Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 100-117).

There are currently an estimated 33.2 million people living with human immunodeficiency virus (HIV) worldwide. For these individuals, long-term use of combination antiretroviral therapy (cART) is not feasible for a variety of reasons including major adverse complications, multi-drug resistance, poor adherence, and high cost. Hence, development of novel therapeutic strategies that can reduce the life-long dependency on cART is highly desired. In order to develop effective therapeutic strategies such as a therapeutic vaccine, we need to have a greater understanding of the immune correlates of viral control in chronic HIV infection. In this thesis, we used treatment interruption (TI) as a tool to test the efficacy of several therapeutic approaches and immune parameters for their association with effective control of viral replication. / In Chapter 2 we showed that cART intensification and Remune vaccination resulted in reduced viral load (VL) plateau during sequential TIs. Although HIV-specific immune responses measured by interferon-gamma (IFN-gamma) enzyme-linked immunospot assay (ELISPOT) increased in the same time frame, neither their breadth nor magnitude correlated with the decrease in VL plateau. In Chapter 3 the effect of ALVAC-vCP1425 plus Remune vaccination on HIV proteome-wide HIV-specific responses was monitored using a dual color IFN-gamma/interleukin-2 (IL-2) ELISPOT assay. We observed an increase in the magnitude of HIV-specific IFN-gamma/IL-2 responses, as well as in the breadth of Gag-specific IFN-gamma responses in the vaccinated groups compared to placebo groups. A shift towards an increased contribution of Gag-specific responses to total HIV-specific vaccine induced immune response was associated with longer delay to viral rebound during TI. In Chapters 4 and 5, we examined baseline pre-TI immune parameters and their association with viral rebound and CD4 count change during TI in HIV-infected individuals in the chronic phase of infection experiencing virologic failure before TI (Chapter 4) or with different levels of VL control while on therapy prior to TI (Chapter 5). We saw that chronic antigen stimulation from persistent viremia as well as co-infections such as with cytomegalovirus are associated with T-cell senescence, which may result in less favourable clinical outcomes during TI. / Consequently, results from this thesis contribute to further understanding of immune correlates of viral control in chronic HIV infection. New therapeutic vaccines and interventions should induce polyfunctional HIV-specific immune responses, broad Gag-specific immune responses, as well as reducing chronic antigen stimulation to prevent irreversible T-cell exhaustion. Taken together, these insights could potentially lead to the development of novel treatment interventions that could effectively control viral replication off cART.

The peripheral naive CD4 T cell pool is homeostatically regulated through a balance of thymic production, delivery of survival signals and homeostatic proliferation. CD4 recent thymic emigrants (RTEs) have a high T cell receptor excision circle (TREC) content and express high levels of CD31. We report premature thymic involution in RRMS, initiated by reduced numbers of naive CD4 T cells and various naive CD4 T cell subsets in peripheral blood. Further, CXCR4, a receptor involved in emigration from the thymus, and CD127 and Bcl-2 (survival signals) are upregulated in various naive CD4 T cell subsets in RRMS. As a compensatory process, naive CD4 T cells undergo homeostatic proliferation. This proliferation is a form of peripheral positive selection through self-MHC/self-antigen interaction and thus can contribute to the expansion of autoreactive T cells and predispose to development of RRMS.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

Thesis (Ph. D.)--University of Alabama at Birmingham, 2007. / Title from first page of PDF file (viewed Feb. 17, 2009). Includes bibliographical references.

Thesis (Ph. D.)--University of Virginia, 2008. / Title from title page. Includes bibliographical references. Also available online through Digital Dissertations.

Thesis (M.S.)--University of Missouri--Columbia, 2004. / Typescript. Includes bibliographical references (leaves 97-111). Also issued on the Internet.

