Zhongtian
Yang‡
ab,
Liuju
Li‡
ac,
Jing
Ling
ab,
Tianyan
Liu
ab,
Xiaoshuai
Huang
ac,
Yuqing
Ying
de,
Yun
Zhao
de,
Yan
Zhao
ab,
Kai
Lei
*de,
Liangyi
Chen
*acf and
Zhixing
Chen
*abf
aInstitute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China. E-mail: zhixingchen@pku.edu.cn; lychen@pku.edu.cn
bPeking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
cState Key Laboratory of Membrane Biology, Peking University, Beijing, China
dZhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation, Translational Research of Zhejiang ProvinceSchool of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China. E-mail: leikai@westlake.edu.cn
eInstitute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
fPKU-Nanjing Institute of Translational Medicine, Nanjing, China
First published on 27th July 2020
Modern fluorescence-imaging methods promise to unveil organelle dynamics in live cells. Phototoxicity, however, has become a prevailing issue when boosted illumination applies. Mitochondria are representative organelles whose research heavily relies on optical imaging, yet these membranous hubs of bioenergy are exceptionally vulnerable to photodamage. We report that cyclooctatetraene-conjugated cyanine dyes (PK Mito dyes), are ideal mitochondrial probes with remarkably low photodynamic damage for general use in fluorescence cytometry. In contrast, the nitrobenzene conjugate of Cy3 exhibits enhanced photostability but unaffected phototoxicity compared to parental Cy3. PK Mito Red, in conjunction with Hessian-structural illumination microscopy, enables 2000-frame time-lapse imaging with clearly resolvable crista structures, revealing rich mitochondrial dynamics. In a rigorous stem cell sorting and transplantation assay, PK Mito Red maximally retains the stemness of planarian neoblasts, exhibiting excellent multifaceted biocompatibility. Resonating with the ongoing theme of reducing photodamage using optical approaches, this work advocates the evaluation and minimization of phototoxicity when developing imaging probes.
Meanwhile, state-of-the-art, super-resolution (SR) microscopy has the potential to reveal intricate structures and novel dynamics of mitochondria in live cells in real time.4 SR imaging of mitochondria has been made possible by high-density, environmentally sensitive probes based on the single-molecule on-off switching principle.5 Recently, mitochondrial crista structures in live cells have been visualized with Hessian structured illumination microscopy (Hessian SIM)6 and stimulated emission depletion (STED) microscopy.7–9 Yet, in contrast to long-term SR imaging of other organelles, such as endoplasmic reticulum and the cytoskeleton, mitochondrial imaging is much more susceptible to phototoxicity. Extensive illumination induces rapid swelling of mitochondria, followed by the deformation and abruption of inner-membrane cristae (Fig. 1A). Ultimately, mitochondria transform into round, hollow structures. This process has been consistently observed with multiple types of SR microscopy,7,10 emerging as a major obstacle in preventing the visualization of physiologically relevant mitochondrial dynamics in live cells.
The growing need for better mitochondrial dyes makes it one of the most rapidly evolving fields in fluorescence indicator development,11 with several photostable scaffolds having been applied to mitochondrial imaging.7,9,12,13 Some of these dyes are sufficiently bright and stable to give strong signals even under STED microscopy. However, because the membranous structures of mitochondria are prone to the attack by the reactive oxygen species (ROS) associated with fluorescence excitation, focusing on improved photostability, alone, fails to maintain the health of mitochondria under prolonged light exposure.7 Moreover, because apoptosis can be triggered by the damaged mitochondria through ROS-related pathways,10,14 it is equally important to carefully evaluate the general toxicity of fluorescent probes beyond phototoxicity, particularly in the sorting of sensitive cells based on their metabolic states.
