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Nardone D, Ciaramella A, Cerreta M, Pulcrano S, Bellenchi GC, Leone L, Manco G, Febbraio F. Selymatra: A web application for protein-profiling analysis of mass spectra. Biotechnol Appl Biochem 2022; 69:1821-1829. [PMID: 34487563 PMCID: PMC9912196 DOI: 10.1002/bab.2249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/23/2021] [Indexed: 11/06/2022]
Abstract
Surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry is a variant of the matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. It is used in many cases especially for the analysis of protein profiling and for preliminary screening of biomarkers in complex samples. Unfortunately, these analyses are time consuming and protein identification is generally strictly limited. SELDI-TOF analysis of mass spectra (SELYMATRA) is a web application (WA) developed to reduce these limitations by (i) automating the identification processes and (ii) introducing the possibility to predict proteins in complex mixtures from cells and tissues. The WA architectural pattern is the model-view-controller, commonly used in software development. The WA compares the mass value between two mass spectra (sample vs. control) to extract differences, and, according to the set parameters, it queries a local database to predict most likely proteins based on their masses and different expression amplification. The WA was validated in a cellular model overexpressing a tagged NURR1 receptor, being able to recognize the tagged protein in the profiling of transformed cells. A help page, including a description of parameters for WA use, is available on the website.
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Affiliation(s)
- Davide Nardone
- Department of Science and TechnologyUniversity of Naples ParthenopeNaplesItaly
| | - Angelo Ciaramella
- Department of Science and TechnologyUniversity of Naples ParthenopeNaplesItaly
| | - Mariangela Cerreta
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
| | - Salvatore Pulcrano
- Institute of Genetic and Biophysics “A. Buzzati Traverso”National Research CouncilNaplesItaly
| | - Gian C. Bellenchi
- Institute of Genetic and Biophysics “A. Buzzati Traverso”National Research CouncilNaplesItaly
| | - Linda Leone
- Department of Chemical SciencesUniversity of Naples “Federico II”Naples80126Italy
| | - Giuseppe Manco
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cellular BiologyNational Research CouncilNaples80131Italy
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Nuclear morphometry, epigenetic changes, and clinical relevance in prostate cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 773:77-99. [PMID: 24563344 PMCID: PMC7123969 DOI: 10.1007/978-1-4899-8032-8_4] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nuclear structure alterations in cancer involve global genetic (mutations, amplifications, copy number variations, translocations, etc.) and epigenetic (DNA methylation and histone modifications) events that dramatically and dynamically spatially change chromatin, nuclear body, and chromosome organization. In prostate cancer (CaP) there appears to be early (<50 years) versus late (>60 years) onset clinically significant cancers, and we have yet to clearly understand the hereditary and somatic-based molecular pathways involved. We do know that once cancer is initiated, dedifferentiation of the prostate gland occurs with significant changes in nuclear structure driven by numerous genetic and epigenetic processes. This review focuses upon the nuclear architecture and epigenetic dynamics with potential translational clinically relevant applications to CaP. Further, the review correlates changes in the cancer-driven epigenetic process at the molecular level and correlates these alterations to nuclear morphological quantitative measurements. Finally, we address how we can best utilize this knowledge to improve the efficacy of personalized treatment of cancer.
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Jiang F, Zhou XY, Huang J. The value of surface enhanced laser desorption/ionization-time of flight mass spectrometry at the diagnosis of non-small cell lung cancer: a systematic review. Technol Cancer Res Treat 2013; 13:109-17. [PMID: 23862745 DOI: 10.7785/tcrt.2012.500360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Numbers of studies used surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF-MS) to find novel serum biomarkers for non-small cell lung cancer (NSCLC). It is arguable whether the SELDI technique has its value of diagnostic accuracy for NSCLC. The purpose of our study is to determine the diagnostic accuracy of SELDI-TOF-MS for diagnosing NSCLC. The Cochrane Central Register of Controlled Trials, MEDLINE, Pub Med, EMBASE, the Chinese Biomedical Literature Database, the China Academic Journals Full-text Database, and the Chinese Scientific Journals Database were searched systematically for potential studies. Reference lists of included studies and review articles were also reviewed. All studies that reported data on patients with a confirmed diagnosis of NSCLC and that compared the measurement of SELDI-TOF-MS with pathology standard were considered for inclusion. 11 studies were included in the systematic review. The ranges of the diagnostic value of SELDI-TOF-MS for NSCLC were as follows: sensitivity (SEN) was 0.70~1.00; specificity (SPE) was 0.68~1.00; positive likelihood ratio (PLR) was 2.23~23.14; negative likelihood ratio (NLR) was 0.04~0.43; and diagnostic odds ratio (DOR) was 5.17~621.0, respectively. SELDI-TOF-MS showed high accuracy in identifying NSCLC, and could be a potential screening tool for diagnosing NSCLC patients.
