Extracellular matrix: the central regulator of cell and tissue homeostasis

Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn(II)-Dependent Matrix Metalloproteinase-1

Collagen hydrolysis, catalyzed by Zn(II)-dependent matrix metalloproteinases (MMPs), is a critical physiological process. Despite previous computational investigations into the catalytic mechanisms of MMP-mediated collagenolysis, a significant knowledge gap in understanding remains regarding the influence of conformational sampling and entropic contributions at physiological temperature on enzymatic collagenolysis. In our comprehensive multilevel computational study, employing quantum mechanics/molecular mechanics (QM/MM) metadynamics (MetD) simulations, we aimed to bridge this gap and provide valuable insights into the catalytic mechanism of MMP-1. Specifically, we compared the full enzyme-substrate complex in solution, clusters in solution, and gas-phase to elucidate insights into MMP-1-catalyzed collagenolysis. Our findings reveal significant differences in the catalytic mechanism when considering thermal effects and the dynamic evolution of the system, contrasting with conventional static potential energy surface QM/MM reaction path studies. Notably, we observed a significant stabilization of the critical tetrahedral intermediate, attributed to contributions from conformational flexibility and entropy. Moreover, we found that protonation of the scissile bond nitrogen occurs via proton transfer from a Zn(II)-coordinated hydroxide rather than from a solvent water molecule. Following C-N bond cleavage, the C-terminus remains coordinated to the catalytic Zn(II), while the N-terminus forms a hydrogen bond with a solvent water molecule. Subsequently, the release of the C-terminus is facilitated by the coordination of a water molecule. Our study underscores the pivotal role of protein conformational dynamics at physiological temperature in stabilizing the transition state of the rate-limiting step and key intermediates, compared to the corresponding reaction in solution. These fundamental insights into the mechanism of collagen degradation provide valuable guidance for the development of MMP-1-specific inhibitors.

Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1

Metalloproteinase-1 (MMP-1) catalyzed collagen degradation is essential for a wide variety of normal physiological processes, while at the same time contributing to several diseases in humans. Therefore, a comprehensive understanding of this process is of great importance. Although crystallographic and spectroscopic studies provided fundamental information about the structure and function of MMP-1, the precise mechanism of collagen degradation especially considering the complex and flexible structure of the substrate, remains poorly understood. In addition, how the protein environment dynamically reorganizes at the atomic scale into a catalytically active state capable of collagen hydrolysis remains unknown. In this study, we applied experimentally-guided multiscale molecular modeling methods including classical molecular dynamics (MD), well-tempered (WT) classical metadynamics (MetD), combined quantum mechanics/molecular mechanics (QM/MM) MD and QM/MM MetD simulations to explore and characterize the early catalytic events of MMP-1 collagenolysis. Importantly the study provided a complete atomic and dynamic description of the transition from the open to the closed form of the MMP-1•THP complex. Notably, the formation of catalytically active Michaelis complex competent for collagen cleavage was characterized. The study identified the changes in the coordination state of the catalytic zinc(II) associated with the conformational transformation and the formation of catalytically productive ES complex. Our results confirm the essential role of the MMP-1 catalytic domain's α-helices (hA, hB and hC) and the linker region in the transition to the catalytically competent ES complex. Overall, the results provide unique mechanistic insight into the conformational transformations and associated changes in the coordination state of the catalytic zinc(II) that would be important for the design of effective MMP-1 inhibitors.

Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies

Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.

Scaffold-free cell-based tissue engineering therapies: advances, shortfalls and forecast

Cell-based scaffold-free therapies seek to develop in vitro organotypic three-dimensional (3D) tissue-like surrogates, capitalising upon the inherent capacity of cells to create tissues with efficiency and sophistication that is still unparalleled by human-made devices. Although automation systems have been realised and (some) success stories have been witnessed over the years in clinical and commercial arenas, in vitro organogenesis is far from becoming a standard way of care. This limited technology transfer is largely attributed to scalability-associated costs, considering that the development of a borderline 3D implantable device requires very high number of functional cells and prolonged ex vivo culture periods. Herein, we critically discuss advancements and shortfalls of scaffold-free cell-based tissue engineering strategies, along with pioneering concepts that have the potential to transform regenerative and reparative medicine.

