Assessing Collagen D-Band Periodicity with Atomic Force Microscopy

Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix

The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.

Dissipation and recovery in collagen fibrils under cyclic loading: A molecular dynamics study

The hysteretic behavior exhibited by collagen fibrils, when subjected to cyclic loading, is known to result in both dissipation as well as accumulation of residual strain. On subsequent relaxation, partial recovery has also been reported. Cross-links have been considered to play a key role in overall mechanical properties. Here, we modify an existing coarse-grained molecular dynamics model for collagen fibril with initially cross-linked collagen molecules, which is known to reproduce the response to uniaxial strain, by incorporating reformation of cross-links to allow for possible recovery of the fibril. Using molecular dynamics simulations, we show that our model successfully replicates the key features observed in experimental data, including the movement of hysteresis loops, the time evolution of residual strains and energy dissipation, as well as the recovery observed during relaxation. We also show that the characteristic cycle number, describing the approach toward steady state, has a value similar to that in experiments. We also emphasize the vital role of the degree of cross-linking on the key features of the macroscopic response to cyclic loading.

On the effect of pepsin incubation on type I collagen from horse tendon: Fine tuning of its physico-chemical and rheological properties

Type I collagen is commonly recognized as the gold standard biomaterial for the manufacturing of medical devices for health-care related applications. In recent years, with the final aim of developing scaffolds with optimal bioactivity, even more studies focused on the influence of processing parameters on collagen properties, since processing can strongly affect the architecture of collagen at various length scales and, consequently, scaffolds macroscopic performances. The ability to finely tune scaffold properties in order to closely mimic the tissues' hierarchical features, preserving collagen's natural conformation, is actually of great interest. In this work, the effect of the pepsin-based extraction step on the material final properties was investigated. Thus, the physico-chemical properties of fibrillar type I collagens upon being extracted under various conditions were analyzed in depth. Correlations of collagen structure at the supramolecular scale with its microstructural properties were done, confirming the possibility of tuning rheological, viscoelastic and degradation properties of fibrillar type I collagen.

Extracellular Matrices as Bioactive Materials for In Situ Tissue Regeneration

Bioactive materials based on a nature-derived extracellular matrix (NECM) represent a category of biomedical devices with versatile therapeutic applications in the realms of tissue repair and engineering. With advancements in decellularization technique, the inherent bioactive molecules and the innate nano-structural and mechanical properties are preserved in three-dimensional scaffolds mainly composed of collagens. Techniques such as electrospinning, three-dimensional printing, and the intricate fabrication of hydrogels are developed to mimic the physical structures, biosignalling and mechanical cues of ECM. Until now, there has been no approach that can fully account for the multifaceted properties and diverse applications of NECM. In this review, we introduce the main proteins composing NECMs and explicate the importance of them when used as therapeutic devices in tissue repair. Nano-structural features of NECM and their applications regarding tissue repair are summarized. The origins, degradability, and mechanical property of and immune responses to NECM are also introduced. Furthermore, we review their applications, and clinical features thereof, in the repair of acute and chronic wounds, abdominal hernia, breast deformity, etc. Some typical marketed devices based on NECM, their indications, and clinical relevance are summarized.

Development of a facile method to compute collagen network pathological anisotropy using AFM imaging

Type I collagen, a fundamental extracellular matrix (ECM) component, is pivotal in maintaining tissue integrity and strength. It is also the most prevalent fibrous biopolymer within the ECM, ubiquitous in mammalian organisms. This structural protein provides essential mechanical stability and resilience to various tissues, including tendons, ligaments, skin, bone, and dentin. Collagen has been structurally investigated for several decades, and variation to its ultrastructure by histology has been associated with several pathological conditions. The current study addresses a critical challenge in the field of collagen research by providing a novel method for studying collagen fibril morphology at the nanoscale. It offers a computational approach to quantifying collagen properties, enabling a deeper understanding of how collagen type I can be affected by pathological conditions. The application of Fast Fourier Transform (FFT) coupled with Atomic Force Microscope (AFM) imaging distinguishes not only healthy and diseased skin but also holds potential for automated diagnosis of connective tissue disorders (CTDs), contributing to both clinical diagnostics and fundamental research in this area. Here we studied the changes in the structural parameters of collagen fibrils in Ehlers Danlos Syndrome (EDS). We have used skin extracted from genetically mutant mice that exhibit EDS phenotype as our model system (Col1a1Jrt/+ mice). The collagen fibrils were analyzed by AFM based descriptive-structural parameters, coupled with a 2D Fast Fourier Transform(2D-FFT) approach that automated the analysis of AFM images. In addition, each sample was characterized based on its FFT and power spectral density. Our qualitative data showed morphological differences in collagen fibril clarity (clearness of the collagen fibril edge with their neighbouring fibri), D-banding, orientation, and linearity. We have also demonstrated that FFT could be a new tool for distinguishing healthy from tissues with CTDs by measuring the disorganization of fibrils in the matrix. We have also employed FFT to reveal the orientations of the collagen fibrils, providing clinically relevant phenotypic information on their organization and anisotropy. The result of this study can be used to develop a new automated tool for better diagnosis of CTDs.

Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials

The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward "real-world" applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.

