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Rebenku I, Lloyd CB, Szöllősi J, Vereb G. Pixel-by-pixel autofluorescence corrected FRET in fluorescence microscopy improves accuracy for samples with spatially varied autofluorescence to signal ratio. Sci Rep 2023; 13:2934. [PMID: 36804608 PMCID: PMC9941493 DOI: 10.1038/s41598-023-30098-w] [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: 08/23/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The actual interaction between signaling species in cellular processes is often more important than their expression levels. Förster resonance energy transfer (FRET) is a popular tool for studying molecular interactions, since it is highly sensitive to proximity in the range of 2-10 nm. Spectral spillover-corrected quantitative (3-cube) FRET is a cost effective and versatile approach, which can be applied in flow cytometry and various modalities of fluorescence microscopy, but may be hampered by varying levels of autofluorescence. Here, we have implemented pixel-by-pixel autofluorescence correction in microscopy FRET measurements, exploiting cell-free calibration standards void of autofluorescence that allow the correct determination of all spectral spillover factors. We also present an ImageJ/Fiji plugin for interactive analysis of single images as well as automatic creation of quantitative FRET efficiency maps from large image sets. For validation, we used bead and cell based FRET models covering a range of signal to autofluorescence ratios and FRET efficiencies and compared the approach with conventional average autofluorescence/background correction. Pixel-by-pixel autofluorescence correction proved to be superior in the accuracy of results, particularly for samples with spatially varying autofluorescence and low fluorescence to autofluorescence ratios, the latter often being the case for physiological expression levels.
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Affiliation(s)
- István Rebenku
- grid.7122.60000 0001 1088 8582Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary ,grid.7122.60000 0001 1088 8582ELKH-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Cameron B. Lloyd
- grid.7122.60000 0001 1088 8582Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - János Szöllősi
- grid.7122.60000 0001 1088 8582Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary ,grid.7122.60000 0001 1088 8582ELKH-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary. .,ELKH-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary. .,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, Debrecen, 4032, Hungary.
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2
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Glöckner N, zur Oven-Krockhaus S, Rohr L, Wackenhut F, Burmeister M, Wanke F, Holzwart E, Meixner AJ, Wolf S, Harter K. Three-Fluorophore FRET Enables the Analysis of Ternary Protein Association in Living Plant Cells. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11192630. [PMID: 36235497 PMCID: PMC9571070 DOI: 10.3390/plants11192630] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/19/2022] [Accepted: 09/24/2022] [Indexed: 05/13/2023]
Abstract
Protein-protein interaction studies provide valuable insights into cellular signaling. Brassinosteroid (BR) signaling is initiated by the hormone-binding receptor Brassinosteroid Insensitive 1 (BRI1) and its co-receptor BRI1 Associated Kinase 1 (BAK1). BRI1 and BAK1 were shown to interact independently with the Receptor-Like Protein 44 (RLP44), which is implicated in BRI1/BAK1-dependent cell wall integrity perception. To demonstrate the proposed complex formation of BRI1, BAK1 and RLP44, we established three-fluorophore intensity-based spectral Förster resonance energy transfer (FRET) and FRET-fluorescence lifetime imaging microscopy (FLIM) for living plant cells. Our evidence indicates that RLP44, BRI1 and BAK1 form a ternary complex in a distinct plasma membrane nanodomain. In contrast, although the immune receptor Flagellin Sensing 2 (FLS2) also forms a heteromer with BAK1, the FLS2/BAK1 complexes are localized to other nanodomains. In conclusion, both three-fluorophore FRET approaches provide a feasible basis for studying the in vivo interaction and sub-compartmentalization of proteins in great detail.
