Breast cancer metastasis of a variety of vital organs is a major cause of breast cancer mortality. Autophagy has a crucial role in the metastatic breast cancer progression. As a critical mechanotransducer in the Hippo signalling pathway, YAP regulates cell proliferation and promotes autophagy. Previous publications also demonstrated extracellular matrix could regulate the nucleo-cytoplasmic transport of YAP. However, how YAP signalling connects to the interplay of autophagy and mechanotransduction in breast cancer metastasis remains entirely unknown. Through rapamycin-induced autophagy on the metastatic triple negative breast cancer (TNBC) cells, we observed upregulated YAP transcriptional activity and YAP nuclear localization in TNBC. Thus, we reported that YAP nuclear localization regulates autophagy to promote TNBC metastasis. Culturing TNBC cells on PDMS plates with various matrix stiffness demonstrated that stiff matrix promoted the migration of metastatic breast cancer cells in a YAP-dependent mechanism. Therefore, we proposed that YAP mechanotransduction promotes the migration of metastatic breast cancer cells. Then, we advance in these directions by reporting autophagy-mediated YAP nuclear localization is regulated by the response to stiff matrix when TNBC cells were cultured on different matrix stiffness upon autophagy. In conclusion, we suggest autophagy and mechanotransduction mediates YAP nuclear localization together. These findings expand the unknown gap in the convergence of YAP mechanotransduction and autophagy in metastatic breast cancer. They suggest that metastatic breast cancer cells have the potential to exhibit different YAP signalling when they colonize on a secondary location with a distinct matrix stiffness from primary location. Our study further helped to understand YAP biology and the mechanism of breast cancer metastasis that will shed light on future YAP-targeting therapeutics for metastatic breast cancer. / Thesis / Master of Applied Science (MASc)

<p> A Matrix Stiffness-Modification Technique has been proposed for the inelastic analysis of ·reinforced concrete frames subjected to short term or sustained loads. To check the applicability of the analytical method, two large scale concrete frames were tested under short-term loads and sustained-loads respectively. In addition, data for twenty-two frame tests from other sources has also been compared with the non-linear analysis. Close agreement has. been observed for all the frames considered. It was further concluded that a conventional elastic matrix method using stiffnesses based on a cracked transformed section of concrete does net yield accurate results, especially in the case of sustained loading conditions. From the method developed, comments can therefore be made on present column design practice. </p> / Thesis / Master of Engineering (MEngr)

