Super-resolution microscopy to decipher multi-molecular assemblies

iU-ExM: nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy

Expansion microscopy (ExM) is a highly effective technique for super-resolution fluorescence microscopy that enables imaging of biological samples beyond the diffraction limit with conventional fluorescence microscopes. Despite the development of several enhanced protocols, ExM has not yet demonstrated the ability to achieve the precision of nanoscopy techniques such as Single Molecule Localization Microscopy (SMLM). Here, to address this limitation, we have developed an iterative ultrastructure expansion microscopy (iU-ExM) approach that achieves SMLM-level resolution. With iU-ExM, it is now possible to visualize the molecular architecture of gold-standard samples, such as the eight-fold symmetry of nuclear pores or the molecular organization of the conoid in Apicomplexa. With its wide-ranging applications, from isolated organelles to cells and tissue, iU-ExM opens new super-resolution avenues for scientists studying biological structures and functions.

Bayesian methods in integrative structure modeling

There is a growing interest in characterizing the structure and dynamics of large biomolecular assemblies and their interactions within the cellular environment. A diverse array of experimental techniques allows us to study biomolecular systems on a variety of length and time scales. These techniques range from imaging with light, X-rays or electrons, to spectroscopic methods, cross-linking mass spectrometry and functional genomics approaches, and are complemented by AI-assisted protein structure prediction methods. A challenge is to integrate all of these data into a model of the system and its functional dynamics. This review focuses on Bayesian approaches to integrative structure modeling. We sketch the principles of Bayesian inference, highlight recent applications to integrative modeling and conclude with a discussion of current challenges and future perspectives.

[Closer to the native architecture of the cell using Cryo-ExM]

Most cellular imaging techniques, such as light or electron microscopy, require that the biological sample is first fixed by chemical cross-linking agents. This necessary step is also known to damage molecular nanostructures or even sub-cellular organization. To overcome this problem, another fixation approach was invented more than 40 years ago, which consists in cryo-fixing biological samples, thus allowing to preserve their native state. However, this method has been scarcely used in light microscopy due to the complexity of its implementation. In this review, we present a recently developed super-resolution method called expansion microscopy, which, when coupled with cryo-fixation, allows to visualize at a nanometric resolution the cell architecture as close as possible to its native state.

Small-molecule fluorogenic probes for mitochondrial nanoscale imaging

Mitochondria are inextricably linked to the development of diseases and cell metabolism disorders. Super-resolution imaging (SRI) is crucial in enhancing our understanding of mitochondrial ultrafine structures and functions. In addition to high-precision instruments, super-resolution microscopy relies heavily on fluorescent materials with unique photophysical properties. Small-molecule fluorogenic probes (SMFPs) have excellent properties that make them ideal for mitochondrial SRI. This paper summarizes recent advances in the field of SMFPs, with a focus on the chemical and spectroscopic properties required for mitochondrial SRI. Finally, we discuss future challenges in this field, including the design principles of SMFPs and nanoscopic techniques.

