Although structurally unrelated, the human killer cell immunoglobulin-like (KIR) and the rodent lectin-like Ly49 receptors serve similar functional roles in natural killer (NK) cells. Moreover, both gene families display variegated and mostly mono-allelic expression patterns established at the transcriptional level. DNA methylation, but not histone modifications, has recently been shown to play an important role in maintenance of the expression patterns of KIR genes but the potential role of DNA methylation in the expression of Ly49 genes was unknown. My thesis focuses on the role of epigenetic modifications, especially DNA methylation, in the maintenance of mouse Ly49 gene expression. I show that hypomethylation of the region encompassing the main promoter of Ly49a and Ly49c in primary C57BL/6 (B6) mouse NK cells correlates with expression of these genes. Using B6 x BALB/c Fl hybrid mice, I demonstrate that the expressed allele of Ly49a is hypomethylated while the non-expressed allele is heavily methylated, indicating a role for epigenetics in maintaining mono-allelic Ly49 gene expression. Furthermore, the Ly49a promoter region is heavily methylated in fetal NK cells but variably methylated in non-lymphoid tissues. In apparent contrast to the KIR genes, I show that histone acetylation state of the promoter region strictly correlate with Ly49A and Ly49G expression status. Also, the instability of Ly49G expression on some lymphoid cell lines is at least in part due to changes in the level of histone acetylation of the promoter region. As for the activating Ly49 receptors, it seems that although DNA methylation levels of the promoter regions do correlate with the state of expression of these receptors, the pattern of DNA methylation is different from that of the inhibitory Ly49a and c genes. In conclusion, my results support a role for epigenetic mechanisms in the maintenance of Ly49 expression. Moreover, these epigenetic mechanisms appear to vary among the Ly49 genes and also differ from those governing KIR expression.

Transient uterine Natural Killer (uNK) cells are the predominant leukocytes of early gestational human and murine uteri. Murine uNK cells promote changes in endometrial structure including initiation of perivascular smooth muscle reduction in spiral arteries. Less is known about human uNK cell functions due to sampling constraints. Xenogeneic engraftment of human lymphocyte progenitors to alymphoid mice has been useful in understanding human lymphocyte functions in vivo. Irradiation of recipients is required to create a niche for successful humanization of the mice but renders recipient mice sterile. The goal of my thesis was to develop a protocol enabling engraftment of human hematopoietic stem cells in alymphoid mice that would permit differentiation of functional human uNK cells. I then planned to evaluate human uNK cell functions and their regulation in vivo. Neonatal Rag2-/-Il2rg-/- mice, which lack T cells, B cells and NK cells were preconditioned with 5-fluorouracil and inoculated with syngeneic mouse bone marrow cells. As adults, inoculated female mice conceived and differentiated functional mouse uNK cells. In contrast, neonatally-preconditioned Rag2-/-Il2rg-/- mice inoculated with human cord blood hematopoietic stem cells conceived but differentiated non-lymphoid cells in sites normally occupied by uNK cells. Weekly injections of human IL-15, which is required for NK cell differentiation, proliferation and survival, did not promote uNK cell differentiation. Rather, treatment with IL-15 altered gestational uteri, even in mice receiving neither preconditioning nor hematopoietic stem cells. I was successful in developing a protocol that enables hematopoietic stem cell engraftment in neonatal mice without compromising mouse fertility. However, this model is apparently not suitable for in vivo studies of human uNK cell functions. / Thesis (Master, Anatomy & Cell Biology) -- Queen's University, 2010-08-30 16:27:07.522

In the present study, we characterized the ability of a novel oncolytic rhabdovirus - Maraba MG1 to boost Natural Killer (NK) cell activity. In tandem, we addressed the ability of this enhanced NK cell functionality to reduce the incidence of post-cancer surgery micrometastases. Due to the potential safety barriers associated with the use of a live virus immediately prior to surgery in cancer patients, we generated a single cycle replication virus (MG1-Gless) and UV-inactivated MG1 to stimulate NK cell function and reduce post-operative metastases. Our in vivo data demonstrate that significant NK cell activation and a similar level of reduction in postoperative tumor metastases was achieved with live MG1, MG1-Gless and UV-inactivated MG1, concluding that viral replication is important, but not necessary for NK cell activation. Mechanistically, we observed that dendritic cells (DCs) are necessary intermediates for MG1-induced NK cell activation. Finally, we characterized and compared a panel of UV-inactivated MG1 (2mins to 2hrs) to better understand the requirements for NK cell activation. Our results suggest that intact viral particle and cellular recognition and association are essential for NK cell mediated anti-tumor responses. These findings provide the preclinical rationale to develop safe and viable virotherapy-based interventional protocols that might reduce the risk of metastatic disease after cancer surgery.

