Visualizing insulin vesicle neighborhoods in β cells by cryo-electron tomography

Dysregulated inter-mitochondrial crosstalk in glioblastoma cells revealed by in situ cryo-electron tomography

Glioblastomas (GBMs) are the most lethal primary brain tumors with limited survival, even under aggressive treatments. The current therapeutics for GBMs are flawed due to the failure to accurately discriminate between normal proliferating cells and distinctive tumor cells. Mitochondria are essential to GBMs and serve as potential therapeutical targets. Here, we utilize cryo-electron tomography to quantitatively investigate nanoscale details of randomly sampled mitochondria in their native cellular context of GBM cells. Our results show that compared with cancer-free brain cells, GBM cells own more inter-mitochondrial junctions of several types for communications. Furthermore, our tomograms unveil microtubule-dependent mitochondrial nanotunnel-like bridges in the GBM cells as another inter-mitochondrial structure. These quantified inter-mitochondrial features, together with other mitochondria-organelle and intra-mitochondrial ones, are sufficient to distinguish GBM cells from cancer-free brain cells under scrutiny with predictive modeling. Our findings decipher high-resolution inter-mitochondrial structural signatures and provide clues for diagnosis and therapeutic interventions for GBM and other mitochondria-related diseases.

In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography

Actin mediates insulin secretion in pancreatic β-cells through remodeling. Hampered by limited resolution, previous studies have offered an ambiguous depiction as depolymerization and repolymerization. We report the in situ structure of actin remodeling in INS-1E β-cells during glucose-stimulated insulin secretion at nanoscale resolution. After remodeling, the actin filament network at the cell periphery exhibits three marked differences: 12% of actin filaments reorient quasi-orthogonally to the ventral membrane; the filament network mainly remains as cell-stabilizing bundles but partially reconfigures into a less compact arrangement; actin filaments anchored to the ventral membrane reorganize from a "netlike" to a "blooming" architecture. Furthermore, the density of actin filaments and microtubules around insulin secretory granules decreases, while actin filaments and microtubules become more densely packed. The actin filament network after remodeling potentially precedes the transport and release of insulin secretory granules. These findings advance our understanding of actin remodeling and its role in glucose-stimulated insulin secretion.

Advanced Imaging Techniques for the Characterization of Subcellular Organelle Structure in Pancreatic Islet β Cells

Type 2 diabetes (T2D) affects more than 32.3 million individuals in the United States, creating an economic burden of nearly $966 billion in 2021. T2D results from a combination of insulin resistance and inadequate insulin secretion from the pancreatic β cell. However, genetic and physiologic data indicate that defects in β cell function are the chief determinant of whether an individual with insulin resistance will progress to a diagnosis of T2D. The subcellular organelles of the insulin secretory pathway, including the endoplasmic reticulum, Golgi apparatus, and secretory granules, play a critical role in maintaining the heavy biosynthetic burden of insulin production, processing, and secretion. In addition, the mitochondria enable the process of insulin release by integrating the metabolism of nutrients into energy output. Advanced imaging techniques are needed to determine how changes in the structure and composition of these organelles contribute to the loss of insulin secretory capacity in the β cell during T2D. Several microscopy techniques, including electron microscopy, fluorescence microscopy, and soft X-ray tomography, have been utilized to investigate the structure-function relationship within the β cell. In this overview article, we will detail the methodology, strengths, and weaknesses of each approach. © 2024 American Physiological Society. Compr Physiol 14:5243-5267, 2024.

The D2D3 form of uPAR acts as an immunotoxin and may cause diabetes and kidney disease

Soluble urokinase plasminogen activator receptor (suPAR) is a risk factor for kidney diseases. In addition to suPAR, proteolysis of membrane-bound uPAR results in circulating D1 and D2D3 proteins. We showed that when exposed to a high-fat diet, transgenic mice expressing D2D3 protein developed progressive kidney disease marked by microalbuminuria, elevated serum creatinine, and glomerular hypertrophy. D2D3 transgenic mice also exhibited insulin-dependent diabetes mellitus evidenced by decreased levels of insulin and C-peptide, impaired glucose-stimulated insulin secretion, decreased pancreatic β cell mass, and high fasting blood glucose. Injection of anti-uPAR antibody restored β cell mass and function in D2D3 transgenic mice. At the cellular level, the D2D3 protein impaired β cell proliferation and inhibited the bioenergetics of β cells, leading to dysregulated cytoskeletal dynamics and subsequent impairment in the maturation and trafficking of insulin granules. D2D3 protein was predominantly detected in the sera of patients with nephropathy and insulin-dependent diabetes mellitus. These sera inhibited glucose-stimulated insulin release from human islets in a D2D3-dependent manner. Our study showed that D2D3 injures the kidney and pancreas and suggests that targeting this protein could provide a therapy for kidney diseases and insulin-dependent diabetes mellitus.

