1
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Normandeau F, Ng A, Beaugrand M, Juncker D. Spatial Bias in Antibody Microarrays May Be an Underappreciated Source of Variability. ACS Sens 2021; 6:1796-1806. [PMID: 33973474 DOI: 10.1021/acssensors.0c02613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibody microarrays enable multiplexed protein detection with minimal reagent consumption, but they continue to be plagued by lack of reproducibility. Chemically functionalized glass slides are used as substrates, yet antibody binding spatial inhomogeneity across the slide has not been analyzed in antibody microarrays. Here, we characterize spatial bias across five commercial slides patterned with nine overlapping dense arrays (by combining three buffers and three different antibodies), and we measure signal variation for both antibody immobilization and the assay signal, generating 270 heatmaps. Spatial bias varied across models, and the coefficient of variation ranged from 4.6 to 50%, which was unexpectedly large. Next, we evaluated three layouts of spot replicates-local, random, and structured random-for their capacity to predict assay variation. Local replicates are widely used but systematically underestimate the whole-slide variation by up to seven times; structured random replicates gave the most accurate estimation. Our results highlight the risk and consequences of using local replicates: the underappreciation of spatial bias as a source of variability, poor assay reproducibility, and possible overconfidence in assay results. We recommend the detailed characterization of spatial bias for antibody microarrays and the description and use of distributed positive replicates for research and clinical applications.
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Affiliation(s)
- Frédéric Normandeau
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Andy Ng
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Maiwenn Beaugrand
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - David Juncker
- McGill Genome Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec H3A 2B4, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H3A 2B4, Canada
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2
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Shaffaf T, Ghafar-Zadeh E. COVID-19 Diagnostic Strategies Part II: Protein-Based Technologies. Bioengineering (Basel) 2021; 8:54. [PMID: 33925032 PMCID: PMC8145709 DOI: 10.3390/bioengineering8050054] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/08/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
After the initiation of the current outbreak, humans' lives have been profoundly impacted by COVID-19. During the first months, no rapid and reliable detecting tool was readily available to sufficiently respond to the requirement of massive testing. In this situation, when the development of an effective vaccine requires at least a few months, it is crucial to be prepared by developing and commercializing affordable, accurate, rapid and adaptable biosensors not only to fight Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) but also to be armed to avoid the pandemic in the earliest stages in the future. The COVID-19 diagnostic tools are categorized into two main groups of Nucleic Acid (NA)-based and protein-based tests. To date, nucleic acid-based detection has been announced as the gold-standard strategy for coronavirus detection; however, protein-based tests are promising alternatives for rapid and large-scale screening of susceptible groups. In this review, we discuss the current protein-based biosensing tools, the research advances and the potential protein-detecting strategies for COVID-19 detection. This narrative review aims to highlight the importance of the diagnostic tests, encourage the academic research groups and the companies to eliminate the shortcomings of the current techniques and step forward to mass-producing reliable point-of-care (POC) and point-of-need (PON) adaptable diagnostic tools for large-scale screening in the future outbreaks.
