Derived from and inspired by the adaptive immune system of bacteria, CRISPR has gone from basic biology knowledge to a revolutionizing biotechnological tool, applicable in many research areas such as medicine, industry and agriculture. The full mechanism of CRISPR-Cas9 was first published in 2012 and various CRISPR-Cas systems have already passed the first stages of clinical trials as new gene therapies. The immense research has resulted in continuously growing knowledge of CRISPR systems and the technique seems to have the potential to greatly impact all life on our planet. Therefore, this literature study aims to thoroughly describe the CRISPR-Cas system, and further suggest an undergraduate laboratory exercise involving gene editing with the CRISPR-Cas9 tool. In this paper, we describe the fundamental technical background of the CRISPR-Cas system, especially emphasizing the most studied CRISPR-Cas9 system, its development and applications areas, as well as highlighting its current limitations and ethical concerns. The history of genetic engineering and the discovery of the CRISPR system is also described, along with a comparison with other established gene editing techniques.  This study concludes that a deeper knowledge about CRISPR is important and required since the technique is applicable in many research areas. A laboratory exercise will not only inspire but also provide extended theoretical and practical knowledge for undergraduate students.

<p>  </p> <p>Malignant Peripheral Nerve Sheath Tumor (MPNST) is a form of soft tissue sarcoma arising from peripheral nerve sheath cells. Currently, there is no clinically available targeted therapy because the targetable essential driver genes in this tumor are largely unknown. SMARCAD1 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily A, containing DEAD/H box 1) has been identified as a new tumor suppressor of MPNSTs in zebrafish. Several studies have also linked <em>SMARCAD1</em> with cancer development together. However, the cellular roles of <em>SMARCAD1</em> in human MPNST cells remain unclear. To investigate DNA damage repair functions of SMARCAD1 in human MPNST, we created a doxycycline-inducible Schwannoma cell line by CRISPR-Cas13d, a newly developed mRNA knockdown method. I verified efficiently SMARCAD1 knockdown cell line by western blot. In addition, knockdown of SMARCAD1 inhibits Schwannoma cell proliferation and anchorage-independent growth. It is reported that SMARCAD1 is involved in DNA damage repair mechanisms. I confirmed that loss of SMARCAD1 expression compromises DNA damage repairing function in Schwannoma cells. This result was also verified in two zebrafish <em>smarcad1</em> mutants. In summary, I utilized a novel gene knockdown approach to generate a SMARCAD1 Schwannoma cell line and validated its function in DNA damage repair. This study might provide information for developing a new treatment option for MPNSTs.</p>

