Pools of mutants of minimal complexity but maximal coverage of genes of interest facilitate screening for genes under selection in a particular environment. Prior to this work, mutants were generated by random transposon insertions, which yielded highly complex pools for in vivo studies. Recent advances in polymerase chain reaction (PCR)-based mutagenesis in bacteria using the lambda red recombinase, as well as whole genome sequencing, enable a more directed approach for the generation of mutants. The lambda red approach was used to construct individual mutants in 1,023 Salmonella enterica serovar Typhimurium genes, including almost all genes found in Salmonella, but not in related genera. All the mutations were confirmed simultaneously using a novel amplification strategy to produce labeled ribonucleic acid (RNA) from a T7 RNA polymerase promoter, introduced during the construction of each mutant, followed by hybridization of this labeled RNA to a Typhimurium genome tiling array. To demonstrate the ability to identify fitness phenotypes using our pool of mutants, the pool was subjected to selection by intraperitoneal injection into BALB/c (Bagg Albino) mice and was recovered from the spleen. Changes in the representation of each mutant were monitored using T7 transcripts hybridized to a novel inexpensive minimal microarray. Among the top 120 statistically significant spleen colonization phenotypes, 51 were mutations in genes with no previously known role in this model. Fifteen phenotypes were tested using individual mutants in competitive assays and eleven were confirmed in individual mixed intraperitoneal infection in mice, including the first two examples of attenuation for sRNA mutants in Salmonella. We refer to our method as Array-Based Analysis of Cistrons Under Selection (ABACUS). Among the confirmed mutants identified in the ABACUS screen was a component of the twin arginine transport (Tat) system, tatC, required for transport of folded proteins across the cellular membrane. TatC is the highly conserved component necessary for recognition of the twin arginine containing signal sequence S/T-R-R-x-FL- K. We confirmed [delta] tatC mutants are defective for colonization of the liver and spleen in competitive infections with wild type ATCC14028 after intraperitoneal infection in Salmonella- susceptible (BALB/c). We also found that [delta] tatC mutants were defective for swimming motility, but not swarming motility, which was linked to the ability to elaborate flagellins on the bacterial surface under different conditions.

Deciphering genetic determinants of tumorigenesis is the greatest challenge and promise of the present-day era of biomedical research. As extensive tumor genome characterization efforts of the past decade had revealed, tumor genomes harbor multiple point mutations and gene copy number alterations. This exquisite complexity brings forth the challenge of distinguishing numerous incidental alterations from those that are functionally relevant to tumorigenesis. During the past decade, functional genetic screens have shown their utility in identifying genetic changes that functionally contribute to tumor-specific hallmarks and thus hold a great potential for identifying promising new targets for the rational design of successful anticancer therapies. A key hallmark of cancer cells is their ability to escape signals that govern homeostasis of normal tissue. In normal epithelia, growth and survival of cells is dictated by their physical anchorage to the extracellular matrix, and disruption of proper cell-matrix anchorage triggers cell death. Tumors of epithelial origin develop ways to subvert anoikis signals, which enables both their uncontrollable expansion at the primary site as well as metastatic colonization of distant organs. Understanding the genetic determinants of matrix-independent growth of cancer cells is a promising approach to identify potent and selective anticancer targets. In the work presented in this dissertation, we use an unbiased functional genetic screening approach to test a large set of eight thousand human genes to identify those that are involved in inducing and maintaining resistance of mammary epithelial cells to matrix detachment-induced cell death. We show that a cell adhesion molecule PVRL4 promotes cell survival in the absence of matrix anchorage in normal epithelial cells and in cancer cells. Our work reveals that PVRL4 promotes anchorage-independent growth by promoting cell-to-cell attachment and matrix-independent c-Src activation. PVRL4 is focally and frequently amplified in several types of solid tumors. Growth of orthotopically implanted tumors in vivo is inhibited by blocking PVRL4-driven cell-to-cell attachment with monoclonal antibodies, demonstrating a novel strategy for targeted therapy of cancer.

