In 2015, the United States is expected to have nearly 600,000 deaths attributed to cancer. Of these 600,000 deaths, 90% will be a direct result of cancer metastasis, the spread of cancer throughout the body. During cancer metastasis, circulating tumor cells (CTCs) are shed from primary tumors and migrate through bodily fluids, establishing secondary cancer sites. As cancer metastasis is incredibly lethal, there is a growing emphasis on developing "liquid biopsies" that can screen peripheral blood, search for and identify CTCs. One popular method for capturing CTCs is the use of a detection platform with antibodies specifically suited to recognize and capture cancer cells. These antibodies are immobilized onto the platform and can then bind and capture cells of interest. However, current means to immobilize antibodies often leave them with drastically reduced function. The antibodies are left poorly suited for cell capture, resulting in low cell capture efficiencies. This body of work investigates the use of lipid-based fibers to immobilize proteins in a way that retains protein function, ultimately leading to increased cell capture efficiencies. The resulting increased efficiencies are thought to arise from the retained three-dimensional structure of the protein as well as having a complete coating of the material surface with antibodies that are capable of interacting with their antigens. It is possible to electrospin cholesterol-based fibers that are similar in design to the natural cell membrane, providing proteins a more natural setting during immobilization. Such fibers have been produced from cholesterol-based cholesteryl succinyl silane (CSS). These fibers have previously illustrated a keen aptitude for retaining protein function and increasing cell capture. Herein the work focuses on three key concepts. First, a model is developed to understand the immobilization mechanism used by electrospun CSS fibers. The antibody immobilization and cell capturing abilities of the CSS fibers were compared to that of hydrophobic polycaprolactone (PCL) fibers and hydrophilic plasma-treated PCL fibers. Electrospun CSS fibers were found to immobilize equivalent amounts of protein as hydrophobically immobilized proteins. However, these proteins captured 6 times more cells, indicative of retained protein function. The second key concept was the design and fabrication of a hybridized lipid fiber. Lipid fibers provide improved protein function but fabrication difficulties have limited their adoption. Thus, we sought to fabricate a lipid-polymer hybrid that is easily fabricated while maintaining protein function. The hybrid fiber consists of a PCL backbone with conjugated CSS. The hybrid lipid fibers showed improved protein function. In addition, higher lipid concentrations were directly correlated to higher cell capture efficiencies. The third key concept was on the development of dually functionalized lipid fibers and understanding the resulting cell capture efficiencies. Many platforms are unable to simultaneously search for heterogeneous populations of CTCs–the ability to dually functionalize cell-capturing platforms would address this technological weakness. Studies indicated that dually functionalizing the lipid fibers did not compromise the platforms' abilities to capture the cells of interest. Such dually functionalized fibers allow for a single cell-capture platform to successfully detect heterogeneous populations of CTCs. The body of work encompassed herein describes the use of lipid fibers for antibody immobilization and cell capture. Data from various projects indicate that the use of cholesterol-based fibers produced from electrospun CSS are well suited for protein immobilization. The CSS fibers are able to immobilize equivalent amounts of protein as compared to other immobilization techniques. However, the benefit of these fibers is illustrated by the strong cell-capturing efficiencies, indicating that the immobilized proteins are able to retain their function and selectively target cells of interest. The successful immobilization of proteins and their retained function allows for the development of increasingly sensitive cancer diagnostic tools that are able to screen for CTCs early on in the cancer disease cycle.

