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Wang C, Yang Z, Xu E, Shen X, Wang X, Li Z, Yu H, Chen K, Hu Q, Xia X, Liu S, Guan W. Apolipoprotein C-II induces EMT to promote gastric cancer peritoneal metastasis via PI3K/AKT/mTOR pathway. Clin Transl Med 2021; 11:e522. [PMID: 34459127 PMCID: PMC8351524 DOI: 10.1002/ctm2.522] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/18/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Peritoneal metastasis (PM) occurs frequently in patients with gastric cancer (GC) and confers poor survival. Lipid metabolism acts as a non-negligible regulator in epithelial-mesenchymal transition (EMT), which is crucial for the metastasis of GC. As apolipoprotein C2 (APOC2) is a key activator of lipoprotein lipase for triglyceride metabolism, the exact mechanism of APOC2 remains largely unknown in GC. METHODS Tandem mass tags identified differentially expressed proteins between human PM and GC tissues, and showed that APOC2 overexpressed in PM tissues, which was further confirmed by immunoblotting, immunohistochemistry, and ELISA. Global gene expression changes were identified in APOC2 knockdown cells via RNA-sequencing. The role of APOC2 in lipid metabolism of GC cells was assessed via the Seahorse XF analyzer and lipid staining assays. The biological role of APOC2 in GC cells was determined by 3D Spheroid invasion, apoptosis, colony formation, wound healing, transwell assay, and mouse models. The interaction between APOC2 and CD36 was analyzed by co-immunoprecipitation and biolayer interferometry. The underlying mechanisms were investigated using western blot technique. RESULTS APOC2 overexpressed in GC PM tissues. Upregulation of APOC2 correlated with a poor prognosis in GC patients. APOC2 promoted GC cell invasion, migration, and proliferation via CD36-mediated PI3K/AKT/mTOR signaling activation. Furthermore, APOC2-CD36 axis upregulated EMT markers of GC cells via increasing the phosphorylation of PI3K, AKT, and mTOR. Knockdown either APOC2 or CD36 inhibited the malignant phenotype of cancer cells, and delayed GC PM progression in murine GC models. CONCLUSION APOC2 cooperates with CD36 to induce EMT to promote GC PM via PI3K/AKT/mTOR pathway. APOC2-CD36 axis may be a potential target for the treatment of aggressive GC.
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Affiliation(s)
- Chao Wang
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Zhi Yang
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - En Xu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xiaofei Shen
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xingzhou Wang
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Zijian Li
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - Heng Yu
- Department of General SurgeryNanjing Drum Tower Hospital Clinical College of Nanjing Medical UniversityNanjingChina
| | - Kai Chen
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Qiongyuan Hu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Xuefeng Xia
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Song Liu
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
| | - Wenxian Guan
- Department of General Surgery, Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjingChina
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Zheng JS, Wei RY, Wang Z, Zhu TT, Ruan HR, Wei X, Hou KW, Wu R. Serum proteomics analysis of feline mammary carcinoma based on label-free and PRM techniques. J Vet Sci 2020; 21:e45. [PMID: 32476319 PMCID: PMC7263907 DOI: 10.4142/jvs.2020.21.e45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Feline mammary carcinoma is the third most common cancer that affects female cats. Objectives The purpose of this study was to screen differential serum proteins in feline and clarify the relationship between them and the occurrence of feline mammary carcinoma. Methods Chinese pastoral cats were used as experimental animals. Six serum samples from cats with mammary carcinoma (group T) and six serum samples from healthy cats (group C) were selected. Differential protein analysis was performed using a Label-free technique, while parallel reaction monitoring (PRM) was performed to verify the screened differential proteins. Results A total of 82 differential proteins were detected between group T and group C, of which 55 proteins were down regulated and 27 proteins were up regulated. Apolipoprotein A-I, Apolipoprotein A-II (ApoA-II), Apolipoprotein B (ApoB), Apolipoprotein C-III (ApoC-III), coagulation factor V, coagulation factor X, C1q, albumen (ALB) were all associated with the occurrence of feline mammary carcinoma. Differential proteins were involved in a total of 40 signaling pathways, among which the metabolic pathways associated with feline mammary carcinoma were the complement and coagulation cascade and cholesterol metabolism. According to the Label-free results, ApoB, ApoC-III, ApoA-II, FN1, an uncharacterized protein, and ALB were selected for PRM target verification. The results were consistent with the trend of the label-free. Conclusions This experimen is the first to confirm ApoA-II and ApoB maybe new feline mammary carcinoma biomarkers and to analyze their mechanisms in the development of such carcinoma in feline.
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Affiliation(s)
- Jia San Zheng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ren Yue Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Zheng Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ting Ting Zhu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Hong Ri Ruan
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Xue Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Kai Wen Hou
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Rui Wu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, China.
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de Oliveira G, Paccielli Freire P, Santiloni Cury S, de Moraes D, Santos Oliveira J, Dal-Pai-Silva M, do Reis PP, Francisco Carvalho R. An Integrated Meta-Analysis of Secretome and Proteome Identify Potential Biomarkers of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2020; 12:E716. [PMID: 32197468 PMCID: PMC7140071 DOI: 10.3390/cancers12030716] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is extremely aggressive, has an unfavorable prognosis, and there are no biomarkers for early detection of the disease or identification of individuals at high risk for morbidity or mortality. The cellular and molecular complexity of PDAC leads to inconsistences in clinical validations of many proteins that have been evaluated as prognostic biomarkers of the disease. The tumor secretome, a potential source of biomarkers in PDAC, plays a crucial role in cell proliferation and metastasis, as well as in resistance to treatments, which together contribute to a worse clinical outcome. The massive amount of proteomic data from pancreatic cancer that has been generated from previous studies can be integrated and explored to uncover secreted proteins relevant to the diagnosis and prognosis of the disease. The present study aimed to perform an integrated meta-analysis of PDAC proteome and secretome public data to identify potential biomarkers of the disease. Our meta-analysis combined mass spectrometry data obtained from two systematic reviews of the pancreatic cancer literature, which independently selected 20 studies of the secretome and 35 of the proteome. Next, we predicted the secreted proteins using seven in silico tools or databases, which identified 39 secreted proteins shared between the secretome and proteome data. Notably, the expression of 31 genes of these secretome-related proteins was upregulated in PDAC samples from The Cancer Genome Atlas (TCGA) when compared to control samples from TCGA and The Genotype-Tissue Expression (GTEx). The prognostic value of these 39 secreted proteins in predicting survival outcome was confirmed using gene expression data from four PDAC datasets (validation set). The gene expression of these secreted proteins was able to distinguish high- and low-survival patients in nine additional tumor types from TCGA, demonstrating that deregulation of these secreted proteins may also contribute to the prognosis in multiple cancers types. Finally, we compared the prognostic value of the identified secreted proteins in PDAC biomarkers studies from the literature. This analysis revealed that our gene signature performed equally well or better than the signatures from these previous studies. In conclusion, our integrated meta-analysis of PDAC proteome and secretome identified 39 secreted proteins as potential biomarkers, and the tumor gene expression profile of these proteins in patients with PDAC is associated with worse overall survival.