A side effect of generating an immune system for defense against invading pathogens is the potential to develop destructive cells that recognize self-tissues. Typically, through the "education" of developing immune cells, the organism inactivates potentially self-destructive cells, resulting in what is called self-tolerance. I proposed to explore the molecular mechanisms responsible for the induction and maintenance of tolerance. Our lab has developed a model of induced immune tolerance to skin and islet allografts utilizing a donor-specific transfusion of spleen cells and a brief course of anti-CD40L antibody. Because the difficulty in isolation of tolerant T cells from this system is prohibitive to performing large screens on these cells directly, I have chosen to study an in vitro CD4+Th1 cell line, A.E7, which can be made anergic via stimulation through the T cell receptor in the absence of costimulation. I hypothesized that anergized T cells upregulate genes that are responsible for the induction and maintenance of anergy and therefore exhibit a unique RNA expression profile. I have screened anergic cells using Affymetrix GeneChips and identified a small number of genes that are differentially expressed long-term in the anergic population compared to mock-stimulated and productively activated controls. The results have been confirmed by quantitative RT-PCR for each of the candidates. One of the most promising, the zinc-finger transcription factor Egr-2, was verified to be expressed long-term by western blotting, demonstrating perfect correlation between Egr-2 protein expression and the anergic phenotype. Silencing Egr-2 gene expression by siRNA in A.E7 T cells prior to anergy induction rescues the cells from the inability to phosphorylate ERK-1 and ERK-2 and also results in increased proliferation in response to antigen rechallenge. In this study I report that Egr-2 is specifically expressed long-term in anergic cells, protein expression correlates inversely with responsiveness to antigen rechallenge, and that Egr-2 is required for the full induction of anergy in T cell clones.

There are four serotypes of dengue virus designated dengue 1, 2, 3 and 4 (D1, D2, D3 and D4) and epidemiological studies indicate that a severe complication of dengue virus infection - dengue hemorrhagic fever (DHF) is more likely to occur following a secondary infection. DHF is hypothesized to be immunologically mediated and may be triggered by virus-specific T cells. It is also likely that dengue virus-specific cytotoxic T lymphocytes (CTLs) are important for recovery from dengue virus infections. An analysis of the immune response during acute illness and when the patient has recovered from the infection (immune state) is therefore important as it will provide insights into the immunopathological nature of the disease. This thesis initially examines the CD8+CTL responses in volunteers who have received live attenuated dengue vaccines and then investigates acute and immune T cell responses in children following natural infection with dengue. When this project was initiated, there was little available information on the human CD8+ T cell responses to dengue viruses. PBMC from one donor had generated memory CD8+CTL to the nonstructural protein NS3 of dengue virus. Memory CD8+CTL responses were therefore analyzed to determine the diversity of the T cell response to dengue virus and to identify immunodominant proteins using PBMC from eight healthy adult American volunteers who had received monovalent live-attenuated candidate vaccines of the 4 dengue serotypes. All the donors had specific T cell proliferation to dengue viruses and to other flaviviruses that we tested. CTLs were generated from the stimulated PBMC of all donors and in the seven donors tested, dengue virus-specific CD8+CTL activity was demonstrated. The nonstructural proteins NS3 and NS1.2a and the structural protein E were recognized by CD8+CTLs from six, five and three donors respectively. All donors recognized either NS3 or NS 1.2a. In a donor who received a dengue 4 vaccine, CTL killing was seen in bulk culture against the premembrane protein (prM). This is the first demonstration of a CTL response against the prM protein. The CTL responses using PBMC of two donors were serotype-specific whereas all other donors had serotype-cross reactive responses. For