To improve mitochondrial analysis, we exploited a triplet-state engineering strategy to reduce the phototoxicity of cyanine-based mitochondrial dyes.15 This strategy was originally proposed to minimize photobleaching in dye lasers,55 single-molecule imaging and fluorescence resonance energy transfer (FRET) and has been applied to time-lapse imaging of protein targets in fixed and live cells.16–19 Blanchard and coworkers have further carried out researches showing decreased ROS generation of TSQ-conjugated dyes, suggesting applications towards reducing phototoxicity in biological conditions.20,21 We envision that this promising strategy, if proven compatible inside live cells, could benefit live-cell fluorescence analysis in general, such as in SR imaging and cytometry. We synthesized and evaluated a set of cyanine dyes conjugated with triplet-state quenchers (TSQ) and studied their cell localization and phototoxicity. Conjugation to cyclooctatetraene (COT), but not other tested anti-bleaching quenchers, reduced the phototoxicity of cyanines while strongly fluorescing in the mitochondria. This strategy has resulted in two selected molecules, PK Mito Red and PK Mito Deep Red, that fluoresce in the red and far red emission channels. PK Mito dyes outperform their commercial counterparts in viability during illumination of HeLa cells and isolated cardiomyocytes. Using these dyes, we achieved SR imaging with “crista clear” resolution for a record-long 2000 frames with minimal mitochondrial swelling, indicating that phototoxicity, rather than photostability, limits the duration of SR imaging of mitochondria. Finally, by transplanting PK Mito Red-loaded planarian stem cells into planarians devoid of endogenous SirNeoblasts, we demonstrated the minimal cellular toxicity of the dyes, highlighting their general potential for broad applications in live-cell mitochondrial analysis.
The related process of photobleaching, which occurs when chromophores decompose, also warrants attention (Fig. 1B). Paradoxically, photobleaching receives disproportional attention compared to phototoxicity in SR imaging, although they both stem from triplet states. Selected chromophore scaffolds are elaborately tailored to withstand photo-decomposition; however, these strategies, in principle, do not necessarily translate to low phototoxicity. Moreover, in spite of advocates,25 phototoxicities of newly developed probes were not commonly measured and reported, giving few hints for further molecular engineering.
Because efficient assessments of phototoxicity are crucial, but highly customized for different sample types, we first established a reliable assay to quantify the phototoxicity of mitochondrial dyes.5 An epifluorescence microscope equipped with LED light cubes was used to provide continuous and even illumination over a large field of view covering hundreds of HeLa cells after a 40× objective (Fig. S1†). This illumination scheme provided light intensities comparable to those used in typical fluorescence imaging (up to 3 W cm−2). After exposing stained or unstained HeLa cells to relevant LED illumination for designated durations, the samples were allowed to recover for 2 h before treated with propidium iodide (PI). Subsequently, the illuminated cells were analyzed using a 10× objective. Cells with nuclear red fluorescence were counted as dead. This protocol efficiently measured nearly a hundred cells per run; therefore, reliably reporting cell viability after illumination.
We first evaluated the phototoxicities of excitation lights in the visible channels. While 1.7 W cm−2 green and 1.9 W cm−2 red LED lights exhibited negligible damage to HeLa cells, 2.5 W cm−2 blue LED light, itself, reduced cell viability in 10 min (Fig. S1C†). It is likely that the endogenous chromophores, particularly flavins and cytochromes, were excited by the blue light, resulting in ROS formation. This observation, corroborating previous studies,25 prompted us to develop probes excited by green and red light for minimal phototoxicity.
Because phototoxicity mainly results from the triplet states of excited fluorophores, we chose to exploit strategies that depopulate the triplet states to improve upon the cyanine-based family of mitochondrial dyes.15 Excited triplet states are harmful species that can either sensitize molecular oxygen to singlet oxygen or form highly reactive radicals that collectively account for the majority of the phototoxicity (Fig. 1B). The triplet states of dyes, however, can be depleted using triplet-state quenchers. This depletion process is drastically accelerated when the dye and quencher(s) are covalently conjugated; these bifunctional molecules are termed “self-healing dyes”.15,17,18 This strategy, pioneered by Blanchard and coworkers, has been increasingly applied to minimize photobleaching in single-molecule FRET studies.29 The Blanchard lab further studied the triplet-state quenching process of COT-conjugated cyanines30 and measured their triplet-state lifetime17,30 as well as relative reduction of ROS generation in vitro.20 These findings suggested the potential utility of self-healing dyes in alleviating phototoxicity in biological conditions. Despite the growing demand on reducing photodamage in the field of live-cell imaging, few further attempts along this direction were reported. Therefore, the cellular compatibility of TSQ conjugated fluorophores, such as their permeability and toxicity, demands detailed assessments.
