abstract: Immunotherapy has received great attention recently, as it has become a powerful tool in fighting certain types of cancer. Immunotherapeutic drugs strengthen the immune system's natural ability to identify and eradicate cancer cells. This work focuses on immune checkpoint inhibitor and oncolytic virus therapies. Immune checkpoint inhibitors act as blocking mechanisms against the binding partner proteins, enabling T-cell activation and stimulation of the immune response. Oncolytic virus therapy utilizes genetically engineered viruses that kill cancer cells upon lysing. To elucidate the interactions between a growing tumor and the employed drugs, mathematical modeling has proven instrumental. This dissertation introduces and analyzes three different ordinary differential equation models to investigate tumor immunotherapy dynamics. The first model considers a monotherapy employing the immune checkpoint inhibitor anti-PD-1. The dynamics both with and without anti-PD-1 are studied, and mathematical analysis is performed in the case when no anti-PD-1 is administrated. Simulations are carried out to explore the effects of continuous treatment versus intermittent treatment. The outcome of the simulations does not demonstrate elimination of the tumor, suggesting the need for a combination type of treatment. An extension of the aforementioned model is deployed to investigate the pairing of an immune checkpoint inhibitor anti-PD-L1 with an immunostimulant NHS-muIL12. Additionally, a generic drug-free model is developed to explore the dynamics of both exponential and logistic tumor growth functions. Experimental data are used for model fitting and parameter estimation in the monotherapy cases. The model is utilized to predict the outcome of combination therapy, and reveals a synergistic effect: Compared to the monotherapy case, only one-third of the dosage can successfully control the tumor in the combination case. Finally, the treatment impact of oncolytic virus therapy in a previously developed and fit model is explored. To determine if one can trust the predictive abilities of the model, a practical identifiability analysis is performed. Particularly, the profile likelihood curves demonstrate practical unidentifiability, when all parameters are simultaneously fit. This observation poses concerns about the predictive abilities of the model. Further investigation showed that if half of the model parameters can be measured through biological experimentation, practical identifiability is achieved. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2020

Genetically engineered oncolytic viruses (OVs) have been proven to be effective anti-cancer agents. However, the heterogeneity of tumours and obligate attenuation of OVs to achieve safety can limit their efficacy. Our lab has previously shown that diverse small molecules, which we have termed “Viral Sensitizers”, used in combination with OVs can potentiate the infection of cancer cells by OVs over 1000-fold in some cases, resulting in cancer-specific killing in both in vitro and in vivo tumour models. We observed that a subset of viral sensitizer compounds ultimately acts by reducing the expression of IFNb, thereby inhibiting antiviral signaling. Here, we aimed to further refine the mechanism of action of this class of compounds. Our results suggest that VSe1 and more stable analogs such as VSe1-28 inhibit nuclear accumulation of NF-kB p65 and expression of various antiviral cytokines including, TNFa, IL-6, IFITM1, and MX2 in multiple oncolytic VSV-resistant cancer cell lines but not in normal cells. This was also observed in vivo in CT26wt immune-competent mouse tumour models, where our group has already demonstrated the therapeutic benefit of combining VSe1-28 with oncolytic VSV. Using various biochemical methods, we have determined that VSe1 and its analog VSe1-28 lead to these effects at least in part through covalent modification of NF-kB p65. In sum, this study provides a new understanding of how these novel viral sensitizers work at the molecular level. This new understanding will not only aid in the discovery and development of improved molecules but also their clinical translation in combination with oncolytic viruses.

