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Roy D, Michalet X, Miller EW, Weiss S. Towards optical measurements of membrane potential values in Bacillus subtilis using fluorescence lifetime. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598880. [PMID: 38915670 PMCID: PMC11195253 DOI: 10.1101/2024.06.13.598880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells. While optical measurement based on Nernstian indicators have been successfully used, they do not provide absolute or precise quantification of MP or its changes. We present a novel, calibrated MP recording approach to address this gap. In this study, we used a fluorescence lifetime-based approach to obtain a single-cell resolved distribution of the membrane potential and its changes upon extracellular chemical perturbation in a population of bacterial cells for the first time. Our method is based on (i) a unique VoltageFluor (VF) optical transducer, whose fluorescence lifetime varies as a function of MP via photoinduced electron transfer (PeT) and (ii) a quantitative phasor-FLIM analysis for high-throughput readout. This method allows MP changes to be easily visualized, recorded and quantified. By artificially modulating potassium concentration gradients across the membrane using an ionophore, we have obtained a Bacillus subtilis-specific MP versus VF lifetime calibration and estimated the MP for unperturbed B. subtilis cells to be -65 mV and that for chemically depolarized cells as -14 mV. We observed a population level MP heterogeneity of ~6-10 mV indicating a considerable degree of diversity of physiological and metabolic states among individual cells. Our work paves the way for deeper insights into bacterial electrophysiology and bioelectricity research.
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Affiliation(s)
- Debjit Roy
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
- California Nano Systems Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Evan W. Miller
- Departments of Chemistry, Molecular and Cell Biology, Helen Wills Neuroscience Institute, University of California at Berkeley, CA 94720, USA
| | - Shimon Weiss
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA
- California Nano Systems Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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2
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Smith JT, Liu CJ, Degnan J, Ouellette JN, Conklin MW, Kellner AV, Scribano CM, Hrycyniak L, Oliner JD, Zahm C, Wait E, Eliceiri KW, Rafter J. Label-free fluorescence lifetime imaging for the assessment of cell viability in living tumor fragments. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:S22709. [PMID: 38881557 PMCID: PMC11177118 DOI: 10.1117/1.jbo.29.s2.s22709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024]
Abstract
Significance To enable non-destructive longitudinal assessment of drug agents in intact tumor tissue without the use of disruptive probes, we have designed a label-free method to quantify the health of individual tumor cells in excised tumor tissue using multiphoton fluorescence lifetime imaging microscopy (MP-FLIM). Aim Using murine tumor fragments which preserve the native tumor microenvironment, we seek to demonstrate signals generated by the intrinsically fluorescent metabolic co-factors nicotinamide adenine dinucleotide phosphate [NAD(P)H] and flavin adenine dinucleotide (FAD) correlate with irreversible cascades leading to cell death. Approach We use MP-FLIM of NAD(P)H and FAD on tissues and confirm viability using standard apoptosis and live/dead (Caspase 3/7 and propidium iodide, respectively) assays. Results Through a statistical approach, reproducible shifts in FLIM data, determined through phasor analysis, are shown to correlate with loss of cell viability. With this, we demonstrate that cell death achieved through either apoptosis/necrosis or necroptosis can be discriminated. In addition, specific responses to common chemotherapeutic treatment inducing cell death were detected. Conclusions These data demonstrate that MP-FLIM can detect and quantify cell viability without the use of potentially toxic dyes, thus enabling longitudinal multi-day studies assessing the effects of therapeutic agents on tumor fragments.
