The core of the doctoral thesis "Regulation of signal transduction by leukocyte surface proteins" consists of three publications in international peer-reviewed journals dealing with leukocyte signaling both at the level of individual signaling pathways and in the context of a multicellular organism. Most attention is paid to signaling via the T cell receptor (TCR), which plays a central role in the development and function of T cells and represents a key signaling pathway for proper function of the adaptive component of the immune system. Transmembrane protein tyrosine phosphatase CD148 was considered a negative regulator of TCR signaling through dephosphorylation of LAT and PLCγ1 proteins. This study brings evidence that CD148 is able to modulate signaling also at the level of Lck, both positively and negatively. The net effect of CD148 activity on the TCR signaling is determined by the intracellular biochemical context, notably, the presence of another tyrosine phosphatase CD45. The second project dealt with the characterization of a transmembrane adaptor protein PRR7. This adapter inhibits TCR signaling via down-regulation of the intracellular Lck and cell surface TCR levels. The research concerning the signaling in the environment of a multicellular organism is represented by the analysis of...

CD4+ T cells are critical in the fight against parasitic, bacterial, and viral infections, but are also involved in many autoimmune and pathological disorders. Ligation of the T Cell Receptor (TCR) is the primary signal required for T cell activation proliferation, differentiation and cytokine release. Upon TCR activation, several kinases and adaptor proteins are assembled at the TCR/linker for activation of T cells (LAT) signaling complexes, a process indispensable for optimal signal transduction. One important group of proteins recruited to the TCR/LAT complexes is the GRB2 family of adaptors. Due to their role in mediating signaling complexes, the GRB2 family of adaptors are critical for development, proliferation, and survival of diverse cell types. These proteins have been linked to the initiation and progression of numerous pathological conditions including diabetes, asthma/allergy, and solid and hematopoietic malignancies. Therefore, it is essential to characterize and understand the complete functions of these proteins for the generation of safe and efficient targeting treatments for diseases mediated by these proteins. In T cells, GRB2 and its homologs, GADS and GRAP, are crucial for the propagation of signaling pathways through the TCR and adaptor protein LAT. These proteins recruit distinct sets of proline-rich ligands to LAT thereby inducing multiple signaling pathways such as MAP kinase activation, calcium influx and cellular adhesion. However, the role of GRB2 family members in controlling TCR and LAT mediated signaling in mature human T cells is not completely understood. Moreover, the relative role of GRB2 family members in the extent and timing of the recruitment of SH3 domain ligands to the LAT complex is unknown. Our hypothesis is that these proteins recruit distinct sets of ligands to the LAT complex that can drive differential downstream signaling events. As presented in CHAPTER III, we developed microRNA and shRNA targeting viral vectors to effectively inhibit the expression of GRB2 and GADS in human CD4+ T cells to examine the role of these adaptors in mature human T cells. We also established optimized protocols for high efficacy retro or lentiviral transduction of human T cell lines, activated and "hard-to-transduce" non-activated primary human CD4+ T cells. In CHAPTER IV, we demonstrate the requirement for GRB2 in TCR-induced IL-2 and IFN-γ release. The defects in cytokine release in the absence of GRB2 were attributed to diminished formation of LAT signaling microclusters, which resulted in reduced MAP kinase activation, calcium flux and PLC-γ1 recruitment to LAT signaling clusters. Overall, the data presented in this chapter demonstrate that the ability of GRB2 to facilitate protein clustering is as important in regulating TCR-mediated functions as its capacity to recruit effector proteins. This highlights that GRB2 regulates signaling downstream of adaptors and receptors by both recruiting effector proteins and regulating the formation of signaling complexes. In CHAPTER V, we describe the role for GADS in mediating TCR-induced IL-2 and IFN-γ production. GADS was critical for the recruitment of SLP-76 and PLC-γ1 to the LAT complex and subsequent calcium influx. We also show, in contrast to the current paradigm, that recruitment of GADS/SLP-76 complexes to LAT is not required for TCR-mediated adhesion and cytoskeletal arrangement. Overall, our studies reveal novel mechanisms for the role of GRB2 family members in TCR-mediated signaling. They also provide insight into the mechanisms that regulate growth factor, cytokine and insulin receptors. Importantly, studies presented in this thesis will help us understand the mechanisms of T cell activation and highlight potential new therapies for T cell-mediated diseases, including leukemia, lymphomas, autoimmune disorders and cardiovascular disease.

