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Lindskog C, Backman M, Zieba A, Asplund A, Uhlén M, Landegren U, Pontén F. Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues. J Histochem Cytochem 2020; 68:515-529. [PMID: 32602410 DOI: 10.1369/0022155420936384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.
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Affiliation(s)
- Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Agata Zieba
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Morin E, Sjöberg E, Tjomsland V, Testini C, Lindskog C, Franklin O, Sund M, Öhlund D, Kiflemariam S, Sjöblom T, Claesson-Welsh L. VEGF receptor-2/neuropilin 1 trans-complex formation between endothelial and tumor cells is an independent predictor of pancreatic cancer survival. J Pathol 2018; 246:311-322. [PMID: 30027561 PMCID: PMC6221118 DOI: 10.1002/path.5141] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/16/2018] [Accepted: 07/11/2018] [Indexed: 01/01/2023]
Abstract
Unstable and dysfunctional tumor vasculature promotes cancer progression and spread. Signal transduction by the pro‐angiogenic vascular endothelial growth factor (VEGF) receptor‐2 (VEGFR2) is modulated by VEGFA‐dependent complex formation with neuropilin 1 (NRP1). NRP1 expressed on tumor cells can form VEGFR2/NRP1 trans‐complexes between tumor cells and endothelial cells which arrests VEGFR2 on the endothelial surface, thus interfering with productive VEGFR2 signaling. In mouse fibrosarcoma, VEGFR2/NRP1 trans‐complexes correlated with reduced tumor vessel branching and reduced tumor cell proliferation. Pancreatic ductal adenocarcinoma (PDAC) strongly expressed NRP1 on both tumor cells and endothelial cells, in contrast to other common cancer forms. Using proximity ligation assay, VEGFR2/NRP1 trans‐complexes were identified in human PDAC tumor tissue, and its presence was associated with reduced tumor vessel branching, reduced tumor cell proliferation, and improved patient survival after adjusting for other known survival predictors. We conclude that VEGFR2/NRP1 trans‐complex formation is an independent predictor of PDAC patient survival. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Eric Morin
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Elin Sjöberg
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Vegard Tjomsland
- University of Oslo, Department of Hepato-pancreato-biliary Surgery, Oslo University Hospital, Institute of Clinical Medicine, Oslo, Norway
| | - Chiara Testini
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Cecilia Lindskog
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Oskar Franklin
- Umeå University, Department of Surgery and Perioperative Sciences, Umeå, Sweden
| | - Malin Sund
- Umeå University, Department of Surgery and Perioperative Sciences, Umeå, Sweden
| | - Daniel Öhlund
- Umeå University, Department of Radiation Sciences, Umeå, Sweden.,Umeå University, Wallenberg Centre for Molecular Medicine, Umeå, Sweden
| | - Sara Kiflemariam
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Tobias Sjöblom
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
| | - Lena Claesson-Welsh
- Uppsala University, Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Science for Life Laboratory, Uppsala, Sweden
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Liu J, Liu L, Cao L, Wen Q. Keratin 17 Promotes Lung Adenocarcinoma Progression by Enhancing Cell Proliferation and Invasion. Med Sci Monit 2018; 24:4782-4790. [PMID: 29991674 PMCID: PMC6069497 DOI: 10.12659/msm.909350] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Backgrounds Lung adenocarcinoma (LAC) accounts for the majority of lung cancer, which is the leading cause of cancer-related mortality worldwide. Keratin 17 (KRT17) was reported to promote the tumor development of skin tumor and oral cancer. The aim of this study was to investigate the expression and function of KRT17 in LAC. Material/Methods Immunohistochemical staining and quantitative PCR were performed to explore the expression of KRT17 in both LAC tissues and adjacent normal liver tissues. Chi-square test, univariate analysis, and multivariate analysis were conducted to statistically evaluate the clinical significance of KRT17 in LAC. Proliferation, migration, and invasion capacities of LAC cells were assessed after overexpression or silencing KRT17. Results Both the RNA and protein levels of KRT17 were up-regulated in LAC tissues compared to normal lung tissues. High expression of KRT17 was correlated with advanced TNM stage and poor overall survival. Moreover, KRT17 was identified as a novel independent prognostic factor for LAC patients. Cellular studies showed that KRT17 can enhance the proliferation, migration, and invasion capacities of LAC cells, thereby promoting tumor progression. Conclusions High expression of KRT17 is frequent in LAC tissues, which promotes tumor proliferation and invasion, and is correlated with a poor overall survival. Targeting KRT17 may be a novel direction for LAC drug development.