Three popular TSQs (Trolox, nitrobenzene (NB), and COT) were conjugated to Cy3. Because the attachment of two TSQs with linkers of 2 or 3 chemical bonds has been suggested to optimally enhance photostability,17 the Cy3 derivatives were designed accordingly and synthesized using modular chemistry (Fig. 1C, Compounds 2, 3, and 4, see ESI for details†). The resulting molecules – Cy3-bisTrolox (2), Cy3-bisNB (3), Cy3-bisCOT (4) – along with commercially available ethyl-derived Cy3 (1) were first incubated with HeLa cells (250 nM for 10 min) to assess their mitochondrial localization and fluorescence intensities. All of the four compounds exhibited characteristic mitochondrial distributions in live HeLa cells (Fig. S2†). However, the mitochondria of Cy3-bisTrolox-stained cells were significantly dimmer than those stained with the other three dyes (Fig. 1D). We attributed this result to the differences in the quenchers' molecular weight and hydrophobicity, which gave rise to diverse permeability of the dye derivatives. We then measured the photobleaching of the four molecules embedded in polyvinyl alcohol film under a confocal microscope. Cy3-bisCOT (4) and Cy3-bisNB (3) exhibited the lowest initial bleaching rates, while Cy3-bisTrolox (2) bleached the fastest (Fig. 1E). These data narrowed our selection to Cy3-bisCOT and Cy3-bisNB. Finally, these two dyes and the parental Cy3 molecule were subjected to our phototoxicity assay. Cy3-bisNB (3) and Cy3 (1) were equally phototoxic and killed all illuminated HeLa cells in 5 min, while Cy3-bisCOT (4) had drastically reduced cellular apoptosis with a half-lethal dose of 15 min (Fig. 1F). These results suggested that COT, but not NB, reduces the phototoxicity of Cy3 in mitochondria.
We further compared the phototoxicity of PK Mito dyes with MTR/MTDR using our developed assay. MTR and MTDR killed all the HeLa cells after 5 min of illumination, with half-lethal doses of 2–3 min (Fig. 2C and D). Given that the illumination of cells without dyes resulted in no toxicity at the tested exposure durations (Fig. S5†), the observed cell death is unambiguously attributed to the phototoxicity of the MitoTracker dyes. PK Mito dyes, in contrast, showed significantly less cell death under photodamage. PK Mito Red had a half-lethal dose of 15 min light exposure, while PK Mito Deep Red exhibited a plateau in cell viability of >60%. These results established the remarkably low phototoxicity of COT-conjugated PK Mito dyes covering red and far red channels.
To further demonstrate time-lapse imaging of mitochondria in cardiomyocytes, spinning disk confocal microscope was an ideal instrument due to its high imaging speed and gentle illumination. PK Mito Deep Red could be excited by low-energy red laser, which readily combined with chemical probes of DNA (Hoechst), microtubules (ViaFluor 488), and lysosomes (LysoView 540), and enabled four-color 3D imaging of live cardiomyocytes (Fig. 3B and Movie S1†). Time-lapse z-stacked imaging of a whole cell requires cumulative light exposure over both space and time, inducing considerable phototoxicity. In xyzt mode, cardiomyocytes stained with MTDR typically collapsed after 5–8 3D frames (Fig. 3C). In contrast, PK Mito Deep Red enabled 20-frame imaging composed of 23 z-stacked images before the single cardiomyocyte irreversibly contracted (Fig. 3D). It is noteworthy that most of the mitochondria were still bright at the time of cell contraction. This finding recapitulated the challenge of live-cell mitochondrial imaging, which is often not limited by the photobleaching of the mitochondrial markers, but by the accumulated photodamage. The PK Mito dyes thus offer a viable option to ameliorate the phototoxicity during time-lapse image acquisitions, particularly on vulnerable cardiomyocytes.
To quantify the photodynamic behavior of the dyes, we analyzed the overall intensity profiles of the images over time. MTR-stained mitochondria rapidly brightened in the first tens of frames, followed by a fast fluorescence loss over the first hundreds of frames (Fig. 4D). The first process was attributed to the release of aggregated cationic dyes due to inner membrane depolarization, a consequence of phototoxicity.31 And the subsequent fluorescence loss process reflected photodamage-induced dye diffusion compounded with photobleaching. PKMR-treated mitochondria, in contrast, exhibited a mild and gradual fluorescence decrease throughout the 2000 frames. Frame number at 25% percent fluorescence loss was ∼100 for MTR group and ∼800 for PKMR group (Fig. 4E). Selected line plots across a number of mitochondria were further analyzed. In a typical line plot, the FWHM of Gaussian-fitted peaks were 154 nm and 123 nm, respectively (Fig. S7†), approaching the theoretical resolution of 2D Hessian-SIM. The mitochondrial inner width was measured and plotted for assessing morphological changes over the imaging process. Typical mitochondria stained with PKMR remained their inner width around 500 nm for ∼1200 frames before swelling, while MTR-stained mitochondria started swelling in the first 140 frames (Fig. 4F). On average, PKMR was capable of providing ∼1400 SR images before mitochondria expand to 150% of the original width, while MTR could deliver only ∼170 frames under same conditions (Fig. 4G). Both the morphological and fluorescence intensity data supported PKMR as a steady and reliable marker for maintaining the structural and biochemical integrity of mitochondria under Hessian-SIM.