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Affiliation(s)
- Jason T Smith
- Elephas, Madison, Wisconsin, United States
- Booz Allen Hamilton, McLean, Virginia, United States
| | - Chao J Liu
- Elephas, Madison, Wisconsin, United States
| | | | | | | | | | | | | | | | - Chris Zahm
- Elephas, Madison, Wisconsin, United States
| | - Eric Wait
- Elephas, Madison, Wisconsin, United States
| | - Kevin W Eliceiri
- Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
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3
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Harel M, Arbiv U, Ankri R. Multiplexed near infrared fluorescence lifetime imaging in turbid media. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:026004. [PMID: 38425720 PMCID: PMC10902792 DOI: 10.1117/1.jbo.29.2.026004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/23/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Significance Fluorescence lifetime imaging (FLI) plays a pivotal role in enhancing our understanding of biological systems, providing a valuable tool for non-invasive exploration of biomolecular and cellular dynamics, both in vitro and in vivo. Its ability to selectively target and multiplex various entities, alongside heightened sensitivity and specificity, offers rapid and cost-effective insights. Aim Our aim is to investigate the multiplexing capabilities of near-infrared (NIR) FLI within a scattering medium that mimics biological tissues. We strive to develop a comprehensive understanding of FLI's potential for multiplexing diverse targets within a complex, tissue-like environment. Approach We introduce an innovative Monte Carlo (MC) simulation approach that accurately describes the scattering behavior of fluorescent photons within turbid media. Applying phasor analyses, we enable the multiplexing of distinct targets within a single FLI image. Leveraging the state-of-the-art single-photon avalanche diode (SPAD) time-gated camera, SPAD512S, we conduct experimental wide-field FLI in the NIR regime. Results Our study demonstrates the successful multiplexing of dual targets within a single FLI image, reaching a depth of 1 cm within tissue-like phantoms. Through our novel MC simulation approach and phasor analyses, we showcase the effectiveness of our methodology in overcoming the challenges posed by scattering media. Conclusions This research underscores the potential of NIR FLI for multiplexing applications in complex biological environments. By combining advanced simulation techniques with cutting-edge experimental tools, we introduce significant results in the non-invasive exploration of biomolecular dynamics, to advance the field of FLI research.
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Affiliation(s)
- Meital Harel
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
| | - Uri Arbiv
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
| | - Rinat Ankri
- Ariel University, Department of Physics, Faculty of Natural Science, Ariel, Israel
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4
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Ochoa M, Smith JT, Gao S, Intes X. Computational macroscopic lifetime imaging and concentration unmixing of autofluorescence. JOURNAL OF BIOPHOTONICS 2022; 15:e202200133. [PMID: 36546622 PMCID: PMC10026351 DOI: 10.1002/jbio.202200133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/06/2022] [Accepted: 07/12/2022] [Indexed: 06/17/2023]
Abstract
Single-pixel computational imaging can leverage highly sensitive detectors that concurrently acquire data across spectral and temporal domains. For molecular imaging, such methodology enables to collect rich intensity and lifetime multiplexed fluorescence datasets. Herein we report on the application of a single-pixel structured light-based platform for macroscopic imaging of tissue autofluorescence. The super-continuum visible excitation and hyperspectral single-pixel detection allow for parallel characterization of autofluorescence intensity and lifetime. Furthermore, we exploit a deep learning based data processing pipeline, to perform autofluorescence unmixing while yielding the autofluorophores' concentrations. The full scheme (setup and processing) is validated in silico and in vitro with clinically relevant autofluorophores flavin adenine dinucleotide, riboflavin, and protoporphyrin. The presented results demonstrate the potential of the methodology for macroscopically quantifying the intensity and lifetime of autofluorophores, with higher specificity for cases of mixed emissions, which are ubiquitous in autofluorescence and multiplexed in vivo imaging.
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Affiliation(s)
- Marien Ochoa
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Jason T Smith
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Shan Gao
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Xavier Intes
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York, USA
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5
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Gao S, Li M, Smith JT, Intes X. Design and characterization of a time-domain optical tomography platform for mesoscopic lifetime imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:4637-4651. [PMID: 36187247 PMCID: PMC9484415 DOI: 10.1364/boe.460216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/17/2022] [Accepted: 07/12/2022] [Indexed: 06/16/2023]
Abstract
We report on the system design and instrumental characteristics of a novel time-domain mesoscopic fluorescence molecular tomography (TD-MFMT) system for multiplexed molecular imaging in turbid media. The system is equipped with a supercontinuum pulsed laser for broad spectral excitation, based on a high-density descanned raster scanning intensity-based acquisition for 2D and 3D imaging and augmented with a high-dynamical range linear time-resolved single-photon avalanche diode (SPAD) array for lifetime quantification. We report on the system's spatio-temporal and spectral characteristics and its sensitivity and specificity in controlled experimental settings. Also, a phantom study is undertaken to test the performance of the system to image deeply-seated fluorescence inclusions in tissue-like media. In addition, ex vivo tumor xenograft imaging is performed to validate the system's applicability to the biological sample. The characterization results manifest the capability to sense small fluorescence concentrations (on the order of nanomolar) while quantifying fluorescence lifetimes and lifetime-based parameters at high resolution. The phantom results demonstrate the system's potential to perform 3D multiplexed imaging thanks to spectral and lifetime contrast in the mesoscopic range (at millimeters depth). The ex vivo imaging exhibits the prospect of TD-MFMT to resolve intra-tumoral heterogeneity in a depth-dependent manner.