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Affiliation(s)
- Nina Glöckner
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Sven zur Oven-Krockhaus
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Leander Rohr
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Frank Wackenhut
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Moritz Burmeister
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Eleonore Holzwart
- Centre for Organismal Studies (COS), University of Heidelberg, 69117 Heidelberg, Germany
| | - Alfred J. Meixner
- Institute for Physical & Theoretical Chemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sebastian Wolf
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69117 Heidelberg, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-(0)-7071-2972605
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Lim J, Petersen M, Bunz M, Simon C, Schindler M. Flow cytometry based-FRET: basics, novel developments and future perspectives. Cell Mol Life Sci 2022; 79:217. [PMID: 35352201 PMCID: PMC8964568 DOI: 10.1007/s00018-022-04232-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022]
Abstract
Förster resonance energy transfer (FRET) is a widespread technology used to analyze and quantify protein interactions in multiple settings. While FRET is traditionally measured by microscopy, flow cytometry based-FRET is becoming popular within the last decade and more commonly used. Flow cytometry based-FRET offers the possibility to assess FRET in a short time-frame in a high number of cells thereby allowing stringent and statistically robust quantification of FRET in multiple samples. Furthermore, established, simple and easy to implement gating strategies facilitate the adaptation of flow cytometry based-FRET measurements to most common flow cytometers. We here summarize the basics of flow cytometry based-FRET, highlight recent novel developments in this field and emphasize on exciting future perspectives.
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Affiliation(s)
- JiaWen Lim
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Moritz Petersen
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Maximilian Bunz
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Claudia Simon
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany.
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Szabó Á, Szendi-Szatmári T, Szöllősi J, Nagy P. Quo vadis FRET? Förster's method in the era of superresolution. Methods Appl Fluoresc 2020; 8:032003. [PMID: 32521530 DOI: 10.1088/2050-6120/ab9b72] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although the theoretical foundations of Förster resonance energy transfer (FRET) were laid in the 1940s as part of the quantum physical revolution of the 20th century, it was only in the 1970s that it made its way to biology as a result of the availability of suitable measuring and labeling technologies. Thanks to its ease of application, FRET became widely used for studying molecular associations on the nanometer scale. The development of superresolution techniques at the turn of the millennium promised an unprecedented insight into the structure and function of molecular complexes. Without downplaying the significance of superresolution microscopies this review expresses our view that FRET is still a legitimate tool in the armamentarium of biologists for studying molecular associations since it offers distinct advantages and overcomes certain limitations of superresolution approaches.
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Affiliation(s)
- Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary. MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary
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5
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Weinberg F, Han MKL, Dahmke IN, Del Campo A, de Jonge N. Anti-correlation of HER2 and focal adhesion complexes in the plasma membrane. PLoS One 2020; 15:e0234430. [PMID: 32511274 PMCID: PMC7279600 DOI: 10.1371/journal.pone.0234430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/25/2020] [Indexed: 11/18/2022] Open
Abstract
Excess presence of the human epidermal growth factor receptor 2 (HER2) as well as of the focal adhesion protein complexes are associated with increased proliferation, migratory, and invasive behavior of cancer cells. A cross-regulation between HER2 and integrin signaling pathways has been found, but the exact mechanism remains elusive. Here, we investigated whether HER2 colocalizes with focal adhesion complexes on breast cancer cells overexpressing HER2. For this purpose, vinculin or talin green fluorescent protein (GFP) fusion proteins, both key constituents of focal adhesions, were expressed in breast cancer cells. HER2 was either extracellularly or intracellularly labeled with fluorescent quantum dots nanoparticles (QDs). The cell-substrate interface was analyzed at the location of the focal adhesions by means of total internal reflection fluorescent microscopy or correlative fluorescence- and scanning transmission electron microscopy. Expression of HER2 at the cell-substrate interface was only observed upon intracellular labeling, and was heterogeneous with both HER2-enriched and -low regions. In contrast to an expected enrichment of HER2 at focal adhesions, an anti-correlated expression pattern was observed for talin and HER2. Our findings suggest a spatial anti-correlation between HER2 and focal adhesion complexes for adherent cells.
