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Fredolini C, Pathak KV, Paris L, Chapple KM, Tsantilas KA, Rosenow M, Tegeler TJ, Garcia-Mansfield K, Tamburro D, Zhou W, Russo P, Massarut S, Facchiano F, Belluco C, De Maria R, Garaci E, Liotta L, Petricoin EF, Pirrotte P. Shotgun proteomics coupled to nanoparticle-based biomarker enrichment reveals a novel panel of extracellular matrix proteins as candidate serum protein biomarkers for early-stage breast cancer detection. Breast Cancer Res 2020; 22:135. [PMID: 33267867 PMCID: PMC7709252 DOI: 10.1186/s13058-020-01373-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background The lack of specificity and high degree of false positive and false negative rates when using mammographic screening for detecting early-stage breast cancer is a critical issue. Blood-based molecular assays that could be used in adjunct with mammography for increased specificity and sensitivity could have profound clinical impact. Our objective was to discover and independently verify a panel of candidate blood-based biomarkers that could identify the earliest stages of breast cancer and complement current mammographic screening approaches. Methods We used affinity hydrogel nanoparticles coupled with LC-MS/MS analysis to enrich and analyze low-abundance proteins in serum samples from 20 patients with invasive ductal carcinoma (IDC) breast cancer and 20 female control individuals with positive mammograms and benign pathology at biopsy. We compared these results to those obtained from five cohorts of individuals diagnosed with cancer in organs other than breast (ovarian, lung, prostate, and colon cancer, as well as melanoma) to establish IDC-specific protein signatures. Twenty-four IDC candidate biomarkers were then verified by multiple reaction monitoring (LC-MRM) in an independent validation cohort of 60 serum samples specifically including earliest-stage breast cancer and benign controls (19 early-stage (T1a) IDC and 41 controls). Results In our discovery set, 56 proteins were increased in the serum samples from IDC patients, and 32 of these proteins were specific to IDC. Verification of a subset of these proteins in an independent cohort of early-stage T1a breast cancer yielded a panel of 4 proteins, ITGA2B (integrin subunit alpha IIb), FLNA (Filamin A), RAP1A (Ras-associated protein-1A), and TLN-1 (Talin-1), which classified breast cancer patients with 100% sensitivity and 85% specificity (AUC of 0.93). Conclusions Using a nanoparticle-based protein enrichment technology, we identified and verified a highly specific and sensitive protein signature indicative of early-stage breast cancer with no false positives when assessing benign and inflammatory controls. These markers have been previously reported in cell-ECM interaction and tumor microenvironment biology. Further studies with larger cohorts are needed to evaluate whether this biomarker panel improves the positive predictive value of mammography for breast cancer detection.
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Affiliation(s)
- Claudia Fredolini
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Khyatiben V Pathak
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Luisa Paris
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Kristina M Chapple
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Kristine A Tsantilas
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Matthew Rosenow
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Tony J Tegeler
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA
| | - Davide Tamburro
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Weidong Zhou
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Paul Russo
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Samuele Massarut
- Department of Surgical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081, Aviano, PN, Italy
| | - Francesco Facchiano
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Claudio Belluco
- Department of Surgical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, 33081, Aviano, PN, Italy
| | - Ruggero De Maria
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.,Fondazione Policlinico Universitario "A. Gemelli" - I.R.C.C.S, 00168, Rome, Italy
| | - Enrico Garaci
- University San Raffaele and Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele, Rome, Italy
| | - Lance Liotta
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N 5th St, Phoenix, AZ, 85004, USA.
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2
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Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015; 14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Approximately 18% of all human genes purported to encode proteins have not been directly evidenced at the protein level, according to the validation criteria established by neXtProt, and are considered to be "missing" proteins. One of the goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to identify as many of these missing proteins as possible in human samples using mass spectrometry-based methods. To further this goal, a consortium of C-HPP teams (chromosomes 5, 10, 16, and 19) has joined forces to devise new strategies to identify missing proteins by use of a cell-free in vitro transcription/translation system (IVTT). The proposed strategy employs LC-MS/MS data-dependent acquisition (DDA) and targeted selective reaction monitoring (SRM) methods to scrutinize low-complexity samples derived from IVTT. The optimized assays are then applied to identify missing proteins in human cells and tissues. We describe the approach and show proof-of-concept results for development of LC-SRM assays for identification of 18 missing proteins. We believe that the IVTT system, when coupled with downstream mass spectrometric identification, can be applied to identify proteins that have eluded more traditional methods of detection.