A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography

The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline for preparing multicellular samples for cryo-electron tomography. The pipeline comprises sample isolation, vitrification, and lift-out-based lamella preparation using commercially available instruments. We demonstrate the efficacy of our pipeline by visualizing pancreatic β cells from mouse islets at the molecular level. This pipeline enables the determination of the properties of insulin crystals in situ for the first time, using unperturbed samples.

Direct Visualization and Restoration of Metallic Ion-Induced Subcellular Ultrastructural Remodeling

Analysis of cellular ultrastructure dynamics and metal ions' fate can provide insights into the interaction between living organisms and metal ions. Here, we directly visualize the distribution of biogenic metallic aggregates, ion-induced subcellular reorganization, and the corresponding regulation effect in yeast by the near-native 3D imaging approach, cryo-soft X-ray tomography (cryo-SXT). By comparative 3D morphometric assessment, we observe the gold ions disrupting cellular organelle homeostasis, resulting in noticeable distortion and folding of vacuoles, apparent fragmentation of mitochondria, extreme swelling of lipid droplets, and formation of vesicles. The reconstructed 3D architecture of treated yeast demonstrates ∼65% of Au-rich sites in the periplasm, a comprehensive quantitative assessment unobtained by TEM. We also observe some AuNPs in rarely identified subcellular sites, namely, mitochondria and vesicles. Interestingly, the amount of gold deposition is positively correlated with the volume of lipid droplets. Shifting the external starting pH to near-neutral results in the reversion of changes in organelle architectures, boosting the amount of biogenic Au nanoparticles, and increasing cell viability. This study provides a strategy to analyze the metal ions-living organism interaction from subcellular architecture and spatial localization perspectives.

Multifunctional Nanoprobe for 3D Nanoresolution Imaging of Intact Cell HER2 Protein with Hard X-ray Tomography

Three-dimensional nondestructive, nanoresolution, and in situ visualization of protein spatial localization in a large, thick single cell remains challenging. In this study, we designed a multifunctional iron oxide (Fe@BFK) nanoprobe that possesses fluorescence and hard X-ray imaging signals. This probe can specifically target the human epidermal growth factor receptor 2 (HER2) protein and help optimize the label condition and selection of suitable samples for X-ray imaging. Combining 30 nm resolution synchrotron radiation hard X-ray nanocomputed tomography and the X-ray-sensitive Fe@BFK nanoprobe, a 3D localization of HER2 on SK-BR-3 cells was obtained for the first time. HER2 was mainly localized and cluster-distributed on the cell membrane with a heterogeneous pattern. This study provides a novel method for the in situ and nondestructive synchrotron radiation imaging of the desired protein localization in large, thick cells and evaluation of the true cellular distribution of a nanoprobe with high resolution.

Soft X-ray tomograms provide a structural basis for whole-cell modeling

Developing in silico models that accurately reflect a whole, functional cell is an ongoing challenge in biology. Current efforts bring together mathematical models, probabilistic models, visual representations, and data to create a multi-scale description of cellular processes. A realistic whole-cell model requires imaging data since it provides spatial constraints and other critical cellular characteristics that are still impossible to obtain by calculation alone. This review introduces Soft X-ray Tomography (SXT) as a powerful imaging technique to visualize and quantify the mesoscopic (~25 nm spatial scale) organelle landscape in whole cells. SXT generates three-dimensional reconstructions of cellular ultrastructure and provides a measured structural framework for whole-cell modeling. Combining SXT with data from disparate technologies at varying spatial resolutions provides further biochemical details and constraints for modeling cellular mechanisms. We conclude, based on the results discussed here, that SXT provides a foundational dataset for a broad spectrum of whole-cell modeling experiments.