Abstract Early in the evolution of the vertebrates it is thought that two genomic duplications occurred, providing a basis for the evolution in body plan and neural crest of very early vertebrates and substantive material for further evolution of various gene families such as those making up a number of components of the adaptive vertebrate immune system. While the bony fish possibly had another, genome duplications are not generally a feature of vertebrate evolution and indeed the appearance of an antigen-adaptive immune recognition system may have served to limit the size that various vertebrate genomes, including that of the human, can in fact achieve. This initial step in vertebrate immune evolution, the establishment of recognition of non-self against the unique set of 'self' epitopes for an individual, provided an immensely powerful weapon in immune function with the ability to tailor a defense against as-yet-unseen dangers at any time albeit with the pitfall of autoimmune disease. As the recognition sites of the antigen receptor molecules such as TcR are produced by clonal modification of the segments provided in the germline and are thus not in the genome itself, pathogens have not been able to hijack this one component of the immune system in the way so many other components have been put to use throughout evolution, nor do these components necessarily reveal themselves as associated with disease through genome screens. Importantly, overall immune function is determined not just by the potential repertoire of recognition receptors but also by the ability of immunocompetent cells to migrate in a tissue specific fashion through the use of various chemokines and their receptors. Typical of the hijacking of an immune system component by a pathogen is the use of a chemokine ligand gene in the viral ancestor to SIV and HIV, allowing for virus binding to immunocompetent cells as is seen in the use of the CCR5 chemokine receptor by macrophage-tropic HIV strains. This thesis describes the allele and genotype frequencies for several TcR beta-chain variable segment polymorphisms in a population of MS patients compared with controls before and after stratification for HLA-DR15, polymorphism in the Apo-1 / Fas promoter, the DRB1 Val86/Val86 genotype, CCR5-delta32 and the HLA-DRA promoter. The thesis continues with CCR5-delta32 genotyping in IDDM, MS and SLE cohorts and then examines the question of the population of origin of the delta-32 allele of the CCR5 receptor for chemokine. Here, a case / control comparison of 122 RR-MS patients with 96 normal individuals was made for allele and genotype frequencies and for haplotypes formed by pairs of TCRB markers. Further analysis was made after HLA-DR15 stratification. Linkage disequilibrium was found between pairs of alleles of bv8s1, bv10s1, bv15s1 and bv3s1 loci in both patients and controls. In the RR-MS cohort, an increase in the allele frequency of bv8s1*2 was seen (p = 0.03) and the haplotype bv8s1*2 / bv3s1*1 was increased (p = 0.006), and both were found to be statistically significant. In the DR15-positive group, association between MS and TCRB was seen with the bv8s1*2 allele (p = 0.05) and the bv8s1*2 / bv10s1 haplotypes (p = 0.048), while the haplotype associations seen among the DR15-negative patients included the bv3s1*1 allele (bv10s1*1 / bv3s1*1, p = 0.022; bv8s1*2 / bv3s1*1, p = 0.048). While no associations were found after stratification for SDF1-3'A, Apo-1 / Fas or DRB1 there were modest interactions between bv3s1, bv10s1 and bv15s1 and the HLA-DRA promoter. These results support the involvement of the TCRB region in MS susceptibility. The further study of autoimmune disease here includes genotype analysis of CCR5-delta32 in type 1 diabetes (IDDM) and SLE. CCR5 is the major co-receptor for viral entry used by macrophage-tropic HIV strains and protection from infection is seen in homozygotes for CCR5-delta32. In diabetes, infiltration of pancreatic tissue by autoreactive T-cells involves secretion of multiple cytokines and chemokine receptor expression. Variation in the chemokine receptor CCR5 may result in differences in inflammatory cell migration in response to relevant chemokines. Adolescents with type 1 diabetes were genotyped for CCR5-delta32 (n = 626). The allele frequency was compared with that of 253 non-diabetic adolescents and with that of 92 adults with SLE. A reduced allele frequency was seen in type 1 diabetes compared with controls (0.092 vs 0.123, p = 0.05). This difference was not seen for the cohort of patients with SLE (freq = 0.114). A reduction in the number of CCR5-delta32/delta32 homozygotes, who lack CCR5, in the type 1 diabetes cohort was also seen and while not statistically significant (2 observed compared to 5.25 expected; p = 0.12) is interesting. These results suggest a partial protection from type 1 diabetes for CCR5-delta32 homozygous individuals is possible and that CCR5 has a potential role in the pathogenesis of type 1 diabetes. Global surveys of the CCR5-delta32 allele have confirmed a single mutation event in a Northeastern European population as the source of this allele. Here, Australian Ashkenazi Jews (n = 807) were found to have a CCR5-delta32 allele frequency of 14.6% while Australian Sephardic Jews (n = 35) had a frequency of 5.7% and non-Jewish Australian controls (n = 311) had an allele frequency of 11.25%. Data on birthplace of grandparents showed a gradient with highest CCR5-delta32 frequencies from Eastern European Ashkenazim (~19.5% for those whose four grandparents come only from Russia, Poland, Hungary, Austria and Czechoslovakia; n = 197) which differs significantly from the frequency seen in Ashkenazi Jews from Western Europe (n = 101, p = 0.001). Homozygotes for CCR5-delta32 were genotyped with 3p21 region microsatellites. This has defined