Cancer immunotherapy is emerging as a powerful tool in the treatment of cancer. Multiple clinical trials have established that infusion of tumour-specific T cells can cause regression of advanced tumours and prevent tumour relapse. While tumour-specific T cells are typically rare, engineering methods have been developed to introduce tumour-specific receptors into T cells and engender peripheral blood T cells with the ability to kill tumour cells. These engineering successes notwithstanding, tumour cells demonstrate variable sensitivity to T cell attack. Therefore, to maximize the impact of the engineered T cells, it is necessary to develop therapeutic strategies that render tumour cells sensitive to immune attack. For my thesis research, I sought to develop a high throughput screening assay that would allow me to screen chemical libraries for agents that sensitize tumour cells to T cell attack. My ultimate goal is to define chemical agents that effectively sensitize tumour cells to T cell attack but display a better toxicity profile than existing chemotherapies. To this end, I developed a screen where resistant tumour cells were exposed to T cells engineered with chimeric antigen receptors and positive hits were defined as agents that could enhance killing of the tumour cells. My work explored both murine and human systems and I ultimately decided to use human cells for my screen. Multiple methods for measuring tumour cell killing were evaluated, many tumour lines were screened and I optimized the conditions for generating large numbers of engineered T cells for the screen. The net result of my thesis work is a miniaturized assay that is ready for high throughput screening. / Thesis / Master of Science in Medical Sciences (MSMS)

Multiple myeloma is an aggressive plasma cell cancer that consistently acquires multi-drug resistance and relapses despite initial treatment successes. Patients may go through greater than 10-lines of therapy, highlighting the need for more effective treatment options. Immunotherapies are the latest evolution in targeted cancer treatments, and thus far have displayed impressive results in several hematological cancers, including multiple myeloma. T cells possess robust anti-tumor functions which can be harnessed and refined for the treatment of cancers. Genetic engineering of T cells to express a chimeric antigen receptor (CAR) confers antigen-specific tumor-targeting, and adoptive transfer of patient-derived CAR-engineered T (CAR T) cells has been efficacious in relapsed/refractory multiple myeloma. Despite the high efficacy, CAR T cell therapy for myeloma is associated with serious adverse events, which limits dose levels and patient eligibility. We have developed a novel synthetic antigen receptor platform, called the T cell antigen coupler (TAC) receptor, which has shown comparatively higher efficacy with a reduced pro-inflammatory profile compared with CAR T cells in pre-clinical models. The TAC receptor was purpose-built to co-opt the natural T cell activation machinery and lacks the costimulatory signaling typically incorporated in CAR designs. This thesis investigates strategies to augment TAC T cell function against for multiple myeloma through the evaluation of ancillary pharmacological and protein stimuli that would complement the anti-tumor functions of TAC T cells without modifying the TAC receptor design. In chapter 2, I investigated a strategy combining TAC T cells with the SMAC mimetic LCL161 to provide transient costimulatory effects. While LCL161 boosted TAC T cells survival and proliferation, the drug also enhanced susceptibility of TAC T cells to apoptosis and offered no advantage to the TAC T cells when challenged with myeloma. In chapter 3, I engineered TAC T cells to secrete IL-27 in an attempt to modulate the myeloma microenvironment and support T cell cytolytic function. IL-27 did not enhance the anti-tumor activity of TAC T cells but forced expression of IL-27 led to a reduction in the production of pro-inflammatory cytokines without altering cytotoxicity. In appendix I, I describe the process of optimizing CRISPR/Cas9 editing of primary TAC T cells. This methodology was required for much of the work in chapter 2. Ph.D. Thesis – Arya Afsahi McMaster University – Biochemistry and Biomedical Sciences v In appendix II, I describe an assessment of mRNA-engineering as a method to produce TAC T cells. This approach proved to be therapeutically futile and was not pursued beyond the work described herein. The work presented here highlights methods of combining TAC T cells with a clinically relevant SMAC mimetic, or the cytokine IL-27, and provides insights into the biological mechanisms that are affected by these approaches. / Thesis / Doctor of Philosophy (PhD)

This thesis shows how to use Operations Research tools, e.g. Markov chains, optimization, game theory, and matchings, to understand problems that appear in biological contexts. We focus on two biological systems – the activation of the immune system in response to pathogens, and the metabolism of communities of different species of microbes. In Chapter 1, we study a Markov chain model of the activation of individual T-cells, and use the model to analyze how cells make trade-offs between various metrics such as speed and accuracy. In Chapter 2, we provide a detailed model of microbial community metabolism and show how incorporating aspects of game theory and dynamic stability can improve predictions of the behavior of microbial communities. Chapter 3 takes a matching approach to modeling microbial community metabolism by modeling the relationship between species and their environment using the stable marriage problem.

