1
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Gleneadie HJ, Fernandez-Ruiz B, Sardini A, Van de Pette M, Dimond A, Prinjha RK, McGinty J, French PMW, Bagci H, Merkenschlager M, Fisher AG. Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition. Commun Biol 2023; 6:318. [PMID: 36966198 PMCID: PMC10039851 DOI: 10.1038/s42003-023-04666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked disorder caused by loss of function mutations in the dystrophin gene (Dmd), resulting in progressive muscle weakening. Here we modelled the longitudinal expression of endogenous Dmd, and its paralogue Utrn, in mice and in myoblasts by generating bespoke bioluminescent gene reporters. As utrophin can partially compensate for Dmd-deficiency, these reporters were used as tools to ask whether chromatin-modifying drugs can enhance Utrn expression in developing muscle. Myoblasts treated with different PRC2 inhibitors showed significant increases in Utrn transcripts and bioluminescent signals, and these responses were independently verified by conditional Ezh2 deletion. Inhibition of ERK1/2 signalling provoked an additional increase in Utrn expression that was also seen in Dmd-mutant cells, and maintained as myoblasts differentiate. These data reveal PRC2 and ERK1/2 to be negative regulators of Utrn expression and provide specialised molecular imaging tools to monitor utrophin expression as a therapeutic strategy for DMD.
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Affiliation(s)
- Hannah J Gleneadie
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Beatriz Fernandez-Ruiz
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging Facility, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Hakan Bagci
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK.
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2
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Darling C, Davis SPX, Kumar S, French PMW, McGinty J. Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples. J Biophotonics 2023; 16:e202200232. [PMID: 36087031 DOI: 10.1002/jbio.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.
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Affiliation(s)
- Connor Darling
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Samuel P X Davis
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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3
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Lightley J, Görlitz F, Kumar S, Kalita R, Kolbeinsson A, Garcia E, Alexandrov Y, Bousgouni V, Wysoczanski R, Barnes P, Donnelly L, Bakal C, Dunsby C, Neil MAA, Flaxman S, French PMW. Robust deep learning optical autofocus system applied to automated multiwell plate single molecule localization microscopy. J Microsc 2022; 288:130-141. [PMID: 34089183 DOI: 10.1111/jmi.13020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 04/17/2021] [Accepted: 05/05/2021] [Indexed: 11/27/2022]
Abstract
We presenta robust, long-range optical autofocus system for microscopy utilizing machine learning. This can be useful for experiments with long image data acquisition times that may be impacted by defocusing resulting from drift of components, for example due to changes in temperature or mechanical drift. It is also useful for automated slide scanning or multiwell plate imaging where the sample(s) to be imaged may not be in the same horizontal plane throughout the image data acquisition. To address the impact of (thermal or mechanical) fluctuations over time in the optical autofocus system itself, we utilize a convolutional neural network (CNN) that is trained over multiple days to account for such fluctuations. To address the trade-off between axial precision and range of the autofocus, we implement orthogonal optical readouts with separate CNN training data, thereby achieving an accuracy well within the 600 nm depth of field of our 1.3 numerical aperture objective lens over a defocus range of up to approximately +/-100 μm. We characterize the performance of this autofocus system and demonstrate its application to automated multiwell plate single molecule localization microscopy.
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Affiliation(s)
- Jonathan Lightley
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Frederik Görlitz
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Ranjan Kalita
- Photonics Group, Physics Department, Imperial College London, London, UK
| | | | - Edwin Garcia
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Yuriy Alexandrov
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Vicky Bousgouni
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Riccardo Wysoczanski
- Photonics Group, Physics Department, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Peter Barnes
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise Donnelly
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Chris Bakal
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Christopher Dunsby
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Mark A A Neil
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Seth Flaxman
- Department of Mathematics, Imperial College London, London, UK
| | - Paul M W French
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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4
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Van de Pette M, Dimond A, Galvão AM, Millership SJ, To W, Prodani C, McNamara G, Bruno L, Sardini A, Webster Z, McGinty J, French PMW, Uren AG, Castillo-Fernandez J, Watkinson W, Ferguson-Smith AC, Merkenschlager M, John RM, Kelsey G, Fisher AG. Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice. Nat Commun 2022; 13:2464. [PMID: 35513363 PMCID: PMC9072353 DOI: 10.1038/s41467-022-30022-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
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Affiliation(s)
- Mathew Van de Pette
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Andrew Dimond
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - António M Galvão
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Institute of Animal Reproduction and Food Research of PAS, Department of Reproductive Immunology and Pathology, Olsztyn, Poland
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Steven J Millership
- Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Wilson To
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chiara Prodani
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Gráinne McNamara
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ludovica Bruno
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Zoe Webster
- Transgenics and Embryonic Stem Cell Laboratory, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Anthony G Uren
- Cancer Genomics Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | | | - William Watkinson
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Matthias Merkenschlager
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, CB2 0QQ, UK
| | - Amanda G Fisher
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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5
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Kalita R, Flanagan W, Lightley J, Kumar S, Alexandrov Y, Garcia E, Hintze M, Barkoulas M, Dunsby C, French PMW. Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast. J Biophotonics 2021; 14:e202100144. [PMID: 34390220 DOI: 10.1002/jbio.202100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/17/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
We present a robust, low-cost single-shot implementation of differential phase microscopy utilising a polarisation-sensitive camera to simultaneously acquire four images from which phase contrast images can be calculated. This polarisation-resolved differential phase contrast (pDPC) microscopy technique can be easily integrated with fluorescence microscopy.
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Affiliation(s)
- Ranjan Kalita
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - William Flanagan
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Jonathan Lightley
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Yuriy Alexandrov
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Edwin Garcia
- Photonics Group, Physics Department, Imperial College London, London, UK
| | - Mark Hintze
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Physics Department, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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6
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Guglielmi L, Heliot C, Kumar S, Alexandrov Y, Gori I, Papaleonidopoulou F, Barrington C, East P, Economou AD, French PMW, McGinty J, Hill CS. Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways. Nat Commun 2021; 12:6374. [PMID: 34737283 PMCID: PMC8569018 DOI: 10.1038/s41467-021-26486-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptional effector SMAD4 is a core component of the TGF-β family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-β family morphogens, BMPs and Nodal. We demonstrate that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling. However, unexpectedly, Nodal signaling is maintained, but lacks robustness. This Smad4-independent Nodal signaling is sufficient for mesoderm specification, but not for optimal endoderm specification. Furthermore, using Optical Projection Tomography in combination with 3D embryo morphometry, we have generated a BMP morphospace and demonstrate that Smad4 mutants are morphologically indistinguishable from embryos in which BMP signaling has been genetically/pharmacologically perturbed. Smad4 is thus differentially required for signaling by different TGF-β family ligands, which has implications for diseases where Smad4 is mutated or deleted.
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Affiliation(s)
- Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sunil Kumar
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Yuriy Alexandrov
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Philip East
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Paul M W French
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - James McGinty
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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7
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Cannon TM, Lagarto JL, Dyer BT, Garcia E, Kelly DJ, Peters NS, Lyon AR, French PMW, Dunsby C. Characterization of NADH fluorescence properties under one-photon excitation with respect to temperature, pH, and binding to lactate dehydrogenase. OSA Contin 2021; 4:1610-1625. [PMID: 34458690 PMCID: PMC8367293 DOI: 10.1364/osac.423082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 05/06/2023]
Abstract
Reduced nicotinamide adenine dinucleotide (NADH) is the principal electron donor in glycolysis and oxidative metabolism and is thus recognized as a key biomarker for probing metabolic state. While the fluorescence characteristics of NADH have been investigated extensively, there are discrepancies in the published data due to diverse experimental conditions, instrumentation and microenvironmental parameters that can affect NADH fluorescence. Using a cuvette-based time-resolved spectrofluorimeter employing one-photon excitation at 375 nm, we characterized the fluorescence intensity, lifetime, spectral response, anisotropy and time-resolved anisotropy of NADH in aqueous solution under varying microenvironmental conditions, namely temperature, pH, and binding to lactate dehydrogenase (LDH). Our results demonstrate how temperature, pH, and binding partners each impact the fluorescence signature of NADH and highlight the complexity of the fluorescence data when different parameters produce competing effects. We hope that the data presented in this study will provide a reference for potential sources of variation in experiments measuring NADH fluorescence.
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Affiliation(s)
- Taylor M. Cannon
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- These authors contributed equally to this work and are listed in alphabetical order
| | - Joao L. Lagarto
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- These authors contributed equally to this work and are listed in alphabetical order
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Edwin Garcia
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Douglas J. Kelly
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | | | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- Centre for Pathology, Imperial College London, London, W12 0NN, UK
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8
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Jones B, McGlone ER, Fang Z, Pickford P, Corrêa IR, Oishi A, Jockers R, Inoue A, Kumar S, Görlitz F, Dunsby C, French PMW, Rutter GA, Tan T, Tomas A, Bloom SR. Genetic and biased agonist-mediated reductions in β-arrestin recruitment prolong cAMP signaling at glucagon family receptors. J Biol Chem 2020; 296:100133. [PMID: 33268378 PMCID: PMC7948418 DOI: 10.1074/jbc.ra120.016334] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 01/20/2023] Open
Abstract
Receptors for the peptide hormones glucagon-like peptide-1 (GLP-1R), glucose-dependent insulinotropic polypeptide (GIPR), and glucagon (GCGR) are important regulators of insulin secretion and energy metabolism. GLP-1R agonists have been successfully deployed for the treatment of type 2 diabetes, but it has been suggested that their efficacy is limited by target receptor desensitization and downregulation due to recruitment of β-arrestins. Indeed, recently described GLP-1R agonists with reduced β-arrestin-2 recruitment have delivered promising results in preclinical and clinical studies. We therefore aimed to determine if the same phenomenon could apply to the closely related GIPR and GCGR. In HEK293 cells depleted of both β-arrestin isoforms the duration of G protein–dependent cAMP/PKA signaling was increased in response to the endogenous ligand for each receptor. Moreover, in wildtype cells, “biased” GLP-1, GCG, and GIP analogs with selective reductions in β-arrestin-2 recruitment led to reduced receptor endocytosis and increased insulin secretion over a prolonged stimulation period, although the latter effect was only seen at high agonist concentrations. Biased GCG analogs increased the duration of cAMP signaling, but this did not lead to increased glucose output from hepatocytes. Our study provides a rationale for the development of GLP-1R, GIPR, and GCGR agonists with reduced β-arrestin recruitment, but further work is needed to maximally exploit this strategy for therapeutic purposes.
