Confocal interferometric scattering microscopy reveals 3D nanoscopic structure and dynamics in live cells - PubMed (original) (raw)

Confocal interferometric scattering microscopy reveals 3D nanoscopic structure and dynamics in live cells

Michelle Küppers et al. Nat Commun. 2023.

Abstract

Bright-field light microscopy and related phase-sensitive techniques play an important role in life sciences because they provide facile and label-free insights into biological specimens. However, lack of three-dimensional imaging and low sensitivity to nanoscopic features hamper their application in many high-end quantitative studies. Here, we demonstrate that interferometric scattering (iSCAT) microscopy operated in the confocal mode provides unique label-free solutions for live-cell studies. We reveal the nanometric topography of the nuclear envelope, quantify the dynamics of the endoplasmic reticulum, detect single microtubules, and map nanoscopic diffusion of clathrin-coated pits undergoing endocytosis. Furthermore, we introduce the combination of confocal and wide-field iSCAT modalities for simultaneous imaging of cellular structures and high-speed tracking of nanoscopic entities such as single SARS-CoV-2 virions. We benchmark our findings against simultaneously acquired fluorescence images. Confocal iSCAT can be readily implemented as an additional contrast mechanism in existing laser scanning microscopes. The method is ideally suited for live studies on primary cells that face labeling challenges and for very long measurements beyond photobleaching times.

© 2023. The Author(s).

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1

Fig. 1. Schematics and characterization of the optical setup.

a The main components of a confocal laser scanning microscope (CLSM), which is extended to perform iSCAT microscopy in both wide-field and confocal modes. OBJ objective, BS beam splitter, PH pinhole, DC dichroic mirror, EF emission filter, PMT photomultiplier tube. Inset: Wavefronts of laser illumination (dashed lines) and sample radiation (solid lines) for the three modalities. Lateral and axial point spread functions (PSF) of a 100 nm fluorescence-labeled polystyrene bead for wide-field iSCAT (b, c), confocal iSCAT (d, e), and confocal fluorescence (f, g) modalities. The focus was scanned over 4 μm in steps of 30 nm in c, e, and g. The background was accounted for in each z plane. Curves on the right-hand side depict the intensity profiles along the cross sections shown in each figure. Horizontal and vertical scale bars are 200 nm and 500 nm, respectively. h Scanning electron micrograph of a nanofabricated test sample consisting of two chromium pillars of diameter 45 nm, height 45 nm and center-to-center separation 130 nm. Scale bar is 200 nm. i C-iSCAT image of the sample recorded with a pinhole setting of 0.3 AU at a wavelength of 445 nm. Scale bar is 200 nm. j Cross sections along the white dotted lines from (h, orange) and (i, blue). The green curve also shows a cross section from a C-iSCAT image recorded with a pinhole setting of 1.2 AU. k–n The plasma membrane of a HeLa cell simultaneously imaged in W-iSCAT (k), C-iSCAT (l) and confocal fluorescence (m) modes. The plasma membrane was fluorescence-labeled with GFP-GPI. The W-iSCAT image is flat-fielded, whereas the C-iSCAT image is presented in its raw form. n An overlay of the images in l and m. Scale bars in k–n are 2 μm.

Fig. 2

Fig. 2. 3D imaging of the nucleus and its envelope topography.

C-iSCAT _z_-stack of a HeLa cell recorded at two representative focal planes of the apical nuclear envelope at 3.9 μm (a) and the basal nuclear envelope at 0.6 μm above the cover glass (b). Each image was recorded in 1 s and was background corrected. Scale bars are 5 μm. c Edge sharpness analysis. Three exemplary line cuts with a linewidth of 50 pixels each (green dashed lines) and the average hereof (blue solid line). d 3D representation of the basal and apical nuclear envelope. e Projection along the y z plane (along the white dashed line as indicated in a) of the fluorescence signal simultaneously recorded from the nucleus, which was transfected with mCherry-laminA. f Axial line cut from the basal envelope (symbols) and a Gaussian fit (solid curve) along the dashed line in e. g C-iSCAT counterpart of e. Black arrows indicate the planes of images in a–c. Scale bars for e and g are 2 μm. Contrast color code is same as for a. h Axial line cut of the basal envelope in C-iSCAT (symbols) and a corresponding fit with the model confocal iPSF (solid curve) for height extraction along the dashed line in g. i Evaluated topography of the basal nuclear membrane after multiplane reconstruction. The height varies globally on a range of approximately 900 nm. Scale bar is 2 μm. j Cross section along the horizontal white dashed line in i. The gray dashed line shows the C-iSCAT contrast variations along this cut. The orange curve illustrates the height variations obtained from multiplane reconstruction (see Methods). k Rendered 3D model of a small square section shown in i. l Line cut along the dashed line in the white box in i, emphasizing the nanoscale morphology.

