<p>Dysregulated inflammation underlies the pathogenesis of a myriad of human diseases ranging from cancer to autoimmunity. As coordinators, executers and sentinels of host immunity, T cells represent a compelling target population for immune-modulation. In fact, the antigen-specificity, cytotoxicity and promise of long-lived of immune-protection make T cells ideal vehicles for cancer immunotherapy. Interventions for autoimmune disorders, on the other hand, aim to dampen T cell-mediated inflammation and promote their regulatory functions. Although significant strides have been made in targeting T cells for immune-modulation, current approaches remain less than ideal and leave room for improvement. In this dissertation, I seek to improve on current T cell-targeted immunotherapies, by identifying and preclinically characterizing their mechanisms of action and in vivo therapeutic efficacy.</p><p>CD8+ cytotoxic T cells have potent antitumor activity and therefore are leading candidates for use in cancer immunotherapy. The application of CD8+ T cells for clinical use has been limited by the susceptibility of ex vivo-expanded CD8+ T cells to become dysfunctional in response to immunosuppressive microenvironments. To enhance the efficacy of adoptive cell transfer therapy (ACT), we established a novel microRNA-targeting approach that augments CTL cytotoxicity and preserves immunocompetence. Specifically, we screened for miRNAs that modulate cytotoxicity and identified miR-23a as a strong functional repressor of the transcription factor Blimp-1, which promotes CTL cytotoxicity and effector cell differentiation. In a cohort of advanced lung cancer patients, miR-23a was upregulated in tumor-infiltrating CD8+ T cells, and its expression correlated with impaired antitumor potential of patient CD8+ T cells. We determined that tumor-derived TGF-&#946; directly suppresses CD8+ T cell immune function by elevating miR-23a and downregulating Blimp-1. Functional blockade of miR-23a in human CD8+ T cells enhanced granzyme B expression; and in mice with established tumors, immunotherapy with just a small number of tumor-specific CD8+ T cells in which miR-23a was inhibited robustly hindered tumor progression. Together, our findings provide a miRNA-based strategy that subverts the immunosuppression of CD8+ T cells that is often observed during adoptive cell transfer tumor immunotherapy and identify a TGF&#946;-mediated tumor immune-evasion pathway.</p><p>Having established that miR-23a-inhibition can enhance the quality and functional-resilience of anti-tumor CD8+ T cells, especially within the immune-suppressive tumor microenvironment, we went on to interrogate the translational applicability of this strategy in the context of chimeric antigen receptor (CAR)-modified CD8+ T cells. Although CAR T cells hold immense promise for ACT, CAR T cells are not completely curative due to their in vivo functional suppression by immune barriers &#8210; such as TGF&#946; &#8210; within the tumor microenvironment. Since TGF&#946; poses a substantial immune barrier in the tumor microenvironment, we sought to investigate whether inhibiting miR-23a in CAR T cells can confer immune-competence to afford enhanced tumor clearance. To this end, we retrovirally transduced wildtype and miR-23a-deficient CD8+ T cells with the EGFRvIII-CAR, which targets the PepvIII tumor-specific epitope expressed by glioblastomas (GBM). Our in vitro studies demonstrated that while wildtype EGFRvIII-CAR T cells were vulnerable to functional suppression by TGF&#946;, miR-23a abrogation rendered EGFRvIII-CAR T cells immune-resistant to TGF&#946;. Rigorous preclinical studies are currently underway to evaluate the efficacy of miR-23a-deficient EGFRvIII-CAR T cells for GBM immunotherapy. </p><p>Lastly, we explored novel immune-suppressive therapies by the biological characterization of pharmacological agents that could target T cells. Although immune-suppressive drugs are classical therapies for a wide range of autoimmune diseases, they are accompanied by severe adverse effects. This motivated our search for novel immune-suppressive agents that are efficacious and lack undesirable side effects. To this end, we explored the potential utility of subglutinol A, a natural product isolated from the endophytic fungus Fusarium subglutinans. We showed that subglutinol A exerts multimodal immune-suppressive effects on activated T cells in vitro: subglutinol A effectively blocked T cell proliferation and survival, while profoundly inhibiting pro-inflammatory IFN&#947; and IL-17 production by fully-differentiated effector Th1 and Th17 cells. Our data further revealed that subglutinol A might exert its anti-inflammatory effects by exacerbating mitochondrial damage in T cells, but not in innate immune cells or fibroblasts. Additionally, we demonstrated that subglutinol A significantly reduced lymphocytic infiltration into the footpad and ameliorated footpad swelling in the mouse model of Th1-driven delayed-type hypersensitivity. These results suggest the potential of subglutinol A as a novel therapeutic for inflammatory diseases.</p> / Dissertation

