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Kong SH, Bae JM, Kim JH, Kim SW, Han D, Shin CS. Protein Signatures of Parathyroid Adenoma according to Tumor Volume and Functionality. Endocrinol Metab (Seoul) 2024; 39:375-386. [PMID: 38509667 PMCID: PMC11066450 DOI: 10.3803/enm.2023.1827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/22/2023] [Accepted: 12/21/2023] [Indexed: 03/22/2024] Open
Abstract
BACKGRUOUND Parathyroid adenoma (PA) is a common endocrine disease linked to multiple complications, but the pathophysiology of the disease remains incompletely understood. The study aimed to identify the key regulator proteins and pathways of PA according to functionality and volume through quantitative proteomic analyses. METHODS We conducted a retrospective study of 15 formalin-fixed, paraffin-embedded PA samples from tertiary hospitals in South Korea. Proteins were extracted, digested, and the resulting peptides were analyzed using liquid chromatography-tandem mass spectrometry. Pearson correlation analysis was employed to identify proteins significantly correlated with clinical variables. Canonical pathways and transcription factors were analyzed using Ingenuity Pathway Analysis. RESULTS The median age of the participants was 52 years, and 60.0% were female. Among the 8,153 protein groups analyzed, 496 showed significant positive correlations with adenoma volume, while 431 proteins were significantly correlated with parathyroid hormone (PTH) levels. The proteins SLC12A9, LGALS3, and CARM1 were positively correlated with adenoma volume, while HSP90AB2P, HLA-DRA, and SCD5 showed negative correlations. DCPS, IRF2BPL, and FAM98A were the main proteins that exhibited positive correlations with PTH levels, and SLITRK4, LAP3, and AP4E1 had negative correlations. Canonical pathway analysis demonstrated that the RAN and sirtuin signaling pathways were positively correlated with both PTH levels and adenoma volume, while epithelial adherence junction pathways had negative correlations. CONCLUSION Our study identified pivotal proteins and pathways associated with PA, offering potential therapeutic targets. These findings accentuate the importance of proteomics in understanding disease pathophysiology and the need for further research.
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Affiliation(s)
- Sung Hye Kong
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Jung Hee Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sang Wan Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Dohyun Han
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Chan Soo Shin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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2
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Hassan T, Firdous P, Nissar K, Ahmad MB, Imtiyaz Z. Role of proteomics in surgical oncology. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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3
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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4
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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5
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Boccardo F, Rubagotti A, Nuzzo PV, Argellati F, Savarino G, Romano P, Damonte G, Rocco M, Profumo A. Matrix-assisted laser desorption/ionisation (MALDI) TOF analysis identifies serum angiotensin II concentrations as a strong predictor of all-cause and breast cancer (BCa)-specific mortality following breast surgery. Int J Cancer 2015; 137:2394-402. [PMID: 25994113 DOI: 10.1002/ijc.29609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 04/13/2015] [Accepted: 05/05/2015] [Indexed: 12/15/2022]
Abstract
MALDI-TOF MS was used to recognise serum peptidome profiles predictive of mortality in women affected by early BCa. Mortality was analysed based on signal profiling, and appropriate statistics were used. The results indicate that four signals were increased in deceased patients compared with living patients. Three of the four signals were individually associated with all-cause mortality, but only one having mass/charge ratio (m/z) 1,046.49 was associated with BCa-specific mortality and was the only peak to maintain an independent prognostic role after multivariate analysis. Two groups exhibiting different mortality probabilities were identified after clustering patients based on the expression of the four peptides, but m/z 1,046.49 was exclusively expressed in the cluster exhibiting the worst mortality outcome, thus confirming the crucial value of this peptide. The specific role of this peak was confirmed by competing risk analysis. MS findings were validated by ELISA analysis after demonstrating that m/z 1,046.49 structurally corresponded to Angiotensin II (ATII). In fact, mortality results obtained after arbitrarily dividing patients according to an ATII serum value of 255 pg/ml (which corresponds to the 66(th) percentile value) were approximately comparable to those previously demonstrated when the same patients were analysed according to the expression of signal m/z 1,046.49. Similarly, ATII levels were specifically correlated with BCa-related deaths after competing risk analysis. In conclusion, ATII levels were increased in women who exhibited worse mortality outcomes, reinforcing the evidence that this peptide potentially significantly affects the natural history of early BCa. Our findings also confirm that MALDI-TOF MS is an efficient screening tool to identify novel tumour markers and that MS findings can be rapidly validated through less complex techniques, such as ELISA.
