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Wang N, Zhang L, Ying Q, Song Z, Lu A, Treumann A, Liu Z, Sun T, Ding Z. A reverse phase protein array based phospho-antibody characterization approach and its applicability for clinical derived tissue specimens. Sci Rep 2022; 12:22373. [PMID: 36572710 PMCID: PMC9792559 DOI: 10.1038/s41598-022-26715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022] Open
Abstract
Systematic quantification of phosphoprotein within cell signaling networks in solid tissues remains challenging and precise quantification in large scale samples has great potential for biomarker identification and validation. We developed a reverse phase protein array (RPPA) based phosphor-antibody characterization approach by taking advantage of the lysis buffer compatible with alkaline phosphatase (AP) treatment that differs from the conventional RPPA antibody validation procedure and applied it onto fresh frozen (FF) and formalin-fixed and paraffin-embedded tissue (FFPE) to test its applicability. By screening 106 phospho-antibodies using RPPA, we demonstrated that AP treatment could serve as an independent factor to be adopted for rapid phospho-antibody selection. We also showed desirable reproducibility and specificity in clincical specimens indicating its potential for tissue-based phospho-protein profiling. Of further clinical significance, using the same approach, based on melanoma and lung cancer FFPE samples, we showed great interexperimental reproducibility and significant correlation with pathological markers in both tissues generating meaningful data that match clinical features. Our findings set a benchmark of an efficient workflow for phospho-antibody characterization that is compatible with high-plex clinical proteomics in precison oncology.
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Affiliation(s)
- Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Li Zhang
- grid.412474.00000 0001 0027 0586Department of Pathology, Beijing Cancer Hospital, No 52. Fucheng Rd, Haidian District, Beijing, 100142 China
| | - Qi Ying
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Zhentao Song
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
| | - Aiping Lu
- grid.412474.00000 0001 0027 0586Department of Pathology, Beijing Cancer Hospital, No 52. Fucheng Rd, Haidian District, Beijing, 100142 China
| | - Achim Treumann
- grid.1006.70000 0001 0462 7212Newcastle University Protein and Proteome Analysis, Newcastle University, Devonshire Building, Newcastle upon Tyne, NE1 7RU UK ,KBI Biopharma BV, Leuven, Flanders Belgium
| | - Zhaojian Liu
- grid.27255.370000 0004 1761 1174Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Tao Sun
- grid.27255.370000 0004 1761 1174Department of Haematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies, Floor 22, Overseas Chinese Innovation Zone, Gangxing 3rd Rd, High-Tech and Innovation Zone, Jinan, 250100 China
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2
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Hunt AL, Pierobon M, Baldelli E, Oliver J, Mitchell D, Gist G, Bateman NW, Larry Maxwell G, Petricoin EF, Conrads TP. The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow. Clin Proteomics 2020; 17:9. [PMID: 32165870 PMCID: PMC7061469 DOI: 10.1186/s12014-020-09272-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated the impact of UV laser microdissection (UV LMD) and IR laser capture microdissection (IR LCM) on phosphoprotein abundance of key cancer signaling protein targets assessed by reverse-phase protein microarray (RPPA). Tumor epithelial cells from consecutive thin sections obtained from four high-grade serous ovarian cancers were harvested using either UV LMD or IR LCM methods. Phosphoprotein abundances for ten phosphoproteins that represent important drug targets were assessed by RPPA and revealed no significant differences in phosphoprotein integrity from those obtained using higher-energy UV versus the lower-energy IR laser methods.
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Affiliation(s)
- Allison L. Hunt
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - G. Larry Maxwell
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Thomas P. Conrads
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- 3289 Woodburn Rd, Suite 375, Annandale, VA 22003 USA
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3
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Pre-analytics and tumor heterogeneity. N Biotechnol 2020; 55:30-35. [DOI: 10.1016/j.nbt.2019.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 09/19/2019] [Accepted: 09/29/2019] [Indexed: 12/11/2022]
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4
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Espina V, Mueller C. Solid Pin Protein Array Printing Platforms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:61-75. [DOI: 10.1007/978-981-32-9755-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples. Methods Mol Biol 2018; 1723:33-93. [PMID: 29344854 DOI: 10.1007/978-1-4939-7558-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.
