Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis

The fibrillogenesis influence the binding specificity of collagen to discoidin domain receptor 2 and cell behavior

Collagen is one of the most important natural biopolymers, it plays its role as a load-bearing structure in tissues only after polymerizing into fibrils. DDR2 is a collagen-binding receptor tyrosine kinases, playing a role in the regulation of collagen-cell interactions. Here, we studied the recognition of collagen fibrils by DDR2 and the effect of fibrillogenesis on cell biological activity. Our results showed that for monomeric collagen, the binding affinity of DDR2 to mammalian porcine skin collagen is higher than that to fish collagen. When the assembly of collagen monomers into the collagen fibril, the binding affinity of DDR2 is enhanced. In contrast, the binding ability of the hybrid fibril is stronger than the corresponding black carp skin collagen fibrils, and slightly weaker than corresponding porcine skin collagen fibril. This indicates that the introduction of porcine skin collagen in the co-assembly system can regulate the binding of DDR2 to fish-sourced collagen. We also find that compared to monomers, the fibrillogenesis of collagen promotes cell interaction with the collagen substrate, and has an increased ability to induce cells spreading. Our results confirmed that the physical state of collagen impacts its binding with DDR2 and cell behavior. These findings provide new insights into cell-collagen interactions.

Impact of therapeutic X-ray exposure on collagen I and associated proteins

Biological tissues are exposed to X-rays in medical applications (such as diagnosis and radiotherapy) and in research studies (for example microcomputed X-ray tomography: microCT). Radiotherapy may deliver doses up to 50Gy to both tumour and healthy tissues, resulting in undesirable clinical side effects which can compromise quality of life. Whilst cellular responses to X-rays are relatively well-characterised, X-ray-induced structural damage to the extracellular matrix (ECM) is poorly understood. This study tests the hypotheses that ECM proteins and ECM-rich tissues (purified collagen I and rat tail tendons respectively) are structurally compromised by exposure to X-ray doses used in breast radiotherapy. Protein gel electrophoresis demonstrated that breast radiotherapy equivalent doses can induce fragmentation of the constituent α chains in solubilised purified collagen I. However, assembly into fibrils, either in vitro or in vivo, prevented X-ray-induced fragmentation but not structural changes (as characterised by LC-MS/MS and peptide location fingerprinting: PLF). In subsequent experiments exposure to higher (synchrotron) X-ray doses induced substantial fragmentation of solubilised and fibrillar (chicken tendon) collagen I. LC-MS/MS and PLF analysis of synchrotron-irradiated tendon identified structure-associated changes in collagens I, VI, XII, proteoglycans including aggrecan, decorin, and fibromodulin, and the elastic fibre component fibulin-1. Thus, exposure to radiotherapy X-rays can affect the structure of key tissue ECM components, although additional studies will be required to understand dose dependent effects. STATEMENT OF SIGNIFICANCE: Biological systems are routinely exposed to X-rays during medical treatments (radiotherapy) and in imaging studies (microCT). Whilst the impact of ionising radiation on cells is well characterised, the interactions between X-rays and the extracellular matrix are not. Here, we show that relatively low dose breast radiotherapy X-rays are sufficient to affect the structure of collagen I in both its solubilised and fibrillar forms. Although the impact of intermediate X-ray doses on extracellular proteins was not determined, the high dose exposures which are achievable using a synchrotron source had an even greater effect on the structure of collagen I molecules and, in tendon, on the structures of many accessory extracellular matrix proteins, The unwanted side effects of radiotherapy may therefore be due to not only cellular damage but also damage to the surrounding matrix.

The evolution of adhesive dentistry: From etch-and-rinse to universal bonding systems

OBJECTIVES

This review aimed at presenting the mechanisms and pitfalls of adhesion to enamel and dentin, advances in the materials science and in the development of strategies to improve hybrid layer (HL) longevity.

METHODS

Search of the literature was performed on PubMed, Scopus and Web of Science with keywords related to the structure of the dental substrate, HL degradation mechanisms and strategies to contrast them.

RESULTS

Albeit the advances in the dental materials' properties, HL degradation is still a relevant and current issue in adhesive dentistry. However, adhesive materials have become more resistant and less operator sensitive, and good adhesion is currently in the hands of every practitioner. Numerous novel strategies are being developed, able to improve the resistance of adhesive resins to degradation, their ability to infiltrate and chemically bond to dentin, to remove the unbound/residual water within the HL, reinforce the dentin collagen matrix, and inhibit endogenous metalloproteinases. Many of the strategies have turned to nature in search for powerful biomodifying compounds, and for the inspiration as to mimic naturally occurring regenerative processes.

SIGNIFICANCE

Extensive knowledge on the structure of the dental substrate and the complexity of adhesion to dentin has led to the development of improved formulations of dental adhesives and numerous valid strategies to improve the strength and longevity of the HL. Nevertheless, for many of them the road from bench to chairside still seems long. We encourage practitioners to know their materials well and use the strategies readily available to them.

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability

Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks. STATEMENT OF SIGNIFICANCE: Collagen hydrogels are widely used as scaffolds for tissue engineering due to their support of cellular activity. However, collagen hydrogels often undergo undesired changes in size and shape due to cell-generated forces, and conventional strategies to mitigate this deformation typically compromise either the fibrillar microstructure or cytocompatibility of the collagen. In this study, we introduce an innovative interpenetrating network (IPN) that combines physically self-assembled, fibrillar collagen-ideal for promoting cell adhesion and spreading-with covalently crosslinked, amorphous collagen-ideal for enhancing bulk hydrogel stability. Our IPN design maintains the native fibrillar structure of collagen while significantly improving resistance against cell-induced contraction, providing a promising solution to enhance the performance and reliability of collagen hydrogels for tissue engineering applications.

Modeling collagen fibril degradation as a function of matrix microarchitecture

Collagenolytic degradation is a process fundamental to tissue remodeling. The microarchitecture of collagen fibril networks changes during development, aging, and disease. Such changes to microarchitecture are often accompanied by changes in matrix degradability. In a matrix, the pore size and fibril characteristics such as length, diameter, number, orientation, and curvature are the major variables that define the microarchitecture. In vitro, collagen matrices of the same concentration but different microarchitectures also vary in degradation rate. How do different microarchitectures affect matrix degradation? To answer this question, we developed a computational model of collagen degradation. We first developed a lattice model that describes collagen degradation at the scale of a single fibril. We then extended this model to investigate the role of microarchitecture using Brownian dynamics simulation of enzymes in a multi-fibril three dimensional matrix to predict its degradability. Our simulations predict that the distribution of enzymes around the fibrils is non-uniform and depends on the microarchitecture of the matrix. This non-uniformity in enzyme distribution can lead to different extents of degradability for matrices of different microarchitectures. Our simulations predict that for the same enzyme concentration and collagen concentration, a matrix with thicker fibrils degrades more than that with thinner fibrils. Our model predictions were tested using in vitro experiments with synthetic collagen gels of different microarchitectures. Experiments showed that indeed degradation of collagen depends on the matrix architecture and fibril thickness. In summary, our study shows that the microarchitecture of the collagen matrix is an important determinant of its degradability.

