The growth and morphology of fibroblasts cultured on a physically and chemically modified surface was investigated. The need to understand cellular relationships with surface topography and chemistry is essential in the fields of biomedical engineering and biotechnology. It is well documented that mammalian cell behavior senses and responds to the surrounding micro- and nano- scale environment, but the research defining the chemistry, surface architecture, and material properties for control of this behavior is still in its infancy. The cell response to a substrate is complex, involving membrane proteins, extracellular matrix (ECM), cytoskeletal rearrangement, and changes in gene expression. Conventional cell culture is carried out on two-dimensional (2-D) cell culture platforms, such as polystyrene (PS) or glass, and forces cell behavior to adapt and adhere to an unnatural, planar environment. The biological behavior of these cells is used as a starting point for drug screening, implant design, and metabolic processes, but this is a misrepresentation of cells in their native environment. This discrepancy may be hampering biological research or initiating experimental efforts that are invalid. This body of work seeks to address these issues and contains established protocols for inexpensive, pseudo three-dimensional (3-D) culture scaffolds. The research described offers a multi-disciplinary approach for fabrication of biomaterials to achieve user defined or in vivo cell behavior using human fibroblasts. To provide insight into the design of alternative cell culture templates we have analyzed cell-surface interactions and characterized the surface properties. The substrates fabricated utilized micro-roughened surface topography with 2 – 6 µm wide features and surface chemistry as a method for controlling cell behavior. Surface roughness was templated onto polydimethylsiloxane (PDMS) and PS. The fabricated polymer surfaces have been characterized by atomic force microscopy (AFM), contact angle goniometry, fluorescence microscopy, and infrared (IR) spectroscopy. Initial studies of the textured surface yielded a super-hydrophobic surface with a 154° contact angle and high surface adhesion that was investigated using surface free energy calculations. This was followed by modification of the micro-roughness with self-assembled monolayers (SAMs), proteins, or thin films of polymer for use as a culture platform for cells. Cell behavior on the modified polymers was compared and analyzed against unmodified surfaces and tissue culture PS dishes. Cell morphology on rough PDMS surface was altered by the surface topography decreasing the average cell area to 1760 µm2 compared to an average cell area of 3410 µm2 on smooth PDMS. Gene expression changes were also noted with a 2.3 fold increase in the matrix metalloproteinase, MMP14, in cells on the rough surface compared to cells cultured on Petri dishes. Surface roughness was also combined with other surface modification methods for cell culture, including cell alignment and cell sheet engineering. 50 µm wide lines of fibronectin (FN) patterned on the rough PDMS induced cell directionality while still maintaining a pseudo 3-D culture system creating the first cell culture surface of its kind. The micro-roughness was also templated onto PS and chemically modified with a thermo-responsive polymer. This novel surface produced confluent cell sheets that detached from the surface when cooled below 32°C. Cell sheets cultured on the modified PS surfaces had an increase in FN fibril formation stimulated by the surface roughness when compared to cell sheets detached from a smooth, control surface. The minor alterations to surface topology were proven to be effective in modifying cell biochemical response compared to cells cultured on flat substrates. Differences in surface topography and chemistry stimulated changes in cell adhesion, cytoskeletal arrangement, ECM composition, and gene expression. These cell properties were used as markers for comparison to native cell systems and other reports of 3 D culture scaffolds. The mechanism of altering cell response is discussed in each chapter with respect to the specific type of surface used and compared to cell response and behavior on planar culture systems. New fabrication procedures are described that include the incorporation of other surface modification techniques such as SAMs, surface patterning, and thermo-responsive polymer grafting with surface roughness for original cell culture platforms to mimic an in vivo environment. The research presented here demonstrates that micro- and nano- changes to surface topography have large impacts on the cell-surface relationship which have important implications for research and medical applications involving adherent cells.

Tissue engineering is an interdisciplinary field which aims to create substitutes of damaged tissues by combining cells with biomaterials. Cells are extremely sensitive to their microenvironment and so the cell response to biomaterials can be regulated by different extrinsic stimuli and alterations of biomaterial properties. Successful implant integration into the tissue can therefore be promoted by appropriate surface roughness, chemical composition, adhesion ligand density, as well as the availability of growth factors. This thesis mainly focuses on the development of orthopedic replacements and the improvement of the currently used blood vessel prostheses. Through the study of cell-biomaterial interactions, it was demonstrated that superimposed topography with features ranging from the nano to micro scale promotes cell spreading, proliferation, and the metabolic activity of osteoblast-like cells. Moreover, when comparing the chemical composition of biomaterials for orthopedic implants, higher osteoblast densities were observed on composites with 5-15 vol. % of calcium phosphate nanoparticles, while concentrations of 25 vol. % did not support cell proliferation. Cell viability, however, was not affected. In vivo, a more intensive formation of new bone tissue, was found on samples containing...