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Affiliation(s)
- Tina Shaffaf
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J1P3, Canada
| | - Ebrahim Ghafar-Zadeh
- Biologically Inspired Sensors and Actuators Laboratory (BioSA), York University, Toronto, ON M3J1P3, Canada;
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J1P3, Canada
- Department of Electrical Engineering and Computer Science, Lassonde School of Engineering, York University, Toronto, ON M3J1P3, Canada
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3
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Tian C, Zhang B, Ge C. Effect of CEACAM6 silencing on the biological behavior of human gallbladder cancer cells. Oncol Lett 2020; 20:2677-2688. [PMID: 32782584 PMCID: PMC7400980 DOI: 10.3892/ol.2020.11806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) is abnormally expressed in various malignant tumors and thus represents a potential biomarker, although information regarding its role in gallbladder cancer (GBC) is limited. This study aimed to evaluate the expression of CEACAM6 in GBC and the effect of CEACAM6 gene silencing on the proliferation, migration, invasion and apoptosis of human GBC cells. Immunochemistry was used to evaluate CEACAM6 expression in 95 GBC specimens and 40 peritumoral tissue specimens. GBC-SD and SGC-996 cell lines were used for in vitro experiments. CEACAM6 was knocked down by transfection of targeted small interfering RNA (siRNA), and reverse-transcription quantitative PCR and western blot analysis were used to detect knockdown efficiency. Cell Counting Kit-8 and colony formation assays were undertaken to evaluate cell proliferation. Variations in cell migration and invasion were detected by wound-healing and Transwell assays, respectively. Flow cytometry was applied to measure cell apoptosis and cell cycle distribution. CEACAM6 gene expression was significantly greater in GBC tissues than in peritumoral tissues, and its positive expression was associated with poor prognosis. CEACAM6 mRNA and protein expression in the CEACAM6 siRNA treatment group was significantly lower than that in the negative control group and the blank group. CEACAM6 knockdown inhibited GBC cell proliferation, migration and invasion but promoted cell apoptosis. Western blot analysis of invasion- and apoptosis-related proteins matrix metalloproteinase-2, Vimentin, BCL-2 and BAX further confirmed CEACAM6 mRNA depletion promoted cell apoptosis and inhibited invasion. Additionally, CEACAM6 mRNA depletion affected the progression of the GBC cell cycle to increase cell distribution in G0/G1 phase, and to reduce it in G2/M phase and S phase. These findings indicated that CEACAM6 overexpression may be related to the tumorigenesis and development of GBC. In summary, depletion of CEACAM6 mRNA suppressed the malignant biological behaviors of human gallbladder cancer cells.
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Affiliation(s)
- Chengming Tian
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Bingye Zhang
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Chunlin Ge
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110000, P.R. China
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Dowling P, Murphy S, Zweyer M, Raucamp M, Swandulla D, Ohlendieck K. Emerging proteomic biomarkers of X-linked muscular dystrophy. Expert Rev Mol Diagn 2019; 19:739-755. [PMID: 31359811 DOI: 10.1080/14737159.2019.1648214] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Progressive skeletal muscle wasting is the manifesting symptom of Duchenne muscular dystrophy, an X-linked inherited disorder triggered by primary abnormalities in the DMD gene. The almost complete loss of dystrophin isoform Dp427 causes a multi-system pathology that features in addition to skeletal muscle weakness also late-onset cardio-respiratory deficiencies, impaired metabolism and abnormalities in the central nervous system. Areas covered: This review focuses on the mass spectrometry-based proteomic characterization of X-linked muscular dystrophy with special emphasis on the identification of novel biomarker candidates in skeletal muscle tissues, as well as non-muscle tissues and various biofluids. Individual sections focus on molecular and cellular aspects of the pathogenic changes in dystrophinopathy, proteomic workflows used in biomarker research, the proteomics of the dystrophin-glycoprotein complex and the potential usefulness of newly identified protein markers involved in fibre degeneration, fibrosis and inflammation. Expert opinion: The systematic application of large-scale proteomic surveys has identified a distinct cohort of both tissue- and biofluid-associated protein species with considerable potential for improving diagnostic, prognostic and therapy-monitoring procedures. Novel proteomic markers include components involved in fibre contraction, cellular signalling, ion homeostasis, cellular stress response, energy metabolism and the immune response, as well as maintenance of the cytoskeletal and extracellular matrix.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
| | - Sandra Murphy
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle upon Tyne , UK
| | - Margit Zweyer
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | - Maren Raucamp
- Institute of Physiology II, University of Bonn , Bonn , Germany
| | | | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland , Kildare , Ireland.,Human Health Research Institute, Maynooth University , Kildare , Ireland
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Abstract
INTRODUCTION High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward. Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays. Expert commentary: The choice of appropriate protein microarray platform depends on the specific biological application in hand, with both more focused, lower density and higher density arrays having distinct advantages. Full-length protein arrays offer advantages in biomarker discovery profiling applications, although care is required in ensuring that the protein production and array fabrication methodology is compatible with the required downstream functionality.