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Affiliation(s)
- Francesco Boccardo
- Academic Unit of Medical Oncology, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy.,Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Italy
| | - Alessandra Rubagotti
- Academic Unit of Medical Oncology, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy.,Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Italy
| | - Pier Vitale Nuzzo
- Academic Unit of Medical Oncology, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy.,Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Italy
| | - Francesca Argellati
- Academic Unit of Medical Oncology, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy
| | - Grazia Savarino
- Academic Unit of Medical Oncology, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy.,Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Italy
| | - Paolo Romano
- Biopolymers and Proteomics Unit, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy
| | - Gianluca Damonte
- Department of Experimental Medicine and Center of Excellence for Biomedical Research (CEBR), School of Medicine, University of Genoa, Genoa, Italy
| | - Mattia Rocco
- Biopolymers and Proteomics Unit, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy
| | - Aldo Profumo
- Biopolymers and Proteomics Unit, IRCCS AOU San Martino-IST (San Martino University Hospital and National Cancer Research Institute), Genoa, Italy
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Targeted mass spectrometry analysis of the proteins IGF1, IGF2, IBP2, IBP3 and A2GL by blood protein precipitation. J Proteomics 2015; 113:29-37. [DOI: 10.1016/j.jprot.2014.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/11/2014] [Accepted: 09/23/2014] [Indexed: 11/18/2022]
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7
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Chung L, Baxter RC. Breast cancer biomarkers: proteomic discovery and translation to clinically relevant assays. Expert Rev Proteomics 2013; 9:599-614. [PMID: 23256671 DOI: 10.1586/epr.12.62] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Although the molecular classification and prognostic assessment of breast tumors based on gene expression profiling is well established, a number of proteomic studies that propose potential breast cancer biomarkers has not yet led to any new diagnostic, prognostic or predictive test in wide clinical use. This review examines the current status of breast cancer biomarkers, discusses sample types (including plasma, tumor tissue, nipple aspirate and ductal lavage, as well as cell culture models) and different electrophoretic and mass spectrometry methods that have been widely used for the discovery of proteomic biomarkers in breast cancer, and also considers several approaches to biomarker validation. The pathway leading from the initial proteomic discovery and validation process to translation into a clinically useful test is also discussed.
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Affiliation(s)
- Liping Chung
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
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8
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Iloro I, Gonzalez E, Gutierrez-de Juan V, Mato JM, Falcon-Perez JM, Elortza F. Non-invasive detection of drug toxicity in rats by solid-phase extraction and MALDI-TOF analysis of urine samples. Anal Bioanal Chem 2013; 405:2311-20. [DOI: 10.1007/s00216-012-6644-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/26/2012] [Accepted: 12/11/2012] [Indexed: 11/28/2022]
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9
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Emanuele VA, Panicker G, Gurbaxani BM, Lin JMS, Unger ER. Sensitive and specific peak detection for SELDI-TOF mass spectrometry using a wavelet/neural-network based approach. PLoS One 2012; 7:e48103. [PMID: 23152765 PMCID: PMC3495950 DOI: 10.1371/journal.pone.0048103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 09/24/2012] [Indexed: 01/31/2023] Open
Abstract
SELDI-TOF mass spectrometer's compact size and automated, high throughput design have been attractive to clinical researchers, and the platform has seen steady-use in biomarker studies. Despite new algorithms and preprocessing pipelines that have been developed to address reproducibility issues, visual inspection of the results of SELDI spectra preprocessing by the best algorithms still shows miscalled peaks and systematic sources of error. This suggests that there continues to be problems with SELDI preprocessing. In this work, we study the preprocessing of SELDI in detail and introduce improvements. While many algorithms, including the vendor supplied software, can identify peak clusters of specific mass (or m/z) in groups of spectra with high specificity and low false discover rate (FDR), the algorithms tend to underperform estimating the exact prevalence and intensity of peaks in those clusters. Thus group differences that at first appear very strong are shown, after careful and laborious hand inspection of the spectra, to be less than significant. Here we introduce a wavelet/neural network based algorithm which mimics what a team of expert, human users would call for peaks in each of several hundred spectra in a typical SELDI clinical study. The wavelet denoising part of the algorithm optimally smoothes the signal in each spectrum according to an improved suite of signal processing algorithms previously reported (the LibSELDI toolbox under development). The neural network part of the algorithm combines those results with the raw signal and a training dataset of expertly called peaks, to call peaks in a test set of spectra with approximately 95% accuracy. The new method was applied to data collected from a study of cervical mucus for the early detection of cervical cancer in HPV infected women. The method shows promise in addressing the ongoing SELDI reproducibility issues.