<p>T lymphocytes can be rendered specific against a wide range of antigens by the genetic transfer of a chimeric receptor, a fusion between the antigen-binding domain of an antibody and the signalling domain of a T cell receptor. The use of such chimeric T lymphocytes has shown promising results for cancer therapy. Previous experiments in our laboratory have shown low rates of gene transfer using retroviral vectors. In this study, investigations have been done to increase the number of genetically modified cells. Different enhancers such as PLL and polybrene have previously been used in combination with retroviral transduction. The optimal retroviral protocol in this study showed to be the use of retrovectors produced with twice the normal concentration of the plasmids encoding env and gag-pol rather than the use of the enhancers. A 6-day pre stimulation of T lymphocytes prior transduction together with a centrifugation step increased the rate of modified cells even further. Alternative approaches of gene transfer were also investigated, including plasmid transfection and adenoviral transduction. While transfection protocols yielded low numbers of modified cells, adenoviral vectors showed the highest rate of gene transfer.</p> / <p>Cancer är den sjukdom som idag, efter hjärt-kärl-sjukdomar, kräver flest dödsfall i i-länder. Som en alternativ behandlingsmetod mot cancer pågår just nu forskning om genetiskt förbättrade immunceller, s.k. chimära T lymfocyter, skulle kunna användas för att döda tumörceller. De chimära cellerna är utrustade med en konstgjord receptor som är en fusion av en antikropp och en signalkedja. Det gör att cellerna kan riktas mot ett brett urval av cancertyper. Att få cellerna att ta upp generna som behövs för den konstgjorda receptorn har visats sig vara problematiskt. Den här studien har därför som mål att förbättra cellernas förmåga att ta upp gener. För detta har vi använt oss av retrovirus- och adenovirus-system tillsammans med försök att få cellerna att spontant ta upp generna, sk. plasmid-transfektion. Studien har visat att de båda virussystemen ger högst antal modifierade celler. Olika substanser som tidigare har visat sig förhöja graden av gentillförsel har testats, men vår studie har visat att tillverkningen av virusvektorerna har större påverkan på resultaten än någon av de olika hjälpmedlen.</p>

Chemokines are small immune system proteins mediating leukocyte migration and activation, and are important in many aspects of health and diseases. Some chemokines also have the ability to block HIV-1 infection by binding to the HIV-1 co-receptors CCR5 (CC chemokine receptor 5) and CXCR4 (CXC chemokine receptor 4). The first part of this work is to determine the mechanism of action of a human herpesvirus-8 encoded viral chemokine analog vMIP-II (viral macrophage inflammatory protein-II) by characterizing its interactions with endothelial surface glycosaminoglycans (GAGs) and cell surface receptors. Nuclear magnetic resonance (NMR), mutagenesis and molecular-docking were conducted and results show that vMIP-II tightly binds glycosaminoglycans using residues distributed along one face of the protein, such as R18, R46 and R48, and that there is a shift in the GAG binding site between the monomer and dimer form of vMIP-II where the N-terminus is involved in GAG binding for the dimer. This study, for the first time, provides a model that explains the mechanism of how quaternary structure affects chemokine-GAG binding. Mutagenesis and competition binding assays were conducted to study the receptor-binding mechanism of vMIP-II. Preliminary results suggest that vMIP-II uses the same positively charged binding surface comprising R18, K45, R46 and R48 to interact with the negatively charged N-termini of CCR5 and CXCR4. NMR studies on how vMIP-II interacts with N-terminal peptides of CCR5 and CXCR4 is on-going. The second part of this work was to rationally design HIV-1 entry inhibitors based on our knowledge of the mechanisms of chemokine-receptor binding and HIV-1 cell entry. We successfully designed two chimeric HIV entry inhibitors composed of CCR5-targeting RANTES variants (5P12-RANTES and 5P14-RANTES) linked to a gp41 targeting C-peptide, C37. In in vitro assays, chimeric inhibitors 5P12-linker-C37 and 5P14-linker-C37 showed the highest anti-viral potency yet published with IC50 values as low as 0.001 nM against certain virus strains. On human peripheral blood mononuclear cells, the chimeric inhibitors also exhibited very strong inhibition against R5-tropic and X4-tropic viruses, with IC50 values as low as 0.015 nM and 0.44 nM, respectively. A clear delivery mechanism was observed and characterized. These fully recombinant inhibitors can be easily produced at low cost and are excellent candidates for HIV microbicides.