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Affiliation(s)
- Jessica G Duarte
- a Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine , La Trobe University , Heidelberg , Australia
| | - Jonathan M Blackburn
- b Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Faculty of Health Sciences , University of Cape Town , Observatory, South Africa
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6
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Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC. Current applications of antibody microarrays. Clin Proteomics 2018; 15:7. [PMID: 29507545 PMCID: PMC5830343 DOI: 10.1186/s12014-018-9184-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/19/2018] [Indexed: 12/14/2022] Open
Abstract
The concept of antibody microarrays is one of the most versatile approaches within multiplexed immunoassay technologies. These types of arrays have increasingly become an attractive tool for the exploratory detection and study of protein abundance, function, pathways, and potential drug targets. Due to the properties of the antibody microarrays and their potential use in basic research and clinical analytics, various types of antibody microarrays have already been developed. In spite of the growing number of studies utilizing this technique, few reviews about antibody microarray technology have been presented to reflect the quality and future uses of the generated data. In this review, we provide a summary of the recent applications of antibody microarray techniques in basic biology and clinical studies, providing insights into the current trends and future of protein analysis.
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Affiliation(s)
- Ziqing Chen
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Tea Dodig-Crnković
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Sheng-ce Tao
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200240 China
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7
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Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C. Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach. N Biotechnol 2016; 33:503-13. [PMID: 26703809 DOI: 10.1016/j.nbt.2015.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 11/17/2022]
Abstract
Increasing the understanding of a proteome and how its protein composition is affected by for example different diseases, such as cancer, has the potential to improve strategies for early diagnosis and therapeutics. The Global Proteome Survey or GPS is a method that combines mass spectrometry and affinity enrichment with the use of antibodies. The technology enables profiling of complex proteomes in a species independent manner. The sensitivity of GPS, and other methods relying on affinity enrichment, is largely affected by the activity of the exploited affinity reagent. We here present an improvement of the GPS platform by utilizing an antibody immobilization approach which ensures a controlled immobilization process of the antibody to the magnetic bead support. More specifically, we make use of an antibody format that enables site-directed biotinylation and use this in combination with streptavidin coated magnetic beads. The performance of the expanded GPS platform was evaluated by profiling yeast proteome samples. We demonstrate that the oriented antibody immobilization strategy increases the ability of the GPS platform and results in larger fraction of functional antibodies. Additionally, we show that this new antibody format enabled in-solution capture, i.e. immobilization of the antibodies after sample incubation. A workflow has been established that permit the use of an oriented immobilization strategy for the GPS platform.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Helena Persson
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden; Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden
| | - Carl A K Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village (House 406), SE-223 81 Lund, Sweden.
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8
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9
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Meo AD, Pasic MD, Yousef GM. Proteomics and peptidomics: moving toward precision medicine in urological malignancies. Oncotarget 2016; 7:52460-52474. [PMID: 27119500 PMCID: PMC5239567 DOI: 10.18632/oncotarget.8931] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
Urological malignancies are a major cause of morbidity and mortality worldwide. Advances in early detection, diagnosis, prognosis and prediction of treatment response can significantly improve patient care. Proteomic and peptidomic profiling studies are at the center of kidney, prostate and bladder cancer biomarker discovery and have shown great promise for improved clinical assessment. Mass spectrometry (MS) is the most widely employed method for proteomic and peptidomic analyses. A number of MS platforms have been developed to facilitate accurate identification of clinically relevant markers in various complex biological samples including tissue, urine and blood. Furthermore, protein profiling studies have been instrumental in the successful introduction of several diagnostic multimarker tests into the clinic. In this review, we will provide a brief overview of high-throughput technologies for protein and peptide based biomarker discovery. We will also examine the current state of kidney, prostate and bladder cancer biomarker research as well as review the journey toward successful clinical implementation.