No description available.

During the last 40 years, Drosophila melanogaster has become an invaluable tool in understanding innate immunity. The innate immune system of Drosophila consists of a humoral and a cellular component. While many details are known about the humoral immune system, our knowledge about the cellular immune system is comparatively small. Blood cells or hemocytes constitute the cellular immune system. Three blood types have been described for Drosophila larvae. Plasmatocytes are phagocytes with a plethora of functions. Crystal cells mediate melanization and contribute to wound healing. Plasmatocytes and crystal cells constitute the blood cell repertoire of a healthy larva, whereas lamellocytes are induced in a demand-adapted manner after infection with parasitoid wasp eggs. They are involved in the melanotic encapsulation response against parasites and form melanotic nodules that are also referred to as tumors. In my thesis, I focused on unraveling the mechanisms of how the immune system orchestrates the cellular immune response. In particular, I was interested in the hematopoiesis of lamellocytes. In Article I, we were able to show that ectopic expression of key components of a number of signaling pathways in blood cells induced the development of lamellocytes, led to a proliferative response of plasmatocytes, or to a combination of lamellocyte activation and plasmatocyte proliferation. In Article II, I combined newly developed fluorescent enhancer-reporter constructs specific for plasmatocytes and lamellocytes and developed a “dual reporter system” that was used in live microscopy of fly larvae. In addition, we established flow cytometry as a tool to count total blood cell numbers and to distinguish between different blood cell types. The “dual reporter system” enabled us to differentiate between six blood cell types and established proliferation as a central feature of the cellular immune response. The combination flow cytometry and live imaging increased our understanding of the tempo-spatial events leading to the cellular immune reaction. In Article III, I developed a genetic modifier screen to find genes involved in the hematopoiesis of lamellocytes. I took advantage of the gain-of-function phenotype of the Tl10b mutation characterized by an activated cellular immune system, which induced the formation blood cell tumors. We screened the right arm of chromosome 3 for enhancers and suppressors of this mutation and uncovered ird1. Finally in Article IV, we showed that the activity of the Toll signaling pathway in the fat body, the homolog of the liver, is necessary to activate the cellular immune system and induce lamellocyte hematopoiesis.

A range of biochemically diverse molecules located in the plasma membrane— such as proteins, glycans, and lipids—mediate cellular recognition events, initiation of signalling pathways, and the regulation of processes important for the normal development and function of multicellular organisms. Interactions mediated by cell surface receptors can be challenging to detect in biochemical assays, because they are often highly transient, and membrane-embedded receptors are difficult to solubilise in their native conformation. The biochemical features of low-affinity extracellular protein interactions have therefore necessitated the development of bespoke methods to detect them. Here, I develop a genome-scale cell-based genetic screening approach using CRISPR-Cas9 knockout technology that reveals cellular pathways required for specific cell surface recognition events. Using a panel of high-affinity monoclonal antibodies, I first establish a method from which I identify not only the direct receptor but also other required gene products, such as co-receptors, post-translational modi cations, and transcription factors contributing to antigen expression and subsequent antibody-antigen recognition on the surface of cells. I next adapt this method to identify cellular factors required for receptor interactions for a panel of recombinant proteins corresponding to the ectodomains of cell surface proteins to the endogenous surface receptors present on a range of cell lines. In addition to finding general cellular features recognised by many ectodomains, I also identify direct interaction partners of recombinant protein probes on cell surfaces together with intracellular genes required for such associations. Using this method, I identify IGF2R as a binding partner for the R2 subunit of GABAB receptors, providing a mechanism for the internalisation and regulation of GABAB receptor signalling. The results here demonstrate that this single approach can identify the molecular nature and cell biology of surface receptors without the need to make any prior assumptions regarding their biochemical properties.