an ancestral haplotype on which the mutation first occurred and helped to date this event to between 40 and 50 generations ago or just over a thousand years ago. The population gradient, combined with the dating of the mutation by microsatellite allele frequencies, suggests an origin for the CCR5-delta32 allele in a population ancestral to the Ashkenazim. The distribution in non-Jewish populations in northern Europe has led others to postulate spread of the mutation by Vikings. It is hypothesised here that the link between the two populations could be the kingdom of Khazaria with subsequent admixture into both Swedish Vikings and Ashkenazi Jews. The basic driving force of evolution is through selection and the immune system has a role which, through the survival pressure exerted by viruses and other pathogens, has the potential to exert a great deal of selective force on the various components of this system. The effects of this pronounced selection on an immune system component can be seen for example in the increase of the CCR5-delta32 allele over the last thousand years to the current frequency. As mentioned, some immune system components are not affected by such straightforward selection. In the case of the TCRBV segments, effects on the immune repertoire can occur through MHC interaction at the point of thymic entry and in the effects of various superantigens, but the actual binding pockets that recognise antigen are themselves unable to be selected for (or against). The findings presented in this thesis provide support for the association of TCRBV gene segments with multiple sclerosis and also provide support for the further study of the role of the CCR5-delta32 allele in type 1 diabetes. Furthermore, data presented here suggests that the CCR5-delta32 allele had an origin in the Khazar Kingdom just over a thousand years ago, accounting for the allele frequencies in both the Ashkenazi Jews and in lands frequented by the Vikings. The definition of an extended ancestral haplotype for the CCR5-delta32 allele shows how the effect of selection of an allele of one gene can carry with it specific alleles of a large number of other genes as well.

Glycodelin is a 162 amino acid secreted glycoprotein classified as a member of the lipocalin (carriers of small hydrophobic molecules) superfamily based on the presence of lipocalin signature motifs in its primary sequence. The protein has several isoforms which are expressed by various primate tissues, predominantly reproductive tissues. These isoforms are products of the same gene and hence have the same primary sequence; however, they are differentially glycosylated depending on tissue origin. The individual glycodelin isoforms perform very varied functions, which are largely dictated or modulated by the specific glycans on the molecule. Glycodelin A (GdA) is the major glycodelin isoform of the female reproductive tract; and is subclassified as an immunocalin (lipocalins with immunological function) due to its ability to modulate immune responses. Diverse activities have been associated with GdA; pertaining to determination of cell fate, tissue differentiation and significantly, immunomodulation towards fetal-allograft tolerance. The fetus expresses paternal allo-antigens and would be regarded as non-self or foreign by the maternal immune system. However, several synergistic mechanisms of immunomodulation at the fetal-maternal interface establish tolerance towards fetal antigens, protecting it from rejection. GdA is secreted by the uterine endometrium under progesterone induction, and is therefore the most abundant progesterone-regulated secretory glycoprotein of the uterus at the time of implantation and early pregnancy. GdA has been shown to have immunomodulatory activity targeting innate, humoral and cellular responses. It is inhibitory to T cell and B cell proliferation, and NK cell activity. It stimulates the Th2-type cytokine profile, and inhibits interleukins IL-2 and IL-1 production from mitogenically stimulated lymphocytes and mononuclear cell cultures. It has been reported from our laboratory that GdA induces apoptosis in activated T cells. GdA has also been shown to be inhibitory to B cells and monocytes. Clinical studies correlate subnormal levels of GdA with implantation Synopsis failure, habitual abortion and recurrent miscarriage. Due to its pleiotropic nature namely its diverse activities on different immune cell types; its spatio-temporal restriction of expression by progesterone; and its indispensable requirement for successful pregnancy; GdA is being increasingly recognized as a mechanism towards fetal allograft tolerance. Our laboratory has focused on the T cell inhibitory activity of GdA, with particular emphasis on T cell apoptosis. This study was aimed at delineating the molecular mechanism of GdA-induced apoptosis in activated T cells. Previous results from our laboratory have revealed that GdA-induced apoptosis is caspase dependent; and is not initiated by the extrinsic pathway involving Fas/death receptor signailing or initiator caspase 8. In this thesis, we present evidence that GdA triggers the intrinsic apoptotic program in T cells. Characterization of the apoptotic program initiated by GdA is presented in Chapter 1. We observe that GdA treatment triggers a stress response leading to decrease in mitochondrial transmembrane potential, which indicates mitochondrial membrane permeabilization (MMP). GdA-induced apoptosis can also be blocked by inhibition of caspase 9, the initiator caspase for the intrinsic program. The kinetics of mitochondrial depolarization precede onset of DNA fragmentation in both peripheral blood T cells and Jurkat cells treated with GdA. We also observe caspase 2 activation downstream of the mitochondria. Overexpression of the antiapoptotic protein Bcl-2 is sufficient