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Lu M, Faull KF, Whitelegge JP, He J, Shen D, Saxton RE, Chang HR. Proteomics and Mass Spectrometry for Cancer Biomarker Discovery. Biomark Insights 2017. [DOI: 10.1177/117727190700200005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Proteomics is a rapidly advancing field not only in the field of biology but also in translational cancer research. In recent years, mass spectrometry and associated technologies have been explored to identify proteins or a set of proteins specific to a given disease, for the purpose of disease detection and diagnosis. Such biomarkers are being investigated in samples including cells, tissues, serum/plasma, and other types of body fluids. When sufficiently refined, proteomic technologies may pave the way for early detection of cancer or individualized therapy for cancer. Mass spectrometry approaches coupled with bioinformatic tools are being developed for biomarker discovery and validation. Understanding basic concepts and application of such technology by investigators in the field may accelerate the clinical application of protein biomarkers in disease management.
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Affiliation(s)
- Ming Lu
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Kym F. Faull
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Julian P. Whitelegge
- The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry & Biobehavioral and the Neuropsychiatric Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
| | - Jianbo He
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Dejun Shen
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
| | - Romaine E. Saxton
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
| | - Helena R. Chang
- Gonda/UCLA Breast Cancer Research Laboratory, Los Angeles, California
- Revlon/UCLA Breast Center, Department of Surgery/Oncology, David Geffen School of Medicine, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, Los Angeles, California
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Meleth S, Eltoum IE, Zhu L, Oelschlager D, Piyathilake C, Chhieng D, Grizzle WE. Novel Approaches to Smoothing and Comparing SELDI TOF Spectra. Cancer Inform 2017. [DOI: 10.1177/117693510500100109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background Most published literature using SELDI-TOF has used traditional techniques in Spectral Analysis such as Fourier transforms and wavelets for denoising. Most of these publications also compare spectra using their most prominent feature, ie, peaks or local maximums. Methods The maximum intensity value within each window of differentiable m/z values was used to represent the intensity level in that window. We also calculated the ‘Area under the Curve’ (AUC) spanned by each window. Results Keeping everything else constant, such as pre-processing of the data and the classifier used, the AUC performed much better as a metric of comparison than the peaks in two out of three data sets. In the third data set both metrics performed equivalently. Conclusions This study shows that the feature used to compare spectra can have an impact on the results of a study attempting to identify biomarkers using SELDI TOF data.
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Affiliation(s)
- Sreelatha Meleth
- Department of Medicine, Medical Statistics Section. University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Isam-Eldin Eltoum
- Clinical Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Liu Zhu
- Pathology Chair Office, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Denise Oelschlager
- Pathology Chair Office, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chandrika Piyathilake
- Nutrition Sciences, Biochemistry & Molecular Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David Chhieng
- Clinical Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William E. Grizzle
- Clinical Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Grizzle WE, Semmes OJ, Bigbee W, Zhu L, Malik G, Oelschlager DK, Manne B, Manne U. The Need for Review and Understanding of SELDI/MALDI Mass Spectroscopy Data Prior to Analysis. Cancer Inform 2017. [DOI: 10.1177/117693510500100106] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Multiple studies have reported that surface enhanced laser desorption/ionization time of flight mass spectroscopy (SELDI-TOF-MS) is useful in the early detection of disease based on the analysis of bodily fluids. Use of any multiplex mass spectroscopy based approach as in the analysis of bodily fluids to detect disease must be analyzed with great care due to the susceptibility of multiplex and mass spectroscopy methods to biases introduced via experimental design, patient samples, and/or methodology. Specific biases include those related to experimental design, patients, samples, protein chips, chip reader and spectral analysis. Contributions to biases based on patients include demographics (e.g., age, race, ethnicity, sex), homeostasis (e.g., fasting, medications, stress, time of sampling), and site of analysis (hospital, clinic, other). Biases in samples include conditions of sampling (type of sample container, time of processing, time to storage), conditions of storage, (time and temperature of storage), and prior sample manipulation (freeze thaw cycles). Also, there are many potential biases in methodology which can be avoided by careful experimental design including ensuring that cases and controls are analyzed randomly. All the above forms of biases affect any system based on analyzing multiple analytes and especially all mass spectroscopy based methods, not just SELDI-TOF-MS. Also, all current mass spectroscopy systems have relatively low sensitivity compared with immunoassays (e.g., ELISA). There are several problems which may be unique to the SELDI-TOF-MS system marketed by Ciphergen®. Of these, the most important is a relatively low resolution (±0.2%) of the bundled mass spectrometer which may cause problems with analysis of data. Foremost, this low resolution results in difficulties in determining what constitutes a “peak” if a peak matching approach is used in analysis. Also, once peaks are selected, the peaks may represent multiple proteins. In addition, because peaks may vary slightly in location due to instrumental drift, long term identification of the same peaks may prove to be a challenge. Finally, the Ciphergen® system has some “noise” of the baseline which results from the accumulation of charge in the detector system. Thus, we must be very aware of the factors that may affect the use of proteomics in the early detection of disease, in determining aggressive subsets of cancers, in risk assessment and in monitoring the effectiveness of novel therapies.
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Affiliation(s)
| | | | - William Bigbee
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Liu Zhu
- University of Alabama at Birmingham, Birmingham, AL
| | | | | | - Barkha Manne
- University of Alabama at Birmingham, Birmingham, AL
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Li H, Tang Z, Zhu H, Ge H, Cui S, Jiang W. Proteomic study of benign and malignant pleural effusion. J Cancer Res Clin Oncol 2016; 142:1191-200. [PMID: 26945985 DOI: 10.1007/s00432-016-2130-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 02/08/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Lung adenocarcinoma can easily cause malignant pleural effusion which was difficult to discriminate from benign pleural effusion. Now there was no biomarker with high sensitivity and specificity for the malignant pleural effusion. PURPOSE This study used proteomics technology to acquire and analyze the protein profiles of the benign and malignant pleural effusion, to seek useful protein biomarkers with diagnostic value and to establish the diagnostic model. METHODS We chose the weak cationic-exchanger magnetic bead (WCX-MB) to purify peptides in the pleural effusion, used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to obtain peptide expression profiles from the benign and malignant pleural effusion samples, established and validated the diagnostic model through a genetic algorithm (GA) and finally identified the most promising protein biomarker. RESULTS A GA diagnostic model was established with spectra of 3930.9 and 2942.8 m/z in the training set including 25 malignant pleural effusion and 26 benign pleural effusion samples, yielding both 100 % sensitivity and 100 % specificity. The accuracy of diagnostic prediction was validated in the independent testing set with 58 malignant pleural effusion and 34 benign pleural effusion samples. Blind evaluation was as follows: the sensitivity was 89.6 %, specificity 88.2 %, PPV 92.8 %, NPV 83.3 % and accuracy 89.1 % in the independent testing set. The most promising peptide biomarker was identified successfully: Isoform 1 of caspase recruitment domain-containing protein 9 (CARD9), with 3930.9 m/z, was decreased in the malignant pleural effusion. CONCLUSIONS This model is suitable to discriminate benign and malignant pleural effusion and CARD9 can be used as a new peptide biomarker.