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Affiliation(s)
- Grasieli de Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Paula Paccielli Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Jakeline Santos Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Patrícia Pintor do Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil;
- Experimental Research Unity, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-970, São Paulo, Brazil
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
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4
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Zhao Y, Zhang Q, Zhang L, Zhang W. Preparation of mesoporous carbon material derived from Metal-Organic Frameworks and its application in selective capture of endogenous peptides from human serum. Talanta 2019; 200:443-449. [DOI: 10.1016/j.talanta.2019.02.097] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/11/2019] [Accepted: 02/28/2019] [Indexed: 12/29/2022]
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5
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Bennike TB, Bellin MD, Xuan Y, Stensballe A, Møller FT, Beilman GJ, Levy O, Cruz-Monserrate Z, Andersen V, Steen J, Conwell DL, Steen H. A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation. J Proteome Res 2018; 17:1983-1992. [PMID: 29641209 DOI: 10.1021/acs.jproteome.8b00111] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Blood is an ideal body fluid for the discovery or monitoring of diagnostic and prognostic protein biomarkers. However, discovering robust biomarkers requires the analysis of large numbers of samples to appropriately represent interindividual variability. To address this analytical challenge, we established a high-throughput and cost-effective proteomics workflow for accurate and comprehensive proteomics at an analytical depth applicable for clinical studies. For validation, we processed 1 μL each from 62 plasma samples in 96-well plates and analyzed the product by quantitative data-independent acquisition liquid chromatography/mass spectrometry; the data were queried using feature quantification with Spectronaut. To show the applicability of our workflow to serum, we analyzed a unique set of samples from 48 chronic pancreatitis patients, pre and post total pancreatectomy with islet autotransplantation (TPIAT) surgery. We identified 16 serum proteins with statistically significant abundance alterations, which represent a molecular signature distinct from that of chronic pancreatitis. In summary, we established a cost-efficient high-throughput workflow for comprehensive proteomics using PVDF-membrane-based digestion that is robust, automatable, and applicable to small plasma and serum volumes, e.g., finger stick. Application of this plasma/serum proteomics workflow resulted in the first mapping of the molecular implications of TPIAT on the serum proteome.
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Affiliation(s)
- Tue Bjerg Bennike
- Department of Pathology , Harvard Medical School , Boston , Massachusetts , United States.,Department of Pathology , Boston Children's Hospital , Boston , Massachusetts , United States.,Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States.,Department of Health Science and Technology , Aalborg University , Aalborg , Denmark
| | - Melena D Bellin
- Department of Surgery , University of Minnesota Medical Center , Minneapolis , Minnesota , United States.,Department of Pediatrics , University of Minnesota Medical Center , Minneapolis , Minnesota , United States
| | - Yue Xuan
- Thermo Fisher Scientific , Bremen , Germany
| | - Allan Stensballe
- Department of Health Science and Technology , Aalborg University , Aalborg , Denmark
| | | | - Gregory J Beilman
- Department of Surgery , University of Minnesota Medical Center , Minneapolis , Minnesota , United States
| | - Ofer Levy
- Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States.,Division of Infectious Diseases, Department of Medicine , Boston Children's Hospital , Boston , Massachusetts , United States
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology and Nutrition , The Ohio State University Wexner Medical Center , Columbus , Ohio United States
| | - Vibeke Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland , Hospital of Southern Jutland , Aabenraa , Denmark.,Institute of Molecular Medicine , University of Southern Denmark , Odense , Denmark
| | - Judith Steen
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, and Department of Neurology , Harvard Medical School , Boston , Massachusetts , United States
| | - Darwin L Conwell
- Division of Gastroenterology, Hepatology and Nutrition , The Ohio State University Wexner Medical Center , Columbus , Ohio United States
| | - Hanno Steen
- Department of Pathology , Harvard Medical School , Boston , Massachusetts , United States.,Department of Pathology , Boston Children's Hospital , Boston , Massachusetts , United States.,Precision Vaccines Program , Boston Children's Hospital , Boston , Massachusetts , United States
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6
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Al-Moghrabi NM. BRCA1 promoter methylation in peripheral blood cells and predisposition to breast cancer. J Taibah Univ Med Sci 2017; 12:189-193. [PMID: 31435238 PMCID: PMC6695050 DOI: 10.1016/j.jtumed.2017.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/19/2017] [Accepted: 01/22/2017] [Indexed: 11/08/2022] Open
Abstract
Early onset breast cancer is a common malignancy and cause of death among young women in KSA. In addition, the data from women have demonstrated that most patients present late with an advanced stage. The early detection of this disease would not only save patients' lives but would also have the potential to reduce the budget and the time required for treating and nursing advanced breast cancer patients. This review highlights the risk of developing breast cancer in women with the methylated BRCA1 promoter in their white blood cells and proposes the potential use of this epigenetic modification as a powerful molecular marker for the early detection of breast cancer.
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Affiliation(s)
- Nisreen M. Al-Moghrabi
- Cancer Epigenetic Section, Molecular Oncology Department, King Faisal Specialist Hospital and Research Centre, Riyadh, KSA
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7
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Gan Y, Zhang Q, Chen Y, Zhao Y, Xiong Z, Zhang L, Zhang W. Selective extraction of endogenous peptides from human serum with magnetic mesoporous carbon composites. Talanta 2016; 161:647-654. [PMID: 27769460 DOI: 10.1016/j.talanta.2016.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/25/2016] [Accepted: 09/03/2016] [Indexed: 12/22/2022]
Abstract
Highly sensitive and selective enrichment of endogenous peptides or proteins from complex bio-system takes a significant important place to the proteomic. In this work, a unique Fe3O4@2SiO2@mSiO2-C nanomaterial was synthesized, contributing to the separation and enrichment of low concentration peptides from complex mixture. The highly ordered mesoporous carbon structure render the nanospheres with unique properties of strongly connected pore channels, strong hydrophobic properties, high specific surface area (254.90m2/g), uniform pore size (3.61nm). Which made it a promising candidates for the efficient enrichment of peptides through hydrophobic-hydrophobic interaction with low detection limit (0.2fmol), superb size-exclusion of high molecular weight proteins, highly selectivity for BSA digest (molar ratio of BSA tryptic digests/BSA, 1:400), ideal peptides recovery (about 87.5%), wonderful repeatability (RSD less than 25%). Moreover, the as-prepared Fe3O4@2SiO2@mSiO2-C nanoparticles were successfully enriched 2198 endogenous peptides from human serum, which fully indicated that the mesoporous carbon nanoparticles was a promising candidate for isolating proteins or peptides from complex biologicals.
