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Sandström A, Andersson R, Segersvärd R, Löhr M, Borrebaeck CAK, Wingren C. Serum proteome profiling of pancreatitis using recombinant antibody microarrays reveals disease-associated biomarker signatures. Proteomics Clin Appl 2013; 6:486-96. [PMID: 22930578 DOI: 10.1002/prca.201200051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE Pancreatitis is an inflammatory state of the pancreas, for which high-performing serological biomarkers are lacking. The aim of the present study was to evaluate the use of affinity proteomics for identifying potential markers of disease and stratifying pancreatitis subtypes. EXPERIMENTAL DESIGN High-content, recombinant antibody microarrays were applied for serum protein expression profiling of 113 serum samples from patients with chronic, acute, and autoimmune pancreatitis, as well as healthy controls. The sample groups were compared using supervised classification based on support vector machine analysis. RESULTS This discovery study showed that pancreatitis subtypes could be discriminated with high accuracy. Using unfiltered data, the individual subtypes, as well as the combined pancreatitis cohort, were distinguished from healthy controls with high AUC values (0.96-1.00). Moreover, characteristic protein patterns and AUC values in the range of 0.69-0.95 were observed for the individual pancreatitis entities when compared to each other, and to all other samples combined. CONCLUSIONS AND CLINICAL RELEVANCE This study demonstrated the potential of the antibody microarray approach for stratification of pancreatitis. Distinct candidate multiplex serum biomarker signatures for chronic, acute, and autoimmune pancreatitis were defined, which could enhance our fundamental knowledge of the underlying molecular mechanisms, and potentially lead to improved diagnosis.
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Affiliation(s)
- Anna Sandström
- Department of Immunotechnology, Lund University, Lund, Sweden; CREATE Health, Lund University, Lund, Sweden
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Singh AK, Pandey R, Gill K, Singh R, Saraya A, Chauhan SS, Yadav S, Pal S, Singh N, Dey S. p38β MAP kinase as a therapeutic target for pancreatic cancer. Chem Biol Drug Des 2012; 80:266-73. [PMID: 22515544 DOI: 10.1111/j.1747-0285.2012.01395.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pancreatic cancer is very difficult to diagnose in its early stage. Molecular marker and imaging have not proven to be accurate modalities for screening of pancreatic cancer. This study aims to develop p38β as a protein marker for pancreatic cancer and to design peptide inhibitor against the same. The serum p38β level of pancreatic cancer (n = 35; 5.06 μg/mL) was twofold higher compared to that of the chronic pancreatitis (n = 10; 2.92 μg/mL) and matched normal control (n = 10; 2.86 μg/ml) (p < 0.0005). Peptide inhibitors were designed to inhibit the activity of p38β and the kinetic assay had shown the dissociation constant, (K(D)) to be 3.16 × 10(-8) M and IC(50), 25 nM by Surface Plasmon Resonance (SPR) and Enzyme-Linked Immunosorbent Assay (ELISA), respectively. The peptide inhibitor also significantly reduced viability and induced cytotoxicity in Human Pancreatic carcinoma epithelial-like cell line (PANC-1) cells.
