Os linfócitos T têm um papel central no controle da infecção pelo HIV-1. As respostas mediadas por esses linfócitos contra epitopos do HIV-1 restritos a moléculas HLA de classe I podem estar associadas à proteção natural em indivíduos LTNP. Relatos sugerem que determinados alelos HLA apresentamse mais representados entre os LTNP. Para avaliar esses aspectos na coorte francesa ALT, coletamos células mononucleares de sangue periférico (CMSP) de 24 indivíduos LTNP e verificamos a freqüência de respostas específicas para o HIV-1. Para isso, utilizamos pools de peptídeos sobrepostos de Gag e regiões imunodominantes da RT e Nef, e identificamos epitopos do HIV-1 restritos a moléculas HLA de classe I, associados ou não à proteção, através do ensaio de ELISPOT IFN-?. Todos os indivíduos apresentaram respostas específicas aos pools testados, com uma mediana de 5 (2-12). Todas as proteínas do HIV-1 foram reconhecidas, sendo que Gag-p24 e Nef foram as mais freqüentemente reconhecidas pelas CMSP dos indivíduos avaliados. A intensidade total de resposta de linfócitos T específicos aos pools de Gag, RT e Nef do HIV-1 em cada indivíduo variou de 160 a 12307 SFC/106 CMSP (mediana: 2025). Observamos o reconhecimento de 22 epitopos já descritos na literatura, contidos nas proteínas Gag-p17, Gag-p24 e Nef do HIV-1, restritos a moléculas HLA de classe I, a maioria descrita como protetoras da progressão para a doença. Quatro novos epitopos ainda não descritos na literatura também foram observados. Concluímos que: respostas específicas mediadas por linfócitos T, eficazes e dirigidas contra um amplo painel de epitopos do HIV-1, estão presentes nos indivíduos LTNP; a presença de moléculas HLA de classe I associadas à proteção favorece o reconhecimento preferencial de epitopos do HIV-1 restritos por elas na maioria dos indivíduos LTNP; esses aspectos devem ser levados em conta na perspectiva do desenvolvimento de uma vacina candidata contra o HIV-1. / T lymphocytes (T-L) have a paramount role in the control of HIV-1 infection. The responses mediated by these cells against HLA class I epitopes may be associated to the natural protection in long-term non-progressors (LTNP). The literature suggests that some HLA alleles relate to the protection against the immune dysfunction. The aim of this research is to study the recognition of HIV-1 Gag, Nef and RT epitopes by T-L through an ELISPOT IFN-? assay in the peripheral blood mononuclear cells (PBMC) of 24 LTNP selected from French ALT study group. We evaluated the frequency of anti-HIV-1 responses and identified HLA class I epitopes. All individuals presented specific responses to the pools of peptides tested with a median of 5 (2-12). Gag-p24 and Nef were the most frequently recognized proteins. The magnitude of the responses varied from 160 to 12307 SFC/106 PBMC (median=2025). We observed the recognition of 22 epitopes already described in HIV-1 Gag-p17, Gag-p24 and Nef, restricted to HLA class I molecules reported as protective. We have also observed four new epitopes not already described in the literature. Our results suggest that: HIV-1 responses by T-L are present in LTNP; the presence of HLA class I molecules associated with protection in the majority of LTNP are related to the recognition of MHC restricted HIV-1 epitopes; these aspects must be taken into account in the development of a candidate vaccine against HIV-1.

Dissertation (Ph.D.)--University of South Florida, 2009. / Title from PDF of title page. Document formatted into pages; contains 123 pages. Includes vita. Includes bibliographical references.