Introduction: The development of liver fibrosis is characterised by dramatic changes in the biomechanical composition and mechanical properties of the extracellular matrix (ECM). Increases in matrix stiffness associated with inflammation and fibrosis are implicated in promoting cancer development. Clinical studies have demonstrated a close association between increases in liver stiffness and the incidence of hepatocellular carcinoma (HCC). The effect of changes in matrix stiffness on tissue-resident hepatic progenitor cells (HPC) is unknown. Aberrant HPC proliferation has been implicated in the pathogenesis of HCC. It was hypothesised that changes in the stiffness of the cellular microenvironment are important in regulating the behaviour of liver-resident cell populations and may promote the development of HCC. Aims: i) to determine how changes in the stiffness of the cancer cell niche might regulate proliferation, differentiation and chemotherapeutic resistance in HCC; ii) to determine the relationship between changes in liver stiffness and hepatic progenitor cell (HPC) response in rodent models of chronic liver disease; and iii) to determine whether changes in the stiffness of the HPC niche regulate proliferation and differentiation in these cells. A secondary aim of the thesis was to characterise the pattern of histological changes observed in rodent models of chronic hepatic congestion and whether this might provide insight into the effect of oedema and congestion on the development of liver fibrosis. Methods: Cell culture experiments in HCC (Huh7/ HepG2) and HPC cell lines were performed using a system of ligand-coated polyacrylamide (PA) gel supports of variable stiffness. The stiffness of the PA supports (expressed as shear modulus) was altered across a physiological change (1-12kPa) corresponding to values encountered in normal and fibrotic livers. Thiacetamide and carbon tetrachloride (CCl4) models of liver fibrosis were used to investigate the relationship between increasing liver fibrosis, changes in matrix stiffness and HPC response. The pattern of histological changes in the liver in response to hepatic congestion was assessed in two unrelated murine models of dilated cardiomyopathy; the python and CREB S133A mice. Results: Increases in matrix stiffness, as would be encountered in liver fibrosis, promote HCC cell proliferation. Increasing matrix stiffness is associated with enhanced basal and hepatocyte growth factor-mediated signalling though ERK, PKB/ Akt and STAT3. Stiffness-dependent HCC cell proliferation is modulated by β1-integrin and focal adhesion kinase. Increasing matrix stiffness is associated with a reduction in chemotherapy-induced apoptosis in HCC cells. However, following chemotherapy there was an increase in the frequency of clone-initiating cells for cells maintained in a low stiffness environment. Flow cytometry in HepG2 cells demonstrated that culture in a low stiffness environment was associated with an increase in the frequency of the stem cell markers CD44, CD133 and CXCR-4. This effect was further enhanced in the presence of chemotherapy. There is a close association between HPC numbers and liver stiffness measurements in a rat CCl4 model of chronic liver fibrosis. The major expansion in HPC numbers in this model coincides with a similarly large increase in fibrous tissue deposition. In vitro experiments using PA supports demonstrate that increasing matrix stiffness promotes the proliferation of both primary murine HPCs and an immortalised HPC line (BMOL). Changes in matrix stiffness regulate the expression of hepatocyte and biliary markers in BMOL cells. Histological studies in both the Python and CREB S133A models reveal findings consistent with acute on chronic cardiac hepatopathy (ischaemic hepatitis). Features of chronic passive congestion and centrilobular necrosis are present concurrently and develop rapidly. Bridging fibrosis and cirrhosis are not present. Conclusions: Physiologically-relevant changes in matrix stiffness regulate proliferation, differentiation, chemotherapeutic-resistance and stem cell marker expression in HCC cells. Similarly, increases in matrix stiffness are closely correlated to HPC response in vivo and regulate HPC proliferation and differentiation in vitro.

Le terme invadosome regroupe à la fois les podosomes, dans les cellules normales, et les invadopodes, dans les cellules transformées par l’oncogène Src et les cellules cancéreuses. Ces structures sont capables d’interagir avec et de dégrader la matrice extracellulaire (MEC). Ils sont aussi considérés comme des méchanosenseurs car ils sont capables de sentir la rigidité et la nature de la MEC. Mon travail de thèse s’est focalisé sur l’impact du microenvironnement matriciel sur la formation et l’activité des invadosomes. Au cours d’une première étude, nous avons démontré que les cellules endothéliales microvasculaires forment de façon constitutive des podosomes. L’utilisation de matrices de rigidités contrôlées, a permis la mise en évidence d’une corrélation entre l’augmentation de la rigidité augmentait et le nombre de cellules formant des podosomes ainsi que la taille de ces structures. En plus de la rigidité, d’autres propriétés de la MEC, telles que sa composition moléculaire et son organisation pourraient influencer la formation des invadosomes. Dans une seconde et troisième étude, nous avons pu montrer que seul le collagène fibrillaire de type I était capable d’induire la formation de microdomaines d’actine linéaires qui présentent comme les invadosomes, la capacité de dégrader la MEC. Au vu de leur morphologie originale, nous avons nommés ces structures des invadosomes linéaires (LIs). De façon intéressante, nous avons pu établir que la formation et l’activité de dégradation des LIs étaient indépendantes des intégrines β1 et β3. Au contraire, nous avons démontré que les récepteurs à domaine discoïdine (DDRs) contrôlent la formation et l’activité des LIs. De plus, les voies de signalisation classiques associées aux invadosomes classiques ne sont pas impliquées dans la formation des LIs. Une analyse par spectrométrie de masse des interactants de DDR1 dans un contexte collagène de type I fibrilllaire a permis de mettre en évidence des régulateurs clés et de révéler une voie de signalisation potentiellement impliquée dans la formation des LIs.Ainsi, ce travail de thèse a permis d’identifier la rigidité de la matrice comme un inducteur majeur des podosomes mais aussi la capacité intrinsèque des cellules microvasculaires à former ces structures. De plus, nous avons identifié un nouveau type d’invadosome, les LIs, qui sont associés à un nouveau type de récepteur concernant les invadosomes, les DDRs. / Invadosome is a global term including podosome, found in normal cells, and invadopodia observed in Src-transformed and cancer cells. These structures are specialized cell-matrix contacts able to interact with and degrade the extracellular matrix (ECM). They are considered as mechanosensors as they are able to sense the strength, the nature of the extracellular matrix. My PhD work essentially focuses on the understanding of how matrix microenvironment impacts on invadosome formation and activity. In a first study, we demonstrated that microvascular cell types constitutively form podosomes. Thus, using matrices of controlled rigidity, we found that an increase of stiffness was associated with an enhancement in the number of cells forming podosomes and podosome size. In addition to the matrix rigidity, other microenvironment properties, such as the molecular composition and the organization of the matrix are expected to influence the formation of invadosome.In a second and a third part of this wok, we show that fibrillar type I collagen induce the formation of linear actin microdomains which exhibit invadosome characteristics. In view of their original architecture, we named these new structures, linear invadosomes (LIs).Interestingly, we show that the formation and degradation activity of LIs are independent of β1 and β3-integrins but required discoidin domain receptors (DDRs). Moreover, all the signalling pathways known to induce classical invadosome are not required for the LIs induction. A mass spectrometry analysis of DDR1 partners emphasized key regulators and these results highlight a new potential signalling pathway involved in LIs formation. This work allowed us identifying matrix stiffness as a major inducer of podosomes but also the intrinsic capacity of microvascular cells to form these structures. Moreover, we identify a new type of invadosome, the Linear Invadosome associated with DDRs receptors.