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Affiliation(s)
- Shan Gao
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Mengzhou Li
- Biomedical Engineering Department, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jason T. Smith
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xavier Intes
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Smith JT, Rudkouskaya A, Gao S, Gupta JM, Ulku A, Bruschini C, Charbon E, Weiss S, Barroso M, Intes X, Michalet X. In vitro and in vivo NIR fluorescence lifetime imaging with a time-gated SPAD camera. OPTICA 2022; 9:532-544. [PMID: 35968259 PMCID: PMC9368735 DOI: 10.1364/optica.454790] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/27/2022] [Indexed: 05/20/2023]
Abstract
Near-infrared (NIR) fluorescence lifetime imaging (FLI) provides a unique contrast mechanism to monitor biological parameters and molecular events in vivo. Single-photon avalanche diode (SPAD) cameras have been recently demonstrated in FLI microscopy (FLIM) applications, but their suitability for in vivo macroscopic FLI (MFLI) in deep tissues remains to be demonstrated. Herein, we report in vivo NIR MFLI measurement with SwissSPAD2, a large time-gated SPAD camera. We first benchmark its performance in well-controlled in vitro experiments, ranging from monitoring environmental effects on fluorescence lifetime, to quantifying Förster resonant energy transfer (FRET) between dyes. Next, we use it for in vivo studies of target-drug engagement in live and intact tumor xenografts using FRET. Information obtained with SwissSPAD2 was successfully compared to that obtained with a gated intensified charge-coupled device (ICCD) camera, using two different approaches. Our results demonstrate that SPAD cameras offer a powerful technology for in vivo preclinical applications in the NIR window.
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Affiliation(s)
- Jason T. Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Shan Gao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Juhi M. Gupta
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Arin Ulku
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Edoardo Charbon
- AQUA Lab, Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York 12208, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
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Ochoa M, Rudkouskaya A, Smith JT, Intes X, Barroso M. Macroscopic Fluorescence Lifetime Imaging for Monitoring of Drug-Target Engagement. Methods Mol Biol 2022; 2394:837-856. [PMID: 35094361 PMCID: PMC8941982 DOI: 10.1007/978-1-0716-1811-0_44] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Precision medicine promises to improve therapeutic efficacy while reducing adverse effects, especially in oncology. However, despite great progresses in recent years, precision medicine for cancer treatment is not always part of routine care. Indeed, the ability to specifically tailor therapies to distinct patient profiles requires still significant improvements in targeted therapy development as well as decreases in drug treatment failures. In this regard, preclinical animal research is fundamental to advance our understanding of tumor biology, and diagnostic and therapeutic response. Most importantly, the ability to measure drug-target engagement accurately in live and intact animals is critical in guiding the development and optimization of targeted therapy. However, a major limitation of preclinical molecular imaging modalities is their lack of capability to directly and quantitatively discriminate between drug accumulation and drug-target engagement at the pathological site. Recently, we have developed Macroscopic Fluorescence Lifetime Imaging (MFLI) as a unique feature of optical imaging to quantitate in vivo drug-target engagement. MFLI quantitatively reports on nanoscale interactions via lifetime-sensing of Förster Resonance Energy Transfer (FRET) in live, intact animals. Hence, MFLI FRET acts as a direct reporter of receptor dimerization and target engagement via the measurement of the fraction of labeled-donor entity undergoing binding to its respective receptor. MFLI is expected to greatly impact preclinical imaging and also adjacent fields such as image-guided surgery and drug development.