Physiological mechanical forces accelerate the degradation of bovine lung collagen fibers by bacterial collagenase

Collagen fibers, one of the key load-bearing components of the extracellular matrix, contribute significantly to tissue integrity through their mechanical properties of strain-dependent stiffening. This study investigated the effects of bacterial collagenase on the mechanical behavior of individual bovine lung collagen fibers in the presence or absence of mechanical forces, with a focus on potential implications for emphysema, a condition associated with collagen degradation and alveolar wall rupture. Tensile tests were conducted on individual collagen fibers isolated from bovine lung tissue. The rate of degradation was characterized by the change in fiber Young's modulus during 60 min of digestion under various mechanical conditions mimicking the mechanical stresses on the fibers during breathing. Compared to digestion without mechanical forces, a significantly larger drop of fiber modulus was observed in the presence of static or intermittent mechanical forces. Fiber yield stress was also reduced after digestion indicating compromised fiber failure. By incorporating fibril waviness obtained by scanning electron microscopic images, an analytic model allowed estimation of fibril modulus. A computational model that incorporated waviness and the results of tensile tests was also developed to simulate and interpret the data. The simulation results provided insights into the mechanical consequences of bacterial collagenase and mechanical forces on collagen fibers, revealing both fibril softening and rupture during digestion. These findings shed light on the microscale changes in collagen fiber structure and mechanics under enzymatic digestion and breathing-like mechanical stresses with implications for diseases that are impacted by collagen degradation such as emphysema.

Comparing microstructural and micromechanical deformation of the TMJ disc in two anterior disc displacement models

OBJECTIVE

Anterior disc displacement (ADD) has been used to establish temporomandibular joint disorder (TMD) models. Based on whether preserve of the retrodiscal attachment, the modelling methodologies include ADD with dissecting the retrodiscal attachment (ADDwd) and ADD without dissecting the retrodiscal attachment (ADDwod). This article aims to determine which model better matches the micromechanical and microstructural progression of TMD.

METHODS

Through meticulous microscopic observations, the microstructure and micromechanical deformation of the TMJ discs in ADDwd and ADDwod rabbit models were compared at 2 and 20 weeks.

RESULT

Scanning electron microscopy and transmission electron microscopy showed that collagen fibres became slenderized and straightened, collagen fibrils lost diameter and arrangement in the ADDwd group at 2 weeks. Meanwhile, nanoindentation and atomic electron microscopy showed that the micro- and nano- mechanical properties decreased dramatically. However, the ADDwod group exhibited no significant microstructure and micromechanical deformations at 2 weeks. Dissection of the retrodiscal attachment contribute in the acceleration of disease progression at the early stage, the devastating discal phenotype remained fundamentally the same within the two models at 20 weeks.

CONCLUSION

ADDwod models, induced stable and persistent disc deformation, therefore, can better match the progression of TMD. While ADDwd models can be considered for experiments which aim to obtain advanced phenotype in a short time.

Matrix metalloproteinases in dentin: Assessing their presence, activity, and inhibitors - a review of current trends

INTRODUCTION

Dentin integrity is a critical aspect of tooth structure, with matrix metalloproteinases (MMPs) playing a crucial role in dentinogenesis, caries formation, and dental bonding. It is crucial to accurately assess MMP activity to understand dentin pathophysiology and develop effective clinical strategies.

OBJECTIVES

The study aimed to conduct a thorough review and comprehensive summary of diverse techniques employed in assessing MMPs in dentin.

DATA AND SOURCES

To conduct the research, electronic databases were systematically searched and manual citation searches were performed. A total of 621 articles were identified. After eliminating duplicates and irrelevant studies, 70 articles were included in the review. 25 articles with overlapping methodologies were also excluded.

STUDY SELECTION

The selection criteria were based on the relevance of the studies to MMPs and MMP inhibitors in dentin without regard to the study design. Only peer-reviewed articles published in English were included. The search was restricted to studies published until November 2022.

CONCLUSION

The comprehensive analysis of various studies has yielded 37 techniques for evaluating MMPs and MMP inhibitors, which hold significant promise in creating diagnostic markers and devising targeted therapeutic interventions.

Self-Assembly of Cyclic-Bending Collagen Fibrils by Polyimide Films

The cyclic-bending morphologies of the fibrils formed by the self-assembly of type I collagen (Col) are closely related to the mechanisms of various diseases. Therefore, studies that allow the self-assembly of Col molecules to form cyclic-bending fibrils in vitro are vitally important. In this study, we successfully achieved the cyclic-bending shapes (specifically, a regular hexagonal shape) of Col molecules by controlling the steric structures of polyimide (PI) molecular chains through the film formation process. Specifically, when a single layer of PI film was baked, the PI molecular chains within the film bent in the direction parallel to the substrate surface plane. Repeating the layering and baking processes resulted in 3D structures of the PI molecular chains, which were oriented in the direction perpendicular to the substrate surface plane. This three-dimensional bending would result from the PI molecular chain interactions between the upper and lower layers. When the Col molecules were reacted on these film surfaces, they recognized the structures of the PI molecular chains and self-assembled to form cyclic-bending Col fibrils. Especially, in PI films subjected to three cycles of layering and baking, hemicircular-shaped Col fibrils were observed to be regularly arrayed. Additionally, these regularly cyclic-bending fibrils were aligned in the uniaxial direction through a uniaxial rubbing treatment of the PI films. This successful research is significant both as a method for controlling the morphologies of Col fibrils and as a study that explores the biomedical implications of Col fibril cyclic-bending in the living body.

Pauli Exclusion by n→π* Interactions: Implications for Paleobiology

Proteins have evolved to function in an aqueous environment. Collagen, which provides the bodily scaffold for animals, has a special need to retain its integrity. This need was addressed early on, as intact collagen has been detected in dinosaur fossils, even though peptide bonds have a half-life of only ∼500 years in a neutral aqueous solution. We sought to discover the physicochemical basis for this remarkable resistance to hydrolysis. Using experimental and computational methods, we found that a main-chain acyl group can be protected from hydrolysis by an O···C=O n→π* interaction with a neighboring acyl group. These interactions engage virtually every peptide bond in a collagen triple helix. This protection, which arises from the Pauli exclusion principle, could underlie the preservation of ancient collagen.

Mmp14-dependent remodeling of the pericellular-dermal collagen interface governs fibroblast survival

Dermal fibroblasts deposit type I collagen, the dominant extracellular matrix molecule found in skin, during early postnatal development. Coincident with this biosynthetic program, fibroblasts proteolytically remodel pericellular collagen fibrils by mobilizing the membrane-anchored matrix metalloproteinase, Mmp14. Unexpectedly, dermal fibroblasts in Mmp14-/- mice commit to a large-scale apoptotic program that leaves skin tissues replete with dying cells. A requirement for Mmp14 in dermal fibroblast survival is recapitulated in vitro when cells are embedded within, but not cultured atop, three-dimensional hydrogels of crosslinked type I collagen. In the absence of Mmp14-dependent pericellular proteolysis, dermal fibroblasts fail to trigger β1 integrin activation and instead actuate a TGF-β1/phospho-JNK stress response that leads to apoptotic cell death in vitro as well as in vivo. Taken together, these studies identify Mmp14 as a requisite cell survival factor that maintains dermal fibroblast viability in postnatal dermal tissues.

Effect of Bleaching Treatments on the Mechanical Properties of the Dentin Matrix and on Collagen Biodegradation by Endogenous Protease

This study evaluated the mechanical properties of demineralized dentin matrix submitted to different bleaching treatments, as well as the changes in mass and collagen biodegradation brought about by endogenous protease. Dentin collagen matrices were prepared to receive the following treatments (n=12): no bleaching treatment (C-control), 10% carbamide peroxide (CP-Opalescence PF, Ultradent, South Jordan, UT, USA) 10%/8 hours/ day/14 days, and 40% hydrogen peroxide (HP-Opalescence Boost, Ultradent), 40 minutes per session/3 sessions. The dentin matrices were evaluated for elastic modulus and mass before and after treatments and ultimate tensile strength after treatments. The solution collected during storage was evaluated for hydroxyproline release. There was no statistically significant difference between CP and C in terms of the elastic modulus (p=0.3697) or mass variation (p=0.1333). Dentin beams treated with HP and C presented significant mass loss after the first session (p=0.0003). HP treatment led to complete degradation of collagen matrices after the second bleaching session. After the second session, CP showed higher hydroxyproline concentration than C (p<0.0001). Ultimate tensile strength was lower for CP than C (p=0.0097). CP did not affect the elastic modulus or the dentin collagen matrix mass but did promote hydroxyproline release by endogenous protease and reduce the ultimate tensile strength. HP significantly affected the mechanical properties of dentin and promoted complete degradation of the demineralized dentin collagen matrix.

