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Condello S, Prasad M, Atwani R, Matei D. Tissue transglutaminase activates integrin-linked kinase and β-catenin in ovarian cancer. J Biol Chem 2022; 298:102242. [PMID: 35810788 PMCID: PMC9358478 DOI: 10.1016/j.jbc.2022.102242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 10/26/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecological cancer. OC cells have high proliferative capacity, are invasive, resist apoptosis, and tumors often display rearrangement of extracellular matrix (ECM) components, contributing to accelerated tumor progression. The multifunctional protein tissue transglutaminase (TG2) is known to be secreted in the tumor microenvironment (TME), where it interacts with fibronectin (FN) and the cell surface receptor β1 integrin. However, the mechanistic role of TG2 in cancer cell proliferation is unknown. Here, we demonstrate TG2 directly interacts with and facilitates the phosphorylation and activation of the integrin effector protein integrin-linked kinase (ILK) at Ser246. We show TG2 and p-Ser246-ILK form a complex that is detectable in patient-derived OC primary cells grown on FN-coated slides. In addition, we show co-expression of TGM2 and ILK correlates with poor clinical outcome. Mechanistically, we demonstrate TG2-mediated ILK activation causes phosphorylation of glycogen synthase kinase-3α/β (GSK-3α/β), allowing β-catenin nuclear translocation and transcriptional activity. Furthermore, inhibition of TG2 and ILK using small molecules, neutralizing antibodies, or shRNA-mediated knockdown block cell adhesion to the FN matrix, as well as the Wnt receptor response to the Wnt-3A ligand, and ultimately, cell adhesion, growth, and migration. In conclusion, we demonstrate TG2 directly interacts with and activates ILK in OC cells and tumors, and define a new mechanism which links ECM cues with β-catenin signaling in OC. These results suggest a central role of TG2/FN/integrin clusters in ECM rearrangement and indicate downstream effector ILK may represent a potential new therapeutic target in OC.
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Affiliation(s)
- Salvatore Condello
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202; Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202.
| | - Mayuri Prasad
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202; Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Rula Atwani
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202; Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; Robert H Lurie Comprehensive Cancer Center, Chicago, IL, USA; Jesse Brown VA Medical Center, Chicago, IL, USA
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2
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Pancreatic duct ligation reduces premalignant pancreatic lesions in a Kras model of pancreatic adenocarcinoma in mice. Sci Rep 2020; 10:18344. [PMID: 33110094 PMCID: PMC7591874 DOI: 10.1038/s41598-020-74947-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Pancreatic duct ligation (PDL) in the murine model has been described as an exocrine pancreatic atrophy-inducing procedure. However, its influence has scarcely been described on premalignant lesions. This study describes the histological changes of premalignant lesions and the gene expression in a well-defined model of pancreatic ductal adenocarcinoma by PDL. Selective ligation of the splenic lobe of the pancreas was performed in Ptf1a-Cre(+/ki); K-ras LSLG12Vgeo(+/ki) mice (PDL-Kras mice). Three experimental groups were evaluated: PDL group, controls and shams. The presence and number of premalignant lesions (PanIN 1–3 and Atypical Flat Lesions—AFL) in proximal (PP) and distal (DP) pancreas were studied for each group over time. Microarray analysis was performed to find differentially expressed genes (DEG) between PP and PD. Clinical human specimens after pancreaticoduodenectomy with ductal occlusion were also evaluated. PDL-Kras mice showed an intense pattern of atrophy in DP which was shrunk to a minimal portion of tissue. Mice in control and sham groups had a 7 and 10-time increase respectively of risk of high-grade PanIN 2 and 3 and AFL in their DP than PDL-Kras mice. Furthermore, PDL-Kras mice had significantly less PanIN 1 and 2 and AFL lesions in DP compared to PP. We identified 38 DEGs comparing PP and PD. Among them, several mapped to protein secretion and digestion while others such as Nupr1 have been previously associated with PanIN and PDAC. PDL in Ptf1a-Cre(+/ki); K-ras LSLG12Vgeo(+/ki) mice induces a decrease in the presence of premalignant lesions in the ligated DP. This could be a potential line of research of interest in some cancerous risk patients.
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3
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Goeppert B, Roessler S, Becker N, Zucknick M, Vogel MN, Warth A, Pathil-Warth A, Mehrabi A, Schirmacher P, Mollenhauer J, Renner M. DMBT1 expression in biliary carcinogenesis with correlation of clinicopathological data. Histopathology 2017; 70:1064-1071. [PMID: 28130841 DOI: 10.1111/his.13175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 01/18/2017] [Accepted: 01/24/2017] [Indexed: 12/31/2022]
Abstract
AIMS Deleted in malignant brain tumours 1 (DMBT1) exerts functions in the regulation of epithelial differentiation and inflammation and has been proposed as a tumour suppressor. Because chronic inflammation is a hallmark of cholangiocarcinogenesis, the aim of this study was to investigate the expression of DMBT1 in biliary tract cancer (BTC) and to correlate this expression with clinicopathological data. METHODS AND RESULTS The expression of DMBT1 protein was examined immunohistochemically in 157 BTC patients [41 intrahepatic (ICC), 60 extrahepatic cholangiocarcinomas (ECC) and 56 adenocarcinomas of the gallbladder (GBAC)]. Additionally, 56 samples of high-grade biliary intraepithelial neoplasia (BilIN 3) and 92 corresponding samples of histological non-neoplastic biliary tract tissues were included. DMBT1 expression was increased significantly in BilIN 3 compared to normal tissue (P < 0.0001) and BTC (P < 0.0001). BTC showed no significant difference in DMBT1 expression compared to non-neoplastic biliary tissue (P = 0.315). Absent DMBT1 expression in non-neoplastic biliary tissue of BTC patients was associated with poorer survival (P = 0.027). DMBT1 expression was correlated significantly with patients' age (P < 0.001). CONCLUSION DMBT1 is expressed differently in cholangiocarcinogenesis and poorer patients' survival rates are associated with absent DMBT1 expression in non-neoplastic biliary tissue, suggesting a tumour-suppressive role of DMBT1 in early cholangiocarcinogenesis.
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Affiliation(s)
| | | | - Natalia Becker
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Manuela Zucknick
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Oslo Center for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Monika N Vogel
- Diagnostic and Interventional Radiology, Thoraxklinik, University Hospital Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Anita Pathil-Warth
- Department of Internal Medicine IV, Gastroenterology and Hepatology, University Hospital Heidelberg, Germany
| | - Arianeb Mehrabi
- Department of General Visceral and Transplantation Surgery, University Hospital Heidelberg, Germany
| | | | - Jan Mollenhauer
- Molecular Oncology and Lundbeckfonden Center of Excellence NanoCAN, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Marcus Renner
- Institute of Pathology, University Hospital, Heidelberg, Germany
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4
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Pedersen MH, Hood BL, Beck HC, Conrads TP, Ditzel HJ, Leth-Larsen R. Downregulation of antigen presentation-associated pathway proteins is linked to poor outcome in triple-negative breast cancer patient tumors. Oncoimmunology 2017. [PMID: 28638726 DOI: 10.1080/2162402x.2017.1305531] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a heterogeneous subtype with varying disease outcomes. Tumor-infiltrating lymphocytes (TILs) are frequent in TNBC and have been shown to correlate with outcome, suggesting an immunogenic component in this subtype. However, other factors intrinsic to the cancer cells may also influence outcome. To identify proteins and molecular pathways associated with recurrence in TNBC, 34 formalin-fixed paraffin-embedded (FFPE) primary TNBC tumors were investigated by global proteomic profiling using mass spectrometry. Approximately, half of the patients were lymph node-negative and remained free of local or distant metastasis within 10 y follow-up, while the other half developed distant metastasis. Proteomic profiling identified >4,000 proteins, of which 63 exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. Importantly, downregulation of proteins in the major histocompatibility complex (MHC) class I antigen presentation pathways were enriched, including TAP1, TAP2, CALR, HLA-A, ERAP1 and TAPBP, and were associated with significantly shorter recurrence-free and overall survival. In addition, proteins involved in cancer cell proliferation and growth, including GBP1, RAD23B, WARS and STAT1, also exhibited altered expression in primary tumors of recurrence versus recurrence-free patients. The association between the antigen-presentation pathway and outcome were validated in a second sample set of 10 primary TNBC tumors and corresponding metastases using proteomics and in a large public gene expression database of 249 TNBC and 580 basal-like breast cancer cases. Our study demonstrates that downregulation of antigen presentation is a key mechanism for TNBC cells to avoid immune surveillance, allowing continued growth and spread.