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Affiliation(s)
- Yangyang Gan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Quanqing Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China
| | - Yajing Chen
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Yiman Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China
| | - Zhichao Xiong
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, PR China
| | - Lingyi Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, PR China.
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Vance DT, Dufresne J, Florentinus-Mefailoski A, Tucholska M, Trimble W, Grinstein S, Marshall JG. A phagocytosis assay for oxidized low-density lipoprotein versus immunoglobulin G-coated microbeads in human U937 macrophages. Anal Biochem 2016; 500:24-34. [DOI: 10.1016/j.ab.2016.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/24/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
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9
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Diagnostic and prognostic role of serum protein peak at 6449 m/z in gastric adenocarcinoma based on mass spectrometry. Br J Cancer 2016; 114:929-38. [PMID: 27002935 PMCID: PMC4984799 DOI: 10.1038/bjc.2016.52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/03/2016] [Accepted: 02/09/2016] [Indexed: 02/07/2023] Open
Abstract
Background: Gastric cancer (GC) is a highly aggressive cancer type associated with significant mortality owing to delayed diagnosis and non-specific symptoms observed in the early stages. Therefore, identification of novel specific GC serum biomarkers for screening purposes is an urgent clinical requirement. Methods: This study recruited a total of 432 serum samples from 296 GC patients split into the mining and testing sets. We aimed to screen for reliable protein biomarkers from matched serum samples based on mass spectrometry, followed by comparison with three representative conventional markers using receiver operating characteristic and survival curve analyses to ascertain their potential values as diagnostic and prognostic biomarkers for GC. Results: We identified an apoC-III fragment with confirmation in an independent test set from a second hospital. We found that the diagnostic ability of this fragment performed better than current standard GC diagnostic biomarkers both individually and in combination in distinguishing patients with GC from healthy individuals. Moreover, we found that this apoC-III protein fragment represents a more robust potential prognostic factor for GC than the three conventional markers. Conclusions: In view of these findings, we suggest that apoC-III protein fragment is a novel diagnostic and prognostic biomarker, a complement to conventional biomarkers in detecting GC.
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10
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Liu J, Jiang T, Jiang F, Xu D, Wei L, Wang C, Chen Z, Zhang X, Li J. Comparative proteomic analysis of serum diagnosis patterns of sputum smear-positive pulmonary tuberculosis based on magnetic bead separation and mass spectrometry analysis. Int J Clin Exp Med 2015; 8:2077-2085. [PMID: 25932138 PMCID: PMC4402785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/21/2015] [Indexed: 06/04/2023]
Abstract
A major challenge in pulmonary tuberculosis (TB) control is early and accurate diagnosis of sputum smear negative pulmonary TB (SSN-PTB). The patients with SSN-PTB have to wait for a longer period of time before receiving proper treatment than sputum smear positive pulmonary TB (SSP-PTB) patients due to delay in diagnosis. The purpose of this study is to discover potential serum protein biomarkers for SSN-PTB. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) combined with weak cation exchange (WCX) magnetic beads was used to screen serum samples from SSN-PTB patients (N = 66), SSP-PTB patients (N = 49), and healthy volunteers (N = 80). The serum protein profiles were analyzed with Biomarker Wizard system. A classification model was established using Biomarker Pattern Software (BPS). Fifty-eight protein peaks were identified to exhibit significant differences between SSN-PTB, SSP-PTB and healthy control groups (P < 0.05), among which 6 peaks were found to be down-regulated, while 10 peaks were up-regulated gradually in the healthy control, SSN-PTB, and SSP-PTB groups. Twenty-three discriminating m/z peaks were detected between SSN-PTB patients and healthy controls (P < 0.01, Fold ≥ 1.5). The classification tree combined with three protein peaks (2747.0, 4480.0, and 9410.1 Da) could distinguish SSN-PTB patients from healthy controls with a sensitivity of 83.33% and a specificity of 82.50%. Early diagnosis of SSN-PTB disease is critical in order to reduce morbidity and mortality associated with TB. The study will help to clarify the role of differential proteins in the pathogenesis of TB.
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Affiliation(s)
- Jiyan Liu
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, P. R. China
| | - Tingting Jiang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Feng Jiang
- Dongzhimen Hospital Affiliated to Beijing University of Chinese MedicineBeijing, P. R. China
| | - Dandan Xu
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Liliang Wei
- Department of Respiratory Medicine, The Sixth Hospital of ShaoxingShaoxing, P. R. China
| | - Chong Wang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Zhongliang Chen
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Xing Zhang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Jicheng Li
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
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11
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Quantitative evaluation of peptide-extraction methods by HPLC–triple-quad MS–MS. Anal Bioanal Chem 2014; 407:1595-605. [DOI: 10.1007/s00216-014-8389-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/25/2014] [Accepted: 12/02/2014] [Indexed: 12/23/2022]
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12
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Al-Moghrabi N, Nofel A, Al-Yousef N, Madkhali S, Bin Amer SM, Alaiya A, Shinwari Z, Al-Tweigeri T, Karakas B, Tulbah A, Aboussekhra A. The molecular significance of methylated BRCA1 promoter in white blood cells of cancer-free females. BMC Cancer 2014; 14:830. [PMID: 25403427 PMCID: PMC4289167 DOI: 10.1186/1471-2407-14-830] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/23/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND BRCA1 promoter methylation has been detected in DNA from peripheral blood cells of both breast cancer patients and cancer-free females. However, the pathological significance of this epigenetic change in white blood cells (WBC) remains an open question. In this study, we hypothesized that if constitutional BRCA1 methylation reflects an elevated risk for developing breast cancer (BC), WBC that harbor methylated BRCA1 in both cancer-free females and BC patients should exhibit similar molecular changes. METHODS BRCA1 promoter methylation was examined by methylation-specific PCR in WBC from 155 breast cancer patients and 143 cancer-free females. The Human Breast Cancer EpiTect Methyl II Signature PCR Array and The Human Breast Cancer RT2 Profiler™ PCR Array were used to study the methylation status and the expression profile of several breast cancer-related genes, respectively. In addition, we used label-free MS-based technique to study protein expression in plasma. RESULTS We have shown that 14.2% of BC patients and 9.1% of cancer-free females (carriers) harbored methylated BRCA1 promoter in their WBC. Interestingly, 66.7% of patients harbored methylated BRCA1 promoter in both WBC and tumors. Importantly, we have shown the presence of epigenetic changes in 9 other BC-related genes in WBC of both patients and carriers. Additionally, BRCA1 and 15 other important cancer -related genes were found to be differentially expressed in WBC from patients and carriers as compared to controls. Furthermore, we have shown that the carriers exhibited a unique plasma protein pattern different from those of BC patients and controls, with 10 proteins similarly differentially expressed in patients and carriers as compared to controls. CONCLUSIONS The present results suggest the presence of a strong link between aberrant methylation of the BRCA1 promoter in WBC and breast cancer -related molecular changes, which indicate the potential predisposition of the carriers for developing breast cancer. This informs the potential use of the aberrant methylation of BRCA1 promoter in WBC as a powerful non-invasive molecular marker for detecting predisposed individuals at a very early age.
