1
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Wang S, Luo C, Guo J, Hu R, Shen B, Lin F, Zhang C, Liao C, He J, Wang Y, Qu J, Liu L. Enhancing Therapeutic Response and Overcoming Resistance to Checkpoint Inhibitors in Ovarian Cancer through Cell Cycle Regulation. Int J Mol Sci 2024; 25:10018. [PMID: 39337506 PMCID: PMC11431879 DOI: 10.3390/ijms251810018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 09/11/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Tumor cells invade normal surrounding tissues through continuous division. In this study, we hypothesized that cell cycle regulation changes the immune efficacy of ovarian cancer. To investigate this hypothesis, a Förster resonance energy transfer (FRET) sensor was constructed to characterize the cell activity in real time. Cell shrinkage caused by apoptosis induces the aggregation of proteins on the cell membrane, leading to variations in the fluorescence lifetime of FRET sensors. Moreover, we tracked cell activity across various cycles following co-culture with an immune checkpoint inhibitor. Consequently, we assessed how cell cycle regulation influences immunotherapy in a tumor mouse model. This approach, which involves inhibiting typical cell cycle processes, markedly enhances the effectiveness of immunotherapy. Our findings suggest that modulating the cycle progression of cancer cells may represent a promising approach to enhance the immune response of ovarian cancer cells and the efficacy of immunotherapy based on immune checkpoint inhibitors.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Liwei Liu
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province and Ministry of Education, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; (S.W.); (C.L.); (J.G.); (R.H.); (B.S.); (F.L.); (C.Z.); (C.L.); (J.H.); (Y.W.); (J.Q.)
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2
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Kanno H, Hiramatsu K, Mikami H, Nakayashiki A, Yamashita S, Nagai A, Okabe K, Li F, Yin F, Tominaga K, Bicer OF, Noma R, Kiani B, Efa O, Büscher M, Wazawa T, Sonoshita M, Shintaku H, Nagai T, Braun S, Houston JP, Rashad S, Niizuma K, Goda K. High-throughput fluorescence lifetime imaging flow cytometry. Nat Commun 2024; 15:7376. [PMID: 39231964 PMCID: PMC11375057 DOI: 10.1038/s41467-024-51125-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024] Open
Abstract
Flow cytometry is a vital tool in biomedical research and laboratory medicine. However, its accuracy is often compromised by undesired fluctuations in fluorescence intensity. While fluorescence lifetime imaging microscopy (FLIM) bypasses this challenge as fluorescence lifetime remains unaffected by such fluctuations, the full integration of FLIM into flow cytometry has yet to be demonstrated due to speed limitations. Here we overcome the speed limitations in FLIM, thereby enabling high-throughput FLIM flow cytometry at a high rate of over 10,000 cells per second. This is made possible by using dual intensity-modulated continuous-wave beam arrays with complementary modulation frequency pairs for fluorophore excitation and acquiring fluorescence lifetime images of rapidly flowing cells. Moreover, our FLIM system distinguishes subpopulations in male rat glioma and captures dynamic changes in the cell nucleus induced by an anti-cancer drug. FLIM flow cytometry significantly enhances cellular analysis capabilities, providing detailed insights into cellular functions, interactions, and environments.
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Affiliation(s)
- Hiroshi Kanno
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Miyagi, Japan.
| | - Kotaro Hiramatsu
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- Department of Chemistry, Kyushu University, Fukuoka, Japan
| | - Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
- Research Institute for Electronic Science, Hokkaido University, Hokkaido, Japan
| | - Atsushi Nakayashiki
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Shota Yamashita
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Arata Nagai
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Fan Li
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Fei Yin
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Keita Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | | | - Ryohei Noma
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Bahareh Kiani
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Olga Efa
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Martin Büscher
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Tetsuichi Wazawa
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | | | - Hirofumi Shintaku
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takeharu Nagai
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Osaka, Japan
| | - Sigurd Braun
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jessica P Houston
- Department of Chemical and Materials Engineering, New Mexico State University, Las Cruces, NM, USA
| | - Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Miyagi, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience Graduate School of Biomedical Engineering, Tohoku University, Miyagi, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.
- Institute of Technological Sciences, Wuhan University, Hubei, China.
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
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3
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Sarkar M, Raj R R, Maliekal TT. Finding the partner: FRET and beyond. Exp Cell Res 2024; 441:114166. [PMID: 39029572 DOI: 10.1016/j.yexcr.2024.114166] [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] [Received: 04/09/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
Given the importance of aberrant protein-protein interactions (PPIs) in disease, the recent drug discovery focuses on targeting the altered PPIs to treat the disease. In this context, identifying the atypical PPIs underlying the disease is critical for the development of diagnostics and therapeutics. Various biochemical, biophysical, and genetic methods have been reported to study PPIs. Here, we are giving a short account of those techniques with more emphasis on Förster resonance energy transfer (FRET), which can be used to monitor macromolecular interactions in live cells. Besides the basics of FRET, we explain the modifications of its application, like Single molecule FRET (smFRET), Fluorescence Lifetime Imaging Microscopy-FRET (FLIM-FRET), and photoswitching FRET. While smFRET is extensively used for evaluating the biology of nucleic acids and also to develop diagnostics, FLIM-FRET is widely exploited to study the PPIs underlying neurological disorders and cancer. Photoswitching FRET is a relatively newer technique and it has tremendous potential to unravel the significance of different PPIs. Besides these modifications, there are several advancements in the field by introducing new fluorophores. Identification of lanthanide chelates, quantum dots, and other nanoparticle fluorophores has revolutionized the applications of FRET in diagnostics and basic biology. Yet, these methods can be employed to study the interactions of only two molecules. Since the majority of the PPIs are multimeric complexes, we still need to improve our technologies to study these interactions in live cells in real-time.
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Affiliation(s)
- Meghna Sarkar
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Reshma Raj R
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India.
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4
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Mandrou E, Thomason PA, Paschke PI, Paul NR, Tweedy L, Insall RH. A Reliable System for Quantitative G-Protein Activation Imaging in Cancer Cells. Cells 2024; 13:1114. [PMID: 38994966 PMCID: PMC11240385 DOI: 10.3390/cells13131114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/13/2024] Open
Abstract
Fluorescence resonance energy transfer (FRET) biosensors have proven to be an indispensable tool in cell biology and, more specifically, in the study of G-protein signalling. The best method of measuring the activation status or FRET state of a biosensor is often fluorescence lifetime imaging microscopy (FLIM), as it does away with many disadvantages inherent to fluorescence intensity-based methods and is easily quantitated. Despite the significant potential, there is a lack of reliable FLIM-FRET biosensors, and the data processing and analysis workflows reported previously face reproducibility challenges. Here, we established a system in live primary mouse pancreatic ductal adenocarcinoma cells, where we can detect the activation of an mNeonGreen-Gαi3-mCherry-Gγ2 biosensor through the lysophosphatidic acid receptor (LPAR) with 2-photon time-correlated single-photon counting (TCSPC) FLIM. This combination gave a superior signal to the commonly used mTurquoise2-mVenus G-protein biosensor. This system has potential as a platform for drug screening, or to answer basic cell biology questions in the field of G-protein signalling.
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Affiliation(s)
- Elena Mandrou
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
| | | | | | - Nikki R. Paul
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
| | - Luke Tweedy
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
| | - Robert H. Insall
- CRUK Scotland Institute, Garscube Campus, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK
- Division of Cell & Developmental Biology, University College London, London WC1E 6BT, UK
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5
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Bae S, Sung K, Kim SK. Linear spectral unmixing analysis in single-molecule FRET spectroscopy for fluorophores with large spectral overlap. Phys Chem Chem Phys 2024; 26:16561-16566. [PMID: 38832676 DOI: 10.1039/d4cp00736k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Fluorescence resonance energy transfer (FRET) is a highly useful tool to investigate biomolecular interactions and dynamics in single-molecule spectroscopy and nanoscopy. However, the use of spectrally overlapping dye pairs results in various artifact signals that prevent accurate determination of FRET values. In this paper, an algorithmic method of spectral unmixing was devised to extract FRET values of spectrally overlapping dye pairs at the single molecule level. Application of this method allows the determination of both the donor-acceptor composition and the FRET efficiency of the samples labelled with spectrally overlapping dye pairs.
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Affiliation(s)
- Sohyeon Bae
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
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6
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Nguyen TD, Chen YI, Nguyen AT, Yonas S, Sripati MP, Kuo YA, Hong S, Litvinov M, He Y, Yeh HC, Grady Rylander H. Two-photon autofluorescence lifetime assay of rabbit photoreceptors and retinal pigment epithelium during light-dark visual cycles in rabbit retina. BIOMEDICAL OPTICS EXPRESS 2024; 15:3094-3111. [PMID: 38855698 PMCID: PMC11161359 DOI: 10.1364/boe.511806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 06/11/2024]
Abstract
Two-photon excited fluorescence (TPEF) is a powerful technique that enables the examination of intrinsic retinal fluorophores involved in cellular metabolism and the visual cycle. Although previous intensity-based TPEF studies in non-human primates have successfully imaged several classes of retinal cells and elucidated aspects of both rod and cone photoreceptor function, fluorescence lifetime imaging (FLIM) of the retinal cells under light-dark visual cycle has yet to be fully exploited. Here we demonstrate a FLIM assay of photoreceptors and retinal pigment epithelium (RPE) that reveals key insights into retinal physiology and adaptation. We found that photoreceptor fluorescence lifetimes increase and decrease in sync with light and dark exposure, respectively. This is likely due to changes in all-trans-retinol and all-trans-retinal levels in the outer segments, mediated by phototransduction and visual cycle activity. During light exposure, RPE fluorescence lifetime was observed to increase steadily over time, as a result of all-trans-retinol accumulation during the visual cycle and decreasing metabolism caused by the lack of normal perfusion of the sample. Our system can measure the fluorescence lifetime of intrinsic retinal fluorophores on a cellular scale, revealing differences in lifetime between retinal cell classes under different conditions of light and dark exposure.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Anh-Thu Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Siem Yonas
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Manasa P Sripati
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mitchell Litvinov
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yujie He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
| | - H Grady Rylander
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
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7
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Trujillo J, Khan AS, Adhikari DP, Stoneman MR, Chacko JV, Eliceiri KW, Raicu V. Implementation of FRET Spectrometry Using Temporally Resolved Fluorescence: A Feasibility Study. Int J Mol Sci 2024; 25:4706. [PMID: 38731924 PMCID: PMC11083457 DOI: 10.3390/ijms25094706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Förster resonance energy transfer (FRET) spectrometry is a method for determining the quaternary structure of protein oligomers from distributions of FRET efficiencies that are drawn from pixels of fluorescence images of cells expressing the proteins of interest. FRET spectrometry protocols currently rely on obtaining spectrally resolved fluorescence data from intensity-based experiments. Another imaging method, fluorescence lifetime imaging microscopy (FLIM), is a widely used alternative to compute FRET efficiencies for each pixel in an image from the reduction of the fluorescence lifetime of the donors caused by FRET. In FLIM studies of oligomers with different proportions of donors and acceptors, the donor lifetimes may be obtained by fitting the temporally resolved fluorescence decay data with a predetermined number of exponential decay curves. However, this requires knowledge of the number and the relative arrangement of the fluorescent proteins in the sample, which is precisely the goal of FRET spectrometry, thus creating a conundrum that has prevented users of FLIM instruments from performing FRET spectrometry. Here, we describe an attempt to implement FRET spectrometry on temporally resolved fluorescence microscopes by using an integration-based method of computing the FRET efficiency from fluorescence decay curves. This method, which we dubbed time-integrated FRET (or tiFRET), was tested on oligomeric fluorescent protein constructs expressed in the cytoplasm of living cells. The present results show that tiFRET is a promising way of implementing FRET spectrometry and suggest potential instrument adjustments for increasing accuracy and resolution in this kind of study.
