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Anselmo S, Sancataldo G, Vetri V. Deciphering amyloid fibril molecular maturation through FLIM-phasor analysis of thioflavin T. BIOPHYSICAL REPORTS 2024; 4:100145. [PMID: 38404533 PMCID: PMC10884809 DOI: 10.1016/j.bpr.2024.100145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024]
Abstract
The investigation of amyloid fibril formation is paramount for advancing our understanding of neurodegenerative diseases and for exploring potential correlated therapeutic strategies. Moreover, the self-assembling properties of amyloid fibrils show promise for the development of advanced protein-based biomaterials. Among the methods employed to monitor protein aggregation processes, fluorescence has emerged as a powerful tool. Its exceptional sensitivity enables the detection of early-stage aggregation events that are otherwise challenging to observe. This research underscores the pivotal role of fluorescence analysis, particularly in investigating the aggregation processes of hen egg white lysozyme, a model protein extensively studied for insights into amyloid fibril formation. By combining classical spectroscopies with fluorescence microscopy and by exploiting the fluorescence properties (intensity and lifetime) of the thioflavin T, we were able to noninvasively monitor key and complex molecular aspects of the process. Intriguingly, the fluorescence lifetime imaging-phasor analysis of thioflavin T fluorescence lifetime on structures at different stages of aggregation allowed to decipher the complex fluorescence decay behavior, highlighting that their changes rise from the combination of specific binding to amyloid typical cross-β structures and of the rigidity of the molecular environment.
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Affiliation(s)
- Sara Anselmo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Giuseppe Sancataldo
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica – Emilio Segré, Università degli Studi di Palermo, Palermo, Italy
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2
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Schuty B, Martínez S, Guerra A, Lecumberry F, Magliano J, Malacrida L. Quantitative melanoma diagnosis using spectral phasor analysis of hyperspectral imaging from label-free slices. Front Oncol 2023; 13:1296826. [PMID: 38162497 PMCID: PMC10756080 DOI: 10.3389/fonc.2023.1296826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Melanoma diagnosis traditionally relies on microscopic examination of hematoxylin and eosin (H&E) slides by dermatopathologists to search for specific architectural and cytological features. Unfortunately, no single molecular marker exists to reliably differentiate melanoma from benign lesions such as nevi. This study explored the potential of autofluorescent molecules within tissues to provide molecular fingerprints indicative of degenerated melanocytes in melanoma. Methods Using hyperspectral imaging (HSI) and spectral phasor analysis, we investigated autofluorescence patterns in melanoma compared to intradermal nevi. Using UV excitation and a commercial spectral confocal microscope, we acquired label-free HSI data from the whole-slice samples. Results Our findings revealed distinct spectral phasor distributions between melanoma and intradermal nevi, with melanoma displaying a broader phasor phase distribution, signifying a more heterogeneous autofluorescence pattern. Notably, longer wavelengths associated with larger phases correlated with regions identified as melanoma by expert dermatopathologists using H&E staining. Quantitative analysis of phase and modulation histograms within the phasor clusters of five melanomas (with Breslow thicknesses ranging from 0.5 mm to 6 mm) and five intradermal nevi consistently highlighted differences between the two groups. We further demonstrated the potential for the discrimination of several melanocytic lesions using center-of-mass comparisons of phase and modulation variables. Remarkably, modulation versus phase center of mass comparisons revealed strong statistical significance among the groups. Additionally, we identified the molecular endogenous markers responsible for tissue autofluorescence, including collagen, elastin, NADH, FAD, and melanin. In melanoma, autofluorescence is characterized by a higher phase contribution, indicating an increase in FAD and melanin in melanocyte nests. In contrast, NADH, elastin, and collagen dominate the autofluorescence of the nevus. Discussion This work underscores the potential of autofluorescence and HSI-phasor analysis as valuable tools for quantifying tissue molecular fingerprints, thereby supporting more effective and quantitative melanoma diagnosis.
