An estimated 1,735,350 new cancer diagnosis and 609,640 cancer related deaths are predicted to occur in the United States in 2018. To improve patient prognosis, biomarkers are needed to identify cancer in early stages. When diagnosed at an early stage, cancer is more likely to respond to treatments and patients have a higher survival rate. Consequently, there is an ever-present need to identify biomarkers that can aid in the detection of cancer. Additionally, there is a paradigm shift in the field of cancer treatment towards immunotherapy. Traditional cancer treatments include chemotherapy, radiation, and hormone therapy and are not cancer-specific, which leads to bystander effects on the patient<&trade>s normal organs that often harm the patient and create unnecessary hardship. To alleviate this, immunotherapy utilizes a patient<&trade>s own immune cells to attack and destroy cancer cells via cancer-specific biomarkers. These biomarkers are ideally on the surface of cancer cells and absent from the patient<&trade>s normal cells to avoid healthy tissue destruction. With this new therapy, there is a recent push to find surface antigens for immunotherapy techniques.This dissertation describes the characterization of HPRT as a diagnostic and therapeutic biomarker for the detection and possible treatment of hematological and solid malignancies. We describe the general upregulation of HPRT upon malignancy and show that this elevation in protein expression is independent of stage, which indicates that it would be useful as an early stage diagnostic companion tool. We have preliminarily linked the elevation in HPRT to a mutation in one of its prime transcription factors, p53. Specific mutation in p53 called Gain of Function mutations have shown to influence salvage pathway enzyme expression, and we have shown that mutations in p53 are relevant to the elevated levels of HPRT within several cancer types. In addition, we also found that HPRT associates significantly with the membrane of several cancer cell lines as well as patient samples. We found that HPRT has insignificant expression on normal cells, which suggests it may be useful as a targetable biomarker for immunotherapy. Throughout our analysis, we also determined that HPRT might have a role in immune regulation as an elevation of the protein correlates to the decrease of several pro-inflammatory genes involved in immune activation. The knowledge gained from the data presented in this dissertation have opened up new functions for HPRT outside of simple nucleotide production and have confirmed that HPRT has a unique role in cancer that has not been previously reported.

The ATP-PRTase enzyme catalyses the first committed step of histidine biosynthesis in archaea, bacteria, fungi and plants.1 As the catalyst of an energetically expensive pathway, ATP-PRTase is subject to a sophisticated, multilevel regulatory system.2 There are two families of this enzyme, the long form (HisGL) and the short form (HisGS) that differ in their molecular architecture. A single HisGL chain comprises three domains. Domains I and II house the active site of HisGL while domain III, a regulatory domain, forms the binding site for histidine as an allosteric inhibitor. The long form ATP-PRTase adopts a homo-hexameric quaternary structure.3,4 HisGS comprises a similar catalytic core to HisGL but is devoid of the regulatory domain and associates with a second protein, HisZ, to form a hetero-octameric assembly.5 This thesis explores the allosteric regulation of the short form ATP-PRTase, as well as the functional and evolutionary relationship between the two families. New insight into the mode allosteric inhibition of the short form ATP-PRTase from Lactococcus lactis is reported in chapter two. A conformational change upon histidine binding was revealed by small angle X-ray scattering, illuminating a potential mechanism for the allosteric inhibition of the enzyme. Additionally, characterisation of histidine binding to HisZ by isothermal titration calorimetry, in the presence and absence of HisGS, provided evidence toward the location of the functional allosteric binding site within the HisZ subunit. Chapter three details the extensive effort towards the purification of the short form ATP-PRTase from Neisseria menigitidis, the causative agent of bacterial meningitis. This enzyme is of particular interest as a potential target for novel, potent inhibitors to combat this disease. The attempts to purify the long form ATP-PRTase from E. coli, in order to clarify earlier research on the functional multimeric state of the enzyme, are also discussed. Chapter four reports the investigation of a third ATP-PRTase sequence architecture, in which hisZ and hisGS comprise a single open reading frame, forming a putative fusion enzyme. The engineering of two covalent linkers between HisZ and HisGS from L. lactis and the transfer of the regulatory domain from HisGL to HisGS, is also discussed, in an attempt to delineate the evolutionary pathway of the ATP-PRTase enzymes. Finally, the in vivo activity of each functional and putative ATP-PRTase was assessed by E. coli BW25113∆hisG complementation assays.