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Affiliation(s)
- Vincent A Emanuele
- Chronic and Viral Diseases Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
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10
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Early diagnostic protein biomarkers for breast cancer: how far have we come? Breast Cancer Res Treat 2011; 134:1-12. [PMID: 22179926 DOI: 10.1007/s10549-011-1907-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/29/2011] [Indexed: 12/22/2022]
Abstract
Many studies have used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry or matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to search for blood-based proteins that are related to the presence of breast cancer. We review the biomarkers discovered or targeted measured by these methods and discuss the strengths and weaknesses of these studies. We highlight two proteins that were most often related to breast cancer: C3a des-arginine anaphylatoxin (C3adesArg) (molecular weight: 8,938 Da) and fragments of inter-alpha trypsin inhibitor heavy chain H4 (ITIH4). In addition, we elaborate on three important methodological aspects related to these studies: protein identification, specificity of the markers, and disease heterogeneity. Finally, we propose some points to be addressed in future studies. These include the use of other analytical measurement techniques, need of protein identification, the importance of identical sample handling protocols for cases and controls, and the stratification of the results according to molecular subtypes and stages of breast cancer. Ultimately this may lead to the discovery of new and valid breast cancer specific biomarkers.
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11
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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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12
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Lei L, Wang XJ, Zheng ZG, Huang J, Cao WM, Chen ZH, Shao XY, Cai JF, Ye WW, Lu HY. Identification of serum protein markers for breast cancer relapse with SELDI-TOF MS. Anat Rec (Hoboken) 2011; 294:941-4. [PMID: 21548109 DOI: 10.1002/ar.21399] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 09/14/2010] [Accepted: 10/22/2010] [Indexed: 11/07/2022]
Abstract
Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) was used to screen serum samples to identify protein markers for early breast cancer relapse. We collected 67 serum samples from patients with breast cancer (24 preoperative; 23 postoperative without breast cancer relapse; 20 postoperative with breast cancer relapse). Eight protein peaks varied between the presurgical group and the postsurgical group without breast cancer relapse; 4 protein peaks were differentially expressed between the postsurgical patients without relapse and patients with relapse. The peak at 3964 m/z dropped after surgery and rebounded after relapse (P < 0.01). These results indicate that there are differences in serum protein expression among the three different groups of patients. SELDI-TOF MS could be used to screen blood samples for the early detection of relapse in primary breast cancer patients. Specifically, protein peak at 3964 m/z is a potential biomarker for the detection of early breast cancer relapse.
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Affiliation(s)
- Lei Lei
- Department of Chemotherapy Center, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
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13
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Cairns DA. Statistical issues in quality control of proteomic analyses: Good experimental design and planning. Proteomics 2011; 11:1037-48. [DOI: 10.1002/pmic.201000579] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/26/2010] [Accepted: 11/29/2010] [Indexed: 12/21/2022]
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14
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Huijbers A, Velstra B, Dekker TJA, Mesker WE, van der Burgt YEM, Mertens BJ, Deelder AM, Tollenaar RAEM. Proteomic serum biomarkers and their potential application in cancer screening programs. Int J Mol Sci 2010; 11:4175-93. [PMID: 21151433 PMCID: PMC3000077 DOI: 10.3390/ijms11114175] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 10/16/2010] [Accepted: 10/18/2010] [Indexed: 02/06/2023] Open
Abstract
Early diagnosis of cancer is of pivotal importance to reduce disease-related mortality. There is great need for non-invasive screening methods, yet current screening protocols have limited sensitivity and specificity. The use of serum biomarkers to discriminate cancer patients from healthy persons might be a tool to improve screening programs. Mass spectrometry based proteomics is widely applied as a technology for mapping and identifying peptides and proteins in body fluids. One commonly used approach in proteomics is peptide and protein profiling. Here, we present an overview of profiling methods that have the potential for implementation in a clinical setting and in national screening programs.