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Affiliation(s)
- Abhay Kumar Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Pan S, Chen R, Stevens T, Bronner MP, May D, Tamura Y, McIntosh MW, Brentnall TA. Proteomics portrait of archival lesions of chronic pancreatitis. PLoS One 2011; 6:e27574. [PMID: 22132114 PMCID: PMC3223181 DOI: 10.1371/journal.pone.0027574] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/19/2011] [Indexed: 12/11/2022] Open
Abstract
Chronic pancreatitis is a chronic inflammatory disorder of the pancreas. The etiology is multi-fold, but all lead to progressive scarring and loss of pancreatic function. Early diagnosis is difficult; and the understanding of the molecular events that underlie this progressive disease is limited. In this study, we investigated differential proteins associated with mild and severe chronic pancreatitis in comparison with normal pancreas and pancreatic cancer. Paraffin-embedded formalin-fixed tissues from five well-characterized specimens each of normal pancreas (NL), mild chronic pancreatitis (MCP), severe chronic pancreatitis (SCP) and pancreatic ductal adenocarcinoma (PDAC) were subjected to proteomic analysis using a “label-free” comparative approach. Our results show that the numbers of differential proteins increase substantially with the disease severity, from mild to severe chronic pancreatitis, while the number of dysregulated proteins is highest in pancreatic adenocarcinoma. Important functional groups and biological processes associated with chronic pancreatitis and cancer include acinar cell secretory proteins, pancreatic fibrosis/stellate cell activation, glycoproteins, and inflammatory proteins. Three differential proteins were selected for verification by immunohistochemistry, including collagen 14A1, lumican and versican. Further canonical pathway analysis revealed that acute phase response signal, prothrombin activation pathway, and pancreatic fibrosis/pancreatic stellate cell activation pathway were the most significant pathways involved in chronic pancreatitis, while pathways relating to metabolism were the most significant pathways in pancreatic adenocarcinoma. Our study reveals a group of differentially expressed proteins and the related pathways that may shed light on the pathogenesis of chronic pancreatitis and the common molecular events associated with chronic pancreatitis and pancreatic adenocarcinoma.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SP); (TB)
| | - Ru Chen
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Tyler Stevens
- Digestive Disease Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Mary P. Bronner
- Department of Anatomic Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Damon May
- Fred Hutchinson Cancer Research Center, Molecular Diagnostics Program, Seattle, Washington, United States of America
| | - Yasuko Tamura
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Martin W. McIntosh
- Fred Hutchinson Cancer Research Center, Molecular Diagnostics Program, Seattle, Washington, United States of America
| | - Teresa A. Brentnall
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SP); (TB)
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Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis 2010; 31:2377-87. [PMID: 20589857 DOI: 10.1002/elps.200900762] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The standardization of methods for human body fluid protein isolation is a critical initial step for proteomic analyses aimed to discover clinically relevant biomarkers. Several caveats have hindered pancreatic fluid proteomics, including the heterogeneity of samples and protein degradation. We aim to optimize sample handling of pancreatic fluid that has been collected using a safe and effective endoscopic collection method (endoscopic pancreatic function test). Using SDS-PAGE protein profiling, we investigate (i) precipitation techniques to maximize protein extraction, (ii) auto-digestion of pancreatic fluid following prolonged exposure to a range of temperatures, (iii) effects of multiple freeze-thaw cycles on protein stability, and (iv) the utility of protease inhibitors. Our experiments revealed that TCA precipitation resulted in the most efficient extraction of protein from pancreatic fluid of the eight methods we investigated. In addition, our data reveal that although auto-digestion of proteins is prevalent at 23 and 37 degrees C, incubation on ice significantly slows such degradation. Similarly, when the sample is maintained on ice, proteolysis is minimal during multiple freeze-thaw cycles. We have also determined the addition of protease inhibitors to be assay-dependent. Our optimized sample preparation strategy can be applied to future proteomic analyses of pancreatic fluid.
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Affiliation(s)
- Joao A Paulo
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, Boston, MA 02115, USA
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Cheung W, Darfler MM, Alvarez H, Hood BL, Conrads TP, Habbe N, Krizman DB, Mollenhauer J, Feldmann G, Maitra A. Application of a global proteomic approach to archival precursor lesions: deleted in malignant brain tumors 1 and tissue transglutaminase 2 are upregulated in pancreatic cancer precursors. Pancreatology 2008; 8:608-16. [PMID: 18849643 PMCID: PMC2711211 DOI: 10.1159/000161012] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 07/01/2008] [Indexed: 12/11/2022]
Abstract
BACKGROUND Pancreatic cancer is an almost uniformly fatal disease, and early detection is a critical determinant of improved survival. A variety of noninvasive precursor lesions of pancreatic adenocarcinoma have been identified, which provide a unique opportunity for intervention prior to onset of invasive cancer. Biomarker discovery in precursor lesions has been hampered by the ready availability of fresh specimens, and limited yields of proteins suitable for large scale screening. METHODS We utilized Liquid Tissue, a novel technique for protein extraction from archival formalin-fixed material, and mass spectrometry to conduct a global proteomic analysis of an intraductal papillary mucinous neoplasm (IPMN). Tissue microarrays comprised of 38 IPMNs were used for validation of candidate proteins. RESULTS The proteomic analysis of the IPMN Liquid Tissue lysate resulted in identification of 1,534 peptides corresponding to 523 unique proteins. A subset of 25 proteins was identified that had previously been reported as upregulated in pancreatic cancer. Immunohistochemical analysis for two of these, deleted in malignant brain tumors 1 (DMBT1) and tissue transglutaminase 2 (TGM2), confirmed their overexpression in IPMNs. CONCLUSION Global proteomics analysis using the Liquid Tissue workflow is a feasible approach for unbiased biomarker discovery in limited archival material, particularly applicable to precursor lesions of cancer.