Crossing length scales: X-ray approaches to studying the structure of biological materials

Biological materials have outstanding properties. With ease, challenging mechanical, optical or electrical properties are realised from comparatively `humble' building blocks. The key strategy to realise these properties is through extensive hierarchical structuring of the material from the millimetre to the nanometre scale in 3D. Though hierarchical structuring in biological materials has long been recognized, the 3D characterization of such structures remains a challenge. To understand the behaviour of materials, multimodal and multi-scale characterization approaches are needed. In this review, we outline current X-ray analysis approaches using the structures of bone and shells as examples. We show how recent advances have aided our understanding of hierarchical structures and their functions, and how these could be exploited for future research directions. We also discuss current roadblocks including radiation damage, data quantity and sample preparation, as well as strategies to address them.

Expanding limits of artificial enzymes: unprecedented catalysis by an oxidase nanozyme in activating a structural protein for covalent crosslinking and conferring remarkable proteolytic resistance

Nature has endowed us with some complex enzymes capable of utilizing proteins as their substrates to generate functional proteins through post-translational modification. However, nanozymes' interplay with proteins as substrates is scarce, with their chemistry predominantly established using only small molecule substrates, featuring a significant gap in this area. Due to the huge prospects of nanozymes in biotechnological and therapeutic interventions, studies establishing the unexplored roles of nanozymes in the biological environments and their interplay beyond small molecule substrates warrant immediate attention. In this study, we unveil the unprecedented role of a Mn-based oxidase nanozyme (MnN) in activating a structural protein, collagen, and covalently crosslinking its tyrosine residues with only a trace amount of tannic acid (TA) without compromising its triple-helical structural integrity. While therapeutic applications demand materials prepared from collagen, the current chemical and physical crosslinking of collagen often presents significant challenges such as toxicity, denaturation, or high costs. MnN lucidly accomplishes crosslinking interplay at its 101 facets using oxygen as a co-substrate under mild conditions. This process takes advantage of MnN being active at mild acidic pH where collagen preferentially exists as a soluble triple helix (monomeric form), exposing functionalities and enhancing the crosslinking degree. Importantly, this reaction also confers 100% resistance to collagenase attack on the collagen tendon-derived biological material. The catalyzed TA-tyrosine linkage in the telopeptide region of collagen probably impedes the initial recognition step of collagenase, providing robust protection against its degradative action. Our study not only expands the repertoire of nanozymes' substrates beyond the existing library of small molecules but also establishes a significant step toward designing a gold standard for collagen crosslinking. With biomedical applications demanding biomaterials derived from protein scaffolds with preserved structural integrity, our investigation bridges the gap between nanozymes' chemistry and crosslinking proteins, opening exciting prospects for biomaterial development.

Real-time single-molecule observation of incipient collagen fibrillogenesis and remodeling

The hierarchic assembly of fibrillar collagen into an extensive and ordered supramolecular protein fibril is critical for extracellular matrix function and tissue mechanics. Despite decades of study, we still know very little about the complex process of fibrillogenesis, particularly at the earliest stages where observation of rapidly forming, nanoscale intermediates challenges the spatial and temporal resolution of most existing microscopy methods. Using video rate scanning atomic force microscopy (VRS-AFM), we can observe details of the first few minutes of collagen fibril formation and growth on a mica surface in solution. A defining feature of fibrillar collagens is a 67-nm periodic banding along the fibril driven by the organized assembly of individual monomers over multiple length scales. VRS-AFM videos show the concurrent growth and maturation of small fibrils from an initial uniform height to structures that display the canonical banding within seconds. Fibrils grow in a primarily unidirectional manner, with frayed ends of the growing tip latching onto adjacent fibrils. We find that, even at extremely early time points, remodeling of growing fibrils proceeds through bird-caging intermediates and propose that these dynamics may provide a pathway to mature hierarchic assembly. VRS-AFM provides a unique glimpse into the early emergence of banding and pathways for remodeling of the supramolecular assembly of collagen during the inception of fibrillogenesis.

Heterogeneous Structure and Dynamics of Water in a Hydrated Collagen Microfibril

Collagen type I is well-known for its outstanding mechanical properties which it inherits from its hierarchical structure. Collagen type I fibrils may be viewed as a heterogeneous material made of protein, macromolecules (such as glycosaminoglycans and proteoglycans) and water. Water content modulates the properties of these fibrils. Yet, the properties of water and the fine interactions of water with the protein constituent of these heterofibrils have only received limited attention. Here, we propose to model collagen type I fibrils as a hydrated structure made of tropocollagen molecules assembled in a microfibril crystal. We perform large-scale all-atom molecular dynamics simulations of the hydration of collagen fibrils beyond the onset of disassembly. We found that the structural and dynamic properties of water vary strongly with the level of hydration of the microfibril. More importantly, we found that the properties vary spatially within the 67 nm D-spacing periodic structure. Alteration of the structural and dynamical properties of the collagen microfibril occur first in the gap region. Overall, we identify that the change in the role of water molecules from glue to lubricant between tropocollagen molecules arises around 100% hydration while the microfibril begins to disassemble beyond 130% water content. Our findings are supported by a decrease in hydrogen bonding, recovery of bulk water properties and amorphization of the tropocollagen molecules packing. Our simulations reveal the structure and dynamics of hydrated collagen fibrils with unprecedented spatial resolution from physiological conditions to disassembly. Beyond the process of self-assembly and the emergence of mechanical properties of collagen type I fibrils, our results may also provide new insights into mineralization of collagen fibrils.

Modeling collagen fibril degradation as a function of matrix microarchitecture

Collagenolytic degradation is a process fundamental to tissue remodeling. The microarchitecture of collagen fibril networks changes during development, aging, and disease. Such changes to microarchitecture are often accompanied by changes in matrix degradability. In vitro, collagen matrices of the same concentration but different microarchitectures also vary in degradation rate. How do different microarchitectures affect matrix degradation? To answer this question, we developed a computational model of collagen degradation. We first developed a lattice model that describes collagen degradation at the scale of a single fibril. We then extended this model to investigate the role of microarchitecture using Brownian dynamics simulation of enzymes in a multi-fibril three dimensional matrix to predict its degradability. Our simulations predict that the distribution of enzymes around the fibrils is non-uniform and depends on the microarchitecture of the matrix. This non-uniformity in enzyme distribution can lead to different extents of degradability for matrices of different microarchitectures. Our model predictions were tested using in vitro experiments with synthesized collagen gels of different microarchitectures. Experiments showed that indeed degradation of collagen depends on the matrix architecture and fibril thickness. In summary, our study shows that the microarchitecture of the collagen matrix is an important determinant of its degradability.

Texture maintenance and degradation mechanism of ice-stored grass carp (Ctenopharyngodon idella): A scope of intramuscular connective tissue

Although intramuscular connective tissue (IMCT) is low in fish, its impact on texture cannot be ignored due to its special location. Therefore, this study was aimed to investigate the contribution of IMCT degradation to fish softening and its mechanism induced by endogenous proteases. Results showed that IMCT honeycomb-like structure collapsed entirely on the 10th day of ice storage, along with a decrease of shear force by 36.5%. Meanwhile, IMCT and myofibrils (MF) degradation accelerated softening by 25.1% and 15.3% during 10 days of ice storage, respectively. Next, IMCT deterioration was indicated to be highly correlated with decorin degradation (0.956**), followed by elastin (0.928**) and collagen (0.904**). Ulteriorly, endogenous collagenase was shown to degrade IMCT crucial components, while endogenous cathepsins had little effect. In conclusion, this study confirmed that IMCT played an essential role in maintaining fish texture and was mainly degraded by endogenous collagenase.

