Phasor based analysis of FRET images recorded using spectrally resolved lifetime imaging

FLUTE: A Python GUI for interactive phasor analysis of FLIM data

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.

Exploring protein-protein interactions with large differences in protein expression levels using FLIM-FRET

Many molecular processes within a cell are carried out by molecular machines built from a large number of proteins organized by their protein-protein interactions (PPIs). Exploring PPIs in their cellular context is critical to better understand the proteins functions. Förster resonance energy transfer measured by fluorescence lifetime imaging (FLIM-FRET) enables to monitor PPIs and to map their spatial organization in a living cell with high spatial and temporal specificity. But both the accurate measurement and the interpretation of multi-exponential FLIM-FRET data associated to mixtures of interacting and non-interacting proteins are difficult. Here we show that a simple diagram plot can find interesting visualization properties by clustering pixels with similar decay signatures. FLIM diagram plot can be used to provide valuable information about stoichiometry and binding mode in PPIs, even in the presence of large differences in protein expression levels of the different interacting partners. The proposed FLIM diagram plot is a useful visual approach for a more straightforward interpretation of complex lifetime data. This approach was applied for revealing critical features of PPIs in live Pseudomonas aeruginosa.

Differences between FLIM phasor analyses for data collected with the Becker and Hickl SPC830 card and with the FLIMbox card

The phasor approach to FLIM (Fluorescence Lifetime Imaging Microscopy) is becoming popular due to the powerful fit free analysis and the visualization of the decay at each point in images of cells and tissues. However, although several implementation of the method are offered by manufactures of FLIM accessories for microscopes, the details of the conversion of the decay to phasors at each point in an image requires some consideration. Here, we show that if the decay is not properly acquired, the apparently simple phasor transformation can provide incorrect phasor plots and the results may be misinterpreted. In particular, we show the disagreement in experimental data acquired on the same samples using the two cards (FLIMbox, frequency domain and Becker & Hickl BH 830, time domain) and the effect produced by using the BH 830 card with different settings. This difference in data acquisition translates to the assignment of phasor components calculated using different acquisition parameters. This effect is already present in the original data that are not acquired with the proper parameters for the phasor conversion. We also show that the difference in the resolution of components already exists in the data acquired in the time domain when used with settings that do not allow acquisition of the fluorescence decay on a sufficient large time scale. RESEARCH HIGHLIGHTS: This paper is intended to made researchers aware of some simple requirements for the conversion of time-domain data (typically TCSPC) to phasors. The use of phasors for FLIM analysis has seen a surge of popularity. Since the phasor approach is a fit free method and has a powerful visualization of the data, it appears very simple to use. This paper shows that when the original data in the time domain is not acquired with the proper time range to cover the lifetimes in a sample, the conversion to phasors can produce very erroneous results. These results are appearing more frequently in the literature since many of the manufacturers of FLIM accessories for microscopes are now offering the phasor analysis in their software. Here, we show that the phasor transformation per se cannot correct for the problems with data acquisition and that one is misled to think that the "phasor approach" is a universal fix for the lack of the proper time range for data acquisition.

Rapid fluorescence lifetime estimation with modified phasor approach and Laguerre deconvolution: a comparative study

Fluorescence lifetime imaging has been shown to serve as a valuable tool for interrogating and diagnosis of biological tissue at a mesoscopic level. The ability to analyze fluorescence decay curves to extract lifetime values in real-time is crucial for clinical translation and applications such as tumor margin delineation or intracoronary imaging of atherosclerotic plaques. In this work, we compare the performance of two popular non-parametric (fit-free) methods for determining lifetime values from fluorescence decays in real-time-the Phasor approach and Laguerre deconvolution. We demonstrate results from simulated and experimental data to compare the accuracy and speed of both methods and their dependence on noise and model parameters.

Recent advances in FRET for the study of protein interactions and dynamics

Förster/fluorescence resonance energy transfer (FRET) has been extensively used to detect the binding state or conformation of biomolecules. In the past few decades, various in vitro and in vivo applications of FRET measurement have been developed, including FRET probes, in-cell measurements, single-molecule measurements, and combination with computer simulation. In this review, we describe recent advances in FRET methods for examining biomolecular interactions and dynamics: (i) phasor plot analysis for quantitative analysis of protein interactions, (ii) single-molecule FRET measurement for detecting conformational dynamics in live cells, and (iii) data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein.

Translation Elongation Factor eEF1A2 is a Novel Anticancer Target for the Marine Natural Product Plitidepsin

eEF1A2 is one of the isoforms of the alpha subunit of the eukaryotic Elongation Factor 1. It is overexpressed in human tumors and is endowed with oncogenic properties, favoring tumor cell proliferation while inhibiting apoptosis. We demonstrate that plitidepsin, an antitumor agent of marine origin that has successfully completed a phase-III clinical trial for multiple myeloma, exerts its antitumor activity by targeting eEF1A2. The drug interacts with eEF1A2 with a K_D of 80 nM and a target residence time of circa 9 min. This protein was also identified as capable of binding [¹⁴C]-plitidepsin in a cell lysate from K-562 tumor cells. A molecular modelling approach was used to identify a favorable binding site for plitidepsin at the interface between domains 1 and 2 of eEF1A2 in the GTP conformation. Three tumor cell lines selected for at least 100-fold more resistance to plitidepsin than their respective parental cells showed reduced levels of eEF1A2 protein. Ectopic expression of eEF1A2 in resistant cells restored the sensitivity to plitidepsin. FLIM-phasor FRET experiments demonstrated that plitidepsin localizes in tumor cells sufficiently close to eEF1A2 as to suggest the formation of drug-protein complexes in living cells. Altogether, our results strongly suggest that eEF1A2 is the primary target of plitidepsin.