Recent investigations in nanotechnology show that carbon nanotubes (CNT) have one of the most significant mechanical, electrical and optical properties. Interactions between those areas like electrical, optical and mechanical properties are also very promising in both research and industrial fields. Those unique characteristics are built by mainly the atomistic structure of the carbon nanotubes. In this thesis, the effects of vacant atoms on single walled carbon nanotubes (SWCNT) are investigated using matrix stiffness method. In order to use this technique a linkage between structural mechanics and molecular mechanics is established. A code has been developed to construct the SWCNT with the desired chirality, extracting the vacant atoms with the corresponding atomic bonds between the neighbor nodes and calculating the effect of those vacancies on its vibrational properties. A finite element software is also utilized for validation of the code and results. In order to investigate the convergence of the effect of those vacant nodes a numerous number of analyses have been carried out with randomly positioned vacant atoms. Also consecutive vacant nodes have been positioned in order to investigate the effect on the structural properties through the length of a CNT. In addition to those, as a case study, the reduction in Young&#039 / s modulus property because of the vacancies has also been investigated and the effects are tabulated in the report. It is concluded in this study that the any amount of vacant atoms have substantial effect on modal frequencies and Young&#039 / s modulus. Chirality and the position of the vacancies are the main parameters determining the structural properties of a CNT.

Production of brand new protein-based materials with precise control over the amino acid sequences at single residue level has been made possible by genetic engineering, through which artificial genes can be developed that encode protein-based materials with desired features. As an example, silk-elastinlike protein polymers (SELPs), composed of tandem repeats of amino acid sequence motifs from Bombyx mori (silkworm) silk and mammalian elastin, have been produced in this approach. SELPs have been studied extensively in the past two decades, however, the fundamental mechanism governing the self-assembly process to date still remains largely unresolved. Further, regardless of the unprecedented success when exploited in areas including drug delivery, gene therapy, and tissue augmentation, SELPs scaffolds as a three-dimensional cell culture model system are complicated by the inability of SELPs to provide the embedded tissue cells with appropriate biochemical stimuli essential for cell survival and function. In this dissertation, it is reported that the self-assembly of silk-elastinlike protein polymers (SELPs) into nanofibers in aqueous solutions can be modulated by tuning the curing temperature, the size of the silk blocks, and the charge of the elastin blocks. A core-sheath model was proposed for nanofiber formation, with the silk blocks in the cores and the hydrated elastin blocks in the sheaths. The folding of the silk blocks into stable cores - affected by the size of the silk blocks and the charge of the elastin blocks - plays a critical role in the assembly of silk-elastin nanofibers. The assembled nanofibers further form nanofiber clusters on the microscale, and the nanofiber clusters then coalesce into nanofiber micro-assemblies, interconnection of which eventually leads to the formation of three-dimensional scaffolds with distinct nanoscale and microscale features. SELP-Collagen hybrid scaffolds were also fabricated to enable independent control over the scaffolds' biochemical input and matrix stiffness. It is reported herein that in the hybrid scaffolds, collagen provides essential biochemical cues needed to promote cell attachment and function while SELP imparts matrix stiffness tunability. To obtain tissue-specificity in matrix stiffness that spans over several orders of magnitude covering from soft brain to stiff cartilage, the hybrid SELP-Collagen scaffolds were crosslinked by transglutaminase at physiological conditions compatible for simultaneous cell encapsulation. The effect of the increase in matrix stiffness induced by such enzymatic crosslinking on cellular viability and proliferation was also evaluated using in vitro cell assays.