Strain inhibition of bacterial collagenase is consistent with a collagen fibril uncrimping mechanism in rat tail tendons

Mechanical strain inhibits bacterial collagenase from cleaving collagen. Additionally, the toe region of a soft tissue's force-elongation curve arises from sequentially engaging collagen fibrils as the tissue lengthens. Together, these phenomena suggest that mechanical strain may gradually inhibit collagenase activity through a soft tissue's toe region. Therefore, this investigation sought to test this hypothesis. 92 rat tail tendon fascicles from 3 female sentinel animals underwent preliminary stiffness tests, and their force-elongation curves were fit to a collagen distribution model. This distribution-based model calculated the force magnitude corresponding to p% of collagen fibril engagement. Specimens were separated into one of five levels of p, and that level of force was maintained for two hours while being exposed to 0.054 U/mL of bacterial collagenase from C. histolyticum. The specimens were strained to failure following the creep test, and the relative reduction in stiffness was quantified to estimate the fraction of digested fibrils. Every 10% additional collagen engagement corresponded to a 6.3% (97% highest density interval: 4.3 - 8.4%) retention of stiffness, which indicated collagenase inhibition. The results of this investigation were consistent with a strain-inhibition hypothesis along with the established uncrimping mechanism in the toe region. These results support an interaction between mechanical strain and collagenolysis, which may be valuable for disease prevention or treatment.

A Fast, Robust Method for Quantitative Assessment of Collagen Fibril Architecture from Transmission Electron Micrographs

Collagen is the most abundant protein in mammals; it exhibits a hierarchical organization and provides structural support to a wide range of soft tissues, including blood vessels. The architecture of collagen fibrils dictates vascular stiffness and strength, and changes therein can contribute to disease progression. While transmission electron microscopy (TEM) is routinely used to examine collagen fibrils under normal and pathological conditions, computational tools that enable fast and minimally subjective quantitative assessment remain lacking. In the present study, we describe a novel semi-automated image processing and statistical modeling pipeline for segmenting individual collagen fibrils from TEM images and quantifying key metrics of interest, including fibril cross-sectional area and aspect ratio. For validation, we show first-of-their-kind illustrative results for adventitial collagen in the thoracic aorta from three different mouse models.

Mmp14 is required for matrisome homeostasis and circadian rhythm in fibroblasts

The circadian clock in tendon regulates the daily rhythmic synthesis of collagen-I and the appearance and disappearance of small-diameter collagen fibrils in the extracellular matrix. How the fibrils are assembled and removed is not fully understood. Here, we first showed that the collagenase, membrane type I-matrix metalloproteinase (MT1-MMP, encoded by Mmp14), is regulated by the circadian clock in postnatal mouse tendon. Next, we generated tamoxifen-induced Col1a2-Cre-ERT2::Mmp14 KO mice (Mmp14 conditional knockout (CKO)). The CKO mice developed hind limb dorsiflexion and thickened tendons, which accumulated narrow-diameter collagen fibrils causing ultrastructural disorganization. Mass spectrometry of control tendons identified 1195 proteins of which 212 showed time-dependent abundance. In Mmp14 CKO mice 19 proteins had reversed temporal abundance and 176 proteins lost time dependency. Among these, the collagen crosslinking enzymes lysyl oxidase-like 1 (LOXL1) and lysyl hydroxylase 1 (LH1; encoded by Plod2) were elevated and had lost time-dependent regulation. High-pressure chromatography confirmed elevated levels of hydroxylysine aldehyde (pyridinoline) crosslinking of collagen in CKO tendons. As a result, collagen-I was refractory to extraction. We also showed that CRISPR-Cas9 deletion of Mmp14 from cultured fibroblasts resulted in loss of circadian clock rhythmicity of period 2 (PER2), and recombinant MT1-MMP was highly effective at cleaving soluble collagen-I but less effective at cleaving collagen pre-assembled into fibrils. In conclusion, our study shows that circadian clock-regulated Mmp14 controls the rhythmic synthesis of small diameter collagen fibrils, regulates collagen crosslinking, and its absence disrupts the circadian clock and matrisome in tendon fibroblasts.

Biomimetic human skin model patterned with rete ridges

Rete ridges consist of undulations between the epidermis and dermis that enhance the mechanical properties and biological function of human skin. However, most human skin models are fabricated with a flat interface between the epidermal and dermal layers. Here, we report a micro-stamping method for producing human skin models patterned with rete ridges of controlled geometry. To mitigate keratinocyte-induced matrix degradation, telocollagen-fibrin matrices with and without crosslinks enable these micropatterned features to persist during longitudinal culture. Our human skin model exhibits an epidermis that includes the following markers: cytokeratin 14, p63, and Ki67 in the basal layer, cytokeratin 10 in the suprabasal layer, and laminin and collagen IV in the basement membrane. We demonstrated that two keratinocyte cell lines, one from a neonatal donor and another from an adult diabetic donor, are compatible with this model. We tested this model using an irritation test and showed that the epidermis prevents rapid penetration of sodium dodecyl sulfate. Gene expression analysis revealed differences in keratinocytes obtained from the two donors as well as between 2D (control) and 3D culture conditions. Our human skin model may find potential application for drug and cosmetic testing, disease and wound healing modeling, and aging studies.

Tissue Biology: In Search of a New Paradigm

Animal tissues are made up of multiple cell types that are increasingly well-characterized, yet our understanding of the core principles that govern tissue organization is still incomplete. This is in part because many observable tissue characteristics, such as cellular composition and spatial patterns, are emergent properties, and as such, they cannot be explained through the knowledge of individual cells alone. Here we propose a complex systems theory perspective to address this fundamental gap in our understanding of tissue biology. We introduce the concept of cell categories, which is based on cell relations rather than cell identity. Based on these notions we then discuss common principles of tissue modularity, introducing compositional, structural, and functional tissue modules. Cell diversity and cell relations provide a basis for a new perspective on the underlying principles of tissue organization in health and disease.

Effect of Different Crosslinkers on Denatured Dentin Collagen's Biostability, MMP Inhibition and Mechanical Properties

OBJECTIVE

Sound, natural dentin collagen can be stabilized against enzymatic degradation through exogenous crosslinking treatment for durable bonding; however, the effect on denatured dentin (DD) collagen is unknown. Hence, the ability of different crosslinkers to enhance/restore the properties of DD collagen was assessed.

METHODS

Demineralized natural and DD collagen films (7 mm × 7 mm × 7 µm) and beams (0.8 mm × 0.8 mm × 7 mm) were prepared. DD collagen was experimentally produced by heat or acid exposure, which was then assessed by various techniques. All specimens were then treated with 1 wt% of chemical crosslinker 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/n-hydroxysuccinimide (EDC/NHS) and two structurally different flavonoids-theaflavins (TF) from black tea and type-A proanthocyanidins from cranberry juice (CR) for either 30 s or 1 h. The controls were untreated. Dentin films were assessed for chemical interaction and cross-linking effect by FTIR, biostability against exogenous collagenase by weight loss (WL) and hydroxyproline release (HYP), and endogenous matrix metalloproteinases (MMPs) activity by confocal laser microscopy. Dentin beams were evaluated for tensile properties. Data were analyzed using ANOVA and Tukey's test (α = 0.05).

