Clustered regularly interspaced short palindromic repeats (CRISPR) are derived from a bacterial and archaeal adaptive immune system. The core enzymes of CRISPR are RNA-guided endonucleases that sequence-specifically cleave foreign double-stranded DNA. Improving and controling the properties of the CRISPR system is a crucial step in advancing the therapeutic potential of CRISPR technology. Several classes of these enzymes exist and are being adapted for biotechnology, such as genome engineering. Cas12a (Cpf1) is a Type V CRISPR-associated (Cas) enzyme that naturally uses only one guide RNA, in contrast to Type II CRISPR-Cas9 enzymes. Thus, Cpf1 may represent a simpler, more practical tool for applications such as gene editing and therapeutics. This dissertation comprises four related studies in this area. To better understand the functional requirements for Cpf1-crRNA interaction and develop modified crRNAs suitable for synthetic biology and therapeutic applications, the first study performed nucleotide substitutions in the crRNA. It focused on the protein-interaction motif of the crRNA by incorporating base changes at the 2ʹ position that alter hydrogen-bonding capacity, sugar pucker, and flexibility. DNA substitutions in RNA can probe the importance of A-form structure, 2ʹ-hydroxyl contacts, and conformational constraints within RNA-guided enzymes. In addition, Chemical modifications include 2'-deoxy, 2'-fluoro, 2'- deoxy-arabinonucleic acid, and oxepane. Our study discovered that 2'-fluoro maintains the A-form structure and is compatible with AsCpf1 activity. Biochemical endonuclease activity, gene editing efficiency, Cpf1 binding affinity, and ribonucleoprotein stability were used to assess the tolerance and effects of modification. Characterizing structure-function requirements for Cpf1-crRNA interaction will facilitate better design and tuning of Cpf1 enzymes. The second study established a FRET-based assay in collaboration with a computational collaborator to identify small molecule inhibitors predicted by virtual docking and simulations. This study aims to lay the foundation for efficient, safe implementation of CRISPR-Cpf1. The third study used chemically modified Cas9-guide RNAs to offset known weaknesses of CRISPRi. It takes advantage of the high binding affinity and nuclease resistance of modified guides to potentially reduce the required components for CRISPRi.

Wnt signaling is an evolutionarily conserved pathway that is essential for the development of the metazoan embryo. Wnt signaling controls essential developmental processes including cell fate, cell polarity, dorsal-ventral patterning and tissue movement. Misregulated Wnt signaling can have disastrous effects on the developing human embryo, leading to potentially fatal congenital malformations including anencephaly and spina bifida. In addition to embryonic development, misregulated Wnt signaling has been implicated in human pathologies including colon and breast cancers and skeletal malformations. Wnt signaling is divided into two main pathway branches, canonical or beta-catenin dependent, and non-canonical, sometimes referred to as the planar cell polarity (PCP) pathway. The former branch activates the transcription of the downstream target genes leading to the patterning the dorsal-ventral axis of the developing embryo, whilst the latter has no downstream transcriptional targets but rather acts upon the cytoskeleton to control cell and tissue polarity and movement. Wnt signaling bifurcates into these two branches at the level of the protein Dishevelled (Dvl). The Dishevelled-associated activator of morphogenesis 1 (Daam1) protein was identified via a yeast-two hybrid screen using Dvl as bait. Daam1 interacts directly with Dvl and mediates activation of the small GTPase Rho, a key player in non-canonical Wnt signaling necessary for proper gastrulation in the Xenopus (frog) embryo. In addition to Daam1, vertebrates possess a second Daam, Daam2, originally identified via an in silico screen in humans. Similar to Daam1, frog Daam2 participates in non-canonical Wnt signaling, contributing to proper formation of the embryonic neural tube. However, conflicting opinions on the function of Daam2 have led to discrepancies regarding its position in Wnt signaling and function in development. Daam1/2 have not been extensively investigated at the genetic level, therefore, I employed the genetic model zebrafish (Danio rerio) to further clarify their role in Wnt signaling. Using techniques such as the latest gene-editing system CRISPR/Cas9 and other well-established molecular methods including in situ hybridization, RT-PCR and knockdown using morpholino oligonucleotides, I sought to further establish the role of the Daam protein family in vertebrate embryonic development. Together, my results indicate that the zebrafish Daam1a/b and Daam2 behave similarly to Daam1 and Daam2 in frog, respectively, by participating in the non- canonical Wnt signaling pathway and mediating morphology in the developing zebrafish embryo. / Biology