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Affiliation(s)
- Justin Trujillo
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Aliyah S. Khan
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Dhruba P. Adhikari
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Michael R. Stoneman
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
| | - Jenu V. Chacko
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
| | - Kevin W. Eliceiri
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53705, USA; (J.V.C.); (K.W.E.)
- Departments of Biomedical Engineering and Medical Physics, University of Wisconsin-Madison, Madison, WI 53705, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Valerica Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA; (J.T.); (A.S.K.); (D.P.A.); (M.R.S.)
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8
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Mehl BP, Vairaprakash P, Li L, Hinde E, MacNevin CJ, Hsu CW, Gratton E, Liu B, Hahn KM. Live-cell biosensors based on the fluorescence lifetime of environment-sensing dyes. CELL REPORTS METHODS 2024; 4:100734. [PMID: 38503289 PMCID: PMC10985238 DOI: 10.1016/j.crmeth.2024.100734] [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: 02/03/2022] [Revised: 03/13/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024]
Abstract
In this work, we examine the use of environment-sensitive fluorescent dyes in fluorescence lifetime imaging microscopy (FLIM) biosensors. We screened merocyanine dyes to find an optimal combination of environment-induced lifetime changes, photostability, and brightness at wavelengths suitable for live-cell imaging. FLIM was used to monitor a biosensor reporting conformational changes of endogenous Cdc42 in living cells. The ability to quantify activity using phasor analysis of a single fluorophore (e.g., rather than ratio imaging) eliminated potential artifacts. We leveraged these properties to determine specific concentrations of activated Cdc42 across the cell.
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Affiliation(s)
- Brian P Mehl
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pothiappan Vairaprakash
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Li
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Christopher J MacNevin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chia-Wen Hsu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92617, USA
| | - Bei Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Klaus M Hahn
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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9
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Zhou Y, Wang Y, Zhang D, Liang J. Endomembrane-biased dimerization of ABCG16 and ABCG25 transporters determines their substrate selectivity in ABA-regulated plant growth and stress responses. MOLECULAR PLANT 2024; 17:478-495. [PMID: 38327051 DOI: 10.1016/j.molp.2024.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/28/2023] [Accepted: 02/05/2024] [Indexed: 02/09/2024]
Abstract
ATP-binding cassette (ABC) transporters are integral membrane proteins that have evolved diverse functions fulfilled via the transport of various substrates. In Arabidopsis, the G subfamily of ABC proteins is particularly abundant and participates in multiple signaling pathways during plant development and stress responses. In this study, we revealed that two Arabidopsis ABCG transporters, ABCG16 and ABCG25, engage in ABA-mediated stress responses and early plant growth through endomembrane-specific dimerization-coupled transport of ABA and ABA-glucosyl ester (ABA-GE), respectively. We first revealed that ABCG16 contributes to osmotic stress tolerance via ABA signaling. More specifically, ABCG16 induces cellular ABA efflux in both yeast and plant cells. Using FRET analysis, we showed that ABCG16 forms obligatory homodimers for ABA export activity and that the plasma membrane-resident ABCG16 homodimers specifically respond to ABA, undergoing notable conformational changes. Furthermore, we demonstrated that ABCG16 heterodimerizes with ABCG25 at the endoplasmic reticulum (ER) membrane and facilitates the ER entry of ABA-GE in both Arabidopsis and tobacco cells. The specific responsiveness of the ABCG16-ABCG25 heterodimer to ABA-GE and the superior growth of their double mutant support an inhibitory role of these two ABCGs in early seedling establishment via regulation of ABA-GE translocation across the ER membrane. Our endomembrane-specific analysis of the FRET signals derived from the homo- or heterodimerized ABCG complexes allowed us to link endomembrane-biased dimerization to the translocation of distinct substrates by ABCG transporters, providing a prototypic framework for understanding the omnipotence of ABCG transporters in plant development and stress responses.
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Affiliation(s)
- Yeling Zhou
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
| | - Yuzhu Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Dong Zhang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Jiansheng Liang
- Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China.
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10
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Lin Y, Mos P, Ardelean A, Bruschini C, Charbon E. Coupling a recurrent neural network to SPAD TCSPC systems for real-time fluorescence lifetime imaging. Sci Rep 2024; 14:3286. [PMID: 38331957 PMCID: PMC10853568 DOI: 10.1038/s41598-024-52966-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Fluorescence lifetime imaging (FLI) has been receiving increased attention in recent years as a powerful diagnostic technique in biological and medical research. However, existing FLI systems often suffer from a tradeoff between processing speed, accuracy, and robustness. Inspired by the concept of Edge Artificial Intelligence (Edge AI), we propose a robust approach that enables fast FLI with no degradation of accuracy. This approach couples a recurrent neural network (RNN), which is trained to estimate the fluorescence lifetime directly from raw timestamps without building histograms, to SPAD TCSPC systems, thereby drastically reducing transfer data volumes and hardware resource utilization, and enabling real-time FLI acquisition. We train two variants of the RNN on a synthetic dataset and compare the results to those obtained using center-of-mass method (CMM) and least squares fitting (LS fitting). Results demonstrate that two RNN variants, gated recurrent unit (GRU) and long short-term memory (LSTM), are comparable to CMM and LS fitting in terms of accuracy, while outperforming them in the presence of background noise by a large margin. To explore the ultimate limits of the approach, we derive the Cramer-Rao lower bound of the measurement, showing that RNN yields lifetime estimations with near-optimal precision. To demonstrate real-time operation, we build a FLI microscope based on an existing SPAD TCSPC system comprising a 32[Formula: see text]32 SPAD sensor named Piccolo. Four quantized GRU cores, capable of processing up to 4 million photons per second, are deployed on the Xilinx Kintex-7 FPGA that controls the Piccolo. Powered by the GRU, the FLI setup can retrieve real-time fluorescence lifetime images at up to 10 frames per second. The proposed FLI system is promising and ideally suited for biomedical applications, including biological imaging, biomedical diagnostics, and fluorescence-assisted surgery, etc.
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Affiliation(s)
- Yang Lin
- Advanced Quantum Architecture Laboratory, École polytechnique fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Paul Mos
- Advanced Quantum Architecture Laboratory, École polytechnique fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Andrei Ardelean
- Advanced Quantum Architecture Laboratory, École polytechnique fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Claudio Bruschini
- Advanced Quantum Architecture Laboratory, École polytechnique fédérale de Lausanne, Neuchâtel, 2002, Switzerland
| | - Edoardo Charbon
- Advanced Quantum Architecture Laboratory, École polytechnique fédérale de Lausanne, Neuchâtel, 2002, Switzerland.
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11
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Nguyen TD, Chen YI, Nguyen AT, Chen LH, Yonas S, Litvinov M, He Y, Kuo YA, Hong S, Rylander HG, Yeh HC. Multiplexed imaging in live cells using pulsed interleaved excitation spectral FLIM. OPTICS EXPRESS 2024; 32:3290-3307. [PMID: 38297554 PMCID: PMC11018333 DOI: 10.1364/oe.505667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Multiplexed fluorescence detection has become increasingly important in the fields of biosensing and bioimaging. Although a variety of excitation/detection optical designs and fluorescence unmixing schemes have been proposed to allow for multiplexed imaging, rapid and reliable differentiation and quantification of multiple fluorescent species at each imaging pixel is still challenging. Here we present a pulsed interleaved excitation spectral fluorescence lifetime microscopic (PIE-sFLIM) system that can simultaneously image six fluorescent tags in live cells in a single hyperspectral snapshot. Using an alternating pulsed laser excitation scheme at two different wavelengths and a synchronized 16-channel time-resolved spectral detector, our PIE-sFLIM system can effectively excite multiple fluorophores and collect their emission over a broad spectrum for analysis. Combining our system with the advanced live-cell labeling techniques and the lifetime/spectral phasor analysis, our PIE-sFLIM approach can well unmix the fluorescence of six fluorophores acquired in a single measurement, thus improving the imaging speed in live-specimen investigation.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Anh-Thu Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Limin H. Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Siem Yonas
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mitchell Litvinov
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yujie He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - H. Grady Rylander
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
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12
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Mehlhorn D, Wallmeroth N, Berendzen KW, Grefen C. 2 in 1 Vectors Improve in Planta BiFC and FRET Analysis. Methods Mol Biol 2024; 2772:149-168. [PMID: 38411812 DOI: 10.1007/978-1-0716-3710-4_11] [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: 02/28/2024]
Abstract
Protein-protein interactions (PPIs) play vital roles in all subcellular processes, and a number of tools have been developed for their detection and analysis. Each method has its unique set of benefits and drawbacks that need to be considered prior application. In fact, researchers are spoilt for choice when it comes to deciding which method to use for the initial detection of a PPI and which to corroborate the findings. With constant improvements in microscope development, the possibilities of techniques to study PPIs in vivo, and in real time, are continuously enhanced and expanded. Here, we describe three common approaches, their recent improvements incorporating a 2-in-1 cloning approach, and their application in plant cell biology: ratiometric bimolecular fluorescence complementation (rBiFC), FRET acceptor photobleaching (FRET-AB), and fluorescent lifetime imaging (FRET-FLIM), using Nicotiana benthamiana leaves and Arabidopsis thaliana cell culture protoplasts as transient expression systems.