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Affiliation(s)
- Jianbo Liu
- Department of Public Health, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Lei Liu
- General Department of Health and Geriatrics, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Lina Cao
- General Department of Health and Geriatrics, Yidu Central Hospital of Weifang, Weifang, Shandong, China (mainland)
| | - Qiang Wen
- Third Department of Internal Medicine, Linyi People's Hospital, Linyi, Shandong, China (mainland).,Third Department of Internal Medicine, East District of Linyi People's Hospital, Linyi, Shandong, China (mainland)
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Warford A. In situ hybridisation: Technologies and their application to understanding disease. ACTA ACUST UNITED AC 2015; 50:37-48. [PMID: 26797255 DOI: 10.1016/j.proghi.2015.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/23/2022]
Abstract
In situ hybridisation (ISH) is unique amongst molecular analysis methods in providing for the precise microscopic localisation of genes, mRNA and microRNA in metaphase spreads, cell and tissue preparations. The method is well established as a tool to guide appropriate therapeutic intervention in breast, gastric and lung cancer. With the description of ultrasensitive ISH technologies for low copy mRNA demonstration and the relative ease by which microRNA can be visualised, the applications for research and diagnostic purposes is set to increase dramatically. In this review ISH is considered with emphasis on recent technological developments and surveyed for present and future applications in the context of the demonstration of genes, mRNA and microRNA in health and disease.
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Affiliation(s)
- Anthony Warford
- University of Westminster, 115 New Cavendish Street, London W1W 6UW, United Kingdom.
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Kiflemariam S, Ljungström V, Pontén F, Sjöblom T. Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1600-9. [PMID: 25864925 DOI: 10.1016/j.ajpath.2015.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/08/2015] [Accepted: 02/18/2015] [Indexed: 01/16/2023]
Abstract
The tyrosine kinome and phosphatome harbor oncogenes and tumor suppressor genes and important regulators of angiogenesis and tumor stroma formation. To provide a better understanding of their potential roles in cancer, we analyzed the expression of 85 tyrosine kinases and 42 tyrosine phosphatases by in situ hybridization 48 human normal and 24 tumor tissue specimens. Nine-tenths of the assessed transcripts had tumor cell expression concordant with expression array databases. Further, pan-cancer expression of AATK, PTPRK, and PTPRU and expression of PTPRS in a subset of tumors were observed. To demonstrate tumor subcompartment resolution, we validated the predicted tumor stroma-specific markers HTRA1, HTRA3, MXRA5, MXRA8, and SERPING1 in situ. In addition to known vascular and stromal markers such as PDGFRB, we observed stromal expression of PTK6 and TNS1 and vascular expression of INSR, PTPRF, PTPRG, PTPRU, and TNS1, of which INSR emerged as a tumor-specific vessel marker. This study demonstrates the feasibility of large-scale analyses to chart the transcriptome in situ in human cancers and their ability to identify novel cancer biomarkers.