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Affiliation(s)
- Bruno Schuty
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
| | - Sofía Martínez
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Analía Guerra
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Federico Lecumberry
- Instituto de Ingeniería Eléctrica, Facultad de Ingeniería, Universidad de la República, Montevideo, Uruguay
| | - Julio Magliano
- Unidad Academica de Dermatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Unidad de Bioimagenología Avanzada, Institut Pasteur de Montevideo, Hospital de Clínicas Universidad de la República, Montevideo, Uruguay
- Unidad Academica de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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3
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Gottlieb D, Asadipour B, Kostina P, Ung TPL, Stringari C. FLUTE: A Python GUI for interactive phasor analysis of FLIM data. BIOLOGICAL IMAGING 2023; 3:e21. [PMID: 38487690 PMCID: PMC10936343 DOI: 10.1017/s2633903x23000211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/16/2023] [Accepted: 10/25/2023] [Indexed: 03/17/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique used to probe the local environment of fluorophores. The fit-free phasor approach to FLIM data is increasingly being used due to its ease of interpretation. To date, no open-source graphical user interface (GUI) for phasor analysis of FLIM data is available in Python, thus limiting the widespread use of phasor analysis in biomedical research. Here, we present Fluorescence Lifetime Ultimate Explorer (FLUTE), a Python GUI that is designed to fill this gap. FLUTE simplifies and automates many aspects of the analysis of FLIM data acquired in the time domain, such as calibrating the FLIM data, performing interactive exploration of the phasor plot, displaying phasor plots and FLIM images with different lifetime contrasts simultaneously, and calculating the distance from known molecular species. After applying desired filters and thresholds, the final edited datasets can be exported for further user-specific analysis. FLUTE has been tested using several FLIM datasets including autofluorescence of zebrafish embryos and in vitro cells. In summary, our user-friendly GUI extends the advantages of phasor plotting by making the data visualization and analysis easy and interactive, allows for analysis of large FLIM datasets, and accelerates FLIM analysis for non-specialized labs.
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Affiliation(s)
- Dale Gottlieb
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Bahar Asadipour
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Polina Kostina
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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4
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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5
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Affiliation(s)
- Leonel Malacrida
- Departamento de Fisiopatología, Facultad de Medicina, Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay.
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay.
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6
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Díaz M, Malacrida L. Advanced Fluorescence Microscopy Methods to Study Dynamics of Fluorescent Proteins In Vivo. Methods Mol Biol 2023; 2564:53-74. [PMID: 36107337 DOI: 10.1007/978-1-0716-2667-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescent proteins are standard tools for addressing biological questions in a cell biology laboratory. The genetic tagging of protein of interest with fluorescent proteins opens the opportunity to follow them in vivo and to understand their interactions and dynamics. In addition, the latest advances in optical microscopy image acquisition and processing allow us to study many cellular processes in vivo. Techniques such as fluorescence lifetime microscopy and hyperspectral imaging provide valuable tools for understanding fluorescent protein interactions and their photophysics. Finally, fluorescence fluctuation analysis opens the possibility to address questions of molecular diffusion, protein-protein interactions, and oligomerization, among others, yielding quantitative information on the subject of study. This chapter will cover some of the more important advances in cutting-edge technologies and methods that, combined with fluorescent proteins, open new frontiers for biological studies.
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Affiliation(s)
- Marcela Díaz
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo & Universidad de la República, Montevideo, Uruguay.
