Building a super-resolution fluorescence cryomicroscope

Correlated super-resolution fluorescence microscopy and cryo-electron microscopy enables imaging with both high labeling specificity and high resolution. Naturally, combining two sophisticated imaging techniques within one workflow also introduces new requirements on hardware, such as the need for a super-resolution fluorescence capable microscope that can be used to image cryogenic samples. In this chapter, we describe the design and use of the "cryoscope"; a microscope designed for single-molecule localization microscopy (SMLM) of cryoEM samples that fits right into established cryoEM workflows. We demonstrate the results that can be achieved with our microscope by imaging fluorescently labeled vimentin, an intermediate filament, within U2OS cells grown on EM grids, and we provide detailed 3d models that encompass the entire design of the microscope.

Imaging intracellular components in situ using super-resolution cryo-correlative light and electron microscopy

Super-resolution cryo-correlative light and electron microscopy (SRcryoCLEM) is emerging as a powerful method to enable targeted in situ structural studies of biological samples. By combining the high specificity and localization accuracy of single-molecule localization microscopy (cryoSMLM) with the high resolution of cryo-electron tomography (cryoET), this method enables accurately targeted data acquisition and the observation and identification of biomolecules within their natural cellular context. Despite its potential, the adaptation of SRcryoCLEM has been hindered by the need for specialized equipment and expertise. In this chapter, we outline a workflow for cryoSMLM and cryoET-based SRcryoCLEM, and we demonstrate that, given the right tools, it is possible to incorporate cryoSMLM into an established cryoET workflow. Using Vimentin as an exemplary target of interest, we demonstrate all stages of an SRcryoCLEM experiment: performing cryoSMLM, targeting cryoET acquisition based on single-molecule localization maps, and correlation of cryoSMLM and cryoET datasets using scNodes, a software package dedicated to SRcryoCLEM. By showing how SRcryoCLEM enables the imaging of specific intracellular components in situ, we hope to facilitate adoption of the technique within the field of cryoEM.

Quantification of the intrinsic neural plexus of the heart - The missing link in histological tissue analysis

BACKGROUND AND OBJECTIVE

The heart is under strict regulation of the autonomic nervous system, during which, in a healthy state, the effects of sympathetic and parasympathetic branches are balanced. In recent years, there has been increasing interest in pathological remodeling and outgrowth of cardiac autonomic nerves in relation to arrhythmogenesis. However, the small size of the cardiac nerves in relatively large tissues renders research using histological quantification of these nerves extremely challenging and usually relies on quantification of the nerve density in selected regions of interest only. Our aim was to develop a method to be able to quantify the histological nerve density in transmural tissue sections.

METHODS

Here we describe a novel workflow that enables visualization and quantification of variable innervation types and their heterogeneity within transmural myocardial tissue sections. A custom semiautomatic workflow for the quantification of cardiac nerves involving Python, MATLAB and ImageJ is provided and described in this protocol in a stepwise and detailed manner.

REPRESENTATIVE RESULTS

The results of two example tissue sections are represented in this paper. An example tissue section taken from the infarction core with a high heterogeneity value of 0.20, 63.3% normal innervation, 12.2% hyperinnervation, 3.6% hypoinnervation and 21.0% denervation. The second example tissue section taken from an area of the left ventricle remote from the infarction showed a low heterogeneity value of 0.02, 95.3% normal innervation, 3.8% hyperinnervation, 0.5% hypoinnervation and 0.5% denervation.

CONCLUSIONS

This approach has the potential to be broadly applied to any research involving high-resolution imaging of nerves in large tissues.

High-throughput Analysis of Capillary Density in Skeletal Muscle Cross Sections

Capillary density in skeletal muscles is key to estimate exercise capacity in healthy individuals, athletes, and those with muscle-related pathologies. Here, we present a step-by-step, high-throughput semi-automated method for quantifying capillary density from whole human skeletal muscle cross-sections, in areas of the muscle occupied by myofibers. We provide a detailed protocol for immunofluorescence staining, image acquisition, processing, and quantification. Image processing is performed in ImageJ, and data analysis is conducted in R. The provided protocol allows high-throughput quantification of capillary density. Key features • This protocol builds upon the method and results described in Abbassi-Daloii et al. (2023b). • It includes step-by-step details on image acquisition and image processing of the entire muscle section. • It enables high-throughput and semi-automated image quantification of capillary density. • It provides a robust analysis for determining capillary density over the entire muscle cross section.