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Affiliation(s)
- Ben Jones
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom.
| | - Emma Rose McGlone
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Zijian Fang
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Phil Pickford
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | | | - Atsuro Oishi
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
| | - Ralf Jockers
- Université de Paris, Institut Cochin, INSERM, CNRS, Paris, France
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Sunil Kumar
- Department of Physics, Imperial College London, London, United Kingdom
| | - Frederik Görlitz
- Department of Physics, Imperial College London, London, United Kingdom
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, United Kingdom
| | - Paul M W French
- Department of Physics, Imperial College London, London, United Kingdom
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Tricia Tan
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London, United Kingdom.
| | - Stephen R Bloom
- Section of Endocrinology and Investigative Medicine, Imperial College London, London, United Kingdom
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9
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Fang Z, Chen S, Pickford P, Broichhagen J, Hodson DJ, Corrêa IR, Kumar S, Görlitz F, Dunsby C, French PMW, Rutter GA, Tan T, Bloom SR, Tomas A, Jones B. The Influence of Peptide Context on Signaling and Trafficking of Glucagon-like Peptide-1 Receptor Biased Agonists. ACS Pharmacol Transl Sci 2020; 3:345-360. [PMID: 32296773 PMCID: PMC7155199 DOI: 10.1021/acsptsci.0c00022] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 01/14/2023]
Abstract
Signal bias and membrane trafficking have recently emerged as important considerations in the therapeutic targeting of the glucagon-like peptide-1 receptor (GLP-1R) in type 2 diabetes and obesity. In the present study, we have evaluated a peptide series with varying sequence homology between native GLP-1 and exendin-4, the archetypal ligands on which approved GLP-1R agonists are based. We find notable differences in agonist-mediated cyclic AMP signaling, recruitment of β-arrestins, endocytosis, and recycling, dependent both on the introduction of a His → Phe switch at position 1 and the specific midpeptide helical regions and C-termini of the two agonists. These observations were linked to insulin secretion in a beta cell model and provide insights into how ligand factors influence GLP-1R function at the cellular level.
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Affiliation(s)
- Zijian Fang
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Shiqian Chen
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Philip Pickford
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Johannes Broichhagen
- Department
Chemical Biology, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie (FMP), Berlin, 13125, Germany
| | - David J. Hodson
- Institute
of Metabolism and Systems Research (IMSR), and Centre of Membrane
Proteins and Receptors (COMPARE), University
of Birmingham, Birmingham, B15 2TT, United Kingdom
- Centre
for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, B15 2TT, United Kingdom
| | - Ivan R. Corrêa
- New
England
Biolabs, Ipswich, Massachusetts 01938, United States
| | - Sunil Kumar
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Frederik Görlitz
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Chris Dunsby
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Paul M. W. French
- Department
of Physics, Imperial College London, London, SW7 2BX, United Kingdom
| | - Guy A. Rutter
- Section
of Cell Biology and Functional Genomics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Tricia Tan
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Stephen R. Bloom
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Alejandra Tomas
- Section
of Cell Biology and Functional Genomics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Ben Jones
- Section
of Endocrinology and Investigative Medicine, Imperial College London, London, W12 0NN, United Kingdom
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10
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Davis SPX, Kumar S, Alexandrov Y, Bhargava A, da Silva Xavier G, Rutter GA, Frankel P, Sahai E, Flaxman S, French PMW, McGinty J. Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish. J Biophotonics 2019; 12:e201900128. [PMID: 31386281 PMCID: PMC7065643 DOI: 10.1002/jbio.201900128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/27/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Optical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images. For sparse samples, this can be addressed with iterative algorithms to reconstruct 3D images from undersampled OPT data, but the data processing times present a significant challenge for studies imaging multiple animals. We show here that convolutional neural networks (CNN) can be used in place of iterative algorithms to remove artifacts-reducing processing time for an undersampled in vivo zebrafish dataset from 77 to 15 minutes. We also show that using CNN produces reconstructions of equivalent quality to compressed sensing with 40% fewer projections. We further show that diverse training data classes, for example, ex vivo mouse tissue data, can be used for CNN-based reconstructions of OPT data of other species including live zebrafish.
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Affiliation(s)
| | - Sunil Kumar
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | - Yuriy Alexandrov
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | | | - Gabriela da Silva Xavier
- Department of MedicineImperial College LondonLondonUK
- Institute of Metabolism and Systems ResearchUniversity of BirminghamBirminghamUK
| | - Guy A. Rutter
- Department of MedicineImperial College LondonLondonUK
| | - Paul Frankel
- Division of MedicineUniversity College LondonLondonUK
| | | | - Seth Flaxman
- Department of Mathematics and Data Science InstituteImperial College LondonLondonUK
| | - Paul M. W. French
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | - James McGinty
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
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11
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Jones DC, Kumar S, Lanigan PMP, McGuinness CD, Dale MW, Twitchen DJ, Fisher D, Martineau PM, Neil MAA, Dunsby C, French PMW. Multidimensional luminescence microscope for imaging defect colour centres in diamond. Methods Appl Fluoresc 2019; 8:014004. [DOI: 10.1088/2050-6120/ab4eac] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Lagarto JL, Dyer BT, Peters NS, French PMW, Dunsby C, Lyon AR. In vivo label-free optical monitoring of structural and metabolic remodeling of myocardium following infarction. Biomed Opt Express 2019; 10:3506-3521. [PMID: 31360603 PMCID: PMC6640823 DOI: 10.1364/boe.10.003506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/15/2019] [Accepted: 05/29/2019] [Indexed: 05/14/2023]
Abstract
Cardiac remodeling following myocardial infarction (MI) involves structural and functional alterations in the infarcted and remote viable myocardium that can ultimately lead to heart failure. The underlying mechanisms are not fully understood and, following our previous study of the autofluorescence lifetime and diffuse reflectance signatures of the myocardium in vivo at 16 weeks post MI in rats [Biomed. Opt. Express6(2), 324 (2015)], we here present data obtained at 1, 2 and 4 weeks post myocardial infarction that help follow the temporal progression of these changes. Our results demonstrate that both structural and metabolic changes in the heart can be monitored from the earliest time points following MI using label-free optical readouts, not only in the region of infarction but also in the remote non-infarcted myocardium. Changes in the autofluorescence intensity and lifetime parameters associated with collagen type I autofluorescence were indicative of progressive collagen deposition in tissue that was most pronounced at earlier time points and in the region of infarction. In addition to significant collagen deposition in infarcted and non-infarcted myocardium, we also report changes in the autofluorescence parameters associated with reduced nicotinamide adenine (phosphate) dinucleotide (NAD(P)H) and flavin adenine dinucleotide (FAD), which we associate with metabolic alterations throughout the heart. Parallel measurements of the diffuse reflectance spectra indicated an increased contribution of reduced cytochrome c. Our findings suggest that combining time-resolved spectrofluorometry and diffuse reflectance spectroscopy could provide a useful means to monitor cardiac function in vivo at the time of surgery.
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Affiliation(s)
- João L. Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
- Authors contributed equally to this work
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Authors contributed equally to this work
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Centre for Cardiac Engineering, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, United Kingdom
- Centre for Pathology, Imperial College London Du Cane Road, London W12 0NN, United Kingdom
- Authors contributed equally to this work
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN, United Kingdom
- Authors contributed equally to this work
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13
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Munro I, García E, Yan M, Guldbrand S, Kumar S, Kwakwa K, Dunsby C, Neil MAA, French PMW. Accelerating single molecule localization microscopy through parallel processing on a high-performance computing cluster. J Microsc 2018; 273:148-160. [PMID: 30508256 PMCID: PMC6378585 DOI: 10.1111/jmi.12772] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
Abstract
Super‐resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high‐performance computing (HPC) cluster and quantify the speed advantage for a four‐node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD‐enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software. Lay Description Optical microscopy is now able to provide images with a resolution far beyond the diffraction limit thanks to relatively new super‐resolved microscopy (SRM) techniques, which have revolutionized the ability to study biological structures. One approach to SRM is to randomly switch on and off the emission of fluorescent molecules in an otherwise conventional fluorescence microscope. If only a sparse subset of the fluorescent molecules labelling a sample can be switched on at a time, then each emitter will be, on average, spaced further apart than the diffraction‐limited resolution of the conventional microscope and the separate bright spots in the image corresponding to each emitter can be localised to high precision by finding the centre of each feature using a computer program. Thus, a precise map of the emitter positions can be recorded by sequentially mapping the localisation of different subsets of emitters as they are switched on and others switched off. Typically, this approach, described as single molecule localisation microscopy (SMLM), results in large image data sets that can take many minutes to hours to process, depending on the size of the field of view and whether the SMLM analysis employs a computationally‐intensive iterative algorithm. Such a slow workflow makes it difficult to optimise experiments and to analyse large numbers of samples. Faster SMLM experiments would be generally useful and automated high throughput SMLM studies of arrays of samples, such as cells, could be applied to drug discovery and other applications. However, the time required to process the resulting data would be prohibitive on a normal computer. To address this, we have developed a method to run standard SMLM data analysis software tools in parallel on a high‐performance computing cluster (HPC). This can be used to accelerate the analysis of individual SMLM experiments or it can be scaled to analyse high throughput SMLM data by extending it to run on an arbitrary number of HPC processors in parallel. In this paper we outline the design of our parallelised SMLM software for HPC and quantify the speed advantage when implementing it on four HPC nodes compared to a powerful desktop computer.