Fig. 3

Fig. 3. Structure and dynamics of the endoplasmic reticulum.

a Fluorescence image of the ER network in a COS-7 cell that was transfected with ER-EGFP. b Simultaneously recorded background-corrected C-iSCAT image. ER tubules in the cellular periphery yield a mean iSCAT contrast of 12%. Scale bars in a and b are 1 μm. c Corresponding segmentation of ER after training a conditional generative adversarial network (cGAN). Color map encodes the prediction output of cGAN. d Rendered 3D representation of the tubular network obtained from a z_-stack over the range of 510 nm recorded with Δ_z = 30 nm. e Persistency map calculated using 340 frames over 85 s with a lag period of 5 s. The color code corresponds to the duration each pixel is occupied by a sub-structure of the tubular network. Scale bar is 1 μm. f Time course of the region marked by dashed lines in e. Formation of a ring-like nanodomain (red arrows) and ER sliding (blue arrows) are revealed. g Fluorescence image of an ER sheet labeled with EGFP. Scale bar is 5 μm. h Corresponding C-iSCAT contrast map of the segmented ER sheet. Scale bar is 5 μm. i Pseudo-3D contrast map of the region marked in h indicating axial sheet fluctuations. j Exemplary oscillation profiles at four positions indicated in h. k Dynamic map of the ER sheet shown in h. The color map denotes occurrence of contrast inversions at each pixel over a period of 16 s. Scale bar is 5 μm.

Fig. 4

Fig. 4. Ultrahigh sensitivity in imaging microtubules in live cells.

a Exemplary raw C-iSCAT image of the periphery of a COS-7 cell showing vesicles, ER network and MT. Corresponding CF images of MTs labeled with mEGFP-tubulin (b) and ER tubules labeled with CytERM-mScarlet (c). Scale bars are 1 μm. d Overlay of a–c for a region marked in a. Scale bar is 1 μm. e A cross section along the cut in d, displaying the C-iSCAT (black) and fluorescence signals of MT (cyan) and ER (magenta). The focal plane was adjusted to be able to extract the maximum negative contrast of both MTs and ER tubules. f Exemplary raw C-iSCAT image from the periphery of a COS-7 cell at t = _t_0 and t = t_0 + 20_s. The white arrows indicate the configuration of two visible MTs in between the ER tubular network. ER tubules undergo motor-dependent “sliding” along the length of the MTs. Scale bar is 2 μm. g Optical flow map depicting ER sliding and dynamics of ER nanodomains. Direction and length of the green arrows indicate the direction and amplitude of motion of the ER network. h Time course over 8 s shows the position of the previously identified MT and a vesicle being transported along it. Symbols mark the consecutive locations of the vesicle. Scale bar 1 μm.

Fig. 5

Fig. 5. 3D tracking of clathrin-coated pits and SARS-CoV-2 on the plasma membrane of a live cell.

a Exemplary raw C-iSCAT image of the periphery of a COS-7 cell showing vesicles, ER network and MTs. Scale bar is 2 μm in a–c. b Overlay of single particle trajectories of vesicles detected and tracked in a. Color map encodes the absolute value of the contrast change normalized for each trajectory. c Overlay of a with CF of clathrin labeled with mCerulean3 (cyan). d Close-up of c including clathrin-coated pits. Time course over 75 s shows contrast inversion of a clathrin-coated pit indicated with a white arrow. Scale bar is 500 nm. e Extracted 3D trajectory of the clathrin-coated pit marked in d. Color map encodes the temporal evolution starting from t = 0 s (magenta) to t = 75 s (cyan). CF (f) and C-iSCAT (g) images of a single SARS-CoV-2 particle on a bare cover glass. Scale bar is 200 nm. h Merge of the C-iSCAT and CF (cyan) signals of labeled SARS-CoV-2 particles on the plasma membrane at the periphery of a COS-7 cell. Scale bar is 1 μm. i Color-coded data show a highly dense 2D trajectory of a diffusing SARS-CoV-2 particle obtained in W-iSCAT from the field of view indicated by the white dashed square in f. The star symbols represent the trajectory of the same event recorded simultaneously in the CF channel. Scale bar is 250 nm. j Extracted height displacement of the SARS-CoV-2 particle over time obtained from W-iSCAT images. k 3D representation of the trajectory depicted in i. Colors in i and k follow the same map as in j and encode time over the course of 65 s at a frame rate of 1 kHz.

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