Super-resolution fluorescence imaging of cryosamples does not limit achievable resolution in cryoEM

Correlated super-resolution cryo-fluorescence and cryo-electron microscopy (cryoEM) has been gaining popularity as a method to investigate biological samples with high resolution and specificity. A concern in this combined method (called SR-cryoCLEM), however, is whether and how fluorescence imaging prior to cryoEM acquisition is detrimental to sample integrity. In this report, we investigated the effect of high-dose laser light (405, 488, and 561 nm) irradiation on apoferritin samples prepared for cryoEM with excitation wavelengths commonly used in fluorescence microscopy, and compared these samples to controls that were kept in the dark. We found that laser illumination, of equal duration and intensity as used in cryo-single molecule localization microscopy (cryoSMLM) and in the presence of high concentrations of fluorescent protein, did not affect the achievable resolution in cryoEM, with final reconstructions reaching resolutions of ∼ 1.8 Å regardless of the laser illumination. The finding that super-resolution fluorescence imaging of cryosamples prior to cryoEM data acquisition does not limit the achievable resolution suggests that super-resolution cryo-fluorescence microscopy and in situ structural biology using cryoEM are entirely compatible.

RNF26 binds perinuclear vimentin filaments to integrate ER and endolysosomal responses to proteotoxic stress

Proteotoxic stress causes profound endoplasmic reticulum (ER) membrane remodeling into a perinuclear quality control compartment (ERQC) for the degradation of misfolded proteins. Subsequent return to homeostasis involves clearance of the ERQC by endolysosomes. However, the factors that control perinuclear ER integrity and dynamics remain unclear. Here, we identify vimentin intermediate filaments as perinuclear anchors for the ER and endolysosomes. We show that perinuclear vimentin filaments engage the ER-embedded RING finger protein 26 (RNF26) at the C-terminus of its RING domain. This restricts RNF26 to perinuclear ER subdomains and enables the corresponding spatial retention of endolysosomes through RNF26-mediated membrane contact sites (MCS). We find that both RNF26 and vimentin are required for the perinuclear coalescence of the ERQC and its juxtaposition with proteolytic compartments, which facilitates efficient recovery from ER stress via the Sec62-mediated ER-phagy pathway. Collectively, our findings reveal a scaffolding mechanism that underpins the spatiotemporal integration of organelles during cellular proteostasis.

Modulation of Cathodoluminescence by Surface Plasmons in Silver Nanowires

The waveguide modes in chemically-grown silver nanowires on silicon nitride substrates are observed using spectrally- and spatially-resolved cathodoluminescence (CL) excited by high-energy electrons in a scanning electron microscope. The presence of a long-range, travelling surface plasmon mode modulates the coupling efficiency of the incident electron energy into the nanowires, which is observed as oscillations in the measured CL with the point of excitation by the focused electron beam. The experimental data are modeled using the theory of surface plasmon polariton modes in cylindrical metal waveguides, enabling the complex mode wavenumbers and excitation strength of the long-range surface plasmon mode to be extracted. The experiments yield insight into the energy transfer mechanisms between fast electrons and coherent oscillations in surface charge density in metal nanowires and the relative amplitudes of the radiative processes excited in the wire by the electron.

Quantification of Large Transmural Biopsies Reveals Heterogeneity in Innervation Patterns in Chronic Myocardial Infarction

BACKGROUND

Abnormal cardiac innervation plays an important role in arrhythmogenicity after myocardial infarction (MI). Data regarding reperfusion models and innervation abnormalities in the medium to long term after MI are sparse. Histologic quantification of the small-sized cardiac nerves is challenging, and transmural analysis has not been performed.

OBJECTIVES

This study sought to assess cardiac innervation patterns in transmural biopsy sections in a porcine reperfusion model of MI (MI-R) using a novel method for nerve quantification.