Le cancer de l'ovaire représente la première cause de décès par cancer gynécologique. La survie globale des patientes à 5 ans est inférieure à 30%. Ce sombre pronostic s'explique à la fois par la découverte tardive de la maladie et par le développement d'une chimiorésistance. L'ascite est un fluide exsudatif qui est fréquemment accumulé dans la cavité péritonéale au cours de la progression des cancers de l'ovaire. Ce « microenvironnement tumoral » particulier contribue à la dissémination des cellules cancéreuses et à leurs implantations péritonéales.L'objectif global du travail de thèse a été, d'une part d'évaluer l'influence de l'ascite sur le comportement des cellules cancéreuses ovariennes et d'autre part, d'étudier les mécanismes de résistance à la perte d'ancrage des cellules cancéreuses ovariennes.Nous avons ainsi démontré que l'ascite induit une transition épithélio-mésenchymateuse partielle et que les modifications des comportements cellulaires observées sont dépendantes des intégrines alpha-v.Deux ligands de ces intégrines, la vitronectine et la fibronectine, ont été purifiés selon un protocole original permettant la caractérisation des deux protéines à partir d'une même ascite. Ces protéines ascitiques ont des propriétés différentes selon leur origine, donc selon les patientes dont elles sont issues, et influencent le comportement adhésif des cellules avec un degré variable. L'importance de la signalisation dépendante des intégrines alpha-v et des voies MAP Kinases a également été démontrée dans l'établissement d'une résistance des sphéroïdes tumoraux à l'anoïkis.En perspective, approfondir les connaissances des processus cellulaires et moléculaires conduisant à la dissémination intrapéritonéale et à l'émergence de chimiorésistance ainsi que déterminer le rôle potentiel de protéines ascitiques dans ces processus pourraient permettre la découverte de nouvelles cibles thérapeutiques. / Ovarian cancer is the most lethal gynaecological malignant disease, mainly due to late diagnosis and to acquired chemoresistance. An exudative fluid named ascites is frequently accumulates within the abdominal cavity during ovarian cancer progression. This unique tumor microenvironment contributes to cancer cell dissemination and peritoneal metastasis.The aim of the study was to evaluate the influence of ascites on cancer cell behaviors and to better understand the mechanisms of ovarian cancer cell resistance to the loss of anchorage.We demonstrate that ascites induces a partial epithelial–mesenchymal transition and that the modifications of cell behaviors observed are dependent of alpha-v integrins. A combined purification protocol has been established in order to purify vitronectin and Fibronectin, both ligands of these integrins, from a single pathological sample. These purified ascitic proteins have different molecular features according to the patients and impact the adhesive cell behavior with various degrees.Moreover we showed the importance of alpha-v integrins and MAP Kinases signalling pathways in the anoikis resistance of ovarian cancer spheroids.Our prospects are i) to increase the knowledge of the cellular and molecular processes leading to the intraperitoneal dissemination and to the emergence of chemoresistance and also ii) to determine the potential role of ascitics proteins in these processes. We will expect that these investigations couldlead to the discovery of new therapeutic targets.

Le système immunitaire assure le maintien de l'intégrité de l'organisme, luttant notamment contre les infections. Durant ma thèse, j'ai étudié la réponse immunitaire locale et ses liens avec la réponse systémique chez la Drosophile. La réponse systémique, à l'échelle de l'organisme, est induite dans le corps gras en présence de bactéries dans la cavité générale et la réponse locale a lieu en cas d'accumulation de bactéries au contact d'un épithélium. Certaines infections locales, par voie orale, induisent à la fois une réponse locale et une réponse systémique, en absence de bactéries dans la cavité générale : cela implique l'envoi d'un signal au corps gras par l'intestin. Il a été proposé que ce signal serait le peptidoglycane bactérien diffusant à travers l'intestin. Ma thèse est constituée de deux projets. D'une part, j'ai caractérisé un mode d'infection locale, par voie génitale, induisant une réponse locale et systémique. Par dépôt génital de peptidoglycane, j'ai mis en évidence que cette molécule est le signal induisant la réponse systémique. Selon des données préliminaires, elle diffuserait par transcytose. D'autre part, j'ai étudié la fonction de PGRP-LA. Les PGRP sont des régulateurs et des effecteurs de la réponse immunitaire chez les animaux. L'analyse du transcriptome de trachées larvaires suggère que PGRP-LA participe au maintien d'un niveau basal d'immunité locale. Selon des résultats préliminaires, il serait impliqué dans la réponse du corps gras attenant aux glandes salivaires. Ma thèse apporte donc des informations sur la réponse immunitaire dans les trachées et l'appareil génital et sur la communication entre épithélium génital ou salivaire et corps gras