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Affiliation(s)
- Marien Ochoa
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Alena Rudkouskaya
- Department of Cellular and Molecular Physiology, Albany Medical College, Albany, NY, USA
| | - Jason T Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Margarida Barroso
- Department of Cellular and Molecular Physiology, Albany Medical College, Albany, NY, USA.
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8
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Tian L, Hunt B, Bell MAL, Yi J, Smith JT, Ochoa M, Intes X, Durr NJ. Deep Learning in Biomedical Optics. Lasers Surg Med 2021; 53:748-775. [PMID: 34015146 PMCID: PMC8273152 DOI: 10.1002/lsm.23414] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/02/2023]
Abstract
This article reviews deep learning applications in biomedical optics with a particular emphasis on image formation. The review is organized by imaging domains within biomedical optics and includes microscopy, fluorescence lifetime imaging, in vivo microscopy, widefield endoscopy, optical coherence tomography, photoacoustic imaging, diffuse tomography, and functional optical brain imaging. For each of these domains, we summarize how deep learning has been applied and highlight methods by which deep learning can enable new capabilities for optics in medicine. Challenges and opportunities to improve translation and adoption of deep learning in biomedical optics are also summarized. Lasers Surg. Med. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- L. Tian
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - B. Hunt
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - M. A. L. Bell
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - J. Yi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - J. T. Smith
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - M. Ochoa
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - X. Intes
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, New York NY 12180
| | - N. J. Durr
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Dmitriev RI, Intes X, Barroso MM. Luminescence lifetime imaging of three-dimensional biological objects. J Cell Sci 2021; 134:1-17. [PMID: 33961054 PMCID: PMC8126452 DOI: 10.1242/jcs.254763] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A major focus of current biological studies is to fill the knowledge gaps between cell, tissue and organism scales. To this end, a wide array of contemporary optical analytical tools enable multiparameter quantitative imaging of live and fixed cells, three-dimensional (3D) systems, tissues, organs and organisms in the context of their complex spatiotemporal biological and molecular features. In particular, the modalities of luminescence lifetime imaging, comprising fluorescence lifetime imaging (FLI) and phosphorescence lifetime imaging microscopy (PLIM), in synergy with Förster resonance energy transfer (FRET) assays, provide a wealth of information. On the application side, the luminescence lifetime of endogenous molecules inside cells and tissues, overexpressed fluorescent protein fusion biosensor constructs or probes delivered externally provide molecular insights at multiple scales into protein-protein interaction networks, cellular metabolism, dynamics of molecular oxygen and hypoxia, physiologically important ions, and other physical and physiological parameters. Luminescence lifetime imaging offers a unique window into the physiological and structural environment of cells and tissues, enabling a new level of functional and molecular analysis in addition to providing 3D spatially resolved and longitudinal measurements that can range from microscopic to macroscopic scale. We provide an overview of luminescence lifetime imaging and summarize key biological applications from cells and tissues to organisms.
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Affiliation(s)
- Ruslan I. Dmitriev
- Tissue Engineering and Biomaterials Group, Department of
Human Structure and Repair, Faculty of Medicine and Health Sciences,
Ghent University, Ghent 9000,
Belgium
| | - Xavier Intes
- Department of Biomedical Engineering, Center for
Modeling, Simulation and Imaging for Medicine (CeMSIM),
Rensselaer Polytechnic Institute, Troy, NY
12180-3590, USA
| | - Margarida M. Barroso
- Department of Molecular and Cellular
Physiology, Albany Medical College,
Albany, NY 12208, USA
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10
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Michalet X. An overview of continuous and discrete phasor analysis of binned or time-gated periodic decays. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2021; 11648:116480E. [PMID: 33854272 PMCID: PMC8041354 DOI: 10.1117/12.2577747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived and the locus of the phasors of such modified periodic single-exponential decays is compared to the canonical universal semicircle. The effects of IRF offset, decay truncation and gate shape are also discussed. Finally, modified expressions for the phase and modulus lifetimes are provided for some simple cases. A discussion of a modified phasor calibration approach is presented.