Thesis (Ph.D). / Written for the Dept. of Human Genetics. Title from title page of PDF (viewed 2009/06/08). Includes bibliographical references.

Thesis (Ph.D.). / Written for the Dept. of Medicine, Division of Experimental Medicine. Title from title page of PDF (viewed 2009/06/09). Includes bibliographical references.

Magister Scientiae - MSc / Malaria remains the most important parasitic disease worldwide. It is estimated that over 500 million infections and more that 2.7 million deaths arising from malaria occur each year. Most (90%) of the infections occur in Africa with the most affected groups being children of less than five years of age and women. this dire situation is exacerbated by the emrggence of drug resistant strains of Plasmodium falciparum. The work reported in this thesis focuses on improving the purification of PfHPRT by investigating the characteristics of anion exchange DE-52 chromatography (the first stage of purification), developing an HPLC gel filtration method for examining the quaternary structure of the protein and possible end stage purification, and initialcrystalization trials. a homology model of the open, unligaded PfHPRT is constructed using the atoomic structures of human, T.ccruz and STryphimurium HPRT as templates. / South Africa

Orientadores: Gonçalo Amarante Guimarães Pereira, Francisco Javier Medrano Martin / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T15:38:56Z (GMT). No. of bitstreams: 1 Dantas_DeysedeSouza_D.pdf: 4937353 bytes, checksum: 5c9b26f6ef8ed34e974ca6c8bb0708f2 (MD5) Previous issue date: 2008 / Resumo: Os genes que codificam para a 6-oxopurina fosforribosiltransferase (HPRT, EC2.4.2.8) dos organismos Pyrococcus horikoshii e Schistosoma mansoni foram clonados em vetores de expressão. As proteínas foram expressas e purificadas em larga escala no sistema de expressão de Escherichia coli. Estudos cinéticos mostraram que a enzima de P. horikoshii é capaz de usar hipoxantina, guanina e xantina. Os dois primeiros substratos apresentam uma eficiência catalítica semelhante. A xantina apresenta um valor menor (ao redor de 20 vezes mais baixo), mas a constante catalítica é comparável com a da hipoxantina. A proteína não foi capaz de se ligar a GMP-agarose, mas sim pode ligar o outro substrato da reação reversa, pirofosfato inorgânico, com baixa afinidade (Kd = 4,7 ± 0,1 mM). Os dados de espalhamento dinâmico de luz, gel filtração e espalhamento de raios X a baixo ângulo mostram que esta proteína é um homohexâmero em solução. Este hexâmero é compacto e resistente à ação limitada de enzimas proteolíticas. Estudos de estabilidade frente a agentes químicos mostraram que a proteína é bastante estável resistindo os efeitos da uréia sem desenovelar completamente com a maior concentração do agente (8,0 M). Os dados obtidos com cloreto de guanidina mostraram que a proteína possui, no mínimo, um estado intermediário de desnaturação, como mostram os diferentes perfis obtidos com as diferentes técnicas usadas nos estudos de desnaturação. Os dados preliminares obtidos com a HPRT de S. mansoni mostraram que, na presença da cauda de histidinas, a proteína está presente como um octâmero alongado. Mas, muito provavelmente ela deve ser um tetrâmero. A presença de caudas fusionadas nas proteínas recombinantes pode afetar a estrutura e função das proteínas / Abstract: The genes that code for the 6-oxopurine phosphoribosyltransferase (HPRT, EC2.4.2.8) from the organisms Pyrococcus horikoshii and Schistosoma mansoni were cloned in expression vectors. The proteins were expressed and purified in large scale in the de Escherichia coli expression system. Kinetic studies showed that the enzyme from P. horikoshii is able to use hypoxanthine, guanine and xanthine. The first two substrates show a similar catalytic efficiency. Xanthine show a lower value (around 20 times), but the catalytic constant is comparable to that of hypoxanthine. The protein was unable to bind to GMP-agarose, but was able to bind the other substrate of the reverse reaction, inorganic pyrophosphate, with low affinity (Kd = 4.7 ± 0.1 mM). Dynamic light scattering, gel filtration and small angle X-ray scattering data show that the protein is a homohexamer in solution. This hexamer is compact and resistant to the limited action of proteolytic enzymes. Stability studies with chemical agents showed that the protein is very stable being able to stand the effects of urea without unfolding completely at the highest agent concentration (8.0 M). Data obtained with guanidine hydrochloride showed that the protein presents, at least, one unfolding intermediate state, as can be seen with the different profiles obtained with different techniques used in the unfolding studies. Preliminary data obtained from HPRT from S. mansoni showed that in the presence of the histidine tag, is present as a long octamer. But, most likely it should be a tetramer. The presence of histidine tag fused to the recombinant proteins could affect the structure and function of proteins / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