Calcific aortic valve disease (CAVD) occurs through multiple mutually non-exclusive mechanisms that are mediated by valvular interstitial cells (VICs). VICs undergo pathological differentiation during the progression of valve calcification; however the factors that regulate cellular differentiation are not well defined. Most commonly recognized are biochemical factors that induce pathological differentiation, but little is known regarding the biochemical factors that may suppress this process. Further, the contribution of matrix mechanics in valve pathology has been overlooked, despite increasing evidence of close relationships between changes in tissue mechanics, disease progression and the regulation of cellular response. In this thesis, the effect of matrix stiffness on the differentiation of and calcification by VICs in response to pro-calcific and anti-calcific biochemical factors was investigated. Matrix stiffness modulated the response of VICs to pro-calcific factors, leading to two distinct calcification processes. VICs cultured on the more compliant matrices underwent calcification via osteoblast differentiation, whereas those cultured on the stiffer matrices were prone to myofibroblast differentiation. The transition of fibroblastic VICs to myofibroblasts increased cellular contractility, which led to contraction-mediated, apoptosis-dependent calcification. In addition, C-type natriuretic peptide (CNP), a putative protective molecule against CAVD, was identified. CNP supressed myofibroblast and osteoblast differentiation of VICs, and thereby inhibited calcification in vitro. Matrix stiffness modulated the expression of CNP-regulated transcripts, with only a small number of CNP-regulated transcripts not being sensitive to matrix mechanics. These data demonstrate the combined effects of mechanical and biochemical cues in defining VIC phenotype and responses, with implications for the interpretation of in vitro models of VIC calcification and possibly disease devleopment. The findings from this thesis emphasize the necessity to consider both biochemical and mechanical factors in order to improve fundamental understanding of VIC biology.

Lung cancer is the number one cause of cancer related death worldwide, with more than 1.6 million fatalities each year. Non-small cell lung cancer (NSCLC) accounts for 80-85% of all lung cancers, with KRAS being one of the most prevalent oncogenic driver mutations. Therapeutic approaches for KRAS-mutated NSCLC have been extensively explored due to the US National Cancer Institute RAS Initiative, but methods of directly targeting KRAS or downstream effectors, such as MEK, still have poor results. Previous reports have shown that KRAS-mutated NSCLC activate distinct receptor tyrosine kinases (RTKs) depending on the epithelial or mesenchymal state. Epithelial-to-mesenchymal transition (EMT) is known to play a role in the metastasis and poor prognosis of cancer, and is induced by extracellular matrix (ECM) stiffness. Hallmarks of EMT include loss of E-Cadherin and increase in Vimentin. This research investigates the role of KRAS in EMT transition due to increased ECM stiffness in KRAS mutant NSCLC, and how this affects the efficacy of KRAS and MEK inhibition. To understand how KRAS mutations in NSCLC play a role in this stiffness induced EMT, experiments were performed to detect the gene and protein expression of EMT markers, as well as possible sources of mechanosensing, including primary cilia and receptor tyrosine kinases. We hypothesized that KRAS plays a role in activation of mechanosensors and directly correlates to EMT induced by increased mechanical forces. Results show when KRAS was inhibited and there was increased mechanical forces, either from stretch or substrate stiffness, there was a decreased activation of mechanosensors. KRAS inhibition also prevented the cells from undergoing stiffness-induced EMT. This supports our hypothesis that KRAS plays a key role in ECM stiffness induced EMT. Future studies include examining the mechanism behind this phenomenon and in vivo studies.