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Affiliation(s)
- Ashley Di Meo
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Maria D. Pasic
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine, St. Joseph's Health Centre, Toronto, Ontario, Canada
| | - George M. Yousef
- Department of Laboratory Medicine, and The Keenan Research Centre for Biomedical Science at The Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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10
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Delfani P, Dexlin Mellby L, Nordström M, Holmér A, Ohlsson M, Borrebaeck CAK, Wingren C. Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics. PLoS One 2016; 11:e0159138. [PMID: 27414037 PMCID: PMC4944972 DOI: 10.1371/journal.pone.0159138] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/28/2016] [Indexed: 01/30/2023] Open
Abstract
In the quest for deciphering disease-associated biomarkers, high-performing tools for multiplexed protein expression profiling of crude clinical samples will be crucial. Affinity proteomics, mainly represented by antibody-based microarrays, have during recent years been established as a proteomic tool providing unique opportunities for parallelized protein expression profiling. But despite the progress, several main technical features and assay procedures remains to be (fully) resolved. Among these issues, the handling of protein microarray data, i.e. the biostatistics parts, is one of the key features to solve. In this study, we have therefore further optimized, validated, and standardized our in-house designed recombinant antibody microarray technology platform. To this end, we addressed the main remaining technical issues (e.g. antibody quality, array production, sample labelling, and selected assay conditions) and most importantly key biostatistics subjects (e.g. array data pre-processing and biomarker panel condensation). This represents one of the first antibody array studies in which these key biostatistics subjects have been studied in detail. Here, we thus present the next generation of the recombinant antibody microarray technology platform designed for clinical immunoproteomics.
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Affiliation(s)
- Payam Delfani
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Linda Dexlin Mellby
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
- Immunovia AB, Lund, Sweden
| | | | | | - Mattias Ohlsson
- Computational Biology & Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Carl A. K. Borrebaeck
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology and CREATE Health, Lund University, Medicon Village, Lund, Sweden
- * E-mail:
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11
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Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays. MICROARRAYS 2016; 5:microarrays5020016. [PMID: 27600082 PMCID: PMC5003492 DOI: 10.3390/microarrays5020016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 11/17/2022]
Abstract
Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the antibodies and the solid surfaces plays a central role. In this study, we have taken on the first comprehensive view and evaluated the overall impact of solid surfaces on the recombinant antibody microarray design. The results clearly demonstrated the importance of the surface-antibody interaction and showed the effect of the solid supports on the printing process, the array format of planar arrays (slide- and well-based), the assay performance (spot features, reproducibility, specificity and sensitivity) and assay processing (degree of automation). In the end, two high-end recombinant antibody microarray technology platforms were designed, based on slide-based (black polymer) and well-based (clear polymer) arrays, paving the way for future large-scale protein expression profiling efforts.
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12
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Bader S, Zajac M, Friess T, Ruge E, Rieder N, Gierke B, Heubach Y, Thomas M, Pawlak M. Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA). Mol Cell Proteomics 2015; 14:2775-85. [PMID: 26106084 DOI: 10.1074/mcp.o114.045542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 12/31/2022] Open
Abstract
Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues.
