Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities

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dc.contributor.advisorDheda, Keertanen_ZA
dc.contributor.advisorWarren, Roben_ZA
dc.contributor.advisorDavids, Malikaen_ZA
dc.contributor.authorLenders, Laura Maryen_ZA
dc.date.accessioned2017-01-20T10:33:28Z
dc.date.available2017-01-20T10:33:28Z
dc.date.issued2016en_ZA
dc.description.abstractBACKGROUND: Tuberculosis (TB) remains out of control globally. Recent promising vaccine candidates have failed in clinical trials and host immunity in the lung remains poorly understood. Pathogenesis of pulmonary cavitation, the basis of TB transmission, is poorly understood. The degree of heteroresistance in the human lung remains unclear. METHODOLOGY: Multi- and extensively drug-resistant TB (MDR- and XDR-TB) patients scheduled for therapeutic lung resection surgery in Cape Town were prospectively recruited. Biopsies were obtained from specific positions in and around cavities. Drug-susceptibility testing, strain-type determination, whole-genome sequencing, and whole-transcriptome shotgun sequencing was conducted. RESULTS: Samples were obtained from 2 MDR-TB, 1 pre-XDR-TB and 12 XDR-TB patients, and 10 non- TB controls. There was considerable heterogeneity between sputum and the cavity with respect to genomic and phenotypic profiles of several drugs including ethambutol, moxifloxacin and paraaminosalicylic acid. An anatomically distinct whole-transcriptome-based pathophysiological map of TB cavities was constructed. RNA sequence reads, of which 31% were splice variants, mapped to 19,049 annotated human genes. In peri-cavitary normal-appearing tissue only 33% of pathways showed significant expression change, despite having a similar bacillary burden to diseased tissue. However, in the cavity wall 72% of pathways showed high-intensity increased expression. By contrast, in the cavity center with a high bacillary burden, 53% of these pathways were massively downregulated, differing from airways and sputum. In particular, several neuroendocrine pathways (dopamine, glutamate, synaptic long-term signalling) were significantly downregulated together with those encoding for calcium, retinoic acid-inducible gene-1, and other pathogen-recognition receptors. However, genes encoding for eukaryotic initiation factor-2, triggering receptor expressed on myeloid cell-1 and peroxisome proliferator activated receptor gamma-signalling, amongst others, were upregulated. CONCLUSION: Heterogeneity in genomic and phenotypic profiles within different parts of the cavity and sputum suggests dynamic responses of mycobacterial populations, likely, under the selective pressure of treatment, which has implications for the interpretation and development of TB-specific diagnostic tests. These data may also have important implications for understanding the pathogenesis of failed host immunity and have uncovered several, hitherto, unrecognized pathways and targets that may be useful for the design of vaccines, host-directed therapies, and transmission prevention.en_ZA
dc.identifier.apacitationLenders, L. M. (2016). <i>Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities</i>. (Thesis). University of Cape Town ,Faculty of Health Sciences ,Division of Pulmonology. Retrieved from http://hdl.handle.net/11427/22852en_ZA
dc.identifier.chicagocitationLenders, Laura Mary. <i>"Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities."</i> Thesis., University of Cape Town ,Faculty of Health Sciences ,Division of Pulmonology, 2016. http://hdl.handle.net/11427/22852en_ZA
dc.identifier.citationLenders, L. 2016. Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities. University of Cape Town.en_ZA
dc.identifier.ris TY - Thesis / Dissertation AU - Lenders, Laura Mary AB - BACKGROUND: Tuberculosis (TB) remains out of control globally. Recent promising vaccine candidates have failed in clinical trials and host immunity in the lung remains poorly understood. Pathogenesis of pulmonary cavitation, the basis of TB transmission, is poorly understood. The degree of heteroresistance in the human lung remains unclear. METHODOLOGY: Multi- and extensively drug-resistant TB (MDR- and XDR-TB) patients scheduled for therapeutic lung resection surgery in Cape Town were prospectively recruited. Biopsies were obtained from specific positions in and around cavities. Drug-susceptibility testing, strain-type determination, whole-genome sequencing, and whole-transcriptome shotgun sequencing was conducted. RESULTS: Samples were obtained from 2 MDR-TB, 1 pre-XDR-TB and 12 XDR-TB patients, and 10 non- TB controls. There was considerable heterogeneity between sputum and the cavity with respect to genomic and phenotypic profiles of several drugs including ethambutol, moxifloxacin and paraaminosalicylic acid. An anatomically distinct whole-transcriptome-based pathophysiological map of TB cavities was constructed. RNA sequence reads, of which 31% were splice variants, mapped to 19,049 annotated human genes. In peri-cavitary normal-appearing tissue only 33% of pathways showed significant expression change, despite having a similar bacillary burden to diseased tissue. However, in the cavity wall 72% of pathways showed high-intensity increased expression. By contrast, in the cavity center with a high bacillary burden, 53% of these pathways were massively downregulated, differing from airways and sputum. In particular, several neuroendocrine pathways (dopamine, glutamate, synaptic long-term signalling) were significantly downregulated together with those encoding for calcium, retinoic acid-inducible gene-1, and other pathogen-recognition receptors. However, genes encoding for eukaryotic initiation factor-2, triggering receptor expressed on myeloid cell-1 and peroxisome proliferator activated receptor gamma-signalling, amongst others, were upregulated. CONCLUSION: Heterogeneity in genomic and phenotypic profiles within different parts of the cavity and sputum suggests dynamic responses of mycobacterial populations, likely, under the selective pressure of treatment, which has implications for the interpretation and development of TB-specific diagnostic tests. These data may also have important implications for understanding the pathogenesis of failed host immunity and have uncovered several, hitherto, unrecognized pathways and targets that may be useful for the design of vaccines, host-directed therapies, and transmission prevention. DA - 2016 DB - OpenUCT DP - University of Cape Town LK - https://open.uct.ac.za PB - University of Cape Town PY - 2016 T1 - Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities TI - Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities UR - http://hdl.handle.net/11427/22852 ER - en_ZA
dc.identifier.urihttp://hdl.handle.net/11427/22852
dc.identifier.vancouvercitationLenders LM. Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities. [Thesis]. University of Cape Town ,Faculty of Health Sciences ,Division of Pulmonology, 2016 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/22852en_ZA
dc.language.isoengen_ZA
dc.publisher.departmentDivision of Pulmonologyen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.subject.otherPulmonologyen_ZA
dc.titleMicrobiological, genomic and transcriptomic analyses of human tuberculosis lung cavitiesen_ZA
dc.typeDoctoral Thesis
dc.type.qualificationlevelDoctoral
dc.type.qualificationnamePhDen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceThesisen_ZA
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