The potential of physiologically relevant in vitro cell culture models for studying physiological and pathophysiological phenomena has been widely recognized as replacements for animal and conventional in vitro models. To create models that accurately replicate the structure and function of tissues and organs, it is essential to comprehend the biophysical and mechanical features of the extracellular matrix (ECM) and incorporate them into the in vitro cell culture models. Therefore, we first aimed to investigate how nanotopography can modulate cell behaviors by studying cell behaviors on nanostructures of various aspect ratios on a cobalt-chromium-molybdenum (CoCrMo) alloy surface. We also explored the impact of nanofibrous membranes on the formation of alveolar epithelium, which is critical for lung alveolar interstitium chips. In addition, we investigated the effect of mechanical stretch on cell behaviors and focused on how the dimensionality of the stretch affects cell behaviors. To create physiologically relevant in vitro models based on our findings, we engineered a stem cell niche using a combination of nanofibrous membranes, mechanical stretch, and a soft substrate, and evaluated its impact on stem cell behaviors. Finally, we created a biomimetic human lung interstitium chip for application in physiological and pathophysiological in vitro studies.

<p dir="ltr">Tissue engineering utilizes polymers, cells, and other bioactive factors to promote regeneration within damaged tissue. The main works in this thesis employ naturally derived polymers for use in tissue engineering and explores ways to recapitulate native environments <i>in vitro</i>.</p><p dir="ltr">Collagen (col) is the most prevalent protein in the body. Col type I, II, and III are all fibril-forming collagens that provide structure to tissues. All three types polymerize <i>in vitro</i> to form hydrogels, and these hydrogels have often been studied for use in tissue engineering. Other applications include <i>in vitro </i>tissue models for studies on drug diffusion and drug delivery. Blending collagen types is of particular interest as col I is easier to source and is therefore cheaper than other collagen types. However, to confer biological signals to tissues where col II or III are more abundant (e.g., cartilage or cardiac tissue, respectively), col II or III can be added to col I to form col I/II or col I/III gels, respectively. Additionally, adding multiple types of col to hydrogel models better recapitulates the native environment and can better capture effects on drug diffusion. In this work, compared to col I alone, col I/II hydrogels polymerize more slowly, form more fibril bundles, result in softer hydrogels, and impede transport of larger macromolecules. On the other hand, col I/III gels polymerize at a similar rate to col I, create heterogenous fibril structures, are oftentimes stiffer than col I, and also impede transport of larger macromolecules. Additionally, this work explored the effect of polymerization temperature on blended gel polymerization and properties.</p><p dir="ltr">The second work evaluates col I/II hydrogels for a specific application: cartilage tissue engineering for osteoarthritic applications. Col II is the primary protein found in cartilage. Other components include: glycosaminoglycans, such as hyaluronic acid (HA) and chondroitin sulfate, chondrocytes (cartilage cells), and other small signaling molecules. Building on prior work in the group, high molecular weight hyaluronic acid (HA) was added to col I/II hydrogels, and cartilage differentiation of mesenchymal stem cells (MSCs) was assessed under ideal laboratory conditions and under pro-inflammatory, osteoarthritic conditions (i.e., cytokine-supplemented media of oncostatin M (OSM) at 10 ng/mL and tumor necrosis factor-α (TNF-α) at 20 ng/mL). The addition of HA did not dramatically impact cartilage differentiation of MSCs, however, HA did mitigate the effect of inflammation via downregulation of a degradative enzyme. HA had little impact on inflammatory cytokine production of interleukin (IL)-6 or IL-8, both of which are upregulated during osteoarthritis. However, a linear model suggests that HA and IL-8 are strongly correlated. Thus, this system should be explored further with different HA concentrations or presentations (e.g., chemically modified).</p><p dir="ltr">The last primary chapter of this thesis provides depth to the pro-inflammatory, osteoarthritic model used in the previous chapter. Different pro-inflammatory environments are studied using cytokines found in OA. MSC pellets (used in literature as controls to confirm chondrogenic potential of MSCs) were used to evaluate these inflammatory environments since MSCs are commonly used in tissue engineering. Six treatments were studied: negative control (without the chondrogenic growth factor TGF-β3), positive control (with the chondrogenic growth factor TGF-β3), and four cytokine treatments all with TGF-β3. First, IL-1β at 10 ng/mL was utilized as a comparison to literature. The other three cytokine groups used TNF-α at 20 ng/mL and OSM at 10 ng/mL individually or combined to form the main experimental group, OSM+TNF-α. All cytokine treatment groups limited cartilage production, but OSM decreased production to a statistically lesser extent than other cytokine groups. This trend was similar to observations made via immunostaining of cartilage matrix and gene expression analysis of aggrecan. Furthermore, OSM+TNF-α statistically lowered aggrecan gene expression. In terms of degradation, when compared to all other groups, OSM dramatically increased the protein expression of the degradative enzyme matrix metalloproteinase-13 (MMP-13). Evaluation of inflammatory markers (IL-6 and IL-8) revealed no signal for OSM-treated pellets. TNF-α yielded some signal after 1 week in culture but no signal after two weeks. IL-1β and OSM+TNF-α both resulted in sustained IL-6 and IL-8 expression, however, IL-1β exhibited large variance. Thus, each cytokine contributes to various pathways that are present in OA. Since the combination of OSM and TNF-α appeared to lower cartilage gene expression and resulted in sustained and reproducible IL-6 and IL-8 production, it may serve as a better model of OA than a single cytokine such as IL-1β.</p>