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Affiliation(s)
- Martin H Pedersen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
| | - Brian L Hood
- Womens Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Henry Jackson Foundation for the Advancement of Military Medicine, Annandale, VA, USA
| | - Hans Christian Beck
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Thomas P Conrads
- Womens Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Henry Jackson Foundation for the Advancement of Military Medicine, Annandale, VA, USA
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.,Department of Oncology, Odense University Hospital, Odense C, Denmark
| | - Rikke Leth-Larsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense C, Denmark
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5
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Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0373. [PMID: 27644972 PMCID: PMC5031639 DOI: 10.1098/rsta.2015.0373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jana Jones
- Department of Ancient History, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Dylan Xavier
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Do Seon Lim
- Department of Dental Hygiene, College of Health Sciences, Eulji University, Sungnam, South Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University, College of Medicine, Seoul, South Korea
| | - Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Legal Medicine Section, University of Turin, 10126 Turin, Italy UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Étique and Santé (ADÉS), Faculté de Médecine de Marseille, 13344 Marseille, France
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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Müller H, Weiss C, Renner M, Felderhoff-Müser U, Mollenhauer J. DMBT1 promotes basal and meconium-induced nitric oxide production in human lung epithelial cells in vitro. Histochem Cell Biol 2016; 147:389-397. [DOI: 10.1007/s00418-016-1493-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
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Panis C, Pizzatti L, Souza GF, Abdelhay E. Clinical proteomics in cancer: Where we are. Cancer Lett 2016; 382:231-239. [PMID: 27561426 DOI: 10.1016/j.canlet.2016.08.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 12/25/2022]
Abstract
Proteomics has emerged as a promising field in the post-genomic era. Notwithstanding the great advances provided by gene expression analysis in cancer, the lack of a correlation between gene expression and protein levels has highlighted the need for a proteomic focus on cancer. Although the increasing knowledge regarding cancer biology, a reliable marker to improve diagnosis, prognosis and treatment for cancer patients is not a reality at present. In this review, we address the main considerations regarding proteomics-based studies and their clinical applications on cancer research, highlighting some considerations related to strengths and limitations of proteomics-based studies and its application to clinical practice.
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Affiliation(s)
- Carolina Panis
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil; Laboratório de Mediadores Inflamatórios, Universidade Estadual do Oeste do Paraná, UNIOESTE, Campus Francisco Beltrão, Paraná, Brazil.
| | - Luciana Pizzatti
- Laboratório de Biologia Molecular e Proteômica do Sangue - LABMOPS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Eliana Abdelhay
- Laboratório de Células Tronco, Instituto Nacional de Câncer, INCA, Rio de Janeiro, Brazil
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8
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Huang L, Xu AM, Liu W. Transglutaminase 2 in cancer. Am J Cancer Res 2015; 5:2756-2776. [PMID: 26609482 PMCID: PMC4633903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/12/2015] [Indexed: 06/05/2023] Open
Abstract
The significant influence of tumor microenvironment on malignant cells has been investigated with enthusiasm in this era of targeted therapy. Transglutaminase 2 (TG2, EC 2.3.2.13), a multi-functional enzyme that catalyzes the formation of intermolecular isopeptide bonds between glutamine and lysine side-chains, has been reported to exert important pathophysiological functions. The aim of this review was to investigate the correlation between TG2 and malignant behaviors, which could provide the rationale for novel approaches in anti-cancer therapy. We performed a systematic and electronic search on Medline, Scopus, and Web of Science for relevant publications from inception to April 2015. The bibliographic references of retrieved articles were further reviewed for additional relevant studies. TG2 exerts important physiological functions and plays vital roles in inflammation mainly through its modulation on the structure and stability of extracellular matrix (ECM). It also regulates EMT of diverse malignant cells through various intracellular and extracellular pathways. TG2 also plays an important role in tumor progression and may serve as a novel prognostic biomarker and therapeutic target in various cancer types. TG2 promotes malignant cell mobility, invasion, and metastasis, and induces chemo-resistance of cancer cells, mainly through its pro-crosslink and signaling transduction mediation propensities. In conclusion, TG2 plays vital roles in malignancy progression, and may have important prognostic and therapeutic significances.
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Affiliation(s)
- Lei Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
- Research Centre for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty of Mannheim, Heidelberg UniversityMannheim, Germany
| | - A-Man Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
| | - Wei Liu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
- Liver Transplantation Center, The Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhou, China
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9
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Eckert RL, Fisher ML, Grun D, Adhikary G, Xu W, Kerr C. Transglutaminase is a tumor cell and cancer stem cell survival factor. Mol Carcinog 2015; 54:947-58. [PMID: 26258961 DOI: 10.1002/mc.22375] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 12/15/2022]
Abstract
Recent studies indicate that cancer cells express elevated levels of type II transglutaminase (TG2), and that expression is further highly enriched in cancer stem cells derived from these cancers. Moreover, elevated TG2 expression is associated with enhanced cancer stem cell marker expression, survival signaling, proliferation, migration, invasion, integrin-mediated adhesion, epithelial-mesenchymal transition, and drug resistance. TG2 expression is also associated with formation of aggressive and metastatic tumors that are resistant to conventional therapeutic intervention. This review summarizes the role of TG2 as a cancer cell survival factor in a range of tumor types, and as a target for preventive and therapeutic intervention. The literature supports the idea that TG2, in the closed/GTP-binding/signaling conformation, drives cancer cell and cancer stem cell survival, and that TG2, in the open/crosslinking conformation, is associated with cell death.
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Affiliation(s)
- Richard L Eckert
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Dermatology, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Reproductive Biology, University of Maryland School of Medicine, Baltimore, Maryland.,The Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Matthew L Fisher
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Dan Grun
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Gautam Adhikary
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Wen Xu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Candace Kerr
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland.,The Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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10
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Lee J, Condello S, Yakubov B, Emerson R, Caperell-Grant A, Hitomi K, Xie J, Matei D. Tissue Transglutaminase Mediated Tumor-Stroma Interaction Promotes Pancreatic Cancer Progression. Clin Cancer Res 2015; 21:4482-93. [PMID: 26041746 DOI: 10.1158/1078-0432.ccr-15-0226] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/24/2015] [Indexed: 01/16/2023]
Abstract
PURPOSE Aggressive pancreatic cancer is commonly associated with a dense desmoplastic stroma, which forms a protective niche for cancer cells. The objective of the study was to determine the functions of tissue transglutaminase (TG2), a Ca(2+)-dependent enzyme that cross-links proteins through transamidation and is abundantly expressed by pancreatic cancer cells in the pancreatic stroma. EXPERIMENTAL DESIGN Orthotopic pancreatic xenografts and coculture systems tested the mechanisms by which the enzyme modulates tumor-stroma interactions. RESULTS We show that TG2 secreted by cancer cells effectively molds the stroma by cross-linking collagen, which, in turn, activates fibroblasts and stimulates their proliferation. The stiff fibrotic stromal reaction conveys mechanical cues to cancer cells, leading to activation of the YAP/TAZ transcription factors, promoting cell proliferation and tumor growth. Stable knockdown of TG2 in pancreatic cancer cells leads to decreased size of pancreatic xenografts. CONCLUSIONS Taken together, our results demonstrate that TG2 secreted in the tumor microenvironment orchestrates the cross-talk between cancer cells and stroma fundamentally affecting tumor growth. Our study supports TG2 inhibition in the pancreatic stroma as a novel strategy to block pancreatic cancer progression.
