Biocompatible photoresistant far-red emitting, fluorescent polymer probes, with near-infrared two-photon absorption, for living cell and zebrafish embryo imaging

Establishing Riboglow-FLIM to visualize noncoding RNAs inside live zebrafish embryos

The central role of RNAs in health and disease calls for robust tools to visualize RNAs in living systems through fluorescence microscopy. Live zebrafish embryos are a popular system to investigate multicellular complexity as disease models. However, RNA visualization approaches in whole organisms are notably underdeveloped. Here, we establish our RNA tagging and imaging platform Riboglow-FLIM for complex cellular imaging applications by systematically evaluating FLIM capabilities. We use adherent mammalian cells as models for RNA visualization. Additional complexity of analyzing RNAs in whole mammalian animals is achieved by injecting these cells into a zebrafish embryo system for cell-by-cell analysis in this model of multicellularity. We first evaluate all variable elements of Riboglow-FLIM quantitatively before assessing optimal use in whole animals. In this way, we demonstrate that a model noncoding RNA can be detected robustly and quantitatively inside live zebrafish embryos using a far-red Cy5-based variant of the Riboglow platform. We can clearly resolve cell-to-cell heterogeneity of different RNA populations by this methodology, promising applicability in diverse fields.

Fluorescent Polymer-AS1411-Aptamer Probe for dSTORM Super-Resolution Imaging of Endogenous Nucleolin

Nucleolin is a multifunctional protein involved in essential biological processes. To precisely localize it and unravel its different roles in cells, fluorescence imaging is a powerful tool, especially super-resolution techniques. Here, we developed polymer-aptamer probes, both small and bright, adapted to direct stochastic optical reconstruction microscopy (dSTORM). Well-defined fluorescent polymer chains bearing fluorophores (AlexaFluor647) and a reactive end group were prepared via RAFT polymerization. The reactive end-group was then used for the oriented conjugation with AS1411, a DNA aptamer that recognizes nucleolin with high affinity. Conjugation via strain-promoted alkyne/azide click chemistry (SPAAC) between dibenzylcyclooctyne-ended fluorescent polymer chains and 3'-azido-functionalized nucleic acids proved to be the most efficient approach. In vitro and in cellulo evaluations demonstrated that selective recognition for nucleolin was retained. Their brightness and small size make these polymer-aptamer probes an appealing alternative to immunofluorescence, especially for super-resolution (10-20 nm) nanoscopy. dSTORM imaging demonstrated the ability of our fluorescent polymer-aptamer probe to provide selective and super-resolved detection of cell surface nucleolin.

Assembly of Aggregation-Induced Emission Active Bola-Amphiphilic Macromolecules into Luminescent Nanoparticles Optimized for Two-Photon Microscopy In Vivo

The (Z) and (E)-isomers of an extended tetraphenylethylene-based chromophore with optimized two-photon-induced luminescence properties are separated and functionalized with water-solubilizing pendant polymer groups, promoting their self-assembly in physiological media in the form of small, colloidal stable organic nanoparticles. The two resulting fluorescent suspensions are then evaluated as potential two-photon luminescent contrast agents for intravital epifluorescence and two-photon fluorescence microscopy. Comparisons with previously reported works involving similar fluorophores devoid of polymer side chains illustrate the benefits of later functionalization regarding the control of the self-assembly of the nano-objects and ultimately their biocompatibility toward the imaged organism.

Autofluorescence of Model Polyethylene Terephthalate Nanoplastics for Cell Interaction Studies

This work contributes to fill one of the gaps regarding nanoplastic interactions with biological systems by producing polyethylene terephthalate (PET) model nanoplastics, similar to those found in the marine environment, by means of a fast top-down approach based on mechanical fragmentation. Their size distribution and morphology were characterized by laser diffraction and atomic force microscopy (AFM). Their autofluorescence was studied by spectrofluorimetry and fluorescence imaging, being a key property for the evaluation of their interaction with biota. The emission spectra of label-free nanoplastics were comparable with those of PET nanoplastics labeled with Nile red. Finally, the suitability of label-free nanoplastics for biological studies was assessed by in vitro exposure with Mytilus galloprovincialis hemolymphatic cells in a time interval up to 6 h. The nanoplastic internalization into these cells, known to be provided with phagocytic activity, was assessed by fluorescence microscopy. The obtained results underlined that the autofluorescence of the model PET nanoplastics produced in the laboratory was adequate for biological studies having the potential to overcome the disadvantages commonly associated with several fluorescent dyes, such as the tendency to also stain other organic materials different from plastics, to form aggregates due to intermolecular interactions at high concentrations with a consequent decrease in fluorescence intensity, and to dye desorption from nanoparticles. The results of the autofluorescence study provide an innovative approach for plastic risk assessment.

