC.
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Krisp C, Randall SA, McKay MJ, Molloy MP. Towards clinical applications of selected reaction monitoring for plasma protein biomarker studies. Proteomics Clin Appl 2011; 6:42-59. [PMID: 22213646 DOI: 10.1002/prca.201100062] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 10/21/2011] [Accepted: 10/25/2011] [Indexed: 01/13/2023]
Abstract
The widespread clinical adoption of protein biomarkers with diagnostic, prognostic and/or predictive value remains a formidable challenge for the biomedical community. From discovery to validation, the path to biomarkers of clinical relevance abounds with many protein candidates, yet so few concrete examples have been substantiated. In this review, we focus on the recent adoption of selected reaction monitoring (SRM) of plasma proteins in the path to clinical use for a broad range of diseases including cancer, cardiovascular disease, genetic disorders and various metabolic disorders. Recent progress reveals a promising outlook for clinical applications using SRM, which now provides the routine analysis of clinically relevant protein markers at low nanogram per millilitre in plasma.
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Affiliation(s)
- Christoph Krisp
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
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Findeisen P, Neumaier M. Functional protease profiling for diagnosis of malignant disease. Proteomics Clin Appl 2011; 6:60-78. [PMID: 22213637 DOI: 10.1002/prca.201100058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/27/2011] [Accepted: 10/19/2011] [Indexed: 12/24/2022]
Abstract
Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches.
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Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany.
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DI STASIO MICHELE, VOLPE MARIAGRAZIA, COLONNA GIOVANNI, NAZZARO MELISSA, POLIMENO MIRIAM, SCALA STEFANIA, CASTELLO GIUSEPPE, COSTANTINI SUSAN. A possible predictive marker of progression for hepatocellular carcinoma. Oncol Lett 2011; 2:1247-1251. [PMID: 22848296 PMCID: PMC3406508 DOI: 10.3892/ol.2011.378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/18/2011] [Indexed: 01/01/2023] Open
Abstract
The correlation between decreased levels of selenium and increased DNA damage and oxidative stress shows the significance of this trace element. A number of studies have provided evidence for lower serum, plasma and tissue levels of selenium in patients with various diseases and types of cancer. In this study, liver selenium concentrations were measured in tissue samples of patients with hepatocellular carcinoma (HCC) by atomic absorption spectrometry. The results showed that the selenium concentrations decreased when the malignant grade increased. Furthermore, a significant correlation was found between selenium levels and human selenium binding protein-1 (SELENBP1) down-regulation in the liver. Therefore, we suggest that the evaluation of selenium and SELENBP1 concentrations can be used for improving the prognosis of HCC.
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Affiliation(s)
| | | | - GIOVANNI COLONNA
- Department of Biochemistry and Biophysics and Interdepartmental Research Center for Computational and Biotechnological Sciences (CRISCEB), Second University of Naples, Naples
| | | | | | - STEFANIA SCALA
- ‘G. Pascale Foundation’ National Cancer Institute, Naples
| | - GIUSEPPE CASTELLO
- ‘G. Pascale Foundation’ National Cancer Institute, Cancer Research Center, Mercogliano, Avellino, Italy
| | - SUSAN COSTANTINI
- ‘G. Pascale Foundation’ National Cancer Institute, Cancer Research Center, Mercogliano, Avellino, Italy
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Lee JY, Kim JY, Park GW, Cheon MH, Kwon KH, Ahn YH, Moon MH, Lee HJ, Paik YK, Yoo JS. Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. Mol Cell Proteomics 2011; 10:M111.009290. [PMID: 21940909 DOI: 10.1074/mcp.m111.009290] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A simple mass spectrometric approach for the discovery and validation of biomarkers in human plasma was developed by targeting nonglycosylated tryptic peptides adjacent to glycosylation sites in an N-linked glycoprotein, one of the most important biomarkers for early detection, prognoses, and disease therapies. The discovery and validation of novel biomarkers requires complex sample pretreatment steps, such as depletion of highly abundant proteins, enrichment of desired proteins, or the development of new antibodies. The current study exploited the steric hindrance of glycan units in N-linked glycoproteins, which significantly affects the efficiency of proteolytic digestion if an enzymatically active amino acid is adjacent to the N-linked glycosylation site. Proteolytic digestion then results in quantitatively different peptide products in accordance with the degree of glycosylation. The effect of glycan steric hindrance on tryptic digestion was first demonstrated using alpha-1-acid glycoprotein (AGP) as a model compound versus deglycosylated alpha-1-acid glycoprotein. Second, nonglycosylated tryptic peptide biomarkers, which generally show much higher sensitivity in mass spectrometric analyses than their glycosylated counterparts, were quantified in human hepatocellular carcinoma plasma using a label-free method with no need for N-linked glycoprotein enrichment. Finally, the method was validated using a multiple reaction monitoring analysis, demonstrating that the newly discovered nonglycosylated tryptic peptide targets were present at different levels in normal and hepatocellular carcinoma plasmas. The area under the receiver operating characteristic curve generated through analyses of nonglycosylated tryptic peptide from vitronectin precursor protein was 0.978, the highest observed in a group of patients with hepatocellular carcinoma. This work provides a targeted means of discovering and validating nonglycosylated tryptic peptides as biomarkers in human plasma, without the need for complex enrichment processes or expensive antibody preparations.