RESULTS

Compared with natural collagen, DD collagen showed pronounced structural changes, altered biostability and decreased mechanical properties, which were then improved to various degrees that were dependent on the crosslinkers used, with EDC/NHS being the least effective. Surprisingly, the well-known MMP inhibitor EDC/NHS showed negligible effect on or even increased MMP activity in DD collagen. As compared with control, cross-linking induced by TF and CR significantly increased collagen biostability (reduced WL and HYP release, p < 0.05), MMP inhibition (p < 0.001) and mechanical properties (p < 0.05), regardless of denaturation.

CONCLUSIONS

DD collagen cannot or can only minimally be stabilized via EDC/NHS crosslinking; however, the challenging substrate of DD collagen can be enhanced or restored using the promising flavonoids TF and CR.

Influence of Phosphoric, Glycolic, and Ferulic Acids on Dentin Enzymatic Degradation, Ultimate Tensile Strength, and Permeability

This study evaluated dentin enzymatic degradation based on the total matrix metalloproteinase (MMP) activity of demineralized dentin matrices before and after exposure to phosphoric acid (PA), glycolic acid (GA), and ferulic acid (FA). The release of hydroxyproline (HP), ultimate tensile strength (UTS), and dentin permeability (DP) were also evaluated. Dentin collagen matrices were assessed according to total MMP activity before and after treatment with the tested acids (n=10) for 15 seconds and compared with the control (GM6001 inhibitor). Dentin beams were analyzed for HP release and UTS after the treatments. Dentin discs were tested for DP at a pressure of 5 psi before and after treatment with the acids (n=10). The FA group had a lower percentage of enzymatic inhibition than the PA and GA groups (p<0.0001). No significant difference in UTS was found among the acids (p=0.6824), but HP release was significantly higher in the FA group than in the PA and GA groups (p<0.0001). No significant difference in DP was found for the acids (p=0.0535). GA led to less activation of MMPs and less release of HP, whereas the UTS and DP for GA were like those found for PA. In contrast, FA promoted greater enzymatic activity and greater release of HP, while having similar results to GA and PA regarding mechanical properties.

Single collagen fibrils isolated from high stress and low stress tendons show differing susceptibility to enzymatic degradation by the interstitial collagenase matrix metalloproteinase-1 (MMP-1)

Bovine forelimb flexor and extensor tendons serve as a model for examining high stress, energy storing and low stress, positional tendons, respectively. Previous research has shown structural differences between the collagen fibrils of these tissues. The nanoscale collagen fibrils of flexor tendons are smaller in size, more heavily crosslinked, and respond differently to mechanical loading. Meanwhile, energy storing tendons undergo less collagen turnover compared to positional tendons and are more commonly injured. These observations raise the question of whether collagen fibril structure influences the collagen degradation processes necessary for remodelling. Atomic force microscopy was used to image dry collagen fibrils before and after 5-hour exposure to matrix metalloproteinase-1 (MMP-1) to detect changes in fibril size. Collagen fibrils from three tissue types were studied: bovine superficial digital flexor tendons, matched-pair bovine lateral digital extensor tendons, and rat tail tendons. Compared to control fibrils exposed only to buffer, a significant decrease in fibril cross-sectional area (CSA) following MMP-1 exposure was observed for bovine extensor and rat tail fibrils, with larger fibrils experiencing a greater magnitude of CSA decrease in both fibril types. Fibrils from bovine flexor tendons, on the other hand, showed no decrease in CSA when exposed to MMP-1. The result did not appear to be linked to the small size of flexor fibrils, as equivalently sized extensor fibrils were readily degraded by the enzyme. Increased proteolytic resistance of collagen fibrils from high stress tendons may help to explain the longevity of collagen within these tissues in vivo.

Unraveling the interaction of bisphenol A with collagen and its effect on conformational and thermal stability

Evidence suggests the association of bisphenol A (BPA) with increased collagen (COL) expression in the development of fibrosis. Ultraviolet and fluorescence spectra on collagen-BPA interaction showed that 100 ng/ml of BPA initiated loosening of protein backbone through unfolding with exposure of tyrosine residues resulting in an intermediate "Molten Globule" state, which later aggregated with 1 μg/ml of BPA indicated with an apparent red-shift. Conformational changes with CD and ATR-FTIR showed disappearance of negative band with broadening and shifting of peptide carbonyl groups. Light scattering findings with TEM images presented initial dissolution followed by unordered thick fibrillar bundles with 30 μg/ml BPA. The complex was pH sensitive, with calorimetric thermogram revealing increased thermal stability requiring 83°C to denature. Hydrogen bonds of 2.8 Å with hydrophobic interactions of BPA in all grooves of collagen molecule with same pattern and binding energy (-4.1 to -3.9 kcal/mol) confirmed the intensity of aggregate formation via in-silico docking.

Effects of Riboflavin Collagen Crosslinker on Dentin Adhesive Bonding Efficiency: A Systematic Review and Meta-Analysis

The aim of this study was to evaluate published data regarding riboflavin (RF) as a cross-linker for improved adhesive bond strength to dentin and to analyze previous studies for optimal concentration of riboflavin range suitable for dentin bond. Saliva and distilled water were used as storage media and aging time was 24 h and 6 months. Results of meta-analysis were synthesized using a statistical method of inverse variance in random effects with a 95% Confidence Interval (CI). Cochrane review manager 5.4.1 was used to determine results of the meta-analysis. In total, 3172 articles were found from search databases "PubMed", "Scopus", and "Google Scholar". Six of the fifteen studies were eligible for meta-analysis. Micro tensile strength shows significant improvement with the addition of riboflavin (p < 0.05) compared to without the addition of riboflavin from with 95% CI. A significant difference has been found in micro tensile bond strength between use of the riboflavin cross-linker and without use of the riboflavin crosslinker in the dentin adhesive system. With a 95% confidence interval (CI), the I² for micro tensile strength was 89% with strong heterogeneity, Chi² = 44.76, df = 5 (p < 0.00001), and overall effect size is Z = 2.22 (p = 0.03) after immediate aging. Chiang et al. 2013 shows maximum mean differences which is 38.50 [17.93-59.07]. After 6 months of aging in distilled water or artificial saliva micro tensile bond strength has been increased with the addition of riboflavin (p < 0.05). It can be clearly seen that pooled effect and 95% CI did not cross the line of no effect. With a 95% confidence interval (CI), the I² for micro tensile strength was 96% with strong heterogeneity, Chi² = 117.56, df = 5 (p < 0.00001), and overall effect size is Z = 2.30 (p = 0.02). Subgroup analysis proved a similar effect of distilled water and artificial saliva as storage media on micro tensile bond strength after incorporating riboflavin as a collagen crosslinker. An artificial saliva aged forest plot also showed considerable heterogeneity with I² = 96%; Tau² = 257.32; Chi² = 94.37; df = 2 (p < 0.00001); test for overall effect, Z = 1.06 (p = 0.29). Riboflavin prior to or with bonding is recommended to improve the bonding of different adhesive systems.

A fast, robust method for quantitative assessment of collagen fibril architecture from transmission electron micrographs

Collagen is the most abundant protein in mammals; it exhibits a hierarchical organization and provides structural support to a wide range of soft tissues, including blood vessels. The architecture of collagen fibrils dictates vascular stiffness and strength, and changes therein can contribute to disease progression. While transmission electron microscopy (TEM) is routinely used to examine collagen fibrils under normal and pathological conditions, computational tools that enable fast and minimally subjective quantitative assessment remain lacking. In the present study, we describe a novel semi-automated image processing and statistical modeling pipeline for segmenting individual collagen fibrils from TEM images and quantifying key metrics of interest, including fibril cross-sectional area and aspect ratio. For validation, we show illustrative results for adventitial collagen in the thoracic aorta from three different mouse models.