Thanks to this non-invasive imaging protocol, rich mitochondrial physiological behaviors (as opposed to pathological activitys) were unveiled at unparalleled spatial and temporal resolution. In a typical video of 2000 frames recorded at 10 frames per second, three tip-extension–retraction events were identified (Fig. 4B and Movie S3†). The tip extensions were often less than 1 μm and the dynamic processes lasted 5–10 s. In addition, one kiss-and-run-type mitochondrial interaction was recorded (Movie S2,† Frames 550–750), which lasted for approximately 20 s. Moreover, a mitochondrial hot spot was identified that was particularly active, with dynamic protrusions forming and vanishing several times within 30 s. The duration of these transient events was as short as 1 s (Fig. 4C and Movie S4†). We speculated that these events may be related to the recently discovered mitochondrial nanotunnels3 and tubulations32 (Fig. S8†), whose identification relied heavily on fixed cells examined with electron microscopy and other SR microscopy methods. The diverse mitochondrial dynamics recorded using PK Mito Red – Hessian-SIM, which occurred over durations of 1 to 20 s and distances less than 2 μm, creates a new paradigm for high-throughput image analysis at high spatial resolution and uncompromised temporal resolution. Such an imaging experiment would not have been possible without reagents with superior optical properties and minimal photodamage.
We therefore tested our mitochondrial probes on planarian stem cells, with a long-term goal of understanding their powerful regenerative capacity that confers planarians with “immortal-like” long lifespans36 (Fig. 5A). Despite being an essential organelle for metabolism and aging, the function of mitochondria in planarian stem cell pluripotency and tissue regeneration has not been extensively studied. Adult planarian stem cells, neoblasts, form colonies in vivo after being transplanted into stem-cell-depleted planarian hosts (Fig. 5B).37,38 By combining SiR-DNA and CellTracker Green indicators to identify the proliferating neoblast population, we have previously established an isolation method for neoblasts, referred to as SirNeoblasts, using FACS.39 To leverage the red fluorescence channel, PK Mito Red or MTR were added together with SiR-DNA and CellTracker Green to the isolated planarian cell pellets after maceration, which were then subjected to FACS. PK Mito Red staining clearly distinguished two cell populations of SirNeoblasts that were more distinct than the MTR-stained group (Fig. 5C). Consistently, examination of SirNeoblasts stained with PK Mito Red under a confocal microscope readily identified strongly and weakly fluorescent cells, in contrast to the barely discernible SirNeoblast populations stained with MTR (Fig. S9†). This disparity may be attributed to different mitochondrial membrane potential or to different mitochondrial mass, both of which infer metabolic heterogeneity within SirNeoblasts. The biology behind the different mitochondrial signals in neoblasts is currently under investigation.
Next, we compared the cellular properties of neoblasts isolated using the two mitochondrial dyes. In FACS, cells are first treated with dyes, followed by brief laser irradiations. Both phototoxicity and dark toxicity can possibly affect the viability and stemness of the isolated neoblasts, with the latter one speculated to be dominant. Due to the sensitive nature of stem cells, this assay represents a rigorous test for bio-compatibility of mitochondrial reagents. Compared with unstained SirNeoblasts, PK Mito Red staining did not reduce the viability or nature of stem cells in vitro, as indicated by the pan stem cell marker smedwi-1 (Fig. S10B†). MTR staining, however, slightly but significantly reduced the viability but not the nature of stem cells (Fig. S10A†). Freshly isolated PK Mito Red-stained cells (0 div) had a colony-formation rate of 92% in planarian hosts similar to that of unstained SirNeoblast transplantation,39 but better than the ∼70% success rate of MTR-stained cells (Fig. 5D and E). When the isolated SirNeoblasts were cultured for 1 day before transplantation, a colony-formation rate of ∼55% was retained for PK Mito Red-stained cells compared to 4% for MTR-stained cells (Fig. 5E). The cell numbers were then counted using fluorescent whole-mount in situ hybridization (Fig. 5G). The colony sizes were similar among all three groups but exhibited a slightly lower number in planarians transplanted with 0 div SirNeoblasts labeled with MTR. Later, when 1 day SirNeoblasts were used for transplantation, the planarians that received MTR-stained cells performed the worst, while those receiving PK Mito Red-stained cells performed comparably to those receiving unstained SirNeoblasts (Fig. 5F). Altogether, compared to MTR, PK Mito Red offers a minimally disruptive assay for sorting SirNeoblasts with different mitochondrial states while maintaining maximal stemness. This effect is particularly significant in the neoblasts after 1 day of in vitro culture, highlighting the marked innocuousness of PK Mito Red in stem cell research.