one donor, CTLs specific for E, NSl.2a and NS3 proteins were all HLA-B44 restricted. For the three other donors tested the potential restricting alleles for recognition of NS3 were HLA-B38, A24 and/or B62 and B35. These results indicate that the CD8+CTL responses of humans after immunization with a single serotype of dengue virus are diverse and directed against a variety of proteins. The nonstructural proteins NS3 and NSl.2a appear to be immunodominant and should be considered when designing subunit vaccines for dengue. Previously T cell responses had not been examined in people who have had natural infections with dengue. The HLA diversity between North American Caucasians and populations where dengue is a serious health problem, calls for the analysis of immune responses in people who have been infected with natural circulating strains of the virus. We examined the memory cytotoxic T lymphocytic (CTL) responses of peripheral blood mononuclear cells (PBMC) obtained from patients in Thailand 12 months after natural symptomatic secondary dengue infections. In all four patients analyzed, CTLs were detected in bulk culture PBMC against nonstructural dengue proteins. Numerous CD4+ and CD8+ CTL lines were generated from the bulk cultures of two patients, KPP94-037 and KPP94-024, which were specific for the NSl.2a and NS3 proteins respectively. All CTL lines derived from both patients were crossreactive with other serotypes of dengue virus. The CD8+ NS1.2a specific lines from patient KPP94-037 were HLA-B57 restricted and the CD8+ NS3 specific lines from patient KPP94-024 were HLA-B7 restricted. The CD4+ CTL lines from patient KPP94-037 were HLA-DR7 restricted. A majority of the CD8+CTLs isolated from patient KPP94-024 were found to recognize a.a. 221-232 on NS3. These results demonstrate that after symptomatic secondary natural dengue infections in Thai patients, CTLs are mainly directed against nonstructural proteins and are broadly crossreactive. The data correlate with our observations that nonstructural proteins are immunodominant proteins in volunteers who received dengue vaccines. We were interested in examining CTL responses in children during their acute illness and comparing them to memory CTLs obtained from the same children a year or more after the infection. A detailed analysis on samples from nine patients during their acute illness failed to generate any dengue virus-specific CTL responses. We therefore decided to determine if cell mediated responses are altered during acute dengue infection. Decreased proliferative responses to mitogens and recall antigens have been observed in PBMC obtained during several acute human viral infections. All responses of PBMC during acute illness were compared to the same patients PBMC obtained at least 6 months after their infection. Proliferative responses to PHA, anti-CD3, tetanus toxoid and dengue antigens were significantly decreased in PBMC obtained during the acute infection. The proliferative responses to PHA were restored by the addition of gamma-irradiated autologous immune or allogeneic PBMC. Cell contact with the irradiated PBMC was necessary to restore proliferation. Non-T cells from the acute PBMC of dengue patients did not support proliferation of T cells from control donors in response to PHA, but T cells from the PBMC of patients with acute dengue proliferated if accessory cells from a control donor were present. Addition of anti-CD28 antibodies restored anti-CD3-induced proliferation of the PBMC of some patients. The percentage of monocytes was reduced in the acute sample of PBMC of the dengue patients. Addition of IL-2 or IL-7, but not IL-4 or IL-12 also restored proliferation of acute PBMC stimulated with anti-CD3. The results demonstrate that both quantitative and qualitative defects in the accessory cell population during acute dengue illness result in a depression of in vitro T cell proliferation. The data generated from this project shed light on the nature of the immune responses during acute natural dengue infections. It strengthens the existing data on the human memory CD8+CTL responses to dengue viruses and validates the observations by examining memory CTL responses after natural dengue infection in patients from Thailand. In addition, we demonstrate a profound defect in lymphoproliferative responses during dengue illness.