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Affiliation(s)
- Jiyoon Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Salvatore Condello
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Bakhtiyor Yakubov
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Robert Emerson
- Department of Pathology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Andrea Caperell-Grant
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kiyotaka Hitomi
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Japan
| | - Jingwu Xie
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana. Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana. Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana
| | - Daniela Matei
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana. Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana. Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, Indiana. Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana. Richard L. Roudebush VA Medical Center, Indianapolis, Indiana.
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11
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Nuciforo P, Radosevic-Robin N, Ng T, Scaltriti M. Quantification of HER family receptors in breast cancer. Breast Cancer Res 2015; 17:53. [PMID: 25887735 PMCID: PMC4389676 DOI: 10.1186/s13058-015-0561-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The clinical success of trastuzumab in breast cancer taught us that appropriate tumor evaluation is mandatory for the correct identification of patients eligible for targeted therapies. Although HER2 protein expression by immunohistochemistry (IHC) and gene amplification by fluorescence in situ hybridization (FISH) assays are routinely used to select patients to receive trastuzumab, both assays only partially predict response to the drug. In the case of epidermal growth factor receptor (EGFR), the link between the presence of the receptor or its amplification and response to anti-EGFR therapies could not be demonstrated. Even less is known for HER3 and HER4, mainly due to lack of robust and validated assays detecting these proteins. It is becoming evident that, besides FISH and IHC, we need better assays to quantify HER receptors and categorize the patients for individualized treatments. Here, we present the current available methodologies to measure HER family receptors and discuss the clinical implications of target quantification.
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Affiliation(s)
- Paolo Nuciforo
- Molecular Oncology Laboratory, Vall d'Hebron Institute of Oncology, Passeig Vall d'Hebron 119-129, Barcelona, 08035, Spain.
- Universitat Autònoma de Barcelona, Barcelona, 08035, Spain.
| | - Nina Radosevic-Robin
- ERTICa Research Group, University of Auvergne EA4677, 63000, Clermont-Ferrand, France.
- Biopathology, Jean Perrin Comprehensive Cancer Center, 58 rue Montalembert, 63011, Clermont-Ferrand, France.
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics and Division of Cancer Studies, King's College London, London, SE1 1UL, UK.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK.
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital King's College London School of Medicine, London, SE1 9RT, UK.
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY, 10065, USA.
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12
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Sahasrabuddhe NA, Barbhuiya MA, Bhunia S, Subbannayya T, Gowda H, Advani J, Shrivastav BR, Navani S, Leal P, Roa JC, Chaerkady R, Gupta S, Chatterjee A, Pandey A, Tiwari PK. Identification of prosaposin and transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics. Biochem Biophys Res Commun 2014; 446:863-9. [PMID: 24657443 DOI: 10.1016/j.bbrc.2014.03.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 03/04/2014] [Indexed: 01/11/2023]
Abstract
Gallbladder cancer is an uncommon but lethal malignancy with particularly high incidence in Chile, India, Japan and China. There is a paucity of unbiased large-scale studies investigating molecular basis of gallbladder cancer. To systematically identify differentially regulated proteins in gallbladder cancer, iTRAQ-based quantitative proteomics of gallbladder cancer was carried out using Fourier transform high resolution mass spectrometry. Of the 2575 proteins identified, proteins upregulated in gallbladder cancer included several lysosomal proteins such as prosaposin, cathepsin Z and cathepsin H. Downregulated proteins included serine protease HTRA1 and transgelin, which have been reported to be downregulated in several other cancers. Novel biomarker candidates including prosaposin and transgelin were validated to be upregulated and downregulated, respectively, in gallbladder cancer using tissue microarrays. Our study provides the first large scale proteomic characterization of gallbladder cancer which will serve as a resource for future discovery of biomarkers for gallbladder cancer.
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Affiliation(s)
| | - Mustafa A Barbhuiya
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior 474011, India; School of Studies in Zoology, Jiwaji University, Gwalior, India
| | - Shushruta Bhunia
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior 474011, India
| | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; Amrita School of Biotechnology, Amrita University, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | | | | | - Pamela Leal
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Universidad de La Frontera, CEGIN-BIOREN, Temuco, Chile
| | - Juan Carlos Roa
- Department of Pathology, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Raghothama Chaerkady
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sanjeev Gupta
- Cancer Hospital and Research Institute, Gwalior, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pramod K Tiwari
- Centre for Genomics, Molecular and Human Genetics, Jiwaji University, Gwalior 474011, India; School of Studies in Zoology, Jiwaji University, Gwalior, India.
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13
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Iuga C, Seicean A, Iancu C, Buiga R, Sappa PK, Völker U, Hammer E. Proteomic identification of potential prognostic biomarkers in resectable pancreatic ductal adenocarcinoma. Proteomics 2014; 14:945-55. [PMID: 24459066 DOI: 10.1002/pmic.201300402] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 12/17/2022]
Abstract
Pancreatic cancer is a devastating disease with a mortality rate almost identical with its incidence. In this context, the investigation of the pancreatic cancer proteome has gained considerable attention because profiles of proteins may be able to identify disease states and progression more accurately. Therefore, our objective was to investigate the changes in the proteome of patients suffering from pancreatic ductal adenocarcinoma (PDAC) by a comprehensive quantitative approach. Comparative proteomic profiling by label-free LC-MS/MS analysis of nine matched pairs of tumor and nontumor pancreas samples was used to identify differences in protein levels characteristic for PDAC. In this analysis, 488 proteins were quantified by at least two peptides of which 99 proteins displayed altered levels in PDAC (p < 0.01, fold change >1.3). Screening of data revealed a number of molecules that had already been related to PDAC such as galectin-1 (LEG1), major vault protein, adenylyl cyclase-associated protein 1 (CAP1), but also a potential new prognostic biomarker prolargin (PRELP). The Kaplan-Meier survival analysis revealed a significant correlation of protein abundance of PRELP with postoperative survival of patients with PDAC. For selected proteins the findings were verified by targeted proteomics (SRM), validated by immunohistochemistry and Western blotting and their value as candidate biomarkers is discussed.
