Stiffness tomography exploration of living and fixed macrophages

Dual topologies of myotomal collagen XV and Tenascin C act in concert to guide and shape developing motor axons

During development, motor axons are guided toward muscle target by various extrinsic cues including extracellular matrix (ECM) proteins whose identities and cellular source remain poorly characterized. Here, using single-cell RNAseq of sorted GFP+ cells from smyhc1:gfp-injected zebrafish embryos, we unravel the slow muscle progenitors (SMP) pseudotemporal trajectory at the single-cell level and show that differentiating SMPs are a major source of ECM proteins. The SMP core-matrisome was characterized and computationally predicted to form a basement membrane-like structure tailored for motor axon guidance, including basement membrane-associated ECM proteins, as collagen XV-B, one of the earliest core-matrisome gene transcribed in differentiating SMPs and the glycoprotein Tenascin C. To investigate how contact-mediated guidance cues are organized along the motor path to exert their function in vivo, we used microscopy-based methods to analyze and quantify motor axon navigation in tnc and col15a1b knock-out fish. We show that motor axon shape and growth rely on the timely expression of the attractive cue Collagen XV-B that locally provides axons with a permissive soft microenvironment and separately organizes the repulsive cue Tenascin C into a unique functional dual topology. Importantly, bioprinted micropatterns that mimic this in vivo ECM topology were sufficient to drive directional motor axon growth. Our study offers evidence that not only the composition of ECM cues but their topology critically influences motor axon navigation in vertebrates with potential applications in regenerative medicine for peripheral nerve injury as regenerating nerves follow their original path.

Deep learning strategy for small dataset from atomic force microscopy mechano-imaging on macrophages phenotypes

The cytoskeleton is involved during movement, shaping, resilience, and functionality in immune system cells. Biomarkers such as elasticity and adhesion can be promising alternatives to detect the status of cells upon phenotype activation in correlation with functionality. For instance, professional immune cells such as macrophages undergo phenotype functional polarization, and their biomechanical behaviors can be used as indicators for early diagnostics. For this purpose, combining the biomechanical sensitivity of atomic force microscopy (AFM) with the automation and performance of a deep neural network (DNN) is a promising strategy to distinguish and classify different activation states. To resolve the issue of small datasets in AFM-typical experiments, nanomechanical maps were divided into pixels with additional localization data. On such an enlarged dataset, a DNN was trained by multimodal fusion, and the prediction was obtained by voting classification. Without using conventional biomarkers, our algorithm demonstrated high performance in predicting the phenotype of macrophages. Moreover, permutation feature importance was employed to interpret the results and unveil the importance of different biophysical properties and, in turn, correlated this with the local density of the cytoskeleton. While our results were demonstrated on the RAW264.7 model cell line, we expect that our methodology could be opportunely customized and applied to distinguish different cell systems and correlate feature importance with biophysical properties to unveil innovative markers for diagnostics.

Imaging beyond the surface region: Probing hidden materials via atomic force microscopy

Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.

AFM Stiffness Mapping in Human Aortic Smooth Muscle Cells

Aortic Smooth Muscle Cells (SMCs) play a vital role in maintaining mechanical homeostasis in the aorta. We recently found that SMCs of aneurysmal aortas apply larger traction forces than SMCs of healthy aortas. This result was explained by the significant increase of hypertrophic SMCs abundance in aneurysms. In the present study, we investigate whether the cytoskeleton stiffness of SMCs may also be altered in aneurysmal aortas. For that, we use Atomic Force Microscopy (AFM) nanoindentation with a specific mode that allows subcellular-resolution mapping of the local stiffness across a specified region of interest of the cell. Aortic SMCs from a commercial human lineage (AoSMCs, Lonza) and primary aneurysmal SMCs (AnevSMCs) are cultured in conditions promoting the development of their contractile apparatus, and seeded on hydrogels with stiffness properties of 12kPa and 25kPa. Results show that all SMC exhibit globally a lognormal stiffness distribution, with medians in the range 10-30 kPa. The mean of stiffness distributions is slightly higher in aneurysmal SMCs than in healthy cells (16 kPa versus 12 kPa) but the differences are not statistically significant due to the large dispersion of AFM nanoindentation stiffness. We conclude that the possible alterations previously found in aneurysmal SMCs do not affect significantly the AFM nanoindentation stiffness of their cytoskeleton.