Mechanisms of gut microbiota-immune-host interaction on glucose regulation in type 2 diabetes

Intestinal absorption of food is one of the sources of glucose. Insulin resistance and impaired glucose tolerance caused by lifestyle and diet are the precursors of type 2 diabetes. Patients with type 2 diabetes have trouble controlling their blood sugar levels. For long-term health, strict glycemic management is necessary. Although it is thought to be well correlated with metabolic diseases like obesity, insulin resistance, and diabetes, its molecular mechanism is still not completely understood. Disturbed microbiota triggers the gut immune response to reshape the gut homeostasis. This interaction not only maintains the dynamic changes of intestinal flora, but also preserves the integrity of the intestinal barrier. Meanwhile, the microbiota establishes a systemic multiorgan dialog on the gut-brain and gut-liver axes, intestinal absorption of a high-fat diet affects the host's feeding preference and systemic metabolism. Intervention in the gut microbiota can combat the decreased glucose tolerance and insulin sensitivity linked to metabolic diseases both centrally and peripherally. Moreover, the pharmacokinetics of oral hypoglycemic medications are also influenced by gut microbiota. The accumulation of drugs in the gut microbiota not only affects the drug efficacy, but also changes the composition and function of them, thus may help to explain individual therapeutic variances in pharmacological efficacy. Regulating gut microbiota through healthy dietary patterns or supplementing pro/prebiotics can provide guidance for lifestyle interventions in people with poor glycemic control. Traditional Chinese medicine can also be used as complementary medicine to effectively regulate intestinal homeostasis. Intestinal microbiota is becoming a new target against metabolic diseases, so more evidence is needed to elucidate the intricate microbiota-immune-host relationship, and explore the therapeutic potential of targeting intestinal microbiota.

An intensity-based post-processing tool for 3D instance segmentation of organelles in soft X-ray tomograms

Investigating the 3D structures and rearrangements of organelles within a single cell is critical for better characterizing cellular function. Imaging approaches such as soft X-ray tomography have been widely applied to reveal a complex subcellular organization involving multiple inter-organelle interactions. However, 3D segmentation of organelle instances has been challenging despite its importance in organelle characterization. Here we propose an intensity-based post-processing tool to identify and separate organelle instances. Our tool separates sphere-like (insulin vesicle) and columnar-shaped organelle instances (mitochondrion) based on the intensity of raw tomograms, semantic segmentation masks, and organelle morphology. We validate our tool using synthetic tomograms of organelles and experimental tomograms of pancreatic β-cells to separate insulin vesicle and mitochondria instances. As compared to the commonly used connected regions labeling, watershed, and watershed + Gaussian filter methods, our tool results in improved accuracy in identifying organelles in the synthetic tomograms and an improved description of organelle structures in β-cell tomograms. In addition, under different experimental treatment conditions, significant changes in volumes and intensities of both insulin vesicle and mitochondrion are observed in our instance results, revealing their potential roles in maintaining normal β-cell function. Our tool is expected to be applicable for improving the instance segmentation of other images obtained from different cell types using multiple imaging modalities.

Integrative modeling of the cell

A whole-cell model represents certain aspects of the cell structure and/or function. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.

Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic beta cells

Characterizing relationships between Zn²⁺, insulin, and insulin vesicles is of vital importance to the study of pancreatic beta cells. However, the precise content of Zn²⁺ and the specific location of insulin inside insulin vesicles are not clear, which hinders a thorough understanding of the insulin secretion process and diseases caused by blood sugar dysregulation. Here, we demonstrated the colocalization of Zn²⁺ and insulin in both single extracellular insulin vesicles and pancreatic beta cells by using an X-ray scanning coherent diffraction imaging (ptychography) technique. We also analyzed the elemental Zn²⁺ and Ca²⁺ contents of insulin vesicles using electron microscopy and energy dispersive spectroscopy (EDS) mapping. We found that the presence of Zn²⁺ is an important characteristic that can be used to distinguish insulin vesicles from other types of vesicles in pancreatic beta cells and that the content of Zn²⁺ is proportional to the size of insulin vesicles. By using dual-energy contrast X-ray microscopy and scanning transmission X-ray microscopy (STXM) image stacks, we observed that insulin accumulates in the off-center position of extracellular insulin vesicles. Furthermore, the spatial distribution of insulin vesicles and their colocalization with other organelles inside pancreatic beta cells were demonstrated using three-dimensional (3D) imaging by combining X-ray ptychography and an equally sloped tomography (EST) algorithm. This study describes a powerful method to univocally describe the location and quantitative analysis of intracellular insulin, which will be of great significance to the study of diabetes and other blood sugar diseases.

Automated vitrification of cryo-EM samples with controllable sample thickness using suction and real-time optical inspection

The speed and efficiency of data collection and image processing in cryo-electron microscopy have increased over the last decade. However, cryo specimen preparation techniques have lagged and faster, more reproducible specimen preparation devices are needed. Here, we present a vitrification device with highly automated sample handling, requiring only limited user interaction. Moreover, the device allows inspection of thin films using light microscopy, since the excess liquid is removed through suction by tubes, not blotting paper. In combination with dew-point control, this enables thin film preparation in a controlled and reproducible manner. The advantage is that the quality of the prepared cryo specimen is characterized before electron microscopy data acquisition. The practicality and performance of the device are illustrated with experimental results obtained by vitrification of protein suspensions, lipid vesicles, bacterial and human cells, followed by imaged using single particle analysis, cryo-electron tomography, and cryo correlated light and electron microscopy.