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Affiliation(s)
- Hongqing Li
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Zhonghao Tang
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Huili Zhu
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China.
| | - Haiyan Ge
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Shilei Cui
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Weiping Jiang
- Department of Respiratory Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, 200040, China
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Schwacke J, Millar TP, Hammond CE, Saha A, Hoffman BJ, Romagnuolo J, Hill EG, Smolka AJ. Discrimination of normal and esophageal cancer plasma proteomes by MALDI-TOF mass spectrometry. Dig Dis Sci 2015; 60:1645-54. [PMID: 25577268 DOI: 10.1007/s10620-014-3513-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/29/2014] [Indexed: 12/09/2022]
Abstract
BACKGROUND Most patients presenting with symptoms of esophageal cancer (EC) have advanced disease. Even with resection, the cure rate is extremely low due to local recurrence and metastatic disease. Early detection and effective therapeutic intervention are essential to improve survival. AIMS This study tested the hypothesis that the presence of EC modulates concentrations of specific plasma proteins and peptides, potentially allowing discrimination between EC and controls based on mass spectrometric analysis of the respective plasma proteomes. METHODS Blood samples from 79 esophageal cancer patients and 40 age-matched normal subjects were processed to plasma, and protein/peptide sub-fractions were isolated using HIC8 or WAX-derivatized superparamagnetic beads. Triplicate matrix-assisted laser desorption time-of-flight mass spectra were acquired for specific plasma fractions from each subject. RESULTS HIC8 and WAX-derivatized plasma eluates yielded 79 and 77 candidate features, respectively, and a Random Forest algorithm identified a subset of features whose peak intensities allowed discrimination between cancer patients and controls. Areas under the curve in receiver operating characteristic curves for HIC8 spectra were 0.88 and 0.83 for WAX spectra. The combined feature set discriminated EC from control plasma with 79 % sensitivity and 79 % specificity, with positive and negative test likelihood ratios of >14 and 0.17, respectively. CONCLUSIONS These data lay the foundation for the development of a clinically useful test for esophageal cancer based on statistical analysis of proteomic spectra of patient plasma samples. This approach will be validated by analysis of larger patient cohorts, development of cancer-specific classifiers, and assessment of racial origin imbalances.
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Xiong C, Wang H, Yuan Y, Chai Y, Yuan R. A novel solid-state Ru(bpy)32+ electrochemiluminescence immunosensor based on poly(ethylenimine) and polyamidoamine dendrimers as co-reactants. Talanta 2015; 131:192-7. [DOI: 10.1016/j.talanta.2014.07.072] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
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Kim HS, Kang D, Moon MH, Kim HJ. Identification of pancreatic cancer-associated tumor antigen from HSP-enriched tumor lysate-pulsed human dendritic cells. Yonsei Med J 2014; 55:1014-27. [PMID: 24954332 PMCID: PMC4075362 DOI: 10.3349/ymj.2014.55.4.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/23/2013] [Accepted: 11/04/2013] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Vaccine strategies utilizing dendritic cells (DCs) to elicit anti-tumor immunity are the subject of intense research. Although we have shown that DCs pulsed with heat-treated tumor lysate (HTL) induced more potent anti-tumor immunity than DCs pulsed with conventional tumor lysate (TL), the underlying molecular mechanism is unclear. In order to explore the molecular basis of this approach and to identify potential antigenic peptides from pancreatic cancer, we analyzed and compared the major histocompatibility complex (MHC) ligands derived from TL- and HTL-pulsed dendritic cells by mass spectrophotometry. MATERIALS AND METHODS Human monocyte-derived dendritic cells were pulsed with TL or HTL prior to maturation induction. To delineate differences of MHC-bound peptide repertoire eluted from DCs pulsed with TL or HTL, nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) was employed. RESULTS HTL, but not TL, significantly induced DC function, assessed by phenotypic maturation, allostimulation capacity and IFN-γ secretion by stimulated allogeneic T cells. DCs pulsed with TL or HTL displayed pancreas or pancreatic cancer-related peptides in context of MHC class I and II molecules. Some of the identified peptides had not been previously reported as expressed in pancreatic cancer or cancer of other tissue types. CONCLUSION Our partial lists of MHC-associated peptides revealed the differences between peptide profiles eluted from HTL-and TL-loaded DCs, implying that induced heat shock proteins in HTL chaperone tumor-derived peptides enhanced their delivery to DCs and promoted cross-presentation by DC. These findings may aid in identifying novel tumor antigens or biomarkers and in designing future vaccination strategies.
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Affiliation(s)
- Han-Soo Kim
- Innovative Cell and Gene Therapy Center, International St. Mary's Hospital, Incheon, Korea
| | - Dukjin Kang
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, Korea
| | | | - Hyung Jik Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea.
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Abstract
Multifactorial diseases such as respiratory disease call for a global analysis of such disorders. Recent advances in protein profiling techniques may allow for early diagnosis of respiratory disease, which is crucial for intervention and treatment. In order to reduce false-positive rates, clinical diagnosis requires a high degree of sensitivity and specificity to be an effective screening tool. Protein profiles identified by ProteinChip (Ciphergen Biosystems) technology coupled with mass spectrometry affords a global analysis of clinical samples and is beginning to reach acceptable levels of sensitivity and specificity. Combining the profile with another diagnostic tool enhances the effectiveness of protein profiles to classify disease. Although current efforts have centered on serum protein profiling, the local environment of the lung may be better reflected in proteins of bronchoalveolar lavage or sputum. Identification of biomarkers of disease by protein profiling analyses may lead to an understanding of the mechanisms of this disease and contribute to the discovery of new therapeutics for the prevention and treatment of disease. Advancing these analyses are techniques such as ProteinChip mass spectrometry, laser capture microdissection, tissue microarrays and fluorescently labeled antibody bead arrays, which enable the direct global analysis of complex mixtures. Effective high-throughput and ease of use of clinical testing will arrive with improvements in bioinformatics and decreases in instrumentation costs.
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Affiliation(s)
- Susan E Boggs
- Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr SE, Albuquerque, NM 87108, USA.
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Saha SK, Khuda-Bukhsh AR. Molecular approaches towards development of purified natural products and their structurally known derivatives as efficient anti-cancer drugs: current trends. Eur J Pharmacol 2013; 714:239-48. [PMID: 23819913 DOI: 10.1016/j.ejphar.2013.06.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 06/01/2013] [Accepted: 06/08/2013] [Indexed: 12/14/2022]
Abstract
Several natural products and their derivatives, either in purified or structurally identified form, exhibit immense pharmacological and biological properties, some of them showing considerable anticancer potential. Although the molecular mechanisms of action of some of these products are yet to be elucidated, extensive research in this area continues to generate new data that are clinically exploitable. Recent advancement in molecular biology, high throughput screening, biomarker identifications, target selection and genomic approaches have enabled us to understand salient interactions of natural products and their derivatives with cancer cells vis-à-vis normal cells. In this review we highlight the recent approaches and application of innovative technologies made to improve quality as well as efficiency of structurally identified natural products and their derivatives, particularly in small molecular forms capable of being used in "targeted therapies" in oncology. These products preferentially involve multiple mechanistic pathways and overcome chemo-resistance in tumor types with cumulative action. We also mention briefly a few physico-chemical features that compare natural products with drugs in recent natural product discovery approaches. We further report here a few purified natural products as examples that provide molecular interventions in cancer therapeutics to give the reader a glimpse of the current trends of approach for discovering useful anticancer drugs.