to protect from GdA-induced cellular stress indicating that the apoptotic program can be reversed upstream of the mitochondria. Further, our studies reveal that stress signaling by GdA is not mediated by any of the canonical second messengers of stress signaling, namely, reactive oxygen species; the stress activated protein kinases JNK, p38 MAPK and ERK; intracellular calcium or ceramide. It has been reported that GdA desensitizes T cell receptor (TCR) signaling by decreasing the stability of TCR-triggered phosphoproteins, probably by its association ith the transmembrane tyrosine phosphatase CD45. TCR-desensitization would result in decreased proliferation and cytokine secretion, and has been postulated as the mechanism of T cell-inhibition by GdA. We have tested this theory and Chapter 2 provides evidence that the apoptogenic activity of GdA is not a consequence of its ability to blunt TCR-signaling. Further, GdA-induced apoptosis does not depend on components of the TCR signal cascade namely CD45, the kinase Lck and CTLA4, molecules that are proven transducers of apoptotic signals to the mitochondria in response to diverse stress stimuli. GdA triggers apoptosis in the CD45 deficient cell line J45.01 with similar kinetics of MMP and DNA fragmentation as with Synopsis wildtype cells, demonstrating that CD45 is not the determinant receptor for apoptosis on cells. We also observe that GdA is inhibitory to T cells stimulated with phorbol ester and calcium ionophore, which bypasses TCR-proximal signaling events; and that GdA treatment does not interfere with early T cell activation as evidenced from induction of the activation marker CD69. Thus, GdA initiates mitochondrial stress mediated apoptosis in T cells by a pathway that is distinct and independent from the TCR-coupled signaling pathway. This study presents a novel mode of immunosuppression for GdA and highlights the ability of GdA to suppress the immune response by more than one mechanism. Cell surface glycoproteins undergo alterations in their carbohydrate profiles upon T cell activation and differentiation, and this has a significant role to play in lymphocyte fate and function. One such global alteration in cell surface glycans is a difference in sialylation upon T cell activation and differentiation. While activated T cell have a lesser degree of sialylated surface glycoproteins as compared to naïve T cells, memory T cells are sialylated to a higher extent, and Th2 cells have more cell surface sialic acids than Th1 cells. As GdA is capable of triggering apoptosis in activated T cells, we investigated the requirement of cell surface glycans for differential recognition of T cell subsets by GdA, the results for which are detailed in Chapter 3. We observe that the activity of GdA could be competed out by asialofetuin and not fetuin, suggesting that GdA recognizes terminal galactose residues on asialofetuin glycans, which would be masked by sialic acids in case of fetuin glycans. This assumption was confirmed as the free sugars lactose and galactose, but not annose, could also competitively inhibit GdA activity. We also demonstrate that the lectin-activity of dA is calcium independent, typical of mammalian galectins. Thus, our results reveal GdA to be a novel galactose-specific lectin of the female reproductive tract. This carbohydrate specificity of GdA is responsible for its apoptotic activity on T cells. The selectivity of GdA towards activated T cells is a result of increased exposure of terminal galactose residues on activated T cell surface receptors, as demonstrated by staining of naïve and stimulated T cells with Fluorescent lectin-conjugates of different carbohydrate specificities. We also demonstrate hat GdA shows specificity towards N-liked glycans on cell surface glycoproteins. This is evident from the use of glycan processing inhibitors, which prevent addition of galactose to the core glycan on the nascent polypeptide chain. We observe that inhibition of processing of N-glycans, and not O-glycans, render cells resistant to GdA. Incidentally, we observe that another property of GdA, namely its ability to induce Synopsis epithelial differentiation and apoptosis in the breast cancer cell line MCF-7, is also due to ts galactose-specific lectin activity. It is therefore probable that the diverse functions ssociated with GdA are a consequence of its ability to recognize different glycoprotein receptors on different cell types. We can thus draw a comparison for GdA with the galectins, which are the prototype beta-galactoside binding mammalian lectins with diverse roles in determining cell fate and apoptosis, especially in the immune system. In fact, the immune-related activities of GdA are almost identical to the effects of galectin-1 on the immune system. Galectin-1 has also very recently been shown to play a significant role in fetal-tolerance. This raises a strong possibility of shared receptors for GdA and galectin-1 on the T cell surface, resulting from a shared calcium-independent recognition property for complex glycans with terminal galactose residues. Two predominant galectin-1 receptors on T cells are the glycoproteins CD45 and CD7. We have already observed that though GdA may recognize CD45, this association does not mediate its apoptotic activity. We therefore examined the possibility of the activation-induced glycoprotein CD7 as receptor for GdA. Our experiments reveal that the apoptotic activity of GdA on different T cell lines is dependent on the degree of CD7 expression by these cell lines. Notably, the CD7 negative lymphoma cell line HuT78 was completely resistant to GdA. To confirm CD7 as receptor, we obtained a cell line HuT78.7 in which CD7 expression has been restored by stable transfection. We observed that these CD7 positive cells now responded to GdA comparable to Jurkat cells, and GdA-induced apoptosis in these cells could be completely competed out with asialofetuin, not fetuin. To summarize, our study identifies GdA as a novel pregnancy-related galectin-like lectin of the female reproductive tract, which triggers mitochondrial stress and apoptosis in activated T cells. GdA shares receptors on T cells with galectin-1 due a common carbohydrate recognition property. We identify CD7 as a molecular target for GdA on activated T cells, capable of mediating the apoptotic signal. However, it is likely that GdA also recognizes other galectin receptors on T cells, as it is capable of inhibition by more than one mechanism. This underscores the requirement for redundant mechanisms indispensable for establishment and maintenance of successful pregnancy.

