HiExM: high-throughput expansion microscopy enables scalable super-resolution imaging
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Curated by eLife
eLife assessment
This important study develops a high throughput version of expansion microscopy that can be performed in 96-well plates. The engineered technology is convincing and compatible with standard microplates and automated microscopes and thus will be of broad interest. However, the application is incomplete and would benefit from additional experiments.
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Abstract
Expansion microscopy (ExM) enables nanoscale imaging using a standard confocal microscope through the physical, isotropic expansion of fixed immunolabeled specimens. ExM is widely employed to image proteins, nucleic acids, and lipid membranes in single cells at nanoscale resolution; however, current methods cannot be performed in multi-well cell culture plates which limits the number of samples that can be processed simultaneously. We developed High-throughput Expansion Microscopy (HiExM), a robust platform that enables expansion microscopy of cells cultured in a standard 96-well plate. Our method enables consistent ∼4.2x expansion within individual wells, across multiple wells, and between plates processed in parallel. We also demonstrate that HiExM can be combined with high-throughput confocal imaging platforms greatly improve the ease and scalability of image acquisition. As an example, we analyzed the effects of doxorubicin, a known cardiotoxic agent, in human cardiomyocytes (CMs) based on Hoechst signal intensity. We show a dose dependent effect on nuclear chromatin that is not observed in unexpanded CMs, suggesting that HiExM improves the detection of cellular phenotypes in response to drug treatment. Our method broadens the application of ExM as a tool for scalable super-resolution imaging in biological research applications.Expansion microscopy (ExM) is a flexible, highly accessible, and widely implemented technique for super-resolution imaging of fixed biological specimens. For many ExM users, slide-based sample preparation and manual imaging limit the total volume of data generated and the number of conditions that are tested in parallel. In this work, we develop a simple and inexpensive device that allows the user to perform ExM within the wells of a 96-well plate. We show that samples prepared with our workflow can be imaged with a high-throughput autonomous confocal microscope, allowing for scalable super-resolution image acquisition. Our device retains the accessibility of ExM while extending the application space of ExM to problems that require the analysis of many conditions, treatments, and time points.
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Author response:
Public Reviews:
Reviewer #1 (Public Review):
Summary:
In this manuscript, Day et al. present a high-throughput version of expansion microscopy to increase the throughput of this well-established super-resolution imaging technique. Through technical innovations in liquid handling with custom-fabricated tools and modifications to how the expandable hydrogels are polymerized, the authors show robust ~4-fold expansion of cultured cells in 96-well plates. They go on to show that HiExM can be used for applications such as drug screens by testing the effect of doxorubicin on human cardiomyocytes. Interestingly, the effects of this drug on changing DNA organization were only detectable by ExM, demonstrating the utility of HiExM for such studies.
Overall, this is a very well-written manuscript presenting an important …
Author response:
Public Reviews:
Reviewer #1 (Public Review):
Summary:
In this manuscript, Day et al. present a high-throughput version of expansion microscopy to increase the throughput of this well-established super-resolution imaging technique. Through technical innovations in liquid handling with custom-fabricated tools and modifications to how the expandable hydrogels are polymerized, the authors show robust ~4-fold expansion of cultured cells in 96-well plates. They go on to show that HiExM can be used for applications such as drug screens by testing the effect of doxorubicin on human cardiomyocytes. Interestingly, the effects of this drug on changing DNA organization were only detectable by ExM, demonstrating the utility of HiExM for such studies.
Overall, this is a very well-written manuscript presenting an important technical advance that overcomes a major limitation of ExM - throughput. As a method, HiExM appears extremely useful, and the data generally support the conclusions.
Strengths:
Hi-ExM overcomes a major limitation of ExM by increasing the throughput and reducing the need for manual handling of gels. The authors do an excellent job of explaining each variation introduced to HiExM to make this work and thoroughly characterize the impressive expansion isotropy. The dox experiments are generally well-controlled and the comparison to an alternative stressor (H2O2) significantly strengthens the conclusions.
Weaknesses:
(1) Based on the exceedingly small volume of solution used to form the hydrogel in the well, there may be many unexpanded cells in the well and possibly underneath the expanded hydrogel at the end of this. How would this affect the image acquisition, analysis, and interpretation of HiExM data?