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Affiliation(s)
- Anouck Huijbers
- Department of Surgery, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands; E-Mails: (A.H.); (B.V.); (W.E.M.)
| | - Berit Velstra
- Department of Surgery, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands; E-Mails: (A.H.); (B.V.); (W.E.M.)
| | - Tim J. A. Dekker
- Department of Surgery, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands; E-Mails: (A.H.); (B.V.); (W.E.M.)
| | - Wilma E. Mesker
- Department of Surgery, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands; E-Mails: (A.H.); (B.V.); (W.E.M.)
| | - Yuri E. M. van der Burgt
- Department of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Bart J. Mertens
- Department of Medical Statistics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - André M. Deelder
- Department of Parasitology, Biomolecular Mass Spectrometry Unit, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Rob A. E. M. Tollenaar
- Department of Surgery, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands; E-Mails: (A.H.); (B.V.); (W.E.M.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +317-152-636-10
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15
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Li R, Wang Y, Chen GL, Shi M, Wang XG, Zheng JB. Synthesis and Chromatographic Characteristics of Multidentate Ligand-Boned Silica Stationary Phases. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.8.2201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Peter JF, Otto AM. Magnetic particles as powerful purification tool for high sensitive mass spectrometric screening procedures. Proteomics 2010; 10:628-33. [PMID: 20099258 DOI: 10.1002/pmic.200900535] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The effective isolation and purification of proteins from biological fluids is the most crucial step for a successful protein analysis when only minute amounts are available. While conventional purification methods such as dialysis, ultrafiltration or protein precipitation often lead to a marked loss of protein, SPE with small-sized particles is a powerful alternative. The implementation of particles with superparamagnetic cores facilitates the handling of those particles and allows the application of particles in the nanometer to low micrometer range. Due to the small diameters, magnetic particles are advantageous for increasing sensitivity when using subsequent MS analysis or gel electrophoresis. In the last years, different types of magnetic particles were developed for specific protein purification purposes followed by analysis or screening procedures using MS or SDS gel electrophoresis. In this review, the use of magnetic particles for different applications, such as, the extraction and analysis of DNA/RNA, peptides and proteins, is described.
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Debald M, Wolfgarten M, Walgenbach-Brünagel G, Kuhn W, Braun M. Non-invasive proteomics-thinking about personalized breast cancer screening and treatment. EPMA J 2010. [PMID: 23199085 PMCID: PMC3405342 DOI: 10.1007/s13167-010-0039-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The early diagnosis of breast cancer in potentially curable stages improves prognosis and consecutively reduces mortality of breast cancer patients. Established screening programs have an unfavorable connotation due to significant rates of false negative as well as false positive results leading to overdiagnosis and overtherapy. The combination of a non-invasive breast-cancer-suspectability-biomarker with established clinical diagnostics could help to increase the acceptance of population based breast cancer screening programs by creating an individual risk profile, which is irrespective of mammography quality and interpretation. Recently, non-invasive proteomic biomarkers obtained from blood, saliva or nipple aspiration fluid have been extensively investigated and might play a future role in the personalized management of breast cancer screening. A simple, robust and inexpensive, non-invasive test for screening and diagnosis could easily be performed in every medical practice leading to an affordable, high-throughput instrument. This review describes recently investigated proteomic screening biomarkers that could improve the early diagnosis of breast cancer in the following years.
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Affiliation(s)
- Manuel Debald
- Department of Obstetrics and Gynecology, Center for Integrated Oncology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Matthias Wolfgarten
- Department of Obstetrics and Gynecology, Center for Integrated Oncology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Gisela Walgenbach-Brünagel
- Institute for Clinical Chemistry and Pharmacology, Center for Integrated Oncology, University of Bonn, Bonn, Germany
| | - Walther Kuhn
- Department of Obstetrics and Gynecology, Center for Integrated Oncology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Michael Braun
- Department of Obstetrics and Gynecology, Center for Integrated Oncology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
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Pietrowska M, Polanska J, Marczak L, Behrendt K, Nowicka E, Stobiecki M, Polanski A, Tarnawski R, Widlak P. Mass spectrometry-based analysis of therapy-related changes in serum proteome patterns of patients with early-stage breast cancer. J Transl Med 2010; 8:66. [PMID: 20618994 PMCID: PMC2908576 DOI: 10.1186/1479-5876-8-66] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 07/11/2010] [Indexed: 12/04/2022] Open
Abstract
Background The proteomics approach termed proteome pattern analysis has been shown previously to have potential in the detection and classification of breast cancer. Here we aimed to identify changes in serum proteome patterns related to therapy of breast cancer patients. Methods Blood samples were collected before the start of therapy, after the surgical resection of tumors and one year after the end of therapy in a group of 70 patients diagnosed at early stages of the disease. Patients were treated with surgery either independently (26) or in combination with neoadjuvant chemotherapy (5) or adjuvant radio/chemotherapy (39). The low-molecular-weight fraction of serum proteome was examined using MALDI-ToF mass spectrometry, and then changes in intensities of peptide ions registered in a mass range between 2,000 and 14,000 Da were identified and correlated with clinical data. Results We found that surgical resection of tumors did not have an immediate effect on the mass profiles of the serum proteome. On the other hand, significant long-term effects were observed in serum proteome patterns one year after the end of basic treatment (we found that about 20 peptides exhibited significant changes in their abundances). Moreover, the significant differences were found primarily in the subgroup of patients treated with adjuvant therapy, but not in the subgroup subjected only to surgery. This suggests that the observed changes reflect overall responses of the patients to the toxic effects of adjuvant radio/chemotherapy. In line with this hypothesis we detected two serum peptides (registered m/z values 2,184 and 5,403 Da) whose changes correlated significantly with the type of treatment employed (their abundances decreased after adjuvant therapy, but increased in patients treated only with surgery). On the other hand, no significant correlation was found between changes in the abundance of any spectral component or clinical features of patients, including staging and grading of tumors. Conclusions The study establishes a high potential of MALDI-ToF-based analyses for the detection of dynamic changes in the serum proteome related to therapy of breast cancer patients, which revealed the potential applicability of serum proteome patterns analyses in monitoring the toxicity of therapy.
