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Borgmann DM, Mayr S, Polin H, Schaller S, Dorfer V, Obritzberger L, Endmayr T, Gabriel C, Winkler SM, Jacak J. Single Molecule Fluorescence Microscopy and Machine Learning for Rhesus D Antigen Classification. Sci Rep 2016; 6:32317. [PMID: 27580632 PMCID: PMC5007495 DOI: 10.1038/srep32317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/02/2016] [Indexed: 01/24/2023] Open
Abstract
In transfusion medicine, the identification of the Rhesus D type is important to prevent anti-D immunisation in Rhesus D negative recipients. In particular, the detection of the very low expressed DEL phenotype is crucial and hence constitutes the bottleneck of standard immunohaematology. The current method of choice, adsorption-elution, does not provide unambiguous results. We have developed a complementary method of high sensitivity that allows reliable identification of D antigen expression. Here, we present a workflow composed of high-resolution fluorescence microscopy, image processing, and machine learning that - for the first time - enables the identification of even small amounts of D antigen on the cellular level. The high sensitivity of our technique captures the full range of D antigen expression (including D+, weak D, DEL, D-), allows automated population analyses, and results in classification test accuracies of up to 96%, even for very low expressed phenotypes.
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Affiliation(s)
- Daniela M. Borgmann
- University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232 Hagenberg, Austria
| | - Sandra Mayr
- University of Applied Sciences Upper Austria, School of Applied Health and Social Sciences, Garnisonstrasse 21, 4020 Linz, Austria
| | - Helene Polin
- Red Cross Transfusion Service for Upper Austria, Krankenhausstrasse 7, 4020 Linz, Austria
| | - Susanne Schaller
- University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232 Hagenberg, Austria
| | - Viktoria Dorfer
- University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232 Hagenberg, Austria
| | - Lisa Obritzberger
- University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232 Hagenberg, Austria
| | - Tanja Endmayr
- University of Applied Sciences Upper Austria, School of Applied Health and Social Sciences, Garnisonstrasse 21, 4020 Linz, Austria
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, Krankenhausstrasse 7, 4020 Linz, Austria
| | - Stephan M. Winkler
- University of Applied Sciences Upper Austria, School of Informatics, Communications and Media, Softwarepark 11, 4232 Hagenberg, Austria
| | - Jaroslaw Jacak
- University of Applied Sciences Upper Austria, School of Applied Health and Social Sciences, Garnisonstrasse 21, 4020 Linz, Austria
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2
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Ren CL, Schlapak R, Hager R, Szleifer I, Howorka S. Molecular and Thermodynamic Factors Explain the Passivation Properties of Poly(ethylene glycol)-Coated Substrate Surfaces against Fluorophore-Labeled DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11491-11501. [PMID: 26439134 DOI: 10.1021/acs.langmuir.5b02674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Poly(ethylene glycol) (PEG) nanofilms are used to avert the nonspecific binding of biomolecules on substrate surfaces in biomedicine and bioanalysis including modern fluorescence-based DNA sensing and sequencing chips. A fundamental and coherent understanding of the interactions between fluorophore-tagged DNA, PEG-films, and substrates in terms of molecular and energetic factors is, however, missing. Here we explore a large parameter space to elucidate how PEG layers passivate metal oxide surfaces against Cy3-labeled DNA probes. The driving force for probe adsorption is found to be the affinity of the fluorophore to the substrate, while the high-quality PEG films prevent adsorption to bare ITO surfaces. The amount of nonrepelled, surface-bound DNA strongly depends on oligonucleotide size, PEG chain length, and incubation temperature. To explain these observations, we develop an experimentally validated theory to provide a microscopic picture of the PEG layer and show that adsorbed DNA molecules reside within the film by end-tethering the fluorophore to the ITO surface. To compensate for the local accumulation of negatively charged DNA, counterions condense on the adsorbed probes within the layer. The model furthermore explains that surface passivation is governed by the interdependence of molecular size, conformation, charge, ion condensation, and environmental conditions. We finally report for the first time on the detailed thermodynamic values that show how adsorption results from a balance between large opposing energetic factors. The insight of our study can be applied to rationally engineer PEG nanolayers for improved functional performance in DNA analysis schemes and may be expanded to other polymeric thin films.