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Affiliation(s)
- Cristina Iuga
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, University of Medicine and Pharmacy "Iuliu Haţieganu", Cluj-Napoca, Romania; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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14
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Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer. JOP : JOURNAL OF THE PANCREAS 2013; 14:405-414. [PMID: 23846938 PMCID: PMC4506757 DOI: 10.6092/1590-8577/1508] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/15/2013] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
CONTEXT Formalin-fixed paraffin-embedded (FFPE) tissue is a standard for specimen preservation, and as such FFPE tissue banks are an untapped resource of histologically-characterized specimens for retrospective biomarker investigation for pancreatic disease. OBJECTIVES We use liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to compare FFPE specimens from three different diseases of the exocrine pancreas. DESIGN We investigated the proteomic profile of FFPE pancreatic tissue from 9 archived specimens that were histologically classified as: autoimmune pancreatitis (n=3), chronic pancreatitis (n=3), and pancreatic cancer (n=3), using LC-MS/MS. SETTING This is a proteomic analysis experiment of FFPE pancreatic tissue in an academic center. PATIENTS FFPE tissue specimens were provided by Dana-Farber/Harvard Cancer Center (Boston, MA, USA). INTERVENTIONS FFPE tissue specimens were collected via routine surgical resection procedures. MAIN OUTCOME MEASURES We compared proteins identified from chronic pancreatitis, autoimmune pancreatitis, and pancreatic cancer FFPE pancreatic tissue. RESULTS We identified 386 non-redundant proteins from 9 specimens. Following our filtering criteria, 73, 29, and 53 proteins were identified exclusively in autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer specimens, respectively. CONCLUSIONS We report that differentially-expressed proteins can be identified among FFPE tissues specimens originating from individuals with different histological diagnoses. These proteins merit further confirmation with a greater number of specimens and orthogonal validation, such as immunohistochemistry. The mass spectrometry-based methodology used herein has the potential to enhance diagnostic biomarker and therapeutic target discovery, further advancing pancreatic research.
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Affiliation(s)
- Joao A Paulo
- Department of Pathology, Children’s Hospital Boston
- Proteomics Center, Children’s Hospital Boston
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Vivek Kadiyala
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Scott Brizard
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Peter A Banks
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
| | - Hanno Steen
- Department of Pathology, Children’s Hospital Boston
- Proteomics Center, Children’s Hospital Boston
| | - Darwin L Conwell
- Center for Pancreatic Disease, Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital and Department of Medicine, Harvard Medical School. Boston, MA, USA
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15
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Wang G, Lunardi A, Zhang J, Chen Z, Ala U, Webster KA, Tay Y, Gonzalez-Billalabeitia E, Egia A, Shaffer DR, Carver B, Liu XS, Taulli R, Kuo WP, Nardella C, Signoretti S, Cordon-Cardo C, Gerald WL, Pandolfi PP. Zbtb7a suppresses prostate cancer through repression of a Sox9-dependent pathway for cellular senescence bypass and tumor invasion. Nat Genet 2013; 45:739-746. [PMID: 23727861 PMCID: PMC4036521 DOI: 10.1038/ng.2654] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/02/2013] [Indexed: 12/12/2022]
Abstract
Lrf has been previously described as a powerful proto-oncogene. Here we surprisingly demonstrate that Lrf plays a critical oncosuppressive role in the prostate. Prostate specific inactivation of Lrf leads to a dramatic acceleration of Pten-loss-driven prostate tumorigenesis through a bypass of Pten-loss-induced senescence (PICS). We show that LRF physically interacts with and functionally antagonizes SOX9 transcriptional activity on key target genes such as MIA, which is involved in tumor cell invasion, and H19, a long non-coding RNA precursor for an Rb-targeting miRNA. Inactivation of Lrf in vivo leads to Rb down-regulation, PICS bypass and invasive prostate cancer. Importantly, we found that LRF is genetically lost, as well as down-regulated at both the mRNA and protein levels in a subset of human advanced prostate cancers. Thus, we identify LRF as a context-dependent cancer gene that can act as an oncogene in some contexts but also displays oncosuppressive-like activity in Pten−/− tumors.
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Affiliation(s)
- Guocan Wang
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA.,BCMB Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10021.,Cancer Biology and Genetics Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Andrea Lunardi
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jiangwen Zhang
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Zhenbang Chen
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Ugo Ala
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kaitlyn A Webster
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yvonne Tay
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Enrique Gonzalez-Billalabeitia
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Ainara Egia
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - David R Shaffer
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Brett Carver
- Human Oncology and Pathogenesis Program, Department of Surgery, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Xue-Song Liu
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Riccardo Taulli
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Winston Patrick Kuo
- Department of Developmental Biology, Harvard School Of Dental Medicine, Boston, MA 02115, USA
| | - Caterina Nardella
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA.,Cancer Biology and Genetics Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.,Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA. MA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - William L Gerald
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
| | - Pier Paolo Pandolfi
- Cancer Genetics Program, Beth Israel Deaconess Cancer Center, Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA.,BCMB Program, Weill Graduate School of Medical Sciences, Cornell University, New York, New York 10021.,Cancer Biology and Genetics Program, Sloan-Kettering Institute, 1275 York Avenue, New York, New York 10021, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
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16
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Hembrough T, Thyparambil S, Liao WL, Darfler MM, Abdo J, Bengali KM, Hewitt SM, Bender RA, Krizman DB, Burrows J. Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue. J Mol Diagn 2013; 15:454-65. [PMID: 23672976 DOI: 10.1016/j.jmoldx.2013.03.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 01/17/2013] [Accepted: 03/07/2013] [Indexed: 01/17/2023] Open
Abstract
One of the critical gaps in the clinical diagnostic space is the lack of quantitative proteomic methods for use on formalin-fixed, paraffin-embedded (FFPE) tissue. Herein, we describe the development of a quantitative, multiplexed, mass spectrometry-based selected reaction monitoring (SRM) assay for four therapeutically important targets: epidermal growth factor receptor, human EGF receptor (HER)-2, HER3, and insulin-like growth factor-1 receptor. These assays were developed using the Liquid Tissue-SRM technology platform, in which FFPE tumor tissues were microdissected, completely solubilized, and then subjected to multiplexed quantitation by SRM mass spectrometry. The assays were preclinically validated by comparing Liquid Tissue-SRM quantitation of FFPE cell lines with enzyme-linked immunosorbent assay/electrochemiluminescence quantitation of fresh cells (R(2) > 0.95). Clinical performance was assessed on two cohorts of breast cancer tissue: one cohort of 10 samples with a wide range of HER2 expression and a second cohort of 19 HER2 IHC 3+ tissues. These clinical data demonstrate the feasibility of quantitative, multiplexed clinical analysis of proteomic markers in FFPE tissue. Our findings represent a significant advancement in cancer tissue analysis because multiplexed, quantitative analysis of protein targets in FFPE tumor tissue can be tailored to specific oncological indications to provide the following: i) complementary support for anatomical pathological diagnoses, ii) patient stratification to optimize treatment outcomes and identify drug resistance, and iii) support for the clinical development of novel therapies.
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17
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Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013; 45:205-18. [PMID: 23592010 DOI: 10.1007/s00726-013-1494-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.
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18
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Vincenti DC, Murray GI. The proteomics of formalin-fixed wax-embedded tissue. Clin Biochem 2013; 46:546-51. [DOI: 10.1016/j.clinbiochem.2012.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/06/2012] [Accepted: 10/01/2012] [Indexed: 01/16/2023]
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19
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Pan S, Brentnall TA, Kelly K, Chen R. Tissue proteomics in pancreatic cancer study: discovery, emerging technologies, and challenges. Proteomics 2013; 13:710-21. [PMID: 23125171 DOI: 10.1002/pmic.201200319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/22/2022]
Abstract
Pancreatic cancer is a highly lethal disease that is difficult to diagnose and treat. The advances in proteomics technology, especially quantitative proteomics, have stimulated a great interest in applying this technology for pancreatic cancer study. A variety of tissue proteomics approaches have been applied to investigate pancreatic cancer and the associated diseases. These studies were carried out with various goals, aiming to better understand the molecular mechanisms underlying pancreatic tumorigenesis, to improve therapeutic treatment and to identify cancer associated protein signatures, signaling events as well as interactions between cancer cells and tumor microenvironment. Here, we provide an overview on the tissue proteomics studies of pancreatic cancer reported in the past few years in light of discovery and technology development.