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Affiliation(s)
- I Munro
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - E García
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - M Yan
- Photonics Group, Physics Department, Imperial College London, London, U.K.,Northwest Institute of Nuclear Technology, Xi'an, Shaanxi, P.R. China
| | - S Guldbrand
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - S Kumar
- Photonics Group, Physics Department, Imperial College London, London, U.K.,The Francis Crick Institute, London, U.K
| | - K Kwakwa
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - C Dunsby
- Photonics Group, Physics Department, Imperial College London, London, U.K.,Centre for Pathology, Imperial College London, London, U.K
| | - M A A Neil
- Photonics Group, Physics Department, Imperial College London, London, U.K
| | - P M W French
- Photonics Group, Physics Department, Imperial College London, London, U.K
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14
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Davis SPX, Wisniewski L, Kumar S, Correia T, Arridge SR, Frankel P, McGinty J, French PMW. Slice-illuminated optical projection tomography. Opt Lett 2018; 43:5555-5558. [PMID: 30439894 PMCID: PMC6238829 DOI: 10.1364/ol.43.005555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/24/2018] [Indexed: 06/09/2023]
Abstract
To improve the imaging performance of optical projection tomography (OPT) in live samples, we have explored a parallelized implementation of semi-confocal line illumination and detection to discriminate against scattered photons. Slice-illuminated OPT (sl-OPT) improves reconstruction quality in scattering samples by reducing interpixel crosstalk at the cost of increased acquisition time. For in vivo imaging, this can be ameliorated through the use of compressed sensing on angularly undersampled OPT data sets. Here, we demonstrate sl-OPT applied to 3D imaging of bead phantoms and live adult zebrafish.
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Affiliation(s)
- Samuel P. X. Davis
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | | | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Teresa Correia
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, UK
| | - Simon R. Arridge
- School of Biomedical Engineering and Imaging Sciences, King’s College London, London, UK
| | - Paul Frankel
- Division of Medicine, University College London, London, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, London, UK
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15
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Görlitz F, Guldbrand S, Runcorn TH, Murray RT, Jaso-Tamame AL, Sinclair HG, Martinez-Perez E, Taylor JR, Neil MAA, Dunsby C, French PMW. easySLM-STED: Stimulated emission depletion microscopy with aberration correction, extended field of view and multiple beam scanning. J Biophotonics 2018; 11:e201800087. [PMID: 29978591 DOI: 10.1002/jbio.201800087] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/01/2018] [Accepted: 07/05/2018] [Indexed: 05/06/2023]
Abstract
We demonstrate a simplified set-up for STED microscopy with a straightforward alignment procedure that uses a single spatial light modulator (SLM) with collinear incident excitation and depletion beams to provide phase modulation of the beam profiles and correction of optical aberrations. We show that this approach can be used to extend the field of view for STED microscopy by correcting chromatic aberration that otherwise leads to walk-off between the focused excitation and depletion beams. We further show how this arrangement can be adapted to increase the imaging speed through multibeam excitation and depletion. Fine adjustments to the alignment can be accomplished using the SLM only, conferring the potential for automation.
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Affiliation(s)
- Frederik Görlitz
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Stina Guldbrand
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Timothy H Runcorn
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | - Robert T Murray
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | | | - Hugo G Sinclair
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | | | - James R Taylor
- Femtosecond Optics Group, Department of Physics, Imperial College London, London, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Imperial College London, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
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16
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Lagarto JL, Dyer BT, Talbot CB, Peters NS, French PMW, Lyon AR, Dunsby C. Characterization of NAD(P)H and FAD autofluorescence signatures in a Langendorff isolated-perfused rat heart model. Biomed Opt Express 2018; 9:4961-4978. [PMID: 30319914 PMCID: PMC6179415 DOI: 10.1364/boe.9.004961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 05/22/2023]
Abstract
Autofluorescence spectroscopy is a promising label-free approach to characterize biological samples with demonstrated potential to report structural and biochemical alterations in tissues in a number of clinical applications. We report a characterization of the ex vivo autofluorescence fingerprint of cardiac tissue, exploiting a Langendorff-perfused isolated rat heart model to induce physiological insults to the heart, with a view to understanding how metabolic alterations affect the autofluorescence signals. Changes in the autofluorescence intensity and lifetime signatures associated with reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) were characterized during oxygen- or glucose-depletion protocols. Results suggest that both NAD(P)H and FAD autofluorescence intensity and lifetime parameters are sensitive to changes in the metabolic state of the heart owing to oxygen deprivation. We also observed changes in NAD(P)H fluorescence intensity and FAD lifetime parameter on reperfusion of oxygen, which might provide information on reperfusion injury, and permanent tissue damage or changes to the tissue during recovery from oxygen deprivation. We found that changes in the autofluorescence signature following glucose-depletion are, in general, less pronounced, and most clearly visible in NAD(P)H related parameters. Overall, the results reported in this investigation can serve as baseline for future investigations of cardiac tissue involving autofluorescence measurements.
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Affiliation(s)
- João L Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
- Authors contributed equally to this work
| | - Benjamin T Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
- Authors contributed equally to this work
| | - Clifford B Talbot
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
| | - Nicholas S Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
| | - Alexander R Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London W12 0NN, UK
- Authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2AZ, UK
- Centre for Pathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Authors contributed equally to this work
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17
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Alexandrov Y, Nikolic DS, Dunsby C, French PMW. Quantitative time domain analysis of lifetime-based Förster resonant energy transfer measurements with fluorescent proteins: Static random isotropic fluorophore orientation distributions. J Biophotonics 2018; 11:e201700366. [PMID: 29582566 DOI: 10.1002/jbio.201700366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Förster resonant energy transfer (FRET) measurements are widely used to obtain information about molecular interactions and conformations through the dependence of FRET efficiency on the proximity of donor and acceptor fluorophores. Fluorescence lifetime measurements can provide quantitative analysis of FRET efficiency and interacting population fraction. Many FRET experiments exploit the highly specific labelling of genetically expressed fluorescent proteins, applicable in live cells and organisms. Unfortunately, the typical assumption of fast randomization of fluorophore orientations in the analysis of fluorescence lifetime-based FRET readouts is not valid for fluorescent proteins due to their slow rotational mobility compared to their upper state lifetime. Here, previous analysis of effectively static isotropic distributions of fluorophore dipoles on FRET measurements is incorporated into new software for fitting donor emission decay profiles. Calculated FRET parameters, including molar population fractions, are compared for the analysis of simulated and experimental FRET data under the assumption of static and dynamic fluorophores and the intermediate regimes between fully dynamic and static fluorophores, and mixtures within FRET pairs, is explored. Finally, a method to correct the artefact resulting from fitting the emission from static FRET pairs with isotropic angular distributions to the (incorrect) typically assumed dynamic FRET decay model is presented.
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Affiliation(s)
- Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
| | - Dino S Nikolic
- Quantum Physics and Information Technology Group, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
- Centre for Pathology, Imperial College London, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Light Microscopy, Francis Crick Institute, London, UK
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18
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Sherlock B, Warren SC, Alexandrov Y, Yu F, Stone J, Knight J, Neil MAA, Paterson C, French PMW, Dunsby C. In vivo multiphoton microscopy using a handheld scanner with lateral and axial motion compensation. J Biophotonics 2018; 11:e201700131. [PMID: 28858435 DOI: 10.1002/jbio.201700131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
This paper reports a handheld multiphoton fluorescence microscope designed for clinical imaging that incorporates axial motion compensation and lateral image stabilization. Spectral domain optical coherence tomography is employed to track the axial position of the skin surface, and lateral motion compensation is realised by imaging the speckle pattern arising from the optical coherence tomography beam illuminating the sample. Our system is able to correct lateral sample velocities of up to approximately 65 μm s-1 . Combined with the use of negative curvature microstructured optical fibre to deliver tunable ultrafast radiation to the handheld multiphoton scanner without the need of a dispersion compensation unit, this instrument has potential for a range of clinical applications. The system is used to compensate for both lateral and axial motion of the sample when imaging human skin in vivo.