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Affiliation(s)
- Santu Kumar Saha
- Cytogenetics and Molecular Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani-741235, India
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Tao YL, Li Y, Gao J, Liu ZG, Tu ZW, Li G, Xu BQ, Niu DL, Jiang CB, Yi W, Li ZQ, Li J, Wang YM, Cheng ZB, Liu QD, Bai L, Zhang C, Zhang JY, Zeng MS, Xia YF. Identifying FGA peptides as nasopharyngeal carcinoma-associated biomarkers by magnetic beads. J Cell Biochem 2012; 113:2268-78. [PMID: 22334501 DOI: 10.1002/jcb.24097] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Early diagnosis and treatment is known to improve prognosis for nasopharyngeal carcinoma (NPC). The study determined the specific peptide profiles by comparing the serum differences between NPC patients and healthy controls, and provided the basis for the diagnostic model and identification of specific biomarkers of NPC. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) can be used to detect the molecular mass of peptides. Mass spectra of peptides were generated after extracting and purification of 40 NPC samples in the training set, 21 in the single center validation set and 99 in the multicenter validation set using weak cationic-exchanger magnetic beads. The spectra were analyzed statistically using FlexAnalysis™ and ClinProt™ bioinformatics software. The four most significant peaks were selected out to train a genetic algorithm model to diagnose NPC. The diagnostic sensitivity and specificity were 100% and 100% in the training set, 90.5% and 88.9% in the single center validation set, 91.9% and 83.3% in the multicenter validation set, and the false positive rate (FPR) and false negative rate (FNR) were obviously lower in the NPC group (FPR, 16.7%; FNR, 8.1%) than in the other cancer group (FPR, 39%; FNR, 61%), respectively. So, the diagnostic model including four peptides can be suitable for NPC but not for other cancers. FGA peptide fragments identified may serve as tumor-associated biomarkers for NPC.
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Affiliation(s)
- Ya-Lan Tao
- Department of Radiation Oncology, Cancer Center, Sun Yat-Sen University, Guangzhou, Guangdong, People's Republic of China
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Ueda H, Matsunaga H, Halder SK. Prothymosin α plays multifunctional cell robustness roles in genomic, epigenetic, and nongenomic mechanisms. Ann N Y Acad Sci 2012; 1269:34-43. [DOI: 10.1111/j.1749-6632.2012.06675.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Intracellular and extracellular cytokine-like functions of prothymosin α: implications for the development of immunotherapies. Future Med Chem 2012; 3:1199-208. [PMID: 21806381 DOI: 10.4155/fmc.11.72] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Prothymosin α (ProTα) is a 12.5-kDa, highly acidic protein widely distributed in different cell types expressed intracellularly and extracellularly. ProTα does not contain a secretion-signal sequence and is released by a nonclassical secretory pathway with a cargo protein. New findings on the extracellular function of ProTα have yielded exciting insights into the cytokine-like functions of this host protein that stimulates type I interferon via Toll-like receptor 4. Here, we discuss the intracellular function of ProTα, how new findings of cytokine-like activities of ProTα aid our understanding of mechanisms that direct ProTα functions, and the potential application of these new insights to the development of immunotherapies.
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Tripathi SC, Matta A, Kaur J, Grigull J, Chauhan SS, Thakar A, Shukla NK, Duggal R, Choudhary AR, DattaGupta S, Sharma MC, Ralhan R, Siu KWM. Overexpression of prothymosin alpha predicts poor disease outcome in head and neck cancer. PLoS One 2011; 6:e19213. [PMID: 21573209 PMCID: PMC3088661 DOI: 10.1371/journal.pone.0019213] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 03/29/2011] [Indexed: 12/13/2022] Open
Abstract
Background In our recent study, tissue proteomic analysis of oral pre-malignant lesions (OPLs) and normal oral mucosa led to the identification of a panel of biomarkers, including prothymosin alpha (PTMA), to distinguish OPLs from histologically normal oral tissues. This study aimed to determine the clinical significance of PTMA overexpression in oral squamous cell hyperplasia, dysplasia and head and neck squamous cell carcinoma (HNSCC). Methodology Immunohistochemistry of PTMA protein was performed in HNSCCs (n = 100), squamous cell hyperplasia (n = 116), dysplasia (n = 50) and histologically normal oral tissues (n = 100). Statistical analysis was carried out to determine the association of PTMA overexpression with clinicopathological parameters and disease prognosis over 7 years for HNSCC patients. Results Our immunohistochemical analysis demonstrated significant overexpression of nuclear PTMA in squamous cell hyperplasia (63.8%), dysplasia (50%) and HNSCC (61%) in comparison with oral normal mucosa (ptrend<0.001). Chi-square analysis showed significant association of nuclear PTMA with advanced tumor stages (III+IV). Kaplan Meier survival analysis indicated reduced disease free survival (DFS) in HNSCC patients (p<0.001; median survival 11 months). Notably, Cox-multivariate analysis revealed nuclear PTMA as an independent predictor of poor prognosis of HNSCC patients (p<0.001, Hazard's ratio, HR = 5.2, 95% CI = 2.3–11.8) in comparison with the histological grade, T-stage, nodal status and tumor stage. Conclusions Nuclear PTMA may serve as prognostic marker in HNSCC to determine the subset of patients that are likely to show recurrence of the disease.
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Affiliation(s)
| | - Ajay Matta
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
| | - Jatinder Kaur
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Jorg Grigull
- Department of Mathematics and Statistics, York University, Toronto, Ontario, Canada
| | - Shyam Singh Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Alok Thakar
- Department of Otorhinolaryngology, All India Institute of Medical Sciences, New Delhi, India
| | - Nootan Kumar Shukla
- Department of Surgery, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Duggal
- Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Ajoy Roy Choudhary
- Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | | | - Mehar Chand Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ranju Ralhan
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
- Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases and Department of Otolaryngology – Head and Neck Surgery, Mount Sinai Hospital, Toronto, Ontario, Canada
- Alex and Simona Shnaider Laboratory in Molecular Oncology and Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (RR); (KWMS)
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada
- * E-mail: (RR); (KWMS)
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Time course proteomic profiling of human myocardial infarction plasma samples: An approach to new biomarker discovery. Clin Chim Acta 2011; 412:1086-93. [DOI: 10.1016/j.cca.2011.02.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/30/2011] [Accepted: 02/19/2011] [Indexed: 01/22/2023]
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15
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Ma Z, Liu C, Deng B, Dong S, Tao G, Zhan X, Wang C, Liu S, Qu X. Different protein profile in amniotic fluid with nervous system malformations by surface-enhanced laser desorption-ionization/time-of-flight mass spectrometry (SELDI-TOF-MS) technology. J Obstet Gynaecol Res 2011; 36:1195-203. [PMID: 21114572 DOI: 10.1111/j.1447-0756.2010.01390.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIM To detect the distinct proteins in amniotic fluid (AF) between nervous system malformations fetuses and normal fetuses. MATERIAL AND METHODS Surface-enhanced laser desorption-ionization/time-of-flight mass spectrometry was used to characterize AF peptides in AF between nervous system malformations fetuses and normal fetuses. WCX2 protein chips were used to characterize AF peptides in AF. Protein chips were examined in a PBSIIC protein reader, the protein profiling was collected by ProteinChip software version 3.1 (Ciphergen Biosystems, Fremont, CA, USA) and analyzed by Biomarker Wizard software (Ciphergen Biosystems). Nine distinct proteins were identified in AF between nervous system malformations fetuses and normal fetuses. RESULTS Compared with the control group, three proteins with m/z 4967.5 Da, 5258.0 Da, and 11,717.0 Da were down-regulated, and six proteins with m/z 2540.4 Da, 3107.1 Da, 3396.8 Da, 4590.965 Da, 5589.2 Da and 6429.4 Da up-regulated in nervous system malformations fetuses. CONCLUSION The results suggest that there are distinct proteins in protein profiling of AF between nervous system malformations fetuses and normal fetuses.
