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Studying Glomerular Diseases with Key Insights from Amira Software

By 05.01.2023

Glomerular diseases: understanding function and impact

Glomerular diseases affect the filtering units of the kidneys, the glomeruli. These diseases may lead to pathogenic processes such as inflammation, tumor growth, atrophy, or worse. The most widespread glomerular disease, according to the National Institute of Health (NIH), is diabetic nephropathy or diabetic kidney disease. It is the most common cause of needing dialysis or kidney transplantation and over time may lead to kidney failure. An accurate understanding of the three-dimensional architecture of the glomerular endothelial cell structures could provide insights or possibly even indicate pathways to treatments.

A recent study at Juntendo University in Japan enabled the development of a visual model of the 3D architecture of glomerular endothelial cells (GEnCs) from adult rats using a combination of FIB-SEM (focused ion beam – scanning electron microscopy) images and Thermo Scientific Amira Software, thus advancing scientists’ understanding of the morphology of the GEnCs and improving potential pathologic analyses of glomerular diseases.

FIB-SEM tomography combined with Amira Software

In the study, to clarify the 3D architecture of GEnCs in adult rats, researchers at Juntendo University manually extracted information about GEnCs from serial FIB-SEM images. They then used Amira Software to reconstruct the data as coherent 3D images of complete GEnCs’ structures.

Juxtamesangial region and cell bodies of glomerular endothelial cells (GEnCs)

Juxtamesangial region and cell bodies of glomerular endothelial cells (GEnCs). Source: https://doi.org/10.3389/fcell.2021.653472

The researchers used FIB-SEM tomography to cut the relevant section of the adult rat’s kidney into 250-µm-thick slices. The thin slices were chemically treated, stained, and then dehydrated. The dehydrated samples were embedded in a resin and allowed to harden over several days. The resin-embedded tissue was mounted on a block and imaged with a Thermo Scientific Helios Nanolab 660 FIB-SEM. After aligning serial FIB-SEM images, the target GEnCs were manually segmented on individual FIB-SEM images using Amira Software and then reconstructed using the same software.

This resulted in a single composite 3D image of the entire structure of the glomerular endothelial cells. This image could be rotated and manipulated in ways that gave the researchers the ability to view aspects of the GEnCs not previously seen.

The powerful combination of the Helios Nanolab 660 FIB-SEM images and the 3D reconstruction techniques in Amira Software allowed researchers to reveal not only the luminal surface structures of GEnCs, but also the basal surface structures. Additionally, it revealed characteristics of cellular junctions in GEnCs. And beyond that, the 3D reconstruction of GEnCs showed the structural hierarchy of their subcellular compartments.

Amira Software provides accurate 3D reconstruction

The luminal surface visualized via Amira Software’s reconstructed GEnCs was quite similar to that observed through conventional scanning electron microscopy (SEM), indicating that 3D reconstruction could be performed with high accuracy.

Strong agreement between the results from the two different methods provides assurance that Amira Software’s reconstructed images possess high accuracy. Thus, the 3D architecture of normal GEnCs in adult rats has now been described more clearly and precisely than ever before.

3D reconstruction software enables views of basal cell surfaces and glomerular mesangial cells

This highly accurate visibility of 3D ultrastructures is one of the most important benefits of this FIB-SEM / 3D reconstruction software approach. Conventional SEM is useful for revealing the luminal surface structures of GEnCs; however, it is almost impossible to observe their basal surface structures because the basal cell surface is attached to the glomerular basement membrane (GBM) or supporting framework of the mesangium. These structures obstruct direct views and make the basal cell surface difficult to expose. Amira 3D reconstruction software ultimately resolved this problem by enabling the observation of surface structures from any direction and without interference by the neighboring GBM, mesangium, or podocytes.

Furthermore, color-coded reconstructed images are also helpful in determining the spatial relationship between GEnCs and glomerular mesangial cells. For example, the arrangement of GEnC intercellular and autocellular junctions, or the penetration of mesangial non-adhesive processes into the glomerular capillary lumen, can be assigned contrasting color schemes within Amira Software. Such colorful visualization can bring the spatial relationships into sharp relief.

With these color-coded 3D reconstructions, the GEnCs were found to consist of three major subcellular compartments: the cell body, cytoplasmic ridges, and sieve plates. Two associated subcellular compartments, namely, the globular protrusions and reticular porous structures, were also identified. Further insights into the shape and form of the cells showed that most individual GEnCs made up a “seamless” tubular shape, while some of them formed an autocellular junction to make up a tubular shape.

Read the full research paper from Juntendo University >>

The upshot of this study is that FIB-SEM tomography combined with Amira Software’s 3D reconstruction capabilities provides a powerful approach to better understand the 3D architecture of GEnCs. Moreover, the morphological information revealed in this study will be valuable for the structural analysis of developmental processes in the glomerular capillary system and for advancing the 3D pathologic evaluation of GEnCs in animal and human glomerular diseases.

Learn more about Amira Software >>

 

Citation:

AUTHOR=Kawasaki Yuto, Hosoyamada Yasue, Miyaki Takayuki, Yamaguchi Junji, Kakuta Soichiro, Sakai Tatsuo, Ichimura Koichiro
TITLE=Three-Dimensional Architecture of Glomerular Endothelial Cells Revealed by FIB-SEM Tomography
JOURNAL=Frontiers in Cell and Developmental Biology
VOLUME=9
YEAR=2021
URL=https://www.frontiersin.org/articles/10.3389/fcell.2021.653472
DOI=10.3389/fcell.2021.653472
ISSN=2296-634X

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