Advancements in high-resolution 3D microscopy analysis of endosomal morphology in postmortem Alzheimer's disease brains

Abnormal endo-lysosomal morphology is an early cytopathological feature of Alzheimer's disease (AD) and genome-wide association studies (GWAS) have implicated genes involved in the endo-lysosomal network (ELN) as conferring increased risk for developing sporadic, late-onset AD (LOAD). Characterization of ELN pathology and the underlying pathophysiology is a promising area of translational AD research and drug development. However, rigorous study of ELN vesicles in AD and aged control brains poses a unique constellation of methodological challenges due in part to the small size of these structures and subsequent requirements for high-resolution imaging. Here we provide a detailed protocol for high-resolution 3D morphological quantification of neuronal endosomes in postmortem AD brain tissue, using immunofluorescent staining, confocal imaging with image deconvolution, and Imaris software analysis pipelines. To demonstrate these methods, we present neuronal endosome morphology data from 23 sporadic LOAD donors and one aged non-AD control donor. The techniques described here were developed across a range of AD neuropathology to best optimize these methods for future studies with large cohorts. Application of these methods in research cohorts will help advance understanding of ELN dysfunction and cytopathology in sporadic AD.

Combining RNAscope and immunohistochemistry to visualize inflammatory gene products in neurons and microglia

A challenge for central nervous system (CNS) tissue analysis in neuroscience research has been the difficulty to codetect and colocalize gene and protein expression in the same tissue. Given the importance of identifying gene expression relative to proteins of interest, for example, cell-type specific markers, we aimed to develop a protocol to optimize their codetection. RNAscope fluorescent in situ hybridization (FISH) combined with immunohistochemistry (IHC) in fixed (CNS) tissue sections allows for reliable quantification of gene transcripts of interest within IHC-labeled cells. This paper describes a new method for simultaneous visualization of FISH and IHC in thicker (14-μm), fixed tissue samples, using spinal cord sections. This method's effectiveness is shown by the cell-type-specific quantification of two genes, namely the proinflammatory cytokine interleukin-1beta (IL-1b) and the inflammasome NLR family pyrin domain containing 3 (NLRP3). These genes are challenging to measure accurately using immunohistochemistry (IHC) due to the nonspecificity of available antibodies and the hard-to-distinguish, dot-like visualizations of the labeled proteins within the tissue. These measurements were carried out in spinal cord sections after unilateral chronic constriction injury of the sciatic nerve to induce neuroinflammation in the spinal cord. RNAscope is used to label transcripts of genes of interest and IHC is used to label cell-type specific antigens (IBA1 for microglia, NeuN for neurons). This combination allowed for labeled RNA transcripts to be quantified within cell-type specific boundaries using confocal microscopy and standard image analysis methods. This method makes it easy to answer empirical questions that are intractable with standard IHC or in situ hybridization alone. The method, which has been optimized for spinal cord tissue and to minimize tissue preparation time and costs, is described in detail from tissue collection to image analysis. Further, the relative expression changes in inflammatory genes NLRP3 and IL-1b in spinal cord microglia vs. neurons of somatotopically relevant laminae are described for the first time.

Visualizing Chromosome Territories and Nuclear Architecture of Large Plant Genomes Using Alien Introgressions

Visualization of chromosome territories is a challenging task in plant genomes due to the lack of chromosome-specific probes, especially in species with large genomes. On the other hand, combination of flow sorting, genomic in situ hybridization (GISH), confocal microscopy, and employment of software for 3D modeling enables to visualize and characterize chromosome territories (CT) in interspecific hybrids. Here, we describe the protocol for the analysis of CTs in wheat-rye and wheat-barley hybrids, including amphiploids and introgression forms, where a pair of chromosomes or chromosome arms from one species is introgressed into the genome of another species. In this way, the architecture and dynamics of CTs in various tissues and different stages of cell cycle can be analyzed.