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Affiliation(s)
- X Michalet
- Department of Chemistry & Biochemistry, 607 Charles E. Young Drive E., Los Angeles, CA 90095, USA
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11
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Michalet X. Continuous and discrete phasor analysis of binned or time-gated periodic decays. AIP ADVANCES 2021; 11:035331. [PMID: 33786208 PMCID: PMC7990508 DOI: 10.1063/5.0027834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/22/2021] [Indexed: 05/29/2023]
Abstract
The time-resolved analysis of periodically excited luminescence decays by the phasor method in the presence of time-gating or binning is revisited. Analytical expressions for discrete configurations of square gates are derived, and the locus of the phasors of such modified periodic single-exponential decays is compared to the canonical universal semicircle. The effects of instrument response function offset, decay truncation, and gate shape are also discussed. Finally, modified expressions for the phase and modulus lifetimes are provided for some simple cases. A discussion of a modified phasor calibration approach is presented, and an illustration of the new concepts with examples from the literature concludes this work.
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Affiliation(s)
- Xavier Michalet
- Department of Chemistry and Biochemistry, 607 Charles E. Young Drive E., Los Angeles, California 90095, USA
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12
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Quantification of Trastuzumab-HER2 Engagement In Vitro and In Vivo. Molecules 2020; 25:molecules25245976. [PMID: 33348564 PMCID: PMC7767145 DOI: 10.3390/molecules25245976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/22/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Human EGF Receptor 2 (HER2) is an important oncogene driving aggressive metastatic growth in up to 20% of breast cancer tumors. At the same time, it presents a target for passive immunotherapy such as trastuzumab (TZM). Although TZM has been widely used clinically since 1998, not all eligible patients benefit from this therapy due to primary and acquired drug resistance as well as potentially lack of drug exposure. Hence, it is critical to directly quantify TZM–HER2 binding dynamics, also known as cellular target engagement, in undisturbed tumor environments in live, intact tumor xenograft models. Herein, we report the direct measurement of TZM–HER2 binding in HER2-positive human breast cancer cells and tumor xenografts using fluorescence lifetime Forster Resonance Energy Transfer (FLI-FRET) via near-infrared (NIR) microscopy (FLIM-FRET) as well as macroscopy (MFLI-FRET) approaches. By sensing the reduction of fluorescence lifetime of donor-labeled TZM in the presence of acceptor-labeled TZM, we successfully quantified the fraction of HER2-bound and internalized TZM immunoconjugate both in cell culture and tumor xenografts in live animals. Ex vivo immunohistological analysis of tumors confirmed the binding and internalization of TZM–HER2 complex in breast cancer cells. Thus, FLI-FRET imaging presents a powerful analytical tool to monitor and quantify cellular target engagement and subsequent intracellular drug delivery in live HER2-positive tumor xenografts.
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Ochoa M, Rudkouskaya A, Yao R, Yan P, Barroso M, Intes X. High compression deep learning based single-pixel hyperspectral macroscopic fluorescence lifetime imaging in vivo. BIOMEDICAL OPTICS EXPRESS 2020; 11:5401-5424. [PMID: 33149959 PMCID: PMC7587256 DOI: 10.1364/boe.396771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Single pixel imaging frameworks facilitate the acquisition of high-dimensional optical data in biological applications with photon starved conditions. However, they are still limited to slow acquisition times and low pixel resolution. Herein, we propose a convolutional neural network for fluorescence lifetime imaging with compressed sensing at high compression (NetFLICS-CR), which enables in vivo applications at enhanced resolution, acquisition and processing speeds, without the need for experimental training datasets. NetFLICS-CR produces intensity and lifetime reconstructions at 128 × 128 pixel resolution over 16 spectral channels while using only up to 1% of the required measurements, therefore reducing acquisition times from ∼2.5 hours at 50% compression to ∼3 minutes at 99% compression. Its potential is demonstrated in silico, in vitro and for mice in vivo through the monitoring of receptor-ligand interactions in liver and bladder and further imaging of intracellular delivery of the clinical drug Trastuzumab to HER2-positive breast tumor xenografts. The data acquisition time and resolution improvement through NetFLICS-CR, facilitate the translation of single pixel macroscopic flurorescence lifetime imaging (SP-MFLI) for in vivo monitoring of lifetime properties and drug uptake.