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Affiliation(s)
- Wang Cheung
- Departments of Pathology, Baltimore, Md., USA
| | | | | | - Brian L. Hood
- Department of Pharmacology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pa., USA
| | - Thomas P. Conrads
- Department of Pharmacology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pa., USA
| | - Nils Habbe
- Departments of Pathology, Baltimore, Md., USA
| | | | - Jan Mollenhauer
- Department of Molecular Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany,Department of Molecular Oncology, Institute of Medical Biology, University of Southern Denmark, Odense, Denmark
| | - Georg Feldmann
- Departments of Pathology, Baltimore, Md., USA,*Georg Feldmann, MD, The Sol Goldman Pancreatic Cancer Research Center, Room 316, CRB II, Johns Hopkins University School of Medicine, 1550 Orleans Street, Baltimore, MD 21231 (USA), Tel. +1 410 955 3511, Fax +1 410 614 0671, E-Mail
| | - Anirban Maitra
- Departments of Pathology, Baltimore, Md., USA,Oncology, Johns Hopkins University School of Medicine, Baltimore, Md., USA,Genetic Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Md., USA
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Kim SW, Hwang HJ, Baek YM, Lee SH, Hwang HS, Yun JW. Proteomic and transcriptomic analysis for streptozotocin-induced diabetic rat pancreas in response to fungal polysaccharide treatments. Proteomics 2008; 8:2344-61. [DOI: 10.1002/pmic.200700779] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Löhr JM, Faissner R, Findeisen P, Neumaier M. [Proteome analysis--basis for individualized pancreatic carcinoma therapy?]. Internist (Berl) 2007; 47 Suppl 1:S40-8. [PMID: 16773365 DOI: 10.1007/s00108-006-1634-7] [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] [Indexed: 02/01/2023]
Abstract
Ductal pancreatic adenocarcinoma is a dismal disease, having the worst prognosis of all solid tumors. While genomics and transcriptomics have provided a wealth of data, no contribution has been made to clinical medicine in terms of diagnostic or prognostic markers. Hope lies in yet another novel technology, proteomics. Conceptually, proteomics bears the advantage of incorporating both posttranslational modifications as well as host factors. This is thought to be important in factors influencing survival such as chemoresistance. This tutorial review discusses the state of the art in pancreatic cancer proteomics in light of technical developments. At this moment, proteomics is still at the beginning in clinical application. First results, however, suggest some hope for the development of a new understanding of the molecular biology in pancreatic cancer yielding into very specific markers of disease or allowing a rational and individualized therapy.
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Affiliation(s)
- J M Löhr
- Klinische Kooperationseinheit für Molekulare Gastroenterologie (dkfz E180), II. Medizinische Klinik, Medizinische Fakultät Mannheim der Universität Heidelberg.