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Affiliation(s)
- Sara Kiflemariam
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Tobias Sjöblom
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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O'Hurley G, Sjöstedt E, Rahman A, Li B, Kampf C, Pontén F, Gallagher WM, Lindskog C. Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers. Mol Oncol 2014; 8:783-98. [PMID: 24725481 PMCID: PMC5528533 DOI: 10.1016/j.molonc.2014.03.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/10/2014] [Indexed: 12/19/2022] Open
Abstract
The use of immunohistochemistry (IHC) in clinical cohorts is of paramount importance in determining the utility of a biomarker in clinical practice. A major bottleneck in translating a biomarker from bench-to-bedside is the lack of well characterized, specific antibodies suitable for IHC. Despite the widespread use of IHC as a biomarker validation tool, no universally accepted standardization guidelines have been developed to determine the applicability of particular antibodies for IHC prior to its use. In this review, we discuss the technical challenges faced by the use of immunohistochemical biomarkers and rigorously explore classical and emerging antibody validation technologies. Based on our review of these technologies, we provide strict criteria for the pragmatic validation of antibodies for use in immunohistochemical assays.
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Affiliation(s)
- Gillian O'Hurley
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden; OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland
| | - Evelina Sjöstedt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Arman Rahman
- OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland
| | - Bo Li
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden.
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland; OncoMark Ltd, NovaUCD, Belfield Innovation Park, Belfield, Dublin 4, Ireland.
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85 Uppsala, Sweden
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Andersson S, Konrad A, Ashok N, Pontén F, Hober S, Asplund A. Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection. J Histochem Cytochem 2013; 61:773-84. [PMID: 23920108 PMCID: PMC3808578 DOI: 10.1369/0022155413502360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Antibody-based protein profiling on a global scale using immunohistochemistry constitutes an emerging strategy for mapping of the human proteome, which is crucial for an increased understanding of biological processes in the cell. Immunohistochemistry is often performed indirectly using secondary antibodies for detection, with the benefit of signal amplification. Direct immunohistochemistry instead brings the advantage of multiplexing; however, it requires labeling of the primary antibody. Many antibody-labeling kits do not specifically target IgG and may therefore cause labeling of stabilizing proteins present in the antibody solution. A new conjugation method has been developed that utilizes a modified Z-domain of protein A (ZBPA) to specifically target the Fc part of antibodies. The aim of the present study was to compare the ZBPA conjugation method and a commercially available labeling kit, Lightning-Link, for in situ protein detection. Fourteen antibodies were biotinylated with each method and stained using immunohistochemistry. For all antibodies tested, ZBPA biotinylation resulted in distinct immunoreactivity without off-target staining, regardless of the presence of stabilizing proteins in the buffer, whereas the majority of the Lightning-Link biotinylated antibodies displayed a characteristic pattern of nonspecific staining. We conclude that biotinylated ZBPA domain provides a stringent method for antibody biotinylation, advantageous for in situ protein detection in tissues.
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Affiliation(s)
- Sandra Andersson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden (SA,NA,FP,AA)
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Asplund A, Edqvist PHD, Schwenk JM, Pontén F. Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research. Proteomics 2012; 12:2067-77. [PMID: 22623277 DOI: 10.1002/pmic.201100504] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this review, we present an update on the progress of the Human Protein Atlas, with an emphasis on strategies for validating immunohistochemistry-based protein expression patterns and on the possibilities to extend the map of protein expression patterns for cancer research projects. The objectives underlying the Human Protein Atlas include (i) the generation of validated antibodies toward a major isoform of all proteins encoded by the human genome, (ii) creating an information database of protein expression patterns in normal human tissues, in cells, and in cancer, and (iii) utilizing generated antibodies and protein expression data as tools to identify clinically useful biomarkers. The success of such an effort is dependent on the validity of antibodies as specific binders of intended targets in applications used to map protein expression patterns. The development of strategies to support specific target binding is crucial and remains a challenge as a large fraction of proteins encoded by the human genome is poorly characterized, including the approximately one-third of all proteins lacking evidence of existence. Conceivable methods for validation include the use of paired antibodies, i.e. two independent antibodies targeting different and nonoverlapping epitopes on the same protein as well as comparative analysis of mRNA expression patterns with corresponding proteins.
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Affiliation(s)
- Anna Asplund
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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