B and T cells comprise the two major arms of the adaptive immune response tasked with clearing and preventing infection; molecular recognition in these cells occurs through antibodies and T cell receptors (TCRs), respectively. Highly successful therapeutics, clinical diagnostics and laboratory tools have been engineered from fragments of these parent molecules. The binding specificity, affinity and biophysical characteristics of these fragments determine their potential applications and resulting efficacies. Thus engineering desired properties into antibody and TCR fragments is a major concern of the multi-billion dollar biopharmaceutical industry. Toward this goal, we (1) designed antibody specificity using a novel computational method, (2) engineered thermoresistant Fabs by phage-based selection and (3) modulated binding kinetics for a single-chain TCR. In the first study, de novo modeling was used to generate libraries of FLAG peptide-binding single-chain antibodies. Phage-based screening identified a dominant design, and activity was confirmed after conversion to soluble Fab format. Bioinformatics analysis revealed potential areas for design process improvement. We present the first experimental validation of this in silico design method, which can be used to guide future antibody specificity engineering efforts. In the second study, the variable heavy chain of a moderately stable EE peptide-binding Fab was subjected to random mutagenesis, and variants were selected for resistance to heat inactivation. Thermoresistant clones where biophysically characterized, and structural analysis of selected mutations suggested general mechanisms of stabilization. Framework mutations conferring thermoresistance can be grafted to other antibodies in future Fab stabilization work. In the third study, TCR fragment binding kinetics for a clonotypic antibody were modulated by varying valence during phage-based selection. Binding affinity and kinetics for representative variants depended on the display format used during selection, and all TCR fragments retained binding to native pMHC antigen. This work demonstrates a general engineering platform for tuning protein-protein interactions. Using a combination of computational design and phage-based screening, we have identified antibodies and TCR fragments with improved binding properties or biophysical characteristics. The optimized variants possess a wider range of potential applications compared to their parent molecules, and we detail engineering methods likely to be useful in the engineering of many other protein-based therapeutics. / text

\(CD8^+\) cytotoxic T lymphocytes (CTLs) play a critical role in controlling human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication. The CTL responses that are thought to be the most protective against HIV and SIV are those that are of high frequency, recognize multiple epitopes, and perform multiple antiviral functions. Therefore, current vaccines aim to elicit CTLs possessing these characteristics. However, the phenomenon of immunodominance likely limits the potential of vaccines from generating such CTL responses by restricting the breadth of epitopes recognized by CTLs and the frequency and functionality of these CTL responses. In this dissertation, we explored the relationship between SIV epitope dominance and the functionality of the epitope-specific CTL populations. We also examined factors that contribute to the development of SIV epitope immunodominance hierarchies. We initially investigated the relationship between SIV epitope dominance and the antiviral functionality of the epitope-specific CTL populations in rhesus monkeys. We performed a gene expression analysis in dominant and subdominant epitope-specific CTLs during the acute phase of SIV infection and observed differential expression of a number of genes during this time. Subsequent in vitro functional studies of these epitope-specific CTL populations during the chronic phase of infection confirmed the presence of differences in maturation phenotype and functional capacity of dominant and subdominant epitope-specific CTLs. These studies demonstrate a relationship between epitope dominance and antiviral functionality of epitopespecific CTLs and suggest that dominant and subdominant epitope-specific CTLs may differ in their protective role against HIV acquisition and replication. This has important implications for vaccine design. In subsequent studies, we investigated the contribution of the binding of the peptide:MHC (pMHC) complex to the T cell receptor (TCR) in the development of immunodominance hierarchies. Using surface plasmon resonance, we measured the kinetics and the affinity of the interactions between dominant and subdominant epitope pMHC complexes with their respective TCRs. We found that epitope dominance was associated with higher affinities of pMHC:TCR binding. These findings indicate a molecular interaction that may be manipulated in vaccine-induced CTL responses to enhance their frequency and functional capacity.