Integrin α6 signaling induces STAT3-TET3-mediated hydroxymethylation of genes critical for maintenance of glioma stem cells

Both the extracellular matrix (ECM) and DNA epigenetic regulation are critical for maintaining stem cell phenotype and cancer progression. Whether and how ECM regulates epigenetic alterations to influence cancer stem cells (CSCs) remain to be explored. Here we report that ECM through laminin-integrin α6 upregulates ten-eleven translocation enzyme 3 (TET3) dioxygenase. TET3 in turn mediates DNA cytosine 5’-hydroxymethylation (5hmC) and upregulates genes critical for maintenance of glioma stem cells (GSCs). Activating integrin α6-FAK pathway increases STAT3 activity, TET3 expression and 5hmC levels in GSCs. Moreover, targeting STAT3 disrupts integrin α6-FAK signaling and inhibits TET3⁺ GSC maturation in vivo. STAT3 directly regulates TET3 expression and the two proteins are co-localized with 5hmC in GSC clusters. 5hmC is upregulated by STAT3 at the promoters of several tumorigenic genes, including c-Myc, known to be critical for GSCs. In vivo silencing of TET3 in GSC-enriched tumors reduces 5hmC accumulation and expression of the GSC critical genes, leading to tumor growth inhibition. TET3 expression and 5hmC accumulation also co-segregate with integrin α6 in patient malignant glioma. Thus, ECM- integrin α6-STAT3-TET3 axis regulates hydroxymethylation of genes important for GSCs, thereby increasing GSC tumorigenicity and resistance to therapies.

Role of the Crumbs proteins in ciliogenesis, cell migration and actin organization

Epithelial cell organization relies on a set of proteins that interact in an intricate way and which are called polarity complexes. These complexes are involved in the determination of the apico-basal axis and in the positioning and stability of the cell-cell junctions called adherens junctions at the apico-lateral border in invertebrates. Among the polarity complexes, two are present at the apical side of epithelial cells. These are the Par complex including aPKC, PAR3 and PAR6 and the Crumbs complex including, CRUMBS, PALS1 and PATJ/MUPP1. These two complexes interact directly and in addition to their already well described functions, they play a role in other cellular processes such as ciliogenesis and polarized cell migration. In this review, we will focus on these aspects that involve the apical Crumbs polarity complex and its relation with the cortical actin cytoskeleton which might provide a more comprehensive hypothesis to explain the many facets of Crumbs cell and tissue properties.

More than the genes, the tumor microenvironment in neuroblastoma

Neuroblastoma is the second most common solid tumor in children. Since the seminal discovery of the role of amplification of the MYCN oncogene in the pathogenesis of neuroblastoma in the 1980s, much focus has been on the contribution of genetic alterations in the progression of this cancer. However it is now clear that not only genetic events play a role but that the tumor microenvironment (TME) substantially contributes to the biology of neuroblastoma. In this article, we present a comprehensive review of the literature on the contribution of the TME to the ten hallmarks of cancer in neuroblastoma and discuss the mechanisms of communication between neuroblastoma cells and the TME that underlie the influence of the TME on neuroblastoma progression. We end our review by discussing how the knowledge acquired over the last two decades in this field is now leading to new clinical trials targeting the TME.

Mammary ductal elongation and myoepithelial migration are regulated by the composition of the extracellular matrix

Mammary branching morphogenesis occurs over a period of weeks deep inside an adipocyte-rich stroma. The adipocytes contain light-scattering lipid droplets that limit the depth of penetration of visible light. Organotypic culture methods were developed to enable high-resolution optical monitoring of branching morphogenesis ex vivo. A challenge has been to identify the best culture conditions to model specific developmental events. We recently demonstrated that collagen I induces protrusive invasion in both normal and neoplastic mammary epithelium. In this study, we observed that the abundance of collagen I fibrils correlated strongly with invasive behaviour, even when the collagen I concentration was identical. We found that the extent of fibril assembly was experimentally manipulable by varying the incubation time at 4°C following pH neutralization. We next tested the capacity of collagen I fibrils to induce invasive behaviour when presented in combination with basement membrane proteins (Matrigel). We found that epithelial organoids in mixed gels of collagen I and basement membrane proteins exhibited more extensive branching morphogenesis but did not initiate protrusions into the matrix. Organoids in pure Matrigel produced many small epithelial buds that were bare of myoepithelial cells. Surprisingly, organoids in mixed gels of collagen I and Matrigel produced fewer epithelial buds, the buds elongated further, and the elongating buds remained covered by myoepithelial cells. Our mixed gels therefore provide a more physiologically accurate model of mammary branching morphogenesis. Our results also suggest that changes in the composition of the extracellular matrix could induce migration of epithelial cells past myoepithelial coverage.