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Affiliation(s)
- Dietmar Mehlhorn
- Molecular & Cellular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Niklas Wallmeroth
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kenneth W Berendzen
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
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13
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Perego E, Zappone S, Castagnetti F, Mariani D, Vitiello E, Rupert J, Zacco E, Tartaglia GG, Bozzoni I, Slenders E, Vicidomini G. Single-photon microscopy to study biomolecular condensates. Nat Commun 2023; 14:8224. [PMID: 38086853 PMCID: PMC10716487 DOI: 10.1038/s41467-023-43969-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Biomolecular condensates serve as membrane-less compartments within cells, concentrating proteins and nucleic acids to facilitate precise spatial and temporal orchestration of various biological processes. The diversity of these processes and the substantial variability in condensate characteristics present a formidable challenge for quantifying their molecular dynamics, surpassing the capabilities of conventional microscopy. Here, we show that our single-photon microscope provides a comprehensive live-cell spectroscopy and imaging framework for investigating biomolecular condensation. Leveraging a single-photon detector array, single-photon microscopy enhances the potential of quantitative confocal microscopy by providing access to fluorescence signals at the single-photon level. Our platform incorporates photon spatiotemporal tagging, which allowed us to perform time-lapse super-resolved imaging for molecular sub-diffraction environment organization with simultaneous monitoring of molecular mobility, interactions, and nano-environment properties through fluorescence lifetime fluctuation spectroscopy. This integrated correlative study reveals the dynamics and interactions of RNA-binding proteins involved in forming stress granules, a specific type of biomolecular condensates, across a wide range of spatial and temporal scales. Our versatile framework opens up avenues for exploring a broad spectrum of biomolecular processes beyond the formation of membrane-less organelles.
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Affiliation(s)
- Eleonora Perego
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Sabrina Zappone
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Genoa, Italy
| | - Francesco Castagnetti
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Davide Mariani
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Erika Vitiello
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Jakob Rupert
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Elsa Zacco
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Gian Gaetano Tartaglia
- RNA Systems Biology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Irene Bozzoni
- Non coding RNAs in Physiology and Pathology, Istituto Italiano di Tecnologia, Genoa, Italy
- Department of Biology and Biotechnologies 'C. Darwin', Sapienza University of Rome, Rome, Italy
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.
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14
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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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15
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Zhu H, Kamiya Y, Asanuma H. Illuminating miRNA Inhibition: Visualizing the Interaction between Anti-miRNA Oligonucleotide and Target miRNA Using FRET. ACS Chem Biol 2023; 18:2281-2289. [PMID: 37789826 DOI: 10.1021/acschembio.3c00353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Anti-miRNA oligonucleotides (anti-miRs) effectively and specifically inhibit the function of individual miRNAs and have the potential to serve as a novel class of nucleic acid therapeutic. However, the details of the mechanisms of anti-miRs in cells have not yet been clarified sufficiently. In particular, the localization of the complexes of anti-miRs and target miRNA in cells remains unclear. We previously developed anti-miRs composed of serinol nucleic acid (SNA) that very effectively inhibited miRNA-mediated silencing activity. Here we describe an imaging system based on the fluorescence resonance energy transfer (FRET) designed by miRNAs labeled with fluorophore-quencher pairs and an SNA-based anti-miR labeled with an acceptor dye. We discovered that the anti-miR hybridizes with the miRNA in the miRNA-induced silencing complex (miRISC), which is the active complex formed by miRNA and Ago2 in cells within P-bodies. Based on FRET ratio analysis, we hypothesize that the complex formed by the anti-miR and the miRNA in P-bodies is dynamic, with anti-miR complexing the miRISC, followed by miRNA release and degradation. Our findings provide valuable insights into the mechanism of action of anti-miRs and enable further studies of miRNA-targeted therapeutics.
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Affiliation(s)
- Hongyu Zhu
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Department of Bimolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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16
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Liu C, Liu D, Wang S, Gan L, Yang X, Ma C. Identification of the SNARE complex that mediates the fusion of multivesicular bodies with the plasma membrane in exosome secretion. J Extracell Vesicles 2023; 12:e12356. [PMID: 37700095 PMCID: PMC10497535 DOI: 10.1002/jev2.12356] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/25/2023] [Indexed: 09/14/2023] Open
Abstract
Exosomes play crucial roles in local and distant cellular communication and are involved in various physiological and pathological processes. Tumour-derived exosomes are pivotal to tumorigenesis, but the precise mechanisms underlying their secretion remain elusive. In particular, the SNARE proteins that mediate the fusion of multivesicular bodies (MVBs) with the plasma membrane (PM) in tumour cells are subject to debate. In this study, we identified syntaxin-4, SNAP-23, and VAMP-7 as the SNAREs responsible for exosome secretion in MCF-7 breast cancer cells and found that a SNARE complex consisting of these SNAREs can drive membrane fusion in vitro. Deletion of any of these SNAREs in MCF-7 cells did not affect MVB biogenesis and transportation, indicating their specific involvement in MVB-PM fusion. In addition, syntaxin-4, SNAP-23, and VAMP-7 play equivalent roles in exosome secretion in both HeLa cervical cancer cells and A375 melanoma cells, suggesting their conserved function in exosome secretion. Furthermore, deletion of VAMP-7 in 4T1 mammary carcinoma cells efficiently inhibited exosome secretion and led to significant attenuation of tumour growth and lung metastasis in mouse models, implying that VAMP-7 may hold promise as a novel therapeutic target for breast cancer.
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Affiliation(s)
- Chuqi Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Dexiang Liu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Lu Gan
- National Engineering Research Center for Nanomedicine, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaHuazhong University of Science and TechnologyWuhanChina
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaHuazhong University of Science and TechnologyWuhanChina
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia MedicaHuazhong University of Science and TechnologyWuhanChina
- GBA Research Innovation Institute for NanotechnologyGuangzhouGuangdongP. R. China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
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17
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Rinaldi DA, Kanagy WK, Kaye HC, Grattan RM, Lucero SR, Pérez MP, Wester MJ, Lidke KA, Wilson BS, Lidke DS. Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552060. [PMID: 37609336 PMCID: PMC10441289 DOI: 10.1101/2023.08.04.552060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Immunoreceptor tyrosine-based activation motif (ITAM)-containing Fc receptors are critical components of the innate and adaptive immune systems. FcεRI mediates the allergic response via crosslinking of IgE-bound receptors by multivalent antigens. Yet, the underlying molecular mechanisms that govern the response of FcεRI to specific antigens remain poorly understood. We compared responses induced by two antigens with distinct geometries, high valency DNP-BSA and trivalent DF3, and found unique secretion and receptor phosphorylation profiles that are due to differential recruitment of Lyn and SHIP1. To understand how these two antigens can cause such markedly different outcomes, we used direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging combined with Bayesian Grouping of Localizations (BaGoL) analysis to compare the nanoscale characteristics of FcεRI aggregates. DF3 aggregates were found to be smaller and more densely packed than DNP-BSA aggregates. Using lifetime-based Förster resonance energy transfer (FRET) measurements, we discovered that FcεRI subunits undergo structural rearrangements upon crosslinking with either antigen, and in response to interaction with monovalent antigen presented on a supported lipid bilayer. The extent of conformational change is positively correlated with signaling efficiency. Finally, we provide evidence for forces in optimizing FcεRI signaling, such that immobilizing DF3 on a rigid surface promoted degranulation while increasing DNP-BSA flexibility lowered degranulation. These results provide a link between the physical attributes of allergens, including size, shape, valency, and flexibility, and FcεRI signaling strength. Thus, the antigen modulates mast cell outcomes by creating unique aggregate geometries that tune FcεRI conformation, phosphorylation and signaling partner recruitment.
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Affiliation(s)
- Derek A. Rinaldi
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - William K. Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Present address: Department of Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Hannah C. Kaye
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Rachel M. Grattan
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Shayna R. Lucero
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | | | - Michael J. Wester
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Keith A. Lidke
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
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18
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van Zanten TS, S GP, Mayor S. Quantitative fluorescence emission anisotropy microscopy for implementing homo-fluorescence resonance energy transfer measurements in living cells. Mol Biol Cell 2023; 34:tp1. [PMID: 37144969 DOI: 10.1091/mbc.e22-09-0446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Quantitative fluorescence emission anisotropy microscopy reveals the organization of fluorescently labeled cellular components and allows their characterization in terms of changes in either rotational diffusion or homo-Förster's energy transfer characteristics in living cells. These properties provide insights into molecular organization, such as orientation, confinement, and oligomerization in situ. Here we elucidate how quantitative measurements of anisotropy using multiple microscope systems may be made by bringing out the main parameters that influence the quantification of fluorescence emission anisotropy. We focus on a variety of parameters that contribute to errors associated with the measurement of emission anisotropy in a microscope. These include the requirement for adequate photon counts for the necessary discrimination of anisotropy values, the influence of extinction ratios of the illumination source, the detector system, the role of numerical aperture, and excitation wavelength. All these parameters also affect the ability to capture the dynamic range of emission anisotropy necessary for quantifying its reduction due to homo-FRET and other processes. Finally, we provide easily implementable tests to assess whether homo-FRET is a cause for the observed emission depolarization.