In recent years, there has been a worldwide increase in obesity, which parallels a rise in pathologies, including type 2 diabetes, collectively termed the metabolic syndrome. Chronic, low-grade inflammation has been implicated as a major link between these diseases. Recent work showed the presence of a unique subset of CD4+Foxp3+ regulatory T cells residing in visceral adipose tissue (VAT Treg) with PPAR-g being the key transcription factor responsible for their phenotype and function in controlling adipose tissue inflammation and, thereby, insulin sensitivity. VAT Tregs inversely correlated with insulin resistance. In contrast, there was a dramatic age-associated increase in frequency of VAT Tregs in lean animals, correlating with continued insulin sensitivity, despite significant increases in body and adipose tissue weights. This increase in Treg frequencies was not observed in other lymphoid and non-lymphoid tissues, including the subcutaneous fat depot. We characterized this unique age-associated increase in VAT Tregs through the use of adoptive transfer models, in vivo labeling and tracking systems, parabiosis, and analysis of the T cell receptor (TCR) repertoire used by VAT Tregs. Our findings indicate that the progressive increase in VAT Tregs is not due to conversion of conventional CD4+ T cells nor to substantial infiltration of Tregs from the circulation and secondary lymphoid organs. However, by analyzing the TCR repertoire on a single-cell level we uncovered a striking oligo-clonal expansion of VAT Tregs, suggesting their accumulation results from in situ proliferation. We further showed that this accumulation is dependent on major histocompatibility complex (MHC) class II, but not on CD1d. Finally, we showed that IL-33 was able to induce proliferation of VAT Tregs. In parallel, we extended our analysis of TCR repertoire to the Treg population residing in skeletal muscle. In acute and chronic models of muscle injury, muscle-resident Tregs underwent a substantial clonal expansion, with a particular clone being detected in multiple individuals. Taken together these studies highlight the importance of proliferation as a mechanism of Treg accumulation in tissues in response to acute and chronic inflammation.

<p>T cells and B cells each express unique antigen receptors used to identify, eliminate, and remember pathogens. These receptors are generated through a process known as V(D)J recombination, in which T cell receptor and B cell receptor gene loci undergo genomic recombination. Interestingly, recombination at certain genes is regulated so that a single in-frame rearrangement is present on only one allele per cell. This phenomenon, termed allelic exclusion, requires two steps. First, recombination can occur only on one allele at a time. In the second step, additional recombination must be prevented. Though the mechanism of the second step is well-understood, the first step remains poorly understood.</p><p>The first step of recombination necessitates that alleles rearrange one at a time. This could be achieved either through inefficient recombination or by halting further recombination in the presence of recombination. To separate these mechanisms, we analyzed recombination in nuclei unable to complete recombination. We found that rearrangement events accumulated at antigen receptor loci, suggesting that the presence of recombination does not stop additional rearrangements and asynchronous recombination likely results from inefficient recombination at both alleles.</p><p>Association with repressive subnuclear compartments has been proposed to reduce the recombination efficiency of allelically excluded antigen receptor loci. Of the alleleically excluded loci, <italic>Tcrb</italic> alleles are uniquely regulated during development. Other allelically excluded alleles are positioned at the transcriptionally-repressive nuclear periphery prior to recombination, and relocate to the nuclear interior at the stage in which they recombine. However <italic>Tcrb</italic> alleles remain highly associated with the nuclear periphery during rearrangement. Here we provide evidence that this peripheral subnuclear positioning of <italic>Tcrb</italic> alleles does suppress recombination. We go on to suggest that peripheral localization mediates the first step of allelic exclusion.</p><p>In search of the mechanism by which recombination is suppressed on peripheral <italic>Tcrb</italic> alleles, we investigated the subnuclear localization of a recombinase protein. Two recombinase proteins are required for recombination, one of which is recruited to actively transcribing (and more centrally located) DNA. Here we demonstrate that one recombinase protein is unable to localize to peripheral <italic>Tcrb</italic> alleles, potentially serving as the mechanism by which recombination is suppressed on peripheral alleles.</p> / Dissertation