BACKGROUND: Containing a brain for signal processing and decision making, and a peripheral component for sensation and response, the nervous system provides higher organisms a powerful method of interacting with their environment. The specific neurons involved in pain sensation are known as nociceptors and are the source of normal nociceptive pain signaling to prompt appropriate responses. Though acute hypersensitization can be advantageous by encouraging an organism to allow an injured area to heal, chronic pain conditions can be pathological and can markedly reduce quality of life. While a variety of genes have been associated with congenital pain conditions, two rare cases examined in this study have not had their mutated genes identified. Potassium voltage-gated channel subfamily H member 8, or KCNH8, is involved in regulating action potential production and propagation, and has not been linked with pain processing of any kind to date. Here, a male patient evaluated at Boston Children’s Hospital contains a novel single-base KCNH8 mutation and possesses an extremely low sensitivity to cold temperatures and mechanical pain, but a higher sensitivity to warmer temperatures. A separate protein, intersectin-2, or ITSN2, normally functions in clathrin-mediated endocytosis and exocytosis. A second patient at Boston Children’s Hospital expresses a previously-unseen point mutation in ITSN2 and experiences erythromelalgia, characterized by episodes of intense pain and red, swollen limbs during ambient warm temperatures. Through the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 genome editing, this study will produce these specific genetic mutations in mouse lines to explore their effects on mammalian behavior. OBJECTIVES: This project employs two transgenic mouse models to study the behavioral phenotypes associated with rare potentially damaging mutations in KCNH8 and ITSN2 exhibited in the human patients. Through these experiments, a greater understanding of neural pain signaling and sensitivity changes can occur. METHODS: The differences in temperature preference of KCNH8 and ITSN2 mutant mice compared to wild type mice lacking these mutations was studied using thermal plates under cold and warm conditions. Direct application of acetone and von Frey filaments to mouse paws was used to study cold and mechanical sensitivity. Further testing of stamina, anxiety, coordination, and strength were also evaluated. RESULTS: A marked decrease in sensitivity to von Frey stimulation (p<0.01) and acetone administration (p<0.05) was observed in KCNH8 mutant mice. Thermal preference testing demonstrated a decreased preference for warmer temperatures as compared to wild type mice. In addition, anxiety levels were also observed to be slightly higher in these mutant KCNH8 mice (p<0.05). The mutant ITSN2 mice spent less time at cooler temperatures, though surprisingly they significantly preferred warmer conditions as compared to their wild type littermates. A full and partial reversal of these temperature preferences was demonstrated in cold and heat thermal conditions respectively after intraperitoneal gabapentin injection, which normalized the mice toward wild type behavior. CONCLUSIONS: Data from the KCNH8 mutant mouse model indicates an aversion to warmer temperatures and a decreased ability to detect cold or mechanical pressure, much like the human patient. The mutant ITSN2 mice were less likely to spend time at cooler temperatures, indicating heightened sensory sensitivity, but their preference for warmer temperatures suggests a possible desensitization of the affected nociceptors. These results often mirror the patient’s phenotype, but the preference for ambient warmer environments appears opposite to the patient. As the ITSN2 mice feel discomfort at cooler temperatures, a proposed desensitization at warmer temperatures would result in a more comfortable environment and could explain the observed preference. The trends toward normal neural firing rates achieved through gabapentin injection suggest that the aberrant responses in mutant ITSN2 mice is due to altered sensitization, but additional examination under these conditions with a larger group of mice is necessary to further unravel these signaling pathways. However, these extremely encouraging data introduce two new molecular targets for acute pain control.

Due to its strength, flexibility, and biocompatibility, spider silk is a highly appealing material for applications in the medical field. Unfortunately, natural spider silk is difficult to obtain in large quantities because spiders are territorial and cannibalistic, making them impractical to farm. Synthetic spider silk proteins produced by transgenic hosts such as bacteria and goats have made it possible to obtain the quantities of spider silk needed to study it more fully and to investigate its potential uses. The spider silk proteins produced in our laboratory do not have an optimal purification method to remove all of the non-biocompatible contaminants and have not previously been tested for their biocompatibility. The first focus of this dissertation was to create goat cells that can be used to create new goats. These new goats will produce proteins that can be purified more efficiently and more completely. The second focus of this dissertation was to perform biocompatibility tests on goat-derived spider silk proteins. Prior to performing any biocompatibility tests, a method was established for removing endotoxins – an impurity that causes an immune response in the body – from the proteins. This work has shed light on areas for improvement in the silk protein purification process and laid groundwork for the production of new goat-derived proteins. These steps will help make it possible for synthetic spider silk to progress further toward becoming a viable biomaterial.

CRISPR (clustered regularly interspaced short palindromic repeats)-guided nucleases such as Cas9 remain atop the most exciting biological systems in gene editing and therapeutic potential. The modern adaptation of the Streptococcus pyogenes (Spy) Cas9 machinery for directed DNA editing relies on two major components; a Cas9 protein, and an RNA guide. This study aims at modification of the guide RNA to probe structural requirements and modification tolerance while studying the biochemical properties of the ribonucleoprotein complex. We find that the SpyCas9-RNP is not only capable of heavy substitutions and modifications in the guide, but specific properties can be tuned by careful and directed modifications. DNA substitutions in the 3’ end of the guide RNA improves cleavage activity and efficiency in vitro. Various RNA chemistries such as 2’-fluoro and other RNA mimics maintain biochemical activity but can be used to improve stability against nucleases. Additionally, tethering of the tracrRNA and crRNA together into a sgRNA was found to affect the fundamental properties of the Cas9 protein, improving activity, but reducing target binding affinity and cleavage rate. Directed modification of the guide RNA can be used to exploit certain biochemical properties for effective therapeutic applications.