Die Genregulation ist ein komplexer Prozess, bei dem Zellen die Menge der Genprodukte steuern, um ihre Identität auszubilden und auf Umweltveränderungen zu reagieren. Die CRISPR-Technologie hat genetische Screens revolutioniert und ermöglicht es, mehrere Transkripte gleichzeitig zu untersuchen. In dieser Arbeit werden die Vorteile und Herausforderungen gepoolter CRISPR-Screens zur Erforschung der Genregulation untersucht. Es wird ein CRISPR-ko-Screen in embryonalen Mausstammzellen (mESCs) beschrieben, der pluripotenzerhaltende Transkriptionsfaktoren identifiziert. Es zeigte sich, dass ein Screening mit einer kleinen Bibliothek den Großteil des biologischen Signals eines genomweiten Screens erfasst und die Identifizierung von Genkandidaten mit kleinen Effektgrößen verbessert. Nachfolgend wird CRISPTimeR, eine neue Methode für die Analyse von Zeitreihen von CRISPR-Screens, vorgestellt. Sie basiert auf gemischten linearen Modellen und ermöglicht es, Treffer zu identifizieren und gleichzeitig zeitlich zu klassifizieren. Als Nächstes wurde CRISPRi verwendet, um für die Pluripotenz von mESCs relevante lncRNAs zu untersuchen, was aufgrund ihrer schlechten Annotation und niedrigen Expressionsniveaus schwierig ist. Eine mögliche Lösung ist eine manuell verfeinerte Annotation von Transkriptionsstartstellen und kleinere Bibliotheks-Screens mit empfindlicherer phänotypischer Auslesung. Zudem wurde ein Sättigungsscreen genomischer Regionen rund um den PHOX2B-Lokus, zur Identifikation cis-regulierender Elemente, durchgeführt. Dabei wurden CRISPRa-reaktive Elemente identifiziert, die Gene in der PHOX2B-TAD regulieren, und mit diesen mittels Einzelzell RNA-seq in Verbindung gebracht. Zusammenfassend zeigt diese Arbeit den Wert gepoolter CRISPR-Screens für die Erforschung der Genregulation und Herausforderungen der Analyse nicht-kodierender Elemente. Zusätzlich beschreibt sie ein neues Tool für die Analyse von kodierenden und nicht-kodierenden CRISPR-Screens in Zeitreihen. / Gene regulation is a complex process in which cells control gene product levels to establish identity and respond to environmental changes. CRISPR technology has revolutionized genetic screening, enabling researchers to study multiple transcripts simultaneously. This thesis explores the advantages and challenges of using pooled CRISPR screens to study gene regulation. First, I describe a CRISPR-ko screen in mouse embryonic stem cells (mESCs) to identify transcription factors involved in pluripotency maintenance. I show that a small-library screen captures most of the biological signal observed in a genome-wide screen, and it improves the identification of candidate genes with small effect sizes. Next, introduce CRISPTimeR, a novel method for the analysis time-series CRISPR screens. CRISPTimeR is based on mixed linear models; it allows to use information from a time-series experiment to identify, and simultaneously perform temporal classification on, hits. Next, I use CRISPRi to study lncRNAs relevant to pluripotency in mESCs. Targeting lncRNAs poses challenges due to poor annotation and low expression levels. I suggest to address these issues by using a hand-refined annotation of transcription start sites and by designing small-library screens with more sensitive phenotypic readout. Finally, I describe a saturation screen targeting large genomic regions around the PHOX2B locus, to identify putative cis-regulatory elements. I identified CRISPRa responsive elements involved in regulating the expression of genes within the PHOX2B TAD, which were then matched with the genes they control using single-cell RNA-seq. Overall, in this thesis I demonstrate the value of CRISPR pooled screens for studying gene regulation, while highlighting the challenges associated with targeting non-coding elements and suggesting possible approaches to address these challenges. Moreover, I introduce a novel tool for the analysis of both coding and non-coding time-series CRISPR screens.