Proteomic Analysis of Decellularized Extracellular Matrix: Achieving a Competent Biomaterial for Osteogenesis

Decellularized ECMs have been used as biological scaffolds for tissue repair due to their tissue-specific biochemical and mechanical composition, poorly simulated by other materials. It is used as patches and powders, and it could be further processed via enzymatic digestion under acidic conditions using pepsin. However, part of the bioactivity is lost during the digestion process due to protein denaturation. Here, stepwise digestion was developed to prepare a competent biomaterial for osteogenesis from three different ECM sources. In addition, three different proteases were compared to evaluate the most effective digestion protocol for specific cellular processes. GAGs and peptide quantification showed that the stepwise method yielded a higher concentration of bioactive residues. Circular dichroism analysis also showed that the stepwise approach preserved the secondary structures better. The protein profiles of the digested ECMs were analyzed, and it was found to be highly diverse and tissue-specific. The digestion of ECM from pericardium produced peptides originated from 94 different proteins, followed by 48 proteins in ECM from tendon and 35 proteins in ECM from bone. In addition, digested products from pericardium ECM yielded increased proliferation and differentiation of bone marrow mesenchymal stem cells to mature osteoblasts.

Obesity induces adipose fibrosis and collagen cross-linking through suppressing AMPK and enhancing lysyl oxidase expression

Collagen is the main component of connective tissue surrounding adipocytes. Collagen cross-linking affects adipose remodeling, which is crucial for maintaining function and metabolic homeostasis of adipose tissue. However, the effects of obesity on collagen cross-linking and adipose fibrosis remain to be examined. Therefore, the objective of this study was to investigate obesity-induced collagen cross-linking in adipose tissue and explore the underlying mechanisms. We found that obesity increased mature nonreducible collagen cross-linking in white adipose tissue (WAT) of mice, which was associated with inhibition of AMPK, up-regulation of transforming growth factor-β (TGF-β) signaling and the expression of lysyl oxidase (LOX), a key enzyme catalyzing the synthesis of mature cross-linking products. In SVCs and 3T3-L1 adipocytes, AMPK activation by metformin or AICAR inhibited TGF-β1-induced fibrogenesis and expression of LOX, which was further confirmed by ectopic expression of AMPK WT and K45R mutant. Consistently, in vivo, knocking out AMPK increased fibrosis and collagen cross-linking. Our study showed that AMPK downregulation due to obesity increases TGF-β signaling and LOX expression, which enhances adipose fibrosis and collagen cross-linking. Thus, AMPK is a therapeutic target for ameliorating the obesity-induced fibrosis, improving metabolic health of adipose tissue.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Role of Natural Cross Linkers in Resin-Dentin Bond Durability: A Systematic Review and Meta-Analysis

BACKGROUND

The role of endogenous Matrix Metallo Proteinases in resin dentin bond deterioration over time has been well documented. The present study aimed to systematically review the literature; in vitro and ex vivo studies that assessed the outcomes of natural cross-linkers for immediate and long-term tensile bond strength were included.

METHODS

The manuscript search was carried out in six electronic databases-PubMed/MEDLINE, LILACS, SciELO, Cochrane, Web of Science and DOAJ, without publication year limits. Only manuscripts in English (including the translated articles) were selected, and the last search was performed in December 2020. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement was followed.

RESULTS

From the 128 potentially eligible studies, 48 full-text articles were assessed for eligibility. After eligibility assessment and exclusions, 14 studies were considered for systematic review and seven studies for meta-analysis. Amongst the selected studies for meta-analysis, three had a medium and four had a low risk of bias.

CONCLUSIONS

It was evidenced by the available data that Proanthocyanidin is the most efficient natural cross-linker to date, in preserving the bond strength even after ageing.

Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey

Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.

Regulation and Function of Matrix Metalloproteinase-13 in Cancer Progression and Metastasis

Matrix metalloproteinase-13 (MMP-13) is a member of the Matrix metalloproteinases (MMPs) family of endopeptidases. MMP-13 is produced in low amounts and is well-regulated during normal physiological conditions. Its expression and secretion are, however, increased in various cancers, where it plays multiple roles in tumour progression and metastasis. As an interstitial collagenase, MMP-13 can proteolytically cleave not only collagens I, II and III, but also a range of extracellular matrix proteins (ECMs). Its action causes ECM remodelling and often leads to the release of various sequestered growth and angiogenetic factors that promote tumour cell growth, invasion and angiogenesis. This review summarizes our current understanding of the regulation of MMP-13 expression and secretion and discusses the actions of MMP-13 in cancer progression and metastasis.

The articular cartilage surface is impaired by a loss of thick collagen fibers and formation of type I collagen in early osteoarthritis

Osteoarthritis (OA) is a joint disease affecting millions of patients worldwide. During OA onset and progression, the articular cartilage is destroyed, but the underlying complex mechanisms remain unclear. Here, we uncover changes in the thickness of collagen fibers and their composition at the onset of OA. For articular cartilage explants from knee joints of OA patients, we find that type I collagen-rich fibrocartilage-like tissue was formed in macroscopically intact cartilage, distant from OA lesions. Importantly, the number of thick fibers (>100 nm) has decreased early in the disease, followed by complete absence of thick fibers in advanced OA. We have obtained these results by a combination of high-resolution atomic force microscopy imaging under near-native conditions, immunofluorescence, scanning electron microscopy and a fluorescence-based classification of the superficial chondrocyte spatial organization. Taken together, our data suggests that the loss of tissue functionality in early OA cartilage is caused by a reduction of thick type II collagen fibers, likely due to the formation of type I collagen-rich fibrocartilage, followed by the development of focal defects in later OA stages. We anticipate that such an integrative characterization will be very beneficial for an in-depth understanding of other native biological tissues and the development of sustainable biomaterials. STATEMENT OF SIGNIFICANCE: In early osteoarthritis (OA) the cartilage appears macroscopically intact. However, this study demonstrates that the collagen network already changes in early OA by collagen fiber thinning and the formation of fibrocartilage-like tissue. Both nanoscopic deficiencies already occur in macroscopically intact regions of the human knee joint and are likely connected to processes that result in a weakened extracellular matrix. This study enhances the understanding of earliest progressive cartilage degeneration in the absence of external damage. The results suggest a determination of the mean collagen fiber thickness as a new target for the detection of early OA and a regulation of type I collagen synthesis as a new path for OA treatment.

Mussel-inspired monomer - A new selective protease inhibitor against dentine collagen degradation

OBJECTIVES

To evaluate the inhibitory effect of a novel mussel-inspired monomer (N-(3,4-dihydroxyphenethyl)methacrylamide (DMA) on the soluble and matrix-bound proteases.

METHODS

The inhibitory effect of DMA (0, 1, 5, and 10 mM) and 1 mM chlorhexidine (CHX) dissolved in 50% ethanol/water on soluble recombinant human matrix metalloproteinases (rhMMP-2, -8, and -9), as well as cysteine cathepsins (B and K) were evaluated using both fluorometric assay kits and molecular docking. The effect of CHX and DMA on matrix-bound proteases was examined by in situ zymography, and the fluorescence intensity and relative area were calculated by Image J software. All data obtained were analyzed by one-way ANOVA followed by Tukey test (α = 0.05).

RESULTS

The anti-proteolytic ability of DMA increased in a dose-dependent manner except that of rhMMP-9. Inhibitory effect of 1 mM DMA against rhMMP-2, - 8, - 9, as well as cathepsin B and K was all significantly lower than 1 mM CHX (p < 0.05). The molecular docking analysis was in good agreement with the experimental results, that the binding energy of DMA was lower than CHX for all proteases. In situ zymography revealed that all DMA- and CHX-treated groups significantly inactivated the matrix-bound proteases, with a dramatic reduction of the fluorescence intensity and relative area compared with the control group (p < 0.05).