No description available.

Glioblastoma (GBM) remains the most aggressive primary brain tumor in adults. Since 2005, Standard of Care (SoC) consists of surgical resection followed by radiation and adjuvant chemotherapy with temozolomide. Treatment failure is attributed to intratumoral heterogeneity with populations capable of mechanisms to repair damaged DNA. Given the lack of progress to improve patient outcomes, the current work encompasses how multi-omic approaches can be utilized to uncover novel biology in GBM and develop precision medicines to exploit these cancer specific phenomena. Using patient derived GBM samples I first used the surface marker CD133 to interrogate glioblastoma stem cells, a subpopulation of cells identified to withstand conventional therapies and lead to tumor relapse. I used a genome-wide CRISPR-Cas9 library to conduct an unbiased loss-of-function phenotypic screen to identify regulators of CD133. I then validated SOX2 as a direct transcription factor to PROM1 encoding CD133. These findings further show the untapped potential of CRISPR to uncover novel biology to directly apply to broader fields of stem cells and cancer biology. Next, I combed GBM data sets at transcriptomic and proteomic levels to identify understudied proteins as potential targets for immunotherapies. Glycoprotein nonmetastatic melanoma protein B (GPNMB) has previously been identified as a clinically relevant target in GBM and shown to be active in the tumor immune microenvironment. I found GPNMB to be upregulated in recurrent GBM and macrophage populations which can be exploited in a more comprehensive manner to treat GBM. Through a series of models, I elucidated how GPNMB influences GBM biology, its effectiveness as a target for Chimeric Antigen Receptor T-cells, and how it can be paired with CD133 therapies to provide better coverage of tumor cells. Together, these studies highlight how advances in pre-clinical models and technologies can be leveraged to develop new therapies in a rational manner. / Thesis / Doctor of Science (PhD) / Glioblastoma (GBM) remains an aggressive and incurable brain cancer despite decades of intense research. Treatment failure is due to the untargeted approaches currently undertaken in the clinic. The current work uses multiples methods to interrogate how GBM grows and develops over time. Using GBM samples from consenting patients, I investigated an important population of the tumor using a surface marker CD133 and CRISPR to study which genes influenced it. I then successfully validated SOX2 as a direct regulator of CD133 expression. Next, I combed multiple data sets for a target to kill GBM cells without harming healthy tissue in patients. I found Glycoprotein Non-Metastatic Melanoma Protein B (GPNMB) to be exploitable and used several experimental methods to investigate its role in GBM progression. Finally, we used a novel immunotherapy to eliminate cells which express GPNMB. Together, these findings could apply to the broader field of stem cell biology and be used for a more targeted method to eliminate the cancer entirely.

