New methods to study the composition and structure of the extracellular matrix in natural and bioengineered tissues

Resolving Atomic-Level Dynamics and Interactions of High-Molecular-Weight Hyaluronic Acid by Multidimensional Solid-State NMR

High-molecular-weight (HMW) hyaluronic acid (HA) is a highly abundant natural polysaccharide and a fundamental component of the extracellular matrix (ECM). Its size and concentration regulate tissues' macro- and microenvironments, and its upregulation is a hallmark feature of certain tumors. Yet, the conformational dynamics of HMW-HA and how it engages with the components of the ECM microenvironment remain poorly understood at the molecular level. Probing the molecular structure and dynamics of HMW polysaccharides in a hydrated, physiological-like environment is crucial and also technically challenging. Here, we deploy advanced magic-angle spinning (MAS) solid-state NMR spectroscopy in combination with isotopic enrichment to enable an in-depth study of HMW-HA to address this challenge. This approach resolves multiple coexisting HA conformations and dynamics as a function of environmental conditions. By combining 13C-labeled HA with unlabeled ECM components, we detect by MAS NMR HA-specific changes in global and local conformational dynamics as a consequence of hydration and ECM interactions. These measurements reveal atom-specific variations in the dynamics and structure of the N-acetylglucosamine moiety of HA. We discuss possible implications for interactions that stabilize the structure of HMW-HA and facilitate its recognition by HA-binding proteins. The described methods apply similarly to the studies of the molecular structure and dynamics of HA in tumor contexts and in other biological tissues as well as HMW-HA hydrogels and nanoparticles used for biomedical and/or pharmaceutical applications.

Unveiling extracellular matrix assembly: Insights and approaches through bioorthogonal chemistry

Visualizing cells, tissues, and their components specifically without interference with cellular functions, such as biochemical reactions, and cellular viability remains important for biomedical researchers worldwide. For an improved understanding of disease progression, tissue formation during development, and tissue regeneration, labeling extracellular matrix (ECM) components secreted by cells persists is required. Bioorthogonal chemistry approaches offer solutions to visualizing and labeling ECM constituents without interfering with other chemical or biological events. Although biorthogonal chemistry has been studied extensively for several applications, this review summarizes the recent advancements in using biorthogonal chemistry specifically for metabolic labeling and visualization of ECM proteins and glycosaminoglycans that are secreted by cells and living tissues. Challenges, limitations, and future directions surrounding biorthogonal chemistry involved in the labeling of ECM components are discussed. Finally, potential solutions for improvements to biorthogonal chemical approaches are suggested. This would provide theoretical guidance for labeling and visualization of de novo proteins and polysaccharides present in ECM that are cell-secreted for example during tissue remodeling or in vitro differentiation of stem cells.

Ligand binding of interleukin-8: a comparison of glycosaminoglycans and acidic peptides

Recognition and binding of regulatory proteins to glycosaminoglycans (GAGs) from the extracellular matrix is a process of high biological importance. The interaction between negatively charged sulfate or carboxyl groups of the GAGs and clusters of basic amino acids on the protein is crucial in this binding process and it is believed that electrostatics represent the key factor for this interaction. However, given the rather undirected nature of electrostatics, it is important to achieve a clear understanding of its role in protein-GAG interactions and how specificity and selectivity in these systems can be achieved, when the classical key-lock binding motif is not applicable. Here, we compare protein binding of a highly charged heparin (HP) hexasaccharide with four de novo designed decapeptides of varying negative net charge. The charge density of these peptides was comparable to typical GAGs of the extracellular matrix. We used the regulatory protein interleukin-8 (IL-8) because its interactions with GAGs are well described. All four peptide ligands bind to the same epitope of IL-8 but show much weaker binding affinity as revealed in 1H-15N HSQC NMR titration experiments. Complementary molecular docking and molecular dynamics simulations revealed further atomistic details of the interaction mode of GAG versus peptide ligands. Overall, similar contributions to the binding energy and hydrogen bond formation are determined for HP and the highly charged peptides, suggesting that the entropic loss of the peptides upon binding likely account for the remarkably different affinity of GAG versus peptide ligands to IL-8.