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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7
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Linear Combination Properties of the Phasor Space in Fluorescence Imaging. SENSORS 2022; 22:s22030999. [PMID: 35161742 PMCID: PMC8840623 DOI: 10.3390/s22030999] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
The phasor approach to fluorescence lifetime imaging, and more recently hyperspectral fluorescence imaging, has increased the use of these techniques, and improved the ease and intuitiveness of the data analysis. The fit-free nature of the phasor plots increases the speed of the analysis and reduces the dimensionality, optimization of data handling and storage. The reciprocity principle between the real and imaginary space-where the phasor and the pixel that the phasor originated from are linked and can be converted from one another-has helped the expansion of this method. The phasor coordinates calculated from a pixel, where multiple fluorescent species are present, depends on the phasor positions of those components. The relative positions are governed by the linear combination properties of the phasor space. According to this principle, the phasor position of a pixel with multiple components lies inside the polygon whose vertices are occupied by the phasor positions of these individual components and the distance between the image phasor to any of the vertices is inversely proportional to the fractional intensity contribution of that component to the total fluorescence from that image pixel. The higher the fractional intensity contribution of a vertex, the closer is the resultant phasor. The linear additivity in the phasor space can be exploited to obtain the fractional intensity contribution from multiple species and quantify their contribution. This review details the various mathematical models that can be used to obtain two/three/four components from phasor space with known phasor signatures and then how to obtain both the fractional intensities and phasor positions without any prior knowledge of either, assuming they are mono-exponential in nature. We note that other than for blind components, there are no restrictions on the type of the decay or their phasor positions for linear combinations to be valid-and they are applicable to complicated fluorescence lifetime decays from components with intensity decays described by multi-exponentials.
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8
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Cleland NRW, Al-Juboori SI, Dobrinskikh E, Bruce KD. Altered substrate metabolism in neurodegenerative disease: new insights from metabolic imaging. J Neuroinflammation 2021; 18:248. [PMID: 34711251 PMCID: PMC8555332 DOI: 10.1186/s12974-021-02305-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases (NDs), such as Alzheimer's disease (AD), Parkinson's disease (PD) and multiple sclerosis (MS), are relatively common and devastating neurological disorders. For example, there are 6 million individuals living with AD in the United States, a number that is projected to grow to 14 million by the year 2030. Importantly, AD, PD and MS are all characterized by the lack of a true disease-modifying therapy that is able to reverse or halt disease progression. In addition, the existing standard of care for most NDs only addresses the symptoms of the disease. Therefore, alternative strategies that target mechanisms underlying the neuropathogenesis of disease are much needed. Recent studies have indicated that metabolic alterations in neurons and glia are commonly observed in AD, PD and MS and lead to changes in cell function that can either precede or protect against disease onset and progression. Specifically, single-cell RNAseq studies have shown that AD progression is tightly linked to the metabolic phenotype of microglia, the key immune effector cells of the brain. However, these analyses involve removing cells from their native environment and performing measurements in vitro, influencing metabolic status. Therefore, technical approaches that can accurately assess cell-specific metabolism in situ have the potential to be transformative to our understanding of the mechanisms driving AD. Here, we review our current understanding of metabolism in both neurons and glia during homeostasis and disease. We also evaluate recent advances in metabolic imaging, and discuss how emerging modalities, such as fluorescence lifetime imaging microscopy (FLIM) have the potential to determine how metabolic perturbations may drive the progression of NDs. Finally, we propose that the temporal, regional, and cell-specific characterization of brain metabolism afforded by FLIM will be a critical first step in the rational design of metabolism-focused interventions that delay or even prevent NDs.
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Affiliation(s)
- Nicholas R W Cleland
- Endocrinology, Metabolism and Diabetes, Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Saif I Al-Juboori
- Section of Neonatology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Evgenia Dobrinskikh
- Section of Neonatology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, USA
- Division of Pulmonary Sciences and Critical Care, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Kimberley D Bruce
- Endocrinology, Metabolism and Diabetes, Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, USA.