Indiana University-Purdue University Indianapolis (IUPUI) / The differentiation of naïve CD4+ T cells into subsets of T helper cells (Th) is an essential process that impacts host defense and the pathogenesis of immunemediated diseases. Signal transducers and activators of transcription (STAT) proteins, activated downstream of instructive cytokines, dictate and perpetuate the lineage decision of Th cells through both positive and negative effects. This is accomplished by regulating transcription factors, surface receptors and promoting epigenetic changes in gene expression through chromatin remodeling. Transforming growth factor-β1 (TGF-β1) can induce Foxp3 in developing Th cells and these Foxp3-expressing adaptive T regulatory cells (aTregs) are able to suppress inflammation in vitro and in vivo. To define the mechanism by which STAT proteins regulate Th cell pro- and anti-inflammatory phenotypes, we examined T cells deficient in Stat3, Stat4, and Stat6 as well as T cells expressing two STAT4 isoforms after being cultured in the presence or absence of TGF-β1 and cytokines known to be instructive in Th cell development. The negative effects of STAT proteins are demonstrated by our results indicating STAT3, STAT4 and STAT6 proteins activated downstream of the instructive cytokines IL- 6, IL-12 and IL-4, respectively, negatively regulate the development of TGF-β induced Foxp3 and aTreg development. STAT3, STAT4, and STAT6 utilize a vi Mark H. Kaplan, Ph.D., Chair common mechanism to inhibit aTreg generation by inhibiting STAT5, a positive regulator of Foxp3 expression, from binding to the Foxp3 gene. STAT proteins positively effecting inflammatory immunity are demonstrated by our analysis of STAT4 isoforms and their ability to regulate the production of proinflammatory cytokines downstream of IL-12. STAT4β, a STAT4 splice isoform that lacks a Cterminal domain, and STAT4α, a full-length isoform are both capable of mediating inflammatory cell development. However, STAT4β promotes greater inflammation in vivo than STAT4α independent of its ability to repress Foxp3. Instead, the inflammation correlates with STAT4 isoform-dependent expression of inflammatory cytokines. Thus, cytokine-stimulated STAT proteins orchestrate T helper cell pro- and anti-inflammatory cell phenotypes.

Indiana University-Purdue University Indianapolis (IUPUI) / CD1d is a cell surface glycolipid that, like Major Histocompatibility Complex (MHC) class I and MHC class II molecules, presents antigen. However, instead of peptides, CD1d presents lipids to Natural Killer (NK) T cells, a subset of T cells that express both NK cell markers and the T cell receptor and produces both T helper (Th) 1 and Th2 cytokines. Our lab focuses on the regulation CD1d-mediated antigen presentation. TGF beta is a known regulator of the immune system, such as controlling MHC class II antigen presentation. Further, TGF beta can activate the mitogen activated protein kinase (MAPK) p38, a known negative regulator of CD1d-mediated antigen presentation. Therefore, we hypothesized that TGF beta would be a negative regulator of CD1d-mediated antigen presentation, and our results showed a decrease in antigen presentation by CD1d in response to TGF beta treatment. However, this inhibition was not through p38 activation, as indicated by the absence of a rescue of CD1d-mediated antigen presentation in, TGF beta-treated, p38 dominant negative-expressing cells. Alternatively, the Smad pathway, the canonical pathway activated by TGF beta, was investigated through a lentivirus shRNA-mediated knockdown of Smad2, Smad3 and Smad4 proteins. Smad2 shRNA-expressing cells showed in an increase in CD1d-mediated antigen presentation, suggesting an inhibitory role for Smad2. In contrast, Smad3 shRNA-expressing cells did not differ from control cells. However, as in the case of Smad2, CD1d+ cells in which Smad4 was knocked down, were substantially better at CD1d-mediated antigen presentation than control cells, suggesting that it also negatively regulates antigen presentation. Overall, these studies demonstrate that the canonical TGF beta/Smad pathway regulates an important part of the host’s innate immune response, vis-à-vis CD1d-mediated antigen presentation.

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Host innate and adaptive immune responses must be tightly regulated by an intricate balance between positive and negative signals to ensure their appropriate onset and termination while fighting pathogens and avoiding autoimmunity; persistent pathogens may usurp these regulatory machineries to dampen host immune responses for their persistence in vivo. Here, we demonstrate that miR146a is up‐regulated in monocytes from hepatitis C virus (HCV )‐infected individuals compared to control subjects. Interestingly, miR146a expression in monocytes without HCV infection increased, whereas its level in monocytes with HCV infection decreased, following Toll‐like receptor (TLR ) stimulation. This miR146a induction by HCV infection and differential response to TLR stimulation were recapitulated in vitro in monocytes co‐cultured with hepatocytes with or without HCV infection. Importantly, inhibition of miR146a in monocytes from HCV ‐infected patients led to a decrease in IL ‐23, IL ‐10 and TGF ‐β expressions through the induction of suppressor of cytokine signalling 1 (SOCS 1) and the inhibition of signal transducer and activator transcription 3 (STAT 3), and this subsequently resulted in a decrease in regulatory T cells (Tregs) accumulated during HCV infection. These results suggest that miR146a may regulate SOCS 1/STAT 3 and cytokine signalling in monocytes, directing T‐cell differentiation and balancing immune clearance and immune injury during chronic viral infection.

