Publications

Changes in the mechanical properties of the extracellular matrix (ECM) are a hallmark of disease. Due to its relevance, several in vitro models have been developed for the ECM, including cell-derived matrices (CDMs). CDMs are decellularized natural ECMs assembled by cells that closely mimic the in vivo stromal fibre organization and molecular content. Here, we applied atomic force microscopy-force spectroscopy (AFM-FS) to evaluate the nanomechanical properties of CDMs obtained from patients diagnosed with collagen VI-related congenital muscular dystrophies (COL6-RDs). COL6-RDs are a set of neuromuscular conditions caused by pathogenic variants in any of the three major COL6 genes, which result in deficiency or dysfunction of the COL6 incorporated into the ECM of connective tissues. Current diagnosis includes the genetic confirmation of the disease and categorization of the phenotype based on maximum motor ability, as no direct correlation exists between genotype and phenotype of COL6-RDs. We describe differences in the elastic modulus (E) among CDMs from patients with different clinical phenotypes, as well as the restoration of E in CDMs obtained from genetically edited cells. Results anticipate the potential of the nanomechanical analysis of CDMs as a complementary clinical tool, providing phenotypic information about COL6-RDs and their response to gene therapies.

JTD Keywords: Atomic force microscopy-based force spectroscopy, Bethlem myopathy, Cell-derived matrices, Collagen vi-related congenital muscular dystrophies, Elastic modulus, Extracellular matrix, Extracellular-matrix, Fibroblasts, Gene editin, Microenvironment, Migration, Mode, Muscle, Position, Progenitors, Stiffness

Extracellular matrix (ECM) viscoelasticity has emerged as a potent regulator of physiological and pathological processes, including cancer progression. Spatial confinement within the ECM is also known to influence cell behavior in these contexts. However, the interplay between matrix viscoelasticity and spatial confinement in driving epithelial cell mechanotransduction is not well understood, as it relies on experiments employing purely elastic hydrogels. This work presents an innovative approach to fabricate and micropattern viscoelastic polyacrylamide hydrogels with independently tuneable Young's modulus and stress relaxation, specifically designed to mimic the mechanical properties observed during breast tumor progression, transitioning from a soft dissipative tissue to a stiff elastic one. Using this platform, this work demonstrates that matrix viscoelasticity differentially modulates breast epithelial cell spreading, adhesion, YAP nuclear import and cell migration, depending on the initial stiffness of the matrix. Furthermore, by imposing spatial confinement through micropatterning, this work demonstrates that confinement alters cellular responses to viscoelasticity, including cell spreading, mechanotransduction and migration. These findings establish ECM viscoelasticity as a key regulator of epithelial cell mechanoresponse and highlight the critical role of spatial confinement in soft, dissipative ECMs, which was a previously unexplored aspect.

JTD Keywords: Cell adhesion, Cell movement, Confinement, Dynamics, Elastic modulus, Elasticity, Epithelial cells, Extracellular matrix, Extracellular-matrix, Force transmission, Humans, Hydrogels, Mechanics, Mechanotransduction, cellular, Micropatterning, Migration, Morphology, Motilit, Polyacrylamide hydrogels, Stiffness, Substrate, Viscoelasticit, Viscoelasticity, Viscosity

The properties of thiol-yne click polyethylene glycol (PEG)-based hydrogels, which can be tuned by controlling the cis and trans stereochemistry through the gelation conditions, have been investigated at the micro- and nanoscale using optomechanics, atomistic molecular dynamics (MD) simulations, and nanoindentation. Optomechanical measurements on thin films and computer MD simulations have shown that the trans hydrogel is less porous than the cis hydrogel, which is in agreement with both the swelling behavior and the pore size determined for macroscopic 3D hydrogel samples. On the other hand, results from optomechanical measurements using both static and dynamic modes, as well as nanoindentation profiles obtained for thin films adhered to glass substrates, reflect that the trans hydrogel is stiffer than the cis one. Overall, despite the few drawbacks of the techniques employed in this work, from a qualitative point of view, the properties of click PEG-based hydrogels at the micro- and nanoscale follow a behavior similar to that found for 3D macroscopic samples. Considering the wide range of mechanical properties of human tissues (e.g., Young's modulus ranges from 0.1 kPa to many tens of MPa) and the extensive use of hydrogels in applications such as tissue regeneration and tissue-specific drug delivery, the availability of a hydrogel with tunable properties opens the door to targeted biomedicine.

JTD Keywords: Algorithm, Elastic modulu, Ewal, Injectable hydrogels, Molecular dynamics, Molecular-dynamics, Nanoindentation, Optomechanical sensors, Polyethylene glycol hydrogels, Surface stress, Thiol-yneclick hydrogels

Atomic force microscopy (AFM) has become indispensable for studying biological and medical samples. More than two decades of experiments have revealed that cancer cells are softer than healthy cells (for measured cells cultured on stiff substrates). The softness or, more precisely, the larger deformability of cancer cells, primarily independent of cancer types, could be used as a sensitive marker of pathological changes. The wide application of biomechanics in clinics would require designing instruments with specific calibration, data collection, and analysis procedures. For these reasons, such development is, at present, still very limited, hampering the clinical exploitation of mechanical measurements. Here, we propose a standardized operational protocol (SOP), developed within the EU ITN network Phys2BioMed, which allows the detection of the biomechanical properties of living cancer cells regardless of the nanoindentation instruments used (AFMs and other indenters) and the laboratory involved in the research. We standardized the cell cultures, AFM calibration, measurements, and data analysis. This effort resulted in a step-by-step SOP for cell cultures, instrument calibration, measurements, and data analysis, leading to the concordance of the results (Young's modulus) measured among the six EU laboratories involved. Our results highlight the importance of the SOP in obtaining a reproducible mechanical characterization of cancer cells and paving the way toward exploiting biomechanics for diagnostic purposes in clinics.