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Affiliation(s)
- Sheng Pan
- Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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20
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Krizman DB, Burrows J. Use of formalin-fixed, paraffin-embedded tissue for proteomic biomarker discovery. Methods Mol Biol 2013; 1002:85-92. [PMID: 23625396 DOI: 10.1007/978-1-62703-360-2_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Application of mass spectrometry to proteomic analysis of tissue is a highly desirable approach to discovery of disease biomarkers due to a direct correlation of findings to tissue/disease histology and in many respects obviating the need for model systems of disease. Both frozen and formalin-fixed, paraffin-embedded (FFPE) tissue can be interrogated; however, worldwide access to vastly larger numbers of highly characterized FFPE tissue collections derived from both human and model organisms makes this form of tissue more advantageous. Here, an approach to large-scale, global proteomic analysis of FFPE tissue is described that can be employed to discover differentially expressed proteins between different histological tissue types and thus discover novel protein biomarkers of disease.
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21
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Xiao SY. Intraductal papillary mucinous neoplasm of the pancreas: an update. SCIENTIFICA 2012; 2012:893632. [PMID: 24278753 PMCID: PMC3820567 DOI: 10.6064/2012/893632] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/18/2012] [Indexed: 06/02/2023]
Abstract
Intraductal papillary mucinous neoplasm (IPMN) is a cystic tumor of the pancreas. The etiology is unknown, but increasing evidence suggests the involvement of several tumorigenesis pathways, including an association with hereditary syndromes. IPMN occurs more commonly in men, with the mean age at diagnosis between 64 and 67 years old. At the time of diagnosis, it may be benign, with or without dysplasia, or frankly malignant with an invasive carcinoma. Tumors arising from the main pancreatic duct are termed main-duct IPMNs, those involving the branch ducts, branch-duct IPMNs. In general, small branch-duct IPMNs are benign, particularly in asymptomatic patients, and can be safely followed. In contrast, main-duct tumors should be surgically resected and examined carefully for an invasive component. In the absence of invasion, patient's survival is excellent, from 94 to 100%. For patients with an IPMN-associated invasive carcinoma, the prognosis overall is better than those with a de novo pancreatic ductal adenocarcinoma, with a 5-year survival of 40% to 60% in some series. However, no survival advantage can be demonstrated if the invasive component in an IPMN patient is that of the conventional tubular type (versus mucinous carcinoma). Several histomorphologic variants are recognized, although the clinical significance of this "subtyping" is not well defined.
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Affiliation(s)
- Shu-Yuan Xiao
- Department of Pathology, University of Chicago Medical Center, 5841 South Maryland Avenue, MC6101, Chicago, IL 60637, USA
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22
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Zhu C, Pinsky P, Berg C. Improving Research on Biomarkers for Early Detection and Screening of Cancers. Cancer Biomark 2012. [DOI: 10.1201/b14318-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Srivastava M, Khurana P, Sugadev R. Lung cancer signature biomarkers: tissue specific semantic similarity based clustering of digital differential display (DDD) data. BMC Res Notes 2012; 5:617. [PMID: 23122428 PMCID: PMC3532198 DOI: 10.1186/1756-0500-5-617] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 10/23/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used 'Gene Ontology semantic similarity score' to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. RESULTS Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1-4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4). CONCLUSIONS Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated. All down regulated genes in this panel were highly up regulated in most other types of cancers. These panels of proteins may represent signature biomarkers for lung cancer and will aid in lung cancer diagnosis and disease monitoring as well as in the prediction of responses to therapeutics.
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Affiliation(s)
- Mousami Srivastava
- Bioinformatics Group, Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi-110054, India
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24
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Ali S, Banerjee S, Logna F, Bao B, Philip PA, Korc M, Sarkar FH. Inactivation of Ink4a/Arf leads to deregulated expression of miRNAs in K-Ras transgenic mouse model of pancreatic cancer. J Cell Physiol 2012; 227:3373-80. [PMID: 22213426 DOI: 10.1002/jcp.24036] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human pancreatic cancer (PC) is an aggressive disease, which has been recapitulated in transgenic animal model that provides unique opportunity for mechanistic understanding of disease progression and also for testing the efficacy of novel therapeutics. Emerging evidence suggests deregulated expression of microRNAs (miRNAs) in human PC, and thus we investigated the expression of miRNAs in pancreas tissues obtained from transgenic mouse models of K-Ras (K), Pdx1-Cre (C), K-Ras;Pdx1-Cre (KC), and K-Ras;Pdx1-Cre;INK4a/Arf (KCI), initially from pooled RNA samples using miRNA profiling, and further confirmed in individual specimens by quantitative RT-PCR. We found over-expression of miR-21, miR-221, miR-27a, miR-27b, and miR-155, and down-regulation of miR-216a, miR-216b, miR-217, and miR-146a expression in tumors derived from KC and KCI mouse model, which was consistent with data from KCI-derived RInk-1 cells. Mechanistic investigations revealed a significant induction of EGFR, K-Ras, and MT1-MMP protein expression in tissues from both KC and KCI mouse compared to tissues from K or C, and these results were consistent with similar findings in RInk-1 cells compared to human MIAPaCa-2 cells. Furthermore, miR-155 knock-down in RInk-1 cells resulted in the inhibition of cell growth and colony formation consistent with down-regulation of EGFR, MT1-MMP, and K-Ras expression. In addition, miR-216b which target Ras, and forced re-expression of miR-216b in RInk-1 cells showed inhibition of cell proliferation and colony formation, which was correlated with reduced expression of Ras, EGFR, and MT1-MMP. These findings suggest that these models would be useful for preclinical evaluation of novel miRNA-targeted agents for designing personalized therapy for PC.
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Affiliation(s)
- Shadan Ali
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
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25
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NOTCH1, HIF1A and other cancer-related proteins in lung tissue from uranium miners--variation by occupational exposure and subtype of lung cancer. PLoS One 2012; 7:e45305. [PMID: 23028920 PMCID: PMC3444449 DOI: 10.1371/journal.pone.0045305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 08/21/2012] [Indexed: 12/26/2022] Open
Abstract
Background Radon and arsenic are established pulmonary carcinogens. We investigated the association of cumulative exposure to these carcinogens with NOTCH1, HIF1A and other cancer-specific proteins in lung tissue from uranium miners. Methodology/Principal Findings Paraffin-embedded tissue of 147 miners was randomly selected from an autopsy repository by type of lung tissue, comprising adenocarcinoma (AdCa), squamous cell carcinoma (SqCC), small cell lung cancer (SCLC), and cancer-free tissue. Within each stratum, we additionally stratified by low or high level of exposure to radon or arsenic. Lifetime exposure to radon and arsenic was estimated using a quantitative job-exposure matrix developed for uranium mining. For 22 cancer-related proteins, immunohistochemical scores were calculated from the intensity and percentage of stained cells. We explored the associations of these scores with cumulative exposure to radon and arsenic with Spearman rank correlation coefficients (rs). Occupational exposure was associated with an up-regulation of NOTCH1 (radon rs = 0.18, 95% CI 0.02–0.33; arsenic: rs = 0.23, 95% CI 0.07–0.38). Moreover, we investigated whether these cancer-related proteins can classify lung cancer using supervised and unsupervised classification. MUC1 classified lung cancer from cancer-free tissue with a failure rate of 2.1%. A two-protein signature discriminated SCLC (HIF1A low), AdCa (NKX2-1 high), and SqCC (NKX2-1 low) with a failure rate of 8.4%. Conclusions/Significance These results suggest that the radiation-sensitive protein NOTCH1 can be up-regulated in lung tissue from uranium miners by level of exposure to pulmonary carcinogens. We evaluated a three-protein signature consisting of a physiological protein (MUC1), a cancer-specific protein (HIF1A), and a lineage-specific protein (NKX2-1) that could discriminate lung cancer and its major subtypes with a low failure rate.
