Mechanical and Systems Biology of Cancer

Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control basic mechanical properties, such as cell tension, stiffness, and engagement with the extracellular environment, which can lead to extracellular matrix remodeling. Intracellular mechanics can alter signaling and transcription factors, impacting cell decision making. Additionally, signaling from soluble and mechanical factors in the extracellular environment, such as substrate stiffness and ligand density, can modulate cytoskeletal dynamics. Computational models closely integrated with experimental support, incorporating cancer-specific parameters, can provide quantitative assessments and serve as predictive tools toward dissecting the feedback between signaling and mechanics and across multiple scales and domains in tumor progression.Comment: 18 pages, 3 figure

Breaking through the glioblastoma micro-environment via extracellular vesicles

Glioblastoma (GBM) is the most common and most aggressive brain tumour. Prognosis remains poor, despite the combined treatment of radio- and chemotherapy following surgical removal. GBM cells coexist with normal non-neoplastic cells, including endothelial cells, astrocytes and immune cells, constituting a complex and dynamic tumour micro-environment (TME). Extracellular vesicles (EVs) provide a critical means of bidirectional inter-cellular communication in the TME. Through delivery of a diverse range of genomic, lipidomic and proteomic cargo to neighbouring and distant cells, EVs can alter the phenotype and function of the recipient cell. As such, EVs have demonstrated their role in promoting angiogenesis, immune suppression, invasion, migration, drug resistance and GBM recurrence. Moreover, EVs can reflect the phenotype of the cells within the TME. Thus, in conjunction with their accessibility in biofluids, they can potentially serve as a biomarker reservoir for patient prognosis, diagnosis and predictive therapeutic response as well as treatment follow-up. Furthermore, together with the ability of EVs to cross the blood–brain barrier undeterred and through the exploitation of their cargo, EVs may provide an effective mean of drug delivery to the target site. Unveiling the mechanisms by which EVs within the GBM TME are secreted and target recipient cells may offer an indispensable understanding of GBM that holds the potential to provide a better prognosis and overall quality of life for GBM patients

Exploring the Production of Extracellular Matrix by Astrocytes in Response to Mimetic Traumatic Brain Injury

Following injury to the central nervous system, extracellular modulations are apparent at the site of injury, often resulting in a glial scar. Astrocytes are mechanosensitive cells, which can create a neuroinhibitory extracellular environment in response to injury. The aim for this research was to gain a fundamental understanding of the affects a diffuse traumatic brain injury has on the astrocyte extracellular environment after injury. To accomplish this, a bioreactor culturing astrocytes in 3D constructs delivered 150G decelerations with 20% biaxial strain to mimic a traumatic brain injury. Experiments were designed to compare the potential effects of media type, number of impacts, and impacts with or without strain. Multiple impacts on astrocytes resulted in increased apoptosis, supporting cumulative effects of multiple traumatic brain injury events. Surprisingly, the expression of glial fibrillary acidic protein and S100B by astrocytes was downregulated following injury. With multiple impacts, astrocytes downregulated collagen and glycosaminoglycan expression at acute time points. Suppression of matrix metalloproteinase-2 coupled with unchanging production of transforming growth factor beta-1 and tissue inhibitor of metalloproteinase-1 indicates an inability to degrade damaged ECM or produce new ECM. This was supported by long-term studies which indicate significant decreases in chondroitin sulfate proteoglycan and collagen I accumulation. This could suggest astrocytes experiencing damaging mechanical stimulation enter a survival state ceasing to moderate the extracellular environment at short time points after injury

Characterization of an electron conduit between bacteria and the extracellular environment

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning ß-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment

Increased Hematopoietic Extracellular RNAs and Vesicles in the Lung during Allergic Airway Responses.

Extracellular RNAs (exRNAs) can be released by numerous cell types in vitro, are often protected within vesicles, and can modify recipient cell function. To determine how the composition and cellular sources of exRNAs and the extracellular vesicles (EVs) that carry them change in vivo during tissue inflammation, we analyzed bronchoalveolar lavage fluid (BALF) from mice before and after lung allergen challenge. In the lung, extracellular microRNAs (ex-miRNAs) had a composition that was highly correlated with airway-lining epithelium. Using cell type-specific membrane tagging and single vesicle flow, we also found that 80% of detected vesicles were of epithelial origin. After the induction of allergic airway inflammation, miRNAs selectively expressed by immune cells, including miR-223 and miR-142a, increased and hematopoietic-cell-derived EVs also increased >2-fold. These data demonstrate that infiltrating immune cells release ex-miRNAs and EVs in inflamed tissues to alter the local extracellular environment

A Serpin shapes the extracellular environment to prevent influenza A virus maturation

Interferon-stimulated genes (ISGs) act in concert to provide a tight barrier against viruses. Recent studies have shed light on the contribution of individual ISG effectors to the antiviral state, but most have examined those acting on early, intracellular stages of the viral life cycle. Here, we applied an image-based screen to identify ISGs inhibiting late stages of influenza A virus (IAV) infection. We unraveled a directly antiviral function for the gene SERPINE1, encoding plasminogen activator inhibitor 1 (PAI-1). By targeting extracellular airway proteases, PAI-1 inhibits IAV glycoprotein cleavage, thereby reducing infectivity of progeny viruses. This was biologically relevant for IAV restriction in vivo. Further, partial PAI-1 deficiency, attributable to a polymorphism in human SERPINE1, conferred increased susceptibility to IAV in vitro. Together, our findings reveal that manipulating the extracellular environment to inhibit the last step in a virus life cycle is an important mechanism of the antiviral response

In wound repair vimentin mediates the transition of mesenchymal leader cells to a myofibroblast phenotype.