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Affiliation(s)
- Sabine Bader
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Magdalena Zajac
- §Pharma Research & Early Development, Roche Innovation Centre Welwyn, 6 Falcon Way, Shire Park, Welwyn Garden City, Herts, AL7 1TW, United Kingdom
| | - Thomas Friess
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Elisabeth Ruge
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Natascha Rieder
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Berthold Gierke
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Yvonne Heubach
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Marlene Thomas
- ‖Roche Pharma AG, Emil-Barell-Str. 1, 79639, Grenzach-Wyhlen, Germany
| | - Michael Pawlak
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany;
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13
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Husi H, Skipworth RJE, Cronshaw A, Stephens NA, Wackerhage H, Greig C, Fearon KCH, Ross JA. Programmed cell death 6 interacting protein (PDCD6IP) and Rabenosyn-5 (ZFYVE20) are potential urinary biomarkers for upper gastrointestinal cancer. Proteomics Clin Appl 2015; 9:586-96. [PMID: 25644331 DOI: 10.1002/prca.201400111] [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: 08/14/2014] [Revised: 12/02/2014] [Accepted: 01/27/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE Cancer of the upper digestive tract (uGI) is a major contributor to cancer-related death worldwide. Due to a rise in occurrence, together with poor survival rates and a lack of diagnostic or prognostic clinical assays, there is a clear need to establish molecular biomarkers. EXPERIMENTAL DESIGN Initial assessment was performed on urine samples from 60 control and 60 uGI cancer patients using MS to establish a peak pattern or fingerprint model, which was validated by a further set of 59 samples. RESULTS We detected 86 cluster peaks by MS above frequency and detection thresholds. Statistical testing and model building resulted in a peak profiling model of five relevant peaks with 88% overall sensitivity and 91% specificity, and overall correctness of 90%. High-resolution MS of 40 samples in the 2-10 kDa range resulted in 646 identified proteins, and pattern matching identified four of the five model peaks within significant parameters, namely programmed cell death 6 interacting protein (PDCD6IP/Alix/AIP1), Rabenosyn-5 (ZFYVE20), protein S100A8, and protein S100A9, of which the first two were validated by Western blotting. CONCLUSIONS AND CLINICAL RELEVANCE We demonstrate that MS analysis of human urine can identify lead biomarker candidates in uGI cancers, which makes this technique potentially useful in defining and consolidating biomarker patterns for uGI cancer screening.
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Affiliation(s)
- Holger Husi
- Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK.,School of Clinical Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Andrew Cronshaw
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | - Carolyn Greig
- School of Clinical Sciences, University of Edinburgh, Edinburgh, UK.,School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, Birmingham, UK
| | | | - James A Ross
- School of Clinical Sciences, University of Edinburgh, Edinburgh, UK
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14
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Discovery and validation of an INflammatory PROtein-driven GAstric cancer Signature (INPROGAS) using antibody microarray-based oncoproteomics. Oncotarget 2015; 5:1942-54. [PMID: 24722433 PMCID: PMC4039123 DOI: 10.18632/oncotarget.1879] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study aimed to improve gastric cancer (GC) diagnosis by identifying and validating an INflammatory PROtein-driven GAstric cancer Signature (hereafter INPROGAS) using low-cost affinity proteomics. The detection of 120 cytokines, 43 angiogenic factors, 41 growth factors, 40 inflammatory factors and 10 metalloproteinases was performed using commercially available human antibody microarray-based arrays. We identified 21 inflammation-related proteins (INPROGAS) with significant differences in expression between GC tissues and normal gastric mucosa in a discovery cohort of matched pairs (n=10) of tumor/normal gastric tissues. Ingenuity pathway analysis confirmed the "inflammatory response", "cellular movement" and "immune cell trafficking" as the most overrepresented biofunctions within INPROGAS. Using an expanded independent validation cohort (n = 22), INPROGAS classified gastric samples as "GC" or "non-GC" with a sensitivity of 82% (95% CI 59-94) and a specificity of 73% (95% CI 49-89). The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. The positive predictive value and negative predictive value in this validation cohort were 75% (95% CI 53-90) and 80% (95% CI 56-94), respectively. Antibody microarray analyses of the GC-associated inflammatory proteome identified a 21-protein INPROGAS that accurately discriminated GC from noncancerous gastric mucosa.