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26
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Hembrough T, Thyparambil S, Liao WL, Darfler MM, Abdo J, Bengali KM, Taylor P, Tong J, Lara-Guerra H, Waddell TK, Moran MF, Tsao MS, Krizman DB, Burrows J. Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue. Clin Proteomics 2012; 9:5. [PMID: 22554165 PMCID: PMC3464929 DOI: 10.1186/1559-0275-9-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Analysis of key therapeutic targets such as epidermal growth factor receptor (EGFR) in clinical tissue samples is typically done by immunohistochemistry (IHC) and is only subjectively quantitative through a narrow dynamic range. The development of a standardized, highly-sensitive, linear, and quantitative assay for EGFR for use in patient tumor tissue carries high potential for identifying those patients most likely to benefit from EGFR-targeted therapies. METHODS A mass spectrometry-based Selected Reaction Monitoring (SRM) assay for the EGFR protein (EGFR-SRM) was developed utilizing the Liquid Tissue®-SRM technology platform. Tissue culture cells (n = 4) were analyzed by enzyme-linked immunosorbent assay (ELISA) to establish quantitative EGFR levels. Matching formalin fixed cultures were analyzed by the EGFR-SRM assay and benchmarked against immunoassay of the non-fixed cultured cells. Xenograft human tumor tissue (n = 10) of non-small cell lung cancer (NSCLC) origin and NSCLC patient tumor tissue samples (n = 23) were microdissected and the EGFR-SRM assay performed on Liquid Tissue lysates prepared from microdissected tissue. Quantitative curves and linear regression curves for correlation between immunoassay and SRM methodology were developed in Excel. RESULTS The assay was developed for quantitation of a single EGFR tryptic peptide for use in FFPE patient tissue with absolute specificity to uniquely distinguish EGFR from all other proteins including the receptor tyrosine kinases, IGF-1R, cMet, Her2, Her3, and Her4. The assay was analytically validated against a collection of tissue culture cell lines where SRM analysis of the formalin fixed cells accurately reflects EGFR protein levels in matching non-formalin fixed cultures as established by ELISA sandwich immunoassay (R2 = 0.9991). The SRM assay was applied to a collection of FFPE NSCLC xenograft tumors where SRM data range from 305amol/μg to 12,860amol/μg and are consistent with EGFR protein levels in these tumors as previously-reported by western blot and SRM analysis of the matched frozen tissue. In addition, the SRM assay was applied to a collection of histologically-characterized FFPE NSCLC patient tumor tissue where EGFR levels were quantitated from not detected (ND) to 670amol/μg. CONCLUSIONS This report describes and evaluates the performance of a robust and reproducible SRM assay designed for measuring EGFR directly in FFPE patient tumor tissue with accuracy at extremely low (attomolar) levels. This assay can be used as part of a complementary or companion diagnostic strategy to support novel therapies currently under development and demonstrates the potential to identify candidates for EGFR-inhibitor therapy, predict treatment outcome, and reveal mechanisms of therapeutic resistance.
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Affiliation(s)
- Todd Hembrough
- Onco Plex Diagnostics Inc, 9620 Medical Center Drive, Rockville, Maryland, 20850, USA.
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Fowler CB, Waybright TJ, Veenstra TD, O'Leary TJ, Mason JT. Pressure-assisted protein extraction: a novel method for recovering proteins from archival tissue for proteomic analysis. J Proteome Res 2012; 11:2602-8. [PMID: 22352854 PMCID: PMC3320745 DOI: 10.1021/pr201005t] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Formaldehyde-fixed, paraffin-embedded (FFPE) tissue repositories
represent a valuable resource for the retrospective study of disease
progression and response to therapy. However, the proteomic analysis
of FFPE tissues has been hampered by formaldehyde-induced protein
modifications, which reduce protein extraction efficiency and may
lead to protein misidentification. Here, we demonstrate the use of
heat augmented with high hydrostatic pressure (40,000 psi) as a novel
method for the recovery of intact proteins from FFPE mouse liver.
When FFPE mouse liver was extracted using heat and elevated pressure,
there was a 4-fold increase in protein extraction efficiency, a 3-fold
increase in the extraction of intact proteins, and up to a 30-fold
increase in the number of nonredundant proteins identified by mass
spectrometry, compared to matched tissue extracted with heat alone.
More importantly, the number of nonredundant proteins identified in
the FFPE tissue was nearly identical to that of matched fresh-frozen
tissue.
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Affiliation(s)
- Carol B Fowler
- Department of Biophysics, Armed Forces Institute of Pathology, Rockville, Maryland, United States
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Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas 2012; 41:175-85. [PMID: 22015969 PMCID: PMC3368275 DOI: 10.1097/mpa.0b013e318227a6b7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVES FFPE tissue is a standard method of specimen preservation for hospital pathology departments. Formalin-fixed paraffin-embedded tissue banks are a resource of histologically characterized specimens for retrospective biomarker investigation. We aim to establish liquid chromatography coupled with tandem mass spectrometry analysis of FFPE pancreatic tissue as a suitable strategy for the study of the pancreas proteome. METHODS We investigated the proteomic profile of FFPE pancreatic tissue specimens, using liquid chromatography coupled with tandem mass spectrometry, from 9 archived specimens that were histologically classified as normal (n = 3), chronic pancreatitis (n = 3), and pancreatic cancer (n = 3). RESULTS We identified 525 nonredundant proteins from 9 specimens. Implementing our filtering criteria, 78, 15, and 21 proteins were identified exclusively in normal, chronic pancreatitis, and pancreatic cancer specimens, respectively. Several proteins were identified exclusively in specimens with no pancreatic disease: spink 1, retinol dehydrogenase, and common pancreatic enzymes. Similarly, proteins were identified exclusively in chronic pancreatitis specimens: collagen α1 (XIV), filamin A, collagen α3 (VI), and SNC73. Proteins identified exclusively in pancreatic cancer included annexin 4A and fibronectin. CONCLUSIONS We report that differentially expressed proteins can be identified among FFPE tissue specimens originating from individuals with different pancreatic histologic findings. The mass spectrometry-based method used herein has the potential to enhance biomarker discovery and chronic pancreatitis research.