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Affiliation(s)
- Thomas S van Zanten
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Greeshma Pradeep S
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
| | - Satyajit Mayor
- Cell Biology Group, National Centre for Biological Sciences, UAS-GKVK Campus, Tata Institute for Fundamental Research, Bangalore 560065, India
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19
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Alam SR, Mahadevan MS, Periasamy A. Detecting RNA-Protein Interactions With EGFP-Cy3 FRET by Acceptor Photobleaching. Curr Protoc 2023; 3:e689. [PMID: 36821783 DOI: 10.1002/cpz1.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Förster Resonance Energy Transfer (FRET) is a great tool for cell biologists to investigate molecular interactions in live specimens. FRET is a distance-dependent phenomenon which can detect molecular interactions at distances between 1-10 nm. Several FRET approaches are reported in the literature for live and fixed cells to study protein-protein interactions; this protocol provides details of acceptor photobleaching as a FRET method to study RNA-Protein interactions. Cy3-labeled RNA foci (FRET acceptors) are photobleached at the intra-cellular site of interest (the nuclei) and the intensity of the EGFP-tagged proteins (FRET donors) at that same site are measured pre- and post- photobleaching. In principle, FRET is detected if the intensity of EGFP increases after photobleaching of Cy3. This protocol describes necessary steps and appropriate controls to conduct FRET measurements by the acceptor photobleaching method. Successful applications of this protocol will provide data to support the conclusion that EGFP-labeled proteins directly interact with Cy3-labeled RNA at the site of photobleaching. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: FRET in fixed cells Alternate Protocol: FRET in live cells.
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Affiliation(s)
- Shagufta Rehman Alam
- W. M. Keck Center for Cellular Imaging, University of Virginia, Charlottesville, Virginia
| | - Mani S Mahadevan
- Department of Pathology, University of Virginia, Charlottesville, Virginia
| | - Ammasi Periasamy
- W. M. Keck Center for Cellular Imaging, University of Virginia, Charlottesville, Virginia.,Departments of Biology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia
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20
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Kellerer T, Janusch J, Freymüller C, Rühm A, Sroka R, Hellerer T. Comprehensive Investigation of Parameters Influencing Fluorescence Lifetime Imaging Microscopy in Frequency- and Time-Domain Illustrated by Phasor Plot Analysis. Int J Mol Sci 2022; 23:15885. [PMID: 36555522 PMCID: PMC9781030 DOI: 10.3390/ijms232415885] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Having access to fluorescence lifetime, researchers can reveal in-depth details about the microenvironment as well as the physico-chemical state of the molecule under investigation. However, the high number of influencing factors might be an explanation for the strongly deviating values of fluorescent lifetimes for the same fluorophore reported in the literature. This could be the reason for the impression that inconsistent results are obtained depending on which detection and excitation scheme is used. To clarify this controversy, the two most common techniques for measuring fluorescence lifetimes in the time-domain and in the frequency-domain were implemented in one single microscopy setup and applied to a variety of fluorophores under different environmental conditions such as pH-value, temperature, solvent polarity, etc., along with distinct state forms that depend, for example, on the concentration. From a vast amount of measurement results, both setup- and sample-dependent parameters were extracted and represented using a single display form, the phasor-plot. The measurements showed consistent results between the two techniques and revealed which of the tested parameters has the strongest influence on the fluorescence lifetime. In addition, quantitative guidance as to which technique is most suitable for which research task and how to perform the experiment properly to obtain consistent fluorescence lifetimes is discussed.
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Affiliation(s)
- Thomas Kellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
- Faculty of Physics, Soft Condensed Matter, Ludwig-Maximilians-University, 80539 Munich, Germany
| | - Janko Janusch
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
- Laser-Forschungslabor, LIFE Center, Department of Urology, University Hospital, Ludwig-Maximilians-University, 82152 Planegg, Germany
- Department of Urology, University Hospital, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Christian Freymüller
- Laser-Forschungslabor, LIFE Center, Department of Urology, University Hospital, Ludwig-Maximilians-University, 82152 Planegg, Germany
- Department of Urology, University Hospital, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Adrian Rühm
- Laser-Forschungslabor, LIFE Center, Department of Urology, University Hospital, Ludwig-Maximilians-University, 82152 Planegg, Germany
- Department of Urology, University Hospital, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Ronald Sroka
- Laser-Forschungslabor, LIFE Center, Department of Urology, University Hospital, Ludwig-Maximilians-University, 82152 Planegg, Germany
- Department of Urology, University Hospital, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Thomas Hellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, 80335 Munich, Germany
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21
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The BrightEyes-TTM as an open-source time-tagging module for democratising single-photon microscopy. Nat Commun 2022; 13:7406. [PMID: 36456575 PMCID: PMC9715684 DOI: 10.1038/s41467-022-35064-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Fluorescence laser-scanning microscopy (LSM) is experiencing a revolution thanks to new single-photon (SP) array detectors, which give access to an entirely new set of single-photon information. Together with the blooming of new SP LSM techniques and the development of tailored SP array detectors, there is a growing need for (i) DAQ systems capable of handling the high-throughput and high-resolution photon information generated by these detectors, and (ii) incorporating these DAQ protocols in existing fluorescence LSMs. We developed an open-source, low-cost, multi-channel time-tagging module (TTM) based on a field-programmable gate array that can tag in parallel multiple single-photon events, with 30 ps precision, and multiple synchronisation events, with 4 ns precision. We use the TTM to demonstrate live-cell super-resolved fluorescence lifetime image scanning microscopy and fluorescence lifetime fluctuation spectroscopy. We expect that our BrightEyes-TTM will support the microscopy community in spreading SP-LSM in many life science laboratories.
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22
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Fluorescent Organic Small Molecule Probes for Bioimaging and Detection Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238421. [PMID: 36500513 PMCID: PMC9737913 DOI: 10.3390/molecules27238421] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022]
Abstract
The activity levels of key substances (metal ions, reactive oxygen species, reactive nitrogen, biological small molecules, etc.) in organisms are closely related to intracellular redox reactions, disease occurrence and treatment, as well as drug absorption and distribution. Fluorescence imaging technology provides a visual tool for medicine, showing great potential in the fields of molecular biology, cellular immunology and oncology. In recent years, organic fluorescent probes have attracted much attention in the bioanalytical field. Among various organic fluorescent probes, fluorescent organic small molecule probes (FOSMPs) have become a research hotspot due to their excellent physicochemical properties, such as good photostability, high spatial and temporal resolution, as well as excellent biocompatibility. FOSMPs have proved to be suitable for in vivo bioimaging and detection. On the basis of the introduction of several primary fluorescence mechanisms, the latest progress of FOSMPs in the applications of bioimaging and detection is comprehensively reviewed. Following this, the preparation and application of fluorescent organic nanoparticles (FONPs) that are designed with FOSMPs as fluorophores are overviewed. Additionally, the prospects of FOSMPs in bioimaging and detection are discussed.
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23
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Condensation of SEUSS promotes hyperosmotic stress tolerance in Arabidopsis. Nat Chem Biol 2022; 18:1361-1369. [DOI: 10.1038/s41589-022-01196-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/03/2022] [Indexed: 11/16/2022]
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24
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Zhan X, Drummond-Main C, Greening D, Yao J, Chen SWR, Appendino JP, Au PYB, Turner RW. Cannabidiol counters the effects of a dominant-negative pathogenic Kv7.2 variant. iScience 2022; 25:105092. [PMID: 36157585 PMCID: PMC9490039 DOI: 10.1016/j.isci.2022.105092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/04/2022] Open
Abstract
Epilepsy and neurodevelopmental disorders can arise from pathogenic variants of KCNQ (Kv7) channels. A patient with developmental and epileptic encephalopathy exhibited an in-frame deletion of histidine 260 on Kv7.2. Coexpression of Kv7.2 mutant (mut) subunits with Kv7.3 invoked a decrease in current density, a depolarizing shift in voltage for activation, and a decrease in membrane conductance. Biotinylation revealed an increased level of surface Kv7.2mut compared to Kv7.3 with no change in total membrane protein expression. Super-resolution and FRET imaging confirmed heteromeric channel formation and a higher expression density of Kv7.2mut. Cannabidiol (1 μM) offset the effects of Kv7.2mut by inducing a hyperpolarizing shift in voltage for activation independent of CB1 or CB2 receptors. These data reveal that the ability for cannabidiol to reduce the effects of a pathogenic Kv7.2 variant supports its use as a potential therapeutic to reduce seizure activity. A patient with epileptic encephalopathy exhibits a Kv7.2 deletion at H260 (Kv7.2mut) Kv7.2mut shows increased expression at the membrane compared to Kv7.3 Kv7.2mut acts in a dominant-negative manner to reduce Kv7 conductance Cannabidiol acts on Kv7.x activation voltage to offset the effects of Kv7.2mut
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Affiliation(s)
- Xiaoqin Zhan
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Chris Drummond-Main
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Dylan Greening
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Jinjing Yao
- Libin Cardiovascular Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - S W R Chen
- Libin Cardiovascular Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - J P Appendino
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Pediatric Department, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - P Y Billie Au
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Medical Genetics, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ray W Turner
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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25
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Zapata-Mercado E, Biener G, McKenzie DM, Wimley WC, Pasquale EB, Raicu V, Hristova K. The efficacy of receptor tyrosine kinase EphA2 autophosphorylation increases with EphA2 oligomer size. J Biol Chem 2022; 298:102370. [PMID: 35970390 PMCID: PMC9512837 DOI: 10.1016/j.jbc.2022.102370] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022] Open
Abstract
The receptor tyrosine kinase (RTK) EphA2 is expressed in epithelial and endothelial cells and controls the assembly of cell-cell junctions. EphA2 has also been implicated in many diseases, including cancer. Unlike most RTKs, which signal predominantly as dimers, EphA2 readily forms high-order oligomers upon ligand binding. Here, we investigated if a correlation exists between EphA2 signaling properties and the size of the EphA2 oligomers induced by multiple ligands, including the widely used ephrinA1-Fc ligand, the soluble monomeric m-ephrinA1, and novel engineered peptide ligands. We used fluorescence intensity fluctuation (FIF) spectrometry to characterize the EphA2 oligomer populations induced by the different ligands. Interestingly, we found that different monomeric and dimeric ligands induce EphA2 oligomers with widely different size distributions. Our comparison of FIF brightness distribution parameters and EphA2 signaling parameters reveals that the efficacy of EphA2 phosphorylation on tyrosine 588, an autophosphorylation response contributing to EphA2 activation, correlates with EphA2 mean oligomer size. However, we found that other characteristics, such as the efficacy of AKT inhibition and ligand bias coefficients, appear to be independent of EphA2 oligomer size. Taken together, this work highlights the utility of FIF in RTK signaling research and demonstrates a quantitative correlation between the architecture of EphA2 signaling complexes and signaling features.