Nuclear bone morphogenetic protein 2 (nBMP2) is a nuclear variant of the secreted growth factor BMP2. Experiments in nBmp2NLStm mutant mice, which lack nBMP2 in the nucleus, have shown that nBMP2 affects intracellular calcium transport in skeletal muscle and hippocampal neurons. The objective of this study was to determine whether nBMP2 affects the immune system, since activation of lymphocytes and other immune cells depends on intracellular calcium transport. We found that spleens in nBmp2NLStm mutant mice were 24% smaller than in wild type mice. The white pulp of the spleen contains many immune cells, particularly B and T lymphocytes and reduced spleen size in the nBmp2NLStm mutant mice could be caused by a reduced number of lymphocytes migrating to the spleen. When mutants and wild types were challenged with an intravenous infection of 10^7 CFU of S. aureus, they showed similar immune responses. Samples of blood, liver, spleen, kidney and lymph nodes cultured three days after infection showed no difference in post infection bacterial load between mutant and wild type. Likewise, post-infection weight loss and percent survival were similar between mutant and wild type, suggesting that the innate immune response is functional in nBmp2NLStm mice. However, when mice were challenged with a secondary infection, immune response and spleen function were severely impaired. Mutant mice showed higher levels of bacteria remaining in the blood and had lower rate of survival to day 3 after secondary infection. In addition, CD4+ and CD8+ T-cell levels within mutant lymph nodes were significantly reduced, indicating that nBMP2 is involved in the secondary immune response.

No description available.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to be the greatest global crisis of the 21st century and has led to a devastating state of human health and societal infrastructure. Such calamity was met with immense determination from the scientific community to uncover the immunological and virological basis of its accompanying disease and resulted in remarkable feats of public health response and therapeutic design. As SARS-CoV-2 continues to evolve and elicits a heterogenous disease presentation across different demographics, we aimed to define the circulating and tissue-localized immune memory generated following SARS-CoV-2 infection, as well as determine the immunological properties governing severe disease. Using human tissues from seropositive organ donors, we showed that SARS-CoV-2-specific immune memory was present in circulation, lymphoid, and mucosal sites up to 6 months post infection. B and T cell populations mounted against SARS-CoV-2 showed significant correlations between circulating and tissue-resident memory lymphocytes, suggesting local and systemic tissue coordination of cellular and humoral immunity against SARS-CoV-2, set for optimal protection against future infectious challenges. Next, we presented a comprehensive, longitudinal study of the peripheral blood immune system following pediatric SARS-CoV-2 infection and provided new insight on the immunological underpinnings of multisystem inflammatory syndrome in children (MIS-C). Acute MIS-C and pediatric COVID-19 differ in their effector module elicitation, activating opposing type 1 and type 2 immune responses respectively. We reveal that MIS-C presents with a unique peripheral T cell signature marked by activation, exhaustion, and tissue-residency at the proteomic and transcriptional level, along with a major Vβ-biased clonal expansion. Despite the considerable immune dysregulation during acute disease, children recovered from MIS-C maintain stable humoral immunity up to 18 months post hospitalization at comparable levels to seropositive groups, and generate robust, functional T cell memory in greater magnitude than seropositive children. Together, we report a near-complete restoration in global T cell phenotype and function in children following MIS-C, as well as the robust production of competent SARS-CoV-2 specific memory. Finally, following our queries into SARS-CoV-2-specific antiviral immunity, we sought to delineate the dynamics of human follicular immune responses and its role in generating and maintaining humoral immunity across a lifespan. Using healthy pediatric and adult donor tissues to examine blood, lymphoid, and mucosal tissues, our results reveal that TFH cells predominate the CD4+ T-cell memory pool in lymphoid sites in early life and decline in frequency with age. Further, pediatric and adult TFH cells differ in their functional capacities, with pediatric TFH cells expressing higher levels of markers associated with signal regulation and germinal center function, while adult TFH cells demonstrate a TH17-like identity. Further, early life TFH cells in lymphoid exhibit marked TCR repertoire overlap. Together, these results indicate a differential propensity for follicular responses in early life and adulthood, with important implications in considering immunomodulatory strategies in different life stages.