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Affiliation(s)
- Zhe Ma
- Department of Ultrasound Basic Medicine, Qilu Hospital, Shandong University, Shandong Province, China
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Application of serum protein fingerprint in diagnosis of coronary artery disease. Clin Biochem 2011; 44:185-91. [DOI: 10.1016/j.clinbiochem.2010.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 10/04/2010] [Accepted: 10/06/2010] [Indexed: 11/24/2022]
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Wang Z, Li XQ, Wang KZ, Deng MM, Xu L. Serum protein fingerprinting for diagnosis and prognosis evaluation of colorectal cancer. Shijie Huaren Xiaohua Zazhi 2010; 18:3745-3751. [DOI: 10.11569/wcjd.v18.i35.3745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify differentially expressed proteins for diagnosis and prognosis evaluation of colorectal cancer by serum protein fingerprint in colorectal cancer patients.
METHODS: Serum protein fingerprinting was performed by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) in 45 colorectal cancer patients, 14 colorectal cancer having a good prognosis (no postoperative recurrence and metastasis), 13 colorectal cancer patients having a poor prognosis (having recurrence or metastasis), 24 patients with benign gastrointestinal disease, and 155 healthy controls. The Biomarker Wizard software was used to identify differential proteins. Two respective artificial neural network (ANN) models were developed for diagnosis and prognosis evaluation of colorectal cancer.
RESULTS: Seven proteins that displayed significant differential expression were identified (all P < 0.01), and their molecular weight was 4 955 Da, 5 325 Da, 5 890 Da, 6 615 Da, 7 739 Da, 8 109 Da, and 8 575 Da, respectively. Using these seven protein markers, we developed an artificial neural network model for diagnosis of colorectal cancer. Furthermore, five proteins that had a molecular weight of 4 955 Da, 5 325 Da, 5 890 Da, 6 615 Da, and 7 739 Da were used to develop an artificial neural network model for evaluation of the prognosis of colorectal cancer. The sensitivity, specificity, negative predictive value, positive predictive value, and accuracy of the diagnostic model were 82.22%, 80.45%, 94.74%, 51.39% and 80.80%, respectively. The coincidence rate of the prognostic model for evaluation of recurrence and metastasis was 62.96%.
CONCLUSION: SELDI-TOF-MS serum protein fingerprinting allows identification of differentially expressed proteins in colorectal cancer to develop models for diagnosis and prognosis evaluation of the disease.
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Zhang CM, Zhang JL, Zhang Q, Zhang Z, Zhang HP, Sun QC, Ding X, Liu YL, Sheyhidin I. Identification of esophageal carcinoma-associated proteins by proteomics in Han, Uygur and Kazakh patients with esophageal carcinoma in Xinjiang, China. Shijie Huaren Xiaohua Zazhi 2010; 18:1773-1779. [DOI: 10.11569/wcjd.v18.i17.1773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To conduct a serum protein profile analysis in Han, Uygur and Kazakh patients with esophageal carcinoma (EC) in Xinjiang, China.
METHODS: Serum samples from patients with EC (43 Han, 43 Uygur and 41 Kazakh subjects) were detected by weak cation exchange (CM10) protein chip assay using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) technology to screen differentially expressed serum markers for EC.
RESULTS: The peaks at the mass to charge ratios (M/Z) 4 310.0109, 8 713.0142 and 7 993.0223 were significantly different between Han and Uygur EC patients (P < 0.05). The peaks at M/Z 4 310.0184, 8 167.9277, 8 158.1117, 13 789.4864, 8 067.7056, 4 611.9098, 7 993.4422 and 16 146.8706 were significantly different between Han and Kazakh EC patients (P < 0.05). The peaks at M/Z 9 161.7944, 4 611.6342, 6 649.6163 and 4 979.3807 were significantly different between Uygur and Kazakh EC patients (P < 0.05). The peat at M/Z 4 310.0109 was highly expressed in Uygur and Kazakh patients but lowly expressed in Han patients.
CONCLUSION: The protein fingerprints are significantly different among Han, Uygur and Kazakh EC patients in Xinjiang, China, which can be used to build a diagnostic model of EC.
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Sharma SV, Haber DA, Settleman J. Cell line-based platforms to evaluate the therapeutic efficacy of candidate anticancer agents. Nat Rev Cancer 2010; 10:241-53. [PMID: 20300105 DOI: 10.1038/nrc2820] [Citation(s) in RCA: 421] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Efforts to discover new cancer drugs and predict their clinical activity are limited by the fact that laboratory models to test drug efficacy do not faithfully recapitulate this complex disease. One important model system for evaluating candidate anticancer agents is human tumour-derived cell lines. Although cultured cancer cells can exhibit distinct properties compared with their naturally growing counterparts, recent technologies that facilitate the parallel analysis of large panels of such lines, together with genomic technologies that define their genetic constitution, have revitalized efforts to use cancer cell lines to assess the clinical utility of new investigational cancer drugs and to discover predictive biomarkers.
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Affiliation(s)
- Sreenath V Sharma
- Center for Molecular Therapeutics, Massachusetts General Hospital Cancer Center and Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA
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20
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Kanmura S, Uto H, Sato Y, Kumagai K, Sasaki F, Moriuchi A, Oketani M, Ido A, Nagata K, Hayashi K, Stuver SO, Tsubouchi H. The complement component C3a fragment is a potential biomarker for hepatitis C virus-related hepatocellular carcinoma. J Gastroenterol 2010; 45:459-67. [PMID: 20012107 DOI: 10.1007/s00535-009-0160-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/28/2009] [Indexed: 02/04/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has a high mortality rate, and early detection of HCC improves patient survival. However, the molecular diagnostic markers for early HCC have not been fully elucidated. The aim of this study was to identify novel diagnostic markers for HCC. METHODS Serum protein profiles of 45 hepatitis C virus infection (HCV)-related HCC patients (HCV-HCC) were compared to 42 HCV-related chronic liver disease patients without HCC (HCV-CLD) and 21 healthy volunteers using the ProteinChip SELDI system. One of the identified proteins was evaluated as a diagnostic marker for HCC in patients with HCV. RESULTS Five protein peaks (4067, 4470, 7564, 7929, and 8130 m/z) had p-values less than 1 x 10(-7) and were significantly increased in the sera of HCV-HCC patients compared to HCV-CLD patients and healthy volunteers. Among these proteins, an 8130 m/z peak was the most differentially expressed and identified as the complement component 3a (C3a) fragment. For HCV-HCC and HCV-CLD, the relative intensity of this C3a fragment had the best area under the ROC curve [0.70], followed by des-gamma-carboxy prothrombin (DCP) [0.68], lectin-bound alpha fetoprotein (AFP-L3) [0.58] and AFP [0.53] for HCC. A combined analysis of the C3a fragment, AFP and DCP led to a 98% positive identification rate. In addition, the measurable C3a fragment in some HCC patients was not only significantly higher in the year of HCC onset compared to the pre-onset year, but also decreased after treatment. CONCLUSIONS The 8130 m/z C3a fragment is a potential marker for the early detection of HCV-related HCC.