SIGNIFICANCE

Under the prerequisite condition that the overall inhibitory performance on matrix-bound proteases was comparable by DMA and CHX, the more selective property of DMA could avoid inducing potential negative effects by suppressing MMP-9 when applied in dental treatment compared with CHX.

A primer for ZooMS applications in archaeology

Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited.

Prokaryotic Collagen-Like Proteins as Novel Biomaterials

Collagens are the major structural component in animal extracellular matrices and are critical signaling molecules in various cell-matrix interactions. Its unique triple helical structure is enabled by tripeptide Gly-X-Y repeats. Understanding of sequence requirements for animal-derived collagen led to the discovery of prokaryotic collagen-like protein in the early 2000s. These prokaryotic collagen-like proteins are structurally similar to mammalian collagens in many ways. However, unlike the challenges associated with recombinant expression of mammalian collagens, these prokaryotic collagen-like proteins can be readily expressed in E. coli and are amenable to genetic modification. In this review article, we will first discuss the properties of mammalian collagen and provide a comparative analysis of mammalian collagen and prokaryotic collagen-like proteins. We will then review the use of prokaryotic collagen-like proteins to both study the biology of conventional collagen and develop a new biomaterial platform. Finally, we will describe the application of Scl2 protein, a streptococcal collagen-like protein, in thromboresistant coating for cardiovascular devices, scaffolds for bone regeneration, chronic wound dressing and matrices for cartilage regeneration.

Mechanistic Insight into the Fragmentation of Type I Collagen Fibers into Peptides and Amino Acids by a Vibrio Collagenase

Vibrio collagenases of the M9A subfamily are closely related to Vibrio pathogenesis for their role in collagen degradation during host invasion. Although some Vibrio collagenases have been characterized, the collagen degradation mechanism of Vibrio collagenase is still largely unknown. Here, an M9A collagenase, VP397, from marine Vibrio pomeroyi strain 12613 was characterized, and its fragmentation pattern on insoluble type I collagen fibers was studied. VP397 is a typical Vibrio collagenase composed of a catalytic module featuring a peptidase M9N domain and a peptidase M9 domain and two accessory bacterial prepeptidase C-terminal domains (PPC domains). It can hydrolyze various collagenous substrates, including fish collagen, mammalian collagens of types I to V, triple-helical peptide [(POG)₁₀]₃, gelatin, and 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-o-Arg (Pz-peptide). Atomic force microscopy (AFM) observation and biochemical analyses revealed that VP397 first assaults the C-telopeptide region to dismantle the compact structure of collagen and dissociate tropocollagen fragments, which are further digested into peptides and amino acids by VP397 mainly at the Y-Gly bonds in the repeating Gly-X-Y triplets. In addition, domain deletion mutagenesis showed that the catalytic module of VP397 alone is capable of hydrolyzing type I collagen fibers and that its C-terminal PPC2 domain functions as a collagen-binding domain during collagenolysis. Based on our results, a model for the collagenolytic mechanism of VP397 is proposed. This study sheds light on the mechanism of collagen degradation by Vibrio collagenase, offering a better understanding of the pathogenesis of Vibrio and helping in developing the potential applications of Vibrio collagenase in industrial and medical areas. IMPORTANCE Many Vibrio species are pathogens and cause serious diseases in humans and aquatic animals. The collagenases produced by pathogenic Vibrio species have been regarded as important virulence factors, which occasionally exhibit direct pathogenicity to the infected host or facilitate other toxins' diffusion through the digestion of host collagen. However, our knowledge concerning the collagen degradation mechanism of Vibrio collagenase is still limited. This study reveals the degradation strategy of Vibrio collagenase VP397 on type I collagen. VP397 binds on collagen fibrils via its C-terminal PPC2 domain, and its catalytic module first assaults the C-telopeptide region and then attacks the Y-Gly bonds in the dissociated tropocollagen fragments to release peptides and amino acids. This study offers new knowledge regarding the collagenolytic mechanism of Vibrio collagenase, which is helpful for better understanding the role of collagenase in Vibrio pathogenesis and for developing its industrial and medical applications.

Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis

The collagenases of Vibrio species, many of which are pathogens, have been regarded as an important virulence factor. However, there is little information on the structure and collagenolytic mechanism of Vibrio collagenase. Here, we report the crystal structure of the collagenase module (CM) of Vibrio collagenase VhaC and the conformation of VhaC in solution. Structural and biochemical analyses and molecular dynamics studies reveal that triple-helical collagen is initially recognized by the activator domain, followed by subsequent cleavage by the peptidase domain along with the closing movement of CM. This is different from the peptidolytic mode or the proposed collagenolysis of Clostridium collagenase. We propose a model for the integrated collagenolytic mechanism of VhaC, integrating the functions of VhaC accessory domains and its collagen degradation pattern. This study provides insight into the mechanism of bacterial collagenolysis and helps in structure-based drug design targeting of the Vibrio collagenase.

The collagenolytic mechanism of Vibrio collagenase, a virulence factor, remains unclear. Here, the authors report the structure of Vibrio collagenase VhaC and propose the mechanism for collagen recognition and degradation, providing new insight into bacterial collagenolysis.

Directing Cholangiocyte Morphogenesis in Natural Biomaterial Scaffolds

Patients with Alagille syndrome carry monogenic mutations in the Notch signaling pathway and face complications such as jaundice and cholestasis. Given the presence of intrahepatic ductopenia in these patients, Notch2 receptor signaling is implicated in driving normal biliary development and downstream branching morphogenesis. As a result, in vitro model systems of liver epithelium are needed to further mechanistic insight of biliary tissue assembly. Here, primary human intrahepatic cholangiocytes as a candidate population for such a platform are systematically evaluated, and conditions that direct their branching morphogenesis are described. It is found that extracellular matrix presentation, coupled with mitogen stimulation, promotes biliary branching in a Notch-dependent manner. These results demonstrate the utility of using 3D scaffolds for mechanistic investigation of cholangiocyte branching and provide a gateway to integrate biliary architecture in additional in vitro models of liver tissue.

Collagen crosslinking: effect on structure, mechanics and fibrosis progression

Biophysical properties of extracellular matrix (ECM), such as matrix stiffness, viscoelasticity and matrix fibrous structure, are emerging as important factors that regulate progression of fibrosis and other chronic diseases. The biophysical properties of the ECM can be rapidly and profoundly regulated by crosslinking reactions in enzymatic or non-enzymatic manners, which further alter the cellular responses and drive disease progression. In-depth understandings of crosslinking reactions will be helpful to reveal the underlying mechanisms of fibrosis progression and put forward new therapeutic targets, whereas related reviews are still devoid. Here, we focus on the main crosslinking mechanisms that commonly exist in a plethora of chronic diseases (e.g. fibrosis, cancer, osteoarthritis) and summarize current understandings including the biochemical reaction, the effect on ECM properties, the influence on cellular behaviors, and related studies in disease model establishment. Potential pharmaceutical interventions targeting the crosslinking process and relevant clinical studies are also introduced. Limitations of pharmaceutical development may be due to the lack of systemic investigations related to the influence on crosslinking mechanism from micro to macro level, which are discussed in the last section. We also propose the unclarified questions regarding crosslinking mechanisms and potential challenges in crosslinking-targeted therapeutics development.

Bioinformatics analysis identified MMP14 and COL12A1 as immune-related biomarkers associated with pancreatic adenocarcinoma prognosis

BACKGROUND

Pancreatic adenocarcinoma (PAAD) is one of the most common malignant tumors with high mortality rates and a poor prognosis. There is an urgent need to determine the molecular mechanism of PAAD tumorigenesis and identify promising biomarkers for the diagnosis and targeted therapy of the disease.