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Freidl GS, Bruin ED, Schipper M, Koopmans M. Exploring novel sero-epidemiological tools-Effect of different storage conditions on longitudinal stability of microarray slides comprising influenza A-, measles- and Streptococcus pneumoniae antigens. J Virol Methods 2017; 245:53-60. [PMID: 28315717 DOI: 10.1016/j.jviromet.2017.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 10/20/2022]
Abstract
In this study we evaluated the long-term stability of a microarray-based serological screening platform, containing antigens of influenza A, measles and Streptococcus pneumoniae, as part of a preparedness research program aiming to develop assays for syndromic disease detection. Spotted microarray slides were kept at four different storage regimes with varying temperature and humidity conditions. We showed that under the standard storage condition in a temperature-controlled (21°C) and desiccated environment (0% relative humidity), microarray slides remained stable for at least 22 months without loss of antigen quality, whereas the other three conditions (37°C, desiccated; Room temperature, non-desiccated; Frozen, desiccated) produced acceptable results for some antigens (influenza A, S.pneumoniae), but not for others (measles). We conclude that these arrays for multiplex antibody testing can be prepared and stored for prolonged periods of time, which aids laboratory-preparedness and facilitates sero-epidemiological studies.
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Affiliation(s)
- Gudrun S Freidl
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands; Virology Department, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
| | - Erwin de Bruin
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands; Virology Department, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
| | - Maarten Schipper
- Department for Statistics, Informatics and Mathematical Modelling, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
| | - Marion Koopmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, the Netherlands; Virology Department, Centre for Infectious Diseases Research, Diagnostics and Screening, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands.
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7
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Abstract
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets. Here, two approaches for the computational analysis of RPPA data are detailed: the identification of similar patterns of protein expression by hierarchical cluster analysis and the modeling of protein interactions and signaling relationships by network analysis. The protocols use freely available, cross-platform software, are easy to implement, and do not require any programming expertise. Serving as data-driven starting points for further in-depth analysis, validation, and biological experimentation, these and related bioinformatic approaches can accelerate the functional interpretation of RPPA data.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK.
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8
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Pin E, Stratton S, Belluco C, Liotta L, Nagle R, Hodge KA, Deng J, Dong T, Baldelli E, Petricoin E, Pierobon M. A pilot study exploring the molecular architecture of the tumor microenvironment in human prostate cancer using laser capture microdissection and reverse phase protein microarray. Mol Oncol 2016; 10:1585-1594. [PMID: 27825696 DOI: 10.1016/j.molonc.2016.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
The cross-talk between tumor epithelium and surrounding stromal/immune microenvironment is essential to sustain tumor growth and progression and provides new opportunities for the development of targeted treatments focused on disrupting the tumor ecology. Identification of novel approaches to study these interactions is of primary importance. Using laser capture microdissection (LCM) coupled with reverse phase protein microarray (RPPA) based protein signaling activation mapping we explored the molecular interconnection between tumor epithelium and surrounding stromal microenvironment in 18 prostate cancer (PCa) specimens. Four specimen-matched cellular compartments (normal-appearing epithelium and its adjacent stroma, and malignant epithelium and its adjacent stroma) were isolated for each case. The signaling network analysis of the four compartments unraveled a number of molecular mechanisms underlying the communication between tumor cells and stroma in the context of the tumor microenvironment. In particular, differential expression of inflammatory mediators like IL-8 and IL-10 by the stroma cells appeared to modulate specific cross-talks between the tumor cells and surrounding microenvironment.
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Affiliation(s)
- Elisa Pin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA; Division of Experimental Oncology 2, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Steven Stratton
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Claudio Belluco
- Department of Surgical Oncology, CRO-IRCCS, National Cancer Institute, Aviano, Italy
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ray Nagle
- Division of Cancer Prevention and Control, University of Arizona Cancer Center, Tucson, AZ, USA
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Jianghong Deng
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Ting Dong
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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9
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Atak A, Mukherjee S, Jain R, Gupta S, Singh VA, Gahoi N, K P M, Srivastava S. Protein microarray applications: Autoantibody detection and posttranslational modification. Proteomics 2016; 16:2557-2569. [PMID: 27452627 DOI: 10.1002/pmic.201600104] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/09/2016] [Accepted: 07/19/2016] [Indexed: 12/18/2022]
Abstract
The discovery of DNA microarrays was a major milestone in genomics; however, it could not adequately predict the structure or dynamics of underlying protein entities, which are the ultimate effector molecules in a cell. Protein microarrays allow simultaneous study of thousands of proteins/peptides, and various advancements in array technologies have made this platform suitable for several diagnostic and functional studies. Antibody arrays enable researchers to quantify the abundance of target proteins in biological fluids and assess PTMs by using the antibodies. Protein microarrays have been used to assess protein-protein interactions, protein-ligand interactions, and autoantibody profiling in various disease conditions. Here, we summarize different microarray platforms with focus on its biological and clinical applications in autoantibody profiling and PTM studies. We also enumerate the potential of tissue microarrays to validate findings from protein arrays as well as other approaches, highlighting their significance in proteomics.