The hydrogel footprint covers approximately 5% of the surface within an individual well and only cells within this area are embedded in the polymerized hydrogel for subsequent processing steps. Cells that are outside of this footprint are not incorporated into the gel, meaning that these cells are digested by Proteinase K and subsequently washed away by the excess water exchange in the gel swelling step. Note that different cell types may require higher or lower concentrations of Proteinase K to adequately digest cells for expansion while maintaining fluorescence signal. Given the compatibility of HiExM with 96-well plates, this titration can be performed rapidly in a single experiment. Although cells outside of the hydrogel footprint are removed prior to imaging, we do occasionally observe Hoechst signal that appears to be underneath the gels. We believe this signal is likely from excess DNA from digested cells that was not fully washed out in the gel swelling step. This signal is both spatially and morphologically distinct from the nuclear signal of intact cells and it does not affect image acquisition, analysis, or data interpretation.
(2) It is unclear why the expansion factor is so variable between plates (e.g., Figure 2H). This should be discussed in more detail.
The variability in expansion factor across plates can likely be attributed to the small volume (~250 nL) deposited by the device posts. Small variations in gel volume could impact gel polymerization compared to standard ExM gels. For example, gels in HiExM are more sensitive to evaporation because they are ~1000x smaller than standard expansion gel preparations due to an increased air-liquid-interface. Evaporation in HiExM gels increases monomer and cross linker concentrations, leading to variation in expansion factor across plates. We note that expansion factor is robust within well plates and that variance is slightly increased between plates. These differences will be discussed in the revised manuscript.
(3) The authors claim that CF dyes are more resistant to bleaching than other dyes. However, in Figure. S3, it appears that half of the CF dyes tested still show bleaching, and no data is shown supporting the claim that Alexa dyes bleach. It would be helpful to include data supporting the claim that Alexa dyes bleach more than CF dyes and the claim that CF dyes in general are resistant to bleaching should be modified to more accurately reflect the data shown.
We did not show data using Alexa dyes because these fluorophores are highly sensitive to photobleaching using Irgacure and thus we could not obtain images. In contrast, some CF dyes are more robust to bleaching in HiExM including CF488A, CF568, and CF633 dyes. We have recently adapted our protocol to PhotoExM chemistry which is compatible with a wider range of fluorophores as described by Günay et al. (2023) and as shown in current Fig. S11.
(4) Related to the above point, it appears that Figure S11 may be missing the figure legend. This makes it hard to understand how HiExM can use other photo-inducible polymerization methods and dyes other than CF dyes.
The following figure legend will be included in the revised manuscript. Fig. S11: Example of a cell expanded in HiExM using Photo-ExM gel chemistry. Photo-ExM does not require an anoxic environment for gel deposition and polymerization, improving ease of use of HiExM. Mitochondria were stained with an Alexa 647 conjugated secondary antibody, indicating that HiExM is compatible with additional fluorophores when combined with Photo-ExM.
(5) The use of automated high-content imaging is impressive. However, it is unclear to me how the increased search space across the extended planar area and focal depths in expanded samples is overcome. It would be helpful to explain this automated imaging strategy in more detail.
We imaged plates on the Opera Phenix using the PreciScan Acquisition Software in Harmony. In brief, each well is imaged at 5x magnification in the Hoechst channel to capture the full well at low resolution. Hoechst is used for this step given its signal brightness, ubiquity across established staining protocols, and spectral independence from most fluorophores commonly conjugated to secondary antibodies. Using this information, the microscope detects regions of interest (nuclei) based on criteria including size, brightness, circularity, etc. Finally, the positional information for each region is stored, and the microscope automatically images those regions at 63x magnification. The working distance for the objective used in this study is 600 µm which is sufficient to capture the entirety of expanded cells in the Z direction. This strategy allows minimizes off-target imaging and allows robust image acquisition even in cultures with lower seeding density. A detailed description of the automated imaging strategy will be included in the revised manuscript.
(6) The general method of imaging pre- and post-expansion is not entirely clear to me. For example, on page 5 the authors state that pre-expansion imaging was done at the center of each gel. Is pre-expansion imaging done after the initial gel polymerization? If so, this would assume that the gelation itself has no effect on cell size and shape if these gelled but not yet expanded cells are used as the reference for calculating expansion factor and isotropy.
Pre-expansion imaging is performed after staining is complete, but prior to the application of AcX, which is the first step of the HiExM protocol. Following staining and imaging, plates can be sealed with paraffin and stored at 4˚C for up to a week prior to starting the expansion protocol. We typically image 61 fields of view at the center of the well plate (where the gel will be deposited) to obtain sufficient pre-expansion images as shown in Figure 2b (left). After pre-expansion imaging, we perform the HiExM protocol followed by image acquisition. We then tile all the images, as shown in Figure 2b, and compare tiled images from the same well pre- and post-expansion to manually identify the same cells. Comparisons of the pre- and post-expansion images of the same cell are then used to calculate expansion factor and isotropy measurements as described. This detailed description will be included in the revised manuscript.