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Affiliation(s)
| | | | | | - Aránzazu Del Campo
- INM – Leibniz Institute for New Materials, Saarbrücken, Germany
- Department of Chemistry, University of Saarland, Saarbrücken, Germany
| | - Niels de Jonge
- INM – Leibniz Institute for New Materials, Saarbrücken, Germany
- Department of Physics, University of Saarland, Saarbrücken, Germany
- * E-mail:
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6
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Abstract
In the past decades, investigation of protein-protein interactions in situ in living or intact cells has gained expanding importance as structure/function relationships proposed from bulk biochemistry and molecular modeling experiments required confirmation at the cellular level. Förster (fluorescence) resonance energy transfer (FRET)-based methods are excellent tools for determining proximity and supramolecular organization of biomolecules at the cell surface or inside the cell. This could well be the basis for the increasing popularity of FRET. In fact, the number of publications exploiting FRET has exploded since the turn of the millennium. Interestingly, most applications are microscope-based, and only a fraction employs flow cytometry, even though the latter offers great statistical power owed to the potentially huge number of individually measured cells. However, with the increased availability of multi-laser flow cytometers, strategies to obtain absolute FRET efficiencies can now be relatively facilely implemented. In this chapter, we intend to provide generally useable protocols for measuring FRET in flow cytometry. After a concise theoretical introduction, recipes are provided for successful labeling techniques and measurement approaches. The simple, quenching-based population-level measurement, the classic ratiometric, intensity-based technique providing cell-by-cell actual FRET efficiencies, and a more advanced version of the latter, allowing for cell-by-cell autofluorescence correction are described. An Excel macro pre-loaded with spectral data of the most commonly used fluorophores is also provided for easy calculation of average FRET efficiencies. Finally, points of caution are given to help design proper experiments and critically interpret the results.
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Affiliation(s)
- László Ujlaky-Nagy
- Department of Biophysics and Cell Biology, MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, Faculty of Pharmacy, University of Debrecen, Debrecen, Hungary.
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7
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Distinct ErbB2 receptor populations differentially interact with beta1 integrin in breast cancer cell models. PLoS One 2017; 12:e0174230. [PMID: 28306722 PMCID: PMC5357064 DOI: 10.1371/journal.pone.0174230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/05/2017] [Indexed: 11/30/2022] Open
Abstract
ErbB2 is a member of the ErbB family of tyrosine kinase receptors that plays a major role in breast cancer progression. Located at the plasma membrane, ErbB2 forms large clusters in spite of the presence of growth factors. Beta1 integrin, membrane receptor of extracellular matrix proteins, regulates adhesion, migration and invasiveness of breast cancer cells. Physical interaction between beta1 integrin and ErbB2 has been suggested although published data are contradictory. The aim of the present work was to study the interaction between ErbB2 and beta1 integrin in different scenarios of expression and activation. We determined that beta1 integrin and ErbB2 colocalization is dependent on the expression level of both receptors exclusively in adherent cells. In suspension cells, lack of focal adhesions leave integrins free to diffuse on the plasma membrane and interact with ErbB2 even at low expression levels of both receptors. In adherent cells, high expression of beta1 integrin leaves unbound receptors outside focal complexes that diffuse within the plasma membrane and interact with ErbB2 membrane domains. Superresolution imaging showed the existence of two distinct populations of ErbB2: a major population located in large clusters and a minor population outside these structures. Upon ErbB2 overexpression, receptors outside large clusters can freely diffuse at the membrane and interact with integrins. These results reveal how expression levels of beta1 integrin and ErbB2 determine their frequency of colocalization and show that extracellular matrix proteins shape membrane clusters distribution, regulating ErbB2 and beta1 integrin activity in breast cancer cells.
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8
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Szöllősi J, Vereb G, Nagy P. The flow of events: How the sequence of molecular interactions is seen by the latest, user-friendly high throughput flow cytometric FRET. Cytometry A 2016; 89:881-885. [DOI: 10.1002/cyto.a.22994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/12/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Affiliation(s)
- János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine; University of Debrecen; Debrecen Hungary
- MTA-DE Cell Biology and Signaling Research Group, Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen; Debrecen Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine; University of Debrecen; Debrecen Hungary
| | - Péter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine; University of Debrecen; Debrecen Hungary
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9
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Steffens A, Bräutigam A, Jakoby M, Hülskamp M. The BEACH Domain Protein SPIRRIG Is Essential for Arabidopsis Salt Stress Tolerance and Functions as a Regulator of Transcript Stabilization and Localization. PLoS Biol 2015; 13:e1002188. [PMID: 26133670 PMCID: PMC4489804 DOI: 10.1371/journal.pbio.1002188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
Abstract
Members of the highly conserved class of BEACH domain containing proteins (BDCPs) have been established as broad facilitators of protein-protein interactions and membrane dynamics in the context of human diseases like albinism, bleeding diathesis, impaired cellular immunity, cancer predisposition, and neurological dysfunctions. Also, the Arabidopsis thaliana BDCP SPIRRIG (SPI) is important for membrane integrity, as spi mutants exhibit split vacuoles. In this work, we report a novel molecular function of the BDCP SPI in ribonucleoprotein particle formation. We show that SPI interacts with the P-body core component DECAPPING PROTEIN 1 (DCP1), associates to mRNA processing bodies (P-bodies), and regulates their assembly upon salt stress. The finding that spi mutants exhibit salt hypersensitivity suggests that the local function of SPI at P-bodies is of biological relevance. Transcriptome-wide analysis revealed qualitative differences in the salt stress-regulated transcriptional response of Col-0 and spi. We show that SPI regulates the salt stress-dependent post-transcriptional stabilization, cytoplasmic agglomeration, and localization to P-bodies of a subset of salt stress-regulated mRNAs. Finally, we show that the PH-BEACH domains of SPI and its human homolog FAN (Factor Associated with Neutral sphingomyelinase activation) interact with DCP1 isoforms from plants, mammals, and yeast, suggesting the evolutionary conservation of an association of BDCPs and P-bodies.
