Name: Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy (Video) | JoVE Journal
Uploaded: 2022-06-09T13:00:00.000+00:00
Duration: 9 min 12 s
Description: Learn 3D reconstruction of interorganelle contact sites in hepatocytes using serial section electron microscopy. This robust protocol enables visualization of membrane interactions without requiring specialized volume electron microscopes.

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5 minutes

We thank Joanna Hanley, Rebecca Fiadeiro, and Ania Straatman-Iwanowska for expert technical assistance. We also thank Stefan lab members and Ian J. White for helpful discussions. J.J.B. is supported by MRC funding to the MRC Laboratory of Molecular Cell Biology at UCL, award code MC_U12266B. C.J.S. is supported by MRC funding to the MRC Laboratory of Molecular Cell Biology University Unit at UCL, award code MC_UU_00012/6. P.G. is funded by the European Research Council, grant code ERC-2013-StG-337057.

The authors have no conflicts of interest to disclose.

An accessible vEM technique for visualizing organelle structure and interactions in 3D is described in this protocol. The morphology of interorganelle contacts in hepatocytes is presented as a case study here. However, this approach has also been applied to investigate a variety of other samples and research areas, including Schwann cell-endothelial interactions in peripheral nerves45, Weibel Palade Body biogenesis in endothelial cells46, cargo secretion in kidney cells<sup...

Since their invention in the 1930s, electron microscopes have allowed researchers to visualize the structural components of cells and tissues1,2. Most investigations have provided 2D information, as building 3D models requires painstaking serial section collection, manual photography, negative processing, manual tracing, and the creation and assembly of 3D models from sheets of glass, plastic, or Styrofoam3,4. Almost 70 years later, there have been considerable advances in numerous aspects of the process, from microscope performance, serial section collection, automated digital imaging, sophisticated software and hardware for 3D reconstruction, visualization, and analysis to alternative approaches for what is now collectively termed volume EM (vEM). These vEM techniques are generally considered to provide 3D ultrastructural information at nanometer resolutions across micron scales and encompass transmission electron microscopy (TEM) and newer scanning electron microscopy (SEM) techniques; see reviews5,6,7,8.
For example, focused ion beam SEM (FIB-SEM) uses a focused ion beam inside an SEM to mill away the surface of the block between sequential SEM imaging scans of the block&#39;s surface, allowing the repeated automated milling/imaging of a sample and building up a 3D dataset for reconstruction9,10. In contrast, serial block face SEM (SBF-SEM) uses an ultramicrotome inside the SEM to remove material from the block face prior to imaging11,12, while array tomography is a nondestructive process that requires the collection of serial sections, onto coverslips, wafers, or tape, prior to setting up an automated workflow of imaging the region of interest in sequential sections in the SEM to generate the 3D dataset13. Similar to array tomography, serial section TEM (ssTEM) requires physical sections to be collected ahead of imaging; however, these sections are collected on TEM grids and imaged in a TEM14,15,16. ssTEM can be extended by performing tilt tomography17,18,19. Serial tilt tomography provides the best resolution in x, y, and z, and while it has been used to reconstruct whole cells20, it is reasonably challenging. This protocol focuses on the practical aspects of ssTEM as the most accessible vEM technique available to many EM labs who may not currently have access to specialized sectioning or vEM instruments but would benefit from generating 3D vEM data.
Serial ultramicrotomy for 3D reconstruction has previously been considered challenging. It was difficult to cut straight ribbons of even section thickness, be able to arrange and pick up ribbons of the correct size, in the correct order, onto grids with sufficient support, but without grid bars obscuring regions of interest, and most importantly, without losing sections, as an incomplete series may prevent full 3D reconstruction21. However, improvements to commercial ultramicrotomes, diamond cutting and trimming knives22,23, electron lucent support films on grids21,24, and adhesives for aiding section adhesion and ribbon preservation13,21 are just some of the incremental advances over the years that have made the technique more routine in many labs. Once serial sections have been collected, serial imaging in TEM is straightforward and can provide EM images with subnanometer px sizes in x and y, allowing high-resolution interrogation of the subcellular structures-a potential requirement for many research questions. The case study presented here demonstrates the use of ssTEM and 3D reconstruction in the study of endoplasmic reticulum (ER)-organelle contacts in liver hepatocytes, where&#160;ER-organelle contacts were first observed25,26.
While being contiguous with the nuclear envelope, the ER also makes close contacts with numerous other cell organelles, including lysosomes, mitochondria, lipid droplets, and the plasma membrane27. ER-organelle contacts have been implicated in lipid metabolism28, phosphoinositide and calcium signaling29, autophagy regulation, and stress response30,31. The ER-organelle contacts and other interorganelle contacts are highly dynamic structures that respond to cellular metabolic needs and extracellular cues. They have been shown to vary morphologically in their size and shape and the distances between organelle membranes32,33. It is thought that these ultrastructural differences are likely to reflect their different protein/lipid compositions and function34,35. However, it is still a challenging task to define interorganelle contacts and analyze them36. Hence, a reliable yet simple protocol to examine and characterize interorganelle contacts is required for further investigations.
As ER-organelle contacts can range from 10 to 30 nm in membrane-to-membrane separation, the gold standard for identification has historically been TEM. Thin-section TEM has revealed specific subdomain localization for resident ER proteins at distinct membrane contacts37. Traditionally, this has revealed ER-organelle contacts with nm resolution but often only presented a 2D view of these interactions. However, vEM approaches reveal the ultrastructural presentation and context of these contact sites in 3D, enabling full reconstruction of contacts and more accurate classification of contacts (point vs. tubular vs. cisternal-like) and quantification38,39. In addition to being the first cell type where ER-organelle contacts were observed25,26, hepatocytes have an extensive system of other interorganelle contacts that serve vital roles in their architecture and physiology28,40. However, thorough morphological characterization of ER-organelle and other interorganelle contacts in hepatocytes is still lacking. Accordingly, how interorganelle contacts form and remodel during regeneration and repair is of particular relevance to hepatocyte biology and liver function.