Bottom-up Coarse-Graining: Principles and Perspectives

Large-scale computational molecular models provide scientists a means to investigate the effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship between variations on the molecular scale and macroscopic observable properties facilitates an understanding of the molecular interactions driving the properties of real world materials and complex systems (e.g., those found in biology, chemistry, and materials science). As a result, discovering an explicit, systematic connection between microscopic nature and emergent mesoscopic behavior is a fundamental goal for this type of investigation. The molecular forces critical to driving the behavior of complex heterogeneous systems are often unclear. More problematically, simulations of representative model systems are often prohibitively expensive from both spatial and temporal perspectives, impeding straightforward investigations over possible hypotheses characterizing molecular behavior. While the reduction in resolution of a study, such as moving from an atomistic simulation to that of the resolution of large coarse-grained (CG) groups of atoms, can partially ameliorate the cost of individual simulations, the relationship between the proposed microscopic details and this intermediate resolution is nontrivial and presents new obstacles to study. Small portions of these complex systems can be realistically simulated. Alone, these smaller simulations likely do not provide insight into collectively emergent behavior. However, by proposing that the driving forces in both smaller and larger systems (containing many related copies of the smaller system) have an explicit connection, systematic bottom-up CG techniques can be used to transfer CG hypotheses discovered using a smaller scale system to a larger system of primary interest. The proposed connection between different CG systems is prescribed by (i) the CG representation (mapping) and (ii) the functional form and parameters used to represent the CG energetics, which approximate potentials of mean force (PMFs). As a result, the design of CG methods that facilitate a variety of physically relevant representations, approximations, and force fields is critical to moving the frontier of systematic CG forward. Crucially, the proposed connection between the system used for parametrization and the system of interest is orthogonal to the optimization used to approximate the potential of mean force present in all systematic CG methods. The empirical efficacy of machine learning techniques on a variety of tasks provides strong motivation to consider these approaches for approximating the PMF and analyzing these approximations.

Live cell microscopy: From image to insight

Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.

Pulling back the curtain: The hidden functions of receptor tyrosine kinases in development

Receptor tyrosine kinases (RTKs) are a conserved superfamily of transmembrane growth factor receptors that drive numerous cellular processes during development and in the adult. Upon activation, multiple adaptors and signaling effector proteins are recruited to binding site motifs located within the intracellular domain of the RTK. These RTK-effector interactions drive subsequent intracellular signaling cascades involved in canonical RTK signaling. Genetic dissection has revealed that alleles of Fibroblast Growth Factor receptors (FGFRs) that lack all canonical RTK signaling still retain some kinase-dependent biological activity. Here we examine how genetic analysis can be used to understand the mechanism by which RTKs drive multiple developmental processes via canonical signaling while revealing noncanonical activities. Recent data from both FGFRs and other RTKs highlight potential noncanonical roles in cell adhesion and nuclear signaling. The data supporting such functions are discussed as are recent technologies that have the potential to provide valuable insight into the developmental significance of these noncanonical activities.

Early upregulation of cytosolic phospholipase A2α in motor neurons is induced by misfolded SOD1 in a mouse model of amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a fatal multifactorial neurodegenerative disease characterized by the selective death of motor neurons. Cytosolic phospholipase A₂ alpha (cPLA₂α) upregulation and activation in the spinal cord of ALS patients has been reported. We have previously shown that cPLA₂α upregulation in the spinal cord of mutant SOD1 transgenic mice (SOD1^G93A) was detected long before the development of the disease, and inhibition of cPLA₂α upregulation delayed the disease's onset. The aim of the present study was to determine the mechanism for cPLA₂α upregulation.

METHODS

Immunofluorescence analysis and western blot analysis of misfolded SOD1, cPLA₂α and inflammatory markers were performed in the spinal cord sections of SOD1^G93A transgenic mice and in primary motor neurons. Over expression of mutant SOD1 was performed by induction or transfection in primary motor neurons and in differentiated NSC34 motor neuron like cells.

RESULTS

Misfolded SOD1 was detected in the spinal cord of 3 weeks old mutant SOD1^G93A mice before cPLA₂α upregulation. Elevated expression of both misfolded SOD1 and cPLA₂α was specifically detected in the motor neurons at 6 weeks with a high correlation between them. Elevated TNFα levels were detected in the spinal cord lysates of 6 weeks old mutant SOD1^G93A mice. Elevated TNFα was specifically detected in the motor neurons and its expression was highly correlated with cPLA₂α expression at 6 weeks. Induction of mutant SOD1 in primary motor neurons induced cPLA₂α and TNFα upregulation. Over expression of mutant SOD1 in NSC34 cells caused cPLA₂α upregulation which was prevented by antibodies against TNFα. The addition of TNFα to NSC34 cells caused cPLA₂α upregulation in a dose dependent manner.