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Affiliation(s)
| | - Andrea Bräutigam
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Düsseldorf, Germany
- Plant Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- * E-mail:
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Radbruch H, Bremer D, Mothes R, Günther R, Rinnenthal JL, Pohlan J, Ulbricht C, Hauser AE, Niesner R. Intravital FRET: Probing Cellular and Tissue Function in Vivo. Int J Mol Sci 2015; 16:11713-27. [PMID: 26006244 PMCID: PMC4463726 DOI: 10.3390/ijms160511713] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/13/2015] [Indexed: 12/02/2022] Open
Abstract
The development of intravital Förster Resonance Energy Transfer (FRET) is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo-ratiometrically and time-resolved by fluorescence lifetime imaging-and show their concrete application in the context of neuroinflammation in adult mice.
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Affiliation(s)
- Helena Radbruch
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
| | - Daniel Bremer
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Ronja Mothes
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Robert Günther
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | | | - Julian Pohlan
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Carolin Ulbricht
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
- Immundynamics and Intravital Microscopy, Charité-University of Medicine, Berlin 10117, Germany.
| | - Anja E Hauser
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
- Immundynamics and Intravital Microscopy, Charité-University of Medicine, Berlin 10117, Germany.
| | - Raluca Niesner
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
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Shrestha D, Jenei A, Nagy P, Vereb G, Szöllősi J. Understanding FRET as a research tool for cellular studies. Int J Mol Sci 2015; 16:6718-56. [PMID: 25815593 PMCID: PMC4424985 DOI: 10.3390/ijms16046718] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/18/2015] [Indexed: 01/06/2023] Open
Abstract
Communication of molecular species through dynamic association and/or dissociation at various cellular sites governs biological functions. Understanding these physiological processes require delineation of molecular events occurring at the level of individual complexes in a living cell. Among the few non-invasive approaches with nanometer resolution are methods based on Förster Resonance Energy Transfer (FRET). FRET is effective at a distance of 1-10 nm which is equivalent to the size of macromolecules, thus providing an unprecedented level of detail on molecular interactions. The emergence of fluorescent proteins and SNAP- and CLIP- tag proteins provided FRET with the capability to monitor changes in a molecular complex in real-time making it possible to establish the functional significance of the studied molecules in a native environment. Now, FRET is widely used in biological sciences, including the field of proteomics, signal transduction, diagnostics and drug development to address questions almost unimaginable with biochemical methods and conventional microscopies. However, the underlying physics of FRET often scares biologists. Therefore, in this review, our goal is to introduce FRET to non-physicists in a lucid manner. We will also discuss our contributions to various FRET methodologies based on microscopy and flow cytometry, while describing its application for determining the molecular heterogeneity of the plasma membrane in various cell types.
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Affiliation(s)
- Dilip Shrestha
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary.
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen 4032, Hungary.
| | - Attila Jenei
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary.
| | - Péter Nagy
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary.
| | - György Vereb
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary.
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen 4032, Hungary.
| | - János Szöllősi
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Nagyerdei Krt. 98, Debrecen 4032, Hungary.
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, Debrecen 4032, Hungary.