Issues to be considered when studying cancer in vitro

Various cancer treatment approaches have shown promising results when tested preclinically. The results of clinical trials, however, are often disappointing. While searching for the reasons responsible for their failures, the relevance of experimental and preclinical models has to be taken into account. Possible factors that should be considered, including cell modifications during in vitro cultivation, lack of both the relevant interactions and the structural context in vitro have been summarized in the present review.

Focal adhesion-chromatin linkage controls tumor cell resistance to radio- and chemotherapy

Cancer resistance to therapy presents an ongoing and unsolved obstacle, which has clear impact on patient's survival. In order to address this problem, novel in vitro models have been established and are currently developed that enable data generation in a more physiological context. For example, extracellular-matrix- (ECM-) based scaffolds lead to the identification of integrins and integrin-associated signaling molecules as key promoters of cancer cell resistance to radio- and chemotherapy as well as modern molecular agents. In this paper, we discuss the dynamic nature of the interplay between ECM, integrins, cytoskeleton, nuclear matrix, and chromatin organization and how this affects the response of tumor cells to various kinds of cytotoxic anticancer agents.

MR elastography of liver tumours: value of viscoelastic properties for tumour characterisation

OBJECTIVES

To assess the value of the viscoelastic parameters in the characterisation of liver tumours at MR elastography.

PATIENTS AND METHODS

Ninety-four patients with liver tumours >1 cm prospectively underwent MR elastography using 50-Hz mechanical waves and a full three-directional motion-sensitive sequence. The model-free viscoelastic parameters (the complex shear modulus and its real and imaginary parts, i.e. the storage and loss moduli) were calculated in 72 lesions after exclusion of cystic, treated or histopathologically undetermined tumours.

RESULTS

We observed higher absolute shear modulus and loss modulus in malignant versus benign tumours (3.38 ± 0.26 versus 2.41 ± 0.15 kPa, P < 0.01 and 2.25 ± 0.26 versus 1.05 ± 0.13 kPa, P < 0.001, respectively). Moreover, the loss modulus of hepatocellular carcinomas was significantly higher than in benign hepatocellular tumours. The storage modulus did not differ significantly between malignant and benign tumours. The area under the receiver-operating characteristic curve of loss modulus was significantly larger than that of the absolute shear modulus and storage modulus when comparing malignant and benign lesions.

CONCLUSIONS

The increased loss modulus is a better discriminator between benign and malignant tumours than the increased storage modulus or absolute value of the shear modulus.

KEY POINTS

• Magnetic Resonance elastography is a new method of assessing the liver. • Increased loss modulus is an indicator of malignancy in hepatic tumours. • Loss modulus is a better discriminator than absolute shear modulus values. • The viscoelastic properties of lesions offer promise for characterising liver tumours.

Morphologic complexity of the pericellular matrix in the annulus of the human intervertebral disc

The pericellular region of the extracellular matrix (ECM) contains collagens, proteoglycans and other noncollagenous matrix proteins. Although such specialized pericellular ECM has been well studied in articular cartilage, little is known about the pericellular matrix in the disc. In the study reported here, pericellular matrix was studied in annulus tissue from 52 subjects ranging in age from 17-74 years. In aging/degenerating intervertebral discs, cells were identified that formed a distinctive cocoon of encircling pericellular ECM. Immunohistochemical studies identified types I, II, III and VI collagen in these pericellular sites with diverse morphological features. Similar types of changes in the pericellular matrix were observed in both surgical specimens and control donor discs. Results indicate the need for future studies to address why such specialized matrix regions form around certain disc cells and to determine the consequences of these unusual matrix regions on annular lamellar organization and function.