METHODS

Transmural biopsy sections from 4 swine (n = 83) at 3 months after MI-R and 3 controls (n = 38) were stained with picrosirius red (fibrosis) and beta-III-tubulin (autonomic nerves). Biopsy sections were classified as infarct core, border zone, or remote zone. Each biopsy section was analyzed with a custom software pipeline, allowing calculation of nerve density and classification into innervation types at the 1 × 1-mm resolution level. Relocation of the classified squares to the original biopsy position enabled transmural quantification and innervation heterogeneity assessment.

RESULTS

Coexisting hyperinnervation, hypoinnervation, and denervation were present in all transmural MI-R biopsy sections. The innervation heterogeneity was greatest in the infarct core (median: 0.14; IQR: 0.12-0.15), followed by the border zone (median: 0.05; IQR: 0.04-0.07; P = 0.02) and remote zone (median: 0.02; IQR: 0.02-0.03; P < 0.0001). Only in the border zone was a positive linear relation between fibrosis and innervation heterogeneity observed (R = 0.79; P < 0.0001).

CONCLUSIONS

This novel method allows quantification of nerve density and heterogeneity in large transmural biopsy sections. In the chronic phase after MI-R, alternating innervation patterns were identified within the same biopsy section. Persistent innervation heterogeneity, in particular in the border zone biopsy sections, may contribute to late arrhythmogenicity.

Selecting optimal support grids for super-resolution cryogenic correlated light and electron microscopy

Cryogenic transmission electron microscopy (cryo-TEM) and super-resolution fluorescence microscopy are two popular and ever improving methods for high-resolution imaging of biological samples. In recent years, the combination of these two techniques into one correlated workflow has gained attention as a promising route towards contextualizing and enriching cryo-TEM imagery. A problem that is often encountered in the combination of these methods is that of light-induced damage to the sample during fluorescence imaging that renders the sample structure unsuitable for TEM imaging. In this paper, we describe how absorption of light by TEM sample support grids leads to sample damage, and we systematically explore the importance of parameters of grid design. We explain how, by changing the grid geometry and materials, one can increase the maximum illumination power density in fluorescence microscopy by up to an order of magnitude. Finally, we demonstrate the significant improvements in super-resolution image quality that are enabled by the selection of support grids that are optimally suited for correlated cryo-microscopy.

Measuring cryo-TEM sample thickness using reflected light microscopy and machine learning

In cryo-transmission electron microscopy (cryo-TEM), sample thickness is one of the most important parameters that governs image quality. When combining cryo-TEM with other imaging methods, such as light microscopy, measuring and controlling the sample thickness to ensure suitability of samples becomes even more critical due to the low throughput of such correlated imaging experiments. Here, we present a method to assess the sample thickness using reflected light microscopy and machine learning that can be used prior to TEM imaging of a sample. The method makes use of the thin-film interference effect that is observed when imaging narrow-band LED light sources reflected by thin samples. By training a neural network to translate such reflection images into maps of the underlying sample thickness, we are able to accurately predict the thickness of cryo-TEM samples using a light microscope. We exemplify our approach using mammalian cells grown on TEM grids, and demonstrate that the thickness predictions are highly similar to the measured sample thickness. The open-source software described herein, including the neural network and algorithms to generate training datasets, is freely available at github.com/bionanopatterning/thicknessprediction. With the recent development of in situ cellular structural biology using cryo-TEM, there is a need for fast and accurate assessment of sample thickness prior to high-resolution imaging. We anticipate that our method will improve the throughput of this assessment by providing an alternative method to screening using cryo-TEM. Furthermore, we demonstrate that our method can be incorporated into correlative imaging workflows to locate intracellular proteins at sites ideal for high-resolution cryo-TEM imaging.

Quantitative analysis of myofiber type composition in human and mouse skeletal muscles

Skeletal muscles are composed of different myofiber types characterized by the expression of myosin heavy chain isoforms, which can be affected by physical activity, aging, and pathological conditions. Here, we present a step-by-step high-throughput semi-automated approach for performing myofiber type quantification of entire human or mouse muscle tissue sections, including immunofluorescence staining, image acquisition, processing, and quantification. For complete details on the use and execution of this protocol, please refer to Abbassi-Daloii et al. (2022).1.

A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location

Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.