Made available in DSpace on 2015-12-06T23:47:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2009 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Uma das principais causas de falência terapêutica é o surgimento de cepas resistentes aos inibidores da transcriptase reversa (IRT) e da protease (IP). O processo de replicação do vírus HIV – 1 promove alta taxa de mutação devido aos erros inerentes à atividade da transcriptase reversa. Portanto, é comum em indivíduos sob tratamento e com carga viral detectável, o surgimento e seleção de cepas resistentes. O Estado de São Paulo é considerado como um dos epicentros da epidemia de Aids no Brasil, sendo que o município de Santos possui um dos maiores portos da América Latina e devido às rotas de comércio internacional atua como introdutor e difusor do HIV – 1 no sudeste brasileiro, com uma alta incidência de infecção, alta prevalência da resistência antirretroviral primária e de alta prevalência de vírus recombinante B/F. Tem sido também reconhecido que a falência virológica ao tratamento antirretroviral é alta nesta cidade, entretanto, não existem dados recentes e abrangentes a respeito da caracterização genotípica, da freqüência dos subtipos e resistência primária do HIV – 1. O objetivo do estudo foi avaliar os perfis virológico e imunológico e a resistência primária em pacientes virgens de tratamento aos medicamentos antirretrovirais e os fatores relacionados à falência virológica após 48 semanas de HAART nesta população. Foram analisados os prontuários dos pacientes recém diagnosticados e cadastrados no ano de 2000 e 2001, num total de 594 pacientes. Destes pacientes estudados no período citado, apenas 315 realizaram os exames de quantificação da carga viral e a contagem da subpopulações dos linfócitos TCD4+/TCD8+ no momento do seu diagnóstico. Posteriormente dos 315 pacientes foram selecionados 80 virgens de tratamento aos antirretrovirais, para a realização do exame de genotipagem, no qual foram comparados os perfis demográficos do HIV – 1 entre os indivíduos com sucesso virológico versus falência virológica após 48 semanas de iniciação aos antirretrovirais. Os pacientes que realizaram a genotipagem (N=80), foram divididos em dois grupos: Grupo 1 (N=43) são os pacientes que após a introdução do tratamento aos antirretrovirais não conseguiram atingir os níveis de quantificação de carga viral abaixo de 50 cópias/mL, isto é a carga viral se manteve detectável após seis meses de tratamento. Grupo 2 (N=37) são os pacientes que conseguiram se manter com os níveis de quantificação da carga viral, indetectáveis após seis meses de tratamento. Todos os indivíduos estudados iniciaram HAART, sendo que foram considerados aderentes aos antirretrovirais, de acordo com a frequência que obtiveram as suas medicações prescritas pelo médico e a partir de uma farmácia centralizada. O HIV - 1 foi seqüenciado na região pol a partir do plasma em amostras armazenadas a – 80° C, coletadas imediatamente antes do início do tratamento. Ao avaliar os pacientes (N=315) a contagem média das células TCD4+ foi de 320 células/µL. Destes pacientes 98 (31%) tinham TCD4+ menor que 200 células/µL, 69 (22%) TCD4+ entre 200 e 350 células/µL; 57 (18%) TCD4+ entre 350 e 500 células/µL e 91 (29%) com TCD4+ acima de 500 células/µL, mostrando a importância do diagnóstico. Em relação a carga viral a média foi de 180.000 cópias/ml e o “log” médio foi de 4,28. Ainda referente a quantificação da carga viral avaliou-se que 40,2% estavam, acima de 30.000 cópias/mL e 22% maior que 100.000 cópias/mL, indicando uma imunossupressão e mostrando a importância do diagnóstico precoce do vírus HIV-1. A determinação da contagem das subpopulações dos linfócitos TCD4+ e a quantificação da Carga viral do HIV – 1, ambos exames representam a pedra angular no acompanhamento, estadiamento e a avaliação da resposta terapêutica dos antirretrovirais. Deve-se considerar também que a determinação da contagem das subpopulações dos linfócitos TCD4+ é um indicador do estágio evolutivo da doença, bem como o determinante fundamental na terapêutica. Avaliar as condições imunológicas dos pacientes recém diagnosticados, que chegam ao serviço de referência em Aids de Santos, é de grande valia, no momento que inicia o tratamento médico, sendo justificado pelos resultados apresentados, no qual destacamos que 53% dos pacientes tinham contagem de TCD4+ menor que 350 células/µL do total estudado (N=315), indicando uma imunossupressão, mostrando nitidamente a importância do diagnóstico precoce pelo HIV-1, sabendo que, segundo os critérios do Consenso Nacional Brasileiro de tratamento para a infecção pelo vírus HIV -1, os mesmos já deveriam estar fazendo uso de medicações antirretrovirais. Quando analisamos a resistência primária dos pacientes do Grupo 1 (N=43) 21 (48,8%) comparada com o Grupo 2 (N=37) 6 (16,2%), ao longo de 48 semanas concluímos que os pacientes do grupo 1 por apresentarem maior prevalência de mutações relacionadas à resistência aos fármacos antirretrovirais prescritos (p<0,005), eles não conseguiram atingir os níveis de quantificação de carga viral abaixo de 50 cópias/mL, isto é, a carga viral se manteve detectável após seis meses de tratamento até final do estudo. Em relação às classes dos medicamentos antirretrovirais, os pacientes do grupo 1 e 2 apresentaram resistência de 16.2% aos IRTNN; 20% aos IRTN e 2,5% aos IP. Quanto a resistência de pelo menos duas classes de ARVs (IRTNN e IRTN) foram 5% e não foi observado nenhum paciente resistente as três classes de ARVs. Na determinação da prevalência dos subtipos do HIV – 1 baseada nas seqüências do gene pol, a classificação filogenética das seqüências puras foi de 80% do subtipo B e 7,5% F. Quanto as seqüências recombinantes B/F foi de 12,5% mostrando uma preocupação epidemiológica na cadeia de transmissão porque essas cepas recombinantes estão infectando novos indivíduos e predominando nos pacientes recém diagnosticados. Não foram encontradas diferenças significativas basais observadas na carga viral e níveis de TCD4+ com relação aos antirretrovirais utilizados ou a demografia entre os 2 grupos, pacientes portadores de vírus resistentes e tipo selvagem. A prevalência de 33,7% de resistência primária aos antirretrovirais entre os pacientes foi considerada extremamente elevada nesta região, portanto, em regiões atípicas como a cidade de Santos, seria de grande valia apoiar o conceito de realizar exames de genotipagem antes de iniciar o tratamento antirretroviral, fato fundamental, efetivo e econômico para o serviço público, embora alguns indivíduos com resistência primária têm conseguido uma supressão viral empírica sob HAART, a estreita associação entre a resistência primária e falência virológica pode sugerir que essa resistência dificulte gradativamente a atividade dos antirretrovirais. / One of the main causes of therapeutic failure is the appearance of strains resistant to reverse transcriptase inhibitors (NRTIs) and protease (PI). The process of replication of HIV - 1 promotes high rate of mutation due to errors inherent in the activity of reverse transcriptase. Therefore, it is common in individuals under treatment and with detectable viral load, the appearance and selection of resistant strains. The State of São Paulo is considered one of the epicenters of the AIDS epidemic in Brazil, and the city of Santos has one of the biggest ports of Latin America and because the routes of international trade acts as a diffuser and introducer of HIV -1 in the Southeast Brazil, with a high incidence of infection, high prevalence of primary antiretroviral resistance and high prevalence of recombinant viruses B/F. It has also been recognized that virological failure to antiretroviral treatment is high in this city, however, there are no recent and comprehensive data on the genetic characterization of the frequency of subtypes and primary resistance of HIV–1. The objective of the study was to evaluate the virological and immunological profiles and primary resistance in patients naïve to antiretroviral drugs treatment and the factors related to virological failure after 48 weeks of HAART in this population. We analyzed the charts of newly diagnosed patients registered in 2000 and 2001, as a total of 594 patients. From these patients studied during the period cited, only 315 were tested for quantification of viral load and counts of lymphocyte subpopulations of CD4+T cells/+ TCD8 at the time of diagnosis. Later among the 315 patients were selected 80 naïve to antiretroviral treatment, for the test for genotyping, in which were compared the demographic profiles of HIV-1 among individuals with virological success versus virological failure after 48 weeks of initiation of antiretroviral. Patients in which we performed genotyping (n = 80) were divided into two groups: Group 1 (N=43) are the patients