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Affiliation(s)
- Chun-lai Ren
- National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University , Nanjing 210093, China
| | | | - Roland Hager
- Center for Advanced Bioanalysis GmbH, Linz, Austria
| | - Igal Szleifer
- Department of Biomedical Engineering, Department of Chemistry and Chemistry of Life Processes Institute, Northwestern University , Evanston, Illinois 60208, United States
| | - Stefan Howorka
- Center for Advanced Bioanalysis GmbH, Linz, Austria
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London , London, United Kingdom
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3
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Bissonnette L, Bergeron MG. Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine. Expert Rev Mol Diagn 2014; 6:433-50. [PMID: 16706745 DOI: 10.1586/14737159.6.3.433] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.
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Affiliation(s)
- Luc Bissonnette
- Département de Biologie Médicale (Microbiologie), Faculté de Médecine, Université Laval, Québec City, Canada.
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4
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Mörwald H, Wurm S, Crailsheim K, Wechselberger C. Prion protein facilitates hormone-induced differentiation of mammary gland epithelial cells. Biochem Biophys Res Commun 2007; 360:746-51. [PMID: 17631862 DOI: 10.1016/j.bbrc.2007.06.154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Accepted: 06/25/2007] [Indexed: 10/23/2022]
Abstract
Expression of prion protein has been reported for a variety of cell types including neuronal cells, haematopoietic stem cells, lymphocytes, fibroblasts, and epithelial cells. However, the characterization of the physiological roles exhibited by this protein is still in progress and multiple biological functions have been described to date. In this study we have characterized the contribution of prion protein during hormone-induced differentiation of mouse mammary gland epithelial cells. We present evidence that prion expression enhances the differentiation-capabilities of these cells indicating novel physiological roles during mammary gland development. In addition we were able to demonstrate the presence of prion molecules resistant to mild proteinase digestion in differentiated mammary gland epithelial cells. This represents the first report of proteinase-resistant prion proteins in a physiological, non-pathogenic context.
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Affiliation(s)
- Helene Mörwald
- Upper Austrian Research GmbH, Center for Biomedical Nanotechnology, Scharitzerstrasse 6-8, 4020 Linz, Austria
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5
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Paar C, Wurm S, Pfarr W, Sonnleitner A, Wechselberger C. Prion protein resides in membrane microclusters of the immunological synapse during lymphocyte activation. Eur J Cell Biol 2007; 86:253-64. [PMID: 17449139 DOI: 10.1016/j.ejcb.2007.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/19/2007] [Accepted: 03/07/2007] [Indexed: 12/22/2022] Open
Abstract
Expression of prion protein (PrP) has been reported for a variety of cell types including neuronal cells, haematopoietic stem cells, antigen-presenting cells, as well as lymphocytes. However, besides this widespread occurrence little is known about the physiological roles exhibited by this enigmatic protein. In this study, the contribution of PrP to the classical T-lymphocyte activation process was characterized by clustering the T-cell receptor component CD3epsilon as well as PrP with soluble and surface-immobilized antibodies, respectively. We present evidence that PrP is a component of signaling structures recently described as plasma membrane microclusters established during T-lymphocyte activation. The formation of immunological synapses, however, did not depend on the presence of PrP as proven by siRNA knockdown experiments, indicating very subtle physiological roles of PrP in vivo within the immune system.
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Affiliation(s)
- Christian Paar
- Upper Austrian Research GmbH, Center for Biomedical Nanotechnology, Scharitzerstrasse 6-8, A-4020 Linz, Austria
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6
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Wurm S, Wechselberger C. Prion protein modifies TGF-β induced signal transduction. Biochem Biophys Res Commun 2006; 349:525-32. [PMID: 16942751 DOI: 10.1016/j.bbrc.2006.08.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 08/11/2006] [Indexed: 10/24/2022]
Abstract
Members of the transforming growth factor-beta (TGF-beta) superfamily regulate a multitude of cellular processes as well as the expression of various proteins such as, e.g., matrix metalloproteinases (MMPs). These endopeptidases selectively degrade components of the extracellular matrix as well as non-matrix substrates like growth factors and cell surface receptors. MMPs are activated during embryonic development, morphogenesis, and tissue resorption/remodeling as well as in pathological conditions such as deranged wound healing and cancer metastasis. In this report we demonstrate that over-expression of cellular prion protein in mouse mammary gland epithelial cells is able to modulate TGF-beta induced signal transduction leading to a synergistic increase of secreted MMP-2 activity. This correlates with elevated substrate detachment of cells grown as an epithelial monolayer as well as interfering with morphogenesis of cells cultured in a three-dimensional collagen type I matrix.