(7) In the dox experiments, are only 4 expanded nuclei analyzed? It is unclear in the Figure 3 legend what the replicates are because for the unexpanded cells, it says the number of nuclei but for expanded it only says n=4. If only 4 nuclei are analyzed, this does not play to the strengths of HiExM by having high throughput.
We performed the DOX titration assay across four different well plates (i.e. n=4). For each condition, the total number of nuclei measured was 56, 71, 64, 92, and 62 for DMSO, 1nM, 10nM, 100nM, and 1µM, respectively. For SEM calculations, we included the number of technical replicates to avoid underestimating error. We have revised the Figure 3 legend to better reflect the experimental details.
(8) I am not sure if the analysis of dox-treated cells is accurate for the overall phenotype because only a single slice at the midplane is analyzed. It would be helpful to show, at least in one or two example cases, that this trend of changing edge intensity occurs across the whole 3D nucleus.
We will repeat our analysis on a subset of images using multiple optical sections for each nucleus reported. These new data will be included in the revised manuscript.
(9) It would be helpful to provide an actual benchmark of imaging speed or throughput to support the claims on page 8 that HiExM can be combined with autonomous imaging to capture thousands of cells a day. What is the highest throughput you have achieved so far?
The parameters that dictate imaging speed in HiExM include exposure time, z-stack height, and number of channels. Depending on the signal intensity for a given channel, exposure times vary from 200ms to 1000ms. For z-stack height, we found that imaging 65 sections with 1µm spacing allowed for robust identification of each region of interest in the 5x pre-scan. As an example, collecting images for a full well plate (e.g., 20 images per well with 4 channels) requires approximately 24 hours of autonomous image acquisition using the Opera Phenix. Depending on cell size, this yields imaging data for between 1200 cells (1 cell per field of view) to 6000 cells (5 cells per field of view). Different autonomous imagers as well as improving staining techniques that increase signal:noise can be expected to significantly decrease the exposure time as it will reduce the number of z-stacks needed for each region.
Reviewer #2 (Public Review):
Summary:
In the present work, the authors present an engineering solution to sample preparation in 96-well plates for high-throughput super-resolution microscopy via Expansion Microscopy. This is not a trivial problem, as the well cannot be filled with the gel, which would prohibit the expansion of the gel. A device was engineered that can spot a small droplet of hydrogel solution and keep it in place as it polymerizes. It occupies only a small portion of space at the center of each well, the gel can expand into all directions, and imaging and staining can proceed by liquid handling robots and an automated microscope.
Strengths:
In contrast to Reference 8, the authors' system is compatible with standard 96 well imaging plates for high-throughput automated microscopy and automated liquid handling for most parts of the protocol. They thus provide a clear path towards high-throughput ExM and high-throughput super-resolution microscopy, which is a timely and important goal.
Weaknesses:
The assay they chose to demonstrate what high-throughput ExM could be useful for, is not very convincing. But for this reviewer that is not important.
We appreciate this reviewer’s point. We believe the data provide an example of the power of HiExM for collecting thousands of nanoscale images that would benefit experiments that require many samples (e.g., conditions, replicates, timepoints, etc.). The ability to generate large data sets also enables quantitative analysis of images with appropriate statistical power. The intention of this experiment was to provide a proof-of-concept example of the robustness, accessibility, and experimental design flexibility of HiExM.
Reviewer #3 (Public Review):
Summary:
Day et al. introduced high-throughput expansion microscopy (HiExM), a method facilitating the simultaneous adaptation of expansion microscopy for cells cultured in a 96-well plate format. The distinctive features of this method include 1) the use of a specialized device for delivering a minimal amount (~230 nL) of gel solution to each well of a conventional 96-well plate, and 2) the application of the photochemical initiator, Irgacure 2959, to successfully form and expand the toroidal gel within each well.
Strengths:
This configuration eliminates the need for transferring gels to other dishes or wells, thereby enhancing the throughput and reproducibility of parallel expansion microscopy. This methodological uniqueness indicates the applicability of HiExM in detecting subtle cellular changes on a large scale.