that after the introduction of antiretroviral treatment failed to achieve the quantification levels of viral load below 50 copies/mL, in other words, the viral load remained detectable after six months of treatment. Group 2 (N=37) patients who were able to remain with the quantification of viral load on undetectable levels after six months of treatment. All studied subjects started HAART, which were considered adherent to antiretroviral according to how often they obtained their medications prescribed by a doctor and from a centralized drugstore. The HIV-1 was sequenced in the pol region from plasma samples stored at – 176ºC, collected immediately before starting treatment. When evaluating the patients (N=315) the average cell count CD4+T cells was 320 cells/µL. 98 (31%) of these patients had CD4+T cells below 200 cells/µL, 69 (22%) CD4+T cells between 200 and 350 cells/µL, 57 (18%) CD4+T cells between 350 and 500 cells/µL and 91 (29%) with CD4+T cells above 500 cells/µL, showing the importance of diagnosis. In relation to the average viral load was 180,000 copies/mL and the "log" average was 4.28. Still concerning the quantification of viral load assessed that 40.2% were above 30,000 copies/mL and 22% higher than 100,000 copies/mL, indicating an immunosuppression and showing the importance of early diagnosis of HIV-1. The determination of the counts of lymphocyte subpopulations of CD4+T cells and quantification of viral load of HIV-1, both tests represent a cornerstone in monitoring, staging and assessment of antiretroviral therapeutic response. One should also consider that the determination of the counts of lymphocyte subpopulations of CD4+T cells is an indicator of the stage of the disease, and the decisive role in therapy. To evaluate the immunological conditions of patients newly diagnosed who come to the referral service on AIDS of Santos, is of great value in the moment you start the treatment, being justified by the results presented, in which is highlighted that 53% of patients had counting CD4+T cells below 350 cells/ul from the total studied (N=315), indicating a immunosuppression, showing clearly the importance of early diagnosis of HIV-1, knowing that according to the criteria of the Brazilian Consensus for the treatment of HIV-1 infection, they should already be using antiretroviral medications. When we analyze the primary resistance of the patients in Group 1 (N = 43) 21 (48.8%) compared with Group 2 (N = 37) 6 (16.2%) during over 48 weeks we conclude that group 1 patients, due to higher prevalence of mutations associated with resistance to antiretroviral drugs prescribed (p<0.005), failed to achieve the quantification of viral load below 50 copies/mL, in other words, viral load remained detectable after six months of treatment by the end of the study. Concerning the classes of antiretroviral drugs, patients in group 1 and 2 showed resistance of 16.2% to IRTNN; 20% to IRTN and 2.5% to PI. Regarding the resistance of at least two classes of ARVs (IRTNN and IRTN) were 5% and there was no studied patient resistant to at least two of the three classes of ARVs. In determining the prevalence of subtypes of HIV -1 based on the pol gene sequences, the phylogenetic classification of pure sequences was 80% of subtype B and 7.5% F. As the sequences recombinant B/F it was 12.5% showing a concern in the epidemiological chain of transmission because these recombinant strains are infecting new individuals and are predominant in newly diagnosed patients. No significant baseline differences were observed in viral load and levels of CD4 + T cells regarding the antiretroviral used or the demographics between the 2 groups, patients with resistant virus and patients with the wild type. The 33.7% prevalence of primary resistance to antiretroviral among patients was considered extremely high in this region, so as atypical regions in the city of Santos, would be of great value to support the concept of conducting examinations of genotyping before starting treatment antiretroviral, indeed essential, effective and economical for the public service, although some individuals with primary resistance have achieved an empirical viral suppression under HAART, the close association between primary resistance and virological failure may suggest that this resistance make the activity of antiretroviral gradually difficult. / FAPESP: 2004/15856-9 / BV UNIFESP: Teses e dissertações