Three-Dimensional Simultaneous Imaging of Nucleic Acids and Proteins During Influenza Virus Infection in Single Cells Using Confocal Microscopy

Three-dimensional imaging is a powerful tool for examining the spatial distribution of intracellular molecules like nucleic acids, proteins, and organelles in cells and tissues. Multicolor fluorescence imaging coupled with three-dimensional spatial information provide a platform to explore the relationship between different cellular features and molecules. We have previously developed a pipeline to study the intracellular localization of influenza virus genomic segments within an infected cell. Here, we describe the staining of multiple viral RNA segments in cells infected with influenza virus by combined fluorescence in situ hybridization (FISH) and immunofluorescence and quantification of colocalization between viral segments. This chapter will cover the acquisition and analysis of 3D images by the widely used laser scanning confocal microscope. These strategies can be applied to a wide range of biological processes and modified to examine colocalization of other cellular features.

Analysis of Intracellular Vesicles in B Lymphocytes: Antigen Traffic in the Spotlight

All eukaryotic cells are delimited by the plasma membrane, separating the cell from its environment. Two critical cellular pathways, the endocytic and the exocytic vesicle networks, shuttle material in and out the cell, respectively. The substantial development of cell biological imaging techniques, along with improved fluorescent probes and image analysis tools, has been instrumental in increasing our understanding of various functions and regulatory mechanisms of various intracellular vesicle subpopulations and their dynamics. Here, using B lymphocytes (B cells) as a model system, we provide a protocol for 3D analysis of the intracellular vesicle traffic in either fixed or living cells using spinning disk confocal microscopy. We also describe the usage of image deconvolution to improve the resolution, particularly important for vesicular networks in lymphocytes due to the small size of these cells. Lastly, we describe two types of quantitative analysis: vesicle distribution/clustering toward the microtubule organizing center (MTOC), and colocalization analysis with endolysosomal markers.

A method for quantification of vesicular compartments within cells using 3D reconstructed confocal z-stacks: Comparison of ImageJ and Imaris to count early endosomes within basal forebrain cholinergic neurons

BACKGROUND

Phenotypic changes in vesicular compartments are an early pathological hallmark of many peripheral and central diseases. For example, accurate assessment of early endosome pathology is crucial to the study of Down syndrome (DS) and Alzheimer's disease (AD), as well as other neurological disorders with endosomal-lysosomal pathology.

NEW METHOD

We describe a method for quantification of immunolabeled early endosomes within transmitter-identified basal forebrain cholinergic neurons (BFCNs) using 3-dimensional (3D) reconstructed confocal z-stacks employing Imaris software.

RESULTS

Quantification of 3D reconstructed z-stacks was performed using two different image analysis programs: ImageJ and Imaris. We found ImageJ consistently overcounted the number of early endosomes present within individual BFCNs. Difficulty separating densely packed early endosomes within defined BFCNs was observed in ImageJ compared to Imaris.

COMPARISON WITH EXISTING METHODS

Previous methods quantifying endosomal-lysosomal pathology relied on confocal microscopy images taken in a single plane of focus. Since early endosomes are distributed throughout the soma and neuronal processes of BFCNs, critical insight into the abnormal early endosome phenotype may be lost as a result of analyzing only a single image of the perikaryon. Rather than relying on a representative sampling, this protocol enables precise, direct quantification of all immunolabeled vesicles within a defined cell of interest.

CONCLUSIONS

Imaris is an ideal program for accurately counting punctate vesicles in the context of dual label confocal microscopy. Superior image resolution and detailed algorithms offered by Imaris make precise and rigorous quantification of individual early endosomes dispersed throughout a BFCN in 3D space readily achievable.

Cell Tracking Profiler - a user-driven analysis framework for evaluating 4D live-cell imaging data

Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a 'ground truth' for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.

Exocytosis of Progeny Infectious Varicella-Zoster Virus Particles via a Mannose-6-Phosphate Receptor Pathway without Xenophagy following Secondary Envelopment