Molecular-biological annotation data is continuously being collected, curated and made accessible in numerous public data sources. Integration of this data is a major challenge in bioinformatics. We present the GenMapper system that physically integrates heterogeneous annotation data in a flexible way and supports large-scale analysis on the integrated data. It uses a generic data model to uniformly represent different kinds of annotations originating from different data sources. Existing associations between objects, which represent valuable biological knowledge, are explicitly utilized to drive data integration and combine annotation knowledge from different sources. To serve specific analysis needs, powerful operators are provided to derive tailored annotation views from the generic data representation. GenMapper is operational and has been successfully used for large-scale functional profiling of genes.

Despite the progress made in cancer research, cancer remains one of the leading causes of death worldwide. Although the development of new cancer treatments has improved cancer patients' survival rate, a significant number of patients experience refractory and recurrence events with serious side effects. It is known that the immune system actively participates in eliminating cancer. However, cancer cells can develop mechanisms to evade the immune system resulting in immunotolerance. Immunotherapy aids the patient's immune system's ability to recognize and eliminate cancer cells. During the last three decades, immunotherapy has gradually emerged as an effective and more specific approach to treat cancer. Particularly monoclonal antibodies and adoptive cell therapies such as chimeric antigen receptor (CAR) T-cells have proven highly effective. Nevertheless, the success of these novel therapies depends on discovering suitable tumor targets. Recently, we reported localization of Thymidine Kinase 1 (TK1) to the plasma membrane of certain cancer cells but have not found such localization on normal cells. Similarly, another nucleotide salvage pathway enzyme Hypoxanthine Guanine Phosphoribosyltransferase (HPRT), has also been reported to be localized to the plasma membrane of certain cancer cells. Thus, TK1 and HPRT membrane-associated forms can be potential tumor targets for cancer immunotherapy. This dissertation describes the immunotargeting of TK1 for the selective elimination of tumor cells and the surface localization of HPRT on the plasma membrane of cancer cells. Using hybridoma and phage display technologies, we developed monoclonal antibodies (mAb) and isolated human single domain antibodies (sdAb) specific to human TK1. We confirmed that antibodies and sdAbs could target TK1 on the plasma membrane of lung, breast and colon cancer cells, but not on healthy cells. In addition, we demonstrated that cancer cells expressing membrane-associated TK1 (mTK1) co-cultured with human mononuclear cells (MNC) were selectively eliminated through antibody-dependent cell-mediated cytotoxicity (ADCC) when anti-TK1 mAbs were added. Furthermore, we designed novel TK1 specific tumor targeting receptors and expressed them in human T cells and human macrophages. Finally, we proposed using both TK1 and HPRT as biomarkers for the early detection and monitoring of follicular lymphoma (FL), a disease that is usually detected at advanced stages. The knowledge generated from the data presented in this dissertation indicates that TK1 and HPRT may be suitable immunotherapeutic targets for antibody-based and adoptive cell-based therapies against both liquid and solid malignancies. It also proposes the incorporation of TK1 and HPRT as molecular biomarkers for the early detection and monitoring of FL.