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Affiliation(s)
- Shuji Kanmura
- Digestive Disease and Life-style Related Disease Health Research, Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8520, Japan
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Tang J, Liu Y, Qi D, Yao G, Deng C, Zhang X. On-plate-selective enrichment of glycopeptides using boronic acid-modified gold nanoparticles for direct MALDI-QIT-TOF MS analysis. Proteomics 2010; 9:5046-55. [PMID: 19834891 DOI: 10.1002/pmic.200900033] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this study, an on-plate-selective enrichment method is developed for fast and efficient glycopeptide investigation. Gold nanoparticles were first spotted and sintered on a stainless-steel plate, then modified with 4-mercaptophenylboronic acid to provide porous substrate with large specific surface and dual functions. These spots were used to selectively capture glycopeptides from peptide mixtures and the captured target peptides could be analyzed by MALDI-MS simply by deposition of 2,5-dihydroxybenzoic acid matrix. Horseradish peroxidase was employed as a standard glycoprotein to investigate the enrichment efficiency. In this way, the enrichment, washing and detection steps can all be fulfilled on a single MALDI target plate. The relatively small sample amount needed, low detection limit and rapid selective enrichment have made this on-plate strategy promising for online enrichment of glycopeptides, which could be applied in high-throughput proteome research.
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Affiliation(s)
- Jia Tang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, P. R. China
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Abstract
Bladder cancer is one of the most expensive cancers from diagnosis to death of the patient due to life-long surveillance involving upper tract imaging, urinary cytology, and cystoscopy. Cytology has been historically used in conjunction with cystoscopy to help detect disease that may be missed by routine cystoscopy (e.g., carcinoma in situ and upper tract disease). Urine cytology is highly cytopathologist dependent and has reasonable sensitivity for detecting high grade disease. However, its sensitivity drops precipitously with regard to well-differentiated low grade cancers. Intensive investigations have been undertaken using proteomics to find an alternative to cystoscopy and cytology. Urine proteomic markers currently evaluated critically in the literature include bladder tumor antigen, nuclear matrix protein 22, BLCA-4, hyaluronic acid, hyaluronidase, cytokeratin 8, cytokeratin 18, cytokeratin 19, tissue polypeptide antigen, and tissue polypeptide-specific antigen. Markers used as alternatives to cystoscopy must be accurate with high sensitivity and specificity, cost effective for life-long surveillance, and minimally invasive to minimize the burden to the patient. To date, no proteomic marker has been developed that can replace cystoscopy for the detection of bladder cancer. However, several urinary markers appear to have higher sensitivity albeit lower specificity than cytology and can be used to supplement cystoscopy. Some of those markers are herein described in this chapter. By defining and characterizing the current state of the art in protein based markers, we are poised to evaluate and benchmark newly discovered protein biomarkers that will be isolated through new proteomics based investigations of urine.
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Affiliation(s)
- Kris E Gaston
- Department of Urology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit1373, Houston, TX 77030, USA
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Jing J, Qiao Y, Suginami H, Taniguchi F, Shi H, Wang X. Two novel serum biomarkers for endometriosis screened by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry and their change after laparoscopic removal of endometriosis. Fertil Steril 2009; 92:1221-1227. [DOI: 10.1016/j.fertnstert.2008.08.078] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 07/28/2008] [Accepted: 08/04/2008] [Indexed: 11/24/2022]
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24
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Strenziok R, Hinz S, Wolf C, Conrad T, Krause H, Miller K, Schrader M. Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J Urol 2009; 28:193-7. [PMID: 19529944 DOI: 10.1007/s00345-009-0434-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 05/25/2009] [Indexed: 10/20/2022] Open
Abstract
PURPOSE Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF MS) allows rapid protein profiling of complex biological mixtures. We analyzed testicular germ cell cancer serum samples to differentiate between cancer and controls with a special focus on beta-hCG-negative seminomas. METHODS Proteomic spectra were generated by the ProteinChip system and analyzed by the proteomic platform "proteomic.net". For statistical analysis, an artificial intelligence learning algorithm was used. RESULTS The classification algorithm correctly identified the pattern in 90.4% of the patients. Decision trees predicted seminomas with 91.5% sensitivity and 89.4% specificity. Seminoma patients with normal beta-hCG serum level were correctly predicted with 80% sensitivity and 70% specificity. CONCLUSIONS Our study demonstrates protein profiles of testicular germ cell cancer patients that differ in a highly significant degree from normal controls. Validation of these findings may enable proteomic profiling to become a valuable tool, especially for aftercare.
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Affiliation(s)
- Romy Strenziok
- Charité-Universitätsmedizin Berlin, Urologische Klinik und Hochschulambulanz, Hindenburgdamm 30, 12200 Berlin, Germany.
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25
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Abstract
Diagnostic oncoproteomics is the application of proteomic techniques for the diagnosis of malignancies. A new mass spectrometric technology involves surface enhanced laser desorption ionization combined with time-of flight mass analysis (SELDI-TOF-MS), using special protein chips. After the description of the relevant principles of the technique, including approaches to proteomic pattern diagnostics, applications are reviewed for the diagnosis of ovarian, breast, prostate, bladder, pancreatic, and head and neck cancers, and also several other malignancies. Finally, problems and prospects of the approach are discussed.
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Affiliation(s)
- John Roboz
- Division of Hematology-Oncology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
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26
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Shi L, Zhang J, Wu P, Feng K, Li J, Xie Z, Xue P, Cai T, Cui Z, Chen X, Hou J, Zhang J, Yang F. Discovery and identification of potential biomarkers of pediatric acute lymphoblastic leukemia. Proteome Sci 2009; 7:7. [PMID: 19291297 PMCID: PMC2662805 DOI: 10.1186/1477-5956-7-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 03/16/2009] [Indexed: 12/22/2022] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is a common form of cancer in children. Currently, bone marrow biopsy is used for diagnosis. Noninvasive biomarkers for the early diagnosis of pediatric ALL are urgently needed. The aim of this study was to discover potential protein biomarkers for pediatric ALL. Methods Ninety-four pediatric ALL patients and 84 controls were randomly divided into a "training" set (45 ALL patients, 34 healthy controls) and a test set (49 ALL patients, 30 healthy controls and 30 pediatric acute myeloid leukemia (AML) patients). Serum proteomic profiles were measured using surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy (SELDI-TOF-MS). A classification model was established by Biomarker Pattern Software (BPS). Candidate protein biomarkers were purified by HPLC, identified by LC-MS/MS and validated using ProteinChip immunoassays. Results A total of 7 protein peaks (9290 m/z, 7769 m/z, 15110 m/z, 7564 m/z, 4469 m/z, 8937 m/z, 8137 m/z) were found with differential expression levels in the sera of pediatric ALL patients and controls using SELDI-TOF-MS and then analyzed by BPS to construct a classification model in the "training" set. The sensitivity and specificity of the model were found to be 91.8%, and 90.0%, respectively, in the test set. Two candidate protein peaks (7769 and 9290 m/z) were found to be down-regulated in ALL patients, where these were identified as platelet factor 4 (PF4) and pro-platelet basic protein precursor (PBP). Two other candidate protein peaks (8137 and 8937 m/z) were found up-regulated in the sera of ALL patients, and these were identified as fragments of the complement component 3a (C3a). Conclusion Platelet factor (PF4), connective tissue activating peptide III (CTAP-III) and two fragments of C3a may be potential protein biomarkers of pediatric ALL and used to distinguish pediatric ALL patients from healthy controls and pediatric AML patients. Further studies with additional populations or using pre-diagnostic sera are needed to confirm the importance of these findings as diagnostic markers of pediatric ALL.