Translation control is crucial during virus-host interaction, in which the host relies on the translation machinery to mount an antiviral response or induce the inflammation response to reduce virus spread, while the virus aims to take control of this system to thwart the host defense while producing viral progeny. The field of oncolytic virus (OV) therapy relies on replicating, engineered viruses that preferentially infect tumor cells to induce direct oncolysis or promote an antitumor immune response. Despite the importance of translation control in virus-host interaction, not much has been described on the interaction at the translation level between OV and cancer cells. I propose that this knowledge gap could reveal significant improvements in OV efficacy in treating cancer. In my first study, I set out to characterize the translatome of an infection-resistant breast cancer cell line infected by three clinically advanced OVs to identify residual antiviral activity in cancer cells regulated by translation control. I found the inositol phosphatase Inpp5e to be a novel antiviral gene that is translationally induced during infection via a transcript variant shift. Mechanistically, I showed that the majority of Inpp5e transcripts in uninfected cells contain a long 5’ UTR that harbor four translationally inhibitory upstream reading frames (uORF). Yet, OV infection induced the expression of a shorter 5’ UTR with a spliced intron that removes three uORFs, derepressing the translation of Inpp5e mRNA. CRISPR-Cas9 knockout of Inpp5e also enhanced the infectivity of oncolytic HSV1 and VSV. My study suggests the existence of a class of translationally regulated antiviral genes in cancer cells. In my second study, I sought to adapt the translation of transgenes to the unique translation condition imposed by the infecting virus via the incorporation of a viral 5’UTR. I identified HSV1 5’UTRs by locating the transcription start site of most HSV1 genes using RNA-seq data, then determined the 5’UTR of US11 as a potent translation enhancer during HSV1 infection. Incorporation of this 5’UTR into the transgene expression cassette inserted into the HSV1 genome enhanced transgene expression significantly at the translation level. In my third study, I set out to explore the mechanism of miR-223 mediated inflammation inhibition. miR-223 is a protective miRNA in the context of atherogenesis via suppressing inflammatory signaling. Using transcriptome and translatome profiling (RNA-seq and Ribo-seq), I found that the inhibitory effect of miR-223 on inflammation occurs primarily at the translation level. Overall, my work highlights the importance of translation control in OV-cancer cells interaction, as well as in inflammation-related diseases.

Immunotherapy is a promising tool in the fight against cancer and aims to recruit patients own immune systems to seek out and destroy malignant cells. Options such as oncolytic viruses (OVs), autologous tumour vaccines and chimeric antigen receptors have shown clinical success to date, yet there remain significant hurdles to overcome. Here, we demonstrate a novel vaccine combining irrCell priming and infected cell boosting dramatically improves the tumour-specific CTL response against CT26 tumours and can be further enhanced using additional immunogenic factors (armed OVs, adjuvants). We also developed a novel fluorescence-based high-throughput screening platform to identify compounds that sensitize resistant solid tumours to killing by CAR-T cells, which ultimately revealed cardiac glycosides as putative tumour sensitizers. Overall, this thesis identifies several novel enhancers of the anticancer immune response, including a heterologous irr:ICV vaccine regimen and the potential ability to identify molecules to overcome resistance to CAR-T therapy.

Pancreatic cancer (PC) is a highly aggressive disease with unmet therapeutic needs. Recent advances in the use of oncolytic viruses (OVs) as cancer therapeutic agents bring new hope to fight the notorious disease that is PC. Although OVs have shown promising results in certain cancers, some tumors remain resistant to OV therapy due to their inherent residual antiviral mechanisms. We hypothesized that the use of OV-encoded artificial microRNAs (amiRNAs) could help target the cellular antiviral components associated with the observed OV resistance and could also sensitize neighboring tumor cells to OV therapy and small molecule inhibitors through the secretion of amiRNA-containing extracellular vesicles (EVs) from infected cells. To find such amiRNAs, a viral surrogate library encoding ~16,000 unique amiRNAs was passaged in pancreatic cancer cell lines to enrich for sequences that could enhance OV replication. An amiRNA that improves PC cell killing when expressed from an OV was identified. Target identification of this amiRNA (amiR-4) revealed ARID1A as a key player in resistance to OV therapy in pancreatic cancers. This target is of particular interest, since its downregulation acts in a synthetic lethal fashion with inhibition of the EZH2 methyltransferase. Combining VSV51-amiR-4 with a small molecule inhibitor of EZH2 enhances PC cell death. Moreover, amiR-4 is packaged in cancer cell-secreted EVs which can reach neighboring naïve cells to sensitize them to EZH2 inhibition-mediated cell death and to spread the OV-mediated tumor killing effect throughout the tumor. This data translates into tumor debulking and survival in animal models of highly aggressive PC. This work not only broadens our knowledge on the resistance of select tumors to oncolytic virotherapy and the EV-mediated bystander killing effect in OV-infected tumors, but it also establishes OVs as a novel tool to produce anti-cancer therapeutic EVs in situ to improve therapeutic gain. Ultimately, our work provides new hope for a cure to the grim disease that is PC.