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12
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Szalóki N, Doan-Xuan QM, Szöllősi J, Tóth K, Vámosi G, Bacsó Z. High throughput FRET analysis of protein-protein interactions by slide-based imaging laser scanning cytometry. Cytometry A 2013; 83:818-29. [DOI: 10.1002/cyto.a.22315] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 04/24/2013] [Accepted: 05/12/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Nikoletta Szalóki
- Department of Biophysics and Cell Biology; Medical and Health Science Center, Research Center for Molecular Medicine, University of Debrecen; Nagyerdei krt. 98; H-4032; Debrecen; Hungary
| | - Quang Minh Doan-Xuan
- Department of Biophysics and Cell Biology; Medical and Health Science Center, Research Center for Molecular Medicine, University of Debrecen; Nagyerdei krt. 98; H-4032; Debrecen; Hungary
| | | | - Katalin Tóth
- German Cancer Research Center (DKFZ), Biophysics of Macromolecules (B040); Im Neuenheimer Feld 580; D-69120; Heidelberg; Germany
| | - György Vámosi
- Department of Biophysics and Cell Biology; Medical and Health Science Center, Research Center for Molecular Medicine, University of Debrecen; Nagyerdei krt. 98; H-4032; Debrecen; Hungary
| | - Zsolt Bacsó
- Department of Biophysics and Cell Biology; Medical and Health Science Center, Research Center for Molecular Medicine, University of Debrecen; Nagyerdei krt. 98; H-4032; Debrecen; Hungary
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13
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Petrás M, Lajtos T, Friedländer E, Klekner A, Pintye E, Feuerstein BG, Szöllosi J, Vereb G. Molecular interactions of ErbB1 (EGFR) and integrin-β1 in astrocytoma frozen sections predict clinical outcome and correlate with Akt-mediated in vitro radioresistance. Neuro Oncol 2013; 15:1027-40. [PMID: 23595626 DOI: 10.1093/neuonc/not046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Treatment of astrocytoma is frequently hampered by radioresistance of the tumor. In addition to overexpression of ErbB1/EGFR, functional crosstalk between receptor tyrosine kinases and cell adhesion molecules may also contribute to therapy resistance. METHODS Acceptor photobleaching FRET was implemented on frozen sections of clinical astrocytoma to check the role of ErbB1-integrin-β1 interaction. U251 glioma subclones were obtained by introducing extra CHR7 material or the ErbB1 gene to test the relevance and mechanism of this interaction in vitro. RESULTS Grade IV tumors showed higher ErbB1 and integrin-β1 expression and greater ErbB1-integrin-β1 heteroassociation than did grade II tumors. Of these, the extent of molecular association was a single determinant of tumor grade and prognosis in stepwise logistic regression. In vitro, integrin-β1 was upregulated, and radiosensitivity was diminished by ectopic ErbB1 expression. Great excess of ErbB1 provided colony forming advantage over medium excess but did not yield better radiation resistance or faster proliferation and decreased to medium level over time, whereas integrin-β1 levels remained elevated and defined the extent of radioresistance. Increased expression of ErbB1 and integrin-β1 was paralleled by decreasing ErbB1 homoassociation and increasing ErbB1-integrin-β1 heteroassociation. Microscopic two-sided FRET revealed that pixels with higher ErbB1-integrin-β1 heteroassociation exhibited lowed ErbB1 homoassociation, indicating competition for association partners among these molecules. Boosted Akt phosphorylation response to EGF accompanied this shift toward heteroassociation, and the consequentially increased radioresistance could be reverted by inhibiting PI3K. CONCLUSION The clinically relevant ErbB1-integrin-β1 heteroassociation may be used as a target of both predictive diagnostics and molecular therapy.
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Affiliation(s)
- Miklós Petrás
- Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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15
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Fábián Á, Horváth G, Vámosi G, Vereb G, Szöllősi J. TripleFRET measurements in flow cytometry. Cytometry A 2013; 83:375-85. [PMID: 23504771 DOI: 10.1002/cyto.a.22267] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 12/18/2012] [Accepted: 01/23/2013] [Indexed: 02/01/2023]
Abstract
A frequently used method for viewing protein interactions and conformation, Förster (fluorescence) resonance energy transfer (FRET), has traditionally been restricted to two fluorophores. Lately, several methods have been introduced to expand FRET methods to three species. We present a method that allows the determination of FRET efficiency in three-dye systems on a flow cytometer. TripleFRET accurately reproduces energy transfer efficiency values measured in two-dye systems, and it can indicate the presence of trimeric complexes, which is not possible with conventional FRET methods. We also discuss the interpretation of energy transfer values obtained with tripleFRET in relation to spatial distribution of labeled molecules, specifically addressing the limitations of using total energy transfer to determine molecular distance.