Human Natural Killer (NK) cells are regulated by a variety of germ-line encoded activating and inhibitory receptors. Broadly, activating receptors detect ligands that are expressed or up-regulated on cancerous or infected cells, while inhibitory receptors bind self-molecules to induce tolerance against healthy cells. Highly homologous pairs of activating and inhibitory receptors are also expressed on NK cells, including Killer Ig-like Receptors KIR2DL1 and KIR2DS1, which bind the same ligands, class I MHC proteins from the C2 group. Here, two super-resolution microscopy techniques, stimulated emission depletion (STED) and ground state depletion microscopy followed by individual molecule return (GSDIM) were used to examine the nanometre-scale organization of KIR2DL1 and KIR2DS1, as well as molecules engaged in their signalling. Both receptors were observed to constitutively assemble in nanometre-scale clusters at the surface of NK cells but displayed differential patterns of clustering - the activating receptor KIR2DS1 formed nanoclusters 2.3-fold larger than its inhibitory counterpart KIR2DL1. Site-directed mutagenesis established that the size of nanoclusters was controlled by transmembrane amino-acid 233, a lysine in KIR2DS1. Mutated variant of KIR2DS1 in which lysine 233 was substituted with alanine formed significantly smaller clusters than the wild-type KIR2DS1. Reciprocally, substitution of isoleucine found at position 233 in KIR2DL1 sequence with lysine resulted in the receptor assembling into larger clusters. Super-resolution microscopy also revealed two ways in which KIR nanoclusters impact signalling. First, KIR2DS1 and DAP12 nanoclusters were juxtaposed in the resting-cell state but coalesced upon receptor ligation. Second, quantitative super-resolution microscopy revealed that membrane-proximal clusters of the kinase ZAP-70 or phosphatase SHP-1, as well as their phosphorylated active forms, were more often found in contact with larger KIR nanoclusters. Together, this work has established that size of KIR nanoclusters depends on the transmembrane sequence and impacts downstream signalling.

Philosophiae Doctor - PhD / The current diagnostic, prognostic, predictive and therapeutic monitoring methods used for breast cancer are limited. Thus, research into more specific, sensitive and effective strategies is required. Breast cancer is the most prevalent form of cancer in women worldwide and accounts for the most common cause of death in women every year. Cancer development is characterized by a wide spread of genetic abnormalities of gene sequences that can be used in detecting and monitoring treatment of the disease as a result of altered gene expression patterns which leave a trail of biomarkers. Seven candidate genes (Gene 1-7) were identified from a previous in silico study and their gene products (BRG 1-7) were annotated to be good candidate breast cancer biomarkers. Differential gene expression analysis using quantitative real-time PCR (qRT-PCR) validated the over-expression of Gene 3, Gene 4 and Gene 7 in a breast cancer cell line (MCF7), of which Gene 7, annotated as a Natural killer group 2, member D (NKG2D) ligand, was observed to be the most over-expressed gene. The innate immune system is the first line of the body's physiological defense against diseases and the natural killer (NK) cells, are central to mediating this type of immunity. NK cells are activated when a specific surface receptor such as the NKG2D receptor binds its ligands expressed by tumor cells. To evade being detected by the immune system, cancer cells are reported to shed off the NKG2D ligands and are expected to be present in the bodily fluids of cancer patients. Also, chemotherapeutics have been reported to suppress the natural anti-tumour immune response, thus should be taken into account when designing optimal therapy for cancer patients. The aim of this research was to validate these candidate genes as effective breast cancer biomarkers using several in silico methods as well as molecular techniques and study the effect of Gene 7 on modulating the effect of several pro-apoptotic compounds. The in silico part of the study investigated the functional, protein interaction, pathways, and tissue expression specificity of the candidate biomarkers using computational software such as