A novel method for visualization and quantification of nerve density in transmural biopsies after myocardial infarction

Introduction

Abnormal cardiac innervation plays an important role in arrhythmogenicity after myocardial infarction (MI). To study the innervation state after cardiac damage and ventricular arrhythmias, accurate quantification of nerve density is important. However, as cardiac nerves are very small structures, the histological quantification of nerves requires high resolution images, thus far proved extremely challenging and has never been performed transmurally.

Aim

To develop a method to analyze nerve density in large transmural biopsies after MI.

Method

Transmural myocardial biopsies from 4 swine, 3 months after MI, were stained with Picrosirius Red (fibrosis) and Beta-III-Tubulin (autonomic nerves). Fibrosis cut-offs were used to classify the biopsies into MI core (&gt;59.8%), borderzone (BZ) (14.3–59.8%) or remote zone (RZ) (&lt;14.3%). Each biopsy was quantified with a custom software pipeline, involving Python, Matlab and ImageJ. The biopsy was graphically divided into a 1x1mm grid. Using fixed values, nerve and myocardial tissue areas were thresholded and subjected to a quality check and artefact removal, followed by further division into 0.1x0.1mm squares. The nerve density per square was calculated and classified into denervation, hypoinnervation, normal innervation and hyperinnervation according to cut-offs (5th, 95th percentile) derived from 3 control swine. Finally, squares were located back to the original position within the biopsy allowing visualization and quantification of the different innervation types. Currently these steps are being integrated into an easy-to-use framework.

Results

In all 121 analyzed biopsies (experimental swine n=83, control n=38), areas with variable nerve densities were observed, although the areas with denervation, hypo- and hyperinnervation were largest in the MI core and BZ. Normal innervation was observed in 94.9% (93.8–96.0%) of the total biopsy area in the RZ, decreased in the BZ biopsies, 87.9% (85.1–92.4%, p&lt;0.001), and even lower in the MI core, 72.8% (66.3–75.8%, p&lt;0.001). The percentage of denervation and hypoinnervation per biopsy was highest in the core biopsies, 16.7% (13.5–23.5%) and 3.8% (2.9–5.0%) respectively, lower in the BZ, 2.6% (1.6–6.5%, p&lt;0.008) and 1.2% (0.8–1.7%, p=0.015) and even lower in the RZ, 1.2% (0.7–1.8%, p&lt;0.001), 0.6% (0.3–1.3, p&lt;0.001). Hyperinnervation was observed mainly in the BZ, 5.3% (3.7–9.4%) and remarkably, also in the core, 5.3% (3.7–9.4%, p&gt;0.999), whilst being low in the RZ 2.6% (1.7–4.3%, p=0.002 and p=0.038 respectively).

Conclusion

This novel method allows successful visualization and quantification of nerve density after cardiac damage in transmural biopsies. Strikingly, alternating areas of different innervation types could be identified within the same biopsy after MI, indicating a potentially heterogenous substrate for arrhythmias. This method has the potential to be broadly applied to any research involving high resolution imaging of nerves in large tissues.

Funding Acknowledgement

Type of funding sources: None.

Apparent Lack of BRAF V600E Derived HLA Class I Presented Neoantigens Hampers Neoplastic Cell Targeting by CD8+ T Cells in Langerhans Cell Histiocytosis