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Gu Q, Sivanandam TM. Optimizing scan parameters for antibody microarray experiments: accelerating robust systems diagnostics for life sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:385-98. [PMID: 24754828 DOI: 10.1089/omi.2013.0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microarray experiments are a centerpiece of postgenomics life sciences and the current efforts to develop systems diagnostics for personalized medicine. The majority of antibody microarray experiments are fluorescence-based, which utilizes a scanner to convert target signals into image files for subsequent quantification. Certain scan parameters such as the laser power and photomultiplier tube gain (PMT) can influence the readout of fluorescent intensities and thus may affect data quantitation. To date, however, there is no consensus of how to determine the optimal settings of microarray scanners. Here we show that different settings of the laser power and PMT not only affect the signal intensities but also the accuracy of antibody microarray experiments. More importantly, we demonstrate an experimental approach using two fluorescent dyes to determine optimal settings of scan parameters for microarray experiments. These measures provide added quality control of microarray experiments, and thus help to improve the accuracy of quantitative outcome in microarray experiments in the above contexts.
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Affiliation(s)
- Qiang Gu
- 1 Department of Neurobiology and Anatomy, Wake Forest University School of Medicine , Medical Center Boulevard, Winston-Salem, North Carolina
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Abstract
Affinity proteomics, represented by antibody arrays, is a multiplex technology for high-throughput protein expression profiling of crude proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are individually deposited in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified using mainly fluorescence as the mode of detection. The binding pattern is then converted into a relative protein expression map, or protein atlas, delineating the composition of the sample at the molecular level. The technology provides unique opportunities for various applications, such as protein expression profiling, biomarker discovery, disease diagnostics, prognostics, evidence-based therapy selection, and disease monitoring. Here, we describe the generation and use of planar antibody arrays for serum protein profiling.
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Borrebaeck CAK, Sturfelt G, Wingren C. Recombinant antibody microarray for profiling the serum proteome of SLE. Methods Mol Biol 2014; 1134:67-78. [PMID: 24497355 DOI: 10.1007/978-1-4939-0326-9_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Systemic lupus erythematosus (SLE) is a severe autoimmune connective tissue disease. Our current knowledge about the serum proteome, or serum biomarker panels, reflecting disease and disease status is still very limited. Affinity proteomics, represented by recombinant antibody arrays, is a novel, multiplex technology for high-throughput protein expression profiling of crude serum proteomes in a highly specific, sensitive, and miniaturized manner. The antibodies are deposited one by one in an ordered pattern, an array, onto a solid support. Next, the sample is added, and any specifically bound proteins are detected and quantified. The binding pattern is then converted into a relative protein expression map, or protein map, deciphering the composition of the sample at the molecular level. The methodology provides unique opportunities for delineating serum biomarkers reflecting SLE, thus paving the way for improved diagnosis, classification, and prognosis.
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Affiliation(s)
- Carl A K Borrebaeck
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
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Gromov P, Gromova I, Olsen CJ, Timmermans-Wielenga V, Talman ML, Serizawa RR, Moreira JM. Tumor interstitial fluid — A treasure trove of cancer biomarkers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2259-70. [DOI: 10.1016/j.bbapap.2013.01.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/09/2013] [Accepted: 01/14/2013] [Indexed: 12/11/2022]
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Pauly F, Dexlin-Mellby L, Ek S, Ohlin M, Olsson N, Jirström K, Dictor M, Schoenmakers S, Borrebaeck CAK, Wingren C. Protein Expression Profiling of Formalin-Fixed Paraffin-Embedded Tissue Using Recombinant Antibody Microarrays. J Proteome Res 2013; 12:5943-53. [DOI: 10.1021/pr4003245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Frida Pauly
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Linda Dexlin-Mellby
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Sara Ek
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Niclas Olsson
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michael Dictor
- Department of Clinical Sciences, Pathology, Lund University, Skåne University Hospital, Lund, Sweden
| | | | - Carl A. K. Borrebaeck
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
| | - Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden
- CREATE Health, Lund University, Medicon Village, Lund, Sweden