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Affiliation(s)
- Feng Jiang
- Department of Cardiology, Affiliated Hospital of Lu Zhou Medical College, Lu Zhou, Sichuan, China 646000.
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Hu QY, Su J, Jiang H, Wang LL, Jia YQ. Potential role of proteomics in the diagnosis of lymphoma: a meta-analysis. Int J Lab Hematol 2012; 35:367-78. [PMID: 23216964 DOI: 10.1111/ijlh.12032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/10/2012] [Indexed: 02/05/2023]
Abstract
Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) has been approved for identifying biomarkers and diagnosing many diseases such as lymphomas. It is arguable whether the SELDI technique has its value of diagnostic accuracy for lymphomas. The purpose of our study is to determine the diagnostic accuracy of SELDI-TOF-MS for diagnosing lymphomas. The Cochrane Central Register of Controlled Trials, MEDLINE, Pub Med, EMBASE, the Chinese Biomedical Literature Database, the China Academic Journals Full-text Database, and the Chinese Scientific Journals Database were searched systematically for potential studies. Reference lists of included studies and review articles were also reviewed. All studies that reported data on patients with a confirmed diagnosis of lymphomas and that compared the measurement of SELDI-TOF-MS with pathology standard were considered for inclusion. Eleven studies were included in the systematic review. The ranges of the diagnostic value of SELDI-TOF-MS for lymphoma were as follows: sensitivity (SEN) was 0.69-0.96; specificity (SPE) was 0.70-1.00; positive likelihood ratio (PLR) was 2.99-96.09; negative likelihood ratio (NLR) was 0.04-0.35; and diagnostic odds ratio (DOR) was 18.13-1250.71, respectively. Further, we analysed serum samples as a subgroup, and the pooled endpoints were as follows: pooled SEN was 0.89 (0.85-0.91); pooled SPE was 0.91 (0.88-0.93); pooled PLR was 12.35 (5.36-28.44); pooled NLR was 0.13 (0.09-0.20); and pooled DOR was 101.04 (39.57-258.04), respectively. SELDI-TOF-MS showed high accuracy in identifying lymphoma and could be a useful screening tool for diagnosing lymphoma patients.
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Affiliation(s)
- Q-Y Hu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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Jiang H, Wang XH, Yu XM, Zheng ZG. Detection and Prognostic Analysis of Serum Protein Expression in Esophageal Squamous Cell Cancer. Asian Pac J Cancer Prev 2012; 13:1579-82. [DOI: 10.7314/apjcp.2012.13.4.1579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Berrade L, Garcia AE, Camarero JA. Protein microarrays: novel developments and applications. Pharm Res 2010; 28:1480-99. [PMID: 21116694 PMCID: PMC3137928 DOI: 10.1007/s11095-010-0325-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Protein microarray technology possesses some of the greatest potential for providing direct information on protein function and potential drug targets. For example, functional protein microarrays are ideal tools suited for the mapping of biological pathways. They can be used to study most major types of interactions and enzymatic activities that take place in biochemical pathways and have been used for the analysis of simultaneous multiple biomolecular interactions involving protein-protein, protein-lipid, protein-DNA and protein-small molecule interactions. Because of this unique ability to analyze many kinds of molecular interactions en masse, the requirement of very small sample amount and the potential to be miniaturized and automated, protein microarrays are extremely well suited for protein profiling, drug discovery, drug target identification and clinical prognosis and diagnosis. The aim of this review is to summarize the most recent developments in the production, applications and analysis of protein microarrays.
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Affiliation(s)
- Luis Berrade
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, PSC 616, Los Angeles, California 90033, USA
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Qiong-ying H, Wang KZ, Ding YH, Zheng LF, Liang SH, Lei ZM, Fu WG, Yan L. Application of SELDI-TOF-MS Coupled With an Artificial Neural Network Model to the Diagnosis of Pancreatic Cancer. Lab Med 2010. [DOI: 10.1309/lmh6tuomqkx6v2dn] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Glen A, Evans CA, Gan CS, Cross SS, Hamdy FC, Gibbins J, Lippitt J, Eaton CL, Noirel J, Wright PC, Rehman I. Eight-plex iTRAQ analysis of variant metastatic human prostate cancer cells identifies candidate biomarkers of progression: An exploratory study. Prostate 2010; 70:1313-32. [PMID: 20623638 DOI: 10.1002/pros.21167] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Due to the heterogeneity in the biological behavior of prostate cancer, biomarkers that can reliably distinguish indolent from aggressive disease are urgently needed to inform treatment choices. METHODS We employed 8-plex isobaric Tags for Relative and Absolute Quantitation (iTRAQ), to profile the proteomes of two distinct panels of isogenic prostate cancer cells with varying growth and metastatic potentials, in order to identify novel biomarkers associated with progression. The LNCaP, LNCaP-Pro5, and LNCaP-LN3 panel of cells represent a model of androgen-responsive prostate cancer, while the PC-3, PC-3M, and PC-3M-LN4 panel represent a model of androgen-insensitive disease. RESULTS Of the 245 unique proteins identified and quantified (>or=95% confidence; >or=2 peptides/protein), 17 showed significant differential expression (>or=+/-1.5), in at least one of the variant LNCaP cells relative to parental cells. Similarly, comparisons within the PC-3 panel identified 45 proteins to show significant differential expression in at least one of the variant PC-3 cells compared with parental cells. Differential expression of selected candidates was verified by Western blotting or immunocytochemistry, and corresponding mRNA expression was determined by quantitative real-time PCR (qRT-PCR). Immunostaining of prostate tissue microarrays for ERp5, one of the candidates identified, showed a significant higher immunoexpression in pre-malignant lesions compared with non-malignant epithelium (P < 0.0001, Mann-Whitney U-test), and in high Gleason grade (4-5) versus low grade (2-3) cancers (P < 0.05). CONCLUSIONS Our study provides proof of principle for the application of an 8-plex iTRAQ approach to uncover clinically relevant candidate biomarkers for prostate cancer progression.