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Tanca A, Pagnozzi D, Addis MF. Setting proteins free: Progresses and achievements in proteomics of formalin-fixed, paraffin-embedded tissues. Proteomics Clin Appl 2011; 6:7-21. [DOI: 10.1002/prca.201100044] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/01/2011] [Accepted: 09/13/2011] [Indexed: 12/25/2022]
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Alkhas A, Hood BL, Oliver K, Teng PN, Oliver J, Mitchell D, Hamilton CA, Maxwell GL, Conrads TP. Standardization of a Sample Preparation and Analytical Workflow for Proteomics of Archival Endometrial Cancer Tissue. J Proteome Res 2011; 10:5264-71. [DOI: 10.1021/pr2007736] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Addie Alkhas
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Brian L. Hood
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Kate Oliver
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Pang-ning Teng
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Julie Oliver
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - David Mitchell
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - Chad A. Hamilton
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, Maryland, United States
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
| | - G. Larry Maxwell
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
- Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Fairfax, Virgina, United States
| | - Thomas P. Conrads
- Women’s Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Department of Defense, Annandale, Virgina, United States
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Martínez VG, Moestrup SK, Holmskov U, Mollenhauer J, Lozano F. The conserved scavenger receptor cysteine-rich superfamily in therapy and diagnosis. Pharmacol Rev 2011; 63:967-1000. [PMID: 21880988 DOI: 10.1124/pr.111.004523] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The scavenger receptor cysteine-rich (SRCR) superfamily of soluble or membrane-bound protein receptors is characterized by the presence of one or several repeats of an ancient and highly conserved protein module, the SRCR domain. This superfamily (SRCR-SF) has been in constant and progressive expansion, now up to more than 30 members. The study of these members is attracting growing interest, which parallels that in innate immunity. No unifying function has been described to date for the SRCR domains, this being the result of the limited knowledge still available on the physiology of most members of the SRCR-SF, but also of the sequence versatility of the SRCR domains. Indeed, involvement of SRCR-SF members in quite different functions, such as pathogen recognition, modulation of the immune response, epithelial homeostasis, stem cell biology, and tumor development, have all been described. This has brought to us new information, unveiling the possibility that targeting or supplementing SRCR-SF proteins could result in diagnostic and/or therapeutic benefit for a number of physiologic and pathologic states. Recent research has provided structural and functional insight into these proteins, facilitating the development of means to modulate the activity of SRCR-SF members. Indeed, some of these approaches are already in use, paving the way for a more comprehensive use of SRCR-SF members in the clinic. The present review will illustrate some available evidence on the potential of well known and new members of the SRCR-SF in this regard.
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Affiliation(s)
- Vanesa Gabriela Martínez
- Center Esther Koplowitz, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
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Byrum S, Avaritt NL, Mackintosh SG, Munkberg JM, Badgwell BD, Cheung WL, Tackett AJ. A quantitative proteomic analysis of FFPE melanoma. J Cutan Pathol 2011; 38:933-6. [PMID: 21883366 DOI: 10.1111/j.1600-0560.2011.01761.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Brand RE, Nolen BM, Zeh HJ, Allen PJ, Eloubeidi MA, Goldberg M, Elton E, Arnoletti JP, Christein JD, Vickers SM, Langmead CJ, Landsittel DP, Whitcomb DC, Grizzle WE, Lokshin AE. Serum biomarker panels for the detection of pancreatic cancer. Clin Cancer Res 2011; 17:805-16. [PMID: 21325298 DOI: 10.1158/1078-0432.ccr-10-0248] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE Serum-biomarker based screening for pancreatic cancer could greatly improve survival in appropriately targeted high-risk populations. EXPERIMENTAL DESIGN Eighty-three circulating proteins were analyzed in sera of patients diagnosed with pancreatic ductal adenocarcinoma (PDAC, n = 333), benign pancreatic conditions (n = 144), and healthy control individuals (n = 227). Samples from each group were split randomly into training and blinded validation sets prior to analysis. A Metropolis algorithm with Monte Carlo simulation (MMC) was used to identify discriminatory biomarker panels in the training set. Identified panels were evaluated in the validation set and in patients diagnosed with colon (n = 33), lung (n = 62), and breast (n = 108) cancers. RESULTS Several robust profiles of protein alterations were present in sera of PDAC patients compared to the Healthy and Benign groups. In the training set (n = 160 PDAC, 74 Benign, 107 Healthy), the panel of CA 19-9, ICAM-1, and OPG discriminated PDAC patients from Healthy controls with a sensitivity/specificity (SN/SP) of 88/90%, while the panel of CA 19-9, CEA, and TIMP-1 discriminated PDAC patients from Benign subjects with an SN/SP of 76/90%. In an independent validation set (n = 173 PDAC, 70 Benign, 120 Healthy), the panel of CA 19-9, ICAM-1 and OPG demonstrated an SN/SP of 78/94% while the panel of CA19-9, CEA, and TIMP-1 demonstrated an SN/SP of 71/89%. The CA19-9, ICAM-1, OPG panel is selective for PDAC and does not recognize breast (SP = 100%), lung (SP = 97%), or colon (SP = 97%) cancer. CONCLUSIONS The PDAC-specific biomarker panels identified in this investigation warrant additional clinical validation to determine their role in screening targeted high-risk populations.
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Affiliation(s)
- Randall E Brand
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Mehta K, Han A. Tissue Transglutaminase (TG2)-Induced Inflammation in Initiation, Progression, and Pathogenesis of Pancreatic Cancer. Cancers (Basel) 2011; 3:897-912. [PMID: 24212645 PMCID: PMC3756395 DOI: 10.3390/cancers3010897] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 02/01/2011] [Accepted: 02/14/2011] [Indexed: 12/26/2022] Open
Abstract
Pancreatic cancer (PC) is among the deadliest cancers, with a median survival of six months. It is generally believed that infiltrating PC arises through the progression of early grade pancreatic intraepithelial lesions (PanINs). In one model of the disease, the K-ras mutation is an early molecular event during progression of pancreatic cancer; it is followed by the accumulation of additional genetic abnormalities. This model has been supported by animal studies in which activated K-ras and p53 mutations produced metastatic pancreatic ductal adenocarcinoma in mice. According to this model, oncogenic K-ras induces PanIN formation but fails to promote the invasive stage. However, when these mice are subjected to caerulein treatment, which induces a chronic pancreatitis-like state and inflammatory response, PanINs rapidly progress to invasive carcinoma. These results are consistent with epidemiologic studies showing that patients with chronic pancreatitis have a much higher risk of developing PC. In line with these observations, recent studies have revealed elevated expression of the pro-inflammatory protein tissue transglutaminase (TG2) in early PanINs, and its expression increases even more as the disease progresses. In this review we discuss the implications of increased TG2 expression in initiation, progression, and pathogenesis of pancreatic cancer.
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Affiliation(s)
- Kapil Mehta
- Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; E-Mail:
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Amy Han
- Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; E-Mail:
- Graduate School of Biomedical Sciences, The University of Texas Health Science Center, Houston, TX 77030, USA
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Ralton LD, Murray GI. The use of formalin fixed wax embedded tissue for proteomic analysis: Table 1. J Clin Pathol 2011; 64:297-302. [DOI: 10.1136/jcp.2010.086835] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The potential of proteomic approaches to elucidate disease pathogenesis and biomarker discovery is increasingly being recognised. These studies are usually based on the use of fresh tissue samples. Problems in obtaining and storing fresh frozen samples, especially either for the investigation of rare diseases or for the study of microscopic disease foci, have led to the investigation of the possible use of formalin fixed wax embedded tissue for proteomic biomarker detection Overcoming problems with protein cross-linking associated with formalin fixation of tissues, especially by using heat-mediated retrieval techniques combined with highly sensitive methods for protein separation and identification are now emerging, giving promise to the use of formalin fixed wax embedded tissues for proteomic analysis. Formalin fixed wax embedded tissues, together with their associated clinical and pathological information outcome may provide significant potential opportunities for proteomics research. Such studies of formalin fixed wax embedded tissue will allow access to already acquired clinical tissue samples which can be readily correlated with clinical, pathological and outcome data. It also provides access to rare types of tissue/diseases that would be either difficult to collect prospectively in a timely manner or are unlikely to be available as fresh samples. The purpose of this review is to provide an overview of the issues associated with the use of formalin fixed wax embedded tissues for proteomics.