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Affiliation(s)
- M. Ochoa
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - A. Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - R. Yao
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - P. Yan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - M. Barroso
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - X. Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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Rudkouskaya A, Sinsuebphon N, Ochoa M, Chen SJ, Mazurkiewicz JE, Intes X, Barroso M. Multiplexed non-invasive tumor imaging of glucose metabolism and receptor-ligand engagement using dark quencher FRET acceptor. Theranostics 2020; 10:10309-10325. [PMID: 32929350 PMCID: PMC7481426 DOI: 10.7150/thno.45825] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/25/2020] [Indexed: 12/31/2022] Open
Abstract
Rationale: Following an ever-increased focus on personalized medicine, there is a continuing need to develop preclinical molecular imaging modalities to guide the development and optimization of targeted therapies. Near-Infrared (NIR) Macroscopic Fluorescence Lifetime Förster Resonance Energy Transfer (MFLI-FRET) imaging offers a unique method to robustly quantify receptor-ligand engagement in live intact animals, which is critical to assess the delivery efficacy of therapeutics. However, to date, non-invasive imaging approaches that can simultaneously measure cellular drug delivery efficacy and metabolic response are lacking. A major challenge for the implementation of concurrent optical and MFLI-FRET in vivo whole-body preclinical imaging is the spectral crowding and cross-contamination between fluorescent probes. Methods: We report on a strategy that relies on a dark quencher enabling simultaneous assessment of receptor-ligand engagement and tumor metabolism in intact live mice. Several optical imaging approaches, such as in vitro NIR FLI microscopy (FLIM) and in vivo wide-field MFLI, were used to validate a novel donor-dark quencher FRET pair. IRDye 800CW 2-deoxyglucose (2-DG) imaging was multiplexed with MFLI-FRET of NIR-labeled transferrin FRET pair (Tf-AF700/Tf-QC-1) to monitor tumor metabolism and probe uptake in breast tumor xenografts in intact live nude mice. Immunohistochemistry was used to validate in vivo imaging results. Results: First, we establish that IRDye QC-1 (QC-1) is an effective NIR dark acceptor for the FRET-induced quenching of donor Alexa Fluor 700 (AF700). Second, we report on simultaneous in vivo imaging of the metabolic probe 2-DG and MFLI-FRET imaging of Tf-AF700/Tf-QC-1 uptake in tumors. Such multiplexed imaging revealed an inverse relationship between 2-DG uptake and Tf intracellular delivery, suggesting that 2-DG signal may predict the efficacy of intracellular targeted delivery. Conclusions: Overall, our methodology enables for the first time simultaneous non-invasive monitoring of intracellular drug delivery and metabolic response in preclinical studies.
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Affiliation(s)
- Alena Rudkouskaya
- Department of Cellular and Molecular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Nattawut Sinsuebphon
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Marien Ochoa
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Sez-Jade Chen
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Joseph E. Mazurkiewicz
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA
| | - Xavier Intes
- Center for Modeling, Simulation, and Imaging in Medicine, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Margarida Barroso
- Department of Cellular and Molecular Physiology, Albany Medical College, Albany, NY 12208, USA
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15
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Smith JT, Ochoa M, Intes X. UNMIX-ME: spectral and lifetime fluorescence unmixing via deep learning. BIOMEDICAL OPTICS EXPRESS 2020; 11:3857-3874. [PMID: 33014571 PMCID: PMC7510912 DOI: 10.1364/boe.391992] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 05/18/2023]
Abstract
Hyperspectral fluorescence lifetime imaging allows for the simultaneous acquisition of spectrally resolved temporal fluorescence emission decays. In turn, the acquired rich multidimensional data set enables simultaneous imaging of multiple fluorescent species for a comprehensive molecular assessment of biotissues. However, to enable quantitative imaging, inherent spectral overlap between the considered fluorescent probes and potential bleed-through must be considered. Such a task is performed via either spectral or lifetime unmixing, typically independently. Herein, we present "UNMIX-ME" (unmix multiple emissions), a deep learning-based fluorescence unmixing routine, capable of quantitative fluorophore unmixing by simultaneously using both spectral and temporal signatures. UNMIX-ME was trained and validated using an in silico framework replicating the data acquisition process of a compressive hyperspectral fluorescent lifetime imaging platform (HMFLI). It was benchmarked against a conventional LSQ method for tri and quadri-exponential simulated samples. Last, UNMIX-ME's potential was assessed for NIR FRET in vitro and in vivo preclinical applications.