<table><tbody><tr><td>0.22 &amp;micro;m syringe filter</td><td>Sarstedt</td><td>83.1826.001</td><td></td></tr><tr><td>Aluminum trays</td><td>Agar Scientific</td><td>AGG3912</td><td></td></tr><tr><td>Amira v6</td><td>ThermoFisher</td><td></td><td>https://www.thermofisher.com</td></tr><tr><td>Chloroform</td><td>Fisher</td><td>C/4960/PB08</td><td></td></tr><tr><td>DDSA/Dodecenyl Succinic Anhydride</td><td>TAAB</td><td>T027</td><td>Epon ingredient</td></tr><tr><td>Diamond knife</td><td>DiaTOME</td><td>ultra 45&amp;deg;</td><td></td></tr><tr><td>DMP-30/2,4,6-tri (Dimethylaminomethyl) phenol</td><td>TAAB</td><td>D032</td><td>Epon ingredient</td></tr><tr><td>Dumont Tweezers N5</td><td>Agar Scientific</td><td>AGT5293</td><td></td></tr><tr><td>Fiji</td><td></td><td></td><td>https://imagej.net/</td></tr><tr><td>Fiji TrakEM2 plugin</td><td></td><td></td><td>https://imagej.net/</td></tr><tr><td>Formaldehyde 36% solution</td><td>TAAB</td><td>F003</td><td></td></tr><tr><td>Formvar coated slot grid</td><td>Homemade</td><td></td><td>Alternative: EMS diasum (FF2010-Cu)</td></tr><tr><td>Glass bottle with applicator rod</td><td>Medisca</td><td>6258</td><td></td></tr><tr><td>Glass vials</td><td>Fisher Scientific</td><td>15364769</td><td></td></tr><tr><td>Gluteraldehyde 25% solution</td><td>TAAB</td><td>G011</td><td></td></tr><tr><td>MNA/Methyl Nadic Anhydride</td><td>TAAB</td><td>M011</td><td>Epon ingredient</td></tr><tr><td>Osmium Tetroxide 2% solution</td><td>TAAB</td><td>O005</td><td></td></tr><tr><td>Potassium Ferricyanide</td><td>Sigma-Aldrich</td><td>P-8131</td><td></td></tr><tr><td>Propylene oxide</td><td>Fisher Scientific</td><td>E/0050/PB08</td><td></td></tr><tr><td>Reuseable adhesive</td><td>Blue Tack</td><td></td><td></td></tr><tr><td>Reynolds Lead Citrate</td><td>TAAB</td><td>L037</td><td>Section stain</td></tr><tr><td>Sodium Cacodylate</td><td>Sigma-Aldrich</td><td>C-0250</td><td>to make 0.1 M Caco buffer</td></tr><tr><td>Super Glue</td><td>RS Components</td><td>918-6872</td><td>Cyanoacrylate glue, Step 1.3</td></tr><tr><td>TAAB 812 Resin</td><td>TAAB</td><td>T023</td><td>Epon ingredient</td></tr><tr><td>Tannic acid</td><td>TAAB</td><td>T046</td><td></td></tr><tr><td>Triton X-100</td><td>Sigma-Aldrich</td><td>T9284</td><td></td></tr><tr><td>Two part Epoxy Resin</td><td>RS Components</td><td>132-605</td><td>Alternative: Step 2.13</td></tr><tr><td>Ultramicrotome</td><td>Leica</td><td>UC7</td><td></td></tr><tr><td>Vibrating microtome</td><td>Leica</td><td></td><td>100 &amp;micro;m thick slices, 0.16 mm/s cutting at 1 mm amplitude .</td></tr><tr><td>Weldwood Original Contact cement</td><td>DAP</td><td>107</td><td>Contact adhesive: Step 3.1.4</td></tr></tbody></table>