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Löhr JM. Pancreatic cancer — Outlook: gene therapy. THE CHINESE-GERMAN JOURNAL OF CLINICAL ONCOLOGY 2007; 6:181-186. [DOI: 10.1007/s10330-007-0049-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
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Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, Goodlett DR, Aebersold R, Brentnall TA. Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas 2007; 34:70-9. [PMID: 17198186 PMCID: PMC2423229 DOI: 10.1097/01.mpa.0000240615.20474.fd] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVES Pancreatitis is an inflammatory condition of the pancreas. However, it often shares many molecular features with pancreatic cancer. Biomarkers present in pancreatic cancer frequently occur in the setting of pancreatitis. The efforts to develop diagnostic biomarkers for pancreatic cancer have thus been complicated by the false-positive involvement of pancreatitis. METHODS In an attempt to develop protein biomarkers for pancreatic cancer, we previously use quantitative proteomics to identify and quantify the proteins from pancreatic cancer juice. Pancreatic juice is a rich source of proteins that are shed by the pancreatic ductal cells. In this study, we used a similar approach to identify and quantify proteins from pancreatitis juice. RESULTS In total, 72 proteins were identified and quantified in the comparison of pancreatic juice from pancreatitis patients versus pooled normal control juice. Nineteen of the juice proteins were overexpressed, and 8 were underexpressed in pancreatitis juice by at least 2-fold compared with normal pancreatic juice. Of these 27 differentially expressed proteins in pancreatitis, 9 proteins were also differentially expressed in the pancreatic juice from pancreatic cancer patient. CONCLUSIONS Identification of these differentially expressed proteins from pancreatitis juice provides useful information for future study of specific pancreatitis-associated proteins and to eliminate potential false-positive biomarkers for pancreatic cancer.
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Affiliation(s)
- Ru Chen
- Division of Gastroenterology/Department of Medicine, University of Washington, Seattle, WA
| | - Sheng Pan
- Institute for Systems Biology, Seattle, WA
| | | | - Kara White Moyes
- Division of Gastroenterology/Department of Medicine, University of Washington, Seattle, WA
| | - Mary P. Bronner
- Department of Anatomic Pathology, Cleveland Clinic Foundation, Cleveland, OH
| | - David R. Goodlett
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Ruedi Aebersold
- Institute for Molecular Systems Biology, ETH Zurich and Faculty of Sciences, University of Zurich, Switzerland
| | - Teresa A. Brentnall
- Division of Gastroenterology/Department of Medicine, University of Washington, Seattle, WA
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Chen R, Pan S, Aebersold R, Brentnall TA. Proteomics studies of pancreatic cancer. Proteomics Clin Appl 2007; 1:1582-1591. [PMID: 18633454 PMCID: PMC2467510 DOI: 10.1002/prca.200700414] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2007] [Indexed: 01/12/2023]
Abstract
Pancreatic cancer is the fourth leading cause of cancer death in the United States, with 4% survival 5 years after diagnosis. Biomarkers are desperately needed to improve earlier, more curable cancer diagnosis and to develop new effective therapeutic targets. The development of quantitative proteomics technologies in recent years offers great promise for understanding the complex molecular events of tumorigenesis at the protein level, and has stimulated great interest in applying the technology for pancreatic cancer studies. Proteomic studies of pancreatic tissues, juice, serum/plasma, and cell lines have recently attempted to identify differentially expressed proteins in pancreatic cancer to dissect the abnormal signaling pathways underlying oncogenesis, and to detect new biomarkers. It can be expected that the continuing evolution of proteomics technology with better resolution and sensitivity will greatly enhance our capability in combating pancreatic cancer.
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Affiliation(s)
- Ru Chen
- GI Division / Department of Medicine, University of Washington, Seattle, WA 98195
| | - Sheng Pan
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Ruedi Aebersold
- Institute for Systems Biology, Seattle, WA 98103
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - Teresa A. Brentnall
- GI Division / Department of Medicine, University of Washington, Seattle, WA 98195
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Abstract
Early-stage chronic pancreatitis may be undetected as a clinical entity. However, it may carry a definite risk for subsequent secondary damage, depending on the etiology of the disease. Therefore, the most important question is whether indeed the patient in question does have early-stage chronic pancreatitis rather than oligosymptomatic advanced-stage chronic pancreatitis. This can be easily determined by appropriate imaging such as abdominal computed tomography. For early changes, endoscopic ultrasound is superior to any other technique. Endosonography may also tell about anatomical obstacles (e.g., papillary stenosis, pancreas divisum) that may be treated to prevent progression of the disease. Treatment options at this stage are endoscopic for the most part. Depending on the etiology and familiar/hereditary background of the given patient, one must look further into molecular markers. Such markers may give an estimate on the progression or dynamics of the disease in the future and include mutations in the cationic (PRSS1) and anionic (PRSS2) trypsinogen genes as well as mutations in the serine protease (SPINK1) or cystic fibrosis (CFTR) genes. Admitted ly, these are not markers of early-stage chronic pancreatitis but must be investigated if and when such pathogenesis is suspected. Further, rare forms of chronic pancreatitis, such as autoimmune pancreatitis, which can be cured by appropriate medical treatment with steroids, must be excluded. Markers for autoimmune pancreatitis are elevated serum IgG, especially IgG4, and autoantibodies to carbonic anhydrase (type II) and lactoferrin. It is noteworthy that these markers, present in almost every Asian patient with autoimmune pancreatitis, are mostly lacking in Caucasian populations of patients with autoimmune pancreatitis.