La protéine Damaged DNA-Binding 2 (DDB2) est connue pour son rôle dans la réparation de l'ADN lésé par les UV. Cependant, le laboratoire a montré que cette protéine est surexprimée naturellement dans les cellules tumorales mammaires non métastatiques et active leur prolifération, en favorisant leur entrée en phase de transition G1/S du cycle cellulaire. Il a été montré que cette nouvelle activité biologique de DDB2 dépend de sa capacité à intervenir dans la transcription de gènes cibles, comme celui codant l'enzyme anti-oxydante, la superoxyde dismutase à manganèse (SOD Mn). Sur la base que DDB2 est peu ou pas exprimée dans les cellules tumorales mammaires métastatiques, ce travail a consisté à étudier le rôle de cette protéine dans les capacités invasives de ces cellules. Dans un 1er temps, nous avons montré que les cellules tumorales mammaires hautement métastatiques (MDA-MB231 et SKBR3), lorsqu'elles surexpriment DDB2 après introduction de son gène, ont des capacités migratrices et invasives in vitro, ainsi que des propriétés in vivo à développer des métastases pulmonaires, fortement réduites, en association avec une diminution importante de l'expression de la métalloprotéase matricielle 9 (MMP-9). De même, lors d'une analyse rétrospective sur 92 échantillons cliniques provenant de patientes, une corrélation inverse entre l'expression de DDB2 et le haut grade (SBR>ou =3) des tumeurs mammaires est observée. Dans un 2ème temps, nous avons identifié le mécanisme moléculaire par lequel DDB2 agit négativement sur les capacités invasives des cellules tumorales mammaires. Nous avons montré que DDB2 intervient positivement sur l'expression du gène codant I kappa B alpha (IkBa), en se fixant sur une séquence d'ADN localisée dans la région proximale du promoteur, qui entraîne en conséquence une forte diminution de l'activité du facteur de transcription NF-kB. Ce dernier est connu pour son rôle dans les capacités invasives et migratrices des cellules tumorales mammaires métastatiques, en régulant de nombreux gènes cibles comme celui codant la MMP-9. Nous avons montré, que l?inhibition de l'expression d'IkBa, par ARN interférence restaure en partie les propriétés invasives des cellules tumorales mammaires métastatiques surexprimant DDB2, en association avec une réexpression de MMP-9. Dans un 3ème temps, nous avons également montré dans les cellules tumorales mammaires métastatiques, que l?expression constitutivement élevée de la SOD Mn, en l'absence de DDB2, dépend de l'activité conjointe des facteurs de transcription NF-kB et Sp1, révélant ainsi un autre mécanisme moléculaire impliqué dans les propriétés invasives de ces cellules. L'ensemble de ce travail contribue ainsi à mieux comprendre comment les cellules tumorales mammaires progressent vers un statut invasif et renforce également l'idée que DDB2 présente un intérêt clinique potentiel, comme marqueur prédictif de la progression métastatique des tumeurs mammaires. Enfin, la relation entre la DDB2, NF-kB et la SOD Mn représente une voie intéressante pour le développement de nouvelles thérapies anticancéreuses.