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Affiliation(s)
- Ben Sherlock
- Department of Physics, Imperial College London, London, UK
| | - Sean C Warren
- Department of Physics, Imperial College London, London, UK
| | | | - Fei Yu
- Department of Physics, University of Bath, Bath, UK
| | - James Stone
- Department of Physics, University of Bath, Bath, UK
| | | | - Mark A A Neil
- Department of Physics, Imperial College London, London, UK
| | - Carl Paterson
- Department of Physics, Imperial College London, London, UK
| | | | - Chris Dunsby
- Department of Physics, Imperial College London, London, UK
- Centre for Pathology, Imperial College London, London, UK
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19
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Van de Pette M, Abbas A, Feytout A, McNamara G, Bruno L, To WK, Dimond A, Sardini A, Webster Z, McGinty J, Paul EJ, Ungless MA, French PMW, Withers DJ, Uren A, Ferguson-Smith AC, Merkenschlager M, John RM, Fisher AG. Visualizing Changes in Cdkn1c Expression Links Early-Life Adversity to Imprint Mis-regulation in Adults. Cell Rep 2017; 18:1090-1099. [PMID: 28147266 PMCID: PMC5300902 DOI: 10.1016/j.celrep.2017.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/22/2016] [Accepted: 01/07/2017] [Indexed: 12/13/2022] Open
Abstract
Imprinted genes are regulated according to parental origin and can influence embryonic growth and metabolism and confer disease susceptibility. Here, we designed sensitive allele-specific reporters to non-invasively monitor imprinted Cdkn1c expression in mice and showed that expression was modulated by environmental factors encountered in utero. Acute exposure to chromatin-modifying drugs resulted in de-repression of paternally inherited (silent) Cdkn1c alleles in embryos that was temporary and resolved after birth. In contrast, deprivation of maternal dietary protein in utero provoked permanent de-repression of imprinted Cdkn1c expression that was sustained into adulthood and occurred through a folate-dependent mechanism of DNA methylation loss. Given the function of imprinted genes in regulating behavior and metabolic processes in adults, these results establish imprinting deregulation as a credible mechanism linking early-life adversity to later-life outcomes. Furthermore, Cdkn1c-luciferase mice offer non-invasive tools to identify factors that disrupt epigenetic processes and strategies to limit their long-term impact. Allele-specific expression of imprinted Cdkn1c imaged in vivo using bioluminescence Chromatin-modifying drugs applied in utero transiently de-repress Cdkn1c imprinting In utero exposure to low-protein diet permanently disrupts the Cdkn1c imprint Folate supplements during gestation protect against loss of Cdkn1c imprinting
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Affiliation(s)
- Mathew Van de Pette
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Allifia Abbas
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amelie Feytout
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Gráinne McNamara
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ludovica Bruno
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Wilson K To
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Andrew Dimond
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alessandro Sardini
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Zoe Webster
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Eleanor J Paul
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Mark A Ungless
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anthony Uren
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Amanda G Fisher
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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20
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Lagarto J, Hares JD, Dunsby C, French PMW. Development of Low-Cost Instrumentation for Single Point Autofluorescence Lifetime Measurements. J Fluoresc 2017; 27:1643-1654. [PMID: 28540652 PMCID: PMC5583312 DOI: 10.1007/s10895-017-2101-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 01/25/2023]
Abstract
Autofluorescence lifetime measurements, which can provide label-free readouts in biological tissues, contrasting e.g. different types and states of tissue matrix components and different cellular metabolites, may have significant clinical potential for diagnosis and to provide surgical guidance. However, the cost of the instrumentation typically used currently presents a barrier to wider implementation. We describe a low-cost single point time-resolved autofluorescence instrument, exploiting modulated laser diodes for excitation and FPGA-based circuitry for detection, together with a custom constant fraction discriminator. Its temporal accuracy is compared against a "gold-standard" instrument incorporating commercial TCSPC circuitry by resolving the fluorescence decays of reference fluorophores presenting single and double exponential decay profiles. To illustrate the potential to read out intrinsic contrast in tissue, we present preliminary measurements of autofluorescence lifetime measurements of biological tissues ex vivo. We believe that the lower cost of this instrument could enhance the potential of autofluorescence lifetime metrology for clinical deployment and commercial development.
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Affiliation(s)
- João Lagarto
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK.
| | - Jonathan D Hares
- Kentech Instruments Ltd., Howbery Park, Wallingford, OX10 8BD, UK
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ, UK
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21
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Noble E, Kumar S, Görlitz FG, Stain C, Dunsby C, French PMW. In vivo label-free mapping of the effect of a photosystem II inhibiting herbicide in plants using chlorophyll fluorescence lifetime. Plant Methods 2017; 13:48. [PMID: 28638436 PMCID: PMC5472976 DOI: 10.1186/s13007-017-0201-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/08/2017] [Indexed: 06/19/2023]
Abstract
BACKGROUND In order to better understand and improve the mode of action of agrochemicals, it is useful to be able to visualize their uptake and distribution in vivo, non-invasively and, ideally, in the field. Here we explore the potential of plant autofluorescence (specifically chlorophyll fluorescence) to provide a readout of herbicide action across the scales utilising multiphoton-excited fluorescence lifetime imaging, wide-field single-photon excited fluorescence lifetime imaging and single point fluorescence lifetime measurements via a fibre-optic probe. RESULTS Our studies indicate that changes in chlorophyll fluorescence lifetime can be utilised as an indirect readout of a photosystem II inhibiting herbicide activity in living plant leaves at three different scales: cellular (~μm), single point (~1 mm2) and macroscopic (~8 × 6 mm2 of a leaf). Multiphoton excited fluorescence lifetime imaging of Triticum aestivum leaves indicated that there is an increase in the spatially averaged chlorophyll fluorescence lifetime of leaves treated with Flagon EC-a photosystem II inhibiting herbicide. The untreated leaf exhibited an average lifetime of 560 ± 30 ps while the leaf imaged 2 h post treatment exhibited an increased lifetime of 2000 ± 440 ps in different fields of view. The results from in vivo wide-field single-photon excited fluorescence lifetime imaging excited at 440 nm indicated an increase in chlorophyll fluorescence lifetime from 521 ps in an untreated leaf to 1000 ps, just 3 min after treating the same leaf with Flagon EC, and to 2150 ps after 27 min. In vivo single point fluorescence lifetime measurements demonstrated a similar increase in chlorophyll fluorescence lifetime. Untreated leaf presented a fluorescence lifetime of 435 ps in the 440 nm excited chlorophyll channel, CH4 (620-710 nm). In the first 5 min after treatment, mean fluorescence lifetime is observed to have increased to 1 ns and then to 1.3 ns after 60 min. For all these in vivo plant autofluorescence lifetime measurements, the plants were not dark-adapted. CONCLUSIONS We demonstrate that the local impact of a photosystem II herbicide on living plant leaves can be conveniently mapped in space and time via changes in autofluorescence lifetime, which we attribute to changes in chlorophyll fluorescence. Using portable fibre-optic probe instrumentation originally designed for label-free biomedical applications, this capability could be deployed outside the laboratory for monitoring the distribution of herbicides in growing plants.
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Affiliation(s)
- Elizabeth Noble
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
- Institute of Chemical Biology, Imperial College London, London, SW7 2AZ UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
| | - Frederik G. Görlitz
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
| | - Chris Stain
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
- Centre for Pathology, Imperial College London, London, SW7 2AZ UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, London, SW7 2AZ UK
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22
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Görlitz F, Kelly DJ, Warren SC, Alibhai D, West L, Kumar S, Alexandrov Y, Munro I, Garcia E, McGinty J, Talbot C, Serwa RA, Thinon E, da Paola V, Murray EJ, Stuhmeier F, Neil MAA, Tate EW, Dunsby C, French PMW. Open Source High Content Analysis Utilizing Automated Fluorescence Lifetime Imaging Microscopy. J Vis Exp 2017:55119. [PMID: 28190060 PMCID: PMC5352269 DOI: 10.3791/55119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We present an open source high content analysis instrument utilizing automated fluorescence lifetime imaging (FLIM) for assaying protein interactions using Förster resonance energy transfer (FRET) based readouts of fixed or live cells in multiwell plates. This provides a means to screen for cell signaling processes read out using intramolecular FRET biosensors or intermolecular FRET of protein interactions such as oligomerization or heterodimerization, which can be used to identify binding partners. We describe here the functionality of this automated multiwell plate FLIM instrumentation and present exemplar data from our studies of HIV Gag protein oligomerization and a time course of a FRET biosensor in live cells. A detailed description of the practical implementation is then provided with reference to a list of hardware components and a description of the open source data acquisition software written in µManager. The application of FLIMfit, an open source MATLAB-based client for the OMERO platform, to analyze arrays of multiwell plate FLIM data is also presented. The protocols for imaging fixed and live cells are outlined and a demonstration of an automated multiwell plate FLIM experiment using cells expressing fluorescent protein-based FRET constructs is presented. This is complemented by a walk-through of the data analysis for this specific FLIM FRET data set.
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Affiliation(s)
- Frederik Görlitz
- Photonics Group, Department of Physics, Imperial College London;
| | - Douglas J Kelly
- Photonics Group, Department of Physics, Imperial College London
| | - Sean C Warren
- Photonics Group, Department of Physics, Imperial College London
| | - Dominic Alibhai
- Institute for Chemical Biology, Department of Chemistry, Imperial College London
| | - Lucien West
- MRC Clinical Sciences Centre, Hammersmith Hospital
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London
| | | | - Ian Munro
- Photonics Group, Department of Physics, Imperial College London
| | - Edwin Garcia
- Photonics Group, Department of Physics, Imperial College London
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London
| | - Clifford Talbot
- Photonics Group, Department of Physics, Imperial College London
| | - Remigiusz A Serwa
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | - Emmanuelle Thinon
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | | | | | - Frank Stuhmeier
- Pfizer Global Research and Development, Pfizer Limited, Sandwich, Kent, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College London
| | - Edward W Tate
- Chemical Biology Section, Department of Chemistry, Imperial College London
| | - Christopher Dunsby
- Photonics Group, Department of Physics, Imperial College London; Centre for Histopathology, Imperial College London
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London
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23
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Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PMW, Chin JW, Gervasio FL, Tate EW, Katan M. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Alan R. Lowe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- London Centre for Nanotechnology, 17-19 Gower St, London, WC1H 0AH, UK
- Division of Biosciences, Birkbeck College, Malet St, London, WC1E 7HX, UK
| | - Giorgio Saladino
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jason W. Chin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Luigi Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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24
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Sparks H, Görlitz F, Kelly DJ, Warren SC, Kellett PA, Garcia E, Dymoke-Bradshaw AKL, Hares JD, Neil MAA, Dunsby C, French PMW. Characterisation of new gated optical image intensifiers for fluorescence lifetime imaging. Rev Sci Instrum 2017; 88:013707. [PMID: 28147687 DOI: 10.1063/1.4973917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report the characterisation of gated optical image intensifiers for fluorescence lifetime imaging, evaluating the performance of several different prototypes that culminate in a new design that provides improved spatial resolution conferred by the addition of a magnetic field to reduce the lateral spread of photoelectrons on their path between the photocathode and microchannel plate, and higher signal to noise ratio conferred by longer time gates. We also present a methodology to compare these systems and their capabilities, including the quantitative readouts of Förster resonant energy transfer.