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Affiliation(s)
- Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gabriel Biener
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA
| | - Daniel M McKenzie
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - William C Wimley
- Tulane University School of Medicine, Department of Biochemistry and Molecular Biology, New Orleans, Louisiana, USA
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.
| | - Valerica Raicu
- Department of Physics, University of Wisconsin, Milwaukee, Wisconsin, USA; Department of Biological Sciences, University of Wisconsin, Milwaukee, Wisconsin, USA.
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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26
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Spatola Rossi T, Pain C, Botchway SW, Kriechbaumer V. FRET-FLIM to Determine Protein Interactions and Membrane Topology of Enzyme Complexes. Curr Protoc 2022; 2:e598. [PMID: 36300920 DOI: 10.1002/cpz1.598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Determining protein-protein interactions is vital for gaining knowledge on cellular and metabolic processes including enzyme complexes and metabolons. Förster resonance energy transfer with fluorescence lifetime imaging microscopy (FRET-FLIM) is an advanced imaging methodology that allows for the quantitative detection of protein-protein interactions. In this method, proteins of interest for interaction studies are fused to different fluorophores such as enhanced green fluorescent protein (eGFP; donor molecule) and monomeric red fluorescent protein (mRFP; acceptor molecule). Energy transfer between the two fluorophore groups can only occur efficiently when the proteins of interest are in close physical proximity, around ≤10 nm, and therefore are most likely interacting. FRET-FLIM measures the decrease in excited-state lifetime of the donor fluorophore (eGFP) with and without the presence of the acceptor (mRFP) and can therefore give information on protein-protein interactions and the membrane topology of the tested protein. Here we describe the production of fluorescent protein fusions for FRET-FLIM analysis in tobacco leaf epidermal cells using Agrobacterium-mediated plant transformation and a FRET-FLIM data acquisition and analysis protocol in plant cells. These protocols are applicable and can be adapted for both membrane and soluble proteins in different cellular localizations. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Protein expression in tobacco leaf cells via transient Agrobacterium-mediated plant transformation Basic Protocol 2: FRET-FLIM data acquisition and analysis.
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Affiliation(s)
- Tatiana Spatola Rossi
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Charlotte Pain
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | - Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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27
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Zhu X, Wang X, Zhang H, Zhang F. Luminescence Lifetime Imaging Based on Lanthanide Nanoparticles. Angew Chem Int Ed Engl 2022; 61:e202209378. [DOI: 10.1002/anie.202209378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Xinyan Zhu
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Fudan University Shanghai 200433 China
| | - Xiaohan Wang
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Fudan University Shanghai 200433 China
| | - Hongxin Zhang
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Fudan University Shanghai 200433 China
| | - Fan Zhang
- Department of Chemistry State Key Laboratory of Molecular Engineering of Polymers Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials Fudan University Shanghai 200433 China
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28
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Guaglianone G, Torrado B, Lin YF, Watkins MC, Wysocki VH, Gratton E, Nowick JS. Elucidating the Oligomerization and Cellular Interactions of a Trimer Derived from Aβ through Fluorescence and Mass Spectrometric Studies. ACS Chem Neurosci 2022; 13:2473-2482. [PMID: 35892278 PMCID: PMC9389591 DOI: 10.1021/acschemneuro.2c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/15/2022] [Indexed: 01/20/2023] Open
Abstract
Aβ oligomers play a central role in the neurodegeneration observed with Alzheimer's disease. Our laboratory has developed covalently stabilized trimers derived from residues 17-36 of Aβ as model systems for studying Aβ oligomers. In the current study, we apply the emerging techniques of fluorescence lifetime imaging microscopy (FLIM) and native mass spectrometry (native MS) to better understand the assembly and interactions of the oligomer model system 2AT-L in aqueous solutions and with cells. 2AT-L and fluorescently labeled 2AT-L analogues assemble in the membrane-like environment of SDS-PAGE, showing diffuse bands of oligomers in equilibrium. Native ion mobility-mass spectrometry (native IM-MS) of 2AT-L allows for the identification of discrete oligomers in solution and shows similar patterns of oligomer formation between 2AT-L and fluorescently labeled analogues. Fluorescence microscopy with SH-SY5Y cells reveals that fluorescently labeled 2AT-L analogues colocalize within lysosomes. FLIM studies with phasor analysis further elucidate the assembly of 2AT-L within cells and establish the occurrence of FRET, indicating the presence of oligomers within cells. Collectively, these multiple complementary techniques help better understand the complex behavior of the 2AT-L model system.
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Affiliation(s)
- Gretchen Guaglianone
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Belén Torrado
- Laboratory
for Fluorescence Dynamics, Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - Yu-Fu Lin
- Resource
for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Matthew C. Watkins
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Vicki H. Wysocki
- Resource
for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Enrico Gratton
- Laboratory
for Fluorescence Dynamics, Biomedical Engineering, University of California, Irvine, California 92697, United States
| | - James S. Nowick
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
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29
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Phelps C, Huang T, Wang J, Nan X. Multipair Förster Resonance Energy Transfer via Spectrally Resolved Single-Molecule Detection. J Phys Chem B 2022; 126:5765-5771. [PMID: 35897122 PMCID: PMC9377335 DOI: 10.1021/acs.jpcb.2c03249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/20/2022] [Indexed: 02/08/2023]
Abstract
Förster resonance energy transfer (FRET) is a powerful tool for studying molecular interactions. Its use for studying interactions involving more than two molecules, however, has been limited by spectral crosstalk among the fluorophores. Here, we report multispectral FRET (msFRET) for imaging multiple pairs of interactions in parallel by spectrally resolving single fluorescent molecules. By using a dual (positional and spectral) channel and wide-field imaging configuration, fluorophores with emission maxima as close as 6-10 nm could be reliably distinguished. We demonstrate msFRET by continuously monitoring the hybridization dynamics among 2 × 2 pairs of DNA oligos in parallel using Cy3 and Cy3.5 as donors and Cy5 and Cy5.5 as acceptors. Aside from studying molecular interactions, msFRET may also find applications in probing fluorophore photophysics during FRET and in multiplexed superresolution imaging.
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Affiliation(s)
- Carey Phelps
- Department
of Biomedical Engineering, and Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Tao Huang
- Department
of Biomedical Engineering, and Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Jing Wang
- Department
of Biomedical Engineering, and Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
| | - Xiaolin Nan
- Department
of Biomedical Engineering, and Knight Cancer Early Detection Advanced
Research Center, Oregon Health and Science
University, 2730 S. Moody Avenue, Portland, Oregon 97201, United
States
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30
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Zhu X, Wang X, Zhang H, Zhang F. Luminescence Lifetime Imaging Based on Lanthanide Nanoparticles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xinyan Zhu
- Fudan University chemistry department Room 631, Advanced materials lab,2205 songhu road, yangpu district,Shanghai 200438 Shanghai CHINA
| | | | | | - Fan Zhang
- Fudan University Chemistry 2205 Songhu Road 200438 Shanghai CHINA
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31
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Wang Y, Zhou Y, Liang J. Characterization of Organellar-Specific ABA Responses during Environmental Stresses in Tobacco Cells and Arabidopsis Plants. Cells 2022; 11:2039. [PMID: 35805123 PMCID: PMC9265483 DOI: 10.3390/cells11132039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Abscisic acid (ABA) is a critical phytohormone involved in multifaceted processes in plant metabolism and growth under both stressed and nonstressed conditions. Its accumulation in various tissues and cells has long been established as a biomarker for plant stress responses. To date, a comprehensive understanding of ABA distribution and dynamics at subcellular resolution in response to environmental cues is still lacking. Here, we modified the previously developed ABA sensor ABAleon2.1_Tao3 (Tao3) and targeted it to different organelles including the endoplasmic reticulum (ER), chloroplast/plastid, and nucleus through the addition of corresponding signal peptides. Together with the cytosolic Tao3, we show distinct ABA distribution patterns in different tobacco cells with the chloroplast showing a lower level of ABA in both cell types. In a tobacco mesophyll cell, organellar ABA displayed specific alterations depending on osmotic stimulus, with ABA levels being generally enhanced under a lower and higher concentration of salt and mannitol treatment, respectively. In Arabidopsis roots, cells from both the meristem and elongation zone accumulated ABA considerably in the cytoplasm upon mannitol treatment, while the plastid and nuclear ABA was generally reduced dependent upon specific cell types. In Arabidopsis leaf tissue, subcellular ABA seemed to be less responsive when stressed, with notable increases of ER ABA in epidermal cells and a reduction of nuclear ABA in guard cells. Together, our results present a detailed characterization of stimulus-dependent cell type-specific organellar ABA responses in tobacco and Arabidopsis plants, supporting a highly coordinated regulatory network for mediating subcellular ABA homeostasis during plant adaptation processes.
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Affiliation(s)
- Yuzhu Wang
- Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China;
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yeling Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiansheng Liang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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32
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Hedde PN, Barylko B, Binns DD, Jameson DM, Albanesi JP. Differential Mobility and Self-Association of Arc/Arg3.1 in the Cytoplasm and Nucleus of Living Cells. ACS Chem Neurosci 2022; 13:876-882. [PMID: 35319179 DOI: 10.1021/acschemneuro.1c00744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Arc, also known as Arg3.1, is an activity-dependent immediate-early gene product that plays essential roles in memory consolidation. A pool of Arc is located in the postsynaptic cytoplasm, where it promotes AMPA receptor endocytosis and cytoskeletal remodeling. However, Arc is also found in the nucleus, with a major portion being associated with promyelocytic leukemia nuclear bodies (PML-NBs). Nuclear Arc has been implicated in epigenetic control of gene transcription associated with learning and memory. In this study, we use a battery of fluorescence nanoimaging approaches to characterize the behavior of Arc ectopically expressed in heterologous cells. Our results indicate that in the cytoplasm, Arc exists predominantly as monomers and dimers associated with slowly diffusing particles. In contrast, nuclear Arc is almost exclusively monomeric and displays a higher diffusivity than cytoplasmic Arc. We further show that Arc moves freely and rapidly between PML-NBs and the nucleoplasm and that its movement within PML-NBs is relatively unobstructed.