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Affiliation(s)
- Ákos Fábián
- Department of Biophysics and Cell Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
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16
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Roszik J, Tóth G, Szöllősi J, Vereb G. Validating pharmacological disruption of protein-protein interactions by acceptor photobleaching FRET imaging. Methods Mol Biol 2013; 986:165-178. [PMID: 23436412 DOI: 10.1007/978-1-62703-311-4_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Proteins are the major targets of drug discovery and many of the new drugs are designed to exert their effect by disrupting protein-protein interactions. Validation of the inhibition of molecular interactions is generally done by biochemical methods, however, these are often not feasible when the interaction is not stable enough. Fluorescence resonance energy transfer (FRET) is an excellent tool for determining direct molecular interactions between two molecules in the cell membrane or inside cells in their natural state. Although originally established as a flow cytometric approach, FRET has been adapted for microscopy, allowing for analysis of sub-cellular co-localization at the single cell level. In this chapter, we provide theoretical introduction to the phenomenon of FRET, and a protocol - including labeling techniques, measurement, and evaluation of microscopy images - of the simplest microscopic FRET approach, acceptor photobleaching FRET. This technique is generally usable for studying protein interactions and requires only a standard confocal laser scanning microscope. To demonstrate the value of image based FRET for testing pharmacological disruption of protein-protein interactions, we show how inhibition of the hetero-dimerization of ErbB2 and ErbB1 by the humanized monoclonal antibody pertuzumab can be validated using this technique.
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Affiliation(s)
- Janos Roszik
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, Hungary
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17
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Fábián ÁI, Rente T, Szöllosi J, Mátyus L, Jenei A. Strength in numbers: effects of acceptor abundance on FRET efficiency. Chemphyschem 2011; 11:3713-21. [PMID: 20936620 DOI: 10.1002/cphc.201000568] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fluorescence resonance energy transfer (FRET) is a strongly distance-dependent process between a donor and an acceptor molecule, which can be used for sensitive distance measurements and characterization of molecular interactions at the nanometer level. The original mathematical description of this process, however, is only valid for the interaction of one donor with one acceptor. This criterion is not always met, especially in biological systems, where multiple structures can interact simultaneously, often making distance estimations based on transfer efficiency values error-prone. Herein we investigate how the interaction of multiple acceptors and donors influences the transfer efficiency value in an intramolecular cellular FRET system by manipulating the fluorophore/protein ratio of the fluorophore-conjugated antibodies. We show that the labeling ratio of the acceptor has the largest influence on measured transfer efficiency and decreasing or increasing the acceptor labeling ratio can be utilized to manipulate the FRET response of the acceptor-donor pair and therefore is a tool for optimizing sensitivity of FRET measurements.
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Affiliation(s)
- Ákos I Fábián
- Department of Biophysics and Cell Biology, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
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18
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Abstract
Most cell death in vertebrates proceeds through the intrinsic pathway of apoptosis and results from unregulated increase of mitochondrial membrane permeability. Bcl2-associated X protein (Bax) and Bcl2-antagonist/killer protein (Bak), the effector proapoptotic members of the Bcl-2 family, are, in their active state, the principal accomplices for this permeabilization process. How exactly Bax and Bak are activated has been a matter of major investigation in the last decade, and suitable tools offered by quantitative cytometric methodologies have significantly contributed to the understanding of the function of Bcl-2 family members. Here, we review the most relevant findings in this field and highlight one common trait that has emerged from the diverse new theories: a crucial role in the control of Bax/Bak activation has to be attributed to the BH3-only subset of the Bcl-2 family. BH3-only proteins exert their proapoptotic activity by hierarchical and tightly tuned interactions with other Bcl-2 family members and operate as sensors of intracellular/extracellular death signals and vectors of information to the core apoptotic machinery. Given their essential role in apoptosis, BH3-only molecules are proposed as molecular targets for the cure of diseases associated with abnormal cell death, as in the case with neurodegenerative conditions. As well, they are explored as possible tools for cancer therapy, according to the concept that molecules mimicking the BH3 domain of these proteins could selectively and efficiently cooperate in the cell killing by chemotherapeutic drugs. A few BH3 mimetics are currently being tested in clinical trials of hematologic and solid tumors. Nevertheless, the knowledge about the cellular and molecular mechanisms that regulate responsiveness to BH3 therapy has to be further expanded and will benefit from recent advances in cytometric quantitative technologies.