three-dimensional characterization of interorganelle contact sites in hepatocytes using serial section electron microscopy

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy

Transmission electron microscopy has been long considered to be the gold standard for the visualization of cellular ultrastructure. However, analysis is often limited to two dimensions, hampering the ability to fully describe the three-dimensional (3D) ultrastructure and functional relationship between organelles. Volume electron microscopy (vEM) describes a collection of techniques that enable the interrogation of cellular ultrastructure in 3D at mesoscale, microscale, and nanoscale resolutions. 
This protocol provides an accessible and robust method to acquire vEM data using serial section transmission EM (TEM) and covers the technical aspects of sample processing through to digital 3D reconstruction in a single, straightforward workflow. To demonstrate the usefulness of this technique, the 3D ultrastructural relationship between the endoplasmic reticulum and mitochondria and their contact sites in liver hepatocytes is presented. Interorganelle contacts serve vital roles in the transfer of ions, lipids, nutrients, and other small molecules between organelles. However, despite their initial discovery in hepatocytes, there is still much to learn about their physical features, dynamics, and functions. 
Interorganelle contacts can display a range of morphologies, varying in the proximity of the two organelles to one another (typically ~10-30 nm) and the extent of the contact site (from punctate contacts to larger 3D cisternal-like contacts). The examination of close contacts requires high-resolution imaging, and serial section TEM is well suited to visualize the 3D ultrastructural of interorganelle contacts during hepatocyte differentiation, as well as alterations in hepatocyte architecture associated with metabolic diseases.

For this technique, regions of interest are selected based on the biological research aim and identified prior to the trimming and sectioning of embedded tissue. Similarly, the size of the block face may be dictated by the research question; in this case, the sample was trimmed to leave a block face of approximately 0.3 mm x 0.15 mm (Figure 4A). This allowed for two grids of 9 serial sections per grid, providing 18 serial sections and incorporating a volume of liver tissue of a volume of app...

A simple and comprehensive protocol to acquire three-dimensional details of membrane contact sites between organelles in hepatocytes from the liver or cells in other tissues.

Transmission electron microscopy has been long considered to be the gold standard for the visualization of cellular ultrastructure. However, analysis is ...

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Learn 3D reconstruction of interorganelle contact sites in hepatocytes using serial section electron microscopy. This robust protocol enables visualization of membrane interactions without requiring specialized volume electron microscopes.

Three-dimensional Characterization of Interorganelle Contact Sites in Hepatocytes using Serial Section Electron Microscopy

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