Selenoprotein H (SELENOH) is a nucleolar oxidoreductase with DNA binding properties whose function is not well understood. To determine the functional and physiological roles of SELENOH, a knockout of SELENOH was generated in cell lines using CRISPR/Cas9-mediated genomic deletion and in mice by targeted disruption. Based on the sequenced genome, the results of deduced protein sequences indicated various forms of mutants in the CRISPR/Cas9-mediated knockout, including a frame-shift by aberrant splicing and truncated SELENOH by early termination of the translation process. Loss of SELENOH in HeLa cells induced slow cell proliferation, the formation of giant multinucleated cells, accumulation of unrepaired DNA damage and oxidative stress, and cellular senescence. SELENOH cells were enlarged and possessed a single large nucleolus. Atomic force microscope showed increased stiffness in the nucleoli of SELENOH knockout cells, which suggests that SELENOH maintains the flexible structure of the nucleolus. Furthermore, the knockout of SELENOH led to a large-scale reorganization of the nucleolar architecture with the movement of nucleolar protein into nucleolar cap regions in response to oxidative stress. The nucleolar reorganization is dependent on ATM signaling. Altogether, results suggest that SELENOH appears to be a sensor of oxidative stress that plays critical roles in redox regulation and genome maintenance within the nucleolus. To determine the physiological role of SELENOH in vivo, Selenoh knockout mice were generated by targeted deletion through homologous recombination. Selenoh+/− mice were fertile and phenotypically indistinguishable from wild-type littermates. Results from matings of Selenoh+/− mice showed a significantly reduced fraction of Selenoh−/− offspring on the basis of Mendelian segregation. Since some Selenoh−/− were born, it is likely that Selenoh is a partially essential gene in mice. Live-born Selenoh−/− mice were viable and born without apparent phenotypes. Selenoh−/− mice at 2-month of age showed increased GPX activity in the lung but not in the brain and liver. Furthermore, loss of Selenoh resulted in the aggravated formation of aberrant crypt foci in the colon of Selenoh+/− mice that were injected with azoxymethane. Altogether, SELENOH has critical roles in embryogenesis and colorectal carcinogenesis.

NK cell based anti-tumour therapies demonstrate high efficacy in targeting hematological malignancies, however, treatments for advanced solid tumours face challenges. The immunosuppressive environment produced by tumours prevents NK cells from maintaining cytotoxic activity and reducing tumour burden. Enhancing NK cell activation is essential to improve their function against solid tumours. Genetic manipulation of primary NK cells with viral and non-viral methods has seen a drastic improvement in recent years. Lentiviral vectors are being used to generate CAR-NK cells ex vivo, while refinement of electroporation protocols has allowed for the generation of stable gene knockouts in primary NK cells. To establish and validate the generation of a stable knockout in primary human NK cells we focused on targeting the NCAM-1 (CD56) surface adhesion molecule. The high surface expression of CD56 in NK cells makes it a suitable target to establish the knockout protocol. Furthermore, despite its levels of expression being correlated to different functional phenotypes, the role of CD56 in NK cell function is not understood. Here we have shown that current lentiviral transduction protocols are not viable methods to deliver the sgRNA/Cas9 system into primary NK cells. However, we found that nucleofection of the sgRNA/Cas9 complex into NK cells is an efficient method to generate gene knockouts. Using newly generated CD56KO NK cells we have shown that the expression of CD56 has no effect on NK cell cytotoxicity, cytokine production, proliferation, and in vivo tissue trafficking. In parallel, we have also identified an intracellular pathway that is active in the tumour microenvironment and could inhibit NK cell function. Recent studies on the intracellular signaling of the E3 ubiquitin-protein ligase Cbl-b have highlighted its role in inhibiting NK cell tumour lytic and anti-metastatic activity. Immunosuppressive factors produced by tumours activate the Cbl-b pathway, leading to the targeted degradation of signaling proteins required for NK cell activation. We have shown that Cbl-b is upregulated in ex vivo expanded NK cells cultured with GAS6 or ovarian cancer ascites. Therefore, the generation of human primary Cbl-bKO NK cells could be a beneficial asset to enhance NK cell cancer immunotherapy. / Thesis / Master of Science (MSc)