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9
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Sorrells JE, Iyer RR, Yang L, Bower AJ, Spillman DR, Chaney EJ, Tu H, Boppart SA. Real-time pixelwise phasor analysis for video-rate two-photon fluorescence lifetime imaging microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:4003-4019. [PMID: 34457395 PMCID: PMC8367245 DOI: 10.1364/boe.424533] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 05/06/2023]
Abstract
Two-photon fluorescence lifetime imaging microscopy (FLIM) is a widely used technique in biomedical optical imaging. Presently, many two-photon time-domain FLIM setups are limited by long acquisition and postprocessing times that decrease data throughput and inhibit the ability to image fast sub-second processes. Here, we present a versatile two-photon FLIM setup capable of video-rate (up to 25 fps) imaging with graphics processing unit (GPU)-accelerated pixelwise phasor analysis displayed and saved simultaneously with acquisition. The system uses an analog output photomultiplier tube in conjunction with 12-bit digitization at 3.2 GHz to overcome the limited maximum acceptable photon rate associated with the photon counting electronics in many FLIM systems. This allows for higher throughput FLIM acquisition and analysis, and additionally enables the user to assess sample fluorescence lifetime in real-time. We further explore the capabilities of the system to examine the kinetics of Rhodamine B uptake by human breast cancer cells and characterize the effect of pixel dwell time on the reduced nicotinamide adenine dinucleotide and reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H) autofluorescence lifetime estimation accuracy.
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Affiliation(s)
- Janet E. Sorrells
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rishyashring R. Iyer
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lingxiao Yang
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew J. Bower
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Darold R. Spillman
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric J. Chaney
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haohua Tu
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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10
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Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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11
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Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging. Nat Methods 2021; 18:542-550. [PMID: 33859440 PMCID: PMC10161785 DOI: 10.1038/s41592-021-01108-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 03/03/2021] [Indexed: 02/02/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) and spectral imaging are two broadly applied methods for increasing dimensionality in microscopy. However, their combination is typically inefficient and slow in terms of acquisition and processing. By integrating technological and computational advances, we developed a robust and unbiased spectral FLIM (S-FLIM) system. Our method, Phasor S-FLIM, combines true parallel multichannel digital frequency domain electronics with a multidimensional phasor approach to extract detailed and precise information about the photophysics of fluorescent specimens at optical resolution. To show the flexibility of the Phasor S-FLIM technology and its applications to the biological and biomedical field, we address four common, yet challenging, problems: the blind unmixing of spectral and lifetime signatures from multiple unknown species, the unbiased bleedthrough- and background-free Förster resonance energy transfer analysis of biosensors, the photophysical characterization of environment-sensitive probes in living cells and parallel four-color FLIM imaging in tumor spheroids.
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12
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Gunther G, Malacrida L, Jameson DM, Gratton E, Sánchez SA. LAURDAN since Weber: The Quest for Visualizing Membrane Heterogeneity. Acc Chem Res 2021; 54:976-987. [PMID: 33513300 PMCID: PMC8552415 DOI: 10.1021/acs.accounts.0c00687] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Any chemist studying the interaction of molecules with lipid assemblies will eventually be confronted by the topic of membrane bilayer heterogeneity and may ultimately encounter the heterogeneity of natural membranes. In artificial bilayers, heterogeneity is defined by phase segregation that can be in the nano- and micrometer range. In biological bilayers, heterogeneity is considered in the context of small (10-200 nm) sterol and sphingolipid-enriched heterogeneous and highly dynamic domains. Several techniques can be used to assess membrane heterogeneity in living systems. Our approach is to use a fluorescent reporter molecule immersed in the bilayer, which, by changes in its spectroscopic properties, senses physical-chemistry aspects of the membrane. This dye in combination with microscopy and fluctuation techniques can give information about membrane heterogeneity at different temporal and spatial levels: going from average fluidity to number and diffusion coefficient of nanodomains. LAURDAN (6-dodecanoyl-2-(dimethylamino) naphthalene), is a fluorescent probe designed and synthesized in 1979 by Gregorio Weber with the purpose to study the phenomenon of dipolar relaxation. The spectral displacement observed when LAURDAN is either in fluid or gel phase permitted the use of the technique in the field of membrane dynamics. The quantitation of the spectral displacement was first addressed by the generalized polarization (GP) function in the cuvette, a ratio of the difference in intensity at two wavelengths divided by their sum. In 1997, GP measurements were done for the first time in the microscope, adding to the technique the spatial resolution and allowing the visualization of lipid segregation both in liposomes and cells. A new prospective to the membrane heterogeneity was obtained when LAURDAN fluorescent lifetime measurements were done in the microscope. Two channel lifetime imaging provides information on membrane polarity and dipole relaxation (the two parameters responsible for the spectral shift of LAURDAN), and the application of phasor analysis allows pixel by pixel understanding of these two parameters in the membrane. To increase temporal resolution, LAURDAN GP was combined with fluctuation correlation spectroscopy (FCS) and the motility of nanometric highly packed structures in biological membranes was registered. Lately the application of phasor analysis to spectral images from membranes labeled with LAURDAN allows us to study the full spectra pixel by pixel in an image. All these methodologies, using LAURDAN, offer the possibility to address different properties of membranes depending on the question being asked. In this Account, we will focus on the principles, advantages, and limitations of different approaches to orient the reader to select the most appropriate technique for their research.