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Affiliation(s)
- H Sparks
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - F Görlitz
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - D J Kelly
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - S C Warren
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - P A Kellett
- Kentech Instruments Ltd., Howbery Park, Wallingford OX10 8BD, United Kingdom
| | - E Garcia
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | | | - J D Hares
- Kentech Instruments Ltd., Howbery Park, Wallingford OX10 8BD, United Kingdom
| | - M A A Neil
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - C Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
| | - P M W French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW, United Kingdom
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25
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Cortés E, Huidobro PA, Sinclair HG, Guldbrand S, Peveler WJ, Davies T, Parrinello S, Görlitz F, Dunsby C, Neil MAA, Sivan Y, Parkin IP, French PMW, Maier SA. Plasmonic Nanoprobes for Stimulated Emission Depletion Nanoscopy. ACS Nano 2016; 10:10454-10461. [PMID: 27794591 DOI: 10.1021/acsnano.6b06361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plasmonic nanoparticles influence the absorption and emission processes of nearby emitters due to local enhancements of the illuminating radiation and the photonic density of states. Here, we use the plasmon resonance of metal nanoparticles in order to enhance the stimulated depletion of excited molecules for super-resolved nanoscopy. We demonstrate stimulated emission depletion (STED) nanoscopy with gold nanorods with a long axis of only 26 nm and a width of 8 nm. These particles provide an enhancement of up to 50% of the resolution compared to fluorescent-only probes without plasmonic components irradiated with the same depletion power. The nanoparticle-assisted STED probes reported here represent a ∼2 × 103 reduction in probe volume compared to previously used nanoparticles. Finally, we demonstrate their application toward plasmon-assisted STED cellular imaging at low-depletion powers, and we also discuss their current limitations.
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Affiliation(s)
| | | | | | | | - William J Peveler
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | | | | | | | | | | | - Yonatan Sivan
- Unit of Electro-optics Engineering, Ben-Gurion University , Beer-Sheba 8410501, Israel
| | - Ivan P Parkin
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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26
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Warren SC, Kim Y, Stone JM, Mitchell C, Knight JC, Neil MAA, Paterson C, French PMW, Dunsby C. Adaptive multiphoton endomicroscopy through a dynamically deformed multicore optical fiber using proximal detection. Opt Express 2016; 24:21474-84. [PMID: 27661887 DOI: 10.1364/oe.24.021474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This paper demonstrates multiphoton excited fluorescence imaging through a polarisation maintaining multicore fiber (PM-MCF) while the fiber is dynamically deformed using all-proximal detection. Single-shot proximal measurement of the relative optical path lengths of all the cores of the PM-MCF in double pass is achieved using a Mach-Zehnder interferometer read out by a scientific CMOS camera operating at 416 Hz. A non-linear least squares fitting procedure is then employed to determine the deformation-induced lateral shift of the excitation spot at the distal tip of the PM-MCF. An experimental validation of this approach is presented that compares the proximally measured deformation-induced lateral shift in focal spot position to an independent distally measured ground truth. The proximal measurement of deformation-induced shift in focal spot position is applied to correct for deformation-induced shifts in focal spot position during raster-scanning multiphoton excited fluorescence imaging.
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27
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Kwakwa K, Savell A, Davies T, Munro I, Parrinello S, Purbhoo MA, Dunsby C, Neil MAA, French PMW. easySTORM: a robust, lower-cost approach to localisation and TIRF microscopy. J Biophotonics 2016; 9:948-957. [PMID: 27592533 DOI: 10.1002/jbio.201500324] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/21/2016] [Accepted: 01/31/2016] [Indexed: 06/06/2023]
Abstract
TIRF and STORM microscopy are super-resolving fluorescence imaging modalities for which current implementations on standard microscopes can present significant complexity and cost. We present a straightforward and low-cost approach to implement STORM and TIRF taking advantage of multimode optical fibres and multimode diode lasers to provide the required excitation light. Combined with open source software and relatively simple protocols to prepare samples for STORM, including the use of Vectashield for non-TIRF imaging, this approach enables TIRF and STORM imaging of cells labelled with appropriate dyes or expressing suitable fluorescent proteins to become widely accessible at low cost.
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Affiliation(s)
- Kwasi Kwakwa
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ.
| | - Alexander Savell
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
- Institute of Chemical Biology, Imperial College London, London, SW7 2AZ
| | - Timothy Davies
- MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN
| | - Ian Munro
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
| | - Simona Parrinello
- MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London, W12 0NN
| | - Marco A Purbhoo
- Section of Hepatology, QEQM Hospital, Imperial College London, London, W2 1PG, UK
| | - Chris Dunsby
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
- Centre for Pathology, Imperial College London, London, W12 0NN
| | - Mark A A Neil
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
| | - Paul M W French
- Photonics Group, Physics Department, Imperial College London, London, SW7 2AZ
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28
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Sherlock B, Yu F, Stone J, Warren S, Paterson C, Neil MAA, French PMW, Knight J, Dunsby C. Tunable fibre-coupled multiphoton microscopy with a negative curvature fibre. J Biophotonics 2016; 9:715-720. [PMID: 26989868 DOI: 10.1002/jbio.201500290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/20/2016] [Accepted: 01/27/2016] [Indexed: 06/05/2023]
Abstract
Negative curvature fibre (NCF) guides light in its core by inhibiting the coupling of core and cladding modes. In this work, an NCF was designed and fabricated to transmit ultrashort optical pulses for multiphoton microscopy with low group velocity dispersion (GVD) at 800 nm. Its attenuation was measured to be <0.3 dB m(-1) over the range 600-850 nm and the GVD was -180 ± 70 fs(2) m(-1) at 800 nm. Using an average fibre output power of ∼20 mW and pulse repetition rate of 80 MHz, the NCF enabled pulses with a duration of <200 fs to be transmitted through a length of 1.5 m of fibre over a tuning range of 180 nm without the need for dispersion compensation. In a 4 m fibre, temporal and spectral pulse widths were maintained to within 10% of low power values up to the maximum fibre output power achievable with the laser system used of 278 mW at 700 nm, 808 mW at 800 nm and 420 mW at 860 nm. When coupled to a multiphoton microscope, it enabled imaging of ex vivo tissue using excitation wavelengths from 740 nm to 860 nm without any need for adjustments to the set-up.
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Affiliation(s)
- Ben Sherlock
- Department of Physics, Imperial College London, London, SW7 2AZ, UK.
| | - Fei Yu
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Jim Stone
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Sean Warren
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Carl Paterson
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Mark A A Neil
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
| | - Jonathan Knight
- Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Chris Dunsby
- Department of Physics, Imperial College London, London, SW7 2AZ, UK
- Centre for Histopathology, Imperial College London, London, SW7 2AZ, UK
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29
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Margineanu A, Chan JJ, Kelly DJ, Warren SC, Flatters D, Kumar S, Katan M, Dunsby CW, French PMW. Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM). Sci Rep 2016; 6:28186. [PMID: 27339025 PMCID: PMC4919659 DOI: 10.1038/srep28186] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/19/2016] [Indexed: 11/09/2022] Open
Abstract
We present a high content multiwell plate cell-based assay approach to quantify protein interactions directly in cells using Förster resonance energy transfer (FRET) read out by automated fluorescence lifetime imaging (FLIM). Automated FLIM is implemented using wide-field time-gated detection, typically requiring only 10 s per field of view (FOV). Averaging over biological, thermal and shot noise with 100's to 1000's of FOV enables unbiased quantitative analysis with high statistical power. Plotting average donor lifetime vs. acceptor/donor intensity ratio clearly identifies protein interactions and fitting to double exponential donor decay models provides estimates of interacting population fractions that, with calibrated donor and acceptor fluorescence intensities, can yield dissociation constants. We demonstrate the application to identify binding partners of MST1 kinase and estimate interaction strength among the members of the RASSF protein family, which have important roles in apoptosis via the Hippo signalling pathway. KD values broadly agree with published biochemical measurements.
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Affiliation(s)
- Anca Margineanu
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Jia Jia Chan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Douglas J. Kelly
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Sean C. Warren
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
- Imperial College London, Institute of Chemical Biology, London, SW7 2AZ, London, UK
| | - Delphine Flatters
- Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques in silico, Inserm UMR-S 973, 35 rue Helene Brion, 75013 Paris, France
| | - Sunil Kumar
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Matilda Katan
- University College London, Institute of Structural and Molecular Biology, Darwin building, Gower St., London, WC1E 6BT, UK
| | - Christopher W. Dunsby
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
| | - Paul M. W. French
- Imperial College London, Dept. Physics, Photonics Lab., Blackett building, Prince Consort Road, London, SW7 2AZ, UK
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30
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Andrews N, Ramel MC, Kumar S, Alexandrov Y, Kelly DJ, Warren SC, Kerry L, Lockwood N, Frolov A, Frankel P, Bugeon L, McGinty J, Dallman MJ, French PMW. Visualising apoptosis in live zebrafish using fluorescence lifetime imaging with optical projection tomography to map FRET biosensor activity in space and time. J Biophotonics 2016; 9:414-24. [PMID: 26753623 PMCID: PMC4858816 DOI: 10.1002/jbio.201500258] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/25/2015] [Accepted: 11/27/2015] [Indexed: 05/14/2023]
Abstract
Fluorescence lifetime imaging (FLIM) combined with optical projection tomography (OPT) has the potential to map Förster resonant energy transfer (FRET) readouts in space and time in intact transparent or near transparent live organisms such as zebrafish larvae, thereby providing a means to visualise cell signalling processes in their physiological context. Here the first application of FLIM OPT to read out biological function in live transgenic zebrafish larvae using a genetically expressed FRET biosensor is reported. Apoptosis, or programmed cell death, is mapped in 3-D by imaging the activity of a FRET biosensor that is cleaved by Caspase 3, which is a key effector of apoptosis. Although apoptosis is a naturally occurring process during development, it can also be triggered in a variety of ways, including through gamma irradiation. FLIM OPT is shown here to enable apoptosis to be monitored over time, in live zebrafish larvae via changes in Caspase 3 activation following gamma irradiation at 24 hours post fertilisation. Significant apoptosis was observed at 3.5 hours post irradiation, predominantly in the head region.
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Affiliation(s)
- Natalie Andrews
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ, UK
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Marie-Christine Ramel
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Douglas J Kelly
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Sean C Warren
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Louise Kerry
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
| | - Nicola Lockwood
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
- COMPLEX, University College London, Gower Street, London, WC1E 6BT, UK
| | - Antonina Frolov
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Paul Frankel
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Laurence Bugeon
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
| | - James McGinty
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | | | - Paul M W French
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK.
