To establish efficient expression of their genes, retroviruses integrate proviral copies into the genomes of the cells they have infected. Epigenetic events, however, silence expression of the integrated proviruses. This silencing protects host cells from harmful viral spread, but also creates a reservoir of latent proviruses that subsequently hinders the cure of retroviral (e.g., HIV-1) infections. Furthermore, the silencing of retrovirus-derived integrative vectors complicates their application in transgenesis and gene therapy. The goal of this thesis is to describe the interaction between retroviral expression and host (epi)genomic environment at the site of proviral integration. To pursue the goal, we sought to define the (epi)genomic environment of the proviruses, which expression is not affected by the epigenetic silencing. Diverse retroviral vectors derived from avian sarcoma and leukosis virus (ASLV), murine leukemia virus (MLV), and human immunodeficiency virus type 1 (HIV-1) were used as model retroviral systems, and expression stability of the vectors in human cell lines was examined. In order to identify the features unique to integration sites of the active proviruses, we sorted the cells positive for the proviral expression, identified their proviral integration sites, and compared them to...

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The expression of retroviral genes depends on the establishment of the provirus - the DNA copy of retroviral genome integrated into the host genome. The transcriptional state of provirus is then influenced by the environment at the site of integration. The phenomenon of proviral silencing is an obstacle to the usage of retroviral vectors and a barrier to the eradication of human immunodeficiency virus type 1 (HIV-1) from infected individuals. Taking advantage of single cell clones bearing one provirus, this diploma thesis investigates the distribution of (epi)genomic features at the sites occupied by stably expressed proviruses. In total, long-term expression profiles of 245 and 255 clones carrying avian sarcoma-leucosis virus (ASLV) and HIV-1, respectively, were obtained. The database-based analysis of 42 integration sites of ASLV and three integration sites of HIV-1 proviruses shows that proviral stable expression highly correlates with the transcriptional start sites (TSS) at the sites of integration. Histone marks characteristic for the proximity of active TSSs and regulatory elements at the sites of integration of stably expressed proviruses confirm this finding. The results presented in this thesis could inspire other analyses investigating the relationship between the integration site and the...

Os vetores retrovirais representam uma das melhores opções para transferência e terapia gênica, pois fornecem expressão do transgene em longo prazo. Entretanto, a inserção do provírus pode causar mutagênese insercional, induzindo proto-oncogenes. Eventos deste tipo têm sido descritos em protocolos clínicos para o tratamento de SCID-X1, doença granulomatosa crônica e talessemia beta, quando vetores retrovirais (oncorretrovirus) foram utilizados. Atualmente, existem poucos métodos simples e rápidos para revelar e quantificar a expansão clonal. Assim, descrevemos a construção uma biblioteca de vetores contendo uma marcação aleatória, denominada código de barras. O sequenciamento do código de barras permitirá revelar, caracterizar e até quantificar a expansão clonal de uma população de células transduzidas. Esta metodologia ajudará a testar novos arranjos de promotores e genes terapêuticos, para o desenvolvimento de vetores mais seguros contribuindo para a redução da probabilidade de um evento de proliferação clonal desencadeado pela mutagênese insercional. / Retroviral vectors represent one of the best options for gene transfer and therapy, where long-term transgene expression is required. However, insertion of the provirus can cause insertional mutagenesis, which may have adverse consequences, such as induction of proto-oncogenes. Such events have been described in clinical trials for the treatment of SCID-X1, chronic granulomatous disease and beta thalessemia with some retroviral vectors. Currently, there are few simple and quick methods that can reveal and quantify clonal expansion. Thus, we describe the construction of a vector library containing random markers, called \"barcodes\". The sequencing of the barcode could reveal, characterize and quantify the clonal expansion of a transduced cells population. This methodology will be valuable to test new arrangements of promoters and therapeutic genes, allowing the development of safer vectors, helping to reduce the probability of clonal proliferation events triggered by insertional mutagenesis.