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Cecconi D, Palmieri M, Donadelli M. Proteomics in pancreatic cancer research. Proteomics 2011; 11:816-28. [PMID: 21229586 DOI: 10.1002/pmic.201000401] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/12/2010] [Accepted: 08/25/2010] [Indexed: 12/13/2022]
Abstract
In this review, we give an overview of the actual role of proteomic technologies in the study of pancreatic cancers (PCs). We describe PC proteomics on the basis of sample origins, i.e. tissues, body fluids, and PC cell lines. As regards PC tissues, we report the identification of a number of candidate biomarkers of precursor lesions that may allow early diagnosis of this neoplasia. Moreover, we describe cytoskeletal and hypoxia-regulated proteins that confirm the involvement of cytoskeleton modifications and metabolism adaptations in carcinogenesis. We also discuss the most important biomarkers identified by proteomic analysis involved in local invasion and distant metastasis, and in the cross-talk between pancreatic tumor and the surrounding stroma. Furthermore, we report novel candidate biomarkers identified in serum, plasma, and pancreatic juice of cancer patients compared with cancer-free controls. Proteomic alterations in PC cell line models as compared to normal controls and studies on cell lines treated with drugs or new agents to understand their mechanism of pharmacological action or the onset of drug resistance are also presented. Finally, we discuss the recent improvements obtained in classical 2-DE and high-throughput proteomic strategies able to allow the overcoming of relevant proteomic drawbacks.
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Affiliation(s)
- Daniela Cecconi
- Department of Biotechnology, University of Verona, Verona, Italy.
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Kwon RS, Simeone DM. The use of protein-based biomarkers for the diagnosis of cystic tumors of the pancreas. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:413646. [PMID: 22110950 PMCID: PMC3202124 DOI: 10.1155/2011/413646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 08/15/2011] [Indexed: 12/18/2022]
Abstract
Proteomics is a powerful method used to identify, characterize, and quantify proteins within biologic samples. Pancreatic cystic neoplasms are a common clinical entity and represent a diagnostic and management challenge due to difficulties in accurately diagnosing cystic lesions with malignant potential and assessing the risk of malignant degeneration. Currently, cytology and other biomarkers in cyst fluid have had limited success in accurately distinguishing both the type of cystic neoplasm and the presence of malignancy. Emerging data suggests that the use of protein-based biomarkers may have greater utility in helping clinicians correctly diagnose the type of cyst and to identify which cystic neoplasms are malignant. Several candidate proteins have been identified within pancreatic cystic neoplasms as potential biomarkers. Future studies will be needed to validate these findings and move these biomarkers into the clinical setting.
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Affiliation(s)
- Richard S. Kwon
- 1Department of Internal Medicine, University of Michigan, 1500 E. Medical Center Drive, Taubman 3912, Ann Arbor, MI 48109-5362, USA
| | - Diane M. Simeone
- 2Departments of Surgery and Molecular and Integrative Physiology, University of Michigan, 1500 E. Medical Center Drive, Taubman 2210B, Ann Arbor, MI 48109-5343, USA
- *Diane M. Simeone:
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Markaryan A, Nelson EG, Helseth LD, Hinojosa R. Proteomic analysis of formalin-fixed celloidin-embedded whole cochlear and laser microdissected spiral ganglion tissues. Acta Otolaryngol 2010; 130:984-9. [PMID: 20148753 DOI: 10.3109/00016481003591749] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CONCLUSION The results of this study demonstrate that proteomic analysis can be successfully performed on formalin-fixed celloidin-embedded (FFCE) archival human cochlear tissues. OBJECTIVE To investigate the feasibility of analyzing protein expression in archival cochlear tissues. MATERIAL AND METHODS A new methodology, referred to as Liquid Tissue(TM), was used to extract proteins from human cochlear tissue sections and spiral ganglion tissue isolated by laser microdissection (LMD). Protein identification was performed by bioinformatic analysis of high resolution tandem mass spectrometric data from fractionated tryptic peptide samples. RESULTS Twenty-six proteins were identified with a minimum of 2 unique peptides and 450 proteins were identified with 1 unique peptide at a confidence level of 95% in cochlear tissue. Ten proteins were identified with a minimum of 2 unique peptides and 485 proteins were identified with 1 unique peptide at a confidence level of 95% in spiral ganglion tissue.
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Affiliation(s)
- Adam Markaryan
- Section of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Chicago, IL 60637,, USA
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McKinney KQ, Lee YY, Choi HS, Groseclose G, Iannitti DA, Martinie JB, Russo MW, Lundgren DH, Han DK, Bonkovsky HL, Hwang SI. Discovery of putative pancreatic cancer biomarkers using subcellular proteomics. J Proteomics 2010; 74:79-88. [PMID: 20807598 DOI: 10.1016/j.jprot.2010.08.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/16/2010] [Accepted: 08/24/2010] [Indexed: 01/07/2023]
Abstract
Pancreatic cancer (PC) is a highly aggressive disease that frequently remains undetected until it has progressed to an advanced, systemic stage. Successful treatment of PC is hindered by the lack of early detection. The application of proteomic analysis to PC combined with subcellular fractionation has introduced new possibilities in the field of biomarker discovery. We utilized matched pairs of pancreas tumor and non-tumor pancreas from patients undergoing tumor resection. The tissues were treated to obtain cellular protein fractions corresponding to cytosol, membrane, nucleus and cytoskeleton. The fractions were then separated by molecular weight and digested with trypsin, followed by liquid chromatography and tandem mass spectrometry. The spectra obtained were searched using Sequest engine and combined into a single analysis file to obtain a semi-quantitative number, spectral count, using Scaffold software. We identified 2393 unique proteins in non-tumor and cancer pancreas. Utilizing PLGEM statistical analysis we determined 104 proteins were significantly changed in cancer. From these, we further validated four secreted proteins that are up-regulated in cancer and have potential for development as minimally-invasive diagnostic markers. We conclude that subcellular fractionation followed by gel electrophoresis and tandem mass spectrometry is a powerful strategy for identification of differentially expressed proteins in pancreatic cancer.
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Affiliation(s)
- Kimberly Q McKinney
- Proteomics Laboratory for Clinical and Translational Research, Carolinas HealthCare System, Charlotte, NC, USA
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You J, Fitzgerald A, Cozzi PJ, Zhao Z, Graham P, Russell PJ, Walsh BJ, Willcox M, Zhong L, Wasinger V, Li Y. Post-translation modification of proteins in tears. Electrophoresis 2010; 31:1853-61. [DOI: 10.1002/elps.200900755] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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41
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Pavlou MP, Diamandis EP. The cancer cell secretome: a good source for discovering biomarkers? J Proteomics 2010; 73:1896-906. [PMID: 20394844 DOI: 10.1016/j.jprot.2010.04.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/22/2010] [Accepted: 04/06/2010] [Indexed: 01/06/2023]
Abstract
Cancer is a leading cause of death. Early detection is usually associated with better clinical outcomes. Recent advances in genomics and proteomics raised hopes that new biomarkers for diagnosis, prognosis or monitoring therapeutic response will soon be discovered. Proteins secreted by cancer cells, referred also as "the cancer cell secretome", is a promising source for biomarker discovery. In this review we will summarize recent advances in cancer cell secretome analysis, focusing on the five most fatal cancers (lung, breast, prostate, colorectal, and pancreatic). For each cancer type we will describe the proteomic approaches utilized for the identification of novel biomarkers. Despite progress, identification of markers that are superior to those currently used has proven to be a difficult task and very few, if any, newly discovered biomarker has entered the clinic the last 10 years.
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Affiliation(s)
- Maria P Pavlou
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
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42
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Hood BL, Stewart NA, Conrads TP. Development of High-Throughput Mass Spectrometry–Based Approaches for Cancer Biomarker Discovery and Implementation. Clin Lab Med 2009; 29:115-38. [DOI: 10.1016/j.cll.2009.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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