Extracellular matrix as a driver for intratumoral heterogeneity

The architecture of an organ is built through interactions between its native cells and its connective tissue consisting of stromal cells and the extracellular matrix (ECM). Upon transformation through tumorigenesis, such interactions are disrupted and replaced by a new set of intercommunications between malignantly transformed parenchyma, an altered stromal cell population, and a remodeled ECM. In this perspective, we propose that the intratumoral heterogeneity of cancer cell phenotypes is an emergent property of such reciprocal intercommunications, both biochemical and mechanical-physical, which engender and amplify the diversity of cell behavioral traits. An attempt to assimilate such findings within a framework of phenotypic plasticity furthers our understanding of cancer progression.

Physics of Brain Cancer: Multiscale Alterations of Glioblastoma Cells under Extracellular Matrix Stiffening

The biology and physics underlying glioblastoma is not yet completely understood, resulting in the limited efficacy of current clinical therapy. Recent studies have indicated the importance of mechanical stress on the development and malignancy of cancer. Various types of mechanical stress activate adaptive tumor cell responses that include alterations in the extracellular matrix (ECM) which have an impact on tumor malignancy. In this review, we describe and discuss the current knowledge of the effects of ECM alterations and mechanical stress on GBM aggressiveness. Gradual changes in the brain ECM have been connected to the biological and physical alterations of GBM cells. For example, increased expression of several ECM components such as glycosaminoglycans (GAGs), hyaluronic acid (HA), proteoglycans and fibrous proteins result in stiffening of the brain ECM, which alters inter- and intracellular signaling activity. Several mechanosensing signaling pathways have been identified that orchestrate adaptive responses, such as Hippo/YAP, CD44, and actin skeleton signaling, which remodel the cytoskeleton and affect cellular properties such as cell–cell/ECM interactions, growth, and migration/invasion of GBM cells. In vitro, hydrogels are used as a model to mimic the stiffening of the brain ECM and reconstruct its mechanics, which we also discuss. Overall, we provide an overview of the tumor microenvironmental landscape of GBM with a focus on ECM stiffening and its associated adaptive cellular signaling pathways and their possible therapeutic exploitation.

Matrix stiffness and its influence on pancreatic diseases

The matrix stiffness of the extracellular matrix(ECM), which is the slow elastic force on cells, has gradually become investigated. And a higher stiffness could induce changes in cell biological behaviors and activation of internal signaling pathways. Imbalanced stiffness of ECM is associated with a number of diseases, including pancreatic disease. In this review, we discuss the components of the ECM and the increased stiffness caused by unbalanced ECM changes. Next, we describe how matrix stiffness transmits mechanical signals and what signaling pathways are altered within the cell in detail. Finally, we discuss the effect of ECM on the behavior of pancreatic diseases from the perspective of matrix stiffness.

Investigation of the structure of regulatory proteins interacting with glycosaminoglycans by combining NMR spectroscopy and molecular modeling - the beginning of a wonderful friendship

The interaction of regulatory proteins with extracellular matrix or cell surface-anchored glycosaminoglycans (GAGs) plays important roles in molecular recognition, wound healing, growth, inflammation and many other processes. In spite of their high biological relevance, protein-GAG complexes are significantly underrepresented in structural databases because standard tools for structure determination experience difficulties in studying these complexes. Co-crystallization with subsequent X-ray analysis is hampered by the high flexibility of GAGs. NMR spectroscopy experiences difficulties related to the periodic nature of the GAGs and the sparse proton network between protein and GAG with distances that typically exceed the detection limit of nuclear Overhauser enhancement spectroscopy. In contrast, computer modeling tools have advanced over the last years delivering specific protein-GAG docking approaches successfully complemented with molecular dynamics (MD)-based analysis. Especially the combination of NMR spectroscopy in solution providing sparse structural constraints with molecular docking and MD simulations represents a useful synergy of forces to describe the structure of protein-GAG complexes. Here we review recent methodological progress in this field and bring up examples where the combination of new NMR methods along with cutting-edge modeling has yielded detailed structural information on complexes of highly relevant cytokines with GAGs.