A perspective view on the nanomotion detection of living organisms and its features

The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tools to monitor the response of single cells to chemical or pharmaceutical stimuli. Recently, it has been demonstrated that all living organisms oscillate at a nanometric scale and that these oscillations stop as soon as the organisms die. These nanometric scale oscillations can be detected by depositing living cells onto a micro-fabricated cantilever and by monitoring its displacements with an atomic force microscope-based electronics. Such devices, named nanomotion sensors, have been employed to determine the resistance profiles of life-threatening bacteria within minutes, to evaluate, among others, the effect of chemicals on yeast, neurons, and cancer cells. The data obtained so far demonstrate the advantages of nanomotion sensing devices in rapidly characterizing microorganism susceptibility to pharmaceutical agents. Here, we review the key aspects of this technique, presenting its major applications. and detailing its working protocols.

Nanomechanical sub-surface mapping of living biological cells by force microscopy

Atomic force microscopy allows for the nanomechanical surface characterization of a multitude of types of materials with highest spatial precision in various relevant environments. In recent years, researchers have refined this methodology to analyze living biological materials in vitro. The atomic force microscope thus has become an essential instrument for the (in many cases) non-destructive, high-resolution imaging of cells and visualization of their dynamic mechanical processes. Mapping force versus distance curves and the local evaluation of soft samples allow the operator to "see" beneath the sample surface and to capture the local mechanical properties. In this work, we combine atomic force microscopy with fluorescence microscopy to investigate cancerous epithelial breast cells in culture medium. With unprecedented spatial resolution, we provide tomographic images for the local elasticity of confluent layers of cells. For these particular samples, a layer of higher elastic modulus located directly beneath the cell membrane in comparison with the average elastic properties was observed. Strikingly, this layer appears to be perforated at unique locations of the sample surface of weakest mechanical properties where distinct features were visible permitting the tip to indent farthest into the cell's volume. We interpret this layer as the cell membrane mechanically supported by the components of the cytoskeleton that is populated with sites of integral membrane proteins. These proteins act as breaking points for the indenter thus explaining the mechanical weakness at these locations. In contrast, the highest mechanical strength of the cell was found at locations of the cell cores as cross-checked by fluorescence microscopy images of staining experiments, in particular at nucleoli sites as the cumulative elastic modulus there comprises cytoskeletal features and the tight packing ribosomal DNA of the cell.

Biomechanical Heterogeneity of Living Cells: Comparison between Atomic Force Microscopy and Finite Element Simulation

Atomic force microscopy (AFM) indentation is a popular method for characterizing the micromechanical properties of soft materials such as living cells. However, the mechanical data obtained from deep indentation measurements can be difficult and problematic to interpret as a result of the complex geometry of a cell, the nonlinearity of indentation contact, and constitutive relations of heterogeneous hyperelastic soft components. Living MDA-MB-231 cells were indented by spherical probes to obtain morphological and mechanical data that were adopted to build an accurate finite element model (FEM) for a parametric study. Initially, a 2D-axisymmetric numerical model was constructed with the main purpose of understanding the effect of geometrical and mechanical properties of constitutive parts such as the cell body, nucleus, and lamellipodium. A series of FEM deformation fields were directly compared with atomic force spectroscopy in order to resolve the mechanical convolution of heterogeneous parts and quantify Young's modulus and the geometry of nuclei. Furthermore, a 3D finite element model was constructed to investigate indentation events located far from the axisymmetric geometry. In this framework, the joint FEM/AFM approach has provided a useful methodology and a comprehensive characterization of the heterogeneous structure of living cells, emphasizing the deconvolution of geometrical structure and the true elastic modulus of the cell nucleus.

