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Nikolić S, Oasa S, Krmpot AJ, Terenius L, Belić MR, Rigler R, Vukojević V. Mapping the Direction of Nucleocytoplasmic Transport of Glucocorticoid Receptor (GR) in Live Cells Using Two-Foci Cross-Correlation in Massively Parallel Fluorescence Correlation Spectroscopy (mpFCS). Anal Chem 2023; 95:15171-15179. [PMID: 37782779 PMCID: PMC10585663 DOI: 10.1021/acs.analchem.3c01427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023]
Abstract
Nucleocytoplasmic transport of transcription factors is vital for normal cellular function, and its breakdown is a major contributing factor in many diseases. The glucocorticoid receptor (GR) is an evolutionarily conserved, ligand-dependent transcription factor that regulates homeostasis and response to stress and is an important target for therapeutics in inflammation and cancer. In unstimulated cells, the GR resides in the cytoplasm bound to other molecules in a large multiprotein complex. Upon stimulation with endogenous or synthetic ligands, GR translocation to the cell nucleus occurs, where the GR regulates the transcription of numerous genes by direct binding to glucocorticoid response elements or by physically associating with other transcription factors. While much is known about molecular mechanisms underlying GR function, the spatial organization of directionality of GR nucleocytoplasmic transport remains less well characterized, and it is not well understood how the bidirectional nucleocytoplasmic flow of GR is coordinated in stimulated cells. Here, we use two-foci cross-correlation in a massively parallel fluorescence correlation spectroscopy (mpFCS) system to map in live cells the directionality of GR translocation at different positions along the nuclear envelope. We show theoretically and experimentally that cross-correlation of signals from two nearby observation volume elements (OVEs) in an mpFCS setup presents a sharp peak when the OVEs are positioned along the trajectory of molecular motion and that the time position of the peak corresponds to the average time of flight of the molecule between the two OVEs. Hence, the direction and velocity of nucleocytoplasmic transport can be determined simultaneously at several locations along the nuclear envelope. We reveal that under ligand-induced GR translocation, nucleocytoplasmic import/export of GR proceeds simultaneously but at different locations in the cell nucleus. Our data show that mpFCS can characterize in detail the heterogeneity of directional nucleocytoplasmic transport in a live cell and may be invaluable for studies aiming to understand how the bidirectional flow of macromolecules through the nuclear pore complex (NPC) is coordinated to avoid intranuclear transcription factor accretion/abatement.
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Affiliation(s)
- Stanko
N. Nikolić
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Sho Oasa
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Aleksandar J. Krmpot
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Lars Terenius
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Milivoj R. Belić
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Rudolf Rigler
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Vladana Vukojević
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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Fukushima R, Yamamoto J, Kinjo M. Empirical Bayes method using surrounding pixel information for number and brightness analysis. Biophys J 2021; 120:2156-2171. [PMID: 33812845 PMCID: PMC8390835 DOI: 10.1016/j.bpj.2021.03.033] [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: 08/28/2020] [Revised: 03/13/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Number and brightness (N&B) analysis is useful for monitoring the spatial distribution of the concentration and oligomeric state of fluorescently labeled proteins in cells. N&B analysis is based on the statistical analysis of fluorescence images by using the method of moments (MoM). Furthermore, N&B analysis can determine the particle number and particle brightness, which indicate the concentration and oligomeric state, respectively. However, the statistical accuracy and precision are limited in actual experiments with fluorescent proteins, owing to low excitation and the limited number of images. In this study, we applied maximum likelihood (ML) estimation and maximum a posteriori (MAP) estimation coupled with the empirical Bayes (EB) method (referred to as EB-MAP). In EB-MAP, we constructed a simple prior distribution for a pixel to utilize the information of the surrounding pixels. To evaluate the accuracy and precision of our method, we conducted simulations and experiments and compared the results of MoM, ML, and EB-MAP. The results showed that MoM estimated the particle number with many outliers. The outliers hampered the visibility of the spatial distribution and cellular structure. In contrast, EB-MAP suppressed the number of outliers and improved the visibility notably. The precision of EB-MAP was better by an order of magnitude in terms of particle number and 1.5 times better in terms of particle brightness compared with those of MoM. The proposed method (EB-MAP-N&B) is applicable to studies on fluorescence imaging and would aid in accurately recognizing changes in the concentration and oligomeric state in cells. Our results hold significant importance because quantifying the concentration and oligomeric state would contribute to the understanding of dynamic processes in molecular mechanism in cells.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Johtaro Yamamoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan; Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
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Biophysical research in Hokkaido University, Japan. Biophys Rev 2020; 12:233-236. [PMID: 32347462 DOI: 10.1007/s12551-020-00649-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/11/2020] [Indexed: 10/24/2022] Open
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Otosu T, Ishii K, Tahara T. Multifocus Fluorescence Correlation Spectroscopy with Spatially Separated Excitation Beams. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takuhiro Otosu
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Yamamoto J, Kinjo M. Full fiber-optic fluorescence correlation spectroscopy. OPTICS EXPRESS 2019; 27:14835-14841. [PMID: 31163925 DOI: 10.1364/oe.27.014835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
A full fiber-optic fluorescence correlation spectroscopy (FF-FCS) technique has been developed without the use of objectives and dichroic mirrors. To achieve this, an excitation laser has been focused onto a sample by a lensed optical fiber or a gradient index lens attached on the terminal surface of the optical fiber. The FF-FCS system does not exhibit a higher sensitivity than the conventional FCS system; however, it is much simpler and smaller. This work demonstrates the feasibility of FF-FCS by measuring fluorescent beads. In the future, we expect FF-FCS to be widely used as a laboratory tool and an embedded tool for quality-control systems, such as cytometers.
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