Characterization of defined sulfated heparin-like oligosaccharides by electrospray ionization ion trap mass spectrometry

Glycosaminoglycans (GAG) as long, unbranched polysaccharides are major components of the extracellular matrix. Many studies provided additional evidence of a specific binding between mediators and sulfated GAG, at which the sulfation code-which means the number and positions of sulfate groups along the polysaccharide chain-plays an important role. GAG from natural sources are very inhomogeneous regarding their sulfation patterns and molecular weight. Additionally, there is a high risk of contamination. This results in a growing interest in the careful characterization of native GAG and the synthesis of artificial GAG. Additionally, chemically oversulfated GAG analogues show many favorable properties. However, the structural characterization of these carbohydrates by mass spectrometry remains challenging. One significant problem is the sulfate loss during the ionization, which increases with the number of sulfate residues. We used the sulfated pentasaccharide fondaparinux as model substance to optimize sample preparation and measurement conditions, compared different established desalination methods and already existing protocols for sulfated oligosaccharides, and investigated their impact on the quality of the mass spectra. After optimization of the measurement conditions, we could establish a gentle and fast protocol for the mass spectrometry characterization of (fully) sulfated, artificial GAG-like oligosaccharides with minimized sulfate loss in the positive and negative ion mode. Here, the negative ion mode was more sensitive in comparison with the positive one, and fondaparinux species with sulfate loss were not detectable under the optimized conditions in the positive ion mode.

Decellularized tissues as platforms for in vitro modeling of healthy and diseased tissues

Biomedical engineers are at the forefront of developing novel treatments to improve human health, however, many products fail to translate to clinical implementation. In vivo pre-clinical animal models, although the current best approximation of complex disease conditions, are limited by reproducibility, ethical concerns, and poor accurate prediction of human response. Hence, there is a need to develop physiologically relevant, low cost, scalable, and reproducible in vitro platforms to provide reliable means for testing drugs, biomaterials, and tissue engineered products for successful clinical translation. One emerging approach of developing physiologically relevant in vitro models utilizes decellularized tissues/organs as biomaterial platforms for 2D and 3D models of healthy and diseased tissue. Decellularization is a process that removes cellular content and produces tissue-specific extracellular matrix scaffolds that can more accurately recapitulate an organ/tissue's native microenvironment compared to other natural or synthetic materials. Decellularized tissues hold enormous potential for in vitro modeling of various disease phenotypes and tissue responses to drugs or external conditions such as aging, toxin exposure, or even implantation. In this review, we highlight the need for in vitro models, the advantages and limitations of implementing decellularized tissues, and considerations of the decellularization process. We discuss current research efforts towards applying decellularized tissues as platforms to generate in vitro models of healthy and diseased tissues, and where we foresee the field progressing. A variety of organs/tissues are discussed, including brain, heart, kidney, large intestine, liver, lung, skeletal muscle, skin, and tongue. STATEMENT OF SIGNIFICANCE: Many biomedical products fail to reach clinical translation due to animal model limitations. Development of physiologically relevant in vitro models can provide a more economic, scalable, and reproducible means of testing drugs/therapeutics for successful clinical translation. The use of decellularized tissues as platforms for in vitro models holds promise, as these scaffolds can effectively replicate native tissue complexity, but is not widely explored. This review discusses the need for in vitro models, the promise of decellularized tissues as biomaterial substrates, and the current research applying decellularized tissues towards the creation of in vitro models. Further, this review provides insights into the current limitations and future of such in vitro models.

Design Parameters of Tissue-Engineering Scaffolds at the Atomic Scale

Stem-cell behavior is regulated by the material properties of the surrounding extracellular matrix, which has important implications for the design of tissue-engineering scaffolds. However, our understanding of the material properties of stem-cell scaffolds is limited to nanoscopic-to-macroscopic length scales. Herein, a solid-state NMR approach is presented that provides atomic-scale information on complex stem-cell substrates at near physiological conditions and at natural isotope abundance. Using self-assembled peptidic scaffolds designed for nervous-tissue regeneration, we show at atomic scale how scaffold-assembly degree, mechanics, and homogeneity correlate with favorable stem cell behavior. Integration of solid-state NMR data with molecular dynamics simulations reveals a highly ordered fibrillar structure as the most favorable stem-cell scaffold. This could improve the design of tissue-engineering scaffolds and other self-assembled biomaterials.