The field of synthetic biology seeks to revolutionize the scope and scale of what is currently feasible by genetic engineering. By focusing on engineering general signal processing platforms using modular genetic parts and devices rather than `one-off' systems, synthetic biologists aim to enable plug-and-play genetic circuits readily adaptable to different contexts. For mammalian systems, the goal of synthetic biology is to create sophisticated research tools and gene therapies. While several isolated parts and devices exist for mammalian systems there are few signal processing platforms available. We addressed this need by creating a transcriptional regulatory framework using programmable zinc finger (ZF) and TALE transcription factors and a conceptual framework for logical T-cell receptor signaling. We first engineered a large set of ZF activator and repressor transcription factors and response promoters. ZFs are scalable elements as they can be engineered to bind to given DNA sequences. We demonstrated that we could ‘tune’ the activity of the ZF transcription factors by fusing them to protein homo-dimerization domains and by modifying their response promoters. We also created OR and NOR logic gates using hybrid promoters and AND and NAND logic gates by reconstituting split zinc finger activators and repressors with split inteins. Next, using a computational algorithm we designed a series of TALE transcriptional activators and repressors predicted to be orthogonal to all 2kb human promoter regions and thus minimally interfere with endogenous gene expression. TALEs can be designed to bind to even longer DNA sequences than ZFs, however off-target binding is predicted to occur. We tested our computationally designed TALEs in human cells demonstrating that they activated their intended target genes, but not their likely endogenous off-target genes, nor synthetic promoters with binding site mismatches. Finally, we created a conceptual framework for logical T-cell-mediated killing of target cells expressing combinations of surface antigens. The systems consist of conventional and novel chimeric antigen receptors (CARs) containing inhibitory or co-stimulatory cytoplasmic signaling domains. In co-incubation assays of engineered T-cells with target cells we demonstrated a functioning OR-Gate system and progress toward development of a functional NOT-Gate system using the CD300a and CD45 inhibitory receptor domains.

Disulfide bond formation is an essential process for the folding and biological activity of most extracellular proteins; however, it may become the limiting step when the production of these proteins is attempted in heterologous hosts such as Escherichia coli. The rearrangement of incorrect disulfide bonds between cysteines that do not normally interact in the native structure of a protein is carried out by disulfide isomerase enzymes. The disulfide isomerase present in the bacterial secretory compartment (the periplasmic space) is the homodimeric enzyme DsbC. The objective of this dissertation was to understand the key features of how DsbC catalyzes disulfide bond isomerization. Chimeric disulfide isomerases comprising of protein domains that share a similar function, or are homologous to domains of DsbC were constructed in an effort to understand the effect of the domain orientation in the dimeric protein, and the need for a substrate binding region in disulfide isomerases. We successfully created a series of fusion enzymes, FkpA-DsbAs, which catalyze in vivo disulfide isomerization with comparable efficiency to DsbC. These enzymes comprise of the peptide binding region of the periplasmic chaperone FkpA, which is functionally and structurally similar to the binding domain of DsbC but share no amino acid homology with it, fused to the bacterial oxidase DsbA. In addition, these chimeric enzymes were shown to assist in the initial formation of disulfide bonds, a function that is normally exhibited only by DsbA. Directed evolution of the FkpA-DsbA proteins conferred improved resistance to CuCl₂, a phenotype dependent on disulfide bond isomerization and highlighted the importance of an optimal catalytic site. The bacterial disulfide isomerase DsbC is a homodimeric V-shaped enzyme that consists of a dimerization domain, two α-helical linkers and two opposing catalytic domains. The functional significance of the existence of two catalytic domains of DsbC is not well understood yet. The fact that identical subunits naturally dimerize to generate DsbC has so far limited the study of the individual catalytic sites in the homodimer. In chapter 3 we discuss the engineering, in vivo function, and biochemical characterization chapter 3 we discuss the engineering, in vivo function, and biochemical characterization of DsbC variants covalently linked via (Gly3Ser) flexible linkers. We have either inactivated one of the catalytic sites (CGYC), or entirely removed one of the catalytic domains while maintaining the putative binding area intact. Our results support the hypotheses that dual catalytic domains in DsbC are not necessary for disulfide bond isomerization, but are important in terms of increasing the effective concentration of catalytic equivalents, and that the availability of a substrate binding region is a determining feature in isomerization. Finally, we have carried out initial studies to map the residues and sequence motifs that are recognized in substrate proteins that interact with DsbC. Although the main putative binding region of DsbC has been localized within the limits of the hydrophobic cleft that emerges from the interaction of the N-terminal domains of this enzyme, and, a few native substrates have already been identified, no information on the features of substrate proteins that are recognized by the enzyme has been reported. To address this problem, we have screened two different, 15 amino-acid random peptide libraries for binding to DsbC. We have successfully isolated several peptides with high affinity for the enzyme. Possible consensus binding motifs were identified and their significance in substrate recognition will be examined in future studies. / text