Cette thèse a pour objectif le développement d'une technologie de tri cellulaire reposant sur le principe de la chromatographie d'affinité, pour des applications médicales. Pour cela les mécanismes gouvernant la capture spécifique des cellules dans une colonne chromatographique ont été étudiés. Dans un premier temps une étude sur un système modèle met en évidence le rôle prépondérant de l'étape de transport permettant la rencontre entre les cellules et la surface de capture. Le transport est principalement assuré par la sédimentation des cellules. Cela implique que la vitesse d'écoulement dans la colonne est un paramètre déterminant pour optimiser cette étape de rencontre. La capture de cellules est ensuite étudiée dans son ensemble : la rencontre et la formation du lien spécifique. Selon la vitesse d'écoulement deux régimes se distinguent. Pour des vitesses inférieures à 10-3 m.s-1 la cinétique de capture est gouvernée par la cinétique de rencontre. Pour des vitesses plus élevées toutes les rencontres n'aboutissent pas à une capture spécifique. La cinétique de capture est alors limitée par le transport et par la formation du lien. Cette étude expérimentale permet de dimensionner la technique de tri par chromatographie selon les besoins de l'application considérée. En particulier le tri à grande échelle (jusqu'à 1012 cellules) par chromatographie d'affinité est envisageable en ce qui concerne la durée de séparation et les dimensions de la colonne. / Development of cell sorting system based on affinity chromatography for medical application is the goal of this thesis. We study mechanisms responsible for specific cell capture in chromatographic column. First an experimental study on system model emphasize the importance of the transport step, which allows the encounter between cells and surface of capture. Cell sedimentation in the main way of transport. That means flow velocity is a key parameter to optimize this transport step. Then the whole cell capture is studied : encounter and specific link formation. Depending on the flow velocity, there are two regimens. Until a velocity of 10-3 m.s-1, kinetics of capture is governed by encounter kinetics. For higher velocity, only fraction of encounters leads to cell capture. The capture kinetics depends not only on transport, but also on kinetics of formation of specific link. This experimental study allows us to design cell affinity chromatography depending on the need of each application. Especially, cell sorting at industrial scale is conceivable concerning the separation duration and column dimensions.

Panarthropoda is a monophyletic group comprised of arthropods and lobopods, molting animals with a segmented body, paired appendages, dorsal brain, and ventral nerve cords. Evolutionary Developmental Biology (EvoDevo) is an interdisciplinary field that seeks to understand how changes in development form the basis for variations in morphology and phenotypic evolution, including the genetic network underlying these processes. To study the evolution of panarthropods from such an EvoDevo perspective, one typically uses standard molecular techniques. A first step here is to investigate the expression of a gene of interest in order to find out where and when it is transcribed during development. A hallmark of EvoDevo studies is its comparative character, often with respect to model organisms such as the fruit fly Drosophila melanogaster. Recently developed single-cell RNA sequencing technologies allow the profiling of a plethora of gene expression on the level of individual cells, and thus provide a much more detailed insight into gene expression. In Paper I, I applied standard molecular techniques used in EvoDevo research such as PCR, gene cloning, probe synthesis and whole mount in situ hybridization, to investigate the embryonic expression patterns of the tiptop/teashirt (tio/tsh) and spalt (sal) genes in a range of arthropods representing all main groups of this phylum, and an onychophoran. In the arthropod model Drosophila, these genes act as trunk-specifiers, and the objective of my work was to find out if this is conserved in Arthropoda or even Panarthropoda as a whole. I provide comprehensive data on arthropod tio/tsh and sal expression, including the first data from an onychophoran. The results support the idea that tio/tsh genes are involved in the development of ‘trunk’ segments by regulating limb development. In addition, my data suggest that the function of Sal is unlikely to be conserved in trunk vs head development. Early expression of sal, however, is in line with a potential homeotic function of this gene, at least in Arthropoda. In Paper II, I provide an embryonic tissue dissociation protocol for embryos of the common house spider Parasteatoda tepidariorum that I developed and that I successfully applied for single-cell RNA sequencing. In addition, I report on the progress of this experiment, and provide and discuss preliminary results.