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Affiliation(s)
- Fabio Ghiotto
- Department of Experimental Medicine, Human Anatomy Section, University of Genoa, Genoa 16132, Italy
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19
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Roszik J, Lisboa D, Szöllosi J, Vereb G. Evaluation of intensity-based ratiometric FRET in image cytometry--approaches and a software solution. Cytometry A 2009; 75:761-7. [PMID: 19591240 DOI: 10.1002/cyto.a.20747] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intensity-based ratiometric FRET (fluorescence resonance energy transfer) method is a powerful technique for following molecular interactions in living cells. Since it is not based on irreversibly destroying the donor or the acceptor fluorophores, the time course of changes in FRET efficiency values can be monitored by this method. ImageJ, a sophisticated software tool for many types of image processing allows users to extend it with programs for various purposes. Implementing intensity-based ratiometric FRET with ImageJ vastly enhances the applicability of the FRET method. We developed an efficient ImageJ plugin, RiFRET, which calculates FRET efficiency on a pixel-by-pixel basis from ratiometric FRET images. It allows the user to correct for channel cross-talk (bleed-through) and to calculate FRET from image stacks, i.e., from 3D data sets. Semiautomatic processing for larger datasets is also included in the program. Furthermore, several options for calibrating FRET efficiency calculations were tested and their applicability to various expression systems is discussed. Although the ratiometric FRET method is widely applied, our plugin is the first freely available software for evaluating such FRET data. The program is user friendly and provides reliable, standardized results.
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Affiliation(s)
- János Roszik
- Department of Biophysics and Cell Biology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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20
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Nagy P, Szöllősi J. Proximity or no proximity: That is the question-But the answer is more complex. Cytometry A 2009; 75:813-5. [DOI: 10.1002/cyto.a.20782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Leuchowius KJ, Weibrecht I, Landegren U, Gedda L, Söderberg O. Flow cytometricin situproximity ligation analyses of protein interactions and post-translational modification of the epidermal growth factor receptor family. Cytometry A 2009; 75:833-9. [DOI: 10.1002/cyto.a.20771] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Teodori L, Bushnell T, Campanella L, Tárnok A. GFP: from humble beginnings to Nobel winnings--the color that changed cytometry. Cytometry A 2009; 73A:1109-10. [PMID: 18985727 DOI: 10.1002/cyto.a.20673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Laura Teodori
- BAS-BIOTECMED, Italian Agency for New Technology, Energy and the Environment, Rome, Italy
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23
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Xu H, Eck PK, Baidoo KE, Choyke PL, Brechbiel MW. Toward preparation of antibody-based imaging probe libraries for dual-modality positron emission tomography and fluorescence imaging. Bioorg Med Chem 2009; 17:5176-81. [PMID: 19505829 PMCID: PMC2759299 DOI: 10.1016/j.bmc.2009.05.048] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 05/15/2009] [Accepted: 05/20/2009] [Indexed: 01/28/2023]
Abstract
Two novel imaging agents trastuzumab-Cy5.5-CHX-A''1 and cetuximab-Cy7-CHX-A''2, bearing both a chelating moiety (CHX-A'') for sequestering metallic radionuclides ((86)Y or (111)In) and the near infrared dye Cy5.5/Cy7, were prepared by a novel modular synthetic strategy as examples of dual-labeled, antibody-based imaging probe library. Fluorescent microscopy illustrated that 1 and 2 strongly bind to HER2-expressing cancer cells (e.g., NIH3T3-HER2(+), SKOV-3) and to EGFR-expressing cancer cells (e.g., A431), respectively, thereby demonstrating that the functionality of the targeting moiety is conserved. Hence, the described novel synthesis strategy can be applied to engineer other tumor-targeted monoclonal antibody based probes for multimodality imaging.