Weaknesses:
To demonstrate the potential utility of HiExM in cell phenotyping, drug studies, and toxicology investigations, the authors treated hiPS-derived cardiomyocytes with a low dose of doxycycline (dox) and quantitatively assessed changes in nuclear morphology. However, this reviewer is not fully convinced of the validity of this specific application. Furthermore, some data about the effect of expansion require reconsideration.
The application we chose was intended as a proof of concept. We believe the data provide an example of the power of HiExM for collecting thousands of nanoscale images that would benefit experiments that require many samples (e.g., conditions, replicates, timepoints, etc.). The ability to generate large data sets also enables quantitative analysis of images with appropriate statistical power. The intention of this experiment was to provide a proof-of-concept example of the robustness, accessibility, and experimental design flexibility of HiExM.
The variability in expansion factor across plates can likely be attributed to the small volume (~250 nL) deposited by the device posts. Small variations in gel volume could impact gel polymerization compared to standard ExM gels. For example, gels in HiExM are more sensitive to evaporation because they are ~1000x smaller than standard expansion gel preparations due to an increased air-liquid-interface. Evaporation in HiExM gels increases monomer and cross linker concentrations, leading to variation in expansion factor across plates. We note that expansion factor is robust within well plates and that variance is slightly increased between plates. These differences will be discussed in the revised manuscript.
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eLife assessment
This important study develops a high throughput version of expansion microscopy that can be performed in 96-well plates. The engineered technology is convincing and compatible with standard microplates and automated microscopes and thus will be of broad interest. However, the application is incomplete and would benefit from additional experiments.
-
Reviewer #1 (Public Review):
Summary:
In this manuscript, Day et al. present a high-throughput version of expansion microscopy to increase the throughput of this well-established super-resolution imaging technique. Through technical innovations in liquid handling with custom-fabricated tools and modifications to how the expandable hydrogels are polymerized, the authors show robust ~4-fold expansion of cultured cells in 96-well plates. They go on to show that HiExM can be used for applications such as drug screens by testing the effect of doxorubicin on human cardiomyocytes. Interestingly, the effects of this drug on changing DNA organization were only detectable by ExM, demonstrating the utility of HiExM for such studies.
Overall, this is a very well-written manuscript presenting an important technical advance that overcomes a major …
Reviewer #1 (Public Review):
Summary:
In this manuscript, Day et al. present a high-throughput version of expansion microscopy to increase the throughput of this well-established super-resolution imaging technique. Through technical innovations in liquid handling with custom-fabricated tools and modifications to how the expandable hydrogels are polymerized, the authors show robust ~4-fold expansion of cultured cells in 96-well plates. They go on to show that HiExM can be used for applications such as drug screens by testing the effect of doxorubicin on human cardiomyocytes. Interestingly, the effects of this drug on changing DNA organization were only detectable by ExM, demonstrating the utility of HiExM for such studies.
Overall, this is a very well-written manuscript presenting an important technical advance that overcomes a major limitation of ExM - throughput. As a method, HiExM appears extremely useful, and the data generally support the conclusions.
Strengths:
Hi-ExM overcomes a major limitation of ExM by increasing the throughput and reducing the need for manual handling of gels. The authors do an excellent job of explaining each variation introduced to HiExM to make this work and thoroughly characterize the impressive expansion isotropy. The dox experiments are generally well-controlled and the comparison to an alternative stressor (H2O2) significantly strengthens the conclusions.
Weaknesses:
(1) Based on the exceedingly small volume of solution used to form the hydrogel in the well, there may be many unexpanded cells in the well and possibly underneath the expanded hydrogel at the end of this. How would this affect the image acquisition, analysis, and interpretation of HiExM data?
(2) It is unclear why the expansion factor is so variable between plates (e.g., Figure 2H). This should be discussed in more detail.
(3) The authors claim that CF dyes are more resistant to bleaching than other dyes. However, in Figure. S3, it appears that half of the CF dyes tested still show bleaching, and no data is shown supporting the claim that Alexa dyes bleach. It would be helpful to include data supporting the claim that Alexa dyes bleach more than CF dyes and the claim that CF dyes in general are resistant to bleaching should be modified to more accurately reflect the data shown.
(4) Related to the above point, it appears that Figure S11 may be missing the figure legend. This makes it hard to understand how HiExM can use other photo-inducible polymerization methods and dyes other than CF dyes.
(5) The use of automated high-content imaging is impressive. However, it is unclear to me how the increased search space across the extended planar area and focal depths in expanded samples is overcome. It would be helpful to explain this automated imaging strategy in more detail.
