Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments. The R package is based on a mathematical model in which cell state alterations occur due to stochastic transitions between distinct cell states whose rates only depend on the current state of a cell. CellTrans is an automated tool for estimating the underlying transition probabilities from appropriately prepared data. We point out potential analytical challenges in the quantification of these cell transitions and explain how CellTrans handles them. The applicability of CellTrans is demonstrated on publicly available data on the evolution of cell state compositions in cancer cell lines. We show that CellTrans can be used to (1) infer the transition probabilities between different cell states, (2) predict cell line compositions at a certain time, (3) predict equilibrium cell state compositions, and (4) estimate the time needed to reach this equilibrium. We provide an implementation of CellTrans in R, freely available via GitHub (https://github.com/tbuder/CellTrans).

Die rheumatoide Arthritis (RA) ist eine chronisch-entzündliche Bindegewebserkrankung mit bevorzugtem Befall der Gelenke. Es bestimmen Knorpel- und Knochendestruktionen das Krankheitsbild. Eine Schlüsselrolle in der Pathogenese nehmen proliferierende, synoviale Fibroblasten (RASF) durch Auflösung der extrazellulären Matrix (EZM), durch Interaktion mit immunkompetenten Zellen und durch Produktion pro-inflammatorischer Zytokine ein. Die vorliegende Arbeit zeigt die Migrationseigenschaften von RASF und zwei verschiedenen murinen (LS48) und humanen (TK188) Fibroblastenzelllinien in einem In-vitro-Migrationsassay. Es wird der Einfluss von Antikörpern sowie verschiedener EZM-Komponenten auf die Migration der Zelllinien untersucht. Die nachfolgende Analyse phänotypischer Charakteristika stellt dabei die besondere Rolle der genannten Fibroblastenzelllinien heraus, welche eine Reihe von Gemeinsamkeiten untereinander und mit RASF besitzen. Sie zeigen ebenso erhöhte Migrationsaktivität unter dem Einfluss eines Chemoattraktants und besitzen ähnliche Destruktionsmuster von Kollagenmatrizen. Beide Zellreihen exprimieren mehr RASF-typische Proteasen, Adhäsionsmoleküle und immunologisch agierende Proteine als nicht pathologisch transformierte Fibroblasten. Ebenso weisen sie eine gesteigerte Stoffwechselaktivität und Proliferationstätigkeit auf. Diese in vitro erbrachten Hinweise auf mögliche Knorpeldestruktionen sollten Anlass für weitere In-vivo-Studien zu den genannten Zelllinien geben.

Confronted with the global demographic changes and the increasing pressure on modern healthcare system, there has been a surge of developing new technology platforms in the past decades. Droplet microfluidics is a prominent example of such technology platforms, which offers an efficient format for massively parallelized screening of a large number of samples and holds great promise to boost the throughput and reduce the costs of modern biomedical activities. Despite recent achievements, the realization of a compact and generic screening system which is suited for resource-limited settings and point-of-care applications remains elusive. To address the above challenges, the dissertation focuses on the development of a compact multifunctional droplet micro-magnetofluidic system by exploring the advantages of magnetic in-flow detection principles. The methodologies behind a novel technique for biomedical applications, namely, magnetic in-flow cytometry have been put forth, which encompass magnetic indexing schemes, quantitative multiparametric analytics and magnetically-activated sorting. A magnetic indexing scheme is introduced and intrinsic to the magnetofluidic system. Two parameters characteristic of the magnetic signal when detecting magnetically functionalized objects, i.e. signal amplitude and peak width, providing information which is necessary to perform quantitative analysis in the spirit of optical cytometry has been proposed and realized. Magnetically-activated sorting is demonstrated to actively select individual droplets or to purify a population of droplets of interest. Together with the magnetic indexing scheme and multiparametric analytic technique, this functionality synergistically enables controlled synthesis, quality administration and screening of encoded magnetic microcarriers, which is crucial for the practical realization of magnetic suspension arrays technologies. Furthermore, to satisfy the needs of cost-efficient fabrication and high-volume delivery, an approach to fabricate magnetofluidic devices on flexible foils is demonstrated. The resultant device retains high performance of its rigid counterpart and exhibits excellent mechanical properties, which promises long-term stability in practical applications.