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Affiliation(s)
- Nisreen Al-Moghrabi
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Asmaa Nofel
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Nujoud Al-Yousef
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Safia Madkhali
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Suad M Bin Amer
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Ayodele Alaiya
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Zakia Shinwari
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Taher Al-Tweigeri
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Bedri Karakas
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Asma Tulbah
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
| | - Abdelilah Aboussekhra
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, PO BOX 3354, 11211 Riyadh, Kingdom of Saudi Arabia
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Xiong Z, Ji Y, Fang C, Zhang Q, Zhang L, Ye M, Zhang W, Zou H. Facile Preparation of Core-Shell Magnetic Metal-Organic Framework Nanospheres for the Selective Enrichment of Endogenous Peptides. Chemistry 2014; 20:7389-95. [DOI: 10.1002/chem.201400389] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Indexed: 01/11/2023]
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Nolen BM, Brand RE, Prosser D, Velikokhatnaya L, Allen PJ, Zeh HJ, Grizzle WE, Lomakin A, Lokshin AE. Prediagnostic serum biomarkers as early detection tools for pancreatic cancer in a large prospective cohort study. PLoS One 2014; 9:e94928. [PMID: 24747429 PMCID: PMC3991628 DOI: 10.1371/journal.pone.0094928] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/21/2014] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The clinical management of pancreatic cancer is severely hampered by the absence of effective screening tools. METHODS Sixty-seven biomarkers were evaluated in prediagnostic sera obtained from cases of pancreatic cancer enrolled in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). RESULTS The panel of CA 19-9, OPN, and OPG, identified in a prior retrospective study, was not effective. CA 19-9, CEA, NSE, bHCG, CEACAM1 and PRL were significantly altered in sera obtained from cases greater than 1 year prior to diagnosis. Levels of CA 19-9, CA 125, CEA, PRL, and IL-8 were negatively associated with time to diagnosis. A training/validation study using alternate halves of the PLCO set failed to identify a biomarker panel with significantly improved performance over CA 19-9 alone. When the entire PLCO set was used for training at a specificity (SP) of 95%, a panel of CA 19-9, CEA, and Cyfra 21-1 provided significantly elevated sensitivity (SN) levels of 32.4% and 29.7% in samples collected <1 and >1 year prior to diagnosis, respectively, compared to SN levels of 25.7% and 17.2% for CA 19-9 alone. CONCLUSIONS Most biomarkers identified in previously conducted case/control studies are ineffective in prediagnostic samples, however several biomarkers were identified as significantly altered up to 35 months prior to diagnosis. Two newly derived biomarker combinations offered advantage over CA 19-9 alone in terms of SN, particularly in samples collected >1 year prior to diagnosis. However, the efficacy of biomarker-based tools remains limited at present. Several biomarkers demonstrated significant velocity related to time to diagnosis, an observation which may offer considerable potential for enhancements in early detection.
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Affiliation(s)
- Brian M. Nolen
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Randall E. Brand
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Denise Prosser
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Liudmila Velikokhatnaya
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
| | - Peter J. Allen
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Herbert J. Zeh
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - William E. Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Aleksey Lomakin
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Anna E. Lokshin
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, United States of America
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Ob/Gyn, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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He J, Zeng ZC, Xiang ZL, Yang P. Mass spectrometry-based serum peptide profiling in hepatocellular carcinoma with bone metastasis. World J Gastroenterol 2014; 20:3025-3032. [PMID: 24659894 PMCID: PMC3961966 DOI: 10.3748/wjg.v20.i11.3025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/14/2013] [Accepted: 01/02/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the potential of serum peptides as a diagnostic tool for hepatocellular carcinoma (HCC) with bone metastasis.
METHODS: Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) was used to characterize the serum peptide profile of HCC patients with bone metastasis. Serum samples from 138 HCC patients (66 cases with and 72 cases without bone metastasis) were randomly assigned into a training set (n = 76) and a test set (n = 62). Differential serum peptides were examined using ClinProt magnetic bead-based purification followed by MALDI-TOF-MS. The sequences of differentially expressed serum peptides were identified using liquid chromatography-mass spectrometry. A diagnostic model was established using a learning algorithm of radial basis function neural network verified by a single blind trial. Receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic power of the established model.
RESULTS: Ten peptide peaks were significantly different between HCC patients with or without bone metastasis (P < 0.001). Sequences of seven peptides with mass to charge ratios (m/z) of 1780.7, 1866.5, 2131.6, 2880.4, 1532.4, 2489.8, and 2234.3 were successfully identified. These seven peptides were derived from alpha-fetoprotein, prothrombin, serglycin, isoform 2 of inter-alpha-trypsin inhibitor heavy chain H4, isoform 1 of autophagy-related protein 16-2, and transthyretin and fibrinogen beta chains, respectively. The recognition rate and predictive power of a diagnostic model established on the basis of six significant peptides (m/z for these six peptides were 1535.4, 1780.7, 1866.5, 2131.6, 2880.4, and 2901.9) were 89.47% and 82.89%, respectively. The sensitivity and specificity of this model based upon a single blind trial were 85.29% and 85.71%, respectively. ROC analysis found that the AUC (area under the ROC curve) value was 0.911.
CONCLUSION: Our study suggested that serum peptides may serve as a diagnosis tool for HCC bone metastasis.