Contact with fibrillar collagen inhibits melanoma cell proliferation by up-regulating p27KIP1

It is known that the extracellular matrix regulates normal cell proliferation, and it is assumed that anchorage-independent malignant cells escape this regulatory function. Here we demonstrate that human M24met melanoma cells remain responsive to growth regulatory signals that result from contact with type I collagen and that the effect on proliferation depends on the physical structure of the collagen. On polymerized fibrillar collagen, M24met cells are growth arrested at the G(1)/S checkpoint and maintain high levels of p27(KIP1) mRNA and protein. In contrast, on nonfibrillar (denatured) collagen, the cells enter the cell cycle, and p27(KIP1) is down-regulated. These growth regulatory effects involve contact between type I collagen and the collagen-binding integrin alpha(2)beta(1), which appears restricted in the presence of fibrillar collagen. Thus melanoma cells remain sensitive to negative growth regulatory signals originating from fibrillar collagen, and the proteolytic degradation of fibrils is a mechanism allowing tumor cells to escape these restrictive signals.

Regulation of urokinase plasminogen activator (uPA) activity by E-cadherin and hormones in mammary epithelial cells

Urokinase plasminogen activator (uPA) is involved in proteolysis of extracellular matrix during development and tumor cell invasion. In the present study, we examined the regulation of uPA in hormone-responsive, noninvasive mammary epithelial cells by using fibrinolytic and caseinolytic enzyme activity assays. Urokinase PA expression was activated after contact with fibrin and initiation of cell-cell interactions that were mediated by E-cadherin. Fibrinolysis occurred in zones surrounding cellular aggregates. Stromal matrix proteins that disrupted aggregation or anti-E-cadherin antibodies that inhibited cellular compaction inhibited fibrinolysis perhaps by increasing cell-matrix adhesion or preventing E-cadherin signaling, respectively. Aggregation required the presence of divalent cations and was inhibited by serum and ethylene diaminetetraacetic acid, whereas serine protease inhibitors reduced uPA activity without affecting aggregation. Inhibitors of PA (type 2; PAI-2) and a specific antisense uPA oligonucleotide also reduced enzymatic activity, suggesting that fibrinolysis depends on translational regulation of uPA. In addition, the activation of plasmin from plasminogen was inhibited by anti-E-cadherin antibodies and PAI-2, consistent with a role for uPA. The data also support a role for transcriptional regulation of uPA activity because treatment of cells with progesterone, hydrocortisone, or dexamethasone inhibited uPA activation on fibrin without affecting cellular aggregation. Estradiol and insulin did not alter, whereas human chorionic gonadotropin and prolactin increased uPA activity. The expression of the 55-kDa uPA activity was consistent with specific hormone action and correlated with protein expression by immunoblotting. Therefore, the alteration of downstream signaling events by hormones may affect uPA production. These results indicate that uPA is an enzyme that may be important in the degradation of extracellular matrix during development and that specific E-cadherin interactions and hormones can regulate its activity. Investigation of the regulation of uPA in these cells may be useful in understanding and manipulating mammary gland remodeling. J. Cell. Physiol. 181:1-13, 1999. Published 1999 Wiley-Liss, Inc.

Ultrastructural and immunohistochemical studies of the periendothelial matrix in human melanoma: evidence for an amorphous matrix containing laminin

Angiogenesis and the extracellular matrix are fundamental to tumor progression from in situ to invasive and metastatic disease. Laminin, a major glycoprotein integrated into basement membranes, is observed in angiogenesis and tumorigenesis. A recent study described an association between melanoma cells and endothelial cells via an amorphous matrix containing laminin. In the current study, we have examined 45 cases of human primary and metastatic melanomas by electron microscopy for the presence of an amorphous matrix. We observed an amorphous matrix without a clearly delineated lamina or basement membrane in 41 of the 45 melanomas studied. 28 cases with tissue blocks available for study were examined by immunohistochemistry for the expression of laminin and type IV collagen. We observed the presence of an angiocentric matrix containing laminin in 24 of the 28 melanomas studied. Since laminin is involved in tumor migration, the presence of laminin between melanoma cells and small vessels suggests a role for this material in periendothelial tumor migration. However, further study is required to characterize the nature of this material and the mechanisms involved.