Stiffness tomography of eukaryotic intracellular compartments by atomic force microscopy

Precise localization and biophysical characterization of cellular structures is a key to the understanding of biological processes happening both inside the cell and at the cell surface. Atomic force microscopy is a powerful tool to study the cell surface - topography, elasticity, viscosity, interactions - and also the viscoelastic behavior of the underlying cytoplasm, cytoskeleton or the nucleus. Here, we demonstrate the ability of atomic force microscopy to also map and characterize organelles and microorganisms inside cells, at the nanoscale, by combining stiffness tomography with super-resolution fluorescence and electron microscopy. By using this correlative approach, we could both identify and characterize intracellular compartments. The validation of this approach was performed by monitoring the stiffening effect according to the metabolic status of the mitochondria in living cells in real-time.

Atomic force microscopy methodology and AFMech Suite software for nanomechanics on heterogeneous soft materials

Atomic force microscopy has proven to be a valuable technique to characterize the mechanical and morphological properties of heterogeneous soft materials such as biological specimens in liquid environment. Here we propose a 3-step method in order to investigate biological specimens where heterogeneity hinder a quantitative characterization: (1) precise AFM calibration, (2) nano-indentation in force volume mode, (3) array of finite element simulations built from AFM indentation events. We combine simulations to determine internal geometries, multi-layer material properties, and interfacial friction. In order to easily perform this analysis from raw AFM data to simulation comparison, we propose a standalone software, AFMech Suite comprising five interacting interfaces for simultaneous calibration, morphology, adhesion, mechanical, and simulation analysis. We test the methodology on soft hydrogels with hard spherical inclusions, as a soft-matter model system. Finally, we apply the method on E. coli bacteria supported on soft/hard hydrogels to prove usefulness in biological field.

Atomic force microscopy is an indispensable method in characterizing soft materials but the complexity of biological samples makes reproducible measurements difficult. Here the authors use a 3-step method to investigate biological specimens in which vertical and lateral heterogeneity hinders a precise quantitative characterization.

Identification of nanoparticles and nanosystems in biological matrices with scanning probe microscopy

Identification of nanoparticles and nanosystems into cells and biological matrices is a hot research topic in nanobiotechnologies. Because of their capability to map physical properties (mechanical, electric, magnetic, chemical, or optical), several scanning probe microscopy based techniques have been proposed for the subsurface detection of nanomaterials in biological systems. In particular, atomic force microscopy (AFM) can be used to reveal stiff nanoparticles in cells and other soft biomaterials by probing the sample mechanical properties through the acquisition of local indentation curves or through the combination of ultrasound-based methods, like contact resonance AFM (CR-AFM) or scanning near field ultrasound holography. Magnetic force microscopy can detect magnetic nanoparticles and other magnetic (bio)materials in nonmagnetic biological samples, while electric force microscopy, conductive AFM, and Kelvin probe force microscopy can reveal buried nanomaterials on the basis of the differences between their electric properties and those of the surrounding matrices. Finally, scanning near field optical microscopy and tip-enhanced Raman spectroscopy can visualize buried nanostructures on the basis of their optical and chemical properties. Despite at a still early stage, these methods are promising for detection of nanomaterials in biological systems as they could be truly noninvasive, would not require destructive and time-consuming specific sample preparation, could be performed in vitro, on alive samples and in water or physiological environment, and by continuously imaging the same sample could be used to dynamically monitor the diffusion paths and interaction mechanisms of nanomaterials into cells and biological systems. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

3D depth profiling of the interaction between an AFM tip and fluid polymer solutions