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Affiliation(s)
- Linan Shi
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Graduate University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jun Zhang
- Center for Experimental Medicine, 306 Hospital of PLA, Beijing 100101, PR China
| | - Peng Wu
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Kai Feng
- Center for Experimental Medicine, 306 Hospital of PLA, Beijing 100101, PR China
| | - Jing Li
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Graduate University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhensheng Xie
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Peng Xue
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Tanxi Cai
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ziyou Cui
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Graduate University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiulan Chen
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Graduate University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Junjie Hou
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.,Graduate University of the Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jianzhong Zhang
- Center for Experimental Medicine, 306 Hospital of PLA, Beijing 100101, PR China
| | - Fuquan Yang
- Proteomic Platform, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China
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27
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Li YZ, Hu CJ, Leng XM, Zhao GF, Li N, Xu Y. Promising Diagnostic Biomarkers for Primary Biliary Cirrhosis Identified With Magnetic Beads and MALDI-TOF-MS. Anat Rec (Hoboken) 2009; 292:455-60. [PMID: 19248174 DOI: 10.1002/ar.20870] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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Time course proteomic profile of rat acute myocardial infarction by SELDI-TOF MS analysis. Int J Cardiol 2009; 131:225-33. [DOI: 10.1016/j.ijcard.2007.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 08/30/2007] [Accepted: 10/20/2007] [Indexed: 11/21/2022]
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Metzger J, Luppa PB, Good DM, Mischak H. Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm. Crit Rev Clin Lab Sci 2009; 46:129-52. [PMID: 19404829 PMCID: PMC5769463 DOI: 10.1080/10408360902805261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single biomarker detection is common in clinical laboratories due to the currently available method spectrum. For various diseases, however, no specific single biomarker could be identified. A strategy to overcome this diagnostic void is to shift from single analyte detection to multiplexed biomarker profiling. Mass spectrometric methods were employed for biomarker discovery in body fluids. The enormous complexity of biofluidic proteome compartments implies upstream fractionation. For this reason, mass spectrometry (MS) was coupled to two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization, or capillary electrophoresis (CE). Differences in performance and operating characteristics make them differentially suited for routine laboratory applications. Progress in the field of clinical proteomics relies not only on the use of an adequate technological platform, but also on a fast and efficient proteomic workflow including standardized sample preparation, proteomic data processing, statistical validation of biomarker selection, and sample classification. Based on CE-MS analysis, we describe how proteomic technology can be implemented in a clinical laboratory environment. In the last part of this review, we give an overview of CE-MS-based clinical studies and present information on identity and biological significance of the identified peptide biomarkers providing evidence of disease-induced changes in proteolytic processing and posttranslational modification.
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Affiliation(s)
- Jochen Metzger
- Mosaiques Diagnostics and Terapeutics AG, Mellendorfer Str. 7-9, Hannover 30625, Germany.
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30
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Abstract
BACKGROUND Proteomics has evolved into a large-scale biomarker discovery program; however, these initiatives are viewed as failing owing to a lack of successful implementation of new protein biomarkers in the diagnostic arena. New approaches to proteomics biomarker discovery and validation may be the key to boosting clinical proteomics into diagnostics. OBJECTIVE To review the technologies and the mindsets behind proteomic biomarker discovery and discuss suitable methods for the detection of protein variants and their use as potential biomarkers of disease states. METHODS A literature review of recent research on proteomic biomarkers and through experience with biomarker discovery research was surveyed and described. Emphasis was placed on top-down proteomics approaches for the discovery and routine screening of protein variation. CONCLUSION Protein variation is an untapped resource in the biomarker space, but only a selected few forms of proteomics applications are suitable for their analysis. Such variation could have a significant impact in disease diagnostics and therapeutic intervention.
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Affiliation(s)
- Urban A Kiernan
- Senior Research Scientist, Intrinsic Bioprobes, Inc. - R&D, 2155 E Conference Dr Tempe, AZ 85284, USA +1 480 804 1778 ; +480 804 0778 ;
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31
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Kiga C, Sakurai H, Goto H, Hayashi K, Shimada Y, Saiki I. Proteomic identification of haptoglobin as a stroke plasma biomarker in spontaneously hypertensive stroke-prone rats. Life Sci 2008; 83:625-31. [DOI: 10.1016/j.lfs.2008.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/11/2008] [Accepted: 08/26/2008] [Indexed: 10/21/2022]
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32
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Metzger J, Schanstra JP, Mischak H. Capillary electrophoresis–mass spectrometry in urinary proteome analysis: current applications and future developments. Anal Bioanal Chem 2008; 393:1431-42. [DOI: 10.1007/s00216-008-2309-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 06/11/2008] [Accepted: 07/18/2008] [Indexed: 11/30/2022]
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Liu W, Li X, Ding F, Li Y. Using SELDI-TOF MS to identify serum biomarkers of rheumatoid arthritis. Scand J Rheumatol 2008; 37:94-102. [PMID: 18415765 DOI: 10.1080/03009740701747152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVES No satisfactory biomarkers are currently available to screen for rheumatoid arthritis (RA). We have developed and evaluated surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for detection and analysis of multiple proteins for distinguishing individuals with RA from control individuals. METHODS A total of 156 serum samples from 90 RA patients, 30 patients with ankylosing spondylitis (AS), and 36 healthy individuals were examined by SELDI technology. Spectral data were analysed by the support vector machine (SVM) approach and potential biomarkers were chosen for system training and were used to construct a diagnostic model. RESULTS Pattern 1, consisting of four protein peaks with m/z values of 3899, 4594, 7566, and 13,842, distinguished RA from the healthy samples with sensitivity of 90.0% and a specificity of 91.7%. Pattern 2, consisting of m/z peaks 4287 and 6471, distinguished RA from AS with a sensitivity of 86.7% and a specificity of 85.0%. CONCLUSION The combination of SELDI-TOF MS and SVM could facilitate the discovery of better biomarkers for RA and also provide a useful tool for molecular diagnosis in the future.
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Affiliation(s)
- W Liu
- Department of Rheumatology, Shandong University Qilu Hospital, Jinan, P.R. China
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34
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Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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35
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Kiehntopf M, Siegmund R, Deufel T. Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations. Clin Chem Lab Med 2008; 45:1435-49. [PMID: 17970700 DOI: 10.1515/cclm.2007.351] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Surface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding also of the limitations of this technology and various pitfalls in biomarker discovery. Bearing these in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the pre-analytical as well as the analytical phase and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false-significant results studies must be designed carefully and control groups accurately selected. In addition, appropriate tools, already established for analysis of highly complex microarray data, need to be applied to protein profiling data. To validate the significance of any candidate biomarker derived from pilot studies in appropriately designed prospective multi-center studies is mandatory; reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required; only a few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.
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Affiliation(s)
- Michael Kiehntopf
- Institut für Klinische Chemie und Laboratoriumsdiagnostik, Universitätsklinikum Jena, Jena, Germany.
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36
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Hu CJ, Li YZ, Zhao GF, Li N, Xu Y, Tong DW, Zhang SL. Screening for specific biomarkers in serum for diagnosis of primary biliary cirrhosis using proteomic fingerprint technology. Shijie Huaren Xiaohua Zazhi 2008; 16:277-283. [DOI: 10.11569/wcjd.v16.i3.277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen for the potential protein biomarkers in serum for the diagnosis of primary biliary cirrhosis (PBC) using proteomic fingerprint technology.
METHODS: Proteomic fingerprint technology combining magnetic beads with MALDI-TOF-MS was used to profile and compare the serum proteins from 44 patients with PBC, 32 patients with other hepatic diseases and 43 healthy blood donors. Proteomic patterns associated with PBC were identified by Biomarker Patterns Software. Model of biomarkers was constructed and evaluated using the Biomarker Patterns Software.
RESULTS: A total of 69 discriminating m/z peaks were identified that were related to PBC (P < 0.05). The model of biomarkers constructed by the Biomarker Patterns Software based on the four biomarkers (3445, 4260, 8133 and 16290) generated excellent separation between the PBC and control groups. The sensitivity was 93.3% and the specificity was 95.1%. Blind test data indicated a sensitivity of 92.9% and a specificity of 82.4%.