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Wingren C. Novel type of protein chip for multiplex detection of autoantibodies. Expert Rev Proteomics 2013; 10:417-20. [PMID: 24088012 DOI: 10.1586/14789450.2013.842900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evaluation of: Akada J, Kamei S, Ito A et al. A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients. Proteome Sci. 11(1), 33 (2013). Unlocking the proteome and delivering biomarkers to the clinic will be critical for early and improved diagnosis and prognosis. Conventional protein microarrays have evolved as a promising proteomic technology with great potential for protein expression profiling in health and disease. In this study, Akada et al. explore a new type of protein chip, interfaced with a dual-color fluorescence-based read-out, for screening of autoantibodies in serum. Uniquely, the recombinant antigens were microarray adapted by molecular design to contain a five-cysteine tag for immobilization and green fluorescent protein for detection (color 1). The engineered antigens were immobilized on in-house-designed maleimide-incorporated diamond-like carbon substrates and subsequently heat treated in a solution of denaturing and reducing agents before any specifically bound serum autoantibodies were detected (color 2). The authors used a 4-plex array targeting hepatocellular carcinoma-related autoantibodies in the sera of hepatitis C virus-positive patients as model system to demonstrate proof-of-concept.
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Affiliation(s)
- Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, SE-22381 Lund, Sweden
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Knowledge-based identification of soluble biomarkers: hepatic fibrosis in NAFLD as an example. PLoS One 2013; 8:e56009. [PMID: 23405244 PMCID: PMC3566090 DOI: 10.1371/journal.pone.0056009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/04/2013] [Indexed: 01/01/2023] Open
Abstract
The discovery of biomarkers is often performed using high-throughput proteomics-based platforms and is limited to the molecules recognized by a given set of purified and validated antigens or antibodies. Knowledge-based, or systems biology, approaches that involve the analysis of integrated data, predominantly molecular pathways and networks may infer quantitative changes in the levels of biomolecules not included by the given assay from the levels of the analytes profiled. In this study we attempted to use a knowledge-based approach to predict biomarkers reflecting the changes in underlying protein phosphorylation events using Nonalcoholic Fatty Liver Disease (NAFLD) as a model. Two soluble biomarkers, CCL-2 and FasL, were inferred in silico as relevant to NAFLD pathogenesis. Predictive performance of these biomarkers was studied using serum samples collected from patients with histologically proven NAFLD. Serum levels of both molecules, in combination with clinical and demographic data, were predictive of hepatic fibrosis in a cohort of NAFLD patients. Our study suggests that (1) NASH-specific disruption of the kinase-driven signaling cascades in visceral adipose tissue lead to detectable changes in the levels of soluble molecules released into the bloodstream, and (2) biomarkers discovered in silico could contribute to predictive models for non-malignant chronic diseases.
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Souchelnytskyi S. INDIVIDUALIZATION OF CANCER TREATMENT: CONTRIBUTION OF OMICS TECHNOLOGIES TO CANCER DIAGNOSTIC. BIOTECHNOLOGIA ACTA 2013. [DOI: 10.15407/biotech6.04.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Progress and Trends in Complement Therapeutics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 735:1-22. [PMID: 22990692 DOI: 10.1007/978-1-4614-4118-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past few years have proven to be a highly successful and exciting period for the field of complement-directed drug discovery and development. Driven by promising experiences with the first marketed complement drugs, increased knowledge about the involvement of complement in health and disease, and improvements in structural and analytical techniques as well as animal models of disease, the field has seen a surge in creative approaches to therapeutically intervene at various stages of the cascade. An impressive panel of compounds that show promise in clinical trials is meanwhile being lined up in the pipelines of both small biotechnology and big pharmaceutical companies. Yet with this new focus on complement-targeted therapeutics, important questions concerning target selection, point and length of intervention, safety, and drug delivery emerge. In view of the diversity of the clinical disorders involving abnormal complement activity or regulation, which include both acute and chronic diseases and affect a wide range of organs, diverse yet specifically tailored therapeutic approaches may be needed to shift complement back into balance. This chapter highlights the key changes in the field that shape our current perception of complement-targeted drugs and provides a brief overview of recent strategies and emerging trends. Selected examples of complement-related diseases and inhibitor classes are highlighted to illustrate the diversity and creativity in field.
