1
|
Fazel M, Jazani S, Scipioni L, Vallmitjana A, Zhu S, Gratton E, Digman MA, Pressé S. Building Fluorescence Lifetime Maps Photon-by-Photon by Leveraging Spatial Correlations. ACS PHOTONICS 2023; 10:3558-3569. [PMID: 38406580 PMCID: PMC10890823 DOI: 10.1021/acsphotonics.3c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) has become a standard tool in the quantitative characterization of subcellular environments. However, quantitative FLIM analyses face several challenges. First, spatial correlations between pixels are often ignored as signal from individual pixels is analyzed independently thereby limiting spatial resolution. Second, existing methods deduce photon ratios instead of absolute lifetime maps. Next, the number of fluorophore species contributing to the signal is unknown, while excited state lifetimes with <1 ns difference are difficult to discriminate. Finally, existing analyses require high photon budgets and often cannot rigorously propagate experimental uncertainty into values over lifetime maps and number of species involved. To overcome all of these challenges simultaneously and self-consistently at once, we propose the first doubly nonparametric framework. That is, we learn the number of species (using Beta-Bernoulli process priors) and absolute maps of these fluorophore species (using Gaussian process priors) by leveraging information from pulses not leading to observed photon. We benchmark our framework using a broad range of synthetic and experimental data and demonstrate its robustness across a number of scenarios including cases where we recover lifetime differences between species as small as 0.3 ns with merely 1000 photons.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Sina Jazani
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Songning Zhu
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine, Irvine, California 92697, United States; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, California 92697, United States
| | - Steve Pressé
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, Arizona 85287, United States; School of Molecular Science, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Wassermann LM, Scheckenbach M, Baptist AV, Glembockyte V, Heuer-Jungemann A. Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212024. [PMID: 36932052 DOI: 10.1002/adma.202212024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
Collapse
Affiliation(s)
- Lea M Wassermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Anna V Baptist
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| |
Collapse
|
4
|
Fazel M, Vallmitjana A, Scipioni L, Gratton E, Digman MA, Pressé S. Fluorescence lifetime: Beating the IRF and interpulse window. Biophys J 2023; 122:672-683. [PMID: 36659850 PMCID: PMC9989884 DOI: 10.1016/j.bpj.2023.01.014] [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: 09/09/2022] [Revised: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Fluorescence lifetime imaging captures the spatial distribution of chemical species across cellular environments employing pulsed illumination confocal setups. However, quantitative interpretation of lifetime data continues to face critical challenges. For instance, fluorescent species with known in vitro excited-state lifetimes may split into multiple species with unique lifetimes when introduced into complex living environments. What is more, mixtures of species, which may be both endogenous and introduced into the sample, may exhibit 1) very similar lifetimes as well as 2) wide ranges of lifetimes including lifetimes shorter than the instrumental response function or whose duration may be long enough to be comparable to the interpulse window. By contrast, existing methods of analysis are optimized for well-separated and intermediate lifetimes. Here, we broaden the applicability of fluorescence lifetime analysis by simultaneously treating unknown mixtures of arbitrary lifetimes-outside the intermediate, Goldilocks, zone-for data drawn from a single confocal spot leveraging the tools of Bayesian nonparametrics (BNP). We benchmark our algorithm, termed BNP lifetime analysis, using a range of synthetic and experimental data. Moreover, we show that the BNP lifetime analysis method can distinguish and deduce lifetimes using photon counts as small as 500.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Science, Arizona State University, Tempe, Arizona.
| |
Collapse
|