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Affiliation(s)
- German Gunther
- Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone P. 1007, Santiago 8380492, Chile
| | - Leonel Malacrida
- Advanced Microscopy and Biophotonics Unit, Hospital de Clínicas, Universidad de la República, Montevideo-Uruguay. Advanced Bioimaging Unit, Institut Pasteur Montevideo, Av. Italia s/n, 90600 Montevideo, Uruguay
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, Biosciences 222, Honolulu, Hawaii 96813, United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, 3210 Natural Sciences II, University of California, Irvine, Irvine, California 92697-2725, United States
| | - Susana A Sánchez
- Departamento de Polímeros, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile
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13
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Vallmitjana A, Torrado B, Dvornikov A, Ranjit S, Gratton E. Blind Resolution of Lifetime Components in Individual Pixels of Fluorescence Lifetime Images Using the Phasor Approach. J Phys Chem B 2020; 124:10126-10137. [PMID: 33140960 DOI: 10.1021/acs.jpcb.0c06946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The phasor approach is used in fluorescence lifetime imaging microscopy for several purposes, notably to calculate the metabolic index of single cells and tissues. An important feature of the phasor approach is that it is a fit-free method allowing immediate and easy to interpret analysis of images. In a recent paper, we showed that three or four intensity fractions of exponential components can be resolved in each pixel of an image by the phasor approach using simple algebra, provided the component phasors are known. This method only makes use of the rule of linear combination of phasors rather than fits. Without prior knowledge of the components and their single exponential decay times, resolution of components and fractions is much more challenging. Blind decomposition has been carried out only for cuvette experiments wherein the statistics in terms of the number of photons collected is very good. In this paper, we show that using the phasor approach and measurements of the decay at phasor harmonics 2 and 3, available using modern electronics, we could resolve the decay in each pixel of an image in live cells or mice liver tissues with two or more exponential components without prior knowledge of the values of the components. In this paper, blind decomposition is achieved using a graphical method for two components and a minimization method for three components. This specific use of the phasor approach to resolve multicomponents in a pixel enables applications where multiplexing species with different lifetimes and potentially different spectra can provide a different type of super-resolved image content.