Indivíduos infectados pelo vírus da imunodeficiência humana do tipo 1 (HIV-1) que controlam a replicação viral, mesmo na ausência de tratamento com drogas antirretrovirais, representam um exemplo de contenção bemsucedida do vírus. O entendimento das respostas imunes antivirais presentes nestes indivíduos pode auxiliar no delineamento de vacinas, particularmente no caso de estratégias vacinais desenvolvidas para induzir um fenótipo de controle da replicação viral e, assim, diminuir o ritmo da progressão à AIDS e/ou a taxa de transmissão para terceiros. A resposta imune celular contra HIV-1 é geralmente mapeada em ensaios de ELISPOT-IFN-γ empregando-se peptídeos pentadecâmeros sobrepostos por 11 aminoácidos sintetizados a partir de seqüências consensuais do vírus. Contudo, este método pode subestimar a detecção da real amplitude da resposta imune celular contra epitopos contidos na seqüência autóloga do vírus infectivo. Neste trabalho, foram comparadas respostas imunes celulares contra peptídeos 15-meros baseados nas seqüências de vif e nef do consenso do subtipo B do HIV-1 e respostas imunes contra peptídeos HLA-restritos de nove ou 10 aminoácidos baseados tanto nas seqüências de vif e nef do consenso do subtipo B do HIV-1, quanto nas seqüências autólogas dos vírus seqüenciados a partir de seis pacientes controladores da replicação do HIV-1. Nossa análise revelou que três dos seis pacientes investigados mostraram maior amplitude de resposta imune celular contra epitopos em Vif e Nef quando os peptídeos HLA-restritos foram empregados, tenham sido eles preditos a partir da seqüência consensual ou a partir das seqüências do vírus autólogo. O número de respostas positivas aumentou de quatro para 16 em Vif e de oito para 22 em Nef, com o uso dos reagentes HLA-restritos. Estes resultados sugerem que emprego de peptídeos 15-meros pode sub-representar a amplitude real da resposta imune celular envolvidas no controle da replicação do HIV-1 e que o conhecimento acerca das respostas imunes de sucesso em indivíduos controladores pode ser melhorado e ampliado com a revisão dos métodos empregados. / Human immunodeficiency virus type 1 (HIV-1)-infected individuals who spontaneously control viral replication represent an example of successful containment of the AIDS virus. Understanding the anti-viral immune responses in these individuals may help in vaccine design, particularly vaccine strategies designed to induce a controller phenotype and thus, prevent disease progression and decrease risk of transmission. Immune responses against HIV-1 are normally screened using 15-mer peptides overlapped by 11 amino acids from HIV-1 consensus sequences in ELISPOT-IFN-γ assays. However, this method may underestimate the real breadth of the cellular immune responses against the autologous sequence of the infecting virus. We compared cellular immune responses against nef and vif-encoded consensus B 15-mer peptides to responses against HLA class I-predicted minimal optimal epitopes from consensus B and autologous sequences in six patients who have controlled HIV-1 replication. Interestingly, our analysis revealed that three of our patients had broader cellular immune responses against Vif- and Nef-HLA class I-predicted minimal optimal epitopes from either autologous viruses or from the consensus B sequence, when compared to responses against the 15-mer HIV-1 consensus B peptides. The number of positive responses against epitopes in these two HIV-1 proteins increased from four to 16 for Vif and from eight to 22 for Nef. These findings suggest that immune responses assessed using 15-mers peptides may underrepresent the real breadth of the immune control of the infecting virus and the knowledge about the successful responses in controller individuals could be improved after reviewing the employed methods.

Os linfócitos T têm um papel central no controle da infecção pelo HIV-1. As respostas mediadas por esses linfócitos contra epitopos do HIV-1 restritos a moléculas HLA de classe I podem estar associadas à proteção natural em indivíduos LTNP. Relatos sugerem que determinados alelos HLA apresentamse mais representados entre os LTNP. Para avaliar esses aspectos na coorte francesa ALT, coletamos células mononucleares de sangue periférico (CMSP) de 24 indivíduos LTNP e verificamos a freqüência de respostas específicas para o HIV-1. Para isso, utilizamos pools de peptídeos sobrepostos de Gag e regiões imunodominantes da RT e Nef, e identificamos epitopos do HIV-1 restritos a moléculas HLA de classe I, associados ou não à proteção, através do ensaio de ELISPOT IFN-?. Todos os indivíduos apresentaram respostas específicas aos pools testados, com uma mediana de 5 (2-12). Todas as proteínas do HIV-1 foram reconhecidas, sendo que Gag-p24 e Nef foram as mais freqüentemente reconhecidas pelas CMSP dos indivíduos avaliados. A intensidade total de resposta de linfócitos T específicos aos pools de Gag, RT e Nef do HIV-1 em cada indivíduo variou de 160 a 12307 SFC/106 CMSP (mediana: 2025). Observamos o reconhecimento de 22 epitopos já descritos na literatura, contidos nas proteínas