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Affiliation(s)
- Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ákos Végvári
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Justin Saul
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Jin G Park
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Ji Qiu
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - Michael Syring
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Patrick Pirrotte
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Konstantinos Petritis
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States.,Pathology Research, Phoenix Children's Hospital , 1919 East Thomas Road, Phoenix, Arizona 85016, United States
| | - Tony J Tegeler
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | - Meraj Aziz
- Center for Proteomics, Translational Genomics Research Institute , Phoenix, Arizona 85004, United States
| | | | | | | | | | | | | | - Concha Gil
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Felipe Clemente
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Maria Luisa Hernaez
- Department of Microbiology & Proteomics Unit, University Complutense , 28040 Madrid, Spain
| | - Fernando J Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, PRB2-ProteoRed-ISCIII, IDISNA, Ciberhed , 31008 Pamplona, Spain
| | - Carol L Nilsson
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 301 University Boulevard, Galveston, Texas 77555-1074, United States
| | - Frode S Berven
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen , Postbox 7804, N-5009 Bergen, Norway.,The Norwegian Multiple Sclerosis Competence Centre, Department of Neurology, Haukeland University Hospital , Postbox 1400, 5021 Bergen, Norway
| | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Joshua LaBaer
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287, United States
| | - György Marko-Varga
- First Department of Surgery, Tokyo Medical University , 6-7-1 Nishishinjuku Shinjuku-ku, 160-0023 Tokyo, Japan
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3
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Tabb DL, Vega-Montoto L, Rudnick PA, Variyath AM, Ham AJL, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B, Tegeler TJ, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Fisher SJ, Gibson BW, Kinsinger CR, Mesri M, Rodriguez H, Stein SE, Tempst P, Paulovich AG, Liebler DC, Spiegelman C. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res 2010; 9:761-76. [PMID: 19921851 DOI: 10.1021/pr9006365] [Citation(s) in RCA: 409] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35-60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind repeatability of technical replicates on a single instrument by several percent. These findings reinforce the importance of evaluating repeatability as a fundamental characteristic of analytical technologies.
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Affiliation(s)
- David L Tabb
- Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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4
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Paulovich AG, Billheimer D, Ham AJL, Vega-Montoto L, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR, Zimmerman LJ, Fenyo D, Carr SA, Fisher SJ, Gibson BW, Mesri M, Neubert TA, Regnier FE, Rodriguez H, Spiegelman C, Stein SE, Tempst P, Liebler DC. Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol Cell Proteomics 2009; 9:242-54. [PMID: 19858499 DOI: 10.1074/mcp.m900222-mcp200] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize pre-analytical and analytical variation in comparative proteomics experiments.
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5
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Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJL, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2009; 9:225-41. [PMID: 19837981 PMCID: PMC2830836 DOI: 10.1074/mcp.m900223-mcp200] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications.
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Affiliation(s)
- Paul A Rudnick
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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6
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Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJL, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander Å, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Erratum: Corrigendum: Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma. Nat Biotechnol 2009. [DOI: 10.1038/nbt0909-864b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJL, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009; 27:633-41. [PMID: 19561596 DOI: 10.1038/nbt.1546] [Citation(s) in RCA: 819] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 05/31/2009] [Indexed: 01/13/2023]
Abstract
Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low mug/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma.
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Affiliation(s)
- Terri A Addona
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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8
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Huang SK, Darfler MM, Nicholl MB, You J, Bemis KG, Tegeler TJ, Wang M, Wery JP, Chong KK, Nguyen L, Scolyer RA, Hoon DSB. LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis. PLoS One 2009; 4:e4430. [PMID: 19221597 PMCID: PMC2637971 DOI: 10.1371/journal.pone.0004430] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 01/01/2009] [Indexed: 01/14/2023] Open
Abstract
Background Melanoma metastasis status is highly associated with the overall survival of patients; yet, little is known about proteomic changes during melanoma tumor progression. To better understand the changes in protein expression involved in melanoma progression and metastasis, and to identify potential biomarkers, we conducted a global quantitative proteomic analysis on archival metastatic and primary melanomas. Methodology and Findings A total of 16 metastatic and 8 primary cutaneous melanomas were assessed. Proteins were extracted from laser captured microdissected formalin fixed paraffin-embedded archival tissues by liquefying tissue cells. These preparations were analyzed by a LC/MS-based label-free protein quantification method. More than 1500 proteins were identified in the tissue lysates with a peptide ID confidence level of >75%. This approach identified 120 significant changes in protein levels. These proteins were identified from multiple peptides with high confidence identification and were expressed at significantly different levels in metastases as compared with primary melanomas (q-Value<0.05). Conclusions and Significance The differentially expressed proteins were classified by biological process or mapped into biological system networks, and several proteins were implicated by these analyses as cancer- or metastasis-related. These proteins represent potential biomarkers for tumor progression. The study successfully identified proteins that are differentially expressed in formalin fixed paraffin-embedded specimens of metastatic and primary melanoma.