Orientador: Fabio Papes / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-24T14:16:00Z (GMT). No. of bitstreams: 1 Tolentino_FelipeThadeu_M.pdf: 9244448 bytes, checksum: deea9f7963e05d8a997d9b5a554f9708 (MD5) Previous issue date: 2014 / Resumo: O Sistema Sensorial Olfativo de mamíferos é composto por vários subsistemas na cavidade nasal. Dentre estes, destacam-se o sistema olfativo principal e o sistema olfativo acessório ou vomeronasal. O primeiro realiza a detecção geral de odores e parece participar também da detecção de algumas substâncias que levam a respostas comportamentais instintivas (feromônios), enquanto o último é especializado na detecção desta classe de semioquímicos. A detecção dos estímulos sensoriais olfativos resulta em informações importantes que dependem de vias complexas para sua interpretação e para a geração de respostas apropriadas por parte do sistema nervoso central. Existem vários pontos ainda desconhecidos sobre o funcionamento do sistema olfativo, tanto no que diz respeito aos mecanismos moleculares subjacentes à escolha dos receptores a serem expressos por um dado neurônio sensorial ¿ sendo que cada neurônio olfativo expressa apenas um receptor dentro de uma grande família multi-gênica ¿ quanto em relação ao processamento da informação sensorial em centros cerebrais superiores. Neurônios sensoriais olfativos cultivados eficientemente in vitro seriam extremamente úteis, pois poderiam ser utilizados como ferramenta para o estudo destes problemas, como a investigação da atividade das células sensoriais olfativas, possibilitando, por exemplo, uma melhor compreensão dos mecanismos genéticos e moleculares por trás da expressão dos receptores olfativos e de suas propriedades de detecção. Neste trabalho foram desenvolvidas ferramentas baseadas em vetores retrovirais com o objetivo de induzir a diferenciação celular de neurônios olfativos in vitro, utilizando uma combinação de fatores de transcrição, por meio de transdução viral em células-alvo (fibroblastos murinos). Os retrovírus produzidos foram testados e algumas combinações de fatores de transcrição foram preliminarmente testadas, sendo capazes de induzir mudanças moleculares em fibroblastos acompanhadas da expressão de marcadores de neurônios sensoriais olfativos / Abstract: The mammalian Olfactory System enables the vast majority of animal species to identify the presence and quality of food, predators, competitors, conspecifics and potential mates in the environment. Olfactory stimuli detected by sensory neurons are interpreted by brain processing pathways to generate appropriate behavioral and endocrine responses. Despite its central importance in mammalian physiology, several aspects about the biology of this sensory system remain uncharacterized. For example, it is known that each olfactory sensory neuron (OSN) in the nasal cavity expresses only one gene out of a large multi-gene family coding for receptors involved in odorant and pheromone detection. However, the molecular mechanisms behind this process of olfactory receptor gene choice are not fully understood. The study of this and many other aspects of olfaction has been made difficult by the lack of appropriate in vitro cellular models. An efficient way to obtain cultured OSNs would thus be extremely useful, enabling researchers to investigate the sensory neuron¿s activity in a controllable environment, avoiding obstacles imposed by the cellular heterogeneity found in sensory organs in vivo. In this study, we aimed at obtaining OSNs directly differentiated from mouse embryonic fibroblasts (MEF) using the forced expression of specific transcription factors via retroviral vectors. We therefore developed tools based on retroviral vectors with the objective of differentiating olfactory sensory neurons in vitro, using viral transduction in target cells (murine fibroblasts) with combinations of select transcription factors. Retroviruses were tested and some combinations of transcription factors were tested on a preliminary basis, which were capable of inducing molecular alterations on fibroblasts followed by the expression of olfactory sensory neuron markers / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Os vetores retrovirais representam uma das melhores opções para transferência e terapia gênica, pois fornecem expressão do transgene em longo prazo. Entretanto, a inserção do provírus pode causar mutagênese insercional, induzindo proto-oncogenes. Eventos deste tipo têm sido descritos em protocolos clínicos para o tratamento de SCID-X1, doença granulomatosa crônica e talessemia beta, quando vetores retrovirais (oncorretrovirus) foram utilizados. Atualmente, existem poucos métodos simples e rápidos para revelar e quantificar a expansão clonal. Assim, descrevemos a construção uma biblioteca de vetores contendo uma marcação aleatória, denominada código de barras. O sequenciamento do código de barras permitirá revelar, caracterizar e até quantificar a expansão clonal de uma população de células transduzidas. Esta metodologia ajudará a testar novos arranjos de promotores e genes terapêuticos, para o desenvolvimento de vetores mais seguros contribuindo para a redução da probabilidade de um evento de proliferação clonal desencadeado pela mutagênese insercional. / Retroviral vectors represent one of the best options for gene transfer and therapy, where long-term transgene expression is required. However, insertion of the provirus can cause insertional mutagenesis, which may have adverse consequences, such as induction of proto-oncogenes. Such events have been described in clinical trials for the treatment of SCID-X1, chronic granulomatous disease and beta thalessemia with some retroviral vectors. Currently, there are few simple and quick methods that can reveal and quantify clonal expansion. Thus, we describe the construction of a vector library containing random markers, called \"barcodes\". The sequencing of the barcode could reveal, characterize and quantify the clonal expansion of a transduced cells population. This methodology will be valuable to test new arrangements of promoters and therapeutic genes, allowing the development of safer vectors, helping to reduce the probability of clonal proliferation events triggered by insertional mutagenesis.

Despite recent advances in antiretroviral therapy, nearly 37 million people continue to live with human immunodeficiency virus (HIV). Basic and applied research on the assembly of HIV could be enhanced by using a genetically tractable organism, such as yeast, rather than mammalian cells. While previous studies showed that expression of the HIV Gag polyprotein in Saccharomyces cerevisiae spheroplasts resulted in the production of virus-like particles (VLPs), many questions regarding the utility of yeast in HIV assembly remain uninvestigated. Here, we report use of S. cerevisiae for both the production of VLPs with selectively packaged RNA and to evaluate the human Y-box-binding protein 1 (YB-1) in selective RNA packaging into VLPs. Our data reveal: (1) When co-expressed alongside HIV-1 Gag, an RNA mammalian expression cassette is selectively encapsidated and released in VLPs produced from spheroplasts; (2) Inclusion of the 5’UTR-5’Gag RNA upstream of the mammalian expression cassette greatly increased the selectivity to which non-viral RNA was packaged into VLPs; and (3) heterologous expression of the human YB-1 protein in S. cerevisiae did not facilitate the selective packaging of viral RNA into VLPs, likely due to inability to bind upstream elements in the HIV-1 viral RNA. Overall, this research provides a key first step in the use of yeast for the production of viral vectors used in gene therapy, and lays a foundation for further experiments investigating the role of YB-1 and other host proteins in selective RNA packaging.