CONCLUSIONS

Motor neurons expressing elevated cPLA₂α and TNFα are in an inflammatory state as early as at 6 weeks old mutant SOD1^G93A mice long before the development of the disease. Accumulated misfolded SOD1 in the motor neurons induced cPLA₂α upregulation via induction of TNFα.

Ground state depletion microscopy as a tool for studying microglia-synapse interactions

Ground state depletion followed by individual molecule return microscopy (GSDIM) has been used in the past to study the nanoscale distribution of protein co-localization in living cells. We now demonstrate the successful application of GSDIM to archival human brain tissue sections including from Alzheimer's disease cases as well as experimental tissue samples from mouse and zebrafish larvae. Presynaptic terminals and microglia and their cell processes were visualized at a resolution beyond diffraction-limited light microscopy, allowing clearer insights into their interactions in situ. The procedure described here offers time and cost savings compared to electron microscopy and opens the spectrum of molecular imaging using antibodies and super-resolution microscopy to the analysis of routine formalin-fixed paraffin sections of archival human brain. The investigation of microglia-synapse interactions in dementia will be of special interest in this context.

Putting the axonal periodic scaffold in order

Neurons rely on a unique organization of their cytoskeleton to build, maintain and transform their extraordinarily intricate shapes. After decades of research on the neuronal cytoskeleton, it is exciting that novel assemblies are still discovered thanks to progress in cellular imaging methods. Indeed, super-resolution microscopy has revealed that axons are lined with a periodic scaffold of actin rings, spaced every 190nm by spectrins. Determining the architecture, composition, dynamics, and functions of this membrane-associated periodic scaffold is a current conceptual and technical challenge, as well as a very active area of research. This short review aims at summarizing the latest research on the axonal periodic scaffold, highlighting recent progress and open questions.

Improving the resolution of fluorescence nanoscopy using post-expansion labeling microscopy

The visualization of the cell ultrastructure and molecular complexes has long been reserved for electron microscopy owing to its nanometric resolution. In recent years, this monopoly has been challenged by super-resolution (SR) fluorescence microscopy, which allows the visualization of cell structures with high spatial resolution, approaching virtually molecular dimensions. However, the resolution of current SR microscopy does not systematically reach the level of the ultrastructural information provided by electron microscopy. In this review, we are discussing the potential of revealing cell ultrastructure using the recent method of expansion microscopy (ExM). In particular, we are discussing the limitations that exist in SR and ExM methods that prevent the visualization of nanometric molecular assemblies and how post-labeling expansion could help alleviate them to reveal the molecular cartography of cells with unprecedented details.

Molecular and cellular correlates in Kv channel clustering: entropy-based regulation of cluster ion channel density

Scaffold protein-mediated ion channel clustering at unique membrane sites is important for electrical signaling. Yet, the mechanism(s) by which scaffold protein-ion channel interactions lead to channel clustering or how cluster ion channel density is regulated is mostly not known. The voltage-activated potassium channel (Kv) represents an excellent model to address these questions as the mechanism underlying its interaction with the post-synaptic density 95 (PSD-95) scaffold protein is known to be controlled by the length of the extended ‘ball and chain’ sequence comprising the C-terminal channel region. Here, using sub-diffraction high-resolution imaging microscopy, we show that Kv channel ‘chain’ length regulates Kv channel density with a ‘bell’-shaped dependence, reflecting a balance between thermodynamic considerations controlling ‘chain’ recruitment by PSD-95 and steric hindrance due to the spatial proximity of multiple channel molecules. Our results thus reveal an entropy-based mode of channel cluster density regulation that mirrors the entropy-based regulation of the Kv channel-PSD-95 interaction. The implications of these findings for electrical signaling are discussed.