In the atomic force microscopy (AFM) investigation of soft polymers and liquids, the tip-sample interaction is dominated by long-range van der Waals forces, capillary forces and adhesion. Furthermore, the tip can indent several tens of nanometres into the surface, and it can pull off a polymer filament from the surface. Therefore, measuring the unperturbed shape of a polymeric fluid can be challenging. Here, we study the tip-sample interaction with polystyrene droplets swollen in chloroform vapour, where we can utilize the solvent vapour concentration to adjust the specimen's mechanical properties from a stiff solid to a fluid film. With the same AFM tip, we use two different AFM force spectroscopy methods to measure three-dimensional (3D) depth profiles of the tip-sample interaction: force-distance (FD) curves and amplitude-phase-distance (APD) curves. The 3D depth profiles reconstructed from FD and APD measurements provide detailed insight into the tip-sample interaction mechanism for a fluid polymer solution. The fluid's intrinsic relaxation time, which we measure with an AFM-based step-strain experiment, is essential for understanding the tip-sample interaction mechanism. Furthermore, measuring 3D depth profiles and using APD data to reconstruct the unperturbed surface comprise a versatile methodology for obtaining accurate dimensional measurements of fluid and gel-like objects on the nanometre scale.

Detection of stiff nanoparticles within cellular structures by contact resonance atomic force microscopy subsurface nanomechanical imaging

Detecting stiff nanoparticles buried in soft biological matrices by atomic force microscopy (AFM) based techniques represents a new frontier in the field of scanning probe microscopies, originally developed as surface characterization methods. Here we report the detection of stiff (magnetic) nanoparticles (NPs) internalized in cells by using contact resonance AFM (CR-AFM) employed as a potentially non-destructive subsurface characterization tool. Magnetite (Fe₃O₄) NPs were internalized in microglial cells from cerebral cortices of mouse embryos of 18 days by phagocytosis. Nanomechanical imaging of cells was performed by detecting the contact resonance frequencies (CRFs) of an AFM cantilever held in contact with the sample. Agglomerates of NPs internalized in cells were visualized on the basis of the local increase in the contact stiffness with respect to the surrounding biological matrix. A second AFM-based technique for nanomechanical imaging, i.e., HarmoniX™, as well as magnetic force microscopy and light microscopy were used to confirm the CR-AFM results. Thus, CR-AFM was demonstrated as a promising technique for subsurface imaging of nanomaterials in biological samples.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Nanoscale adhesion forces between the fungal pathogen Candida albicans and macrophages

The development of fungal infections is tightly controlled by the interaction of fungal pathogens with host immune cells. While the recognition of specific fungal cell wall components by immune receptors has been widely investigated, the molecular forces involved are not known. In this Communication, we show the ability of single-cell force spectroscopy to quantify the specific adhesion forces between the fungal pathogen Candida albicans and macrophages. The Candida-macrophage adhesion force is strong, up to ∼3000 pN, and corresponds to multiple cumulative bonds between lectin receptors expressed on the macrophage membrane and mannan carbohydrates on the fungal cell surface. Adhesion force signatures show constant force plateaus, up to >100 μm long, reflecting the extraction of elongated tethers from the macrophage membrane, a phenomenon which may increase the duration of intercellular adhesion. Adhesion strengthens with time, suggesting that the macrophage membrane engulfs the pathogen quickly after initial contact, leading to its internalization. The force nanoscopy method developed here holds great promise for understanding and controlling the early stages of microbe-immune interactions.