Abstract Early in the evolution of the vertebrates it is thought that two genomic duplications occurred, providing a basis for the evolution in body plan and neural crest of very early vertebrates and substantive material for further evolution of various gene families such as those making up a number of components of the adaptive vertebrate immune system. While the bony fish possibly had another, genome duplications are not generally a feature of vertebrate evolution and indeed the appearance of an antigen-adaptive immune recognition system may have served to limit the size that various vertebrate genomes, including that of the human, can in fact achieve. This initial step in vertebrate immune evolution, the establishment of recognition of non-self against the unique set of 'self' epitopes for an individual, provided an immensely powerful weapon in immune function with the ability to tailor a defense against as-yet-unseen dangers at any time albeit with the pitfall of autoimmune disease. As the recognition sites of the antigen receptor molecules such as TcR are produced by clonal modification of the segments provided in the germline and are thus not in the genome itself, pathogens have not been able to hijack this one component of the immune system in the way so many other components have been put to use throughout evolution, nor do these components necessarily reveal themselves as associated with disease through genome screens. Importantly, overall immune function is determined not just by the potential repertoire of recognition receptors but also by the ability of immunocompetent cells to migrate in a tissue specific fashion through the use of various chemokines and their receptors. Typical of the hijacking of an immune system component by a pathogen is the use of a chemokine ligand gene in the viral ancestor to SIV and HIV, allowing for virus binding to immunocompetent cells as is seen in the use of the CCR5 chemokine receptor by macrophage-tropic HIV strains. This thesis describes the allele and genotype frequencies for several TcR beta-chain variable segment polymorphisms in a population of MS patients compared with controls before and after stratification for HLA-DR15, polymorphism in the Apo-1 / Fas promoter, the DRB1 Val86/Val86 genotype, CCR5-delta32 and the HLA-DRA promoter. The thesis continues with CCR5-delta32 genotyping in IDDM, MS and SLE cohorts and then examines the question of the population of origin of the delta-32 allele of the CCR5 receptor for chemokine. Here, a case / control comparison of 122 RR-MS patients with 96 normal individuals was made for allele and genotype frequencies and for haplotypes formed by pairs of TCRB markers. Further analysis was made after HLA-DR15 stratification. Linkage disequilibrium was found between pairs of alleles of bv8s1, bv10s1, bv15s1 and bv3s1 loci in both patients and controls. In the RR-MS cohort, an increase in the allele frequency of bv8s1*2 was seen (p = 0.03) and the haplotype bv8s1*2 / bv3s1*1 was increased (p = 0.006), and both were found to be statistically significant. In the DR15-positive group, association between MS and TCRB was seen with the bv8s1*2 allele (p = 0.05) and the bv8s1*2 / bv10s1 haplotypes (p = 0.048), while the haplotype associations seen among the DR15-negative patients included the bv3s1*1 allele (bv10s1*1 / bv3s1*1, p = 0.022; bv8s1*2 / bv3s1*1, p = 0.048). While no associations were found after stratification for SDF1-3'A, Apo-1 / Fas or DRB1 there were modest interactions between bv3s1, bv10s1 and bv15s1 and the HLA-DRA promoter. These results support the involvement of the TCRB region in MS susceptibility. The further study of autoimmune disease here includes genotype analysis of CCR5-delta32 in type 1 diabetes (IDDM) and SLE. CCR5 is the major co-receptor for viral entry used by macrophage-tropic HIV strains and protection from infection is seen in homozygotes for CCR5-delta32. In diabetes, infiltration of pancreatic tissue by autoreactive T-cells involves secretion of multiple cytokines and chemokine receptor expression. Variation in the chemokine receptor CCR5 may result in differences in inflammatory cell migration in response to relevant chemokines. Adolescents with type 1 diabetes were genotyped for CCR5-delta32 (n = 626). The allele frequency was compared with that of 253 non-diabetic adolescents and with that of 92 adults with SLE. A reduced allele frequency was seen in type 1 diabetes compared with controls (0.092 vs 0.123, p = 0.05). This difference was not seen for the cohort of patients with SLE (freq = 0.114). A reduction in the number of CCR5-delta32/delta32 homozygotes, who lack CCR5, in the type 1 diabetes cohort was also seen and while not statistically significant (2 observed compared to 5.25 expected; p = 0.12) is interesting. These results suggest a partial protection from type 1 diabetes for CCR5-delta32 homozygous individuals is possible and that CCR5 has a potential role in the pathogenesis of type 1 diabetes. Global surveys of the