O presente trabalho teve como objetivos a clonagem, expressão e purificação da proteína HGPRT de Leishimania tarentolae, para a caracterização e cristalização dessa enzima, a fim do seu estudo estrutural e funcional. O gene da HGPRT foi amplificado a partir de uma biblioteca genômica de Leishmania tarentolae da cepa UC Lambda ZAP Express BamHI-Sal3A I. Esse gene foi clonado no vetor de expressão pET29a(+) e usado na transformação da bactéria Escherichia coli BL21 (DE3). Esse sistema de expressão apresentou uma superexpressão da proteína recombinante, que foi purificada em cromatografia de forma iônica, com o uso da coluna de troca anônica POROS 20HQ. A proteína purificada foi utilizada para sua caracterização, como a determinação das constantes cinéticas (Km, Vmax e Kcat) para os diferentes substratos. A proteína foi encontrada como dímero em solução e o pI de aproximadamente 8,2. Além disso, essa proteína foi utilizada nos ensaios de cristalização pelo método de difusão de vapor em gotas suspensas. Os cristais obtidos foram utilizados nos testes da difração de raios-X sendo coletado um conjunto de dados no Laboratório Nacional de Luz Síncroton. Os dados de difração de raios-X foram processados com o uso do pacote de programa HKL. A resolução da estrutura cristalográfica foi obtida pelo método de substituição molecular através do programa AmoRe. Para o refinamento da estrutura foram utilizados os programas de refinamento automático CNS e REFMAC, e a manipulação na estação gráfica foi realizada através do programa O. A estrutura da HGPRT foi resolvida a 2,1 &#197 de resolução com os fatores de concordância Rwork e Rfree finais de 17,34 e 21,53%, respectivamente. / The aims of this work were the cloning, expression and purification of the protein HGPRT from Leishimania tarentolae, for the characterization and crystallization of the enzyme for it structural and functional study. The full-length hgprt gene was isolated from a leishmania tarentolae UC strain Lambda ZAP Express BamHI-Sal3A I genomic library. This gene was cloned in the expression vector pET29a+, and used in the transformation of the bacteria Escherichia coli BL21(DE3). This expression system presented a super-expression of the recombinant protein, which was purified by ionic change chromatography, utilizing the anionic change column POROS 20HQ. The purified protein was utilized for its characterization, including its kinetics constants (Km, Vmax e Kcat) for different substrates. The protein was found to be a dimmer in solution with pI close to 8.2. Besides, this protein was used in the crystallization assays by the steam diffusion in suspended drop technique. The obtained crystals were utilized in the x-ray diffraction studies. The data collection was performed in the Laboratório Nacional de Luz Síncroton. The X-ray diffraction data were processed utilizing the package program HKL. The crystallographic structure resolution was obtained by the molecular replacement method from the AmoRe program. For the structure refinement, the automatic refinement programs CNS and REFMAC were used, and the graphic manipulation was made through the O program. The structure of the HGPRT was resolved with 2,1 &#197 of resolution and final agreement factors Rwork and Rfree of 17,34% and 21,53%, respectively.