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Li C, Xia G, Jianqing Z, Mei Y, Ge B, Li Z. Serum differential protein identification of Xinjiang Kazakh esophageal cancer patients based on the two-dimensional liquid-phase chromatography and LTQ MS. Mol Biol Rep 2014; 41:2893-905. [PMID: 24469726 DOI: 10.1007/s11033-014-3145-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 01/13/2014] [Indexed: 01/30/2023]
Abstract
The aim of this study was to investigate the impact of chemo-radiotherapy on serum protein expression of the esophageal cancer patients and discover potential biomarkers by detecting serum proteins mass spectrometry of the healthy Kazakh people in Xinjiang as well as the patients before and after their chemo-radiotherapy. In order to separate and compare the three serum samples (the healthy group's, the patients' before and after chemo-radiotherapy) with two-dimensional protein liquid chromatography system (Proteome LabTM PF-2D), then detect the differential protein spots with linear trap quadruple mass spectrometer (LTQ MS/MS). (1) The Kazakh esophageal cancer patients got 21 expressed protein spots peaks with significant difference after chemo-radiotherapy compared with before; before the treatment there were 10 different expressed protein spots compared with the healthy group, and after it there were four peaks in the expression of protein spots compared with the healthy group. (2) After LTQ mass spectrometric detection, 22 proteins were up-regulated in serum samples of the healthy group, 22 were up-regulated of the patients before medical treatment and 5 were up-regulated after chemo-radiotherapy. (3) 8 proteins including APOA1 can be served as serum markers in Kazakh esophageal cancer diagnosis, and proteins like CLU can be served as serum markers in judging the resistance and sensitivity towards chemo-radiotherapy. (4) The abnormal expressions of APOC2, APOC3, Antithrombin-III in esophageal cancer were discovered for the first time. Specific protein spots related to Xinjiang Kazakh esophageal cancer diagnosis and chemo-radiotherapy can be identified in the serum, which will probably become a maker in Kazakh esophageal cancer diagnosis and therapeutic evaluation.
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Affiliation(s)
- Cui Li
- Internal Medicine VIP of the First Affiliated Hospital of Xinjiang Medical University, No. 137, Liyushan Road, Xinshi District, Urumqi, 830011, Xinjiang, China
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Ma W, Zhang Y, Miao W, Zhang C, Yu M, Zhang Y, Guo J, Lu H, Wang C. Precisely designed rattle-type mTiO2@P(NIPAM-co-MBA) microspheres with screening gel network for highly selective extraction of phosphopeptidome. RSC Adv 2014. [DOI: 10.1039/c4ra05822d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Rattle-type mTiO2@P(NIPAM-co-MBA) microspheres with a screening gel network shell were elaborately designed and fabricated for highly selective extraction of endogenous phosphopeptidome.
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Affiliation(s)
- Wanfu Ma
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433, China
| | - Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032, People's Republic of China
| | - Weili Miao
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032, People's Republic of China
| | - Cheng Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032, People's Republic of China
| | - Meng Yu
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433, China
| | - Yuting Zhang
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433, China
| | - Jia Guo
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433, China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032, People's Republic of China
| | - Changchun Wang
- State Key Laboratory of Molecular Engineering of Polymers
- Department of Macromolecular Science
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433, China
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Harima Y, Ikeda K, Utsunomiya K, Komemushi A, Kanno S, Shiga T, Tanigawa N. Apolipoprotein C-II is a potential serum biomarker as a prognostic factor of locally advanced cervical cancer after chemoradiation therapy. Int J Radiat Oncol Biol Phys 2013; 87:1155-61. [PMID: 24120821 DOI: 10.1016/j.ijrobp.2013.08.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/30/2013] [Accepted: 08/19/2013] [Indexed: 01/07/2023]
Abstract
PURPOSE To determine pretreatment serum protein levels for generally applicable measurement to predict chemoradiation treatment outcomes in patients with locally advanced squamous cell cervical carcinoma (CC). METHODS AND MATERIALS In a screening study, measurements were conducted twice. At first, 6 serum samples from CC patients (3 with no evidence of disease [NED] and 3 with cancer-caused death [CD]) and 2 from healthy controls were tested. Next, 12 serum samples from different CC patients (8 NED, 4 CD) and 4 from healthy controls were examined. Subsequently, 28 different CC patients (18 NED, 10 CD) and 9 controls were analyzed in the validation study. Protein chips were treated with the sample sera, and the serum protein pattern was detected by surface-enhanced laser desorption and ionization-time-of-flight mass spectrometry (SELDI-TOF MS). Then, single MS-based peptide mass fingerprinting (PMF) and tandem MS (MS/MS)-based peptide/protein identification methods, were used to identify protein corresponding to the detected peak. And then, turbidimetric assay was used to measure the levels of a protein that indicated the best match with this peptide peak. RESULTS The same peak 8918 m/z was identified in both screening studies. Neither the screening study nor the validation study had significant differences in the appearance of this peak in the controls and NED. However, the intensity of the peak in CD was significantly lower than that of controls and NED in both pilot studies (P=.02, P=.04) and validation study (P=.01, P=.001). The protein indicated the best match with this peptide peak at 8918 m/z was identified as apolipoprotein C-II (ApoC-II) using PMF and MS/MS methods. Turbidimetric assay showed that the mean serum levels of ApoC-II tended to decrease in CD group when compared with NED group (P=.078). CONCLUSION ApoC-II could be used as a biomarker for detection in predicting and estimating the radiation treatment outcome of patients with CC.
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Affiliation(s)
- Yoko Harima
- Department of Radiology, Takii Hospital, Kansai Medical University, Moriguchi, Osaka, Japan.
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Choi JW, Liu H, Shin DH, Yu GI, Hwang JS, Kim ES, Yun JW. Proteomic and cytokine plasma biomarkers for predicting progression from colorectal adenoma to carcinoma in human patients. Proteomics 2013; 13:2361-74. [PMID: 23606366 DOI: 10.1002/pmic.201200550] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 12/12/2022]
Abstract
In the present study, we screened proteomic and cytokine biomarkers between patients with adenomatous polyps and colorectal cancer (CRC) in order to improve our understanding of the molecular mechanisms behind turmorigenesis and tumor progression in CRC. To this end, we performed comparative proteomic analysis of plasma proteins using a combination of 2DE and MS as well as profiled differentially regulated cytokines and chemokines by multiplex bead analysis. Proteomic analysis identified 11 upregulated and 13 downregulated plasma proteins showing significantly different regulation patterns with diagnostic potential for predicting progression from adenoma to carcinoma. Some of these proteins have not previously been implicated in CRC, including upregulated leucine-rich α-2-glycoprotein, hemoglobin subunit β, Ig α-2 chain C region, and complement factor B as well as downregulated afamin, zinc-α-2-glycoprotein, vitronectin, and α-1-antichymotrypsin. In addition, plasma levels of three cytokines/chemokines, including interleukin-8, interferon gamma-induced protein 10, and tumor necrosis factor α, were remarkably elevated in patients with CRC compared to those with adenomatous polyps. Although further clinical validation is required, these proteins and cytokines can be established as novel biomarkers for CRC and/or its progression from colon adenoma.