Atypical melanocytic nevi of the genital type with a discussion of reciprocal parenchymal-stromal interactions in the biology of neoplasia

Melanocytic lesions of the genital area, especially those on the vulva, may present great difficulty in histological interpretation. A histological diagnosis of malignant melanoma was made in more than one third of 56 genital area melanocytic lesions submitted in consultation to the authors. The median age of the patients with these lesions was 25 years. This article is a clinicopathological study of these lesions and distinguishes them from malignant melanoma. The stroma of the lesions of the genital area was different from the stroma seen in the dysplastic nevi and melanoma. The differences in the stromal form in the diverse lesions is useful in diagnosis and is of profound biological significance. The stroma in the reported lesions and in some lesions of melanocytic neoplasia is described in detail, and its biological significance is discussed. Three sets of cases are used in this comparative study to delineate the clinicopathological nature and the biology of the genital nevi. The 56 cases submitted in consultation constitute the primary series of our work (The Clark Cutaneous Pathology Laboratory Series). These are compared with a series of cases from the Pigmented Lesion Group of the University of Pennsylvania and Pathology Services, Inc, and another series of cases from the Genetic Epidemiology Branch of the National Cancer Institute. The two series used for comparative study contain approximately the same number of cases of dysplastic nevi and malignant melanoma as there are atypical melanocytic nevi of the genital type in the primary series. The total number of cases was studied by comparison of their attributes in a relational database. The clinical data of the primary series was acquired through the use of a questionnaire completed by the contributors. The 56 cases presented two distinctive pathological pictures. One of these is termed atypical melanocytic nevi of the genital type (AMNGT), whereas dysplastic nevi (DN) formed the second of the two pathological pictures. There were 36 AMNGT and 14 DN. The remaining six cases were common nevi without atypia or ill-defined melanocytic hyperplasias. The lesions of AMNGT are usually located on the vulva, but they are seen on the perineum and, rarely, on the mons pubis and in the axilla. Lesions similar to AMNGT have been seen uncommonly on the male genitalia. The stromal patterns were distinctive and related to specific melanocytic lesions. An unclassified (unclass) or nonspecific stromal pattern was associated with AMNGT; a pattern of regression with differentiation (diff-regress) dominated the stroma of common dermal nevi; concentric eosinophilic fibroplasia (cef) and lamellar fibroplasia (lf) were present in dysplastic nevi; fibroplasia with a plaquelike lymphocytic infiltrate (fl) and diffuse eosinophilic fibroplasia (def) were noted in radial growth phase melanoma; and fibroplasia with angiogenesis (fa) or an absence of evidence for parenchymal stromal reciprocal interactions (nopsi) marked thick or deeply invasive vertical growth phase melanomas. Recommendations for management of the lesions are suggested.

CONCLUSIONS

One kind of atypical melanocytic proliferation in the genital area forms a distinctive clinicopathological entity that can be distinguished from melanoma and dysplastic nevi, the AMNGT. Such lesions are more common on the labia minora or the mucosa of the clitoral region than they are on the labia majora. The other common atypical melanocytic proliferation of this area is a dysplastic nevus, which is much more common on the labia majora than on the labia minora. The reciprocal interactions between parenchyma and stroma are discussed as homeostatic processes, a continually functioning template maintaining tissue, organ, and organismal form and function. The progressive disorganization of this template in neoplasia is illustrated and is considered to be a cardinal element in the biology of neoplasia.

The biochemistry of cancer dissemination

The progression of a tumor cell from one of benign delimited proliferation to invasive and metastatic growth is the major cause of poor clinical outcome of cancer patients. Recent research has revealed that this complex process requires many components for successful dissemination and growth of the tumor cell at secondary sites. These include angiogenesis, enhanced extracellular matrix degradation via tumor and host-secreted proteases, tumor cell migration, and modulation of tumor cell adhesion. Each individual component is multifaceted and is discussed within this review with respect to historical and recent findings. The identification of components and their interrelationship have yielded new therapeutic targets leading to the development of agents that may prove effective in the treatment of cancer and its metastatic progression.