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Affiliation(s)
- Monika Pietrowska
- Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice, Poland
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Leth-Larsen R, Lund RR, Ditzel HJ. Plasma membrane proteomics and its application in clinical cancer biomarker discovery. Mol Cell Proteomics 2010; 9:1369-82. [PMID: 20382631 DOI: 10.1074/mcp.r900006-mcp200] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Plasma membrane proteins that are exposed on the cell surface have important biological functions, such as signaling into and out of the cells, ion transport, and cell-cell and cell-matrix interactions. The expression level of many of the plasma membrane proteins involved in these key functions is altered on cancer cells, and these proteins may also be subject to post-translational modification, such as altered phosphorylation and glycosylation. Additional protein alterations on cancer cells confer metastatic capacities, and some of these cell surface proteins have already been successfully targeted by protein drugs, such as human antibodies, that have enhanced survival of several groups of cancer patients. The combination of novel analytical approaches and subcellular fractionation procedures has made it possible to study the plasma membrane proteome in more detail, which will elucidate cancer biology, particularly metastasis, and guide future development of novel drug targets. The technical advances in plasma membrane proteomics and the consequent biological revelations will be discussed herein. Many of the advances have been made using cancer cell lines, but because the main goal of this research is to improve individualized treatment and increase cancer patient survival, further development is crucial to direct analysis of clinically relevant patient samples. These efforts include optimized specimen handling and preparation as well as improved proteomics platforms. Identification of potentially useful proteomics-based biomarkers must be validated in larger, well defined retrospective and prospective clinical studies, and these combined efforts should result in identification of biomarkers that will greatly improve early detection, prognosis, and prediction of treatment response.
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Affiliation(s)
- Rikke Leth-Larsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, JB Winsløwsvej 25.3, 5000 Odense C, Denmark
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Rezeli M, Végvári Á, Marko-Varga G, Laurell T. Isotope labeled internal standards (ILIS) as a basis for quality control in clinical studies using plasma samples. J Proteomics 2010; 73:1219-29. [DOI: 10.1016/j.jprot.2010.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 02/10/2010] [Accepted: 02/15/2010] [Indexed: 02/07/2023]
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Findeisen P, Neumaier M. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective. Clin Chem Lab Med 2009; 47:666-84. [PMID: 19445650 DOI: 10.1515/cclm.2009.159] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.
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Affiliation(s)
- Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of the University of Heidelberg, Heidelberg, Germany.
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22
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Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer. J Transl Med 2009; 7:60. [PMID: 19594898 PMCID: PMC2725033 DOI: 10.1186/1479-5876-7-60] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 07/13/2009] [Indexed: 01/20/2023] Open
Abstract
Background Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints) detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry. Methods Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves. Results We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions) that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity). Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0.0003) increased level of osteopontin in blood of the group of cancer patients studied (however, the plasma level of osteopontin classified cancer samples with 88% sensitivity but only 28% specificity). Conclusion MALDI-ToF spectrometry of serum has an obvious potential to differentiate samples between early breast cancer patients and healthy controls. Importantly, a classifier built on MS-based serum proteome patterns outperforms available protein biomarkers analyzed in blood by immunoassays.