The literature on the egress of different herpesviruses after secondary envelopment is contradictory. In this report, we investigated varicella-zoster virus (VZV) egress in a cell line from a child with Pompe disease, a glycogen storage disease caused by a defect in the enzyme required for glycogen digestion. In Pompe cells, both the late autophagy pathway and the mannose-6-phosphate receptor (M6PR) pathway are interrupted. We have postulated that intact autophagic flux is required for higher recoveries of VZV infectivity. To test that hypothesis, we infected Pompe cells and then assessed the VZV infectious cycle. We discovered that the infectious cycle in Pompe cells was remarkably different from that of either fibroblasts or melanoma cells. No large late endosomes filled with VZV particles were observed in Pompe cells; only individual viral particles in small vacuoles were seen. The distribution of the M6PR pathway (trans-Golgi network to late endosomes) was constrained in infected Pompe cells. When cells were analyzed with two different anti-M6PR antibodies, extensive colocalization of the major VZV glycoprotein gE (known to contain M6P residues) and the M6P receptor (M6PR) was documented in the viral highways at the surfaces of non-Pompe cells after maximum-intensity projection of confocal z-stacks, but neither gE nor the M6PR was seen in abundance at the surfaces of infected Pompe cells. Taken together, our results suggested that (i) Pompe cells lack a VZV trafficking pathway within M6PR-positive large endosomes and (ii) most infectious VZV particles in conventional cell substrates are transported via large M6PR-positive vacuoles without degradative xenophagy to the plasma membrane.IMPORTANCE The long-term goal of this research has been to determine why VZV, when grown in cultured cells, invariably is more cell associated and has a lower titer than other alphaherpesviruses, such as herpes simplex virus 1 (HSV1) or pseudorabies virus (PRV). Data from both HSV1 and PRV laboratories have identified a Rab6 secretory pathway for the transport of single enveloped viral particles from the trans-Golgi network within small vacuoles to the plasma membrane. In contrast, after secondary envelopment in fibroblasts or melanoma cells, multiple infectious VZV particles accumulated within large M6PR-positive late endosomes that were not degraded en route to the plasma membrane. We propose that this M6PR pathway is most utilized in VZV infection and least utilized in HSV1 infection, with PRV's usage being closer to HSV1's usage. Supportive data from other VZV, PRV, and HSV1 laboratories about evidence for two egress pathways are included.

Three-dimensional Reconstruction and Quantification of Proteins and mRNAs at the Single-cell Level in Cultured Cells

Gene expression is often regulated by the abundance, localization, and translation of mRNAs in both space and time. Being able to visualize mRNAs and protein products in single cells is critical to understand this regulatory process. The development of single-molecule RNA fluorescence in situ hybridization (smFISH) allows the detection of individual RNA molecules at the single-molecule and single-cell levels. When combined with immunofluorescence (IF), both mRNAs and proteins in individual cells can be analyzed simultaneously. However, a precise and streamlined quantification method for the smFISH and IF combined dataset is scarce, as existing workflows mostly focus on quantifying the smFISH data alone. Here we detail a method for performing sequential IF and smFISH in cultured cells (as described in Sepulveda et al., 2018 ) and the subsequent statistical analysis of the smFISH and IF data via three-dimensional (3D) reconstruction in a semi-automatic image processing workflow. Although our method is based on analyzing centrosomally enriched mRNAs and proteins, the workflow can be readily adapted for performing and analyzing smFISH and IF data in other biological contexts.

Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus

Fluorescence in situ hybridization (FISH) is commonly used to visualize chromosomal regions or genomic loci within the nucleus, and can largely contribute to unraveling the link between structure and function in the nucleus. Three-dimensional (3D) analyses are required to best capture the nucleus' organizing principles, but the experimental setup and computational analyses are far from trivial. Here, we present a robust workflow for 3D FISH against repeats and single copy loci in embedded intact nuclei from Arabidopsis leaves. We then describe in detail the image acquisition, subsequent image deconvolution before 3D image processing, and the image reconstruction. We developed an automated batch image processing pipeline using a customized, open source plugin implemented in the Imaris environment.

Imaging the Effector CD8 Synapse

Here, we describe 4D imaging of effector CD8+ T cells as they conjugate and kill live targets in vitro and analyze the polarization dynamics of intracellular compartments to this cell-cell interface.

Quantifying Autophagic Structures in Mammalian Cells Using Confocal Microscopy

Autophagy relies on the sequential, hierarchical association of proteins with phagophores, and forming autophagosomes to allow completion of the process. Additionally, the trafficking of the unique transmembrane autophagy-related protein ATG9 is vital for autophagy progression. In this chapter, we discuss methods to monitor autophagosome number using confocal microscopy, by following the association of different autophagosomal markers with the phagophore and completed autophagosome. We also discuss methods to monitor the trafficking of ATG9 in mammalian cells under starvation conditions.