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Affiliation(s)
- Ju Yeon Lee
- Division of Mass Spectrometry, Korea Basic Science Institute, Ochang-Myun, Cheongwon-Gun, Republic of Korea
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Kadowaki M, Sangai T, Nagashima T, Sakakibara M, Yoshitomi H, Takano S, Sogawa K, Umemura H, Fushimi K, Nakatani Y, Nomura F, Miyazaki M. Identification of vitronectin as a novel serum marker for early breast cancer detection using a new proteomic approach. J Cancer Res Clin Oncol 2011; 137:1105-15. [PMID: 21253761 DOI: 10.1007/s00432-010-0974-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 12/28/2010] [Indexed: 01/22/2023]
Abstract
PURPOSE Breast cancer is the most frequent malignancy in women. However, no useful serum markers with high sensitivity and specificity for the detection of early breast cancer have been identified. The search for biological markers of early breast cancer is of continual interest in experimental and clinical breast cancer research. We recently described a simple and highly reproducible three-step proteome analysis for identifying potential disease-marker candidates among the low-abundance serum proteins. METHODS Serum samples from breast ductal carcinoma in situ (DCIS) patients and normal controls were subjected to a three-step serum proteome analysis. The steps were the following: first, immunodepletion of most abundant proteins; second, fractionation using reverse-phase high-performance liquid chromatography; and third, separation using two-dimensional electrophoresis (2-DE). Differences revealed by protein staining were further confirmed by Western blotting, immunohistochemical staining, and enzyme-linked immunosorbent assays (ELISA). RESULTS Twenty-two upregulated and 26 downregulated spots were detected on the 2-DE gels, and a total of 33 proteins were identified by liquid chromatography and tandem mass spectrometry. Western blotting confirmed that the level of vitronectin was significantly increased in DCIS patients compared with that of normal controls. Immunohistochemical staining of vitronectin in breast cancer tissue revealed high expression in small vessel walls surrounding cancer cells and the extracellular matrix of stroma. Moreover, vitronectin serum concentrations, as measured by ELISA, were significantly increased in patients with DCIS or more advanced breast cancer compared with those of normal controls. CONCLUSIONS Vitronectin could serve as a promising serum marker for the detection of primary breast cancer.
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MESH Headings
- Aged
- Biomarkers, Tumor/blood
- Blotting, Western
- Breast Neoplasms/blood
- Breast Neoplasms/diagnosis
- Carcinoma, Ductal, Breast/blood
- Carcinoma, Ductal, Breast/diagnosis
- Carcinoma, Intraductal, Noninfiltrating/blood
- Carcinoma, Intraductal, Noninfiltrating/diagnosis
- Early Detection of Cancer
- Electrophoresis, Gel, Two-Dimensional
- Enzyme-Linked Immunosorbent Assay
- Female
- Humans
- Middle Aged
- Proteome/analysis
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Vitronectin/blood
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Affiliation(s)
- Masami Kadowaki
- Department of General Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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