CCR5-delta32 allele have confirmed a single mutation event in a Northeastern European population as the source of this allele. Here, Australian Ashkenazi Jews (n = 807) were found to have a CCR5-delta32 allele frequency of 14.6% while Australian Sephardic Jews (n = 35) had a frequency of 5.7% and non-Jewish Australian controls (n = 311) had an allele frequency of 11.25%. Data on birthplace of grandparents showed a gradient with highest CCR5-delta32 frequencies from Eastern European Ashkenazim (~19.5% for those whose four grandparents come only from Russia, Poland, Hungary, Austria and Czechoslovakia; n = 197) which differs significantly from the frequency seen in Ashkenazi Jews from Western Europe (n = 101, p = 0.001). Homozygotes for CCR5-delta32 were genotyped with 3p21 region microsatellites. This has defined an ancestral haplotype on which the mutation first occurred and helped to date this event to between 40 and 50 generations ago or just over a thousand years ago. The population gradient, combined with the dating of the mutation by microsatellite allele frequencies, suggests an origin for the CCR5-delta32 allele in a population ancestral to the Ashkenazim. The distribution in non-Jewish populations in northern Europe has led others to postulate spread of the mutation by Vikings. It is hypothesised here that the link between the two populations could be the kingdom of Khazaria with subsequent admixture into both Swedish Vikings and Ashkenazi Jews. The basic driving force of evolution is through selection and the immune system has a role which, through the survival pressure exerted by viruses and other pathogens, has the potential to exert a great deal of selective force on the various components of this system. The effects of this pronounced selection on an immune system component can be seen for example in the increase of the CCR5-delta32 allele over the last thousand years to the current frequency. As mentioned, some immune system components are not affected by such straightforward selection. In the case of the TCRBV segments, effects on the immune repertoire can occur through MHC interaction at the point of thymic entry and in the effects of various superantigens, but the actual binding pockets that recognise antigen are themselves unable to be selected for (or against). The findings presented in this thesis provide support for the association of TCRBV gene segments with multiple sclerosis and also provide support for the further study of the role of the CCR5-delta32 allele in type 1 diabetes. Furthermore, data presented here suggests that the CCR5-delta32 allele had an origin in the Khazar Kingdom just over a thousand years ago, accounting for the allele frequencies in both the Ashkenazi Jews and in lands frequented by the Vikings. The definition of an extended ancestral haplotype for the CCR5-delta32 allele shows how the effect of selection of an allele of one gene can carry with it specific alleles of a large number of other genes as well.

Anaplastic Large Cell Lymphoma (ALCL) is a peripheral T cell lymphoma divided into three distinct entities: ALCL, Anaplastic Lymphoma Kinase (ALK)+, ALCL ALK- and cutaneous ALCL. In the majority of ALCL, ALK+, ALK is expressed as the result of a chromosomal translocation generating Nucleophosmin 1(NPM)-ALK, which is considered the main driver. ALCL have an unusual immunophenotype; they rarely express a T cell receptor (TCR), but are often positive for CD4 and produce cytotoxic proteins such as perforin and Granzyme B, but in the absence of CD8, questioning the origin and pathogenesis of this malignancy. Expression of NPM-ALK in mice from the T-cell specific CD4 promoter gives rise to thymic lymphomas not modelling human ALCL suggesting that other events and/or expression of NPM-ALK at a defined stage of T cell ontogeny is required for peripheral T cell lymphoma development. Indeed, back-crossing the CD4/NPM-ALK line onto a RAG competent, MHC class I restricted ovalbumin-specific TCR, OTI transgenic line (CD4/NPM-ALK/OTI) permits peripheral lymphoma development mimicking human ALCL (but CD4/NPM-ALK/OTII mice still develop thymic lymphoma); tumours contain cells histopathologically identical to ALCL hallmark cells. Interestingly, peripheral tumours developing in this model also lack cell surface expression of the OTI TCR in fitting with observations of a lack of TCR expression on human ALCL. It follows that stimulation of T cells in vivo by infection with MHV-ova prevents lymphomagenesis suggesting that the TCR is detrimental to tumour growth. Indeed, strong stimulation via the TCR of NPM-ALK-expressing primary T cells in vitro, impedes cell proliferation but cell growth is favoured when a weaker stimulus is employed. Overall, data presented in this thesis identifies a potential mechanism of lymphomagenesis accounting for the unusual immunophenotype of ALCL and an explanation as to why cells lack a TCR and associated proximal signaling.