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Perdios L, Bunney TD, Warren SC, Dunsby C, French PMW, Tate EW, Katan M. Time-resolved FRET reports FGFR1 dimerization and formation of a complex with its effector PLCγ1. Adv Biol Regul 2016; 60:6-13. [PMID: 26482290 PMCID: PMC4739061 DOI: 10.1016/j.jbior.2015.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/22/2015] [Indexed: 11/05/2022]
Abstract
In vitro and in vivo imaging of protein tyrosine kinase activity requires minimally invasive, molecularly precise optical probes to provide spatiotemporal mechanistic information of dimerization and complex formation with downstream effectors. We present here a construct with genetically encoded, site-specifically incorporated, bioorthogonal reporter that can be selectively labelled with exogenous fluorogenic probes to monitor the structure and function of fibroblast growth factor receptor (FGFR). GyrB.FGFR1KD.TC contains a coumermycin-induced artificial dimerizer (GyrB), FGFR1 kinase domain (KD) and a tetracysteine (TC) motif that enables fluorescent labelling with biarsenical dyes FlAsH-EDT2 and ReAsH-EDT2. We generated bimolecular system for time-resolved FRET (TR-FRET) studies, which pairs FlAsH-tagged GyrB.FGFR1KD.TC and N-terminal Src homology 2 (nSH2) domain of phospholipase Cγ (PLCγ), a downstream effector of FGFR1, fused to mTurquoise fluorescent protein (mTFP). We demonstrated phosphorylation-dependent TR-FRET readout of complex formation between mTFP.nSH2 and GyrB.FGFR1KD.TC. By further application of TR-FRET, we also demonstrated formation of the GyrB.FGFR1KD.TC homodimer by coumermycin-induced dimerization. Herein, we present a spectroscopic FRET approach to facilitate and propagate studies that would provide structural and functional insights for FGFR and other tyrosine kinases.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK; Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Tom D Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Sean C Warren
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M W French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK.
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Warren SC, Margineanu A, Katan M, Dunsby C, French PMW. Homo-FRET Based Biosensors and Their Application to Multiplexed Imaging of Signalling Events in Live Cells. Int J Mol Sci 2015; 16:14695-716. [PMID: 26133241 PMCID: PMC4519867 DOI: 10.3390/ijms160714695] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/20/2022] Open
Abstract
Multiplexed imaging of Förster Resonance Energy Transfer (FRET)-based biosensors potentially presents a powerful approach to monitoring the spatio-temporal correlation of signalling pathways within a single live cell. Here, we discuss the potential of homo-FRET based biosensors to facilitate multiplexed imaging. We demonstrate that the homo-FRET between pleckstrin homology domains of Akt (Akt-PH) labelled with mCherry may be used to monitor 3'-phosphoinositide accumulation in live cells and show how global analysis of time resolved fluorescence anisotropy measurements can be used to quantify this accumulation. We further present multiplexed imaging readouts of calcium concentration, using fluorescence lifetime measurements of TN-L15-a CFP/YFP based hetero-FRET calcium biosensor-with 3'-phosphoinositide accumulation.
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Affiliation(s)
- Sean C Warren
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Anca Margineanu
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Matilda Katan
- Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London SW7 2AZ, UK.
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Dyer BT, Elder JM, Lagarto J, Harding SE, French PMW, Peters NS, Dunsby C, Lyon AR. 165 Label-free autofluorescence lifetime to assess changes in myocardial fibrosis and metabolism in vivoin a doxorubicin cardiomyopathy heart failure model. Heart 2015. [DOI: 10.1136/heartjnl-2015-308066.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Chen L, Alexandrov Y, Kumar S, Andrews N, Dallman MJ, French PMW, McGinty J. Mesoscopic in vivo 3-D tracking of sparse cell populations using angular multiplexed optical projection tomography. Biomed Opt Express 2015; 6:1253-1261. [PMID: 25909009 PMCID: PMC4399664 DOI: 10.1364/boe.6.001253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/23/2014] [Accepted: 12/25/2014] [Indexed: 05/29/2023]
Abstract
We describe an angular multiplexed imaging technique for 3-D in vivo cell tracking of sparse cell distributions and optical projection tomography (OPT) with superior time-lapse resolution and a significantly reduced light dose compared to volumetric time-lapse techniques. We demonstrate that using dual axis OPT, where two images are acquired simultaneously at different projection angles, can enable localization and tracking of features in 3-D with a time resolution equal to the camera frame rate. This is achieved with a 200x reduction in light dose compared to an equivalent volumetric time-lapse single camera OPT acquisition with 200 projection angles. We demonstrate the application of this technique to mapping the 3-D neutrophil migration pattern observed over ~25.5 minutes in a live 2 day post-fertilisation transgenic LysC:GFP zebrafish embryo following a tail wound.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
- These authors contributed equally to this work
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
- These authors contributed equally to this work
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - Natalie Andrews
- Institute for Chemical Biology, Department of Chemistry, imperial College London, SW7 2AZ,
UK
| | - Margaret J. Dallman
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
- Centre for Integrative Systems Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
- These joint senior authors contributed equally to this paper
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
- These joint senior authors contributed equally to this paper
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Lagarto J, Dyer BT, Talbot C, Sikkel MB, Peters NS, French PMW, Lyon AR, Dunsby C. Application of time-resolved autofluorescence to label-free in vivo optical mapping of changes in tissue matrix and metabolism associated with myocardial infarction and heart failure. Biomed Opt Express 2015; 6:324-46. [PMID: 25780727 PMCID: PMC4354591 DOI: 10.1364/boe.6.000324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 05/03/2023]
Abstract
We investigate the potential of an instrument combining time-resolved spectrofluorometry and diffuse reflectance spectroscopy to measure structural and metabolic changes in cardiac tissue in vivo in a 16 week post-myocardial infarction heart failure model in rats. In the scar region, we observed changes in the fluorescence signal that can be explained by increased collagen content, which is in good agreement with histology. In areas remote from the scar tissue, we measured changes in the fluorescence signal (p < 0.001) that cannot be explained by differences in collagen content and we attribute this to altered metabolism within the myocardium. A linear discriminant analysis algorithm was applied to the measurements to predict the tissue disease state. When we combine all measurements, our results reveal high diagnostic accuracy in the infarcted area (100%) and border zone (94.44%) as well as in remote regions from the scar (> 77%). Overall, our results demonstrate the potential of our instrument to characterize structural and metabolic changes in a failing heart in vivo without using exogenous labels.
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Affiliation(s)
- João Lagarto
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
- Authors contributed equally to this work
| | - Benjamin T. Dyer
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
- Authors contributed equally to this work
| | - Clifford Talbot
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
| | - Markus B. Sikkel
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Nicholas S. Peters
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Paul M. W. French
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
| | - Alexander R. Lyon
- National Heart and Lung Institute, Imperial College London, Du Cane Road, London, W12 0NN
UK
- Authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ
UK
- Authors contributed equally to this work
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36
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Robinson T, Valluri P, Kennedy G, Sardini A, Dunsby C, Neil MAA, Baldwin GS, French PMW, de Mello AJ. Analysis of DNA binding and nucleotide flipping kinetics using two-color two-photon fluorescence lifetime imaging microscopy. Anal Chem 2014; 86:10732-40. [PMID: 25303623 DOI: 10.1021/ac502732s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Uracil DNA glycosylase plays a key role in DNA maintenance via base excision repair. Its role is to bind to DNA, locate unwanted uracil, and remove it using a base flipping mechanism. To date, kinetic analysis of this complex process has been achieved using stopped-flow analysis but, due to limitations in instrumental dead-times, discrimination of the "binding" and "base flipping" steps is compromised. Herein we present a novel approach for analyzing base flipping using a microfluidic mixer and two-color two-photon (2c2p) fluorescence lifetime imaging microscopy (FLIM). We demonstrate that 2c2p FLIM can simultaneously monitor binding and base flipping kinetics within the continuous flow microfluidic mixer, with results showing good agreement with computational fluid dynamics simulations.
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Affiliation(s)
- Tom Robinson
- Institute of Chemical Biology, Department of Chemistry, Imperial College London , London SW7 2AZ, U.K
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37
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Chen L, Kumar S, Kelly D, Andrews N, Dallman MJ, French PMW, McGinty J. Remote focal scanning optical projection tomography with an electrically tunable lens. Biomed Opt Express 2014; 5:3367-75. [PMID: 25360356 PMCID: PMC4206308 DOI: 10.1364/boe.5.003367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/08/2014] [Accepted: 07/23/2014] [Indexed: 05/04/2023]
Abstract
We describe a remote focal scanning technique for optical projection tomography (OPT) implemented with an electrically tunable lens (ETL) that removes the need to scan the specimen or objective lens. Using a 4× objective lens the average spatial resolution is improved by ∼46% and the light collection efficiency by a factor of ∼6.76, thereby enabling increased acquisition speed and reduced light dose. This convenient implementation is particularly appropriate for lower magnifications and larger sample diameters where axial objective scanning would encounter problems with speed and stability.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - Douglas Kelly
- Institute for Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ,
UK
| | - Natalie Andrews
- Institute for Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ,
UK
| | - Margaret J. Dallman
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
- Centre for Integrative Systems Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
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38
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Coda S, Thompson AJ, Kennedy GT, Roche KL, Ayaru L, Bansi DS, Stamp GW, Thillainayagam AV, French PMW, Dunsby C. Fluorescence lifetime spectroscopy of tissue autofluorescence in normal and diseased colon measured ex vivo using a fiber-optic probe. Biomed Opt Express 2014; 5:515-38. [PMID: 24575345 PMCID: PMC3920881 DOI: 10.1364/boe.5.000515] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 10/11/2013] [Accepted: 11/26/2013] [Indexed: 05/20/2023]
Abstract
We present an ex vivo study of temporally and spectrally resolved autofluorescence in a total of 47 endoscopic excision biopsy/resection specimens from colon, using pulsed excitation laser sources operating at wavelengths of 375 nm and 435 nm. A paired analysis of normal and neoplastic (adenomatous polyp) tissue specimens obtained from the same patient yielded a significant difference in the mean spectrally averaged autofluorescence lifetime -570 ± 740 ps (p = 0.021, n = 12). We also investigated the fluorescence signature of non-neoplastic polyps (n = 6) and inflammatory bowel disease (n = 4) compared to normal tissue in a small number of specimens.