Assessing Mitochondrial Movement Within Neurons: Manual Versus Automated Tracking Methods

Owing to the small size of mitochondria and the complexity of their motility patterns, mitochondrial tracking is technically challenging. Mitochondria are often tracked manually; however, this is time-consuming and prone to measurement error. Here, we examined the suitability of four commercial and open-source software alternatives for automated mitochondrial tracking in neurons compared with manual measurements. We show that all the automated tracking tools dramatically underestimated track length, mitochondrial displacement and movement duration, with reductions ranging from 45 to 77% of the values obtained manually. In contrast, mitochondrial velocity was generally overestimated. Only the number of motile mitochondria and their directionality were similar between strategies. Despite these discrepancies, we show that automated tools successfully detected transport alterations after applying an oxidant agent. Thus, automated methods appear to be suitable for assessing relative transport differences between experimental groups, but not for absolute quantification of mitochondrial dynamics. Although useful for objective and time-efficient measurements of mitochondrial movements, results provided by automated methods should be interpreted with caution.

Visualization and quantification of Plasmodium falciparum intraerythrocytic merozoites

Malaria, a leading parasitic killer, is caused by Plasmodium spp. The pathology of the disease starts when Plasmodium merozoites infect erythrocytes to form rings, that matures through a large trophozoite form and develop into schizonts containing multiple merozoites. The number of intra-erythrocytic merozoites is a key-determining factor for multiplication rate of the parasite. Counting of intraerythrocytic merozoites by classical 2-D microscopy method is error prone due to insufficient representation of merozoite in one optical plane of a schizont. Here, we report an alternative 3-D microscopy based automated method for counting of intraerythrocytic merozoites in entire volume of schizont. This method offers a considerable amount of advantages in terms of both, ease and accuracy.

A novel way to statistically analyze morphologic changes in Dmp1-null osteocytes

Recent studies have revealed multiple roles of osteocytes in bone metabolism. However, detailed analyses of the embedded osteocytes in bone structure are still limited because of the high mineral content around these cells. In this study, we developed an innovative technique, the "FITC-Imaris technique", which combines FITC ([2, 5]-Fluorescein isothiocyanate), confocal microscopy and Imaris software. With this method, we could not only visualize the 3-D morphology of embedded osteocytes, but more importantly, we were able to statistically quantitate the osteocyte structure in the cell surface area, total cell volume, and dendrite numbers. Furthermore, we made a side-by-side comparison of the new method with the acid-etched SEM imaging technique, a common imaging method for studies of osteocyte morphology with a much smaller cell depth (< 3 μm). Finally, we used the FITC-Imaris technique to show both the morphological and statistical differences in the osteocyte structure between the Dmp1-null mice (the osteomalacia model) and their age-matched control littermates. We expect that this newly developed technique will become a powerful tool to disclose more roles that osteocytes play in bone health and diseases.

Acid sensitive background potassium channels K2P3.1 and K2P9.1 undergo rapid dynamin-dependent endocytosis

Acid-sensitive, two-pore domain potassium channels, K(2P)3.1 and K(2P)9.1, are implicated in cardiac and nervous tissue responses to hormones, neurotransmitters and drugs. K(2P)3.1 and K(2P)9.1 leak potassium from the cell at rest and directly impact membrane potential. Hence altering channel number on the cell surface drives changes in cellular electrical properties. The rate of K(2P)3.1 and K(2P)9.1 delivery to and recovery from the plasma membrane determines both channel number at the cell surface and potassium leak from cells. This study examines the endocytosis of K(2P)3.1 and K(2P)9.1. Plasma membrane biotinylation was used to follow the fate of internalized GFP-tagged rat K(2P)3.1 and K(2P)9.1 transiently expressed in HeLa cells. Confocal fluorescence images were analyzed using Imaris software, which revealed that both channels are endocytosed by a dynamin-dependent mechanism and over the course of 60 min, move progressively toward the nucleus. Endogenous endocytosis of human K(2P)3.1 and K(2P)9.1 was examined in the lung carcinoma cell line, A549. Endogenous channels are endocytosed over a similar time-scale to the channels expressed transiently in HeLa cells. These findings both validate the use of recombinant systems and identify an endogenous model system in which K(2P)3.1 and K(2P)9.1 trafficking can be further studied.