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Affiliation(s)
- Apurva Atak
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shuvolina Mukherjee
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rekha Jain
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shabarni Gupta
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vedita Anand Singh
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Nikita Gahoi
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Manubhai K P
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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10
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Nishizuka SS, Mills GB. New era of integrated cancer biomarker discovery using reverse-phase protein arrays. Drug Metab Pharmacokinet 2016; 31:35-45. [DOI: 10.1016/j.dmpk.2015.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/26/2015] [Accepted: 11/29/2015] [Indexed: 12/11/2022]
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Miles G, Rae J, Ramalingam SS, Pfeifer J. Genetic Testing and Tissue Banking for Personalized Oncology: Analytical and Institutional Factors. Semin Oncol 2015; 42:713-23. [PMID: 26433552 DOI: 10.1053/j.seminoncol.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Personalized oncology, or more aptly precision oncogenomics, refers to the identification and implementation of clinically actionable targets tailored to an individual patient's cancer genomic information. Banking of human tissue and other biospecimens establishes a framework to extract and collect the data essential to our understanding of disease pathogenesis and treatment. Cancer cooperative groups in the United States have led the way in establishing robust biospecimen collection mechanisms to facilitate translational research, and combined with technological advances in molecular testing, tissue banking has expanded from its traditional base in academic research and is assuming an increasingly pivotal role in directing the clinical care of cancer patients. Comprehensive screening of tumors by DNA sequencing and the ability to mine and interpret these large data sets from well-organized tissue banks have defined molecular subtypes of cancer. Such stratification by genomic criteria has revolutionized our perspectives on cancer diagnosis and treatment, offering insight into prognosis, progression, and susceptibility or resistance to known therapeutic agents. In turn, this has enabled clinicians to offer treatments tailored to patients that can greatly improve their chances of survival. Unique challenges and opportunities accompany the rapidly evolving interplay between tissue banking and genomic sequencing, and are the driving forces underlying the revolution in precision medicine. Molecular testing and precision medicine clinical trials are now becoming the major thrust behind the cooperative groups' clinical research efforts.
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Affiliation(s)
- George Miles
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO.
| | - James Rae
- Department of Internal Medicine & Pharmacology, University of Michigan, Ann Arbor, MI
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory School of Medicine, Winship Cancer Institute, Atlanta, GA
| | - John Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
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12
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Boellner S, Becker KF. Reverse Phase Protein Arrays-Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use. MICROARRAYS 2015; 4:98-114. [PMID: 27600215 PMCID: PMC4996393 DOI: 10.3390/microarrays4020098] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/19/2022]
Abstract
Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.
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Affiliation(s)
- Stefanie Boellner
- Institut für Pathologie, Technische Universität München, Trogerstrasse 18, 81675 München, Germany.
| | - Karl-Friedrich Becker
- Institut für Pathologie, Technische Universität München, Trogerstrasse 18, 81675 München, Germany.