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Affiliation(s)
- Jason T Smith
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- These authors contributed equally
| | - Marien Ochoa
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- These authors contributed equally
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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16
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Ulku A, Ardelean A, Antolovic M, Weiss S, Charbon E, Bruschini C, Michalet X. Wide-field time-gated SPAD imager for phasor-based FLIM applications. Methods Appl Fluoresc 2020; 8:024002. [PMID: 31968310 PMCID: PMC8827132 DOI: 10.1088/2050-6120/ab6ed7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe the performance of a new wide area time-gated single-photon avalanche diode (SPAD) array for phasor-FLIM, exploring the effect of gate length, gate number and signal intensity on the measured lifetime accuracy and precision. We conclude that the detector functions essentially as an ideal shot noise limited sensor and is capable of video rate FLIM measurement. The phasor approach used in this work appears ideally suited to handle the large amount of data generated by this type of very large sensor (512 × 512 pixels), even in the case of small number of gates and limited photon budget.
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Affiliation(s)
- Arin Ulku
- AQUA Lab, Ecole Polytechnique Fédérale de
Lausanne (EPFL), Neuchâtel, Switzerland
| | - Andrei Ardelean
- AQUA Lab, Ecole Polytechnique Fédérale de
Lausanne (EPFL), Neuchâtel, Switzerland
| | - Michel Antolovic
- AQUA Lab, Ecole Polytechnique Fédérale de
Lausanne (EPFL), Neuchâtel, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of
California at Los Angeles (UCLA), Los Angeles, California, United States of
America
| | - Edoardo Charbon
- AQUA Lab, Ecole Polytechnique Fédérale de
Lausanne (EPFL), Neuchâtel, Switzerland
| | - Claudio Bruschini
- AQUA Lab, Ecole Polytechnique Fédérale de
Lausanne (EPFL), Neuchâtel, Switzerland
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, University of
California at Los Angeles (UCLA), Los Angeles, California, United States of
America
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17
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Ankri R, Basu A, Ulku AC, Bruschini C, Charbon E, Weiss S, Michalet X. Single-Photon, Time-Gated, Phasor-Based Fluorescence Lifetime Imaging through Highly Scattering Medium. ACS PHOTONICS 2020; 7:68-79. [PMID: 35936550 PMCID: PMC9355389 DOI: 10.1021/acsphotonics.9b00874] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Fluorescence lifetime imaging (FLI) is increasingly recognized as a powerful tool for biochemical and cellular investigations, including in vivo applications. Fluorescence lifetime is an intrinsic characteristic of any fluorescent dye which, to a large extent, does not depend on excitation intensity and signal level. In particular, it allows distinguishing dyes with similar emission spectra, offering additional multiplexing capabilities. However, in vivo FLI in the visible range is complicated by the contamination by (i) tissue autofluorescence, which decreases contrast, and by (ii) light scattering and absorption in tissues, which significantly reduce fluorescence intensity and modify the temporal profile of the signal. Here, we demonstrate how these issues can be accounted for and overcome, using a new time-gated single-photon avalanche diode array camera, SwissSPAD2, combined with phasor analysis to provide a simple and fast visual method for lifetime imaging. In particular, we show how phasor dispersion increases with increasing scattering and/or decreasing fluorescence intensity. Next, we show that as long as the fluorescence signal of interest is larger than the phantom autofluorescence, the presence of a distinct lifetime can be clearly identified with appropriate background correction. We use these results to demonstrate the detection of A459 cells expressing the fluorescent protein mCyRFP1 through highly scattering and autofluorescent phantom layers. These results showcase the possibility to perform FLI in challenging conditions, using standard, bright, visible fluorophore or fluorescence proteins.
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Affiliation(s)
- Rinat Ankri
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
| | - Arkaprabha Basu
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Arin Can Ulku
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Claudio Bruschini
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Edoardo Charbon
- School of Engineering, École Polytechnique Fédérale de Lausanne, Neuchâtel 1015, Switzerland
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
- Corresponding Authors:.
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18
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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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