Clustered regularly interspaced palindromic repeats (CRISPR) and their associated (Cas) proteins co-opted as biotechnological tools have improved the simplicity and accessibility of gene editing for fields ranging from crop science to the treatment of human disease. These technologies, however, come with an inherent degree of risk associated with off-target events or direct misuse, accidental or intentional, leading to permanent genetic damage to ecosystems, livestock, or people. Naturally occurring anti-CRISPR proteins have been described, as well as synthetic small molecule inhibitors, but each of these approaches, while suitable for certain applications, leaves something to be desired in deliverability or efficacy in the face of many possible adverse CRISPR-related events. Inspired by strides in the field of oligonucleotide therapeutics, we developed the first reported anti-CRISPR nucleic acids for Streptococcus pyogenes (Sp)Cas9 to address the critical need for fail-safe inhibitors of Cas enzymes. These inhibitors, termed small nucleic acid-based inhibitors of Cas9 (SNuBs), comprise two modules which act in tandem to bind and disable the SpCas9 RNP. We have demonstrated that SNuBs inhibit Cas9 in vitro and in human cells. Successive rounds of optimization on our initial designs have yielded inhibitors capable of carrier-free uptake into human cells, high nuclease resistance, and robust inhibition at low stoichiometric concentrations relative to Cas9 and its RNA guide. In their current form, SNuBs quite possibly present the most tenable approach to inhibiting Cas9 in a variety of contexts including therapeutic applications in the near future.

Morbus Cushing ist die häufigste Ursache für endogenes Cushing-Syndrom und führt auf Grund eines kortikotropen Hypophysenadenoms zu einem Glucocorticoid Überschuss und wiederum zu einer hohen Morbidität und Mortalität. Die Ursache hierfür sind unter anderem somatische Mutationen in den Deubiquitinasen USP8 und USP48. Das Ziel dieser Arbeit war es mittels der CRISPR/Cas9-Methode, die Mutationen USP8 und USP48 in Zelllinien zu etablieren und diese für Cushing-Syndrom Analysen zu verwenden. Hierfür wurden in dieser Arbeit gRNAs für USP8 und USP48 designt, welche anschließend in die humane embryonale Zelllinie HEK293AD Zellen transfiziert wurden. Diese Zellen wurden zu monoklonalen Zellen vereinzelt. Ziel war einen Knock-out von USP8 bzw. USP48 zu generieren. Es konnte ein erfolgreicher Zellklon generiert werden mit einem Knock-out von USP48. Ebenfalls konnte ein Genomediting von USP8 in Exon 20 durchgeführt werden. Zusammenfassend konnte die CRISPR/Cas9 Methode für ein M. Cushing-Zellmodells etabliert und eine gute Ausgangsbasis für weitere Experimente (z.B. ein gezielter Knock-in von USP8- und USP48- Mutationen) generiert werden. / Cushing disease (CD) is the most common reason for endogenous Cushing syndrome (CS). It is caused by corticotrope adenoma of the pituitary resulting in hypercortisolism that is associated with high morbidity and mortality. One of the underlying reasons are the activating mutations of the deubiquitinase USP8 and USP48. The objective of this work was to establish the USP8 and USP48 mutations in cell lines by the CRISPR/Cas9 method in order to use them for further CS analyses. Therefore, we designed gRNAs against USP8 and USP48 which were transfected into the human embryonal cell line of HEK293AD cells. Those cells were separated to generate monoclonal cell lines entailing the knock-out of either USP8 or USP48. We successfully provided a cell clone with a knock-out of USP48. Furthermore, we were able to edit the genome of USP8 in exon 20. In summary we were able to establish the CRISPR/Cas9 method for a CD cell model and provided a good baseline for further experiments (i.e., creating a knock-in of USP8 and USP48 mutations).