In the context of photochemistry and molecular design, this work represents a major development in self-healing dyes for mitochondrial imaging in live cells. Covalent conjugation of triplet-state quenchers to fluorophores has been proposed to exhibit reduced phototoxicity according to in vitro ROS measurements.20 This work, along with previous studies, provides firm evidence that self-healing strategy could effectively alleviate phototoxicity when used for live cell imaging applications. An interesting finding in this work suggested that COT effectively reduces phototoxicity, while nitrobenzene, another popular TSQ in reducing photobleaching, does not alleviate photodamage. This result is in accordance with the triplet state lifetime and singlet oxygen generation of Cy5-COT measured by Blanchard et al.20,30 We tentatively attribute this discrepancy to their different mechanisms of triplet-state quenching,30,47,48 in which COT quenches triplet-state through an energy transfer process, while nitrobenzene works through a redox process. A future extension of this strategy would be the upgrade of the dyes to immobilizable versions for permanent labelling of mitochondria.49 Additionally, the findings in this work could potentially inspire the development of advanced probes for various organelles and protein/nucleic acid targets, as well as next generation TSQs. A recent perspective conveys several opinions on self-healing dyes as a strategy for reducing photobleaching.16 We have demonstrated here that reducing phototoxicity represents a new direction for self-healing dyes.
Considering instrumentation, PK Mito dyes have been tested on a range of fluorescence microscopes, including epifluorescence microscope, high-content imager, spinning-disk confocal microscope, and Hessian-SIM. We recommend Hessian-SIM as a synergistic partner of PK Mito dyes due to its strictly budgeted photon flux compared with other SR imaging methods.6 Hessian-SIM can achieve a spatial resolution of ∼120 nm (2D mode using 561 nm excitation) and a temporal resolution of up to 188 Hz. With PK Mito Red, the effective observation window could reach more than 1000 frames. In comparison to other SR imaging methods, our combination is advantageous in not only biocompatibility, but unveils richer mitochondrial inner membrane and crista dynamics spanning different time scales. For example, the observed kiss-and-run fusion lasted 20 s, while a transient dynamic protrusion lasted for only 1 s. These events are reported for the first time in live cells at super-resolution level. Compared to Mito PB Yellow dye – STED imaging methods that offered ∼60 nm spatial and ∼1 s temporal resolutions,7 our approach is advantageous in capturing both fast dynamics and long-duration events, therefore significantly expanding the observation windows of biological processes. In principle, however, PK Mito dyes should generally reduce the photodamage during image acquisitions under a variety of fluorescence microscopies. We expect that the PK Mito dyes could also be applied to STED microscopy,50 multi-photon microscopy,51 and light sheet microscopy.52 Compatibility with single-molecule localization-based SR imaging53 may also be realized after integrating photoactivation/photoswitching modules to the dyes. Finally, we would like to highlight the sorting and transplantation experiments on planarian cells as a closed-loop demonstration of the general toxicity of a new dye.22 In our work, the upgrading of probe molecules and development of instrumentations evolve in parallel, representing a new trend in modern biotechnology.24,54 With the emergence of these biocompatible fluorescent probes, we look forward to their impact on novel cytometry instruments.
In summary, we present COT-conjugated carbocyanine dyes as mitochondrial probes with minimal photodamage and toxicity. They maximally retain the health of mitochondria in live-cell volumetric imaging of cardiomyocytes, in remarkably long time-lapse SR imaging with Hessian-SIM, and in planarian stem-cell sorting for regeneration. We envision a role for these probes in revealing the dynamics of mitochondrial morphology and interactions, as well as mitochondria-related biotechnologies. Methodologically, as a pilot study on mitochondria, it also paves the way for using triplet-state depleted dyes to upgrade the toolkit for non-disruptive investigation of various cellular targets.
Footnotes |
† Electronic supplementary information (ESI) available. See DOI: 10.1039/d0sc02837a |
‡ These authors contributed equally to this work. |
This journal is © The Royal Society of Chemistry 2020 |