Preventing Obstructions of Nanosized Drug Delivery Systems by the Extracellular Matrix

Although nanosized drug delivery systems are promising tools for the treatment of severe diseases, the extracellular matrix (ECM) constitutes a major obstacle that endangers therapeutic success. Mobility of diffusing species is restricted not only by small pore size (down to as low as 3 nm) but also by electrostatic interactions with the network. This article evaluates commonly used in vitro models of ECM, analytical methods, and particle types with respect to their similarity to native conditions in the target tissue. In this cross-study evaluation, results from a wide variety of mobility studies are analyzed to discern general principles of particle-ECM interactions. For instance, cross-linked networks and a negative network charge are essential to reliably recapitulate key features of the native ECM. Commonly used ECM mimics comprised of one or two components can lead to mobility calculations which have low fidelity to in vivo results. In addition, analytical methods must be tailored to the properties of both the matrix and the diffusing species to deliver accurate results. Finally, nanoparticles must be sufficiently small to penetrate the matrix pores (ideally R_d/p < 0.5; d = particle diameter, p = pore size) and carry a neutral surface charge to avoid obstructions. Larger (R_d/p >> 1) or positively charged particles are trapped.

Next generation organoids for biomedical research and applications

Organoids are in vitro cultures of miniature fetal or adult organ-like structures. Their potentials for use in tissue and organ replacement, disease modeling, toxicology studies, and drug discovery are tremendous. Currently, major challenges facing human organoid technology include (i) improving the range of cellular heterogeneity for a particular organoid system, (ii) mimicking the native micro- and matrix-environment encountered by cells within organoids, and (iii) developing robust protocols for the in vitro maturation of organoids that remain mostly fetal-like in cultures. To tackle these challenges, we advocate the principle of reverse engineering that replicates the inner workings of in vivo systems with the goal of achieving functionality and maturation of the resulting organoid structures with the input of minimal intrinsic (cellular) and environmental (matrix and niche) constituents. Here, we present an overview of organoid technology development in several systems that employ cell materials derived from fetal and adult tissues and pluripotent stem cell cultures. We focus on key studies that exploit the self-organizing property of embryonic progenitors and the role of designer matrices and cell-free scaffolds in assisting organoid formation. We further explore the relationship between adult stem cells, niche factors, and other current developments that aim to enhance robust organoid maturation. From these works, we propose a standardized pipeline for the development of future protocols that would help generate more physiologically relevant human organoids for various biomedical applications.

Physicochemical, antioxidant and biocompatible properties of chondroitin sulphate isolated from chicken keel bone for potential biomedical applications

Chicken keel bone cartilage was explored for cheaper and sustainable source for isolation of chondroitin sulphate (CS) for its future use in tissue engineering and pharmaceutical industry. HPSEC analysis displayed two peaks of 100kDa for CS-keel polysaccharide and 1kDa for protein. DLS analysis of CS-keel displayed polydispersity. CS-keel yield was 15% and 53±5% uronic acid content. The quantified percentages of UA-GalNAc4S and UA-GalNAc6S disaccharide in CS-keel were 58% and 42%, respectively. FT-IR identified CS-keel to be chondroitin 4-sulphate. ¹H NMR of CS-keel confirmed the presence of N-acetylgalactosamine and Glucuronic acid. FESEM demonstrated layer structure and AFM displayed the size of CS-keel fibres. DSC, TGA and DTG studies of CS-keel showed T_d at 243°C. In vitro cell proliferation assay and morphological analysis of mouse fibroblast L929 cell lines confirmed the biocompatibility of CS-keel. CS-keel (5mg/ml) exhibited ∼49% antioxidant activity against DPPH and 22% against superoxide radical protecting from oxidative damage. CS-keel demonstrated better (70.3%) emulsifying activity than commercial sodium alginate (60.2%).