Ziel der vorliegenden Arbeit war die nanoskopische Analyse struktureller Differenzierung und Plastizität präsynaptischer aktiver Zonen (AZs) an der NMJ von Drosophila melanogaster mittels hochauflösender, lichtmikroskopischer Bildgebung von Bruchpilot (Brp). In erster Linie wurde das lokalisationsmikroskopische Verfahren dSTORM angewendet. Es wurden neue Analyse-Algorithmen auf der Basis von HDBSCAN entwickelt, um eine objektive, in weiten Teilen automatisierte Quantifizierung bis auf Ebene der Substruktur der AZ zu ermöglichen. Die Differenzierung wurde am Beispiel phasischer und tonischer Synapsen, die an dieser NMJ durch Is- und Ib-Neurone gebildet werden, untersucht. Phasische Is-Synapsen mit hoher Freisetzungswahrscheinlichkeit zeigten kleinere, kompaktere AZs mit weniger Molekülen und höherer molekularer Dichte mit ebenfalls kleineren, kompakteren Brp-Subclustern. Akute strukturelle Plastizität wurde am Beispiel präsynaptischer Homöostase, bei der es zu einer kompensatorisch erhöhten Neurotransmitterfreisetzung kommt, analysiert. Interessanterweise zeigte sich hier ebenfalls eine kompaktere Konfiguration der AZ, die sich auch auf Ebene der Subcluster widerspiegelte, ohne Rekrutierung von Molekülen. Es konnte demonstriert werden, dass sich eine höhere Moleküldichte in der Lokalisationsmikroskopie in eine höhere Intensität und größere Fläche in der konfokalen Mikroskopie übersetzt, und damit der Zusammenhang zu scheinbar gegensätzlichen Vorbefunden hergestellt werden. Die Verdichtung bzw. Kompaktierung erscheint im Zusammenhang mit der Kopplungsdistanz zwischen VGCCs und präsynaptischen Vesikeln als plausibles Muster der effizienten Anordnung molekularer Komponenten der AZ. Die hier eingeführten Analysewerkzeuge und molekularbiologischen Strategien, basierend auf dem CRISPR/Cas9-System, zur Markierung von AZ-Komponenten können zukünftig zur weiteren Klärung der Bedeutung der molekularen Verdichtung als allgemeines Konzept der AZ-Differenzierung beitragen. / The aim of this work was a nanoscopic analysis of structural differentiation and plasticity of presynaptic active zones (AZs) at the NMJ of Drosophila melanogaster using super-resolution light microscopy of Bruchpilot (Brp). The localization microscopy technique dSTORM was primarily used. New analysis algorithms based on HDBSCAN were developed to ensure objective and largely automatized quantification including the substructure of the AZ. Differentiation was assessed using the model of phasic and tonic neurons that are represented by type Is and type Ib neurons at this NMJ. Phasic Is synapses with higher release probability displayed smaller, more compact AZs with less molecules and an enhanced molecular density with smaller, more compact Brp subclusters. For acute structural plasticity the model of presynaptic homeostasis, which is accompanied by a compensatory increase of neurotransmitter release, was used. Interestingly, this again showed a more compact arrangement of the AZ, that was also found in Brp subclusters, without addition of molecules. It could be demonstrated that a higher molecular density in localization microscopy translates into a higher intensity and area in confocal microscopy and, thus, the apparent discrepancy to earlier studies could be explained. With respect to the coupling distance between VGCCs and presynaptic vesicles compaction appears to be a plausible mechanism for an efficient remodeling of AZ components. The analysis tools and molecular biology strategies, based on the CRISPR/Cas9-System, introduced here will be useful to further clarify the importance of molecular compaction as a general concept of AZ differentiation.