DAVID, STRING, KEGG, Genecards and GEA. Also an in silico validation of the prognostic/predictive values of the genes was analysed using SurvExpress, KMplot, and GOBO. Protein expression of selected genes was analysed by Western blot, and immunofluorescence analysis. BRG 7 gene was cloned into pcDNA3.1 vector using recombinant DNA technology while commercial shRNA construct was used to 'knock-down' Gene 7 expression. The two constructs were used to transfect MCF-7 and MCF-12A cells. Over-expression and 'knock down' Gene 7 in transfected cells was confirmed using western blot analysis. Stably transfected cells were then treated with three pro-apoptotic compounds (Camptothecin, Doxorubicin and DMSO) for 24 hours. The apoptotic cells were stained with 3, 4, 5, 6-tetrachloro-2', 4', 5', 7' tetraiodofluorescein (TCTF) and then analysed using flow cytometry. Functional analysis linked Gene 1, Gene 2, Gene 4, Gene 6 and Gene 7 to different cancer related processes. The pathway analysis showed Gene 1, Gene 2, Gene 4 and Gene 7 were involved in pathways that can be linked to cancer modulation. The protein-protein interaction analysis showed only BRG 2 was directly linked to two major hallmarks of cancer (Apoptosis and Autophagy). Breast cancer associated Transcription factors were shown to regulate these genes. Gene 1 and Gene 5 as well as the three genes observed to be highly expressed in the qRT-PCR study were validated to differentially express in breast cancer. An additional protein (BRG 8) was identified and postulated to be a good biomarker candidate for breast cancer based on its direct interaction with BRG 7 and estrogen receptor protein (ESR). The prognostic value of the candidate genes were monitored in two datasets (DATA1 and DATA2) in SurvExpress. DATA1 showed that Gene 6 and Gene 8 while DATA2 showed that Gene 3, Gene 6 and Gene 7 were valuable candidate genes in breast cancer prognosis. The survival curves from the two datasets showed the combined genes could predict the outcome of breast cancer patients undergoing treatments. A plot box output from SurvExpress showed most of the genes were differentially expressed comparing two risk groups. The Kaplan Meier plotter confirmed, Gene 1, Gene 3, Gene 4 and Gene 7 have a significant P-value in predicting the survival outcome based on gene differential expression value. GOBO analysis showed the genes may accurately predict the survival outcome of estrogen positive subtype, ERBB2 subtype of estrogen receptor negative and lymph node negative subtype of ER- tumours, but not all subtype of ER- tumours. Western blot analysis showed BRG 7 may be highly expressed in MCF-7 as compared to MCF-12A, BRG 8 was found to be expressed in all cancer cell types analyzed except for MCF-7 and HT29. BRG 2 was found to be expressed in all cancer types analyzed. immunofluorescence analysis showed BRG 3, BRG 4 and BRG 7 are differentially expressed in breast cancer cell line and are more localized on the cell membrane when compared to the breast non-cancer cell line. Over-expression and gene knock down in cells were successfully confirmed with Western blot analysis. Stably transfected MCF-12A cell for over-expression of BRG7 protein, resulted in cell senescent and the cell stopped growing while stably transfected MCF-7 over-expressing BRG7 did not show any morphological changes. Apoptosis was enhanced in cells treated with camptothecin, doxorubicin and DMSO overexpressing BRG7. Apoptosis was reduced in camptothecin and DMSO treated gene 'knock-down' cells but not doxorucin treated. BRG7 gene 'knock down' in transfected cells showed varying response to all three pro-apoptotic compounds. From this study Gene 3, 5, 7 and 8 and their protein levels were confirmed to be differentially expressed in breast cancer cells and could serve as putative biomarkers for breast cancer. However the variance in the effectiveness of individual genes suggests that the set of genes would perform better than individual gene. The modulating role of BRG7 in drug induced apoptosis, suggest it could probably play an important role in personalised medicine and could serve as a biomarker to monitor the prognosis and/or therapeutic outcome of pro-apoptotic drugs in breast cancer patients. These findings will be further investigated in human breast tissues to validate these data.