Gag-p17, Gag-p24 e Nef do HIV-1, restritos a moléculas HLA de classe I, a maioria descrita como protetoras da progressão para a doença. Quatro novos epitopos ainda não descritos na literatura também foram observados. Concluímos que: respostas específicas mediadas por linfócitos T, eficazes e dirigidas contra um amplo painel de epitopos do HIV-1, estão presentes nos indivíduos LTNP; a presença de moléculas HLA de classe I associadas à proteção favorece o reconhecimento preferencial de epitopos do HIV-1 restritos por elas na maioria dos indivíduos LTNP; esses aspectos devem ser levados em conta na perspectiva do desenvolvimento de uma vacina candidata contra o HIV-1. / T lymphocytes (T-L) have a paramount role in the control of HIV-1 infection. The responses mediated by these cells against HLA class I epitopes may be associated to the natural protection in long-term non-progressors (LTNP). The literature suggests that some HLA alleles relate to the protection against the immune dysfunction. The aim of this research is to study the recognition of HIV-1 Gag, Nef and RT epitopes by T-L through an ELISPOT IFN-? assay in the peripheral blood mononuclear cells (PBMC) of 24 LTNP selected from French ALT study group. We evaluated the frequency of anti-HIV-1 responses and identified HLA class I epitopes. All individuals presented specific responses to the pools of peptides tested with a median of 5 (2-12). Gag-p24 and Nef were the most frequently recognized proteins. The magnitude of the responses varied from 160 to 12307 SFC/106 PBMC (median=2025). We observed the recognition of 22 epitopes already described in HIV-1 Gag-p17, Gag-p24 and Nef, restricted to HLA class I molecules reported as protective. We have also observed four new epitopes not already described in the literature. Our results suggest that: HIV-1 responses by T-L are present in LTNP; the presence of HLA class I molecules associated with protection in the majority of LTNP are related to the recognition of MHC restricted HIV-1 epitopes; these aspects must be taken into account in the development of a candidate vaccine against HIV-1.

Cure rate models, introduced by Boag (1949), are very commonly used while modelling lifetime data involving long time survivors. Applications of cure rate models can be seen in biomedical science, industrial reliability, finance, manufacturing, demography and criminology. In this thesis, cure rate models are discussed under a competing cause scenario, with the assumption of proportional odds (PO) lifetime distributions for the susceptibles, and statistical inferential methods are then developed based on right-censored data. In Chapter 2, a flexible cure rate model is discussed by assuming the number of competing causes for the event of interest following the Conway-Maxwell (COM) Poisson distribution, and their corresponding lifetimes of non-cured or susceptible individuals can be described by PO model. This provides a natural extension of the work of Gu et al. (2011) who had considered a geometric number of competing causes. Under right censoring, maximum likelihood estimators (MLEs) are obtained by the use of expectation-maximization (EM) algorithm. An extensive Monte Carlo simulation study is carried out for various scenarios, and model discrimination between some well-known cure models like geometric, Poisson and Bernoulli is also examined. The goodness-of-fit and model diagnostics of the model are also discussed. A cutaneous melanoma dataset example is used to illustrate the models as well as the inferential methods. Next, in Chapter 3, the destructive cure rate models, introduced by Rodrigues et al. (2011), are discussed under the PO assumption. Here, the initial number of competing causes is modelled by a weighted Poisson distribution with special focus on exponentially weighted Poisson, length-biased Poisson and negative binomial distributions. Then, a damage distribution is introduced for the number of initial causes which do not get destroyed. An EM-type algorithm for computing the MLEs is developed. An extensive simulation study is carried out for various scenarios, and model discrimination between the three weighted Poisson distributions is also examined. All the models and methods of estimation are evaluated through a simulation study. A cutaneous melanoma dataset example is used to illustrate the models as well as the inferential methods. In Chapter 4, frailty cure rate models are discussed under a gamma frailty wherein the initial number of competing causes is described by a Conway-Maxwell (COM) Poisson distribution in which the lifetimes of non-cured individuals can be described by PO model. The detailed steps of the EM algorithm are then developed for this model and an extensive simulation study is carried out to evaluate the performance of the proposed model and the estimation method. A cutaneous melanoma dataset as well as a simulated data are used for illustrative purposes. Finally, Chapter 5 outlines the work carried out in the thesis and also suggests some problems of further research interest. / Thesis / Doctor of Philosophy (PhD)