Supra-organization and optical anisotropies of the extracellular matrix in the amniotic membrane and limbal stroma before and after explant culture

In this research we evaluated the supramolecular organizations and the optical anisotropical properties of the de-epithelialized human amniotic membrane and rabbit limbal stroma, before and after explant culture. Birefringence, monochromatic light spectral absorption and linear dichroism of the main extracellular matrix biopolymers, that is, the fibrillar collagens and proteoglycans, were investigated by polarized light microscopy combined with image analysis. Our results demonstrated that the culture procedure-induced stimuli altered the supra-organizational characteristics (in terms of collagens/proteoglycans spatial orientation and ordered-aggregational state) of the amniotic and limbal extracellular matrix, which led to changes in optical anisotropical properties.

The selected matrix influences the matrix-assisted laser desorption/ionization time-of-flight mass spectral patterns of partially deuterated glycosaminoglycan disaccharides

RATIONALE

If carbohydrates are investigated by nuclear magnetic resonance (NMR) spectroscopy, they are normally dissolved in deuterated solvents, such as D2 O. The incorporation of deuterium leads to a high complexity of subsequently recorded mass spectra and reduced sensitivity because different deuterated ions become detectable. Here, we demonstrate that the applied matrix-assisted laser desorption/ionization (MALDI) matrix solution has a considerable impact on the observed isotopic distribution.

METHODS

Unsaturated disaccharides of chondroitin (CS) and dermatan sulfate (DS) were prepared by enzymatic digestion of the polysaccharides in D2 O and analyzed by MALDI time-of-flight mass spectrometry (TOF MS) using 2,5-dihydroxybenzoic acid (DHB) and 9-aminoacridine (9-AA) according to previously published protocols.

RESULTS

The extent of deuteration of a given compound can be easily determined by using the mass shift between the non-deuterated and deuterated ions. However, such a determination is more difficult when considering sugars due to their high content of exchangeable groups. Therefore, both the solvent and the matrix have a considerable impact on the MS patterns. Additionally, there are significant differences if the spectra are recorded at different laser fluences.

CONCLUSIONS

Great caution should be taken when the deuterium content of disaccharides is determined by MALDI MS. Aside from the use of non-protic solvents, DHB is the matrix of choice, whereas 9-AA shows a considerable influence on the observed isotope pattern in dependence on the applied laser fluence. Copyright © 2016 John Wiley & Sons, Ltd.

Backbone ¹H, ¹⁵N, and ¹³C and side chain ¹³Cβ NMR chemical shift assignment of murine interleukin-10

Almost complete assignment of backbone (1)H, (13)C, (15)N and side chain (13)Cβ resonances for the immune-regulatory cytokine IL-10 is reported. The protein was overexpressed in Escherichia coli and was refolded from inclusion bodies. The point mutation C149Y was introduced to suppress incorrect disulfide bond formation and to improve protein refolding.

Improvement of the digestibility of sulfated hyaluronans by bovine testicular hyaluronidase: a UV spectroscopic and mass spectrometric study

Glycosaminoglycans (GAGs) such as hyaluronan (HA) and chondroitin sulfate (CS) are important, natural polysaccharides which occur in biological (connective) tissues and have various biotechnological and medical applications. Additionally, there is increasing evidence that chemically (over)sulfated GAGs possess promising properties and are useful as implant coatings. Unfortunately, a detailed characterization of these GAGs is challenging: although mass spectrometry (MS) is one of the most powerful tools to elucidate the structures of (poly)saccharides, MS is not applicable to high mass polysaccharides, but characteristic oligosaccharides are needed. These oligosaccharides are normally generated by enzymatic digestion. However, chemically modified (particularly sulfated) GAGs are extremely refractive to enzymatic digestion. This study focuses on the investigation of the digestibility of GAGs with different degrees of sulfation by bovine testicular hyaluronidase (BTH). It will be shown by using an adapted spectrophotometric assay that all investigated GAGs can be basically digested if the reaction conditions are carefully adjusted. However, the oligosaccharide yield correlates reciprocally with the number of sulfate residues per polymer repeating unit. Finally, matrix-laser desorption and ionization (MALDI) MS will be used to study the released oligosaccharides and their sulfation patterns.