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Affiliation(s)
- J-Matthias Löhr
- Molecular Gastroenterology Unit (dkfz E180), Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Theodor Kutzer Ufer 1-3, D-68167, Mannheim, Germany
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Plebani M. Proteomics: the next revolution in laboratory medicine? Clin Chim Acta 2005; 357:113-22. [PMID: 15941565 DOI: 10.1016/j.cccn.2005.03.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 03/09/2005] [Indexed: 01/22/2023]
Abstract
BACKGROUND The identification of specific genetic alterations and protein profiles associated with disease offers a unique opportunity to develop proteomics-based assays for early diagnosis. By identifying proteins in serum/plasma, a minimally invasive tool is used to assess the presence of disease and to monitor response to treatment and/or disease progression. The potential clinical applications of this tool are broad-based, including the diagnosis not only of cancer but also cardiovascular and neuromuscular diseases, organ transplantation associated conditions, and infertility. METHODS A number of competing chromatographic techniques have been proposed for overcoming the complexity and labor-intensive manipulations associated with the traditional technique for proteomic analysis, which is based on two-dimensional gel electrophoretic techniques. However, mass spectrometry has now assumed a central role in most proteomic workflows, and several combinations of ionization sources, analyzers and fragmentations devices have been described and developed. RESULTS Thanks to proteomic applications in the diagnosis of cancer, several research groups have identified proteomic patterns associated with ovarian, prostatic, colorectal and other cancers. While the sensitivity and specificity of these patterns are highly satisfactory, there are still some open questions concerning the standardization, reproducibility, and inter-laboratory agreement of these data. CONCLUSIONS Proteomics, and, in particular, serum mass spectroscopic proteomic pattern diagnostics, is a rapid expanding field of research. The plasma proteoma has an important position at the intersection between genes and diseases, and clinical laboratories must adapt to a new era of tests based on proteomics and genomics. In the future, mass spectrometry will become an essential tool in the clinical laboratory.
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Affiliation(s)
- Mario Plebani
- Department of Laboratory Medicine, University-Hospital of Padova, Via Giustiniani, 2, 35128 Padova, Italy.
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Chen R, Pan S, Brentnall TA, Aebersold R. Proteomic profiling of pancreatic cancer for biomarker discovery. Mol Cell Proteomics 2005; 4:523-33. [PMID: 15684406 DOI: 10.1074/mcp.r500004-mcp200] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pancreatic cancer is a uniformly lethal disease that is difficult to diagnose at early stage and even more difficult to cure. In recent years, there has been a substantial interest in applying proteomics technologies to identify protein biomarkers for early detection of cancer. Quantitative proteomic profiling of body fluids, tissues, or other biological samples to identify differentially expressed proteins represents a very promising approach for improving the outcome of this disease. Proteins associated with pancreatic cancer identified through proteomic profiling technologies could be useful as biomarkers for the early diagnosis, therapeutic targets, and disease response markers. In this article, we discuss recent progress and challenges for applying quantitative proteomics technologies for biomarker discovery in pancreatic cancer.
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Affiliation(s)
- Ru Chen
- GI Division/Department of Medicine, University of Washington, Seattle, WA 98195, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447475 DOI: 10.1002/cfg.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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