The broad objective of this research is to examine the relationship between the cellular micromechanical environment and disease progression in cancer. The mechanical stiffness of cancerous tissue is a key feature that distinguishes it from normal tissue and thus facilitates its detection clinically. While numerous inroads have been achieved toward elucidating molecular mechanisms that underlie diseases such as cancer, quantitative characterization of associated cellular mechanical properties and biophysical attributes remains largely incomplete. To this end, the present research provides insight into the following questions: (1) What is the effect of extracellular matrix (ECM) stiffness and architecture on internal cancer cell rheology and cytoskeletal organization? (2) What are the integrated effects of ECM stiffness and cell metastatic potential on the intracellular rheology and morphology of breast cancer cells? (3) What are the integrated effects of ECM stiffness, ECM architecture, and cell metastatic potential on the motility of breast cancer cells? To examine these phenomena, the present research utilizes a multidisciplinary engineering approach that integrates experimental rheology, theoretical mechanics, confocal microscopy, computational algorithms, and experimental cell biology. Briefly, genetically altered cancer-mimicking cells are cultured within synthetic ECMs of varying mechanical stiffness and structure, where they are then observed using time-lapsed confocal microscopy. Image analyses and computational algorithms are then employed to extract measures of cell migration speed and intracellular stiffness via particle-tracking microrheology techniques. Major results show that ECM stiffness elicits an intracellular mechanical response only within the framework of physiologically relevant matrix environments and that a key cell-matrix attachment protein (the integrin) plays an essential role in this phenomenon. Additional results indicate that a well-known breast cancer-associated biomarker (ErbB2) is responsible for sensitizing mammary cells to ECM stiffness. Finally, results also show that a switch in ECM architecture significantly hinders the migratory capacity of ErbB2-associated cells, which may explain why the ErbB2 biomarker is detected with much higher frequency in early stage breast cancer than in later stage invasive and metastatic cancers. In total, these findings inform the fields of mechanobiology and cancer biology by systematically linking cell rheology, cell motility, matrix mechanics, and disease progression in cancer. / text

Calcific aortic valve disease (CAVD) occurs through multiple mutually non-exclusive mechanisms that are mediated by valvular interstitial cells (VICs). VICs undergo pathological differentiation during the progression of valve calcification; however the factors that regulate cellular differentiation are not well defined. Most commonly recognized are biochemical factors that induce pathological differentiation, but little is known regarding the biochemical factors that may suppress this process. Further, the contribution of matrix mechanics in valve pathology has been overlooked, despite increasing evidence of close relationships between changes in tissue mechanics, disease progression and the regulation of cellular response. In this thesis, the effect of matrix stiffness on the differentiation of and calcification by VICs in response to pro-calcific and anti-calcific biochemical factors was investigated. Matrix stiffness modulated the response of VICs to pro-calcific factors, leading to two distinct calcification processes. VICs cultured on the more compliant matrices underwent calcification via osteoblast differentiation, whereas those cultured on the stiffer matrices were prone to myofibroblast differentiation. The transition of fibroblastic VICs to myofibroblasts increased cellular contractility, which led to contraction-mediated, apoptosis-dependent calcification. In addition, C-type natriuretic peptide (CNP), a putative protective molecule against CAVD, was identified. CNP supressed myofibroblast and osteoblast differentiation of VICs, and thereby inhibited calcification in vitro. Matrix stiffness modulated the expression of CNP-regulated transcripts, with only a small number of CNP-regulated transcripts not being sensitive to matrix mechanics. These data demonstrate the combined effects of mechanical and biochemical cues in defining VIC phenotype and responses, with implications for the interpretation of in vitro models of VIC calcification and possibly disease devleopment. The findings from this thesis emphasize the necessity to consider both biochemical and mechanical factors in order to improve fundamental understanding of VIC biology.