Although structurally unrelated, the human killer cell immunoglobulin-like (KIR) and the rodent lectin-like Ly49 receptors serve similar functional roles in natural killer (NK) cells. Moreover, both gene families display variegated and mostly mono-allelic expression patterns established at the transcriptional level. DNA methylation, but not histone modifications, has recently been shown to play an important role in maintenance of the expression patterns of KIR genes but the potential role of DNA methylation in the expression of Ly49 genes was unknown. My thesis focuses on the role of epigenetic modifications, especially DNA methylation, in the maintenance of mouse Ly49 gene expression. I show that hypomethylation of the region encompassing the main promoter of Ly49a and Ly49c in primary C57BL/6 (B6) mouse NK cells correlates with expression of these genes. Using B6 x BALB/c Fl hybrid mice, I demonstrate that the expressed allele of Ly49a is hypomethylated while the non-expressed allele is heavily methylated, indicating a role for epigenetics in maintaining mono-allelic Ly49 gene expression. Furthermore, the Ly49a promoter region is heavily methylated in fetal NK cells but variably methylated in non-lymphoid tissues. In apparent contrast to the KIR genes, I show that histone acetylation state of the promoter region strictly correlate with Ly49A and Ly49G expression status. Also, the instability of Ly49G expression on some lymphoid cell lines is at least in part due to changes in the level of histone acetylation of the promoter region. As for the activating Ly49 receptors, it seems that although DNA methylation levels of the promoter regions do correlate with the state of expression of these receptors, the pattern of DNA methylation is different from that of the inhibitory Ly49a and c genes. In conclusion, my results support a role for epigenetic mechanisms in the maintenance of Ly49 expression. Moreover, these epigenetic mechanisms appear to vary among the Ly49 genes and also differ from those governing KIR expression. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Natural killer (NK) cells, lymphocytes of the innate immune system, can recognize a wide array of cells via several receptors families such as Ly49 and NKR-P1. The Nkrp1 gene family encode for C-type lectin-like receptors which can recognize their ligands, Clr, on target cells. Nkrp1 and Clr genes are intertwined in the NK gene complex and are thus inherited together. The Nkrp1-Clr genes in 129S6 and BALB/c mouse strains show significant sequence polymorphism compared to those of C57BL/6 mice while the overall gene organization and gene number are conserved. RT-PCR was utilized to study the expression of individual Nkrp1-Clr genes. In situ hybridization was performed to validate expression results from RT-PCR, as well as to verify the cell types in which Nkrp1-Clr genes are expressed. Surprisingly, our expression studies reveal an interesting pattern of expression of Nkrp1 and Clr genes not only in lymphoid tissues but also in the epithelial cells of the intestine, kidney, eye and lung, the myocytes of the heart and skeletal muscle, and possibly some endothelial cells, indicating novel functions of NK cells in these tissues.

The Tumor Necrosis Factor Receptor Superfamily (TNFR) is responsible in regulating a myriad of physiological function including the regulation of the immune system. Among the members include CD137 (4-1BB), an inducible costimulatory receptor known for its potent activation, proliferation, and survival effects on T cells. Stimulation of NK cells with agonistic α-CD137 antibodies are known to increase IFN-γ production and proliferation in NK cells as well as increase efficacy of anti-tumor responses. However, NK cell death has also been seen in certain circumstances, although the mechanism remains to be determined. In vitro stimulation of NK cells revealed that α-CD137 induced NK cell death occurs through both TNFR1 and TNFR2, although the action of TNF-α and TNF-ß remain uncertain. Death was independent of other cytotoxic mechanisms such as granzyme/perforin, Fas-Fas ligand, and TRAIL. During MCMV infection, α-CD137 induces NK cell death during the early phase of infection reducing viral resistance. This causes increased viral proliferation which drives NK cell proliferation, likely through Ly49H-m157 interactions, to high levels by day 4 of infection. The use of α-CD137 as a tumor therapeutic is promising with several applications undergoing clinical trials. However, my results raise concern of other effects including the depletion of NK cells. This may cause a temporary impairment in immune function against pathogenic infections and a compensatory reaction of NK cell proliferation, both of which may cause damage to the host. However, with proper co-stimulation or co-treatments, this impairment may be overcome and prevent adverse effects in patients.