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Treilleux I, Arnedos M, Cropet C, Wang Q, Ferrero JM, Abadie-Lacourtoisie S, Levy C, Legouffe E, Lortholary A, Pujade-Lauraine E, Bourcier AV, Eymard JC, Spaeth D, Bachelot T. Translational studies within the TAMRAD randomized GINECO trial: evidence for mTORC1 activation marker as a predictive factor for everolimus efficacy in advanced breast cancer. Ann Oncol 2015; 26:120-125. [PMID: 25361980 DOI: 10.1093/annonc/mdu497] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Everolimus is an agent frequently associated with specific toxicities. Predictive markers of efficacy are needed to help define which patients could benefit from it. The goal of this exploratory study was to identify potential predictive biomarkers in the mammalian target of rapamycin (mTOR) complex 1 (mTORC1) activation pathway using primary tumor samples collected during the phase II tamoxifen plus everolimus (TAMRAD) trial. PATIENTS AND METHODS Tumor tissues were collected retrospectively from the TAMRAD trial. Immunohistochemistry was carried out using specific antibodies directed toward proteins that result in mTORC1 activation [canonical phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mTOR or alternative pathways]. DNA was extracted from the tumor tissue; mutation screening in the PIK3CA gene (exons 9 and 20) and the KRAS gene (exons 2 and 3) was first carried out using Sanger direct sequencing, and then completed by next-generation sequencing for PIK3CA. An exploratory analysis of everolimus efficacy in terms of a time-to-progression (TTP) increase was carried out in each biomarker subgroup (high versus low expression referring to the median percentage of marked cells). RESULTS A total of 55 primary tumor samples from the TAMRAD trial—25 from the tamoxifen-alone group and 30 from the tamoxifen/everolimus group—were evaluated for biomarkers. The subgroups most likely to have an improvement in TTP with tamoxifen/everolimus therapy, compared with tamoxifen alone, were patients with high p4EBP1, low 4EBP1, low liver kinase B1, low pAkt, and low PI3K. Among the 45 samples screened for mutation status, nine samples (20%; 95% CI 9.6-34.6) had a PIK3CA mutation. KRAS mutation was observed in one patient. CONCLUSIONS A positive correlation between late effectors of mTORC1 activation, a positive correlation between Akt-independent mTORC1 activation, and an inverse correlation between canonical PI3K/Akt/mTOR pathway and everolimus efficacy were observed in this exploratory analysis. However, these correlations need to be validated in larger studies before applying the findings to routine clinical practice.
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Affiliation(s)
- I Treilleux
- Department of Anatomopathology, Centre Léon Bérard, Lyon
| | - M Arnedos
- Oncology Department, Gustave Roussy, Villejuif
| | - C Cropet
- Biostatistics and Therapeutic Evaluation Unit
| | - Q Wang
- Genomic Platform-Translational Research Laboratory, Centre Léon Bérard, Lyon
| | - J-M Ferrero
- Medical Oncology Department, Centre Antoine Lacassagne, Nice
| | | | - C Levy
- Oncology Department, Centre François Baclesse, Caen
| | - E Legouffe
- Hematology and Oncology Department, Clinique de Valdegour, Nimes
| | - A Lortholary
- Oncology Department, Centre Catherine de Sienne, Nantes
| | - E Pujade-Lauraine
- Oncology Department, Université Paris Descartes, AP-HP, Hôpitaux Universitaires Paris Centre, Site Hôtel-Dieu, Paris
| | - A-V Bourcier
- Hematology and Oncology Department, Centre Hospitalier Départemental Les Oudairies, La Roche-Sur-Yon
| | - J-C Eymard
- Department of Medicine, Institut Jean Godinot, Reims
| | - D Spaeth
- Oncology Department, Centre d'Oncologie de Gentilly, Nancy
| | - T Bachelot
- 2B North Department, Department of Medical Oncology and Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France.
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14
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Theiss AP, Chafin D, Bauer DR, Grogan TM, Baird GS. Immunohistochemistry of colorectal cancer biomarker phosphorylation requires controlled tissue fixation. PLoS One 2014; 9:e113608. [PMID: 25409462 PMCID: PMC4237459 DOI: 10.1371/journal.pone.0113608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/28/2014] [Indexed: 12/31/2022] Open
Abstract
Phosphorylated signaling molecules are biomarkers of cancer pathophysiology and resistance to therapy, but because phosphoprotein analytes are often labile, poorly controlled clinical laboratory practices could prevent translation of research findings in this area from the bench to the bedside. We therefore compared multiple biomarker and phosphoprotein immunohistochemistry (IHC) results in 23 clinical colorectal carcinoma samples after either a novel, rapid tissue fixation protocol or a standard tissue fixation protocol employed by clinical laboratories, and we also investigated the effect of a defined post-operative "cold" ischemia period on these IHC results. We found that a one-hour cold ischemia interval, allowed by ASCO/CAP guidelines for certain cancer biomarker assays, is highly deleterious to certain phosphoprotein analytes, specifically the phosphorylated epidermal growth factor receptor (pEGFR), but shorter ischemic intervals (less than 17 minutes) facilitate preservation of phosphoproteins. Second, we found that a rapid 4-hour, two temperature, formalin fixation yielded superior staining in several cases with select markers (pEGFR, pBAD, pAKT) compared to a standard overnight room temperature fixation protocol, despite taking less time. These findings indicate that the future research and clinical utilities of phosphoprotein IHC for assessing colorectal carcinoma pathophysiology absolutely depend upon attention to preanalytical factors and rigorously controlled tissue fixation protocols.