Langerhans Cell Histiocytosis (LCH) is a neoplastic disorder of hematopoietic origin characterized by inflammatory lesions containing clonal histiocytes (LCH-cells) intermixed with various immune cells, including T cells. In 50-60% of LCH-patients, the somatic BRAF ^V600E driver mutation, which is common in many cancers, is detected in these LCH-cells in an otherwise quiet genomic landscape. Non-synonymous mutations like BRAF ^V600E can be a source of neoantigens capable of eliciting effective antitumor CD8⁺ T cell responses. This requires neopeptides to be stably presented by Human Leukocyte Antigen (HLA) class I molecules and sufficient numbers of CD8⁺ T cells at tumor sites. Here, we demonstrate substantial heterogeneity in CD8⁺ T cell density in n = 101 LCH-lesions, with BRAF ^V600E mutated lesions displaying significantly lower CD8⁺ T cell:CD1a⁺ LCH-cell ratios (p = 0.01) than BRAF wildtype lesions. Because LCH-lesional CD8⁺ T cell density had no significant impact on event-free survival, we investigated whether the intracellularly expressed BRAF ^V600E protein is degraded into neopeptides that are naturally processed and presented by cell surface HLA class I molecules. Epitope prediction tools revealed a single HLA class I binding BRAF ^V600E derived neopeptide (KIGDFGLATEK), which indeed displayed strong to intermediate binding capacity to HLA-A^*03:01 and HLA-A^*11:01 in an in vitro peptide-HLA binding assay. Mass spectrometry-based targeted peptidomics was used to investigate the presence of this neopeptide in HLA class I presented peptides isolated from several BRAF ^V600E expressing cell lines with various HLA genotypes. While the HLA-A^*02:01 binding BRAF wildtype peptide KIGDFGLATV was traced in peptides isolated from all five cell lines expressing this HLA subtype, KIGDFGLATEK was not detected in the HLA class I peptidomes of two distinct BRAF ^V600E transduced cell lines with confirmed expression of HLA-A^*03:01 or HLA-A^*11:01. These data indicate that the in silico predicted HLA class I binding and proteasome-generated neopeptides derived from the BRAF ^V600E protein are not presented by HLA class I molecules. Given that the BRAF ^V600E mutation is highly prevalent in chemotherapy refractory LCH-patients who may qualify for immunotherapy, this study therefore questions the efficacy of immune checkpoint inhibitor therapy in LCH.

Homeostasis of soluble proteins and the proteasome post nuclear envelope reformation in mitosis

Upon Nuclear envelope (NE) fragmentation in the prometaphase the nuclear and cytosolic proteomes blend and must be redefined to reinstate homeostasis. Using a molecular GFP ladder, we show that in early mitosis, condensed chromatin excludes cytosolic proteins. When the NE reforms tightly around condensed chromatin in late mitosis, large GFP multimers are automatically excluded from the nucleus. This can be circumvented by limiting DNA condensation with Q15, a Condensin II inhibitor. Soluble small and other NLS-targeted proteins then swiftly enter the expanding nuclear space. We then examined the proteasome, located in cytoplasm and nucleus. A significant fraction of 20S proteasomes is imported by importin IPO5 within 20 minutes following reformation of the nucleus, after which import comes to an abrupt halt. This suggests that maintaining the nuclear-cytosol distribution after mitosis requires chromatin condensation to exclude cytosolic material from the nuclear space and specialized machineries for nuclear import of large protein complexes such as the proteasome.

Utilization of integrated correlative light and electron microscopy (iCLEM) for imaging sedimentary organic matter

We report here a new microscopic technique for imaging and identifying sedimentary organic matter in geologic materials that combines inverted fluorescence microscopy with scanning electron microscopy and allows for sequential imaging of the same region of interest without transferring the sample between instruments. This integrated correlative light and electron microscopy technique is demonstrated with observations from an immature lacustrine oil shale from the Eocene Green River Mahogany Zone and mid-oil window paralic shale from the Upper Cretaceous Tuscaloosa Group. This technique has the potential to allow for identification and characterization of organic matter in shale hydrocarbon reservoirs that is not possible using either light or electron microscopy alone, and may be applied to understanding the organic matter type and thermal regime in which organic nanoporosity forms, thereby reducing uncertainty in the estimation of undiscovered hydrocarbon resources.

Automated sub-5 nm image registration in integrated correlative fluorescence and electron microscopy using cathodoluminescence pointers

In the biological sciences, data from fluorescence and electron microscopy is correlated to allow fluorescence biomolecule identification within the cellular ultrastructure and/or ultrastructural analysis following live-cell imaging. High-accuracy (sub-100 nm) image overlay requires the addition of fiducial markers, which makes overlay accuracy dependent on the number of fiducials present in the region of interest. Here, we report an automated method for light-electron image overlay at high accuracy, i.e. below 5 nm. Our method relies on direct visualization of the electron beam position in the fluorescence detection channel using cathodoluminescence pointers. We show that image overlay using cathodoluminescence pointers corrects for image distortions, is independent of user interpretation, and does not require fiducials, allowing image correlation with molecular precision anywhere on a sample.

A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM

Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the 'tilted' CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.