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Affiliation(s)
- Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, 651 Ilalo Street, BSB 222, University of Hawaii, Honolulu, Hawaii 96813, United States
| | - Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
| | - Derk D. Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, 651 Ilalo Street, BSB 222, University of Hawaii, Honolulu, Hawaii 96813, United States
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
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33
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Vu H, Woodcock JW, Krishnamurthy A, Obrzut J, Gilman JW, Coughlin EB. Visualization of Polymer Dynamics in Cellulose Nanocrystal Matrices Using Fluorescence Lifetime Measurements. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10793-10804. [PMID: 35179343 DOI: 10.1021/acsami.1c21906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Polymer nanocomposites containing self-assembled cellulose nanocrystals (CNCs) are ideal for advanced applications requiring both strength and toughness as the helicoidal structure of the CNCs deflects crack propagation and the polymer matrix dissipates impact energy. However, any adsorbed water layer surrounding the CNCs may compromise the interfacial adhesion between the polymer matrix and the CNCs, thus impacting stress transfer at that interface. Therefore, it is critical to study the role of water at the interface in connecting the polymer dynamics and the resulting mechanical performance of the nanocomposite. Here, we explore the effect of polymer confinement and water content on polymer dynamics in CNC nanocomposites by covalently attaching a fluorogenic water-sensitive dye to poly(diethylene glycol methyl ether methacrylate) (PMEO2MA), to provide insights into the observed mechanical performance. Utilizing fluorescence lifetime imaging microscopy (FLIM), the lifetime of dye fluorescence decay was measured to probe the polymer chain dynamics of PMEO2MA in CNC nanocomposite films. The PMEO2MA chains experienced distinct regions of differing dynamics within Bouligand structures. A correlation was observed between the average fluorescence lifetime and the mechanical performance of CNC films, indicating that polymer chains with high mobility improved the strain and toughness. These studies demonstrated FLIM as a method to investigate polymer dynamics at the nanosecond timescale that can readily be applied to other composite systems.
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Affiliation(s)
- Huyen Vu
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jeremiah W Woodcock
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-3460, United States
| | - Ajay Krishnamurthy
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-3460, United States
| | - Jan Obrzut
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-3460, United States
| | - Jeffrey W Gilman
- Material Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-3460, United States
| | - E Bryan Coughlin
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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34
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It Takes More than Two to Tango: Complex, Hierarchal, and Membrane-Modulated Interactions in the Regulation of Receptor Tyrosine Kinases. Cancers (Basel) 2022; 14:cancers14040944. [PMID: 35205690 PMCID: PMC8869822 DOI: 10.3390/cancers14040944] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022] Open
Abstract
The search for an understanding of how cell fate and motility are regulated is not a purely scientific undertaking, but it can also lead to rationally designed therapies against cancer. The discovery of tyrosine kinases about half a century ago, the subsequent characterization of certain transmembrane receptors harboring tyrosine kinase activity, and their connection to the development of human cancer ushered in a new age with the hope of finding a treatment for malignant diseases in the foreseeable future. However, painstaking efforts were required to uncover the principles of how these receptors with intrinsic tyrosine kinase activity are regulated. Developments in molecular and structural biology and biophysical approaches paved the way towards better understanding of these pathways. Discoveries in the past twenty years first resulted in the formulation of textbook dogmas, such as dimerization-driven receptor association, which were followed by fine-tuning the model. In this review, the role of molecular interactions taking place during the activation of receptor tyrosine kinases, with special attention to the epidermal growth factor receptor family, will be discussed. The fact that these receptors are anchored in the membrane provides ample opportunities for modulatory lipid-protein interactions that will be considered in detail in the second part of the manuscript. Although qualitative and quantitative alterations in lipids in cancer are not sufficient in their own right to drive the malignant transformation, they both contribute to tumor formation and also provide ways to treat cancer. The review will be concluded with a summary of these medical aspects of lipid-protein interactions.
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35
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Live imaging approach of dynamic multicellular responses in ERK signaling during vertebrate tissue development. Biochem J 2022; 479:129-143. [PMID: 35050327 PMCID: PMC8883488 DOI: 10.1042/bcj20210557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022]
Abstract
The chemical and mechanical responses of cells via the exchange of information during growth and development result in the formation of biological tissues. Information processing within the cells through the signaling pathways and networks inherent to the constituent cells has been well-studied. However, the cell signaling mechanisms responsible for generating dynamic multicellular responses in developing tissues remain unclear. Here, I review the dynamic multicellular response systems during the development and growth of vertebrate tissues based on the extracellular signal-regulated kinase (ERK) pathway. First, an overview of the function of the ERK signaling network in cells is provided, followed by descriptions of biosensors essential for live imaging of the quantification of ERK activity in tissues. Then adducing four examples, I highlight the contribution of live imaging techniques for studying the involvement of spatio-temporal patterns of ERK activity change in tissue development and growth. In addition, theoretical implications of ERK signaling are also discussed from the viewpoint of dynamic systems. This review might help in understanding ERK-mediated dynamic multicellular responses and tissue morphogenesis.
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36
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the 'old' field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
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37
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Linders PTA, Ioannidis M, ter Beest M, van den Bogaart G. Fluorescence Lifetime Imaging of pH along the Secretory Pathway. ACS Chem Biol 2022; 17:240-251. [PMID: 35000377 PMCID: PMC8787756 DOI: 10.1021/acschembio.1c00907] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Many cellular processes
are dependent on correct pH levels, and
this is especially important for the secretory pathway. Defects in
pH homeostasis in distinct organelles cause a wide range of diseases,
including disorders of glycosylation and lysosomal storage diseases.
Ratiometric imaging of the pH-sensitive mutant of green fluorescent
protein, pHLuorin, has allowed for targeted pH measurements in various
organelles, but the required sequential image acquisition is intrinsically
slow and therefore the temporal resolution is unsuitable to follow
the rapid transit of cargo between organelles. Therefore, we applied
fluorescence lifetime imaging microscopy (FLIM) to measure intraorganellar
pH with just a single excitation wavelength. We first validated this
method by confirming the pH in multiple compartments along the secretory
pathway and compared the pH values obtained by the FLIM-based measurements
with those obtained by conventional ratiometric imaging. Then, we
analyzed the dynamic pH changes within cells treated with Bafilomycin
A1, to block the vesicular ATPase, and Brefeldin A, to block endoplasmic
reticulum (ER)–Golgi trafficking. Finally, we followed the
pH changes of newly synthesized molecules of the inflammatory cytokine
tumor necrosis factor-α while they were in transit from the
ER via the Golgi to the plasma membrane. The toolbox we present here
can be applied to measure intracellular pH with high spatial and temporal
resolution and can be used to assess organellar pH in disease models.
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Affiliation(s)
- Peter T. A. Linders
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Melina Ioannidis
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Martin ter Beest
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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Chen YI, Chang YJ, Liao SC, Nguyen TD, Yang J, Kuo YA, Hong S, Liu YL, Rylander HG, Santacruz SR, Yankeelov TE, Yeh HC. Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells. Commun Biol 2022; 5:18. [PMID: 35017629 PMCID: PMC8752789 DOI: 10.1038/s42003-021-02938-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a powerful tool to quantify molecular compositions and study molecular states in complex cellular environment as the lifetime readings are not biased by fluorophore concentration or excitation power. However, the current methods to generate FLIM images are either computationally intensive or unreliable when the number of photons acquired at each pixel is low. Here we introduce a new deep learning-based method termed flimGANE (fluorescence lifetime imaging based on Generative Adversarial Network Estimation) that can rapidly generate accurate and high-quality FLIM images even in the photon-starved conditions. We demonstrated our model is up to 2,800 times faster than the gold standard time-domain maximum likelihood estimation (TD_MLE) and that flimGANE provides a more accurate analysis of low-photon-count histograms in barcode identification, cellular structure visualization, Förster resonance energy transfer characterization, and metabolic state analysis in live cells. With its advantages in speed and reliability, flimGANE is particularly useful in fundamental biological research and clinical applications, where high-speed analysis is critical.
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Affiliation(s)
- Yuan-I Chen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yin-Jui Chang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Shih-Chu Liao
- ISS, Inc., 1602 Newton Drive, Champaign, IL, 61822, USA
| | - Trung Duc Nguyen
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jianchen Yang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Yen-Liang Liu
- Master Program for Biomedical Engineering, China Medical University, Taichung, 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, 406040, Taiwan
| | - H Grady Rylander
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Samantha R Santacruz
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Neuroscience, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Electrical and Computer Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Thomas E Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, The University of Texas at Austin, Austin, TX, 78712, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA.
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Rorke EA, Adhikary G, Szmacinski H, Lakowicz JR, Weber DJ, Godoy-Ruiz R, Puranik P, Keillor JW, Gates EW, Eckert RL. Sulforaphane covalently interacts with the transglutaminase 2 cancer maintenance protein to alter its structure and suppress its activity. Mol Carcinog 2022; 61:19-32. [PMID: 34610184 PMCID: PMC8665039 DOI: 10.1002/mc.23356] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/17/2021] [Indexed: 01/03/2023]
Abstract
Type 2 transglutaminase (TG2) functions as an important cancer cell survival protein in a range of cancers including epidermal squamous cell carcinoma. TG2 exists in open and closed conformations each of which has a distinct and mutually exclusive activity. The closed conformation has GTP-binding/GTPase activity while the open conformation functions as a transamidase to catalyze protein-protein crosslinking. GTP-binding/GTPase activity is required for TG2 maintenance of the aggressive cancer phenotype. Thus, identifying agents that convert TG2 from the closed to the open GTP-binding/GTPase inactive conformation is an important cancer prevention/treatment strategy. Sulforaphane (SFN) is an important diet-derived cancer prevention agent that is known to possess a reactive isothiocyanate group and has potent anticancer activity. Using a biotin-tagged SFN analog (Biotin-ITC) and kinetic analysis we show that SFN covalently and irreversibly binds to recombinant TG2 to inhibit transamidase activity and shift TG2 to an open/extended conformation, leading to a partial inhibition of GTP binding. We also show that incubation of cancer cells or cancer cell extract with Biotin-ITC results in formation of a TG2/Biotin-ITC complex and that SFN treatment of cancer cells inhibits TG2 transamidase activity and shifts TG2 to an open/extended conformation. These findings identify TG2 as a direct SFN anticancer target in epidermal squamous cell carcinoma.