Optimizing Laguerre expansion based deconvolution methods for analysing bi-exponential fluorescence lifetime images

Fast deconvolution is an essential step to calibrate instrument responses in big fluorescence lifetime imaging microscopy (FLIM) image analysis. This paper examined a computationally effective least squares deconvolution method based on Laguerre expansion (LSD-LE), recently developed for clinical diagnosis applications, and proposed new criteria for selecting Laguerre basis functions (LBFs) without considering the mutual orthonormalities between LBFs. Compared with the previously reported LSD-LE, the improved LSD-LE allows to use a higher laser repetition rate, reducing the acquisition time per measurement. Moreover, we extended it, for the first time, to analyze bi-exponential fluorescence decays for more general FLIM-FRET applications. The proposed method was tested on both synthesized bi-exponential and realistic FLIM data for studying the endocytosis of gold nanorods in Hek293 cells. Compared with the previously reported constrained LSD-LE, it shows promising results.

A method to quantify FRET stoichiometry with phasor plot analysis and acceptor lifetime ingrowth

FRET is widely used for the study of protein-protein interactions in biological samples. However, it is difficult to quantify both the FRET efficiency (E) and the affinity (Kd) of the molecular interaction from intermolecular FRET signals in samples of unknown stoichiometry. Here, we present a method for the simultaneous quantification of the complete set of interaction parameters, including fractions of bound donors and acceptors, local protein concentrations, and dissociation constants, in each image pixel. The method makes use of fluorescence lifetime information from both donor and acceptor molecules and takes advantage of the linear properties of the phasor plot approach. We demonstrate the capability of our method in vitro in a microfluidic device and also in cells, via the determination of the binding affinity between tagged versions of glutathione and glutathione S-transferase, and via the determination of competitor concentration. The potential of the method is explored with simulations.

Deconvolution of fluorescence lifetime imaging microscopy by a library of exponentials

Fluorescence lifetime microscopy imaging (FLIM) is an optic technique that allows a quantitative characterization of the fluorescent components of a sample. However, for an accurate interpretation of FLIM, an initial processing step is required to deconvolve the instrument response of the system from the measured fluorescence decays. In this paper, we present a novel strategy for the deconvolution of FLIM data based on a library of exponentials. Our approach searches for the scaling coefficients of the library by non-negative least squares approximations plus Thikonov/l₂ or l₁ regularization terms. The parameters of the library are given by the lower and upper bounds in the characteristic lifetimes of the exponential functions and the size of the library, where we observe that this last variable is not a limiting factor in the resulting fitting accuracy. We compare our proposal to nonlinear least squares and global non-linear least squares estimations with a multi-exponential model, and also to constrained Laguerre-base expansions, where we visualize an advantage of our proposal based on Thikonov/l₂ regularization in terms of estimation accuracy, computational time, and tuning strategy. Our validation strategy considers synthetic datasets subject to both shot and Gaussian noise and samples with different lifetime maps, and experimental FLIM data of ex-vivo atherosclerotic plaques and human breast cancer cells.

Extended output phasor representation of multi-spectral fluorescence lifetime imaging microscopy

In this paper, we investigate novel low-dimensional and model-free representations for multi-spectral fluorescence lifetime imaging microscopy (m-FLIM) data. We depart from the classical definition of the phasor in the complex plane to propose the extended output phasor (EOP) and extended phasor (EP) for multi-spectral information. The frequency domain properties of the EOP and EP are analytically studied based on a multiexponential model for the impulse response of the imaged tissue. For practical implementations, the EOP is more appealing since there is no need to perform deconvolution of the instrument response from the measured m-FLIM data, as in the case of EP. Our synthetic and experimental evaluations with m-FLIM datasets of human coronary atherosclerotic plaques show that low frequency indexes have to be employed for a distinctive representation of the EOP and EP, and to reduce noise distortion. The tissue classification of the m-FLIM datasets by EOP and EP also improves with low frequency indexes, and does not present significant differences by using either phasor.

Investigation of the conformational flexibility of DGAT1 peptides using tryptophan fluorescence

The conformational behavior of synthetic peptides corresponding to the putative binding sites of the diacylglycerol acyltransferase 1 enzyme (a polytopic integral membrane protein) was investigated using steady-state and time-resolved fluorescence spectroscopies. Three small linear peptides with 13, 15 and 22 amino acid residues, containing one, two and three Trp residues, respectively, were studied in aqueous solution, in the absence and presence of model membranes. The high flexibility and unordered conformation of the peptides in solution were confirmed by the low Trp polarization values, the high accessibility to water-soluble quencher, and the fast rotational correlation times of the Trp residues. However, upon binding to the lipid systems, the Trp residues were incorporated within the acyl hydrophobic core and their lifetimes and rotational correlation times increased. Phasor plots were employed to analyze intensity decay of peptide-lipid binding and provided a trajectory, in phasor space, that lies along a line connecting the points of the free and bound peptide. This trajectory was analyzed to determine the association constant of the peptide to the model membrane.