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Affiliation(s)
- Jung-Won Choi
- Department of Biotechnology, Daegu University, Kyungsan, Republic of Korea
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Xue A, Chang JW, Chung L, Samra J, Hugh T, Gill A, Butturini G, Baxter RC, Smith RC. Serum apolipoprotein C-II is prognostic for survival after pancreatic resection for adenocarcinoma. Br J Cancer 2013; 107:1883-91. [PMID: 23169340 PMCID: PMC3504954 DOI: 10.1038/bjc.2012.458] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pancreaticoduodenectomy remains a major undertaking. A preoperative blood test, which could confidently predict the benefits of surgery would improve the selection of pancreatic cancer patients for surgery. This study aimed to identify protein biomarkers prognostic for long-term survival and to validate them with clinico-pathological information. METHODS Serum from 40 preoperative patients was used to train for predictive biomarkers using surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI), and the results were verified on 21 independent samples. Two predictive proteins were identified by tryptic peptide mass fingerprinting and sequencing, and validated on serum from another 57 patients by enzyme-linked immunosorbent assay (ELISA). The influence of these proteins on growth and invasion of two cancer cell lines was tested in-vitro. RESULTS The SELDI panel of m/z 3700, 8222 and 11 522 peaks predicted <12 months' survival (ROC AUC: 0.79, 0.64-0.90; P<0.039). When CA19-9 was added, the ROC AUC increased to 0.95 (0.84-0.99; P<0.0001). The six subjects in the verification group who died within 12 months were correctly classified. The m/z 8222 and 11 522 proteins were identified as Serum ApoC-II and SAA-1, respectively. In the validation samples, ELISA results confirmed that ApoC-II was predictive of survival (Kaplan-Meier P<0.009), but not SAA-I. ApoC-II, CA19-9 and major-vessel involvement independently predicted survival. ApoC-II and SAA-1 increased cell growth and invasion of both cancer cell lines. CONCLUSION Serum ApoC-II, CA19-9 and major-vessel invasion independently predict survival and improves selection of patients for pancreaticoduodenectomy.
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Affiliation(s)
- A Xue
- Department of Gastrointestinal Surgery, University of Sydney, Kolling Institute of Medical Research, St Leonards NSW 2065, Australia
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Huang Y, Zhang X, Jiang W, Wang Y, Jin H, Liu X, Xu C. Discovery of serum biomarkers implicated in the onset and progression of serous ovarian cancer in a rat model using iTRAQ technique. Eur J Obstet Gynecol Reprod Biol 2012; 165:96-103. [DOI: 10.1016/j.ejogrb.2012.06.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/29/2012] [Accepted: 06/26/2012] [Indexed: 10/28/2022]
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Kolusheva S, Yossef R, Kugel A, Hanin-Avraham N, Cohen M, Rubin E, Porgador A. A novel "reactomics" approach for cancer diagnostics. SENSORS 2012; 12:5572-85. [PMID: 22778601 PMCID: PMC3386700 DOI: 10.3390/s120505572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 03/30/2012] [Accepted: 04/23/2012] [Indexed: 02/06/2023]
Abstract
Non-invasive detection and monitoring of lethal diseases, such as cancer, are considered as effective factors in treatment and survival. We describe a new disease diagnostic approach, denoted “reactomics”, based upon reactions between blood sera and an array of vesicles comprising different lipids and polydiacetylene (PDA), a chromatic polymer. We show that reactions between sera and such a lipid/PDA vesicle array produce chromatic patterns which depend both upon the sera composition as well as the specific lipid constituents within the vesicles. The chromatic patterns were processed through machine-learning algorithms, and the bioinformatics analysis could distinguish both between cancer-bearing and healthy patients, respectively, as well between two types of cancers. Size-separation and enzymatic digestion experiments indicate that lipoproteins are the primary components in sera which react with the chromatic biomimetic vesicles. This colorimetric reactomics concept is highly generic, robust, and does not require a priori knowledge upon specific disease markers in sera. Therefore, it could be employed as complementary or alternative approach for disease diagnostics.
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Affiliation(s)
- Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (S.K.); (N.H.-A.)
| | - Rami Yossef
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (R.Y.); (A.K.); (M.C.); (E.R.)
| | - Aleksandra Kugel
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (R.Y.); (A.K.); (M.C.); (E.R.)
| | - Nirit Hanin-Avraham
- Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (S.K.); (N.H.-A.)
| | - Meital Cohen
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (R.Y.); (A.K.); (M.C.); (E.R.)
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (R.Y.); (A.K.); (M.C.); (E.R.)
| | - Angel Porgador
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva 84105, Israel; E-Mails: (R.Y.); (A.K.); (M.C.); (E.R.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +972-8-647-7283; Fax: +972-8-647-7626
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Identification of potential serum biomarkers for Wilms tumor after excluding confounding effects of common systemic inflammatory factors. Mol Biol Rep 2011; 39:5095-104. [PMID: 22160518 DOI: 10.1007/s11033-011-1305-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 11/30/2011] [Indexed: 02/08/2023]
Abstract
Wilms tumor is the most common pediatric tumor of the kidney. Previous studies have identified several serum biomarkers for Wilms tumor; however, they lack sufficient specificity and may not adequately distinguish Wilms tumor from confounding conditions. To date, no specific protein biomarker has been confirmed for this pediatric tumor. To identify novel serum biomarkers for Wilms tumor, we used proteomic technologies to perform protein profiling of serum samples from pre-surgery and post-surgery patients with Wilms tumor and healthy controls. Some common systemic inflammatory factors were included to control for systemic inflammation. By comparing protein peaks among the three groups of sera, we identified two peaks (11,526 and 4,756 Da) showing significant differential expression not only between pre-surgery and control sera but also between pre-surgery and post-surgery sera. These two peaks were identified as serum amyloid A1 (SAA1) and apolipoprotein C-III (APO C-III). Western blot analysis confirmed that both proteins were expressed at higher levels in pre-surgery sera than in post-surgery and control sera. Using the method of leave-1-out for cross detection, we demonstrate that detection of these two candidate biomarkers had high sensitivity and specificity in discriminating pre-surgery sera from post-surgery and normal control sera. Taken together, these findings suggest that SAA1 and APO C-III are two potential biomarkers for Wilms tumor.