A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods

Single-molecule localization microscopy (SMLM) is a relatively new imaging modality, winning the 2014 Nobel Prize in Chemistry, and considered as one of the key super-resolution techniques. SMLM resolution goes beyond the diffraction limit of light microscopy and achieves resolution on the order of 10-20 nm. SMLM thus enables imaging single molecules and study of the low-level molecular interactions at the subcellular level. In contrast to standard microscopy imaging that produces 2D pixel or 3D voxel grid data, SMLM generates big data of 2D or 3D point clouds with millions of localizations and associated uncertainties. This unprecedented breakthrough in imaging helps researchers employ SMLM in many fields within biology and medicine, such as studying cancerous cells and cell-mediated immunity and accelerating drug discovery. However, SMLM data quantification and interpretation methods have yet to keep pace with the rapid advancement of SMLM imaging. Researchers have been actively exploring new computational methods for SMLM data analysis to extract biosignatures of various biological structures and functions. In this survey, we describe the state-of-the-art clustering methods adopted to analyze and quantify SMLM data and examine the capabilities and shortcomings of the surveyed methods. We classify the methods according to (1) the biological application (i.e., the imaged molecules/structures), (2) the data acquisition (such as imaging modality, dimension, resolution, and number of localizations), and (3) the analysis details (2D versus 3D, field of view versus region of interest, use of machine-learning and multi-scale analysis, biosignature extraction, etc.). We observe that the majority of methods that are based on second-order statistics are sensitive to noise and imaging artifacts, have not been applied to 3D data, do not leverage machine-learning formulations, and are not scalable for big-data analysis. Finally, we summarize state-of-the-art methodology, discuss some key open challenges, and identify future opportunities for better modeling and design of an integrated computational pipeline to address the key challenges.

Bridging the Molecular-Cellular Gap in Understanding Ion Channel Clustering

The clustering of many voltage-dependent ion channel molecules at unique neuronal membrane sites such as axon initial segments, nodes of Ranvier, or the post-synaptic density, is an active process mediated by the interaction of ion channels with scaffold proteins and is of immense importance for electrical signaling. Growing evidence indicates that the density of ion channels at such membrane sites may affect action potential conduction properties and synaptic transmission. However, despite the emerging importance of ion channel density for electrical signaling, how ion channel-scaffold protein molecular interactions lead to cellular ion channel clustering, and how this process is regulated are largely unknown. In this review, we emphasize that voltage-dependent ion channel density at native clustering sites not only affects the density of ionic current fluxes but may also affect the conduction properties of the channel and/or the physical properties of the membrane at such locations, all changes that are expected to affect action potential conduction properties. Using the concrete example of the prototypical Shaker voltage-activated potassium channel (Kv) protein, we demonstrate how insight into the regulation of cellular ion channel clustering can be obtained when the molecular mechanism of ion channel-scaffold protein interaction is known. Our review emphasizes that such mechanistic knowledge is essential, and when combined with super-resolution imaging microscopy, can serve to bridge the molecular-cellular gap in understanding the regulation of ion channel clustering. Pressing questions, challenges and future directions in addressing ion channel clustering and its regulation are discussed.

Innovative particle standards and long-lived imaging for 2D and 3D dSTORM

Direct stochastic optical reconstruction microscopy (dSTORM), developed in the last decade, has revolutionised optical microscopy by enabling scientists to visualise objects beyond the resolution provided by conventional microscopy (200 nm). We developed an innovative method based on blinking particle standards and conditions for long-lived imaging over several weeks. Stable localisation precisions within the 10 nm-range were achieved for single virions and in cellulo 2D imaging of centrosomes, as well as their reliable reconstruction in 3D dSTORM.

Super-resolution microscopy: successful applications in centrosome study and beyond

Centrosome is the main microtubule-organizing center in most animal cells. Its core structure, centriole, also assembles cilia and flagella that have important sensing and motility functions. Centrosome has long been recognized as a highly conserved organelle in eukaryotic species. Through electron microscopy, its ultrastructure was revealed to contain a beautiful nine-symmetrical core 60 years ago, yet its molecular basis has only been unraveled in the past two decades. The emergence of super-resolution microscopy allows us to explore the insides of a centrosome, which is smaller than the diffraction limit of light. Super-resolution microscopy also enables the compartmentation of centrosome proteins into different zones and the identification of their molecular interactions and functions. This paper compiles the centrosome architecture knowledge that has been revealed in recent years and highlights the power of several super-resolution techniques.