Droplet microfluidics is an emerging technology for analysis of single cells and biomolecules at high throughput. The controlled encapsulation of particles along with the surrounding microenvironment in discrete droplets, which acts as miniaturized reaction vessels, allows millions of particles to be screened in parallel. By utilizing the unit operations developed to generate, manipulate and analyze droplets, this technology platform has been used to miniaturize a wide range of complex biological assays including, but not limited to, directed evolution, rare cell detection, single cell transcriptomics, rare mutation detection and drug screening. The aim of this thesis is to develop droplet microfluidics based methods for analysis of single cells and nucleic acids. In Paper I, a method for time-series analysis of mammalian cells, using automated fluorescence microscopy and image analysis technique is presented. The cell-containing droplets were trapped on-chip and imaged continuously to assess the viability of hundreds of isolated individual cells over time. This method can be used for studying the dynamic behavior of cells. In Paper II, the influence of droplet size on cell division and viability of mammalian cell factories during cultivation in droplets is presented. The ability to achieve continuous cell division in droplets will enable development of mammalian cell factory screening assays in droplets. In Paper III, a workflow for detecting the outcome of droplet PCR assay using fluorescently color-coded beads is presented. This workflow was used to detect the presence of DNA biomarkers associated with poultry pathogens in a sample. The use of color-coded detection beads will help to improve the scalability of the detection panel, to detect multiple targets in a sample. In Paper IV, a novel unit operation for label-free enrichment of particles in droplets using acoustophoresis is presented. This technique will be useful for developing droplet-based assays that require label-free enrichment of cells/particles and removal of droplet content. In general, droplet microfluidics has proven to be a versatile tool for biological analysis. In the years to come, droplet microfluidics could potentially be used to improve clinical diagnostics and bio-based production processes. / <p>QC 20160926</p>

L’organisme humain présente de nombreuses constantes de régénération tissulaires et c’est cette caractéristique essentielle qui maintient l’équilibre physiologique. Toutefois, l’existence de lésions importantes provoquée par un déséquilibre interne ou externe peut empêcher l’organisme de s’auto-régénerer. Dans ce cas, l’application des biomatériaux développés pour des applications biomédicales peuvent améliorer le processus de guérison. Pour les applications en tissus durs, les biomatériaux doivent posséder des propriétés similaires aux matrices naturelles tant sur le plan biologique que physico-mécanique. Dans les applications en bioingénierie osseuse, les composites à base de collagène (Col) et d’hydroxiapatite (HA) sont devenus tellement performant qu’ils peuvent être classifiés comme des matériaux biomimétiques. Cette thèse propose la production d’une matrice 3-D poreuse à base d’HA et de Col (50:50wt%). Ce composite réticulé par le glutaraldéhyde a été caractérisé par des différentes techniques et servira de support pour la culture cellulaire. Des cellules estromales ostéoprogénitrices ont été cultivées dans un environnement statique et dynamique (deux vitesse de flux) et leurs capacités de colonisation ainsi que leurs comportements d’adhésion, de prolifération, de différentiation seront observés. A travers les résultats de diffraction de rayons X et de spectroscopie infrarouge, il est possible d’affirmer la présence dans la matrice collagène d’une phase minérale peu cristalline constituée par de l’hydroxiapatite carbonatée du type-B déficiente en calcium. La viabilité cellulaire a été fortement influencée par les systèmes de culture au cours des 21 jours. Les résultats du système dynamique en haute vitesse montrent une excellente capacité du composite à supporter les processus cellulaires. Les cellules sont capables d’adhérer, de proliférer et de coloniser la matrice tridimensionnelle. / The progress in Tissue Engineering area allows the development of biomaterials that mimic the properties of natural tissues. For biomedical applications in mineralized tissues, composites based on hydroxyapatite (HA) and collagen (Col) have presented good results when implanted in vivo. The aim of this work was to produce a 3-D matrix and to observe the cell behaviour when stromal cells are cultured in contact with HA-Col scaffold under static and dynamic conditions. For in vitro biological evaluation, osteoprogenitor human cells (Stro+1A cells) were grown and their colonization capacity and adhesion, proliferation and differentiation behaviour were quantified. Two perfusion flow rates (0,03ml/min and 0,3ml/min) were proposed for dynamic culture. The HA-Col composite was prepared by reorganization of Col fibrils simultaneously with HA crystal nucleation and precipitation from calcium and phosphate rich solutions. Afterwards, the composites were crosslinked and sterilized by gamma radiation. Stro+1A cells were inoculated (5x105 cells/sample) into the scaffolds and cultured over 21 days in a humid incubator at 37°C and 5% CO2. Infrared spectroscopy and X-ray diffraction results suggested a calcium-deficient hydroxyapatite as mineral phase. About cell culture, the cell number increased under higher flow rate dynamic culture. By scanning electron microscopy and histological sections, we observed cells adhered and spread inside colonized scaffolds.

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