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Qin H, Gao P, Wang F, Zhao L, Zhu J, Wang A, Zhang T, Wu R, Zou H. Highly Efficient Extraction of Serum Peptides by Ordered Mesoporous Carbon. Angew Chem Int Ed Engl 2011; 50:12218-21. [DOI: 10.1002/anie.201103666] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 09/27/2011] [Indexed: 01/04/2023]
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Qin H, Gao P, Wang F, Zhao L, Zhu J, Wang A, Zhang T, Wu R, Zou H. Highly Efficient Extraction of Serum Peptides by Ordered Mesoporous Carbon. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103666] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Cohen M, Yossef R, Erez T, Kugel A, Welt M, Karpasas MM, Bones J, Rudd PM, Taieb J, Boissin H, Harats D, Noy K, Tekoah Y, Lichtenstein RG, Rubin E, Porgador A. Serum apolipoproteins C-I and C-III are reduced in stomach cancer patients: results from MALDI-based peptidome and immuno-based clinical assays. PLoS One 2011; 6:e14540. [PMID: 21267442 PMCID: PMC3022591 DOI: 10.1371/journal.pone.0014540] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/22/2010] [Indexed: 12/11/2022] Open
Abstract
Finding new peptide biomarkers for stomach cancer in human sera that can be implemented into a clinically practicable prediction method for monitoring of stomach cancer. We studied the serum peptidome from two different biorepositories. We first employed a C8-reverse phase liquid chromatography approach for sample purification, followed by mass-spectrometry analysis. These were applied onto serum samples from cancer-free controls and stomach cancer patients at various clinical stages. We then created a bioinformatics analysis pipeline and identified peptide signature discriminating stomach adenocarcinoma patients from cancer-free controls. Matrix Assisted Laser Desorption/Ionization–Time of Flight (MALDI-TOF) results from 103 samples revealed 9 signature peptides; with prediction accuracy of 89% in the training set and 88% in the validation set. Three of the discriminating peptides discovered were fragments of Apolipoproteins C-I and C-III (apoC-I and C-III); we further quantified their serum levels, as well as CA19-9 and CRP, employing quantitative commercial-clinical assays in 142 samples. ApoC-I and apoC-III quantitative results correlated with the MS results. We then employed apoB-100-normalized apoC-I and apoC-III, CA19-9 and CRP levels to generate rules set for stomach cancer prediction. For training, we used sera from one repository, and for validation, we used sera from the second repository. Prediction accuracies of 88.4% and 74.4% were obtained in the training and validation sets, respectively. Serum levels of apoC-I and apoC-III combined with other clinical parameters can serve as a basis for the formulation of a diagnostic score for stomach cancer patients.
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Affiliation(s)
- Meital Cohen
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Rami Yossef
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Tamir Erez
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Aleksandra Kugel
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michael Welt
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Mark M. Karpasas
- Analytical Research Services & Instrumentation Unit, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Jonathan Bones
- Oxford Glycobiology Laboratory, The National Institute for Bioprocessing Research & Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
| | - Pauline M. Rudd
- Oxford Glycobiology Laboratory, The National Institute for Bioprocessing Research & Training (NIBRT), Conway Institute, University College Dublin, Dublin, Ireland
| | | | | | - Dror Harats
- The Bert Stassburger Lipid Center, Sheba Medical Center, Ramat Gan, Israel
| | - Karin Noy
- The Life Sciences Department, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Yoram Tekoah
- The Avram and Stella Goren-Goldstein Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Rachel G. Lichtenstein
- The Avram and Stella Goren-Goldstein Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Angel Porgador
- The Shraga Segal Department of Microbiology and Immunology and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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Charro N, Hood BL, Faria D, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Couto FM, Conrads TP, Penque D. Serum proteomics signature of cystic fibrosis patients: a complementary 2-DE and LC-MS/MS approach. J Proteomics 2010; 74:110-26. [PMID: 20950718 DOI: 10.1016/j.jprot.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/17/2010] [Accepted: 10/05/2010] [Indexed: 01/01/2023]
Abstract
Complementary 2D-PAGE and 'shotgun' LC-MS/MS approaches were combined to identify medium and low-abundant proteins in sera of Cystic Fibrosis (CF) patients (mild or severe pulmonary disease) in comparison with healthy CF-carrier and non-CF carrier individuals aiming to gain deeper insights into the pathogenesis of this multifactorial genetic disease. 78 differentially expressed spots were identified from 2D-PAGE proteome profiling yielding 28 identifications and postulating the existence of post-translation modifications (PTM). The 'shotgun' approach highlighted altered levels of proteins actively involved in CF: abnormal tissue/airway remodeling, protease/antiprotease imbalance, innate immune dysfunction, chronic inflammation, nutritional imbalance and Pseudomonas aeruginosa colonization. Members of the apolipoproteins family (VDBP, ApoA-I, and ApoB) presented gradually lower expression from non-CF to CF-carrier individuals and from those to CF patients, results validated by an independent assay. The multifunctional enzyme NDKB was identified only in the CF group and independently validated by WB. Its functions account for ion sensor in epithelial cells, pancreatic secretion, neutrophil-mediated inflammation and energy production, highlighting its physiological significance in the context of CF. Complementary proteomics-based approaches are reliable tools to reveal pathways and circulating proteins actively involved in a heterogeneous disease such as CF.
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Affiliation(s)
- Nuno Charro
- Laboratório de Proteómica, Departamento de Genética, INSA, I.P., Lisboa, Portugal
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29
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Gomes CPC, Freire MS, Pires BRB, Vasconcelos ÉAR, Rocha TL, de Fátima Grossi-de-Sá M, Rezende TMB, Mehta Â, Pereira RW, Petriz BA, da Cruz AD, Pescara IC, Franco OL. Comparative proteomical and metalloproteomical analyses of human plasma from patients with laryngeal cancer. Cancer Immunol Immunother 2010; 59:173-81. [PMID: 19629479 PMCID: PMC11029877 DOI: 10.1007/s00262-009-0741-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 07/08/2009] [Indexed: 01/31/2023]
Abstract
Laryngeal cancer is a significant disease worldwide, which presents an increasing incidence. Two contrasting ideas of the immune system role during cancer development are accepted: (1) it fights tumor cells, and (2) it aids tumor progression. Thus, there is no clear understanding about the immune response in laryngeal cancer. Furthermore, since tobacco is the main cause of laryngeal cancer and it contains various carcinogenic components, including metallic elements, these may play a role on cancer development. Plasmas of patients with laryngeal cancer and of healthy smokers were evaluated by 2D gel electrophoresis and mass spectrometry. Proteins were detected on every gel around pH 4.0-10.0 from molecular mass of 10-60 kDa. Few differences were found among cancer and control patients. However, three spots gathered between pI 7.3 and 7.6 with different molecular masses appeared exclusively in cancer profiles. From ten spots identified, six correspond to immune system components, including the three differential ones. The latter were observed only in cancer patients. The presence of several trace elements in the identified proteins was determined by inductively coupled plasma mass spectrometry, where chromium was increased in all proteins analyzed from patients with cancer. This study reinforces the importance of the immune response as target in the understanding and treatment of laryngeal cancer and the possibility that chromium is important in the carcinogenic progress.