CONCLUSION: Biomarkers for PBC can be discovered in serum by MALDI-TOF-MS combining the use of magnetic beads. The pattern of combined markers provides a powerful and reliable diagnostic method for PBC with a high sensitivity and specificity.
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Schiffer E, Mischak H, Theodorescu D, Vlahou A. Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform. World J Urol 2008; 26:67-74. [PMID: 18175124 DOI: 10.1007/s00345-007-0234-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/11/2007] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Bladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures. METHODS Proteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical "target-driven" analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential. CONCLUSIONS This review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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Liu WJ, Qin HL. Application of proteomic techniques in research on biomarkers for colorectal cancer. Shijie Huaren Xiaohua Zazhi 2007; 15:3836-3841. [DOI: 10.11569/wcjd.v15.i36.3836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers in humans, and is often diagnosed at an intermediate or late stage with poor prognosis. Early detection may improve prognosis greatly. Current biomarkers (such as CEA and CA-199) lack sensitivity and specificity for general population screening. Hence, there is a great need for new biomarkers for early detection of CRC. Recently, proteomics has rapidly developed and been applied to every field in the life sciences, especially tumor research. Proteomic techniques give us the possibility to discover early diagnostic and prognostic biomarkers for CRC. In this study, the utilization of proteomics techniques in research on biomarkers for CRC is reviewed briefly.
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Malik G, Rojahn E, Ward MD, Gretzer MB, Partin AW, Semmes OJ, Veltri RW. SELDI protein profiling of dunning R-3327 derived cell lines: identification of molecular markers of prostate cancer progression. Prostate 2007; 67:1565-75. [PMID: 17705230 DOI: 10.1002/pros.20646] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND We recently demonstrated the protein expression profiling of Dunning rat tumor cell lines of varying metastatic potential (G (0%), AT-1 ( approximately 20%), and MLL (100%)) using SELDI-TOF-MS. As a parallel effort, we have been pursuing the identification of the protein(s) comprising the individual discriminatory "peaks" and evaluating their utility as potential biomarkers for prostate cancer progression. METHODS To identify the observed SELDI-TOF-MS m/z (mass/charge) values with discriminatory expression between different sublines, we employed a combination of chemical pre-fractionation, liquid chromatography, gel electrophoresis and tandem mass spectroscopy. Identified proteins were then verified by immuno-assay and Western analysis. RESULTS A 17.5 K m/z SELDI-TOF-MS peak was found to retain discriminatory value in each of two separate study-sets with an increased expression in the metastatic MLL line. Sequence identification and subsequent immunoassays verified that Histone H2B is the observed 17.5 K m/z SELDI peak. SELDI-based immuno-assay and Western Blotting revealed that Histone H2B is specifically over-expressed in metastatic MLL lines. CONCLUSIONS SELDI-TOF MS analysis of the Dunning prostate cancer cell lines confirmed the consistent overexpression of a 17.5 K m/z peak in metastatic MLL subline. The 17.5 kDa protein from MLL has been isolated and identified as Histone H2B.
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Affiliation(s)
- Gunjan Malik
- Center for Biomedical Proteomics, Virginia Prostate Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
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Theodorescu D, Mischak H. Mass spectrometry based proteomics in urine biomarker discovery. World J Urol 2007; 25:435-43. [PMID: 17703310 DOI: 10.1007/s00345-007-0206-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 07/13/2007] [Indexed: 11/28/2022] Open
Abstract
All organisms contain 1,000s of proteins and peptides in their body fluids, which undergo disease-specific changes. Advances in the understanding of the functional relevance of these polypeptides under different (patho)physiological conditions and the identification of indicative changes with disease would greatly enhance diagnosis and therapy. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its lower molecular weight, the peptidome can be assessed without the need for sample manipulation like tryptic digests. This advantage facilitates comparative analysis but it also raises technical challenges differing from those in proteomics. The first part of this manuscript, is focused on the low-molecular-weight urinary proteome and reviews methodological aspects of sample collection, preparation, analysis, and data evaluation. The second part summarizes the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
- Dan Theodorescu
- Department of Molecular Physiology, University of Virginia, Charlottesville, USA
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Mischak H, Julian BA, Novak J. High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine. Proteomics Clin Appl 2007; 1:792. [PMID: 20107618 PMCID: PMC2811330 DOI: 10.1002/prca.200700043] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Indexed: 11/09/2022]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
| | | | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
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42
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Hartwell SK, Pathanon K, Fongmoon D, Kongtawelert P, Grudpan K. Exploiting flow injection system with mini-immunoaffinity chromatographic column for chondroitin sulfate proteoglycans assay. Anal Bioanal Chem 2007; 388:1839-46. [PMID: 17579847 DOI: 10.1007/s00216-007-1361-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 10/23/2022]
Abstract
A flow injection (FI) system with a mini-immunoaffinity chromatographic column was used to perform on-line assays of specific proteoglycans. The 300-microL mini-column contained beads coupled with monoclonal antibodies against the specific sulfation pattern of chondroitin sulfate proteoglycans, which have been reported to be a potential biomarker for cancer. The amount of these proteoglycans present was estimated indirectly from their protein content using the Bradford assay, which is an alternative to a direct carbohydrate assay. The system developed was tested by assaying for chondroitin sulfate proteoglycans in sera from patients with various cancers and comparing the results to those obtained for sera from healthy people. The results indicated that this approach could be used as a cost-effective alternative system for determining the amount of these specific biomarker proteoglycans. The column could be reused at least 90 times, with each run consisting of 200 microL of serum sample diluted twofold; an analysis rate of 30 min per run was achieved, as compared to 4 h for a batch procedure.
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Affiliation(s)
- Supaporn Kradtap Hartwell
- Department of Chemistry, Faculty of Science and Institute for Science and Technology Research and Development, Chiang Mai University, Chiang Mai, 50200, Thailand.
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43
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Differential proteomics in malignant and normal liver cell lines. Chin J Cancer Res 2007. [DOI: 10.1007/s11670-007-0094-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Bharti A, Ma PC, Salgia R. Biomarker discovery in lung cancer--promises and challenges of clinical proteomics. MASS SPECTROMETRY REVIEWS 2007; 26:451-66. [PMID: 17407130 DOI: 10.1002/mas.20125] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Lung cancer is a devastating illness with an overall poor prognosis. To effectively address this disease, early detection and novel therapeutics are required. Early detection of lung cancer is challenging, in part because of the lack of adequate tumor biomarkers. The goal of this review is to summarize the knowledge of current biomarkers in lung cancer, with a focus on important serum biomarkers. The current knowledge on the known serum cytokines and tumor biomarkers of lung cancer will be presented. Emerging trends and new findings in the search for novel diagnostic and therapeutic tumor biomarkers using proteomics technologies and platforms are emphasized, including recent advances in mass spectrometry to facilitate tumor biomarker discovery program in lung cancer. It is our hope that validation of these new research platforms and technologies will result in improved early detection, prognostication, and finally the treatment of lung cancer with potential novel molecularly targeted therapeutics.