METHODS

Three GEO datasets (GSE62165, GSE15471 and GSE62452) were analyzed to obtain differentially expressed genes (DEGs). The PPI networks and hub genes were identified through the STRING database and MCODE plugin in Cytoscape software. GO and KEGG enrichment pathways were analyzed by the DAVID database. The GEPIA database was utilized to estimate the prognostic value of hub genes. Furthermore, the roles of MMP14 and COL12A1 in immune infiltration and tumor-immune interaction and their biological functions in PAAD were explored by TIMER, TISIDB, GeneMANIA, Metascape and GSEA.

RESULTS

A total of 209 common DEGs in the three datasets were obtained. GO function analysis showed that the 209 DEGs were significantly enriched in calcium ion binding, serine-type endopeptidase activity, integrin binding, extracellular matrix structural constituent and collagen binding. KEGG pathway analysis showed that DEGs were mainly enriched in focal adhesion, protein digestion and absorption and ECM-receptor interaction. The 14 genes with the highest degree of connectivity were defined as the hub genes of PAAD development. GEPIA revealed that PAAD patients with upregulated MMP14 and COL12A1 expression had poor prognoses. In addition, TIMER analysis revealed that MMP14 and COL12A1 were closely associated with the infiltration levels of macrophages, neutrophils and dendritic cells in PAAD. TISIDB revealed that MMP14 was strongly positively correlated with CD276, TNFSF4, CD70 and TNFSF9, while COL12A1 was strongly positively correlated with TNFSF4, CD276, ENTPD1 and CD70. GSEA revealed that MMP14 and COL12A1 were significantly enriched in epithelial mesenchymal transition, extracellular matrix receptor interaction, apical junction, and focal adhesion in PAAD development.

CONCLUSIONS

Our study revealed that overexpression of MMP14 and COL12A1 is significantly correlated with PAAD patient poor prognosis. MMP14 and COL12A1 participate in regulating tumor immune interactions and might become promising biomarkers for PAAD.

Targeting mechanosensitive MDM4 promotes lung fibrosis resolution in aged mice

Aging is a strong risk factor and an independent prognostic factor for progressive human idiopathic pulmonary fibrosis (IPF). Aged mice develop nonresolving pulmonary fibrosis following lung injury. In this study, we found that mouse double minute 4 homolog (MDM4) is highly expressed in the fibrotic lesions of human IPF and experimental pulmonary fibrosis in aged mice. We identified MDM4 as a matrix stiffness-regulated endogenous inhibitor of p53. Reducing matrix stiffness down-regulates MDM4 expression, resulting in p53 activation in primary lung myofibroblasts isolated from IPF patients. Gain of p53 function activates a gene program that sensitizes lung myofibroblasts to apoptosis and promotes the clearance of apoptotic myofibroblasts by macrophages. Destiffening of the fibrotic lung matrix by targeting nonenzymatic cross-linking or genetic ablation of Mdm4 in lung (myo)fibroblasts activates the Mdm4-p53 pathway and promotes lung fibrosis resolution in aged mice. These findings suggest that mechanosensitive MDM4 is a molecular target with promising therapeutic potential against persistent lung fibrosis associated with aging.

Prostaglandin F2α agonists induced enhancement in collagen1 expression is involved in the pathogenesis of the deepening of upper eyelid sulcus

Previous our study reported that three-dimension (3D) cultures of human orbital fibroblasts (HOFs) replicated the etiology of deepening of the upper eyelid sulcus (DUES) caused by prostaglandin F2α analogues (PGF2α-ags). To examine this further, the effects of PGF2α-ags on HOFs were characterized by (1) lipid staining (2D; two-dimension, 3D), (2) comparison of the 3D organoid sizes of preadipocytes (DIF-) or adipocytes (DIF+) that had been treated with various concentrations of several PGF2α-ags, (3) physical stiffness (3D), and (4) the mRNA expression of adipogenic related genes, extracellular matrix (ECM), tissue inhibitors of metalloproteinases (TIMPs) and matrix metalloproteinases (MMPs) (3D). PGF2α-ags caused a dramatic down-sizing of the 3D DIF+ organoids and this reduction was concentration dependent. The effects caused by PGF2α-ags were also observed in 3D preadipocytes. Micro-squeezer analysis clearly indicated that PGF2α-ags induced an increase in their physical solidity. The size of each organoid under several conditions was inversely correlated with the mRNA expression profile of collagen1 (COL1), TIMP2, and MMP2 and 9. These findings indicate that PGF2α-ags affect the expression of COL1, TIMP2, and MMP2 and 9 which, in turn, modulate the 3D ECM network within the organoids, thus resulting in their downsizing.

Collagen biology making inroads into prognosis and treatment of cancer progression and metastasis

Progression through dissemination to tumor-surrounding tissues and metastasis development is a hallmark of cancer that requires continuous cell-to-cell interactions and tissue remodeling. In fact, metastization can be regarded as a tissue disease orchestrated by cancer cells, leading to neoplastic colonization of new organs. Collagen is a major component of the extracellular matrix (ECM), and increasing evidence suggests that it has an important role in cancer progression and metastasis. Desmoplasia and collagen biomarkers have been associated with relapse and death in cancer patients. Despite the increasing interest in ECM and in the desmoplastic process in tumor microenvironment as prognostic factors and therapeutic targets in cancer, further research is required for a better understanding of these aspects of cancer biology. In this review, published evidence correlating collagen with cancer prognosis is retrieved and analyzed, and the role of collagen and its fragments in cancer pathophysiology is discussed.

Collagen Mimetic Peptides

Since their first synthesis in the late 1960s, collagen mimetic peptides (CMPs) have been used as a molecular tool to study collagen, and as an approach to develop novel collagen mimetic biomaterials. Collagen, a major extracellular matrix (ECM) protein, plays vital roles in many physiological and pathogenic processes. Applications of CMPs have advanced our understanding of the structure and molecular properties of a collagen triple helix-the building block of collagen-and the interactions of collagen with important molecular ligands. The accumulating knowledge is also paving the way for developing novel CMPs for biomedical applications. Indeed, for the past 50 years, CMP research has been a fast-growing, far-reaching interdisciplinary field. The major development and achievement of CMPs were documented in a few detailed reviews around 2010. Here, we provided a brief overview of what we have learned about CMPs-their potential and their limitations. We focused on more recent developments in producing heterotrimeric CMPs, and CMPs that can form collagen-like higher order molecular assemblies. We also expanded the traditional view of CMPs to include larger designed peptides produced using recombinant systems. Studies using recombinant peptides have provided new insights on collagens and promoted progress in the development of collagen mimetic fibrillar self-assemblies.

Prostaglandin F2α Agonists Negatively Modulate the Size of 3D Organoids from Primary Human Orbital Fibroblasts

Purpose

To elucidate the molecular etiology of deepening of the upper eyelid sulcus (DUES) induced by prostaglandin (PG) analogs, a three-dimensional (3D) tissue culture system was employed using human orbital fibroblasts (HOFs).

Methods

During adipogenesis, changes in HOF 3D organoid sizes, as well as their lipids stained by BODIPY and expression of the extracellular matrix (ECM) by immunolabeling and/or quantitative PCR, were studied in the presence or absence of either 100-nM bimatoprost acid or 100-nM prostaglandin F2α.

Results

The size of the 3D organoids increased remarkably during adipogenesis, but such increases were significantly inhibited by the presence of PG analogs. Staining intensities by BODIPY and mRNA expression of peroxisome proliferator-activated receptor gamma were significantly increased upon adipogenesis but were not influenced by the presence of PG analogs. Unique changes in ECM expression observed with or without adipogenic differentiation were significantly modified by the presence of PG analogs.

Conclusions

Our present study indicates that PG analogs have the potential to modulate the ECM network within HOF 3D organoids. Thus, a 3D tissue culture system may be a suitable strategy for understanding the disease etiology of DUES.