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Affiliation(s)
- Abbey P. Theiss
- Ventana Medical Systems Inc., Tucson, Arizona, United States of America
| | - David Chafin
- Ventana Medical Systems Inc., Tucson, Arizona, United States of America
| | - Daniel R. Bauer
- Ventana Medical Systems Inc., Tucson, Arizona, United States of America
| | - Thomas M. Grogan
- Ventana Medical Systems Inc., Tucson, Arizona, United States of America
| | - Geoffrey S. Baird
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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15
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Tower JI, Lingen MW, Seiwert TY, Langerman A. Impact of warm ischemia on phosphorylated biomarkers in head and neck squamous cell carcinoma. Am J Transl Res 2014; 6:548-557. [PMID: 25360219 PMCID: PMC4212929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 08/21/2014] [Indexed: 06/04/2023]
Abstract
OBJECTIVES To quantitatively and visually characterize changes in phosphorylated biomarker expression in head and neck squamous cell carcinoma specimens from excision through 90 minutes of warm ischemia. MATERIALS AND METHODS Tissue biospecimens were procured prospectively. Head and neck squamous cell carcinoma specimens from 5 patients were subdivided into three parts upon excision, exposed to warm ischemia of 15, 30, or 90 minutes, and routinely biobanked. Relative change in biomarker expression of p-Akt, p-ERK, and p-Stat3 was measured by immunoblot densitometry. Immunofluorescent stains were performed to visually supplement the quantitative analysis. RESULTS From 15 to 30 minutes of ex vivo ischemia, there was a significant decrease in p-Akt (p = 0.045) as the mean intensity fell by 44.9%. This decrease in p-Akt remained significant at the 90 minute time point (p = 0.015). From 15 to 30 minutes of ischemia, there was a trend toward a decline in p-ERK, which became significant by 90 minutes of ex vivo warm ischemia (p = 0.008). These changes were supported by qualitative differences in p-ERK fluorescence at 0 and 90 minutes warm ischemia. CONCLUSION Some phosphorylated biomarkers of HNSCC remain highly dynamic during the period of ex vivo warm ischemia after surgical excision but before biobanking. These findings have critical implications for studies that attempt to correlate protein phosphorylation with clinical outcome. We conclude that ex vivo warm ischemia time is a major determinant of tissue quality that may explain inconsistent results from biomarker research in head and neck squamous cell carcinoma.
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Affiliation(s)
- Jacob I Tower
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, The University of ChicagoChicago, IL 60637, USA
| | - Mark W Lingen
- Department of Pathology, The University of ChicagoChicago, IL 60637, USA
| | - Tanguy Y Seiwert
- Comprehensive Cancer Center, The University of ChicagoChicago, IL 60637, USA
| | - Alexander Langerman
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, The University of ChicagoChicago, IL 60637, USA
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16
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Neumeister VM, Parisi F, England AM, Siddiqui S, Anagnostou V, Zarrella E, Vassilakopolou M, Bai Y, Saylor S, Sapino A, Kluger Y, Hicks DG, Bussolati G, Kwei S, Rimm DL. A tissue quality index: an intrinsic control for measurement of effects of preanalytical variables on FFPE tissue. J Transl Med 2014; 94:467-74. [PMID: 24535259 PMCID: PMC4030875 DOI: 10.1038/labinvest.2014.7] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 12/24/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022] Open
Abstract
While efforts are made to improve tissue quality and control preanalytical variables, pathologists are often confronted with the challenge of molecular analysis of patient samples of unknown quality. Here we describe a first attempt to construct a tissue quality index (TQI) or an intrinsic control that would allow a global assessment of protein status based on quantitative measurement of a small number of selected, informative epitopes. Quantitative immunofluorescence (QIF) of a number of proteins was performed on a series of 93 breast cancer cases where levels of expression were assessed as a function of delayed time to formalin fixation. A TQI was constructed based on the combination of proteins that most accurately reflect increased and decreased levels of expression in proportion to delay time. The TQI, defined by combinations of measurements of cytokeratin, ERK1/2 and pHSP-27 and their relationship to cold ischemic time were validated on a second build of the training series and on two independent breast tissue cohorts with recorded time to formalin fixation. We show an association of negative TQI values (an indicator for loss of tissue quality) with increasing cold ischemic time on both validation cohorts and an association with loss of ER expression levels on all three breast cohorts. Using expression levels of three epitopes, we can begin to assess the likelihood of delayed time to fixation or decreased tissue quality. This TQI represents a proof of concept for the use of epitope expression to provide a mechanism for monitoring tissue quality.