The nonapeptide family of hormones is deeply conserved in evolution. In teleost fishes, as in all vertebrates, two nonapeptide families exist. These are vasotocin (avp) and oxytocin (oxt). While vasotocin has been shown to regulate individual aspects of reproductive physiology in several teleost species, an integrative assessment of its role on male and female reproduction is currently lacking even in widely used fish models, such as the zebrafish (Danio rerio). Taking advantage of the genetic tractability of the zebrafish, and its emerging status as model to study reproductive physiology, I generated avp -/- mutants using a CRISPR/Cas9 based approach to determine reproductive consequences in female and male zebrafish. Following the identification of a female-specific reproductive phenotype which manifests as a reduction in oocyte release and decreased quivering behaviour, I investigated the potential mechanistic basis at the level of the gonad. In avp -/- ovaries, significantly fewer eggs were present compared to WT fishes. When comparing the distribution of oocyte maturation stages, a significantly lower percentage of stage I and higher percentage of stage V oocytes was present in avp-/- ovaries. The altered distribution in oocyte maturation stages coincided with significant decreases in ovarian transcript abundance of nanos2, a germ-cell specific marker suggesting a possible role for Avp in germ-cell maintenance. Additionally, I observed a decrease in the ovarian concentration of the prostaglandin PGF2, which coincided with a reduction in ovarian transcript abundance of pla2g4ab, a paralogue of the phospholipase A2 involved in mobilizing arachidonic acid, a precursor of PGF2,. Together, these finding suggests a role for Avp in PGF2 -mediated ovulation. Because Avp has pleiotropic effects and may thus affect female reproductive physiology indirectly, we assessed somatic growth, a key regulator of sexual maturation in zebrafish, as well as aspects of the endocrine stress axis known to affect oocyte growth in avp -/- mutants. While avp -/- mutants did not exhibit differences in somatic growth up to sexual maturation or GSI, mutants exhibited hypercortisolism. While other zebrafish knock-out mutants exhibiting persistent hypercortisolism do not share the observed reproductive phenotype, future studies investigating potential contributions of pleiotropic Avp effects are nevertheless warranted. Overall, I demonstrate that avp, while not essential, affects female reproductive success, at least iii in part by regulating oocyte maturation. This finding is in line with the recent findings from other vertebrate and invertebrate species, suggesting an evolutionarily ancient role in these processes. It is anticipated that such novel insights into the regulation of female oocyte maturation have in addition to increasing our understanding of female reproduction, translational potential for captive breeding (aquaculture, species conservation) and ecotoxicology (insight into mode of action of specific EDCs).

Cas12a (Cpf1) is a representative type V-A CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) effector RNA-guided DNA endonuclease used widely for genome editing. Identification of Cas12a inhibitors is important for regulating gene editing, enhancing genome editing specificity, and safety for human therapeutics. This study used a fluorescence-based assay to screen diverse drug libraries at a core facility for potential small molecule candidates that can inhibit AsCas12a endonuclease activities. Further validation of the major hit compounds revealed that these small molecules inhibit Cas12a in vitro DNA cis and trans cleavage activities as well as gene editing in cells. IC50 values obtained from gene editing inhibition were even lower than primary screening reported IC50. We determined the impact of the small molecules on the thermal stability of Cas12a, possible binding sites, and binding affinity (Kd) using thermal denaturation experiments. Enzyme kinetics studies were used to investigate the effect of the inhibitors on ribonucleoprotein complex formation. The discovered molecules create a tool for achieving safer applications of CRISPR-Cas12a in biotechnology and therapeutics.

Fusarium graminearum is responsible for causing Fusarium head blight in cereals and maize imposing a significant impact in Canadian agriculture. While a handful of secondary metabolites produced by F. graminearum are recognized as contributors to disease virulence, the functions of numerous molecular products arising from biosynthetic gene clusters expressed during infection remain undiscovered. Presented here are the results of CRISPR-Cas9 mediated gene-deletion experiments disrupting core biosynthetic genes from four biosynthetic gene clusters with reported in-planta transcription: C08, C16, C13 and C70. Both wheat head infection assays and coleoptile infection assays were used to evaluate the pathology phenotypes of transformant strains illustrating potential links between C16 and pathogenicity. Culture medium screening experiments using transformant strains were profiled by UHPLC-HRMS and targeted MS2 experiments to confirm the associated secondary metabolite products and attempt to identify unknown secondary metabolites of the biosynthetic gene clusters. While C08 secondary metabolite remained elusive, confirmation of C16 secondary metabolites led to hypotheses regarding their potential connections to the inhibition of plant immune response and untargeted secondary metabolite profiling of the C13/C70 transformant strains suggests that this BGC may have significant implications for global secondary metabolite production.