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Affiliation(s)
- Alexander Vallmitjana
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Belén Torrado
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
| | - Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, D.C., United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, United States
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14
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Ranjit S, Lanzanò L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol 2020; 17:128-144. [PMID: 32948857 DOI: 10.1038/s41581-020-00337-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, in particular immunofluorescence microscopy, has been used extensively for the assessment of kidney function and pathology for both research and diagnostic purposes. The development of confocal microscopy in the 1950s enabled imaging of live cells and intravital imaging of the kidney; however, confocal microscopy is limited by its maximal spatial resolution and depth. More recent advances in fluorescence microscopy techniques have enabled increasingly detailed assessment of kidney structure and provided extraordinary insights into kidney function. For example, nanoscale precise imaging by rapid beam oscillation (nSPIRO) is a super-resolution microscopy technique that was originally developed for functional imaging of kidney microvilli and enables detection of dynamic physiological events in the kidney. A variety of techniques such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) enable assessment of interaction between proteins. The emergence of other super-resolution techniques, including super-resolution stimulated emission depletion (STED), photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM), has enabled functional imaging of cellular and subcellular organelles at ≤50 nm resolution. The deep imaging via emission recovery (DIVER) detector allows deep, label-free and high-sensitivity imaging of second harmonics, enabling assessment of processes such as fibrosis, whereas fluorescence lifetime imaging microscopy (FLIM) enables assessment of metabolic processes.
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Affiliation(s)
- Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA. .,Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA.
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15
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Smith JT, Yao R, Sinsuebphon N, Rudkouskaya A, Un N, Mazurkiewicz J, Barroso M, Yan P, Intes X. Fast fit-free analysis of fluorescence lifetime imaging via deep learning. Proc Natl Acad Sci U S A 2019; 116:24019-24030. [PMID: 31719196 PMCID: PMC6883809 DOI: 10.1073/pnas.1912707116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Fluorescence lifetime imaging (FLI) provides unique quantitative information in biomedical and molecular biology studies but relies on complex data-fitting techniques to derive the quantities of interest. Herein, we propose a fit-free approach in FLI image formation that is based on deep learning (DL) to quantify fluorescence decays simultaneously over a whole image and at fast speeds. We report on a deep neural network (DNN) architecture, named fluorescence lifetime imaging network (FLI-Net) that is designed and trained for different classes of experiments, including visible FLI and near-infrared (NIR) FLI microscopy (FLIM) and NIR gated macroscopy FLI (MFLI). FLI-Net outputs quantitatively the spatially resolved lifetime-based parameters that are typically employed in the field. We validate the utility of the FLI-Net framework by performing quantitative microscopic and preclinical lifetime-based studies across the visible and NIR spectra, as well as across the 2 main data acquisition technologies. These results demonstrate that FLI-Net is well suited to accurately quantify complex fluorescence lifetimes in cells and, in real time, in intact animals without any parameter settings. Hence, FLI-Net paves the way to reproducible and quantitative lifetime studies at unprecedented speeds, for improved dissemination and impact of FLI in many important biomedical applications ranging from fundamental discoveries in molecular and cellular biology to clinical translation.
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Affiliation(s)
- Jason T Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180;
| | - Ruoyang Yao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Nattawut Sinsuebphon
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208
| | - Nathan Un
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Joseph Mazurkiewicz
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208
| | - Pingkun Yan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180;
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16
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Ranjit S, Datta R, Dvornikov A, Gratton E. Multicomponent Analysis of Phasor Plot in a Single Pixel to Calculate Changes of Metabolic Trajectory in Biological Systems. J Phys Chem A 2019; 123:9865-9873. [PMID: 31638388 DOI: 10.1021/acs.jpca.9b07880] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phasor FLIM in cells undergoing oxidative stress and in mice liver sections have shown the presence of a third autofluorescent component indicative of lipid droplets along with free and enzyme-bound NADH with similar emissions. This third component affects the position and shape of the phasor distribution, pushing it away from the metabolic trajectory. Phasor rule of addition is still valid and was exploited here to create a multicomponent analysis where the phasor distribution can be reassigned to the metabolic trajectory and changes in metabolism can be detected independently of the intensity of this third component. Calculation of multiple components from FLIM imaging data of biological systems is a difficult process, especially if different fluorescent species are present at the same pixel. This paper describes the methodology that can be used to separate these multiple components when they are present in the phasor signature acquired in a single pixel of an image.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States.,Department of Biochemistry and Molecular & Cellular Biology , Georgetown University , Washington , D.C. 20057 , United States