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Affiliation(s)
- Clarissa P. C. Gomes
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Mirna S. Freire
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Bruno R. B. Pires
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Érico A. R. Vasconcelos
- Embrapa (Brazilian Agricultural Research Corporation) Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Universidade de Brasília, Brasília, Brazil
| | - Thales L. Rocha
- Embrapa (Brazilian Agricultural Research Corporation) Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | | | - Taia M. B. Rezende
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Ângela Mehta
- Embrapa (Brazilian Agricultural Research Corporation) Recursos Genéticos e Biotecnologia, Brasília, Brazil
| | - Rinaldo W. Pereira
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Bernardo A. Petriz
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
| | - Aparecido D. da Cruz
- Universidade Católica de Goiás, Pró-Reitoria de Pós-Graduação e Pesquisa, Goiânia, Brazil
| | - Igor C. Pescara
- Laboratório de Espectroscopia Atômica, Hospital da Universidade Católica de Brasília, Brasília, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, Módulo C, 70, Brasília, DF 790-160 Brazil
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Williams D, Ackloo S, Zhu P, Bowden P, Evans KR, Addison CL, Lock C, Marshall JG. Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides. Anal Bioanal Chem 2009; 396:1223-47. [PMID: 20033139 DOI: 10.1007/s00216-009-3345-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022]
Abstract
The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography-electrospray ionization-tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.
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Affiliation(s)
- Declan Williams
- Department of Chemistry and Biology, Faculty of Engineering and Applied Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
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Hu L, Ye M, Zou H. Recent advances in mass spectrometry-based peptidome analysis. Expert Rev Proteomics 2009; 6:433-47. [PMID: 19681678 DOI: 10.1586/epr.09.55] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The peptidome, which is the low-molecular-weight subset of the proteome, has attracted increasing attention in recent years. However, with the interference of high-abundance protein components in complex biological mixtures (e.g., serum), selective extraction of endogenous peptides is the first and most important step before analyzing the peptidome. A number of methods and technologies have now been developed for the selective enrichment, fractionation, quantitative analysis of the endogenous peptides and their application in the potential biomarker discovery. This review will cover the methods and technologies developed in recent years for the peptidome analysis on the selective extraction, multidimensional separation and quantitative analysis, as well as their application for clinical diagnosis and biomarker discovery. The future prospects of the peptidome are also discussed.
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Affiliation(s)
- Lianghai Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
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32
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Chatterji B, Borlak J. A 2-DE MALDI-TOF study to identify disease regulated serum proteins in lung cancer of c-myc transgenic mice. Proteomics 2009; 9:1044-56. [PMID: 19180532 DOI: 10.1002/pmic.200701135] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We previously reported targeted overexpression of c-myc to alveolar epithelium to cause lung cancer. We now extended our studies to the serum proteome of tumor bearing mice. Proteins were extracted with a thiourea-containing lysis buffer and separated by 2-DE at pH 4-7 and 3-10 followed by MALDI-TOF/TOF analysis. Forty-six proteins were identified in tumor bearing mice of which n = 9 were statistically significant. This included disease regulated expression of orosomucoid-8, alpha-2-macroglobulin, apolipoprotein-A1, apolipoprotein-C3, glutathione peroxidase-3, plasma retinol-binding protein, and transthyretin, while expression of apolipoprotein-E was decreased at late stages of disease. Moreover, serum amyloid P component was uniquely expressed at late stages of cancer. It is of considerable importance that most disease regulated proteins carried the E-Box sequence (CACGTG) in the promoter of the coding gene, therefore providing evidence for their regulation by c-myc. Notably, expression of alpha-2-macroglobulin, transthyretin, alpha-1-antitrypsin, and properdin was in common in different lung tumor models, but regulation of orosomucoid-8, apolipoprotein-A1, apolipoprotein-C3, apolipoprotein-E, glutathione peroxidase-3, plasma retinol-binding protein, and serum amyloid P component was unique when the serum proteomes of c-myc and c-raf tumor bearing mice were compared. Therefore, candidate biomarkers to differentiate between atypical adenomatous hyperplasias (AAH) and bronchiolo-alveolar carcinomas (BAC)/papillary adenocarcinomas (PLAC) can be proposed.
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Affiliation(s)
- Bijon Chatterji
- Department of Drug Research and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany
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33
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Geng X, Ke C, Chen G, Liu P, Wang F, Zhang H, Sun X. On-line separation of native proteins by two-dimensional liquid chromatography using a single column. J Chromatogr A 2009; 1216:3553-62. [DOI: 10.1016/j.chroma.2009.01.085] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/16/2022]
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Kojima K, Asmellash S, Klug CA, Grizzle WE, Mobley JA, Christein JD. Applying proteomic-based biomarker tools for the accurate diagnosis of pancreatic cancer. J Gastrointest Surg 2008; 12:1683-90. [PMID: 18709425 DOI: 10.1007/s11605-008-0632-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 07/16/2008] [Indexed: 01/31/2023]
Abstract
BACKGROUND The proteome varies with physiologic and disease states. Few studies have been reported that differentiate the proteome of those with pancreatic cancer. AIM To apply proteomic-based technologies to body fluids. To differentiate pancreatic neoplasia from nonneoplastic pancreatic disease. METHODS Samples from 50 patients (15 healthy (H), 24 cancer (Ca), 11 chronic pancreatitis (CP)) were prospectively collected and underwent analysis. A high-throughput method, using high-affinity solid lipophilic extraction resins, enriched low molecular weight proteins for extraction with a high-speed 200-Hz matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-MS; Bruker Ultraflex III). Samples underwent software processing with FlexAnalysis, Clinprot, MatLab, and Statistica (baseline, align, and normalize spectra). Nonparametric pairwise statistics, multidimensional scaling, hierarchical analysis, and leave-one-out cross validation completed the analysis. Sensitivity (sn) and specificity (sp) of group comparisons were determined. Two top-down-directed protein identification approaches were combined with MALDI-MS and tandem mass spectrometry to fully characterize the most significant protein biomarker. RESULTS Using eight serum features, we differentiated Ca from H (sn 88%, sp 93%), Ca from CP (sn 88%, sp 30%), and Ca from both H and CP combined (sn 88%, sp 66%). In addition, nine features obtained from urine differentiated Ca from both H and CP combined with high efficiency (sn 90%, sp 90%). Interestingly, the plasma samples (considered by the Human Proteome Organization to be the preferred biological fluid) did not show significant differences. Multidimensional scaling indicated that markers from both serum and urine led to a highly effective clinical indicator of each specific disease state. CONCLUSIONS The proteomic analysis of noninvasively acquired biological fluids provided a high level of predictability for diagnosing pancreatic cancer. While the proteomic analysis of serum was capable of screening individuals for pancreatic disease (i.e., CP and Ca vs. H), specific urine biomarkers further distinguished malignancy (Ca) from chronic inflammation (CP).
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Affiliation(s)
- Kyoko Kojima
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
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