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Affiliation(s)
- Ellen A. Rorke
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Gautam Adhikary
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Henryk Szmacinski
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Joseph R. Lakowicz
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - David J. Weber
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Center for Biomolecular Therapueutics, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Raquel Godoy-Ruiz
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Center for Biomolecular Therapueutics, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | - Purushottamachar Puranik
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Center for Biomolecular Therapueutics, University of Maryland School of Medicine, Baltimore, Maryland, 21201
| | | | - Eric W.J Gates
- Department of Chemistry, University of Ottawa, ON, Canada
| | - Richard L. Eckert
- Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, 21201,Center for Biomolecular Therapueutics, University of Maryland School of Medicine, Baltimore, Maryland, 21201
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40
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Leavesley SJ, Annamdevula N, Johnson S, Pleshinger DJ, Rich TC. Automated Image Analysis of FRET Signals for Subcellular cAMP Quantification. Methods Mol Biol 2022; 2483:167-180. [PMID: 35286675 DOI: 10.1007/978-1-0716-2245-2_10] [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: 06/14/2023]
Abstract
A variety of FRET probes have been developed to examine cAMP localization and dynamics in single cells. These probes offer a readily accessible approach to measure localized cAMP signals. However, given the low signal-to-noise ratio of most FRET probes and the dynamic nature of the intracellular environment, there have been marked limitations in the ability to use FRET probes to study localized signaling events within the same cell. Here, we outline a methodology to dissect kinetics of cAMP-mediated FRET signals in single cells using automated image analysis approaches. We additionally extend these approaches to the analysis of subcellular regions. These approaches offer a unique opportunity to assess localized cAMP kinetics in an unbiased, quantitative fashion.
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Affiliation(s)
- Silas J Leavesley
- Department of Chemical and Biomolecular Engineering, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA.
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA.
| | - Naga Annamdevula
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
- Department of Physiology, University of South Alabama, Mobile, AL, USA
| | - Santina Johnson
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - D J Pleshinger
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - Thomas C Rich
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
- Department of Physiology, University of South Alabama, Mobile, AL, USA
- College of Engineering, University of South Alabama, Mobile, AL, USA
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41
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Ems-McClung SC, Walczak CE. Using FLIM-FRET for Characterizing Spatial Interactions in the Spindle. Methods Mol Biol 2022; 2415:221-243. [PMID: 34972958 PMCID: PMC8740612 DOI: 10.1007/978-1-0716-1904-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Proper spindle assembly and the attachment of chromosomes to the spindle are key for the accurate segregation of chromosomes to daughter cells. Errors in these processes can lead to aneuploidy, which is a hallmark of cancer. Understanding the mechanisms that drive spindle assembly will provide fundamental insights into how accurate chromosome segregation is achieved. One challenge in elucidating the complexities of spindle assembly is to visualize protein interactions in space and time. The Xenopus egg extract system has been a valuable tool to probe protein function during spindle assembly in vitro. Tagging proteins with fluorescent proteins and utilizing fluorescence-based approaches, such as Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM), have provided visual clues about the mechanics of spindle assembly and its regulators. However, elucidating how spindle assembly factors are spatially regulated is still challenging. Combining the egg extract system and visual FRET approaches provides a powerful tool to probe the processes involved in spindle assembly. Here we describe how a FLIM-FRET biosensor can be used to study protein-protein interactions in spindles assembled in Xenopus egg extracts. This approach should be readily adaptable to a wide variety of proteins to allow for new insights into the regulation of spindle assembly.
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42
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EIN3 and RSL4 interfere with an MYB-bHLH-WD40 complex to mediate ethylene-induced ectopic root hair formation in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2110004118. [PMID: 34916289 DOI: 10.1073/pnas.2110004118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/30/2022] Open
Abstract
The alternating cell specifications of root epidermis to form hair cells or nonhair cells in Arabidopsis are determined by the expression level of GL2, which is activated by an MYB-bHLH-WD40 (WER-GL3-TTG1) transcriptional complex. The phytohormone ethylene (ET) has a unique effect of inducing N-position epidermal cells to form root hairs. However, the molecular mechanisms underlying ET-induced ectopic root hair development remain enigmatic. Here, we show that ET promotes ectopic root hair formation through down-regulation of GL2 expression. ET-activated transcription factors EIN3 and its homolog EIL1 mediate this regulation. Molecular and biochemical analyses further revealed that EIN3 physically interacts with TTG1 and interferes with the interaction between TTG1 and GL3, resulting in reduced activation of GL2 by the WER-GL3-TTG1 complex. Furthermore, we found through genetic analysis that the master regulator of root hair elongation, RSL4, which is directly activated by EIN3, also participates in ET-induced ectopic root hair development. RSL4 negatively regulates the expression of GL2, likely through a mechanism similar to that of EIN3. Therefore, our work reveals that EIN3 may inhibit gene expression by affecting the formation of transcription-activating protein complexes and suggests an unexpected mutual inhibition between the hair elongation factor, RSL4, and the hair specification factor, GL2. Overall, this study provides a molecular framework for the integration of ET signaling and intrinsic root hair development pathway in modulating root epidermal cell specification.
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43
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Becker L, Janssen N, Layland SL, Mürdter TE, Nies AT, Schenke-Layland K, Marzi J. Raman Imaging and Fluorescence Lifetime Imaging Microscopy for Diagnosis of Cancer State and Metabolic Monitoring. Cancers (Basel) 2021; 13:cancers13225682. [PMID: 34830837 PMCID: PMC8616063 DOI: 10.3390/cancers13225682] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 02/08/2023] Open
Abstract
Hurdles for effective tumor therapy are delayed detection and limited effectiveness of systemic drug therapies by patient-specific multidrug resistance. Non-invasive bioimaging tools such as fluorescence lifetime imaging microscopy (FLIM) and Raman-microspectroscopy have evolved over the last decade, providing the potential to be translated into clinics for early-stage disease detection, in vitro drug screening, and drug efficacy studies in personalized medicine. Accessing tissue- and cell-specific spectral signatures, Raman microspectroscopy has emerged as a diagnostic tool to identify precancerous lesions, cancer stages, or cell malignancy. In vivo Raman measurements have been enabled by recent technological advances in Raman endoscopy and signal-enhancing setups such as coherent anti-stokes Raman spectroscopy or surface-enhanced Raman spectroscopy. FLIM enables in situ investigations of metabolic processes such as glycolysis, oxidative stress, or mitochondrial activity by using the autofluorescence of co-enzymes NADH and FAD, which are associated with intrinsic proteins as a direct measure of tumor metabolism, cell death stages and drug efficacy. The combination of non-invasive and molecular-sensitive in situ techniques and advanced 3D tumor models such as patient-derived organoids or microtumors allows the recapitulation of tumor physiology and metabolism in vitro and facilitates the screening for patient-individualized drug treatment options.
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Affiliation(s)
- Lucas Becker
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, 72076 Tübingen, Germany
| | - Shannon L Layland
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, 72076 Tübingen, Germany
| | - Anne T Nies
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, University of Tübingen, 72076 Tübingen, Germany
| | - Katja Schenke-Layland
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Cardiovascular Research Laboratories, Department of Medicine/Cardiology, David Geffen School of Medicine, UCLA, Los Angeles, CA 90073, USA
| | - Julia Marzi
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
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Wu T, Pang Y, Ai HW. Circularly Permuted Far-Red Fluorescent Proteins. BIOSENSORS 2021; 11:438. [PMID: 34821654 PMCID: PMC8615523 DOI: 10.3390/bios11110438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The color palette of genetically encoded fluorescent protein indicators (GEFPIs) has expanded rapidly in recent years. GEFPIs with excitation and emission within the "optical window" above 600 nm are expected to be superior in many aspects, such as enhanced tissue penetration, reduced autofluorescence and scattering, and lower phototoxicity. Circular permutation of fluorescent proteins (FPs) is often the first step in the process of developing single-FP-based GEFPIs. This study explored the tolerance of two far-red FPs, mMaroon1 and mCarmine, towards circular permutation. Several initial constructs were built according to previously reported circularly permuted topologies for other FP analogs. Mutagenesis was then performed on these constructs and screened for fluorescent variants. As a result, five circularly permuted far-red FPs (cpFrFPs) with excitation and emission maxima longer than 600 nm were identified. Some displayed appreciable brightness and efficient chromophore maturation. These cpFrFPs variants could be intriguing starting points to further engineer far-red GEFPIs for in vivo tissue imaging.
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Affiliation(s)
- Tianchen Wu
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
| | - Yu Pang
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Hui-wang Ai
- Department of Molecular Physiology and Biological Physics, and Center for Membrane and Cell Physiology, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA; (T.W.); (Y.P.)
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
- The UVA Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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45
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Levchenko SM, Pliss A, Peng X, Prasad PN, Qu J. Fluorescence lifetime imaging for studying DNA compaction and gene activities. LIGHT, SCIENCE & APPLICATIONS 2021; 10:224. [PMID: 34728612 PMCID: PMC8563720 DOI: 10.1038/s41377-021-00664-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 05/04/2023]
Abstract
Optical imaging is a most useful and widespread technique for the investigation of the structure and function of the cellular genomes. However, an analysis of immensely convoluted and irregularly compacted DNA polymer is highly challenging even by modern super-resolution microscopy approaches. Here we propose fluorescence lifetime imaging (FLIM) for the advancement of studies of genomic structure including DNA compaction, replication as well as monitoring of gene expression. The proposed FLIM assay employs two independent mechanisms for DNA compaction sensing. One mechanism relies on the inverse quadratic relation between the fluorescence lifetimes of fluorescence probes incorporated into DNA and their local refractive index, variable due to DNA compaction density. Another mechanism is based on the Förster resonance energy transfer (FRET) process between the donor and the acceptor fluorophores, both incorporated into DNA. Both these proposed mechanisms were validated in cultured cells. The obtained data unravel a significant difference in compaction of the gene-rich and gene-poor pools of genomic DNA. We show that the gene-rich DNA is loosely compacted compared to the dense DNA domains devoid of active genes.