| | - Rupsa Datta
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States.,Morgridge Institute for Research , 330 North Orchard Street , Madison , Wisconsin 53715 , United States
| | - Alexander Dvornikov
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States
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17
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Ranjit S, Malacrida L, Stakic M, Gratton E. Determination of the metabolic index using the fluorescence lifetime of free and bound nicotinamide adenine dinucleotide using the phasor approach. JOURNAL OF BIOPHOTONICS 2019; 12:e201900156. [PMID: 31194290 PMCID: PMC6842045 DOI: 10.1002/jbio.201900156] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 05/05/2023]
Abstract
The fluorescence lifetime of nicotinamide adenine dinucleotide (NADH) is commonly used in conjunction with the phasor approach as a molecular biomarker to provide information on cellular metabolism of autofluorescence imaging of cells and tissue. However, in the phasor approach, the bound and free lifetime defining the phasor metabolic trajectory is a subject of debate. The fluorescence lifetime of NADH increases when bound to an enzyme, in contrast to the short multiexponential lifetime displayed by NADH in solution. The extent of fluorescence lifetime increase depends on the enzyme to which NADH is bound. With proper preparation of lactate dehydrogenase (LDH) using oxalic acid (OA) as an allosteric factor, bound NADH to LDH has a lifetime of 3.4 ns and is positioned on the universal semicircle of the phasor plot, inferring a monoexponential lifetime for this species. Surprisingly, measurements in the cellular environments with different metabolic states show a linear trajectory between free NADH at about 0.37 ns and bound NADH at 3.4 ns. These observations support that in a cellular environment, a 3.4 ns value could be used for bound NADH lifetime. The phasor analysis of many cell types shows a linear combination of fractional contributions of free and bound species NADH.
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Affiliation(s)
- Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
- Departamento de Fisiopatología, Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
| | - Milka Stakic
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
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18
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Figueiras E, Silvestre OF, Ihalainen TO, Nieder JB. Phasor-assisted nanoscopy reveals differences in the spatial organization of major nuclear lamina proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118530. [PMID: 31415840 DOI: 10.1016/j.bbamcr.2019.118530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/18/2019] [Accepted: 08/05/2019] [Indexed: 11/15/2022]
Abstract
Phasor-assisted Metal Induced Energy Transfer-Fluorescence Lifetime Imaging Microscopy (MIET-FLIM) nanoscopy is introduced as a powerful tool for functional cell biology research. Thin metal substrates can be used to obtain axial super-resolution via nanoscale distance-dependent MIET from fluorescent dyes towards a nearby metal layer, thereby creating fluorescence lifetime contrast between dyes located at different nanoscale distance from the metal. Such data can be used to achieve axially super-resolved microscopy images, a process known as MIET-FLIM nanoscopy. Suitability of the phasor approach in MIET-FLIM nanoscopy is first demonstrated using nanopatterned substrates, and furthermore applied to characterize the distance distribution of the epithelial basal membrane of a biological cell from the gold substrate. The phasor plot of an entire cell can be used to characterize the full Förster resonance energy transfer (FRET) trajectory as a large distance heterogeneity within the sensing range of about 100 nm from the metal surface is present due to the extended shape of cell with curvatures. In contrast, the different proteins of nuclear lamina show strong confinement close to the nuclear envelope in nanoscale. We find the lamin B layer resides in average at shorter distances from the gold surface compared to the lamin A/C layer located in more extended ranges. This and the observed heterogeneity of the protein layer thicknesses suggests that A- and B-type lamins form distinct networks in the nuclear lamina. Our results provide detailed insights for the study of the different roles of lamin proteins in chromatin tethering and nuclear mechanics.
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Affiliation(s)
- Edite Figueiras
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Oscar F Silvestre
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Teemu O Ihalainen
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, 33014 Tampere, Finland
| | - Jana B Nieder
- Department of Nanophotonics, Ultrafast Bio- and Nanophotonics Group, INL - International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal.
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