JTD Keywords: afm indentation, cancer cells, elastic-moduli, samples, stiffness, Atomic-force microscopy, Biomechanical phenomena, Cell culture techniques, Elastic modulus, Microscopy, atomic force

Drosophila is an amenable system for addressing the mechanics of morphogenesis. We describe a workflow for characterizing the mechanical properties of its ventral nerve cord (VNC), at different developmental stages, in live, flat dissected embryos employing atomic force microscopy (AFM). AFM is performed with spherical probes, and stiffness (Young's modulus) is calculated by fitting force curves with Hertz's contact model. For complete details on the use and execution of this protocol, please refer to Karkali et al. (2022).

JTD Keywords: atomic force microscopy (afm), developmental biology, model organisms, Animals, Atomic force microscopy, Atomic force microscopy (afm), Biology, Developmental biology, Drosophila, Elastic modulus, Microscopy, atomic force, Model organisms, Morphogenesis, Neurociencia, Neuroscience

Tissue elasticity is a critical regulator of cell behavior in normal and diseased conditions like fibrosis and cancer. Since the extracellular matrix (ECM) is a major regulator of tissue elasticity and function, several ECM-based models have emerged in the last decades, including in vitro endogenous ECM, decellularized tissue ECM and ECM hydrogels. The development of such models has urged the need to quantify their elastic properties particularly at the nanometer scale, which is the relevant length scale for cell-ECM interactions. For this purpose, the versatility of atomic force microscopy (AFM) to quantify the nanomechanical properties of soft biomaterials like ECM models has emerged as a very suitable technique. In this chapter we provide a detailed protocol on how to assess the Young's elastic modulus of ECM models by AFM, discuss some of the critical issues, and provide troubleshooting guidelines as well as illustrative examples of AFM measurements, particularly in the context of cancer.

JTD Keywords: 3D ECM hydrogels, Atomic force microscopy, Decellularized tissue, Elastic modulus, Endogenous ECM, Extracellular matrix

There is growing recognition that the mechanical interactions between cells and their local extracellular matrix (ECM) are central regulators of tissue development, homeostasis, repair and disease progression. The unique ability of atomic force microscopy (AFM) to probe quantitatively mechanical properties and forces at the nanometer or micrometer scales in all kinds of biological samples has been instrumental in the recent advances in cell and tissue mechanics. In this review we illustrate how AFM has provided important insights on our current understanding of the mechanobiology of cells, ECM and cell-ECM bidirectional interactions, particularly in the context of soft acinar tissues like the mammary gland or pulmonary tissue. AFM measurements have revealed that intrinsic cell micromechanics is cell-type specific, and have underscored the prominent role of β1 integrin/FAK(Y397) signaling and the actomyosin cytoskeleton in the mechanoresponses of both parenchymal and stromal cells. Moreover AFM has unveiled that the micromechanics of the ECM obtained by tissue decellularization is unique for each anatomical compartment, which may support both its specific function and cell differentiation. AFM has also enabled identifying critical mechanoregulatory proteins involved in branching morphogenesis (MMP14) and acinar differentiation (α3β1 integrin), and has clarified the role of altered tissue mechanics and architecture in a variety of pathologic conditions. Critical technical issues of AFM mechanical measurements like tip geometry effects are also discussed.

JTD Keywords: Atomic force microscopy, Beta1 integrin, Elastic modulus, Extracellular matrix, Morphogenesis, Tissue decellularization

The increasing recognition that tissue elasticity is an important regulator of cell behavior in normal and pathologic conditions such as fibrosis and cancer has driven the development of cell culture substrata with tunable elasticity. Such development has urged the need to quantify the elastic properties of these cell culture substrata particularly at the nanometer scale, since this is the relevant length scale involved in cell-extracellular matrix (ECM) mechanical interactions. To address this need, we have exploited the versatility of atomic force microscopy to quantify the elastic properties of a variety of cell culture substrata used in mechanobiology studies, including floating collagen gels, ECM-coated polyacrylamide gels, and decellularized tissue sections. In this review we summarize major findings in this field from our group within the context of the state-of-the-art in the field, and provide a critical discussion on the applicability and complementarity of currently available cell culture assays with tunable elasticity. In addition, we briefly describe how the limitations of these assays provide opportunities for future research, which is expected to continue expanding our understanding of the mechanobiological aspects that support both normal and diseased conditions.

JTD Keywords: 3D culture, Atomic force microscopy, Elastic modulus, Extracellular matrix, Polyacrylamide