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Affiliation(s)
- Heng Xu
- Radioimmune & Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
| | - Peter K. Eck
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
| | - Kwamena E. Baidoo
- Radioimmune & Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
| | - Peter L. Choyke
- Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
| | - Martin W. Brechbiel
- Radioimmune & Inorganic Chemistry Section, Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1088, USA
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24
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Chapter 12 Reflections on FRET imaging. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s0075-7535(08)00012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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25
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Vámosi G, Damjanovich S, Szöllosi J. Dissecting interacting molecular populations by FRET. Cytometry A 2008; 73:681-4. [PMID: 18636568 DOI: 10.1002/cyto.a.20601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- György Vámosi
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, University of Debrecen, H-4032 Debrecen, Nagyerdei krt. 98, Hungary
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26
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Pentassuglia L, Sawyer DB. The role of Neuregulin-1beta/ErbB signaling in the heart. Exp Cell Res 2008; 315:627-37. [PMID: 18801360 DOI: 10.1016/j.yexcr.2008.08.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2008] [Revised: 08/19/2008] [Accepted: 08/19/2008] [Indexed: 01/13/2023]
Abstract
Products of the Neuregulin-1 (Nrg-1) gene, along with the ErbB family of receptor tyrosine kinases through which Nrg-1 ligands signal, play a critical role during cardiovascular development. Through studies of genetically manipulated mice, as well as studies in cells isolated from adult hearts, it appears that Nrg-1/ErbB signaling is an essential paracrine mediator of cell-cell interactions that not only regulates tissue organization during development, but also helps to maintain cardiac function throughout an organism's life. Studies in cells isolated from the heart demonstrate that Nrg-1 can activate a number of signaling pathways, which mediate cellular adaptations to stress in the myocardium. These observations provide insight as to why ErbB2-targeted cancer treatments have deleterious effects on cardiac function in some cancer patients. Moreover emerging data suggest that Nrg-1 ligands might be useful clinically to restore cardiac function after cardiac injury. In this review we will attempt to synthesize the literature behind this rapidly growing and exciting area of research.
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Affiliation(s)
- Laura Pentassuglia
- Cardiovascular Division, Department of Medicine, Vanderbilt University, Nashville, TN, USA
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27
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Roszik J, Szöllosi J, Vereb G. AccPbFRET: an ImageJ plugin for semi-automatic, fully corrected analysis of acceptor photobleaching FRET images. BMC Bioinformatics 2008; 9:346. [PMID: 18713453 PMCID: PMC2571114 DOI: 10.1186/1471-2105-9-346] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 08/19/2008] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The acceptor photobleaching fluorescence resonance energy transfer (FRET) method is widely used for monitoring molecular interactions in cells. This method of FRET, while among those with the simplest mathematics, is robust, self-controlled and independent of fluorophore amounts and ratios. RESULTS AccPbFRET is a user-friendly, efficient ImageJ plugin which allows fully corrected, pixel-wise calculation and detailed, ROI (region of interest)-based analysis of FRET efficiencies in microscopic images. Furthermore, automatic registration and semi-automatic analysis of large image sets is provided, which are not available in any existing FRET evaluation software. CONCLUSION Despite of the widespread applicability of the acceptor photobleaching FRET technique, this is the first paper where all possible sources of major errors of the measurement and analysis are considered, and AccPbFRET is the only program which provides the complete suite of corrections--for registering image pairs, for unwanted photobleaching of the donor, for cross-talk of the acceptor and/or its photoproduct to the donor channel and for partial photobleaching of the acceptor. The program efficiently speeds up the analysis of large image sets even for novice users and is freely available.
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Affiliation(s)
- János Roszik
- Department of Biophysics and Cell Biology, Research Center for Molecular Medicine, University of Debrecen, Debrecen, Hungary.
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28
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News & views. Biotechnol J 2008. [DOI: 10.1002/biot.200890038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Abstract
One hundred and fifty years after Virchow introduced his fundamental concept of cellular pathology, we now have tools that allow us to unravel the mechanisms of single living cells on a previously unprecedented level of detail. By exploring the molecular cellular phenotype, multiparametric cytometry not only detects specific cellular functions in general but also offers insights into the interaction of single subunits of proteins (e.g., growth factor receptors). Several quantitative and objective techniques allow analysis of single-cell preparations as well as tissue sections to obtain data on different cellular parameters. This opens the way to quantitative and objective histology, which in the future may be possible even without blood or the need to make an incision. To use this huge amount of data for treatment decisions in an individual patient, novel bioinformatic concepts are needed in order to predict the individual course of a disease. The concept of cytomics centers on the cell as the integral unit of all life and explores diseases starting from the cell and going to subcellular units (top-down analysis).
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30
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