Following injury, mesenchymal repair cells are activated to function as leader cells that modulate wound healing. These cells have the potential to differentiate to myofibroblasts, resulting in fibrosis and scarring. The signals underlying these differing pathways are complex and incompletely understood. The ex vivo mock cataract surgery cultures are an attractive model with which to address this question. With this model we study, concurrently, the mechanisms that control mesenchymal leader cell function in injury repair within their native microenvironment and the signals that induce this same cell population to acquire a myofibroblast phenotype when these cells encounter the environment of the adjacent tissue culture platform. Here we show that on injury, the cytoskeletal protein vimentin is released into the extracellular space, binds to the cell surface of the mesenchymal leader cells located at the wound edge in the native matrix environment, and supports wound closure. In profibrotic environments, the extracellular vimentin pool also links specifically to the mesenchymal leader cells and has an essential role in signaling their fate change to a myofibroblast. These findings suggest a novel role for extracellular, cell-surface-associated vimentin in mediating repair-cell function in wound repair and in transitioning these cells to a myofibroblast phenotype

Modeling cell movement in anisotropic and heterogeneous network tissues

Cell motion and interaction with the extracellular matrix is studied deriving a kinetic model and considering its diffusive limit. The model takes into account of chemotactic and haptotactic effects, and obtains friction as a result of the interactions between cells and between cells and the fibrous environment. The evolution depends on the fibre distribution, as cells preferentially move along the fibre direction and tend to cleave and remodel the extracellular matrix when their direction of motion is not aligned with the fibre direction. Simulations are performed to describe the behavior of ensemble of cells under the action of a chemotactic field and in presence of heterogeneous and anisotropic fibre networks

Bioprospecting : the quest for novel extracellular polymers produced by soil-borne bacteria : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, Palmerston North, New Zealand

Bacteria are ubiquitous in nature, and the surrounding environment. Bacterially produced extracellular polymers, and proteins are of particular value in the fields of medicine, food, science, and industry. Soil is an extremely rich source of bacteria with over 100 million per gram of soil, many of which produce extracellular polymers. Approximately 90% of soil-borne bacteria are yet to be cultured and classified. Here we employed an exploratory approach and culture based method for the isolation of soil-borne bacteria, and assessed their capability for extracellular polymer production. Bacteria that produced mucoid (of a mucous nature) colonies were selected for identification, imaging, and polymer production. Here we characterised three bacterial isolates that produced extracellular polymers, with a focus on one isolate that formed potentially novel proteinaceous cell surface appendages. These appendages have an unknown function, however, I suggest they may be important for bacterial communication, signalling, and nutrient transfer. They may also serve to increase the bacteria’s surface area for nutrient adsorption without compromising structural integrity of the cell. The results from this study contribute to the scientific body of knowledge and provide avenues for further research into bacterial appendage formation

Factors contributing to biofilm formation of Yersinia enterocolitica : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Food Technology, Massey University, Palmerston North, New Zealand

Content removed from thesis due to copyright reasons: Wang H., Palmer J., & Flint S. (2015). A rapid method for the nonselective enumeration of Yersinia enterocolitica, a foodborne pathogen associated with pork. Meat Science, 113: 59–61. doi:10.1016/j.meatsci.2015.11.005; Wang H., Tay M., Palmer J., Flint S. (2016) Biofilm formation of Yersinia enterocolitica and its persistence following treatment with different sanitation agents. Food Control, 73, 433-437. doi:10.1016/j.foodcont.2016.08.033Biofilms of pathogenic bacteria are recognised as a threat to food safety. The aim of the present study was to investigate the potential of Yersinia enterocolitica to form biofilms in the pork processing environment and identify the resistance of these biofilms to sanitation. The biofilm formation by Y. enterocolitica was monitored at conditions simulating pork processing environment under daily cleaning routine using an impedance method established in this study. Results showed that Y. enterocolitica had the potential to form biofilm and become resistant to sanitation in a pork processing environment. An investigation into the factors influencing biofilm formation of Y. enterocolitica indicated that the Ca2+ ion increased the level of biofilm formation. In addition, the presence of the virulence plasmid pYV is essential for the biofilm Ca2+ response. Further analysis of the bacterial cell surface properties and extracellular polymeric substance (EPS) composition suggested that the pYV+ cell surfaces are more negatively charged and more hydrophobic than the pYV- cells although no significant difference was observed with the addition of Ca2+. The pYV+ cells appear to produce more exopolysaccharide than the pYV- cells regardless of Ca2+ concentration. Ca2+ was able to increase the yield of extracellular DNA while the presence of pYV appeared to be dispensable in terms of extracellular DNA release. Analysis of cell wall protein revealed one protein expressed in the pYV+ cells but absent in the pYV- cells