Measuring expansion from macro- to nanoscale using NPC as intrinsic reporter

Expansion microscopy is a super-resolution method that allows expanding uniformly biological samples, by increasing the relative distances among fluorescent molecules labeling specific components. One of the main concerns in this approach regards the isotropic behavior at the nanoscale. The present study aims to determine the robustness of such a technique, quantifying the expansion parameters i.e. scale factor, isotropy, uniformity. Our focus is on the nuclear pore complex (NPC), as well-known nanoscale component endowed of a preserved and symmetrical structure localized on the nuclear envelope. Here, we show that Nup153 is a good reporter to quantitatively address the isotropy of the expansion process. The quantitative analysis carried out on NPCs, at different spatial scales, allows concluding that expansion microscopy can be used at the nanoscale to measure subcellular features with an accuracy from 10 to 5 nm. Therefore, it is an excellent method for structural studies of macromolecular complexes.

TNFR1 membrane reorganization promotes distinct modes of TNFα signaling

Signaling by the ubiquitously expressed tumor necrosis factor receptor 1 (TNFR1) after ligand binding plays an essential role in determining whether cells exhibit survival or death. TNFR1 forms distinct signaling complexes that initiate gene expression programs downstream of the transcriptional regulators NFκB and AP-1 and promote different functional outcomes, such as inflammation, apoptosis, and necroptosis. Here, we investigated the ways in which TNFR1 was organized at the plasma membrane at the nanoscale level to elicit different signaling outcomes. We confirmed that TNFR1 forms preassembled clusters at the plasma membrane of adherent cells in the absence of ligand. After trimeric TNFα binding, TNFR1 clusters underwent a conformational change, which promoted lateral mobility, their association with the kinase MEKK1, and activation of the JNK/p38/NFκB pathway. These phenotypes required a minimum of two TNFR1-TNFα contact sites; fewer binding sites resulted in activation of NFκB but not JNK and p38. These data suggest that distinct modes of TNFR1 signaling depend on nanoscale changes in receptor organization.

Subsynaptic Domains in Super-Resolution Microscopy: The Treachery of Images

The application of super-resolution optical microscopy to investigating synaptic structures has revealed a highly heterogeneous and variable intra-synaptic organization. Dense subsynaptic protein assemblies named subsynaptic domains or SSDs have been proposed as structural units that regulate the efficacy of neuronal transmission. However, an in-depth characterization of SSDs has been hampered by technical limitations of super-resolution microscopy of synapses, namely the stochasticity of the signals during the imaging procedures and the variability of the synaptic structures. Here, we synthetize the available evidence for the existence of SSDs at central synapses, as well as the possible functional relevance of SSDs. In particular, we discuss the possible regulation of co-transmission at mixed inhibitory synapses as a consequence of the subsynaptic distribution of glycine receptors (GlyRs) and GABA_A receptors (GABA_ARs).

LAY ABSTRACT

Super-resolution imaging strategies bypass the resolution limit of conventional optical microscopy and have given new insights into the distribution of proteins at synapses in the central nervous system. Neurotransmitter receptors and scaffold proteins appear to occupy specialized locations within synapses that we refer to as subsynaptic domains or SSDs. Interestingly, these SSDs are highly dynamic and their formation seems to be related to the remodeling of synapses during synaptic plasticity. It was also shown that SSDs of pre-and post-synaptic proteins are aligned in so-called nanocolumns, highlighting the role of SSDs in the regulation of synaptic transmission. Despite recent advances, however, the detection of SSDs with super-resolution microscopy remains difficult due to the inherent technical limitations of these approaches that are discussed in this review article.