Developing targeted genome regulation approaches holds much promise for accelerating trait discovery and development in agricultural biotechnology. Clustered Regularly Interspaced Palindromic Repeats (CRISPRs)/CRISPR associated (Cas) system provides bacteria and archaea with an adaptive molecular immunity mechanism against invading nucleic acids through phages and conjugative plasmids. The type II CRISPR/Cas system has been adapted for genome editing purposes across a variety of cell types and organisms. Recently, the catalytically inactive Cas9 (dCas9) protein combined with guide RNAs (gRNAs) were used as a DNA-targeting platform to modulate the expression patterns in bacterial, yeast and human cells. Here, we employed this DNA-targeting system for targeted transcriptional regulation in planta by developing chimeric dCas9-based activators and repressors. For example, we fused to the C-terminus of dCas9 with the activation domains of EDLL and TAL effectors, respectively, to generate transcriptional activators, and the SRDX repression domain to generate transcriptional repressor. Our data demonstrate that the dCas9:EDLL and dCas9:TAD activators, guided by gRNAs complementary to promoter elements, induce strong transcriptional activation on episomal targets in plant cells. Moreover, our data suggest that the dCas9:SRDX repressor and the dCas9:EDLL and dCas9:TAD activators are capable of markedly repressing or activating, respectively, the transcription of an endogenous genomic target. Our data indicate that the CRISPR/dCas9:TFs DNA targeting system can be used in plants as a functional genomic tool and for biotechnological applications.

Šio darbo tikslas buvo gauti monokloninius antikūnus prieš Hendra ir Nipah virusų nukleokapsidės baltymus. Dėl didelės Henipavirus genties virusų nukleokapsidės baltym�� homologijos sunku gauti monokloninius antikūnus, specifiškus konkretaus viruso nukleokapsidės baltymui. Siekiant išspręsti šią problemą, buvo panaudoti chimeriniai rekombinantiniai baltymai, sukonstruoti pelės poliomos viruso pagrindinio kapsidės baltymo VP1 pagrindu, į kurį buvo įterptos nehomologiškos Nipah ir Hendra virusų nukleokapsidės baltymų sekos. Imunizacijoms panaudojus tokius chimerinius baltymus, buvo nustatyta, kad jie sukelia stiprų imuninį atsaką. Buvo sukurti nauji monokloniniai antikūnai, specifiški tik Nipah viruso nukleokapsidės baltymui ir nereaguojantys su Hendra viruso nukleokapsidės baltymu. Taip pat buvo sukurti monokloniniai antikūnai prieš baltymą-nešiklį – pelės poliomos viruso pagrindinį kapsidės baltymą VP1. Naujai sukurtų antikūnų specifiškumas buvo patvirtintas imunofermentinės analizės ir imunoblotingo metodais. Monokloninių antikūnų prieš Hendra viruso nukleokapsidės baltymą gauti nepavyko. / The aim of this study was to generate monoclonal antibodies against Hendra and Nipah virus nucleocapsid proteins. There is high homology between nucleocapsid proteins of Henipavirus genus members, therefore it is difficult to generate monoclonal antibodies that do not show any cross-reactivity with both antigens. This problem was solved by using recombinant chimeric proteins designed by insertion of non-homological segments of Hendra and Nipah virus nucleocapsid proteins into the mouse polyomavirus capsid protein VP1. Mice were immunized with these chimeric proteins and it was determined that they induce a strong immune response. Monoclonal antibodies against Nipah virus nucleocapsid protein as well as carrier protein – mouse polyomavirus capsid protein VP1 – were generated. The specificities of newly developed monoclonal antibodies were confirmed by ELISA and immunoblot. The generation of specific monoclonal antibodies against Hendra virus nucleocapsid protein failed.

Liver metastases are the most common cause of death in colorectal cancer patients. The standard of care and potential for cure for colorectal liver metastases is resection, but often times disease it too extensive for this treatment. Over the years, cancer research has made way for advances in treating progressive disease through immunotherapy. By genetically modifying an individual’s immune system using virally transduced chimeric antigen receptor T cells (CAR-T), patients are better able to receive exquisitely specific T cells to target specific tumors. Furthermore, selective delivery strategies may enhance efficacy while limiting detrimental, systemic adverse effects. Not only this, CAR-Ts have also lead to complete remission in some liquid tumors while maintaining the potential for remission in solid tumors as well. This literature review takes readers through the emergence of the different generations of CAR-T and the various studies including clinical trials that have demonstrated the safety and efficacy of CAR-T. The second portion of this paper will outline the design for a phase II clinical trial using intrahepatic CAR-T therapy in addition to selective internal radiation therapy (SIRT) for refractory CEA+ colorectal liver metastases. Benefits and limitations of using these therapies are further discussed.