År 2020 listade Världshälsoorganisationen (WHO) cancer som den globalt ledande dödsorsaken med över 10 miljoner dödsfall årligen. Av dessa 10 miljoner fall förekommer nästan 70% i låg- till medelinkomstländer - en siffra som på grund av den låga prioriteringen av cancerbehandling- och diagnostik förväntas öka till 85% redan år 2030. Att utveckla enkla, specifika och prisvärda verktyg för diagnostik kommer därför att bli avgörande för förebyggandet av cancer på en global nivå. För att komma ett steg närmare denna utveckling optimerades och testades i denna studie ett mikrofluidiskt system, utvecklat genom layer-bylayer- metoden, baserat på cellulosa nanofibriller med förmågan att isolera och fånga cirkulerande tumörceller. För att uppnå en termodynamisk jämvikt optimerades systemets hydrodynamiska parametrar optimerades för att uppnå en homogen fördelning med hög densitet av det cellulosa-baserade systemet i det mikrofluidiska chippet. Då jämvikt är grundläggande för att maximera det efterföljande beläggningen av antikroppar, och därmed hur effektivt celler isoleras, modifierades parametrar såsom koncentration, flödeshastighet, inkubationstid med fler tills att önskad effekt uppnåtts. Således koncepttestades systemet genom att fånga celler spetsade i blod och därmed demonstrera att systemet kan användas i syfte att isolera cancerceller från blodprov. Detta öppnar upp för utveckling av liknande diagnostiska verktyg som kan användas för att isolera lågfrekventa celler direkt från blod. / In 2020, the World Health Organization (WHO) listed cancer as the leading cause of death worldwide, reaching a staggering number of 10 million cancer-related deaths annually. Of these 10 million deaths, nearly 70% occurred in low- and middle-income countries; a number that is expected to increase to 85% by 2030 due to the lack of resources as well as low priority of the development of cancer treatment and diagnosis. Hence, the development of a sophisticated, specific and affordable diagnostic tool will be crucial for global cancer prevention and control. In this study, a cellulose nanofibril-based Layer-by-Layer system for immuno-capture of tumour cells in a microfluidic device was optimized and tested for the development of a simple and cost-effective diagnostic tool for use in resource-limited areas. In the pursuit of a thermodynamic equilibrium, the hydrodynamic parameters of the system were optimized to achieve a homogeneous distribution with a high surface density of the cellulose-based system across the microfluidic channels. Since an equilibrated system is essential to maximize the antibody coating, and thereby cell capture efficiency, parameters including but not limited to concentration, flow rate and incubation time were altered until a desired effect had been achieved. Thus, as proof-of-concept, the system was tested by capturing cancer cells spiked into whole blood, thereby demonstrating that the system can be utilized for the purpose of isolating cancer cells from blood samples. This paves the way for the development of similar clinical diagnostic tools for the isolation of rare cells directly from whole blood.

Designade ankyrinupprepningsproteiner (DARPiner) är små, mycket stabila antikroppsmimetiska proteiner. I det här projektet användes anti-EpCAM-DARPiner tillsammans med mikrofluidik för att avgära om de kunde fånga upp HCT116-celler mer effektivt än anti-EpCAM-antikroppar. Ytorna på insidan av mikroffluidikkanaler förändrades genom bindning av N-γ-maleimidobutyryl-oxysuccinimidester (GMBS) och merkaptopropyltrietoxysilan (MPTES) för anti-EpCAM-antikroppar och GMBS och (3-aminopropyl)trietoxysilan (APTES) för DARPiner. Båda kanaltyperna testades genom inflöde av cancerceller och helblod blandat med cancerceller. Ingen effektiv och konsekvent celluppfångst åstadkoms trots att det visades att antikropparna och DARPinerna kunde binda till cellerna direkt och att test med fluorescenta DARPiner och antikroppar visade att ytförändringskemin var fungerande. Slutsatsen blev att de mest troliga orsakerna till misslyckandena var att ytförändringskemin påverkade proteinernas bindningsförmåga negativt eller att proteinerna bands till kanalernas yta i fel riktning. DARPiner är fortfarande intressanta för tillämpningar inom mikrofluidik, men vidare förbättring av det experimentella protokollet behövs. / Designed ankyrin repeat proteins (DARPins) are small and highly stable antibody mimetics. In this project, anti-EpCAM DARPins were used in conjunction with microfluidics to determine if they could capture HCT116 cells more effectively than anti-EpCAM antibodies. The inside surfaces of microfluidic chips were modified using N-γ-maleimidobutyryl-oxysuccinimide ester (GMBS) and mercaptopropyltriethoxysilane (MPTES) for anti-EpCAM antibodies, and surface modifications for anti-EpCAM DARPins were made using GMBS and (3-aminopropyl)triethoxysilane (APTES). Both chip types were tested using cancer cells and whole blood mixed with cancer cells. No effective and consistent cell capture was achieved, despite the antibodies and DARPins being shown to be able to bind to the cells directly and tests with fluorescently labelled DARPins and antibodies showing that the surface modification chemistry used was functional. It was concluded that the most likely causes of the failures were surface modifications interfering with the binding ability of the proteins, or improper orientation of the bound proteins. The DARPin remains a protein of interest for microfluidic applications, but further changes and optimisation of the experimental protocol is necessary.