In the present study, we characterized the ability of a novel oncolytic rhabdovirus - Maraba MG1 to boost Natural Killer (NK) cell activity. In tandem, we addressed the ability of this enhanced NK cell functionality to reduce the incidence of post-cancer surgery micrometastases. Due to the potential safety barriers associated with the use of a live virus immediately prior to surgery in cancer patients, we generated a single cycle replication virus (MG1-Gless) and UV-inactivated MG1 to stimulate NK cell function and reduce post-operative metastases. Our in vivo data demonstrate that significant NK cell activation and a similar level of reduction in postoperative tumor metastases was achieved with live MG1, MG1-Gless and UV-inactivated MG1, concluding that viral replication is important, but not necessary for NK cell activation. Mechanistically, we observed that dendritic cells (DCs) are necessary intermediates for MG1-induced NK cell activation. Finally, we characterized and compared a panel of UV-inactivated MG1 (2mins to 2hrs) to better understand the requirements for NK cell activation. Our results suggest that intact viral particle and cellular recognition and association are essential for NK cell mediated anti-tumor responses. These findings provide the preclinical rationale to develop safe and viable virotherapy-based interventional protocols that might reduce the risk of metastatic disease after cancer surgery.

Suppression of anti-tumour immunity by the tumour microenvironment remains a major barrier to the development of broadly effective immunotherapies to treat solid tumours. Cytotoxic natural killer (NK) cells are vital to anti-cancer immunity and have shown clinical efficacy for treating hematologic malignancies. However, NK cell therapies have failed to be effective against solid tumours as cytotoxic NK cells become dysfunctional in the tumour microenvironment. While tumours hinder cytotoxic NK cells, they stimulate the tumour-promoting functions of regulatory NK cells. The mechanisms that dictate NK cell polarization and their fate in the tumour microenvironment remain poorly defined but harbour key therapeutic potential. Glucose-driven cellular metabolism has emerged as a central regulator of NK cell anti-tumour activity. Notably, tumour cells have deregulated metabolism, causing a metabolically hostile environment that is low in glucose and oxygen and high in metabolic waste. In the work presented, we demonstrate that NK cells expanded from cancer patients or healthy donors exert strong anti-tumour activity and dismantle the immunosuppressive tumour microenvironments of advanced ovarian and lung cancer. As a result, expanded NK cells were capable of sensitising initially non-responsive patient tumours to PD1 checkpoint-blockade therapy. Further, we uncover that the activity of cellular metabolic pathways plays a key role in NK cell functional fate in tumour microenvironment. We show that the tumour microenvironment induces paralysis of cytotoxic NK cell glucose metabolism to cause their dysfunction. However, reprogramming of NK cell metabolism through expansion arms expanded NK cells with enhanced metabolic flexibility which enabled their anti- tumour activity to be paradoxically strengthened by the tumour microenvironment. We further identify that regulatory NK cells have a distinct metabolic program compared to cytotoxic NK cells, including lower glucose-driven metabolism, that is amenable with the tumour microenvironment. Our work provides new mechanistic insight into how NK cell fate is regulated and how the pathological environment of a tumour capitalizes on this. This knowledge provides new therapeutic targets to intervene with the suppression of cytotoxic immunity in tumours. Further, this work identifies that expanded NK cells are a promising therapeutic candidate that exploit the metabolic hostility of the tumour microenvironment and synergize with other immunotherapies. / Thesis / Candidate in Philosophy / Harnessing the body’s natural immune defenses against cancer in the form of immunotherapy has emerged as a powerful treatment modality. Over the past decade, immune cell therapies have revolutionized the treatment of blood cancers like leukemia and lymphoma. Yet despite the potential, immune cell therapies have failed to be broadly effective against solid tumours because the anti-cancer activity of immune cells, such as Natural Killer (NK) cells, becomes severely impaired by the tumour environment. In this work, we identify that NK cells expanded from cancer patients and healthy donors overcome suppression by tumours and eliminate detectable tumour in pre-clinical models of advanced ovarian and lung cancer. These expanded NK cells also enhanced the functions of other immunotherapies. Further, we shed new light on how NK cells become dysfunctional in tumours. We uncover that NK cells undergo a metabolic energy crisis in tumours that causes their dysfunction, but that expanded NK cells have increased metabolic fitness which allows them to overcome this energy crisis and remain highly functional. Finally, we also characterize the metabolism of a subset of NK cells that are tumour-promoting and find that they harbour metabolic advantages to thrive in tumours. Overall, our work provides new insight as to how to overcome immunosuppression by tumours. This work identifies that expanded NK cells are a promising therapeutic candidate that exploit the hostility of tumours and synergize with other immunotherapies.