(6) The general method of imaging pre- and post-expansion is not entirely clear to me. For example, on page 5 the authors state that pre-expansion imaging was done at the center of each gel. Is pre-expansion imaging done after the initial gel polymerization? If so, this would assume that the gelation itself has no effect on cell size and shape if these gelled but not yet expanded cells are used as the reference for calculating expansion factor and isotropy.
(7) In the dox experiments, are only 4 expanded nuclei analyzed? It is unclear in the Figure 3 legend what the replicates are because for the unexpanded cells, it says the number of nuclei but for expanded it only says n=4. If only 4 nuclei are analyzed, this does not play to the strengths of HiExM by having high throughput.
(8) I am not sure if the analysis of dox-treated cells is accurate for the overall phenotype because only a single slice at the midplane is analyzed. It would be helpful to show, at least in one or two example cases, that this trend of changing edge intensity occurs across the whole 3D nucleus.
(9) It would be helpful to provide an actual benchmark of imaging speed or throughput to support the claims on page 8 that HiExM can be combined with autonomous imaging to capture thousands of cells a day. What is the highest throughput you have achieved so far?
-
Reviewer #2 (Public Review):
Summary:
In the present work, the authors present an engineering solution to sample preparation in 96-well plates for high-throughput super-resolution microscopy via Expansion Microscopy. This is not a trivial problem, as the well cannot be filled with the gel, which would prohibit the expansion of the gel. A device was engineered that can spot a small droplet of hydrogel solution and keep it in place as it polymerizes. It occupies only a small portion of space at the center of each well, the gel can expand into all directions, and imaging and staining can proceed by liquid handling robots and an automated microscope.
Strengths:
In contrast to Reference 8, the authors' system is compatible with standard 96 well imaging plates for high-throughput automated microscopy and automated liquid handling for most …
Reviewer #2 (Public Review):
Summary:
In the present work, the authors present an engineering solution to sample preparation in 96-well plates for high-throughput super-resolution microscopy via Expansion Microscopy. This is not a trivial problem, as the well cannot be filled with the gel, which would prohibit the expansion of the gel. A device was engineered that can spot a small droplet of hydrogel solution and keep it in place as it polymerizes. It occupies only a small portion of space at the center of each well, the gel can expand into all directions, and imaging and staining can proceed by liquid handling robots and an automated microscope.
Strengths:
In contrast to Reference 8, the authors' system is compatible with standard 96 well imaging plates for high-throughput automated microscopy and automated liquid handling for most parts of the protocol. They thus provide a clear path towards high-throughput exM and high-throughout super-resolution microscopy, which is a timely and important goal.
Weaknesses:
The assay they chose to demonstrate what high-throughput ExM could be useful for, is not very convincing. But for this reviewer that is not important.
-
Reviewer #3 (Public Review):
Summary:
Day et al. introduced high-throughput expansion microscopy (HiExM), a method facilitating the simultaneous adaptation of expansion microscopy for cells cultured in a 96-well plate format. The distinctive features of this method include 1) the use of a specialized device for delivering a minimal amount (~230 nL) of gel solution to each well of a conventional 96-well plate, and 2) the application of the photochemical initiator, Irgacure 2959, to successfully form and expand the toroidal gel within each well.
Strengths:
This configuration eliminates the need for transferring gels to other dishes or wells, thereby enhancing the throughput and reproducibility of parallel expansion microscopy. This methodological uniqueness indicates the applicability of HiExM in detecting subtle cellular changes on a …
Reviewer #3 (Public Review):
Summary:
Day et al. introduced high-throughput expansion microscopy (HiExM), a method facilitating the simultaneous adaptation of expansion microscopy for cells cultured in a 96-well plate format. The distinctive features of this method include 1) the use of a specialized device for delivering a minimal amount (~230 nL) of gel solution to each well of a conventional 96-well plate, and 2) the application of the photochemical initiator, Irgacure 2959, to successfully form and expand the toroidal gel within each well.
Strengths:
This configuration eliminates the need for transferring gels to other dishes or wells, thereby enhancing the throughput and reproducibility of parallel expansion microscopy. This methodological uniqueness indicates the applicability of HiExM in detecting subtle cellular changes on a large scale.
Weaknesses:
To demonstrate the potential utility of HiExM in cell phenotyping, drug studies, and toxicology investigations, the authors treated hiPS-derived cardiomyocytes with a low dose of doxycycline (dox) and quantitatively assessed changes in nuclear morphology. However, this reviewer is not fully convinced of the validity of this specific application. Furthermore, some data about the effect of expansion require reconsideration.
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