Quantitative nanohistology of aging dermal collagen

The skin is the largest organ in the body and is essential for protecting us from environmental stressors such as UV radiation, pollution, and pathogens. As we age, our skin undergoes complex changes that can affect its function, appearance, and health. These changes result from intrinsic (chronological) and extrinsic (environmental) factors that can cause damage to the skin's cells and extracellular matrix. As higher-resolution microscopical techniques, such as Atomic Force Microscopy (AFM), are being deployed to support histology, it is possible to explore the biophysical properties of the dermal scaffold's constituents, such as the collagen network. In this study, we demonstrate the use of our AFM-based quantitative nanohistology, performed directly on unfixed cryosections of 30 donors (female, Caucasian), to differentiate between dermal collagen from different age groups and anatomical sites. The initial 420 (10 × 10 μm²) Atomic Force Microscopy images were segmented into 42,000 (1 × 1 μm²) images before being classified according to four pre-defined empirical collagen structural biomarkers to quantify the structural heterogeneity of the dermal collagen. These markers include interfibrillar gap formation, undefined collagen structure, and registered or unregistered dense collagen fibrillar network with evident D-banding. The structural analysis was also complemented by extensive nanoindentation (∼1,000 curves) performed on individual fibrils from each section, yielding 30,000 indentation curves for this study. Principal Component Analysis was used to reduce the complexity of high-dimensional datasets. The % prevalence of the empirical collagen structural biomarkers between the papillary and reticular dermis for each section proves determinant in differentiating between the donors as a function of their age or the anatomical site (cheek or breast). A case of abnormal biological aging validated our markers and nanohistology approach. This case also highlighted the difference between chronological and biological aging regarding dermal collagen phenotyping. However, quantifying the impact of chronic and pathological conditions on the structure and function of collagen at the sub-micron level remains challenging and lengthy. By employing tools such as the Atomic Force Microscope as presented here, it is possible to start evaluating the complexity of the dermal matrix at the nanoscale and start identifying relevant collagen morphology which could be used toward histopathology standards.

Fluoridated Apatite Coating on Human Dentin via Laser-Assisted Pseudo-Biomineralization with the Aid of a Light-Absorbing Molecule

A simple, area-specific coating technique for fluoridated apatite (FAp) on teeth would be useful in dental applications. Recently, we achieved area-specific FAp coating on a human dentin substrate within 30 min by a laser-assisted biomimetic (LAB) process; pulsed Nd:YAG laser irradiation in a fluoride-containing supersaturated calcium phosphate solution (FCP solution). The LAB-processed, FAp-coated dentin substrate exhibited antibacterial activity against a major oral bacterium, Streptococcus mutans. In the present study, we refined the LAB process with a combination of a dental diode laser and a clinically approved light-absorbing molecule, indocyanine green (ICG). A micron-thick FAp layer was successfully formed on the dentin surface within only 3 min by the refined LAB process, i.e., dental diode laser irradiation in the FCP solution following ICG treatment. The ICG layer precoated on the dentin substrate played a crucial role in inducing rapid pseudo-biomineralization (FAp layer formation) on the dentin surface by absorbing laser light at the solid-liquid interface. In the refined LAB process, the precoated ICG layer was eliminated and replaced with the newly formed FAp layer composed of vertically oriented pillar-like nanocrystals. Cross-sectional ultrastructural analysis revealed a smooth interface between the FAp layer and the dentin substrate. The refined LAB process has potential as a tool for the tooth surface functionalization and hence, is worth further process refinement and in vitro and in vivo studies.

Collagen Remodeling along Cancer Progression Providing a Novel Opportunity for Cancer Diagnosis and Treatment

The extracellular matrix (ECM) is a significant factor in cancer progression. Collagens, as the main component of the ECM, are greatly remodeled alongside cancer development. More and more studies have confirmed that collagens changed from a barrier to providing assistance in cancer development. In this course, collagens cause remodeling alongside cancer progression, which in turn, promotes cancer development. The interaction between collagens and tumor cells is complex with biochemical and mechanical signals intervention through activating diverse signal pathways. As the mechanism gradually clears, it becomes a new target to find opportunities to diagnose and treat cancer. In this review, we investigated the process of collagen remodeling in cancer progression and discussed the interaction between collagens and cancer cells. Several typical effects associated with collagens were highlighted in the review, such as fibrillation in precancerous lesions, enhancing ECM stiffness, promoting angiogenesis, and guiding invasion. Then, the values of cancer diagnosis and prognosis were focused on. It is worth noting that several generated fragments in serum were reported to be able to be biomarkers for cancer diagnosis and prognosis, which is beneficial for clinic detection. At a glance, a variety of reported biomarkers were summarized. Many collagen-associated targets and drugs have been reported for cancer treatment in recent years. The new targets and related drugs were discussed in the review. The mass data were collected and classified by mechanism. Overall, the interaction of collagens and tumor cells is complicated, in which the mechanisms are not completely clear. A lot of collagen-associated biomarkers are excavated for cancer diagnosis. However, new therapeutic targets and related drugs are almost in clinical trials, with merely a few in clinical applications. So, more efforts are needed in collagens-associated studies and drug development for cancer research and treatment.