This thesis describes the establishment of a precise gene targeting methodology in the silkworm Bombyx mori by technologies based on engineered endonucleases. Two classes of engineered endonucleases, ZFNs and full length TALENs were used for creating DSBs at specified sites in the colour marker genes (BmBlos2 and Bmwh3). Direct embryo microinjection of engineered nucleases mRNA were performed and let the nuclease proteins to disrupt the functions of these marker genes by creating DSBs and inducing error prone NHEJ mechanism. These experiments showed that both ZFNs and TALENs could be used for targeted gene disruption in silkworms.

Made available in DSpace on 2014-08-20T13:32:48Z (GMT). No. of bitstreams: 1 tese_silvana_beutinger_marchioro.pdf: 842737 bytes, checksum: 032d940f684cacf69ead32db6268d1cc (MD5) Previous issue date: 2013-06-27 / Mycoplasma hyopneumoniae (M. hyopneumoniae) is the causative agent of enzootic pneumonia (EP) in pigs, a chronic respiratory disease characterized by low mortality and high morbidity, responsible by significant economic losses in the pig industry worldwide. M. hyopneumoniae infection can be controlled by optimizing management practices and housing conditions, as well as with the use of antibiotics and vaccination. Commercial vaccines consist of adjuvanted inactivated whole cell preparations, and are frequently used worldwide in countries with an intensive pig production. The currently available vaccines are beneficial from an economic point of view, but they do not provide a sustainable control of the disease. They cannot prevent colonization of M. hyopneumoniae in the respiratory tract, and do not significantly reduce the transmission of the pathogen. Also, little is known about the exact mechanisms of the partial protection they induce. In this context, the general aims of this thesis were to assess the mode of the action of an existing commercial vaccine on the one hand and to develop and evaluate a new recombinant vaccine against M. hyopneumoniae on the other hand, looking for more effective strategies for disease control. For development of the recombinant vaccine a chimeric protein was developed and evaluated. This protein was based on proteins known to play a role in the adhesion and that were able to induce an immune response and a partial protection against M. hyopneumoniae infection when evaluated individually. From the studies described in this thesis, it can be concluded that intramuscular vaccination with an adjuvanted bacterin is able to stimulate both systemic and local immune responses, and that the new recombinant vaccine developed against EP might be promises strategies to control the disease. / Mycoplasma hyopneumoniae (M. hyopneumoniae) é o agente etiológico da pneumonia enzoótica (EP) suína, uma doença crônica de baixa mortalidade e alta morbidade, responsável por perdas econômicas significativas na cadeia suinícola em todo o mundo. A infecção por M. hyopneumoniae pode ser controlada pela otimização das práticas de manejo e das condições de alojamento, bem como com o uso de antibióticos e vacinação. Vacinas comerciais consistem em preparações de células inteiras inativadas do agente, fornecidas com adjuvante, e são frequentemente utilizadas em todo o mundo. As vacinas disponíveis atualmente são benéficas do ponto de vista econômico, mas elas não fornecem um controle sustentável da doença. Elas não previnem a colonização do M. hyopneumoniae no trato respiratório, e não reduzem significativamente a transmissão do agente patogênico. Além disso, pouco se sabe sobre os mecanismos exatos envolvidos na proteção que elas induzem. Desta forma, os objetivos gerais desta tese foram avaliar o modo de ação de uma vacina comercial existente e desenvolver e avaliar uma nova vacina recombinante contra M. hyopneumoniae, buscando estratégias mais eficazes para o controle da doença. Para o desenvolvimento desta vacina recombinante uma proteína quimérica foi produzida, baseada em proteínas envolvidas na adesão do agente e que foram capazes de induzir uma resposta imune e uma proteção parcial contra a infecção por M. hyopneumoniae quando avaliadas individualmente, e avaliada seu potencial protetor em teste de infecção experimental de suínos. A partir dos estudos descritos nesta tese, pode-se concluir que a vacinação intramuscular com uma bacterina comercial é capaz de estimular tanto uma resposta imune sistêmica quanto local, e que a nova vacina recombinante desenvolvida contra a EP pode ser considerada uma estratégia promissora para o controle da doença.