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Tang XW, Huang S, Wang M, Ji GZ, Fan ZN. Clinical significance of expression of Klotho and β-Catenin in esophageal squamous cell carcinoma. Shijie Huaren Xiaohua Zazhi 2012; 20:3305-3309. [DOI: 10.11569/wcjd.v20.i34.3305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the clinical significance of expression of Klotho and β-Catenin in esophageal carcinoma.
METHODS: Tissue microarray technique and immunohistochemistry were used to examine Klotho and β-Catenin expression in 75 esophageal carcinoma tissue specimens and matched tumor-adjacent esophageal tissue. Correlations between Klotho and β-Catenin expression and clinical and pathological features were then analyzed.
RESULTS: The positive rate of Klotho expression was significantly lower in esophageal carcinoma tissue than in tumor-adjacent tissue (14.9% vs 63.4%, P < 0.05). The expression of Klotho was correlated with tumor invasion and clinical stage (both P < 0.05). The positive rate of β-Catenin expression was significantly higher in esophageal carcinoma tissue than in tumor-adjacent tissue (80.0% vs 16.4%, P < 0.05). The expression of Klotho was correlated with lymph node metastasis and tumor clinical stage (r = -0.276, P < 0.05).
CONCLUSION: The positive rates of Klotho and β-Catenin expression differed significantly between esophageal carcinoma and tumor-adjacent tissue. Klotho and β-Catenin may be used as important markers for esophageal carcinoma and are helpful for prognosis prediction in esophageal carcinoma.
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Kayser K, Borkenfeld S, Djenouni A, Kayser G. History and structures of telecommunication in pathology, focusing on open access platforms. Diagn Pathol 2011; 6:110. [PMID: 22059444 PMCID: PMC3231812 DOI: 10.1186/1746-1596-6-110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 11/07/2011] [Indexed: 11/11/2022] Open
Abstract
Background Telecommunication has matured to a broadly applied tool in diagnostic pathology. Technology and Systems Contemporary with the development of fast electronic communication lines (Integrated digital network services (ISDN), broad band connections, and fibre optics, as well as the digital imaging technology (digital camera), telecommunication in tissue - based diagnosis (telepathology) has matured. Open access (internet) and server - based communication have induced the development of specific medical information platforms, such as iPATH, UICC-TPCC (telepathology consultation centre of the Union International against Cancer), or the Armed Forces Institute of Pathology (AFIP) teleconsultation system. They have been closed, and are subject to be replaced by specific open access forums (Medical Electronic Expert Communication System (MECES) with embedded virtual slide (VS) technology). MECES uses php language, data base driven mySqL architecture, X/L-AMPP infrastructure, and browser friendly W3C conform standards. Experiences The server - based medical communication systems (AFIP, iPATH, UICC-TPCC) have been reported to be a useful and easy to handle tool for expert consultation. Correct sampling and evaluation of transmitted still images by experts reported revealed no or only minor differences to the original images and good practice of the involved experts. β tests with the new generation medical expert consultation systems (MECES) revealed superior results in terms of performance, still image viewing, and system handling, especially as this is closely related to the use of so - called social forums (facebook, youtube, etc.). Benefits and Expectations In addition to the acknowledged advantages of the former established systems (assistance of pathologists working in developing countries, diagnosis confirmation, international information exchange, etc.), the new generation offers additional benefits such as acoustic information transfer, assistance in image screening, VS technology, and teaching in diagnostic sampling, judgement, and verification.
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