Despite the remarkable success of adoptive T cell therapy in the treatment of melanoma and hematological malignancies, therapeutic capacity in a broad range of solid tumours is impaired due to immunosuppressive events that render tumour-specific T cells unable to persist and kill transformed cells. To address some of the limitations of ACT in solid tumours, our laboratory has developed a therapeutic modality utilizing oncolytic virus, which expresses a tumour-associated antigen, known as an oncolytic viral vaccine (OVV), in combination with tumour specific central memory T cells. With this therapeutic approach (ACT), we can achieve robust in vivo expansion of transferred cells resulting in the complete and durable tumour regression in multiple solid murine tumour models. However, we demonstrate that the curative potential is lost when the tumour stage and burden increase as expanded transferred cells differentiate to a dysfunctional state resulting in the progressive decline in the tumour-specific CD8+ T cell response. Thus, we believe that restoring the T cell response in late-stage tumours will lead to enhanced curative potential of ACT in late-stage tumours. We have previously shown that HDACi, MS-275, can enhance the therapeutic capacity of a T cell-based therapy in an aggressive brain tumour model. In addition, concomitant delivery of MS-275 with ACT ensures durable cures through immunomodulatory mechanisms. Strikingly, concomitant delivery of MS-275, a class 1 histone deacetylase inhibitor (HDACi), with ACT in late-stage tumours completely restores the transferred T cell response to similar levels observed in early-stage tumours resulting in the complete regression of advance-stage tumours. Furthermore, MS-275 enhanced the proliferative capacity and tumour-specific cytotoxic function of transferred cells, independently of tumour stage, type and mouse strain. Interestingly, we did not observe a complete reversal of T cell dysfunction, but rather observed that MS-275 conferred unique properties to T cells as the expression of some markers typically associated with T cell dysfunction was enhanced in addition to persistence and proliferation capacity. Moreover, concomitant delivery of MS-275 also restored the therapeutic capacity of endogenously primed tumour-specific CD8+ T cells expanded by an OVV in late-stage tumours, demonstrating the potential for general use for MS-275 in T cell-based therapies. Our data suggests the use of HDACi may potentiate T cell-based immunotherapies to overcome tumour-mediated T cell dysfunction in advanced stage solid tumours. / Thesis / Master of Science in Medical Sciences (MSMS)

Through the years, cancer therapies have progressed rapidly, pouring out novel treatments such as gene therapy, small molecule therapies and immunotherapy. One such immunotherapy, adoptive cell transfer (ACT), augmented through the addition of a chimeric antigen receptor (CAR), has proven success in treatment of hematological malignancies. Additionally, oncolytic viruses (OV) and OV-based (OVV) therapies, have shown promising results in both clinical and pre-clinical studies. In most instances, when applied as a monotherapy, the aforementioned treatment methods are incapable of inducing complete tumour remission. The Wan lab has developed an approach combining ACT with OVV therapies that dramatically increase therapeutic benefit resulting in complete regression of well-established solid tumours. Despite promising results, certain tumours can still escape this combination therapy through antigen loss resulting in antigen negative relapse (ANR). To further augment the therapy, the addition of a secondary receptor (CAR) provides the ACT multiple avenues of attack to prevent ANR. In this dissertation, we define culture conditions that promote strong expression of the CAR alongside confirmation of function in an in vitro setting. Following, it is demonstrated that OVV boosted dual-targeting T cells carry strong T cell activity by measure of cytokine release in vivo. Despite promising T cell activity data, dual-specific T cells are unable to improve tumour control and survival once relapse occurs. The failure to control relapse remains unclear however evidence points towards lack of T cell persistence, poor CAR function in vivo and a lack of endogenous T cell response leading to compounding effects that prevent dual-targeting T cells from preventing ANR. Although dual specific therapies have shown poor efficacy in preventing ANR, further study must be completed to identify areas of improvement – such as persistence, as the potential for success in using dual-targeting T cells coupled with OVVs still lies untapped. / Thesis / Master of Science (MSc)

Epithelial ovarian cancer (EOC) is the most lethal gynecologic cancer and urgently requires new therapies. Oncolytic viruses (OV) are a strong contender. OVs interact with immune components of the TME, which can be altered due to specific genetic mutations. The present study evaluates the impact of specific tumour mutations on the response to carboplatin, the current standard of care, and VSV∆M51, a promising OV candidate. After a study of genetically diverse models, constitutive KRas activation enhanced VSV∆M51 replication in-vitro and sensitivity in syngeneic in-vivo models. VSV∆M51 prolonged survival in syngeneic tumour- bearing mice with KRas, Trp53 and Pten mutations, including one tumour model that did not respond to carboplatin. Response to VSV∆M51 in-vivo was associated with activation of CD4+ and CD8+ T lymphocytes in the peritoneal TME. In summary, VSV∆M51-based immunotherapy has shown promise in diverse murine models of EOC bearing clinically relevant mutations.