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Affiliation(s)
- Susanne Wurm
- Upper Austrian Research GmbH, Center for Biomedical Nanotechnology, 4020 Linz, Austria
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Pammer P, Schlapak R, Sonnleitner M, Ebner A, Zhu R, Hinterdorfer P, Höglinger O, Schindler H, Howorka S. Nanopatterning of biomolecules with microscale beads. Chemphyschem 2006; 6:900-3. [PMID: 15884074 DOI: 10.1002/cphc.200400526] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Patrick Pammer
- Center for Biomedical Nanotechnology, Upper Austrian Research GmbH, Scharitzerstr. 6-8/4, 4020 Linz, Austria
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8
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Schlapak R, Pammer P, Armitage D, Zhu R, Hinterdorfer P, Vaupel M, Frühwirth T, Howorka S. Glass surfaces grafted with high-density poly(ethylene glycol) as substrates for DNA oligonucleotide microarrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:277-85. [PMID: 16378432 DOI: 10.1021/la0521793] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Surfaces carrying a dense layer of poly(ethylene glycol) (PEG) were prepared, characterized, and tested as substrates for DNA oligonucleotide microarrays. PEG bis(amine) with a molecular weight of 2000 was grafted onto silanized glass slides bearing aldehyde groups. After grafting, the terminal amino groups of the PEG layer were derivatized with the heterobifunctional cross-linker succinimidyl 4-[p-maleimidophenyl]butyrate to permit the immobilization of thiol-modified DNA oligonucleotides. The stepwise chemical modification was validated with X-ray photoelectron spectroscopy. Goniometry indicated that the PEG grafting procedure reduced surface inhomogeneities present after the silanization step, while atomic force microscopy and ellipsometry confirmed that the PEG layer was dense and monomolecular. Hybridization assays using DNA oligonucleotides and fluorescence imaging showed that PEG grafting improved the yield in hybridization 4-fold compared to non-PEGylated maleimide-derivatized surfaces. In addition, the PEG layer reduced the nonspecific adsorption of DNA by a factor of up to 13, demonstrating that surfaces with a dense PEG layer represent suitable substrates for DNA oligonucleotide microarrays.
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Affiliation(s)
- Robert Schlapak
- Center for Biomedical Nanotechnology, Upper Austrian Research GmbH, A-4020 Linz, Austria
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9
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Wurm S, Paar C, Sonnleitner A, Sonnleitner M, Höglinger O, Romanin C, Wechselberger C. Co-localization of CD3 and prion protein in Jurkat lymphocytes after hypothermal stimulation. FEBS Lett 2004; 566:121-5. [PMID: 15147880 DOI: 10.1016/j.febslet.2004.03.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2004] [Revised: 03/31/2004] [Accepted: 03/31/2004] [Indexed: 11/16/2022]
Abstract
While long-term effects of temperature treatment in respect of, e.g., gene-expression and cellular function have already been studied in some detail, nothing is known on the physiological responses of lymphocytes during short-term hypothermal shifts. In this report, we characterized the effects of such a stimulation using the human lymphocyte cell line Jurkat E6.1 and present evidence that warming from 4 to 37 degrees C for only 2 min is sufficient to cause co-localization of CD3, prion protein and the lipid-raft ganglioside GM1 paralleling lymphocyte activation as observed by Ca(2+) mobilization and mitogen-activated protein kinase-phosphorylation.
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Affiliation(s)
- Susanne Wurm
- Upper Austrian Research GmbH, Center for Biomedical Nanotechnology, Scharitzerstr. 6-8, 4020 Linz, Austria
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10
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2448450 DOI: 10.1002/cfg.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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