Label-Free Live-Cell Imaging of Internalized Microplastics and Cytoplasmic Organelles with Multicolor CARS Microscopy

As the bioaccumulation of microplastics (MPs) is considered as a potential health risk, many efforts have been made to understand the cellular dynamics and cytotoxicity of MPs. Here, we demonstrate that label-free multicolor coherent anti-Stokes Raman scattering (CARS) microscopy enables separate vibrational imaging of internalized MPs and lipid droplets (LDs) with indistinguishable shapes and sizes in live cells. By simultaneously obtaining polystyrene (PS)- and lipid-specific CARS images at two very different frequencies, 1000 and 2850 cm^-1, respectively, we successfully identify the local distribution of ingested PS beads and native LDs in Caenorhabditis elegans. We further show that the movements of PS beads and LDs in live cells can be separately tracked in real time, which allows us to characterize their individual intracellular dynamics. We thus anticipate that our multicolor CARS imaging method could be of great use to investigate the cellular transport and cytotoxicity of MPs without additional efforts for pre-labeling to MPs.

Benchmarking Density Functional Approximations for Excited-State Properties of Fluorescent Dyes

This study presents an extensive analysis of the predictive power of time-dependent density functional theory in determining the excited-state properties of two groups of important fluorescent dyes, difluoroboranes and hydroxyphenylimidazo[1,2-a]pyridine derivatives. To ensure statistically meaningful results, the data set is comprised of 85 molecules manifesting diverse photophysical properties. The vertical excitation energies and dipole moments (in the electronic ground and excited states) of the aforementioned dyes were determined using the RI-CC2 method (reference) and with 18 density functional approximations (DFA). The set encompasses DFAs with varying amounts of exact exchange energy (EEX): from 0% (e.g., SVWN, BLYP), through a medium (e.g., TPSSh, B3LYP), up to a major contribution of EEX (e.g., BMK, MN15). It also includes range-separated hybrids (CAM-B3LYP, LC-BLYP). Similar error profiles of vertical energy were obtained for both dye groups, although the errors related to hydroxyphenylimidazopiridines are significantly larger. Overall, functionals including 40-55% of EEX (SOGGA11-X, BMK, M06-2X) ensure satisfactory agreement with the reference vertical excitation energies obtained using the RI-CC2 method; however, MN15 significantly outperforms them, providing a mean absolute error of merely 0.04 eV together with a very high correlation coefficient (R2 = 0.98). Within the investigated set of functionals, there is no single functional that would equally accurately determine ground- and excited-state dipole moments of difluoroboranes and hydroxyphenylimidazopiridine derivatives. Depending on the chosen set of dyes, the most accurate μGS predictions were delivered by MN15 incorporating a major EEX contribution (difluoroboranes) and by PBE0 containing a minor EEX fraction (hydroxyphenylimidazopiridines). Reverse trends are observed for μES, i.e., for difluoroboranes the best results were obtained with functionals including a minor fraction of EEX, specifically PBE0, while in the case of hydroxyphenylimidazopiridines, much more accurate predictions were provided by functionals incorporating a major EEX contribution (BMK, MN15).

Multiscale fluorescent tracking of immune cells in the liver with a highly biocompatible far-red emitting polymer probe

The development of innovative immune cell therapies relies on efficient cell tracking strategies. For this, multiscale fluorescence-based analyses of transferred cells into the host with complementary techniques, including flow cytometry for high-throughput cell analysis and two-photon microscopy for deep tissue imaging would be highly beneficial. Ideally, cells should be labelled with a single fluorescent probe combining all the properties required for these different techniques. Due to the intrinsic autofluorescence of most tissues and especially the liver, far-red emission is also an important asset. However, the development of far-red emitting probes suitable for two-photon microscopy and compatible with clearing methods to track labelled immune cells in thick samples, remains challenging. A newly-designed water-soluble far-red emitting polymer probe, 19K-6H, with a large Stokes shift, was thus evaluated for the tracking of primary immune CD8 T cells. These cells, prepared from mouse spleen, were efficiently labelled with the 19K-6H probe, which was internalized via endocytosis and was highly biocompatible at concentrations up to 20 μM. Labelled primary CD8 T cells were detectable in culture by both confocal and two-photon microscopy as well as flow cytometry, even after 3 days of active proliferation. Finally, 19K-6H-labelled primary CD8 T cells were injected to mice in a classical model of immune mediated hepatitis. The efficient tracking of the transferred cells in the liver by flow cytometry (on purified non-parenchymal cells) and by two-photon microscopy on 800 μm thick cleared sections, demonstrated the versatility of the 19K-6H probe.

Innovative particle standards and long-lived imaging for 2D and 3D dSTORM

Direct stochastic optical reconstruction microscopy (dSTORM), developed in the last decade, has revolutionised optical microscopy by enabling scientists to visualise objects beyond the resolution provided by conventional microscopy (200 nm). We developed an innovative method based on blinking particle standards and conditions for long-lived imaging over several weeks. Stable localisation precisions within the 10 nm-range were achieved for single virions and in cellulo 2D imaging of centrosomes, as well as their reliable reconstruction in 3D dSTORM.