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Affiliation(s)
- Svitlana M Levchenko
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260-3000, USA.
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China.
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46
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Tay ZW, Savliwala S, Hensley DW, Fung KLB, Colson C, Fellows BD, Zhou X, Huynh Q, Lu Y, Zheng B, Chandrasekharan P, Rivera-Jimenez SM, Rinaldi-Ramos CM, Conolly SM. Superferromagnetic Nanoparticles Enable Order-of-Magnitude Resolution & Sensitivity Gain in Magnetic Particle Imaging. SMALL METHODS 2021; 5:e2100796. [PMID: 34927972 PMCID: PMC8837195 DOI: 10.1002/smtd.202100796] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Indexed: 05/02/2023]
Abstract
Magnetic nanoparticles have many advantages in medicine such as their use in non-invasive imaging as a Magnetic Particle Imaging (MPI) tracer or Magnetic Resonance Imaging contrast agent, the ability to be externally shifted or actuated and externally excited to generate heat or release drugs for therapy. Existing nanoparticles have a gentle sigmoidal magnetization response that limits resolution and sensitivity. Here it is shown that superferromagnetic iron oxide nanoparticle chains (SFMIOs) achieve an ideal step-like magnetization response to improve both image resolution & SNR by more than tenfold over conventional MPI. The underlying mechanism relies on dynamic magnetization with square-like hysteresis loops in response to 20 kHz, 15 kAm-1 MPI excitation, with nanoparticles assembling into a chain under an applied magnetic field. Experimental data shows a "1D avalanche" dipole reversal of every nanoparticle in the chain when the applied field overcomes the dynamic coercive threshold of dipole-dipole fields from adjacent nanoparticles in the chain. Intense inductive signal is produced from this event resulting in a sharp signal peak. Novel MPI imaging strategies are demonstrated to harness this behavior towards order-of-magnitude medical image improvements. SFMIOs can provide a breakthrough in noninvasive imaging of cancer, pulmonary embolism, gastrointestinal bleeds, stroke, and inflammation imaging.
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Affiliation(s)
- Zhi Wei Tay
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
- Institute of Bioengineering and Bioimaging, Agency for Science, Technology and Research (A*STAR), #02-02 Helios Building, Singapore, 138667, Singapore
| | - Shehaab Savliwala
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611-6005, USA
| | - Daniel W Hensley
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - K L Barry Fung
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Caylin Colson
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Benjamin D Fellows
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Xinyi Zhou
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Quincy Huynh
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Yao Lu
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Bo Zheng
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | - Prashant Chandrasekharan
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
| | | | - Carlos M Rinaldi-Ramos
- Department of Chemical Engineering, University of Florida, Gainesville, FL, 32611-6005, USA
| | - Steven M Conolly
- Department of Bioengineering, 340 Hearst Memorial Mining Building, University of California Berkeley, Berkeley, CA, 94720-1762, USA
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47
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Minner-Meinen R, Weber JN, Albrecht A, Matis R, Behnecke M, Tietge C, Frank S, Schulze J, Buschmann H, Walla PJ, Mendel RR, Hänsch R, Kaufholdt D. Split-HaloTag imaging assay for sophisticated microscopy of protein-protein interactions in planta. PLANT COMMUNICATIONS 2021; 2:100212. [PMID: 34746759 PMCID: PMC8555439 DOI: 10.1016/j.xplc.2021.100212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 05/04/2023]
Abstract
An ever-increasing number of intracellular multi-protein networks have been identified in plant cells. Split-GFP-based protein-protein interaction assays combine the advantages of in vivo interaction studies in a native environment with additional visualization of protein complex localization. Because of their simple protocols, they have become some of the most frequently used methods. However, standard fluorescent proteins present several drawbacks for sophisticated microscopy. With the HaloTag system, these drawbacks can be overcome, as this reporter forms covalent irreversible bonds with synthetic photostable fluorescent ligands. Dyes can be used in adjustable concentrations and are suitable for advanced microscopy methods. Therefore, we have established the Split-HaloTag imaging assay in plants, which is based on the reconstitution of a functional HaloTag protein upon protein-protein interaction and the subsequent covalent binding of an added fluorescent ligand. Its suitability and robustness were demonstrated using a well-characterized interaction as an example of protein-protein interaction at cellular structures: the anchoring of the molybdenum cofactor biosynthesis complex to filamentous actin. In addition, a specific interaction was visualized in a more distinctive manner with subdiffractional polarization microscopy, Airyscan, and structured illumination microscopy to provide examples of sophisticated imaging. Split-GFP and Split-HaloTag can complement one another, as Split-HaloTag represents an alternative option and an addition to the large toolbox of in vivo methods. Therefore, this promising new Split-HaloTag imaging assay provides a unique and sensitive approach for more detailed characterization of protein-protein interactions using specific microscopy techniques, such as 3D imaging, single-molecule tracking, and super-resolution microscopy.
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Affiliation(s)
- Rieke Minner-Meinen
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Jan-Niklas Weber
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Andreas Albrecht
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Rainer Matis
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Maria Behnecke
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Cindy Tietge
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Stefan Frank
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Jutta Schulze
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Henrik Buschmann
- Botany Department, Universität Osnabrück, Barbara Strasse 11, 49076 Osnabrück, Germany
| | - Peter Jomo Walla
- Institut für Physikalische und Theoretische Chemie, Technische Universität Braunschweig, Hagenring 30.023c, 38106 Braunschweig, Germany
| | - Ralf-R. Mendel
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
| | - Robert Hänsch
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
- Center of Molecular Ecophysiology (CMEP), College of Resources and Environment, Southwest University, Tiansheng Road No. 2, Beibei District, 400715 Chongqing, P.R. China
- Corresponding author
| | - David Kaufholdt
- Institut für Pflanzenbiologie, Technische Universität Braunschweig, Humboldtstrasse 1, 38106 Braunschweig, Germany
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Sui P, Li Q, Yu H, Yu M, Zhang Z, Li A, Wang W, Sun X. The construction and modulation of responsive fluorescent materials and nano-assembly with luminescence in solid state. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Zhou Y, Wang Y, Li J, Liang J. In vivo FRET-FLIM reveals ER-specific increases in the ABA level upon environmental stresses. PLANT PHYSIOLOGY 2021; 186:1545-1561. [PMID: 33848331 PMCID: PMC8260131 DOI: 10.1093/plphys/kiab165] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/28/2021] [Indexed: 05/02/2023]
Abstract
Plant hormone abscisic acid (ABA) is essential for regulating plant growth and various stress responses. ABA-mediated signaling depends on local ABA levels rather than the overall cellular ABA concentration. While cellular concentration of ABA can be detected using Förster resonance energy transfer (FRET)-based ABA probes, direct imaging of subcellular ABA levels remains unsolved. Here, we modified the previously reported ABAleon2.1 and generated a new ABA sensor, named ABAleon2.1_Tao3. Via transient expression in tobacco (Nicotiana tabacum) protoplasts, we targeted ABAleon2.1_Tao3s to the endoplasmic reticulum (ER) membrane with the ABA sensing unit facing the cytosol and the ER, respectively, through a nanobody-epitope-mediated protein interaction. Combining FRET with fluorescence lifetime imaging microscopy, ABA-triggered-specific increases in the fluorescence lifetime of the donor mTurquoise in the ABAleon2.1_Tao3 were detected in both transient assays and stably transformed Arabidopsis plants. In tobacco protoplasts, ER membrane-targeted ABAleon2.1_Tao3s showed a generally higher basal level of ABA in the ER than that in the cytosol and ER-specific alterations in the level of ABA upon environmental cues. In ABAleon2.1_Tao3-transformed Arabidopsis roots, mannitol triggered increases in cytosolic ABA in the division zone and increases in ER ABA in the elongation and maturation zone within 1 h after treatment, both of which were abolished in the bg1-2 mutant, suggesting the requirement for BG1 in osmotic stress-triggered early ABA induction in Arabidopsis roots. These data demonstrate that ABAleon2.1_Tao3s can be used to monitor ABA levels in the cytosol and the ER, providing key information on stress-induced changes in the level of ABA in different subcellular compartments.
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Affiliation(s)
- Yeling Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuzhu Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jingwen Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiansheng Liang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China
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Biener G, Stoneman MR, Raicu V. Fluorescence intensity fluctuation analysis of receptor oligomerization in membrane domains. Biophys J 2021; 120:3028-3039. [PMID: 34214533 DOI: 10.1016/j.bpj.2021.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/02/2021] [Accepted: 06/11/2021] [Indexed: 11/26/2022] Open
Abstract
Fluorescence micrographs of the plasma membrane of cells expressing fluorescently labeled G protein-coupled receptors (GPCRs) often exhibit small clusters of pixels (or puncta) with intensities that are higher than those of the surrounding pixels. Although studies of GPCR interactions in uniform membrane areas abound, understanding the details of the GPCR interactions within such puncta as well as the nature of the membrane formations underlying the puncta is hampered by the lack of adequate experimental techniques. Here, we introduce an enhancement of a recently developed method termed fluorescence intensity fluctuation spectrometry, which permits analysis of protein-protein interactions within the puncta in live cell membranes. We applied the novel fluorescence intensity fluctuation data analysis protocol to previously published data from cells expressing human secretin receptors and determined that the oligomer size increases with receptor concentration and duration of treatment with cognate ligand, not only within uniform regions of the membrane (in agreement with previous publications) but also within the puncta. In addition, we found that the number density and fractional area of the puncta increased after treatment with ligand. This method could be applied for probing the evolution in the time of the chain of events that begins with ligand binding and continues with coated pits formation and receptor internalization for other GPCRs and, indeed, other membrane receptors in living cells.
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Affiliation(s)
- Gabriel Biener
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Michael R Stoneman
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Valerică Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin; Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin.
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