Faster cryo specimen preparation can advance cryo electron microscopy (cryoEM). Here, the authors present a vitrification device with automated sample handling for cryoEM of proteins, suspensions and cells, enabling blot-free sample thinning, dew-point control and characterization of cryo grids prior to data acquisition.

Soft X-ray tomography to map and quantify organelle interactions at the mesoscale

Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.

Integrative structural modelling and visualisation of a cellular organelle

Models of insulin secretory vesicles from pancreatic beta cells have been created using the cellPACK suite of tools to research, curate, construct and visualise the current state of knowledge. The model integrates experimental information from proteomics, structural biology, cryoelectron microscopy and X-ray tomography, and is used to generate models of mature and immature vesicles. A new method was developed to generate a confidence score that reconciles inconsistencies between three available proteomes using expert annotations of cellular localisation. The models are used to simulate soft X-ray tomograms, allowing quantification of features that are observed in experimental tomograms, and in turn, allowing interpretation of X-ray tomograms at the molecular level.

The use of soft X-ray tomography to explore mitochondrial structure and function

Background

Mitochondria are cellular organelles responsible for energy production, and dysregulation of the mitochondrial network is associated with many disease states. To fully characterize the mitochondrial network's structure and function, a three-dimensional whole cell mapping technique is required.

Scope of review

This review highlights the use of soft X-ray tomography (SXT) as a relatively high-throughput approach to quantify mitochondrial structure and function under multiple cellular conditions.

Major conclusions

The use of SXT opens the door for mapping cellular rearrangements during critical processes such as insulin secretion, stem cell differentiation, or disease progression. SXT provides unique information such as biochemical compositions or molecular densities of organelles and allows for unbiased, label-free imaging of intact whole cells. Mapping mitochondria in the context of the near-native cellular environment will reveal more information regarding mitochondrial network functions within the cell.

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Soft X-ray tomography (SXT) generates 3D organelle maps of intact cells.

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3D maps reveal the positions of mitochondria and their molecular densities.

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SXT can be used to quantify and compare organelle contacts between conditions.

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SXT is unbiased imaging that identifies the contents of subcellular neighborhoods.

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SXT provides an exciting path for exploring metabolic dysfunction.

Probing β-Cell Biology in Space and Time

β-Cells in the islet of Langerhans have a central role in maintaining energy homeostasis. Understanding the physiology of β-cells and other islet cells requires a deep understanding of their structural and functional organization, their interaction with vessels and nerves, the layout of paracrine interactions, and the relationship between subcellular compartments and protein complexes inside each cell. These elements are not static; they are dynamic and exert their biological actions at different scales of time. Therefore, scientists must be able to investigate (and visualize) short- and long-lived events within the pancreas and β-cells. Current technological advances in microscopy are able to bridge multiple spatiotemporal scales in biology to reveal the complexity and heterogeneity of β-cell biology. Here, I briefly discuss the historical discoveries that leveraged microscopes to establish the basis of β-cell anatomy and structure, the current imaging platforms that allow the study of islet and β-cell biology at multiple scales of resolution, and their challenges and implications. Lastly, I outline how the remarkable longevity of structural elements at different scales in biology, from molecules to cells to multicellular structures, could represent a previously unrecognized organizational pattern in developing and adult β-cells and pancreas biology.

Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography

Characterizing relationships between cell structures and functions requires mesoscale mapping of intact cells showing subcellular rearrangements following stimulation; however, current approaches are limited in this regard. Here, we report a unique application of soft x-ray tomography to generate three-dimensional reconstructions of whole pancreatic β cells at different time points following glucose-stimulated insulin secretion. Reconstructions following stimulation showed distinct insulin vesicle distribution patterns reflective of altered vesicle pool sizes as they travel through the secretory pathway. Our results show that glucose stimulation caused rapid changes in biochemical composition and/or density of insulin packing, increased mitochondrial volume, and closer proximity of insulin vesicles to mitochondria. Costimulation with exendin-4 (a glucagon-like peptide-1 receptor agonist) prolonged these effects and increased insulin packaging efficiency and vesicle maturation. This study provides unique perspectives on the coordinated structural reorganization and interactions of organelles that dictate cell responses.