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Affiliation(s)
- Ajit Bharti
- Center for Molecular Stress Response Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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45
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Driemel O, Murzik U, Escher N, Melle C, Bleul A, Dahse R, Reichert T, Ernst G, von Eggeling F. Protein profiling of oral brush biopsies: S100A8 and S100A9 can differentiate between normal, premalignant, and tumor cells. Proteomics Clin Appl 2007; 1:486-93. [DOI: 10.1002/prca.200600669] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Indexed: 11/06/2022]
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Chang JTC, Chen LC, Wei SY, Chen YJ, Wang HM, Liao CT, Chen IH, Cheng AJ. Increase diagnostic efficacy by combined use of fingerprint markers in mass spectrometry—Plasma peptidomes from nasopharyngeal cancer patients for example. Clin Biochem 2006; 39:1144-51. [PMID: 17014837 DOI: 10.1016/j.clinbiochem.2006.08.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 08/09/2006] [Accepted: 08/15/2006] [Indexed: 10/24/2022]
Abstract
OBJECTIVES There is no plasma marker for detecting nasopharyngeal cancer (NPC). We developed a bead-based affinity fractionated proteomic method to search potential plasma markers for NPC. DESIGN AND METHODS Affinity purification of heparinized plasma with Cu-chelated beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were used to screen potential NPC markers. We compiled MS protein profiles for 47 patients with NPC and compared them to profiles from 28 healthy controls. The spectra were statistically analyzed using flexAnalysis and ClinProt bioinformatics software. Diagnostic efficacy was evaluated by determination of the assay sensitivity and specificity of each marker. RESULTS Twelve mass fingerprint markers differing between cancer and control spectra were found. The sensitivities of these NPC markers are various ranging from 36% to 83%, and the specificities were all over 90%. Combine use of these markers significantly increases diagnostic efficacy. In which, the combined markers (2020 Da and 4635 Da) possess best discriminator with high sensitivity (94%) and specificity (93%). We further identify a C3 fragment, C3f, that may serve as a biomarker for NPC. CONCLUSION The combined use of mass fingerprint markers in plasma proteome will enhance diagnostic efficacy for NPC. This method can be applied to search for novel plasma markers for cancers.
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Akashi T, Nishimura Y, Wakatabe R, Shiwa M, Yamori T. Proteomics-based identification of biomarkers for predicting sensitivity to a PI3-kinase inhibitor in cancer. Biochem Biophys Res Commun 2006; 352:514-21. [PMID: 17137555 DOI: 10.1016/j.bbrc.2006.11.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 11/13/2006] [Indexed: 12/31/2022]
Abstract
To identify biomarkers for predicting sensitivity to phosphatidylinositol 3-kinase (PI3K) inhibitors, we have developed a proteomics-based approach. Using surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF MS), we measured the expression of 393 proteins in 39 human cancer cell lines (JFCR-39), and combined it with our previously established chemosensitivity database to select for proteins whose expressions show significant correlations to drug sensitivities. This integrated approach allowed us to identify peaks from two proteins, 11.6 and 11.8 kDa, that showed significant correlations with the sensitivity to a PI3K inhibitor, LY294002. We found that the 11.8 kDa protein was a phosphorylated form of the 11.6 kDa protein. While the 11.8 kDa protein showed a positive correlation with the sensitivity to LY294002, the 11.6 kDa protein showed a negative correlation with that of the LY294002. The 11.6 kDa protein was purified chromatographically, and was identified by SELDI-TOF MS as the ribosomal P2 protein, which possesses two prospective phosphorylation sites. These results suggested that the phosphorylation status of the ribosomal P2 was responsible for determining the sensitivity to LY294002, and that the ribosomal P2 could be a potential biomarker for predicting chemosensitivity.
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Affiliation(s)
- Tetsuyuki Akashi
- Division of Molecular Pharmacology, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-10-6 Ariake, Tokyo 135-8550, Japan
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Tsai ST, Chen CW, Lora LC, Huang MC, Chen CH, Wang YS. Simultaneous Mass Analysis of Positive and Negative Ions Using a Dual-Polarity Time-of-Flight Mass Spectrometer. Anal Chem 2006; 78:7729-34. [PMID: 17105165 DOI: 10.1021/ac061213v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positive and negative ions produced from matrix-assisted laser desorption/ionization (MALDI) were simultaneously measured using a newly developed dual-polarity time-of-flight mass spectrometer. This instrument is effective not only for express and comprehensive mass analysis but also for studying the ionization mechanisms of biomolecules. It comprises two identical time-of-flight mass analyzers located symmetrically about a MALDI ion source. The ion optics are arranged to be able to extract positive and negative ions synchronously with equal efficiency to each corresponding mass analyzer. Mass spectra of various proteins with molecular weights as large as that of myoglobin monomer and dimer were obtained. The spectral patterns obtained in this work are approximately mirror images with opposite polarities.
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Affiliation(s)
- Shang-Ting Tsai
- Genomics Research Center, Academia Sinica, 128, Academia Road, Section 2, Nankang District, Taipei 115, Taiwan, ROC
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Wang M, Pan JY, Song GR, Chen HB, An LJ, Qu SX. Altered expression of estrogen receptor alpha and beta in advanced gastric adenocarcinoma: correlation with prothymosin alpha and clinicopathological parameters. Eur J Surg Oncol 2006; 33:195-201. [PMID: 17046193 DOI: 10.1016/j.ejso.2006.09.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Accepted: 09/06/2006] [Indexed: 12/18/2022] Open
Abstract
AIMS We aimed to investigate the sources of estrogen receptor alpha (ERalpha), estrogen receptor beta (ERbeta) and estimate the value of both ER subtypes in gastric adenocarcinoma and analyze the possible relationship of prothymosin alpha (ProTalpha) to ERs. METHODS ERs at the mRNA and protein levels in matched advanced gastric adenocarcinomas and surrounding non-cancerous tissues were examined by using reverse transcription-polymerase chain reaction and immunohistochemical (IHC) methods. Cell proliferation related protein ProTalpha was also detected in IHC. The immunoreactive signal, corresponding to the proteins expression level, was quantitatively analyzed. RESULTS Both ERalpha and ERbeta mRNAs were detected in most of the cancer and matched normal tissues analyzed. At the protein level, the percentage of ERalpha and ERbeta positive cases changed. ERalpha immunoreactivity was only detected in poorly differentiated adenocarcinoma and ERalpha positive expression correlated with depth of invasion of the tumors. Compared with non-cancerous tissues, gastric tumors showed decreased ERbeta expression and lost ERbeta. Altered ERbeta in gastric adenocarcinoma correlated with decreased differentiation. And the tumors involved lymph node metastasis showed significantly lower expression level of ERbeta. ProTalpha in ERbeta-positive tumors showed higher expression than that in lost ERbeta tumors. CONCLUSIONS Altered expression of ERalpha and ERbeta in tumors compared with corresponding normal gastric tissues was more common in poorly differentiated adenocarcinomas and related to malignant properties, such as lymph node metastasis. Decreased ERbeta and increased ProTalpha expression in advanced gastric adenocarcinoma indicated that ERbeta may play an anti-proliferation role which is opposed to the role of ProTalpha in gastric epithelium.
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Affiliation(s)
- M Wang
- Department of Bioscience and Biotechnology, Dalian University of Technology, Dalian 116024, China
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50
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Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 2006; 6:5615-27. [PMID: 16991199 DOI: 10.1002/pmic.200600230] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance both diagnosis and therapy of specific diseases. Proteomic methods can provide means to accomplish this grand medical vision. In this review, we will focus on the potential use of proteome analysis for clinical applications, such as disease diagnosis and assessment of response to therapy. We focus on CE coupled with MS (CE-MS) and review in detail different aspects of CE-MS coupling and the results obtained using CE-MS analysis of clinically relevant samples. We also discuss clinical applications of the technology for the diagnosis of renal diseases, urogenital cancer, and arteriosclerosis as well as monitoring the responses to therapeutic interventions.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics & Therapeutics AG, Hanover, Germany
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