Browsing by Author "Colic, Antoinette"

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    Computational analysis of the immunogenicity and sequence diversity of Mycobacterium tuberculosis PPE_MPTR proteins
    (Stellenbosch : Stellenbosch University, 2017-03) Colic, Antoinette; Sampson, Samantha; Christoffels, Alan; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Biomedical Sciences: Molecular Biology and Human Genetics.
    ENGLISH ABSTRACT: Mycobacterium tuberculosis presents a substantial health risk to humans, particularly in Africa. Prevention of infectious diseases via vaccination is the most effective strategy in decreasing prevalence; however the current BCG vaccine against tuberculosis has shown varying levels of efficacy. M. tuberculosis infection represents an on-going interaction between the host and the bacteria, of which we do not yet fully understand all the mechanisms contributing to the pathogenesis at a molecular level. A deeper understanding of host-pathogen interactions is an important step towards developing new and more effective vaccines and therefore combating the disease. Protective immunity against M. tuberculosis is induced by stimulating antigen specific T-cells, which recognise peptide antigens presented by HLA molecules on infected cells. Identifying epitopes that are capable of binding to HLA molecules and eliciting T-cell responses form part of the development of subunit vaccines. An area of mycobacterial biology that is poorly understood is the function of the PE/PPE proteins. These proteins are a large, genetically diverse family of immunogenic proteins that are predicted to play a role in modulating host immune responses. In particular, the PPE major polymorphic tandem repeat (PPE_MPTR) proteins are a subgroup of the PE/PPE proteins which are restricted to pathogenic mycobacterial species and represent one of the most genetically diverse set of proteins within the M. tuberculosis proteome. While many studies have investigated the presence of T-cell epitopes within the PE/PPE family of proteins, no studies have focused specifically on the PPE_MPTR subfamily. Based on the extreme variation in both the length and genetic diversity of the PPE_MPTR proteins, it has been speculated that they may represent a source of antigenic variation which allows the organism to escape antigen-specific host responses. Given the hyper-variable nature of the PPE_MPTR proteins and their possible role in host-pathogen interactions, genetic diversity within the PPE_MPTR proteins may differentially modulate human immune response. Furthermore, epitopes within the PPE_MPTR proteins may be possible subunit vaccine candidates for M. tuberculosis. Conventional experimental techniques used to identify potential epitopes can often be time consuming and expensive. Various computational tools exist to predict binding of peptide sequences to various HLA alleles. Using a collection of known M. tuberculosis epitopes from the Immune Epitope Database (IEDB), an evaluation of the current open source HLA class II prediction tools has been performed, with the results used to inform an in silico identification of human CD4+ T-cell epitopes within the PPE_MPTR proteins. Characterisation of the genetic diversity of these proteins is also an essential step in improving our understanding of this protein family. Publically available whole genome sequence data from strains belonging to various lineages has been used to investigate the level of sequence diversity within these ppe_mptr genes, and the impact of genetic variants on epitope density has been investigated. To date, this study is the most comprehensive analysis of the genetic variation of the ppe_mptr genes. Predicted epitopes have been filtered using a reverse vaccinology approach in order to identify possible subunit vaccine candidates for M. tuberculosis. Findings from epitope prediction analysis support the hypothesis of host-pathogen interactions for the PPE_MPTR proteins. Genetic variation results indicate that certain PPE_MPTR proteins are highly variable while others are relatively conserved across strains, and that genetically diverse regions are less likely to contain epitopes. Therefore no evidence to support antigenic variation was found. Areas of high and low epitope density are correlated to areas of non-repeat and repeat regions within the genome respectively, and therefore epitopes within the PPE_MPTR proteins are conserved non-repeating peptides. This is consistent with previous literature on the conservation of reported M. tuberculosis epitopes within clinical strains. Further studies are therefore needed to determine the role of the variable copy number of repeats found within the PPE_MPTR proteins. Possible vaccine candidates with high predicted population coverage in African countries within the PPE_MPTR proteins have been identified.