O Schistosoma mansoni, parasita responsável pela esquistossomose (barriga dágua), doença que afeta cerca de 300 milhões de pessoas em todo mundo, não possui a via de síntese de purinas, dependendo integralmente da via de salvação de purinas para seu suprimento dessas bases. Uma vez que a terapia se resume a administração de um único fármaco, o praziquantel, diversos casos de resistência do parasita a esse medicamento foram reportadas, sendo assim esta via tem sido citada como alvo potencial para o desenvolvimento de novos fármacos contra a doença. As enzimas adenosina kinase (AK), hipoxantina-guanina fosforibosiltransferase (HGPRT), adenilsuccinato liase (ADSL) e adenilsuccinato sintetase (ADSS) são enzimas chave desta via. Este trabalho faz parte de um projeto maior que visa a obtenção de todas as estruturas das enzimas envolvidas na via de salvação de purinas de Schistosoma mansoni. O cDNA correspondente às enzimas foi amplificado e clonado no vetor de expressão pOPIN; as enzimas AK isoforma 1, HGPRT isoforma 1 e ADSL foram expressas em E. coli Lemo21(DE3) e HGPRT isoforma 3 em E. coli B834(DE3); purificadas em coluna de cobalto agarose por afinidade, concentradas e cristalizadas no kit de cristalização Morpheus (Molecular Dimensions) no Oxford Protein Production Facility (OPPF) em Harwell UK. As coletas de dados por difração de raio-X foram realizadas no Síncrotron Diamond Light Source (DLS) - UK. Foram coletadas duas estruturas de ADSL, a 2.36&Aring; de resolução em complexo com AMP e 2.14&Aring; na forma Apo. A análise das estruturas revelou uma estrutura tetramérica bastante conservada entre as ADSLs, sendo este estado de oligomerização requerido, uma vez que resíduos de três das quatro subunidades compõem o sítio ativo. Apesar do sítio ativo ser altamente conservado entre SmADSL e ADSL humana, a interface dimérica dessas enzimas tem se apresentado suficientemente distintas, o que pode representar um potencial alvo para o desenvolvimento de um inibidor. O ensaio de atividade enzimática de ADSL revelou uma reação endotérmica, indicando que a contribuição da entropia relacionada a grande quantidade de moléculas de água presentes no sítio ativo é importante para a reação cinética. Após diversos experimentos de otimização dos cristais de HGPRT1 e aproximadamente 200 cristais testados, foi obtida uma estrutura em complexo com IMP a 2.8&Aring; de resolução. A análise da estrutura revelou uma estrutura tetramérica. Apesar das subunidades não compartilharem o sítio ativo, este estado de oligomerização é requerido, uma vez que resíduos que compõem o sítio ativo também estão envolvidos em interações na interface dimérica, orientando o resíduo invariável Arg206 na direção do sítio ativo. Foram identificadas quatro mutações na região do sítio ativo entre SmHGPRT e HGPRT humana: Ile149Met, Pro176Arg, Val189Ile e Arg192Lys. Desta forma, a obtenção das estruturas contribui para o entendimento bioquímico desta via essencial para o parasita e de como este pode ser seletivamente privado de recursos. / Schistosoma mansoni is the parasite responsible for schistosomiasis, disease that affects about 300 million people worldwide, and does not have the purine de novo pathway, depending entirely on the purine salvage pathway to supply its demands on purines. Currently, both direct treatment and most disease control initiatives, rely on chemotherapy using a single drug, praziquantel. Concerns over the possibility of resistance developing to praziquantel, has stimulated efforts to develop new drugs for the treatment of schistosomiasis. The purine salvage pathway has been reported as a potential target for developing new drugs against schistosomiasis. Adenosine kinase (AK), hypoxanthine-guanine phosphoribosyltransferase (HGPRT), adenylosuccinate lyase (ADSL), adenylosuccinate synthetase (ADSS) are key enzymes in this pathway. This work is part of a larger project aimed at obtaining all the structures of enzymes involved in purine salvage pathway of Schistosoma mansoni. The cDNA corresponding to the enzymes was amplified and cloned in vector pOPIN, AK isoform 1, HGPRT isoform 1 and ADSL were expressed in E. coli Lemo 21 (DE3) and HGPRT isoform 3 in E. coli B834(DE3); purified in cobalt agarose column, concentrated and crystallized in several conditions of the Morpheus (Molecular Dimensions) crystallization kit at the Oxford Protein Production Facility (OPPF) in Harwell UK. The data collection by xray diffraction were performed at Diamond Light Source UK. Two ADSL structures were obtained, ADSL in complex with AMP at 2.36&Aring; resolution and ADSL Apo form at 2.14&Aring; The analysis revealed a tetrameric structure highly conserved between ADSLs, and this oligomerization state is required since residues three of the four subunits comprise the active site. Despite the active site being highly conserved between human ADSL and SmADSL, the dimeric interface of these enzymes it has been shown sufficiently distinct, which may represent a potential target for the development of an inhibitor. The ADSL enzymatic activity assay showed an endothermic reaction, indicating the contribution of the entropy related to the large quantity of water molecules present in the active site is important for the reaction kinetics. After several optimization experiments of HGPRT1 crystals and about 200 crystals tested was obtained a structure in complex with IMP at 2.8&Aring; resolution. The structure analysis revealed a tetrameric structure. Despite the subunits do not share the active site, this oligomerization state is required, since residues that make up the active site are also involved in interactions in dimeric interface, guiding the invariable residue Arg206 toward the active site. Four mutations were identified in the region of the active site between SmHGPRT and human HGPRT: Ile149Met, Pro176Arg, Val189Ile e Arg192Lys. These structures increase the important structural information available about the Schistosoma mansoni purine salvage pathway and how it can be selectively private resources.