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Affiliation(s)
| | - Fabio Parisi
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Allison M England
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Summar Siddiqui
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Valsamo Anagnostou
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Elizabeth Zarrella
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Yalai Bai
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Sasha Saylor
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Yuval Kluger
- 1] Department of Pathology, Yale University School of Medicine, New Haven, CT, USA [2] Department of Medical Sciences, University of Turin, Turin, Italy
| | - David G Hicks
- Department of Pathology, University of Rochester School of Medicine, Rochester, NY, USA
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Stephanie Kwei
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
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17
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Fowler CB, O'Leary TJ, Mason JT. Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue. Expert Rev Proteomics 2014; 10:389-400. [PMID: 23992421 DOI: 10.1586/14789450.2013.820531] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue and their associated diagnostic records represent an invaluable source of retrospective proteomic information on diseases for which the clinical outcome and response to treatment are known. However, analysis of archival FFPE tissues by high-throughput proteomic methods has been hindered by the adverse effects of formaldehyde fixation and subsequent tissue histology. This review examines recent methodological advances for extracting proteins from FFPE tissue suitable for proteomic analysis. These methods, based largely upon heat-induced antigen retrieval techniques borrowed from immunohistochemistry, allow at least a qualitative analysis of the proteome of FFPE archival tissues. The authors also discuss recent advances in the proteomic analysis of FFPE tissue; including liquid-chromatography tandem mass spectrometry, reverse phase protein microarrays and imaging mass spectrometry.
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Affiliation(s)
- Carol B Fowler
- Laboratory of Proteomics and Protein Science, Washington DC Veterans Affairs Medical Center, Washington, DC, USA.
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18
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Gromov P, Moreira JMA, Gromova I. Proteomic analysis of tissue samples in translational breast cancer research. Expert Rev Proteomics 2014; 11:285-302. [DOI: 10.1586/14789450.2014.899469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Application of molecular technologies for phosphoproteomic analysis of clinical samples. Oncogene 2014; 34:805-14. [PMID: 24608425 DOI: 10.1038/onc.2014.16] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 12/17/2022]
Abstract
The integration of small kinase inhibitors and monoclonal antibodies into oncological practice has opened a new paradigm for treating cancer patients. As proteins are the direct targets of the new generations of targeted therapeutics, many of which are kinase/enzymatic inhibitors, there is an increasing interest in developing technologies capable of monitoring post-translational changes of the human proteome for the identification of new predictive, prognostic and therapeutic biomarkers. It is well known that the vast majority of the activation/deactivation of these drug targets is driven by phosphorylation. This review provides a description of the main proteomic platforms (planar and bead array, reverse phase protein microarray, phosphoflow, AQUA and mass spectrometry) that have successfully been used for measuring changes in phosphorylation level of drug targets and downstream substrates using clinical specimens. Major emphasis was given to the strengths and weaknesses of the different platforms and to the major barriers that are associated with the analysis of the phosphoproteome. Finally, a number of examples of application of the above-mentioned technologies in the clinical setting are reported.
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20
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Thompson SM, Craven RA, Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2013; 7:241-51. [PMID: 23027712 DOI: 10.1002/prca.201200086] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.
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Affiliation(s)
- Seonaid M Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St. James's University Hospital, United Kingdom
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21
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Abstract
The majority of human diseases, including cancer, are characterized by abnormal protein function. Proteins regulate virtually every cellular process and exhibit multiple kinds of post-translational modification that modulate expression levels and activation states, such as phosphorylation by protein kinases. Additionally proteins interact with each other in complex regulatory networks and signal transduction pathways modulated by feedback mechanisms. These pathways are disrupted in disease and altered by therapeutic drugs. Reverse phase protein microarray (RPMA) technology allows simultaneous measurement of numerous phosphorylated, glycosylated, cleaved, or total cellular proteins from complex mixtures in many samples at once. Therefore, RPMAs can provide a portrait of a cell's signaling pathways in diseased states, before and after treatment with drugs, and allows comparison of changes in drug-resistant and sensitive cells. Furthermore, the technology offers a means of connecting genomic abnormalities in cancer to targetable alterations in protein signaling pathways, even for genetic events that seem otherwise undruggable. Consequently, the RPMA platform has great utility in many steps of drug development including target identification, validation of a pharmaceutical agent's efficacy, understanding mechanisms of action, and discovery of biomarkers that predict or guide therapeutic response. RPMAs have become a powerful tool for drug development and are now being integrated into human clinical cancer trials, where they are being used to personalize therapy.