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Affiliation(s)
- Adam Glen
- Department of Human Metabolism, The Mellanby Centre for Bone Research, University of Sheffield Medical School, Sheffield, UK
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Martínez CH, Chalasani V, Chin J. Molecular biomarkers in prostate cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2009; 3:345-353. [PMID: 23485204 DOI: 10.1517/17530050902893303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND After more than two decades of clinical use, serum prostate-specific antigen (PSA) has increased the early diagnosis of prostate cancer, detecting the disease even when small volumes are present. Although stage migration of prostate cancer has occurred, PSA has well-known limitations, despite attempts at refinement and modification, such as the use of PSA velocity, which have been used to improve it. New biomarkers for prostate cancer have been discovered, with promising early results. OBJECTIVE/METHODS This article reviews the ubiquitous current literature on biomarkers in prostate cancer. A search using MEDLINE and EMBASE databases was performed and those articles reporting biomarkers in prostate cancer with clinically significant findings in terms of detection were analyzed. Immunohistochemical markers were not considered for this review. RESULTS/CONCLUSION Despite many markers being promising, no single marker has satisfied the criteria as a perfect candidate. Limited clinical use of IL-6, TGF-β1 and PCA3 has commenced, and further widespread availability of these tests is expected in the coming years. The future lies in artificial neural networks and panels of markers instead of individual assays. Although PSA has some well-known limitations, it is at present the best marker available for prostate cancer when used in conjunction with nomograms or risk calculators.
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Affiliation(s)
- Carlos H Martínez
- University of Western Ontario, London Health Sciences Centre, Division of Urology, 800 Commissioners Road East, London, Ontario, Canada N6A 4G5 +1 519 685 8451 ; +1 519 685 8455 ;
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Evans CA, Glen A, Eaton CL, Larré S, Catto JWF, Hamdy FC, Wright PC, Rehman I. Prostate cancer proteomics: The urgent need for clinically validated biomarkers. Proteomics Clin Appl 2009; 3:197-212. [DOI: 10.1002/prca.200800154] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Indexed: 11/11/2022]
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Surface enhanced laser desorption/ionization (SELDI): tecnología proteómica y su aplicación en oncología. Med Clin (Barc) 2008. [DOI: 10.1016/s0025-7753(08)72265-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jin G, Zhou X, Wang H, Zhao H, Cui K, Zhang XS, Chen L, Hazen SL, Li K, Wong STC. The knowledge-integrated network biomarkers discovery for major adverse cardiac events. J Proteome Res 2008; 7:4013-21. [PMID: 18665624 DOI: 10.1021/pr8002886] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The mass spectrometry (MS) technology in clinical proteomics is very promising for discovery of new biomarkers for diseases management. To overcome the obstacles of data noises in MS analysis, we proposed a new approach of knowledge-integrated biomarker discovery using data from Major Adverse Cardiac Events (MACE) patients. We first built up a cardiovascular-related network based on protein information coming from protein annotations in Uniprot, protein-protein interaction (PPI), and signal transduction database. Distinct from the previous machine learning methods in MS data processing, we then used statistical methods to discover biomarkers in cardiovascular-related network. Through the tradeoff between known protein information and data noises in mass spectrometry data, we finally could firmly identify those high-confident biomarkers. Most importantly, aided by protein-protein interaction network, that is, cardiovascular-related network, we proposed a new type of biomarkers, that is, network biomarkers, composed of a set of proteins and the interactions among them. The candidate network biomarkers can classify the two groups of patients more accurately than current single ones without consideration of biological molecular interaction.
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Affiliation(s)
- Guangxu Jin
- Center for Biotechnology and Informatics, The Methodist Hospital Research Institute & Cornell University, Houston, Texas 77030, USA
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