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Affiliation(s)
- Sharon K. Huang
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
| | - Marlene M. Darfler
- Expression Pathology, Inc., Gaithersburg, Maryland, United States of America
| | - Michael B. Nicholl
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
| | - Jinsam You
- Monarch LifeSciences LLC, Indianapolis, Indiana, United States of America
| | - Kerry G. Bemis
- Monarch LifeSciences LLC, Indianapolis, Indiana, United States of America
| | - Tony J. Tegeler
- Monarch LifeSciences LLC, Indianapolis, Indiana, United States of America
| | - Mu Wang
- Monarch LifeSciences LLC, Indianapolis, Indiana, United States of America
| | - Jean-Pierre Wery
- Monarch LifeSciences LLC, Indianapolis, Indiana, United States of America
| | - Kelly K. Chong
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
| | - Linhda Nguyen
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
| | - Richard A. Scolyer
- Sydney Melanoma Unit, Sydney Cancer Center, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Dave S. B. Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California, United States of America
- * E-mail:
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9
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Wang M, You J, Bemis KG, Tegeler TJ, Brown DPG. Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 2008; 7:329-39. [PMID: 18579615 DOI: 10.1093/bfgp/eln031] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Major technological advances have made proteomics an extremely active field for biomarker discovery and validation in recent years. These improvements have lead to an increased emphasis on larger scale, faster and more efficient methods for protein biomarker discoveries in human tissues, cells and biofluids. However, most current proteomic methodologies for biomarker discovery and validation are not highly automated and generally labour intensive and expensive. Improved automation as well as software programs capable of handling a large amount of data are essential in order to reduce the cost of discovery and increase the throughput. In this review, we will discuss and describe the label-free mass spectrometry-based protein quantification technologies and a case study utilizing one of these methods for biomarker discovery.
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Affiliation(s)
- Mu Wang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 1345 W, 16th Street, Room 312, Indianapolis, IN 46202, USA.
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10
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Janecki DJ, Bemis KG, Tegeler TJ, Sanghani PC, Zhai L, Hurley TD, Bosron WF, Wang M. A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Anal Biochem 2007; 369:18-26. [PMID: 17692277 DOI: 10.1016/j.ab.2007.06.043] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 05/14/2007] [Accepted: 06/29/2007] [Indexed: 11/22/2022]
Abstract
Although significant progress has been made in protein quantification using mass spectrometry during recent years, absolute protein quantification in complex biological systems remains a challenging task in proteomics. The use of stable isotope-labeled standard peptide is the most commonly used strategy for absolute quantification, but it might not be suitable in all instances. Here we report an alternative strategy that employs a stable isotope-labeled intact protein as an internal standard to absolutely quantify the alcohol dehydrogenase (ADH) expression level in a human liver sample. In combination with a new targeted proteomics approach employing the method of multiple reaction monitoring (MRM), we precisely and quantitatively measured the absolute protein expression level of an ADH isoenzyme, ADH1C1, in human liver. Isotope-labeled protein standards are predicted to be particularly useful for measurement of highly homologous isoenzymes such as ADHs where multiple signature peptides can be examined by MRM in a single experiment.
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11
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Tegeler TJ, Mechref Y, Boraas K, Reilly JP, Novotny MV. Microdeposition Device Interfacing Capillary Electrochromatography and Microcolumn Liquid Chromatography with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. Anal Chem 2004; 76:6698-706. [PMID: 15538794 DOI: 10.1021/ac049341b] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A sample deposition device has been constructed and optimized for interfacing CEC and capillary LC columns to MALDI mass spectrometry. For CEC analysis, the device is composed of an inlet buffer reservoir and an outlet buffer reservoir connected to a matrix reservoir through a connection sleeve. The matrix reservoir is connected to a deposition capillary via another connection sleeve. CEC eluent is transported to the matrix reservoir via a capillary that is connected to the deposition capillary by the connection sleeve inside the matrix reservoir. This connection sleeve also acts as a mixing chamber, allowing the CEC eluent to be mixed with matrix prior to deposition. Complex glycan mixtures can be separated by CEC using hydrophilic-phase monolithic columns, with capillary eluent being deposited on a standard MALDI plate along with a suitable matrix solution. Thousands of discrete, highly homogeneous dots can be generated for a subsequent mass spectrometric analysis. With minor modifications, this device is also applicable to capillary LC of peptides using gradient elution. In this configuration, the outlet of the LC column is connected to a deposition capillary inside a matrix reservoir through a connection sleeve that allows mixing of the LC effluent with an appropriate matrix. The device has been evaluated with the tryptic digests of proteins.
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Affiliation(s)
- Tony J Tegeler
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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