Substrate elasticity regulates the behavior of human monocyte-derived macrophages

Macrophages play a key role in atherosclerosis, cancer, and in the response to implanted medical devices. In each of these situations, the mechanical environment of a macrophage can vary from soft to stiff. However, how stiffness affects macrophage behavior remains uncertain. Using substrates of varying stiffness, we show macrophage phenotype and function depends on substrate stiffness. Notably, the cell area increases slightly from a sphere after 18 h on substrates mimicking healthy arterial stiffness (1-5 kPa), whereas macrophages on stiffer substrates (280 kPa-70 GPa) increased in area by nearly eight-fold. Macrophage migration is random regardless of substrate stiffness. The total average track speed was 7.8 ± 0.5 μm/h, with macrophages traveling fastest on the 280-kPa substrate (12.0 ± 0.5 μm/h) and slowest on the 3-kPa substrate (5.0 ± 0.4 μm/h). In addition F-actin organization in macrophages depends on substrate stiffness. On soft substrates, F-actin is spread uniformly throughout the cytoplasm, whereas on stiff substrates F-actin is functionalized into stress fibers. The proliferation rate of macrophages was faster on stiff substrates. Cells plated on the 280-kPa gel had a significantly shorter doubling time than those plated on the softer substrate. However, the ability of macrophages to phagocytose 1-μm particles did not depend on substrate stiffness. In conclusion, the results herein show macrophages are mechanosensitive; they respond to changes in stiffness by modifying their area, migration speed, actin organization, and proliferation rate. These results are important to understanding how macrophages respond in complex mechanical environments such as an atherosclerotic plaque.

Fixed endothelial cells exhibit physiologically relevant nanomechanics of the cortical actin web

It has been unknown whether cells retain their mechanical properties after fixation. Therefore, this study was designed to compare the stiffness properties of the cell cortex (the 50-100 nm thick zone below the plasma membrane) before and after fixation. Atomic force microscopy was used to acquire force indentation curves from which the nanomechanical cell properties were derived. Cells were pretreated with different concentrations of actin destabilizing agent cytochalasin D, which results in a gradual softening of the cell cortex. Then cells were studied 'alive' or 'fixed'. We show that the cortical stiffness of fixed endothelial cells still reports functional properties of the actin web qualitatively comparable to those of living cells. Myosin motor protein activity, tested by blebbistatin inhibition, can only be detected, in terms of cortical mechanics, in living but not in fixed cells. We conclude that fixation interferes with motor proteins while maintaining a functional cortical actin web. Thus, fixation of cells opens up the prospect of differentially studying the actions of cellular myosin and actin.

Imaging living cells surface and quantifying its properties at high resolution using AFM in QI™ mode

Since the last 10 years, AFM has become a powerful tool to study biological samples. However, the classical modes offered (imaging or tapping mode) often damage sample that are too soft or loosely immobilized. If imaging and mechanical properties are required, it requests long recording time as two different experiments must be conducted independently. In this study we compare the new QI™ mode against contact imaging mode and force volume mode, and we point out its benefit in the new challenges in biology on six different models: Escherichia coli, Candida albicans, Aspergillus fumigatus, Chinese hamster ovary cells and their isolated nuclei, and human colorectal tumor cells.

Atomic force microscopy stiffness tomography on living Arabidopsis thaliana cells reveals the mechanical properties of surface and deep cell-wall layers during growth

Cell-wall mechanical properties play a key role in the growth and the protection of plants. However, little is known about genuine wall mechanical properties and their growth-related dynamics at subcellular resolution and in living cells. Here, we used atomic force microscopy (AFM) stiffness tomography to explore stiffness distribution in the cell wall of suspension-cultured Arabidopsis thaliana as a model of primary, growing cell wall. For the first time that we know of, this new imaging technique was performed on living single cells of a higher plant, permitting monitoring of the stiffness distribution in cell-wall layers as a function of the depth and its evolution during the different growth phases. The mechanical measurements were correlated with changes in the composition of the cell wall, which were revealed by Fourier-transform infrared (FTIR) spectroscopy. In the beginning and end of cell growth, the average stiffness of the cell wall was low and the wall was mechanically homogenous, whereas in the exponential growth phase, the average wall stiffness increased, with increasing heterogeneity. In this phase, the difference between the superficial and deep wall stiffness was highest. FTIR spectra revealed a relative increase in the polysaccharide/lignin content.