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Abstract
Background Because screening mammography for breast cancer is less effective for premenopausal women, we investigated the feasibility of a diagnostic blood test using serum proteins. Methods This study used a set of 98 serum proteins and chose diagnostically relevant subsets via various feature-selection techniques. Because of significant noise in the data set, we applied iterated Bayesian model averaging to account for model selection uncertainty and to improve generalization performance. We assessed generalization performance using leave-one-out cross-validation (LOOCV) and receiver operating characteristic (ROC) curve analysis. Results The classifiers were able to distinguish normal tissue from breast cancer with a classification performance of AUC = 0.82 ± 0.04 with the proteins MIF, MMP-9, and MPO. The classifiers distinguished normal tissue from benign lesions similarly at AUC = 0.80 ± 0.05. However, the serum proteins of benign and malignant lesions were indistinguishable (AUC = 0.55 ± 0.06). The classification tasks of normal vs. cancer and normal vs. benign selected the same top feature: MIF, which suggests that the biomarkers indicated inflammatory response rather than cancer. Conclusion Overall, the selected serum proteins showed moderate ability for detecting lesions. However, they are probably more indicative of secondary effects such as inflammation rather than specific for malignancy.
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Gast MCW, Schellens JHM, Beijnen JH. Clinical proteomics in breast cancer: a review. Breast Cancer Res Treat 2008; 116:17-29. [PMID: 19082706 DOI: 10.1007/s10549-008-0263-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 11/24/2008] [Indexed: 12/13/2022]
Abstract
Breast cancer imposes a significant healthcare burden on women worldwide. Early detection is of paramount importance in reducing mortality, yet the diagnosis of breast cancer is hampered by the lack of an adequate detection method. In addition, better breast cancer prognostication may improve selection of patients eligible for adjuvant therapy. Hence, new markers for early diagnosis, accurate prognosis and prediction of response to treatment are warranted to improve breast cancer care. Since proteomics can bridge the gap between the genetic alterations underlying cancer and cellular physiology, much is expected from proteome analyses for the detection of better protein biomarkers. Recent technical advances in mass spectrometry, such as matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and its variant surface-enhanced laser desorption/ionisation (SELDI-) TOF MS, have enabled high-throughput proteome analysis. In the current review, we give a comprehensive overview of the results of expression proteomics (i.e. protein profiling) research performed in breast cancer using these two platforms. Many protein peaks have been reported to bear significant diagnostic, prognostic or predictive value, however, only few candidate markers have been structurally identified yet. In addition, although of pivotal importance in preventing overfitting of data and systematic bias by pre-analytical parameters, validation of biomarker candidates by other, quantitative, methods and/or in new populations is very limited. Moreover, none of the identified candidate biomarkers has been investigated for their utility as breast cancer markers in large, prospective, clinical settings. As such, the candidate biomarkers discussed in this overview have not been validated sufficiently to be used for clinical patient care. Nonetheless, regarding the promising results up to now, MALDI- and SELDI-TOF MS protein profiling studies could eventually fulfil the great promise that protein biomarkers have for improving cancer patient outcome, provided that these studies are performed with adequate statistical power and analytical rigour.
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Affiliation(s)
- Marie-Christine W Gast
- Department of Pharmacy and Pharmacology, The Netherlands Cancer Institute/Slotervaart Hospital, Amsterdam, The Netherlands.
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Palmblad M, Tiss A, Cramer R. Mass spectrometry in clinical proteomics - from the present to the future. Proteomics Clin Appl 2008; 3:6-17. [DOI: 10.1002/prca.200800090] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Indexed: 12/15/2022]
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Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry. J Proteomics 2008; 71:304-17. [DOI: 10.1016/j.jprot.2008.06.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 11/22/2022]
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Callesen AK, Vach W, Jørgensen PE, Cold S, Mogensen O, Kruse TA, Jensen ON, Madsen JS. Reproducibility of Mass Spectrometry Based Protein Profiles for Diagnosis of Breast Cancer across Clinical Studies: A Systematic Review. J Proteome Res 2008; 7:1395-402. [DOI: 10.1021/pr800115f] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anne K. Callesen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Werner Vach
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Per E. Jørgensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Søren Cold
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Ole Mogensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Torben A. Kruse
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Ole N. Jensen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
| | - Jonna S. Madsen
- Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark, Department of Biochemistry, Pharmacology and Genetics, Odense University Hospital, Odense, Denmark, Department of Statistics, University of Southern Denmark, Odense, Denmark, Department of Oncology, Odense University Hospital, Odense, Denmark, and Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark
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