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Affiliation(s)
- Sergio Coda
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
- These authors contributed equally to this work
| | - Alex J. Thompson
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- These authors contributed equally to this work
| | - Gordon T. Kennedy
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Kim L. Roche
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Lakshmana Ayaru
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Devinder S. Bansi
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Gordon W. Stamp
- Department of Histopathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Andrew V. Thillainayagam
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Endoscopy Unit, Department of Gastroenterology, Charing Cross Hospital, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
- These authors contributed equally to this work
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- These authors contributed equally to this work
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
- Department of Histopathology, Imperial College London, Du Cane Road, London, W12 0NN, UK
- These authors contributed equally to this work
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39
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Lenz MO, Sinclair HG, Savell A, Clegg JH, Brown ACN, Davis DM, Dunsby C, Neil MAA, French PMW. 3-D stimulated emission depletion microscopy with programmable aberration correction. J Biophotonics 2014; 7:29-36. [PMID: 23788459 DOI: 10.1002/jbio.201300041] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/03/2013] [Accepted: 06/04/2013] [Indexed: 05/18/2023]
Abstract
We present a stimulated emission depletion (STED) microscope that provides 3-D super resolution by simultaneous depletion using beams with both a helical phase profile for enhanced lateral resolution and an annular phase profile to enhance axial resolution. The 3-D depletion point spread function is realised using a single spatial light modulator that can also be programmed to compensate for aberrations in the microscope and the sample. We apply it to demonstrate the first 3-D super-resolved imaging of an immunological synapse between a Natural Killer cell and its target cell.
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Affiliation(s)
- Martin O Lenz
- Photonics Group, Imperial College London, London SW7 2AZ, UK
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40
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Warren SC, Margineanu A, Alibhai D, Kelly DJ, Talbot C, Alexandrov Y, Munro I, Katan M, Dunsby C, French PMW. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets. PLoS One 2013; 8:e70687. [PMID: 23940626 PMCID: PMC3734241 DOI: 10.1371/journal.pone.0070687] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/20/2013] [Indexed: 12/18/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment.
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Affiliation(s)
- Sean C Warren
- Department of Chemistry, Institute for Chemical Biology, Imperial College London, London, United Kingdom.
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41
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Seidenari S, Arginelli F, Dunsby C, French PMW, König K, Magnoni C, Talbot C, Ponti G. Multiphoton laser tomography and fluorescence lifetime imaging of melanoma: morphologic features and quantitative data for sensitive and specific non-invasive diagnostics. PLoS One 2013; 8:e70682. [PMID: 23923016 PMCID: PMC3724798 DOI: 10.1371/journal.pone.0070682] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/21/2013] [Indexed: 11/19/2022] Open
Abstract
Multiphoton laser tomography (MPT) combined with fluorescence lifetime imaging (FLIM) is a non-invasive imaging technique, based on the study of fluorescence decay times of naturally occurring fluorescent molecules, enabling a non-invasive investigation of the skin with subcellular resolution. The aim of this retrospective observational ex vivo study, was to characterize melanoma both from a morphologic and a quantitative point of view, attaining an improvement in the diagnostic accuracy with respect to dermoscopy. In the training phase, thirty parameters, comprising both cytological descriptors and architectural aspects, were identified. The training set included 6 melanomas with a mean Breslow thickness±S.D. of 0.89±0.48 mm. In the test phase, these parameters were blindly evaluated on a test data set consisting of 25 melanomas, 50 nevi and 50 basal cell carcinomas. Melanomas in the test phase comprised 8 in situ lesions and had a mean thickness±S.D. of 0.77±1.2 mm. Moreover, quantitative FLIM data were calculated for special areas of interest. Melanoma was characterized by the presence of atypical short lifetime cells and architectural disorder, in contrast to nevi presenting typical cells and a regular histoarchitecture. Sensitivity and specificity values for melanoma diagnosis were 100% and 98%, respectively, whereas dermoscopy achieved the same sensitivity, but a lower specificity (82%). Mean fluorescence lifetime values of melanocytic cells did not vary between melanomas and nevi, but significantly differed from those referring to basal cell carcinoma enabling a differential diagnosis based on quantitative data. Data from prospective preoperative trials are needed to confirm if MPT/FLIM could increase diagnostic specificity and thus reduce unnecessary surgical excisions.
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Affiliation(s)
- Stefania Seidenari
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Arginelli
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Karsten König
- Department of Biophotonics and Lasertechnology, Saarland University, Saarbrücken, Germany
- JenLab GmbH, Jena, Germany
| | - Cristina Magnoni
- Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy
| | - Clifford Talbot
- Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Giovanni Ponti
- Department of Clinical and Diagnostic Medicine and Public Health, University Hospital of Modena and Reggio Emilia, Modena, Italy
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42
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Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y, Murray EJ, Stuhmeier F, Tate EW, Neil MAA, Dunsby C, French PMW. Automated fluorescence lifetime imaging plate reader and its application to Förster resonant energy transfer readout of Gag protein aggregation. J Biophotonics 2013. [PMID: 23184449 DOI: 10.1002/jbio.v6.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fluorescence lifetime measurements can provide quantitative readouts of local fluorophore environment and can be applied to biomolecular interactions via Förster resonant energy transfer (FRET). Fluorescence lifetime imaging (FLIM) can therefore provide a high content analysis (HCA) modality to map protein-protein interactions (PPIs) with applications in drug discovery, systems biology and basic research. We present here an automated multiwell plate reader able to perform rapid unsupervised optically sectioned FLIM of fixed and live biological samples and illustrate its potential to assay PPIs through application to Gag protein aggregation during the HIV life cycle. We demonstrate both hetero-FRET and homo-FRET readouts of protein aggregation and report the first quantitative evaluation of a FLIM HCA assay by generating dose response curves through addition of an inhibitor of Gag myristoylation. Z' factors exceeding 0.6 are realised for this FLIM FRET assay.
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Affiliation(s)
- Dominic Alibhai
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington Campus, London, UK
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43
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Alibhai D, Kelly DJ, Warren S, Kumar S, Margineau A, Serwa RA, Thinon E, Alexandrov Y, Murray EJ, Stuhmeier F, Tate EW, Neil MAA, Dunsby C, French PMW. Automated fluorescence lifetime imaging plate reader and its application to Förster resonant energy transfer readout of Gag protein aggregation. J Biophotonics 2013; 6:398-408. [PMID: 23184449 PMCID: PMC3660788 DOI: 10.1002/jbio.201200185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 10/05/2012] [Accepted: 10/14/2012] [Indexed: 05/29/2023]
Abstract
Fluorescence lifetime measurements can provide quantitative readouts of local fluorophore environment and can be applied to biomolecular interactions via Förster resonant energy transfer (FRET). Fluorescence lifetime imaging (FLIM) can therefore provide a high content analysis (HCA) modality to map protein-protein interactions (PPIs) with applications in drug discovery, systems biology and basic research. We present here an automated multiwell plate reader able to perform rapid unsupervised optically sectioned FLIM of fixed and live biological samples and illustrate its potential to assay PPIs through application to Gag protein aggregation during the HIV life cycle. We demonstrate both hetero-FRET and homo-FRET readouts of protein aggregation and report the first quantitative evaluation of a FLIM HCA assay by generating dose response curves through addition of an inhibitor of Gag myristoylation. Z' factors exceeding 0.6 are realised for this FLIM FRET assay.
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Affiliation(s)
- Dominic Alibhai
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Douglas J Kelly
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Sean Warren
- Institute of Chemical Biology, Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2A, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Anca Margineau
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Remigiusz A Serwa
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Emmanuelle Thinon
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | | | - Frank Stuhmeier
- Pfizer Worldwide Research and DevelopmentPfizer Limited, Sandwich, Kent, CT13 9NJ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Mark A A Neil
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
- Centre for Histopathology, Imperial College LondonDu Cane Rd, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College LondonSouth Kensington Campus, London, SW7 2AZ, UK
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44
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Chen L, Andrews N, Kumar S, Frankel P, McGinty J, French PMW. Simultaneous angular multiplexing optical projection tomography at shifted focal planes. Opt Lett 2013; 38:851-3. [PMID: 23503237 DOI: 10.1364/ol.38.000851] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We describe an angular multiplexing technique for optical projection tomography that improves resolution, signal-to-noise ratio, and imaging speed by ameliorating the trade-off between spatial resolution and depth of field and improving the light collection efficiency. Here we demonstrate that imaging at two orthogonal angular projections simultaneously, focused on shifted planes in the sample, improves the average spatial resolution by ~20% and the light collection efficiency by a factor of ~4, thereby enabling increased acquisition speed and reduced light dose.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, London, UK.
