The transciptomic landscape of HIV-TB

Abstract

Includes abstract.Includes bibliographical references.The thesis consists of four main parts. In Part 1 of this thesis I provide a broad overview of HIVTB with an emphasis on systems approaches followed by an overview of a systems-level study aiming at addressing hypotheses relating to transcriptional differences in active tuberculosis and HIV-1 infection, measured in blood and the site of disease in tuberculous pericarditis. The final chapter in this part describes the methods used to generate and analyse the systems-level data, with emphasis on microarray data generation and analysis. Part 2 first presents analysis of transcriptional data generated by RT-PCR at the site of disease compared to blood in study subjects with tuberculous pericarditis, with results showing clear evidence of transcriptional differences between compartments. A Technical Results chapter then provides an overview of the microarray data, and an analytic paradigm based on sample embedding in high-dimensional phenotype space is developed. I then assess the overall quality of the dataset and exclude large-scale systematic bias, while comparison of the IMPI-MA data to exiting TBtranscriptomic data shows a close match. Part 2 concludes with a description of a comprehensive analytic framework developed for the IMPI-MA data. Part 3 presents the results of the analytic pipeline as applied to the transcriptional response in blood to active tuberculosis in an HIV-1 uninfected population. A signature of active tuberculosis is described, and deconvolution analysis finds significant NK cell activation in active tuberculosis. Cell-type specific differential expression identifies CD4 T cells, NK cells and neutrophils as the most likely contributors to the overall “signature” of active tuberculosis. Weighted gene co-expression network analysis reveals multiple modules, whose expression is shown to be differentially regulated based on disease category. Part 4 summarises the results of analysing contrasts in three main contexts: tuberculosis, HIV-1 infection and compartment. Two novel results are presented: Firstly, NK cells are shown to be functionally downregulated at the site of disease, suggesting a possible defence mechanism by M. tuberculosis, and secondly, large-scale metabolic pathway dysregulation at the site of disease, possibly favouring M. tuberculosis, is demonstrated. Part 5 concludes the thesis with a summary and outlines future work