Oncolytic viruses (OVs) are promising tumor-selective treatments, and the efficacy of OV therapies has been shown to depend heavily on the successful delivery and spread of these agents within the tumor mass to generate profound immunostimulatory effects. We have previously reported the potential of vanadium-based compounds such as vanadyl sulfate (VS) as immune-stimulatory enhancers of OV immunotherapy. These compounds, in conjunction with RNA-based OVs such as oncolytic VSVΔ51, improve viral spread and oncolysis, leading to long-term antitumor immunity and prolonged survival in resistant tumor models as previously reported. This effect is associated with a virus-induced antiviral type I IFN response shifting towards a type II IFN response. Here, the systemic impact and the relevant immunological changes following VS/VSVΔ51 combination therapy were investigated to understand the immunological mechanism of action leading to improved antitumor responses. We screened for the secretion of chemokines and cytokines in vivo to understand the mechanism of action regulating the recruitment of immune cells to the tumor in the CT26WT tumor model following treatment. Additionally, the antigen-specific immune response was investigated to further identify the relevant immunological changes following treatment with the VS+VSVΔ51 combination. Our data revealed that VS+VSVΔ51 combination therapy significantly increased the levels of IFN-γ and IL-6, and other key important pro-inflammatory cytokines and chemokines. Improved tumor antigen-specific T-cell responses were observed following the combined therapy. Supported by relevant immunological changes and as a proof of concept for the design of more effective therapeutic regimens, we found that local delivery of VSVΔ51 encoded with IL-12 or with other transgenes in combination with VS further improved therapeutic outcomes in a syngeneic CT26WT colon cancer model. We found that CD8+ T cells and Natural Killer (NK) cells play significant roles in establishing the therapeutic efficacy that we observed; Furthermore, engineering new and targeted therapeutic platforms to impact the antitumor immune response further improves the therapeutic benefits of the combined therapy.

Oncolytic viruses (OVs) have made tremendous strides as a viable cancer therapeutic in recent years; however, variable infectivity rates have since limited clinical efficacy. Residual type 1 interferon (IFN-1) responses are integral to the tumour’s innate antiviral defense and confer resistance to OVs. To combat this, small molecules with viral sensitizing ability can be used in combination to transiently knockdown IFN-1 responses, allowing OVs to gain a foothold for increased infectivity and therapeutic efficacy. Accordingly, we hypothesize that some chemical or genetic manipulations of cellular processes can indirectly antagonize antiviral IFN-1 responses and modulate pro-inflammatory pathways to potentiate oncolytic virotherapy. In this thesis, we identify several avenues to modify cell signalling events to increase OV therapeutic efficacy through IFN-1 inhibition. Firstly, with respect to the demonstrated OV-enhancing effects of vanadium, a pan-phosphatase (PP) inhibitor, we elucidate that its IFN-1 suppressing activity involves activation of the epidermal growth factor receptor (EGFR) pathway via STAT1/2 and NF-κB. Pharmacological inhibition of EGFR abrogated vanadium’s viral sensitizing ability in vivo. Secondly, using high-throughput screening methodology, we identify protein phosphatases that inherently regulate the IFN-1 response as targets for oncolytic vesicular stomatitis virus (VSV∆51) potentiation. Indeed, cloning interfering RNA against one of these PP targets, acid phosphatase 2 (ACP2), into the VSV∆51 platform demonstrated superior infectivity and cancer cell cytotoxicity compared to the non-targeting VSV∆51 control. Thirdly, we characterize pevonedistat, a first in-class neddylation activating enzyme inhibitor, to potentiate OV therapeutic efficacy across several in vitro and in vivo contexts. We demonstrate pevonedistat’s ability to inhibit IFN-1 signalling and pro-inflammatory cytokine production using both neddylation independent and dependent mechanisms. Taken altogether, we dissect multiple signaling mechanisms by which the IFN-1 response can be modulated for the purposes of improving OV therapeutic efficacy. This knowledge can subsequently be directly translated into designing optimized OV strategies for clinical testing.