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45
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Laine R, Stuckey DW, Manning H, Warren SC, Kennedy G, Carling D, Dunsby C, Sardini A, French PMW. Fluorescence lifetime readouts of Troponin-C-based calcium FRET sensors: a quantitative comparison of CFP and mTFP1 as donor fluorophores. PLoS One 2012; 7:e49200. [PMID: 23152874 PMCID: PMC3494685 DOI: 10.1371/journal.pone.0049200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/08/2012] [Indexed: 11/23/2022] Open
Abstract
We have compared the performance of two Troponin-C-based calcium FRET sensors using fluorescence lifetime read-outs. The first sensor, TN-L15, consists of a Troponin-C fragment inserted between CFP and Citrine while the second sensor, called mTFP-TnC-Cit, was realized by replacing CFP in TN-L15 with monomeric Teal Fluorescent Protein (mTFP1). Using cytosol preparations of transiently transfected mammalian cells, we have measured the fluorescence decay profiles of these sensors at controlled concentrations of calcium using time-correlated single photon counting. These data were fitted to discrete exponential decay models using global analysis to determine the FRET efficiency, fraction of donor molecules undergoing FRET and calcium affinity of these sensors. We have also studied the decay profiles of the donor fluorescent proteins alone and determined the sensitivity of the donor lifetime to temperature and emission wavelength. Live-cell fluorescence lifetime imaging (FLIM) of HEK293T cells expressing each of these sensors was also undertaken. We confirmed that donor fluorescence of mTFP-TnC-Cit fits well to a two-component decay model, while the TN-L15 lifetime data was best fitted to a constrained four-component model, which was supported by phasor analysis of the measured lifetime data. If the constrained global fitting is employed, the TN-L15 sensor can provide a larger dynamic range of lifetime readout than the mTFP-TnC-Cit sensor but the CFP donor is significantly more sensitive to changes in temperature and emission wavelength compared to mTFP and, while the mTFP-TnC-Cit solution phase data broadly agreed with measurements in live cells, this was not the case for the TN-L15 sensor. Our titration experiment also indicates that a similar precision in determination of calcium concentration can be achieved with both FRET biosensors when fitting a single exponential donor fluorescence decay model to the fluorescence decay profiles. We therefore suggest that mTFP-based probes are more suitable for FLIM experiments than CFP-based probes.
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Affiliation(s)
- Romain Laine
- Institute of Chemical Biology (ICB), Imperial College of Science, Technology & Medicine, Institute of Chemical Biology (ICB), London, England
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
- * E-mail:
| | - Daniel W. Stuckey
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Hugh Manning
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Sean C. Warren
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Gordon Kennedy
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - David Carling
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Chris Dunsby
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
| | - Alessandro Sardini
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College of Science, Technology & Medicine, London, England
| | - Paul M. W. French
- Photonics Group, Blackett Lab, Imperial College of Science, Technology & Medicine, London, England
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46
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Martins M, Warren S, Kimberley C, Margineanu A, Peschard P, McCarthy A, Yeo M, Marshall CJ, Dunsby C, French PMW, Katan M. Activity of PLCε contributes to chemotaxis of fibroblasts towards PDGF. J Cell Sci 2012; 125:5758-69. [PMID: 22992460 DOI: 10.1242/jcs.110007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Cell chemotaxis, such as migration of fibroblasts towards growth factors during development and wound healing, requires precise spatial coordination of signalling events. Phosphoinositides and signalling enzymes involved in their generation and hydrolysis have been implicated in regulation of chemotaxis; however, the role and importance of specific components remain poorly understood. Here, we demonstrate that phospholipase C epsilon (PLCε) contributes to fibroblast chemotaxis towards platelet-derived growth factor (PDGF-BB). Using PLCe1 null fibroblasts we show that cells deficient in PLCε have greatly reduced directionality towards PDGF-BB without detrimental effect on their basal ability to migrate. Furthermore, we show that in intact fibroblasts, signalling events, such as activation of Rac, are spatially compromised by the absence of PLCε that affects the ability of cells to enlarge their protrusions in the direction of the chemoattractant. By further application of live cell imaging and the use of FRET-based biosensors, we show that generation of Ins(1,4,5)P(3) and recruitment of PLCε are most pronounced in protrusions responding to the PDGF-BB gradient. Furthermore, the phospholipase C activity of PLCε is critical for its role in chemotaxis, consistent with the importance of Ins(1,4,5)P(3) generation and sustained calcium responses in this process. As PLCε has extensive signalling connectivity, using transgenic fibroblasts we ruled out its activation by direct binding to Ras or Rap GTPases, and suggest instead new unexpected links for PLCε in the context of chemotaxis.
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Affiliation(s)
- Marta Martins
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
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47
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Patalay R, Talbot C, Alexandrov Y, Lenz MO, Kumar S, Warren S, Munro I, Neil MAA, König K, French PMW, Chu A, Stamp GWH, Dunsby C. Multiphoton multispectral fluorescence lifetime tomography for the evaluation of basal cell carcinomas. PLoS One 2012; 7:e43460. [PMID: 22984428 PMCID: PMC3439453 DOI: 10.1371/journal.pone.0043460] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/25/2012] [Indexed: 11/19/2022] Open
Abstract
We present the first detailed study using multispectral multiphoton fluorescence lifetime imaging to differentiate basal cell carcinoma cells (BCCs) from normal keratinocytes. Images were acquired from 19 freshly excised BCCs and 27 samples of normal skin (in & ex vivo). Features from fluorescence lifetime images were used to discriminate BCCs with a sensitivity/specificity of 79%/93% respectively. A mosaic of BCC fluorescence lifetime images covering >1 mm2 is also presented, demonstrating the potential for tumour margin delineation. Using 10,462 manually segmented cells from the image data, we quantify the cellular morphology and spectroscopic differences between BCCs and normal skin for the first time. Statistically significant increases were found in the fluorescence lifetimes of cells from BCCs in all spectral channels, ranging from 19.9% (425–515 nm spectral emission) to 39.8% (620–655 nm emission). A discriminant analysis based diagnostic algorithm allowed the fraction of cells classified as malignant to be calculated for each patient. This yielded a receiver operator characteristic area under the curve for the detection of BCC of 0.83. We have used both morphological and spectroscopic parameters to discriminate BCC from normal skin, and provide a comprehensive base for how this technique could be used for BCC assessment in clinical practice.
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Affiliation(s)
- Rakesh Patalay
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
- Department of Dermatology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Clifford Talbot
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Martin O. Lenz
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Sean Warren
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Ian Munro
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Mark A. A. Neil
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | | | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Anthony Chu
- Department of Dermatology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | | | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, United Kingdom
- Department of Medicine, Imperial College Healthcare NHS Trust, London, United Kingdom
- * E-mail:
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48
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Chen L, McGinty J, Taylor HB, Bugeon L, Lamb JR, Dallman MJ, French PMW. Incorporation of an experimentally determined MTF for spatial frequency filtering and deconvolution during optical projection tomography reconstruction. Opt Express 2012; 20:7323-37. [PMID: 22453413 DOI: 10.1364/oe.20.007323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We demonstrate two techniques to improve the quality of reconstructed optical projection tomography (OPT) images using the modulation transfer function (MTF) as a function of defocus experimentally determined from tilted knife-edge measurements. The first employs a 2-D binary filter based on the MTF frequency cut-off as an additional filter during back-projection reconstruction that restricts the high frequency information to the region around the focal plane and progressively decreases the spatial frequency bandwidth with defocus. This helps to suppress "streak" artifacts in OPT data acquired at reduced angular sampling, thereby facilitating faster OPT acquisitions. This method is shown to reduce the average background by approximately 72% for an NA of 0.09 and by approximately 38% for an NA of 0.07 compared to standard filtered back-projection. As a biological illustration, a Fli:GFP transgenic zebrafish embryo (3 days post-fertilisation) was imaged to demonstrate the improved imaging speed (a quarter of the acquisition time). The second method uses the MTF to produce an appropriate deconvolution filter that can be used to correct for the spatial frequency modulation applied by the imaging system.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ, UK.
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49
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Thompson AJ, Coda S, Sørensen MB, Kennedy G, Patalay R, Waitong-Brämming U, De Beule PAA, Neil MAA, Andersson-Engels S, Bendsøe N, French PMW, Svanberg K, Dunsby C. In vivo measurements of diffuse reflectance and time-resolved autofluorescence emission spectra of basal cell carcinomas. J Biophotonics 2012; 5:240-54. [PMID: 22308093 DOI: 10.1002/jbio.201100126] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 12/23/2011] [Accepted: 01/12/2012] [Indexed: 05/20/2023]
Abstract
We present a clinical investigation of diffuse reflectance and time-resolved autofluorescence spectra of skin cancer with an emphasis on basal cell carcinoma. A total of 25 patients were measured using a compact steady-state diffuse reflectance/fluorescence spectrometer and a fibre-optic-coupled multispectral time-resolved spectrofluorometer. Measurements were performed in vivo prior to surgical excision of the investigated region. Singular value decomposition was used to reduce the dimensionality of steady state diffuse reflectance and fluorescence spectra. Linear discriminant analysis was then applied to the measurements of basal cell carcinomas (BCCs) and used to predict the tissue disease state with a leave-one-out methodology. This approach was able to correctly diagnose 87% of the BCCs. With 445 nm excitation a decrease in the spectrally averaged fluorescence lifetime was observed between normal tissue and BCC lesions with a mean value of 886 ps. Furthermore, the fluorescence lifetime for BCCs was lower than that of the surrounding healthy tissue in all cases and statistical analysis of the data revealed that this decrease was significant (p = 0.002).
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Affiliation(s)
- Alex J Thompson
- Photonics Group, Department of Physics, Imperial College, Prince Consort Road, London, UK.
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50
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Soloviev VY, McGinty J, Stuckey DW, Laine R, Wylezinska-Arridge M, Wells DJ, Sardini A, Hajnal JV, French PMW, Arridge SR. Förster resonance energy transfer imaging in vivo with approximated radiative transfer equation. Appl Opt 2011; 50:6583-6590. [PMID: 22193187 PMCID: PMC3492744 DOI: 10.1364/ao.50.006583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We describe a new light transport model, which was applied to three-dimensional lifetime imaging of Förster resonance energy transfer in mice in vivo. The model is an approximation to the radiative transfer equation and combines light diffusion and ray optics. This approximation is well adopted to wide-field time-gated intensity-based data acquisition. Reconstructed image data are presented and compared with results obtained by using the telegraph equation approximation. The new approach provides improved recovery of absorption and scattering parameters while returning similar values for the fluorescence parameters.
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Affiliation(s)
- Vadim Y Soloviev
- Department of Computer Science, University College London, London, UK.
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