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22
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Wulfkuhle JD, Berg D, Wolff C, Langer R, Tran K, Illi J, Espina V, Pierobon M, Deng J, DeMichele A, Walch A, Bronger H, Becker I, Waldhör C, Höfler H, Esserman L, Liotta LA, Becker KF, Petricoin EF. Molecular analysis of HER2 signaling in human breast cancer by functional protein pathway activation mapping. Clin Cancer Res 2012; 18:6426-35. [PMID: 23045247 DOI: 10.1158/1078-0432.ccr-12-0452] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Targeting of the HER2 protein in human breast cancer represents a major advance in oncology but relies on measurements of total HER2 protein and not HER2 signaling network activation. We used reverse-phase protein microarrays (RPMA) to measure total and phosphorylated HER2 in the context of HER family signaling to understand correlations between phosphorylated and total levels of HER2 and downstream signaling activity. EXPERIMENTAL DESIGN Three independent study sets, comprising a total of 415 individual patient samples from flash-frozen core biopsy samples and formalin-fixed and paraffin-embedded (FFPE) surgical and core samples, were analyzed via RPMA. The phosphorylation and total levels of the HER receptor family proteins and downstream signaling molecules were measured in laser capture microdissected (LCM) enriched tumor epithelium from 127 frozen pretreatment core biopsy samples and whole-tissue lysates from 288 FFPE samples and these results were compared with FISH and immunohistochemistry (IHC). RESULTS RPMA measurements of total HER2 were highly concordant (>90% all sets) with FISH and/or IHC data, as was phosphorylation of HER2 in the FISH/IHC(+) population. Phosphorylation analysis of HER family signaling identified HER2 activation in some FISH/IHC(-) tumors and, identical to that seen with FISH/IHC(+) tumors, the HER2 activation was concordant with EGF receptor (EGFR) and HER3 phosphorylation and downstream signaling endpoint activation. CONCLUSIONS Molecular profiling of HER2 signaling of a large cohort of human breast cancer specimens using a quantitative and sensitive functional pathway activation mapping technique reveals IHC(-)/FISH(-)/pHER2(+) tumors with HER2 pathway activation independent of total HER2 levels and functional signaling through HER3 and EGFR.
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Affiliation(s)
- Julia D Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, USA
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23
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Viertler C, Groelz D, Gündisch S, Kashofer K, Reischauer B, Riegman PHJ, Winther R, Wyrich R, Becker KF, Oelmüller U, Zatloukal K. A new technology for stabilization of biomolecules in tissues for combined histological and molecular analyses. J Mol Diagn 2012; 14:458-66. [PMID: 22749745 DOI: 10.1016/j.jmoldx.2012.05.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/08/2012] [Accepted: 05/10/2012] [Indexed: 11/25/2022] Open
Abstract
For accurate diagnosis, prediction of outcome, and selection of appropriate therapies, the molecular characterization of human diseases requires analysis of a broad spectrum of altered biomolecules, in addition to morphological features, in affected tissues such as tumors. In a high-throughput screening approach, we have developed the PAXgene Tissue System as a novel tissue stabilization technology. Comprehensive characterization of this technology in stabilized and paraffin-embedded human tissues and comparison with snap-frozen tissues revealed excellent preservation of morphology and antigenicity, as well as outstanding integrity of nucleic acids (genomic DNA, miRNA, and mRNA) and phosphoproteins. Importantly, PAXgene-fixed, paraffin-embedded tissues provided RNA quantity and quality not only significantly better than that obtained with neutral buffered formalin, but also similar to that from snap-frozen tissue, which currently represents the gold standard for molecular analyses. The PAXgene tissue stabilization system thus opens new opportunities in a variety of molecular diagnostic and research applications in which the collection of snap-frozen tissue is not feasible for medical, logistic, or ethical reasons. Furthermore, this technology allows performing histopathological analyses together with molecular studies in a single sample, which markedly facilitates direct correlation of morphological disease phenotypes with alterations of nucleic acids and other biomolecules.
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