About samples, giving examples: Optimized Single Molecule Localization Microscopy

Super-resolution microscopy has profoundly transformed how we study the architecture of cells, revealing unknown structures and refining our view of cellular assemblies. Among the various techniques, the resolution of Single Molecule Localization Microscopy (SMLM) can reach the size of macromolecular complexes and offer key insights on their nanoscale arrangement in situ. SMLM is thus a demanding technique and taking advantage of its full potential requires specifically optimized procedures. Here we describe how we perform the successive steps of an SMLM workflow, focusing on single-color Stochastic Optical Reconstruction Microscopy (STORM) as well as multicolor DNA Points Accumulation for imaging in Nanoscale Topography (DNA-PAINT) of fixed samples. We provide detailed procedures for careful sample fixation and immunostaining of typical cellular structures: cytoskeleton, clathrin-coated pits, and organelles. We then offer guidelines for optimal imaging and processing of SMLM data in order to optimize reconstruction quality and avoid the generation of artifacts. We hope that the tips and tricks we discovered over the years and detail here will be useful for researchers looking to make the best possible SMLM images, a pre-requisite for meaningful biological discovery.

Monitoring HIV-1 Assembly in Living Cells: Insights from Dynamic and Single Molecule Microscopy

The HIV-1 assembly process is a multi-complex mechanism that takes place at the host cell plasma membrane. It requires a spatio-temporal coordination of events to end up with a full mature and infectious virus. The molecular mechanisms of HIV-1 assembly have been extensively studied during the past decades, in order to dissect the respective roles of the structural and non-structural viral proteins of the viral RNA genome and of some host cell factors. Nevertheless, the time course of HIV-1 assembly was observed in living cells only a decade ago. The very recent revolution of optical microscopy, combining high speed and high spatial resolution, in addition to improved fluorescent tags for proteins, now permits study of HIV-1 assembly at the single molecule level within living cells. In this review, after a short description of these new approaches, we will discuss how HIV-1 assembly at the cell plasma membrane has been revisited using advanced super resolution microscopy techniques and how it can bridge the study of viral assembly from the single molecule to the entire host cell.

Advances in coarse-grained modeling of macromolecular complexes

Recent progress in coarse-grained (CG) molecular modeling and simulation has facilitated an influx of computational studies on biological macromolecules and their complexes. Given the large separation of length-scales and time-scales that dictate macromolecular biophysics, CG modeling and simulation are well-suited to bridge the microscopic and mesoscopic or macroscopic details observed from all-atom molecular simulations and experiments, respectively. In this review, we first summarize recent innovations in the development of CG models, which broadly include structure-based, knowledge-based, and dynamics-based approaches. We then discuss recent applications of different classes of CG models to explore various macromolecular complexes. Finally, we conclude with an outlook for the future in this ever-growing field of biomolecular modeling.

Emerging Picture of Deuterosome-Dependent Centriole Amplification in MCCs

Multiciliated cells (MCCs) have several hair-like structures called cilia, which are required to propel substances on their surface. A cilium is organized from a basal body which resembles a hollow microtubule structure called a centriole. In terminally differentiated MCCs, hundreds of new basal bodies/centrioles are formed via two parallel pathways: the centriole- and deuterosome-dependent pathways. The deuterosome-dependent pathway is also referred to as "de novo" because unlike the centriole-dependent pathway which requires pre-existing centrioles, in the de novo pathway multiple new centrioles are organized around non-microtubule structures called deuterosomes. In the last five years, some deuterosome-specific markers have been identified and concurrent advancements in the super-resolution techniques have significantly contributed to gaining insights about the major stages of centriole amplification during ciliogenesis. Altogether, a new picture is emerging which also challenges the previous notion that deuterosome pathway is de novo. This review is primarily focused on studies that have contributed towards the better understanding of deuterosome-dependent centriole amplification and presents a developing model about the major stages identified during this process.