Lysine-specific Demethylase 1B (KDM1B) is a chromatin regulator which functions as a histone eraser through the removal of the post-translational modifications mono and dimethylation of histone 3 on lysine 4 (H3K4me1/2). This process is enhanced by the formation of a complex with Nuclear Protein Glyoxylate Reductase (NPAC). NPAC resolves the sequestration of the nucleosome histone tail to allow robust demethylation of H3K4me2 by KDM1B, during transcriptional elongation by RNA polymerase 2 (RNAP II). KDM1B is involved in many crucial processes during development. Its physiological functions include the establishment of maternal genomic imprints, reset of the epigenome during somatic cell reprogramming, and regulation of brown adipogenic differentiation. In light of this, the role of KDM1B in human embryonic stem cells (hESCs) is examined through CRISPR/Cas9-editing to further dissect its biological functions during embryogenesis. CRISPR-induced knockouts of KDM1B exhibited similar cell proliferation rate and expression of OCT4 and NANOG pluripotency markers to wildtype cells. Furthermore, KDM1B-/- clones were able to maintain their pluripotency potential by differentiating to all germ layers in teratoma and embryoid body formation assays. In addition, RNA-seq of KDM1B-/- clones showed enrichment of mesoderm lineage-related gene ontology (GO) terms in the downregulated differentially expressed genes. Thus, KDM1B is believed to be dispensable during the pluripotent stage of the cell but proved fundamental during later stages of development.

Salicylic Acid (SA) is an important plant hormone which acts as a therapeutic agent in the plant in response to biotic and abiotic stress. It plays a significant role in growth and development. SABP2, a methyl salicylate esterase is a key player in SA mediated defense signaling. It catalyzes the conversion of mobile methyl salicylate to salicylic acid. During infection, accumulation of salicylic acid in the distal organ in response to the primary infection elsewhere primes the plant to defend against subsequent infection by the mechanism known as Systemic Acquired Resistance (SAR). SIP68, one of the interacting proteins of SABP2 is a glucosyltransferase protein. Glucosyltransferase protein catalyzes the formation of the glycosidic bond by transferring glucose molecule from donor to acceptor molecules. Plant glucosyltransferase is widely distributed in nature playing the dual role of activating and inactivating enzymes. They are also associated with changing the protein stability and solubility of compounds. Since SABP2 has a role in SA mediated defense signaling and glucosyltransferase proteins are associated with physiological function thus, there is a possibility of SIP68 associated with the major or supportive role in either or both functions. The purified recombinant SIP68 protein was tested for glucosyltransferase activity using radioactive method. The purified SIP68 glucosylates various artificially available flavonoid compounds with highest activity detected with Kaempferol (flavonol) followed by quercetin but negligible activity with SA. HPLC based glucosyltransferase assay further verified SIP68 as a flavonoid UDP-glucosyltransferase, not SA glucosyltransferase. Our interest is to further characterize SIP68 and assess its role in plant defense mechanism. Knowing its expression pattern inside plant cell will help us to assess its activity pattern inside the cell. For this enhanced Green Fluorescent Protein (eGFP) tagged SIP68 was transiently expressed inside the plant cell. Confocal microscopy imaging suggests SIP68 likely to be localized in the cytoplasm which will be further confirmed by subcellular fractionation. To assess the role of SIP68 in plant defense mechanism transgenic line expressing altered SIP68 gene was generated using CRISPR Cas9 technique. Verified transgenic line challenged under different biotic and abiotic stress will help us to understand the role of SIP68 in plant defense mechanism. Our research will help us to understand defense mechanism in tobacco model system enabling us to use the knowledge to develop the resistant varieties of crops that are capable of withstanding the adverse condition of pathogenic as well environmental challenges.

Glucosyltransferases catalyze the transfer of glucose molecules from an active donor to acceptor molecules and are involved in many plant processes. SIP68, a tobacco glucosyltransferase protein, is a SABP2-interacting protein. It was identified in a yeast two-hybrid screen using SABP2 as bait and tobacco proteins as prey. SABP2, converts methyl salicylate to salicylic acid (SA) as a part of the signal transduction pathways in SA-mediated defense signaling. Subcellular localization is a crucial aspect of protein functional analysis to assess its biological function. The recombinant SIP68 tagged with eGFP was expressed transiently in Nicotiana benthamiana and observed under confocal microscopy. Fluorescent signals were observed in the epidermal cells. Subcellular fractionation of the tobacco leaves transiently expressing SIP68-+eGFP confirmed that SIP68 is localized in the cytosol. To study the role of SIP68 in plant stress signaling, transgenic lines with altered SIP68 expression were generated using RNAi and CRISPR Cas9 and analyzed.