Advanced Fluorescent Polymer Probes for the Site-Specific Labeling of Proteins in Live Cells Using the HaloTag Technology

We report the site-specific and covalent bioconjugation of fluorescent polymer chains to proteins in live cells using the HaloTag technology. Polymer chains bearing a Halo-ligand precisely located at their α-chain-end were synthesized in a controlled manner owing to the RAFT polymerization process. They were labeled in lateral position by several organic fluorophores such as AlexaFluor 647. The resulting Halo-ligand polymer probe was finally shown to selectively recognize and label HaloTag proteins present at the membrane of live cells using confocal fluorescence microscopy. Such a polymer bioconjugation approach holds great promises for various applications ranging from cell imaging to cell surface functionalization.

Labeling of native proteins with fluorescent RAFT polymer probes: application to the detection of a cell surface protein using flow cytometry

Fluorescent RAFT polymer probes with an activated ester reactive end-group can be advantageously used to label native proteins.

Benzoyl Peroxide Detection in Real Samples and Zebrafish Imaging by a Designed Near-Infrared Fluorescent Probe

A novel near-infrared fluorescence off-on probe, (E)-3,3-dimethyl-1-propyl-2-(2-(6-(2-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyloxy)-2,3-dihydro-1H-xanthen-4-yl)vinyl)-3H-indolium (1), is developed and applied to benzoyl peroxide (BPO) detection in real samples and fluorescence imaging in living cells and zebrafish. When arylboronate as the recognition unit is connected to a stable hemicyanine skeleton, the probe is readily prepared, which exhibits superior analytical performance, such as near-infrared fluorescence emission over 700 nm and high sensitivity with a low detection limit of 47 nM. Upon reaction with BPO, phenylboronic acid pinacol ester is oxidized, followed by hydrolysis and 1,4-elimination of o-quinone methide to release fluorophore. In addtion, the probe displays high selectivity toward BPO over other common substances, which makes it of great potential use in quantitative and simple detection of BPO in wheat flour and antimicrobial agent. More importantly, the probe has been successfully demonstrated for monitoring BPO in living HeLa cells and zebrafish. The probe with superior properties could be of great potential use in other biosystems and in vivo studies.

Fluorescent RAFT polymers bearing a nitrilotriacetic acid (NTA) ligand at the α-chain-end for the site-specific labeling of histidine-tagged proteins

Fluorescent polymer probes bearing a nitrilotriacetic acid ligand at the α−chain-end selectively labeled histidine-tagged recombinant proteins.

Far-Red Fluorescent Lipid-Polymer Probes for an Efficient Labeling of Enveloped Viruses

Far-red emitting fluorescent lipid probes are desirable to label enveloped viruses, for their efficient tracking by optical microscopy inside autofluorescent cells. Most used probes are rapidly released from membranes, leading to fluorescence signal decay and loss of contrast. Here, water-soluble lipid-polymer probes are synthesized harboring hydrophilic or hydrophobic far-red emitting dyes, and exhibiting enhanced brightness. They efficiently label Hepatitis C Virus pseudotyped particles (HCVpp), more stably and reproducibly than commercial probes, and a strong fluorescence signal is observed with a high contrast. Labeling with such probes do not alter virion morphology, integrity, nor infectivity. Finally, it is shown by fluorescence microscopy that these probes enable efficient tracking of labeled HCVpp inside hepatocarcinoma cells used as model hepatocytes, in spite of their autofluorescence up to 700 nm. These novel fluorescent lipid-polymer probes should therefore enable a better characterization of early stages of infection of autofluorescent cells by enveloped viruses.

A two-photon fluorescent sensor revealing drug-induced liver injury via tracking γ-glutamyltranspeptidase (GGT) level in vivo

Currently drug-induced liver injury (DILI) has become a major and challenging public health issue in terms of medicine development and clinical therapy. The level of γ-glutamyl transpeptidase (GGT) has long been regarded as a preclinical/clinical biomarker for prediction of DILI. Herein, we report a two-photon fluorescent sensor for tracking GGT level changes resulted from DILI in vivo. The sensor was prepared by linking a glutamic acid to a dicyanomethylene-4H-pyran (DCM) derivative; and the presence of GGT cleaves γ-glutamyl amide group from the sensor and thereby restores the fluorescence emission (at 635 nm) of DCM moiety under femtosecond pulses at 800 nm. This two-photon sensor exhibits superior sensing performance such as red emission, high photostability and low detection limit (∼0.057 U/L). On a two-photon microscope, the sensor shows a bright red fluorescence in GGT-overexpressing A2780 cells; and it can fluorescently respond to the GGT generated in the liver of zebrafishes as a result of clinical drug (phenytoin) treatment. These findings demonstrate that a commonly-used clinical drug phenytoin can cause remarkable elevation in GGT level in liver, and this sensor may be useful as a marker to detect clinical drug-induced organ damages.