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Deciphering genetic susceptibility to tuberculous meningitis

Bowker, Nicholas Grant (2016-12)

Thesis (MSc)--Stellenbosch University, 2016.

Thesis

ENGLISH SUMMARY: Tuberculous meningitis (TBM) is a type of extrapulmonary tuberculosis (TB) which leads to inflammation of the meninges through small lesions called Rich foci. TBM represents 1% of total TB disease, with the age of onset being around 2-5 years of age. Disease development remains poorly understood, including the mechanism of dissemination across the blood-brain barrier. This study concentrated on the involvement of the host genome in TBM susceptibility. We hypothesised that multiple common variants of moderate effect size are more likely to influence TBM susceptibility than rare variants of large effect. The SAC are a 5-way admixed population with genetic contributions from European, East Asian, South Asian, Bantu-speaking African and KhoeSan groups. Two technologies were used to genotype single nucleotide polymorphisms (SNPs) of varying frequency: exome sequencing and the Illumina® Multi-Ethnic Genotyping Array (MEGA). Exome sequencing involves capture of only the protein-coding regions of the human genome, constituting approximately 1% of the genome. The depth of coverage of exome sequencing enabled the detection of coding SNPs of lower frequency (<1%) which were assessed for association with TBM susceptibility. Ten TBM cases and 10 healthy controls were exome sequenced, with all study participants being from the SAC population. Gene set association tests SKAT-O and SKAT Common Rare were used to assess the association of rare SNPs and the cumulative effect of both common and rare SNPs with susceptibility to TBM, respectively. The SKAT-O analysis included 8 322 gene sets comprising 16 728 SNPs, which did not yield any associations with TBM susceptibility. Ingenuity Pathway Analysis (IPA) of the top-hits of the SKAT-O analysis showed that NOD2 and CYP4F2 are both important in TBM pathogenesis and highlighted these as targets for future study. The SKAT Common Rare analysis included 13 270 gene sets comprised of 53 239 SNPs and was CCP110 associated (p = 5.89x10-6) with TBM susceptibility. In addition, a number of top-hit genes ascribed to the development of the central nervous system (CNS) and innate immune system regulation were highlighted. The role of common variants (>5%) in TBM susceptibility were assessed by conducting a genome-wide association study (GWAS). A total of 123 TBM cases, 400 pulmonary TB (pTB) cases and 477 healthy controls were genotyped on the MEGA array. A GWAS comparing 114 TBM cases to 395 healthy controls showed no association with TBM susceptibility. A second analysis comparing 114 TBM cases to 382 pTB cases was conducted to investigate variants associated with different TB phenotypes. No significant associations were found with progression from pTB to TBM. This study represents the first exome sequencing and GWAS of a TBM cohort and has identified a single previously undescribed association with TBM susceptibility. These results further our understanding of TBM in terms of both SNPs and genes that influence susceptibility. In addition, a number of candidate genes involved in innate immunity have been identified using IPA for further genotypic and functional investigation.

AFRIKAANSE OPSOMMING: Tuberkuleuse meningitis (TBM) is 'n vorm van ekstra-pulmonêre tuberkulose (TB) wat lei tot inflammasie van die meninges deur middel van die vorming van klein letsels bekend as Rich fokusse. TBM verteenwoordig 1% van die totale TB epidemie, met ‘n aanvangsouderdom van ongeveer 2-5 jarige ouderdom. Die ontwikkeling van die siekte, asook die meganisme van beweging van bakterieë oor die bloed-breinskans, word huidiglik nie volkome verstaan nie. Hierdie studie het die rol van die gasheer genoom in TBM vatbaarheid ondersoek. Die hipotese was dat daar ‘n groter waarskynlikheid is dat veelvuldige algemene variante met ‘n matige effekgrootte ‘n rol sal speel in TBM vatbaarheid as raar variant met ‘n groter effekgrootte. Die SAK het genetiese bydraes van 5 verskillende bevolkings, naamlik Europese, Oos-Asiatiese, Suid-Asiatiese, Bantu-sprekende Afrikane en KhoeSan groepe. Twee tegnologieë was gebruik om enkel nukleotied polimorfismes (ENPs) van wisselende frekwensie te genotipeer: eksoom volgordebepaling en die Illumina® Multi-Ethnic Genotyping Array (MEGA). Eksoom volgordebepaling ondersoek slegs proteïen koderende areas van die menslike genoom, wat ongeveer 1% van die genoom uitmaak. Die diepte van dekking van die eksoom volgordebepaling het die opsporing van koderende ENPs met lae frekwensies (<1%) moontlik gemaak en hierdie variante se assosiasie met TBM vatbaarheid is geëvalueer. Eksoom volgordebepaling is uitgevoer op 10 TBM pasiënte en 10 gesonde kontroles van die SAK bevolking. Die geen-stel assosiasie toetse SKAT-O en SKAT Common Rare was gebruik om die assosiasie van skaars ENPs sowel as die kumulatiewe effek van beide algemene en skaars ENPs met TBM vatbaarheid te evalueer. Die SKAT-O analise het 8 322 geen-stelle, bestaande uit 16 728 ENPs, ingesluit wat nie enige assosiasies met TBM vatbaarheid opgelewer het nie. Ingenuity Pathway Analysis (IPA) van die gene, aangedui deur die SKAT-O analise, het getoon dat beide NOD2 en CYP4F2 belangrike rolle in TBM siekte ontwikkeling speel en daarom kandidate vir toekomstige studies is. Die SKAT Common Rare analise het 13 270 geen-stelle, bestaande uit 53 239 ENPs, ingesluit en CCP110 was geassosieer (p = 5.89x10-6) met TBM vatbaarheid. Verder is 'n aantal gene betrokke by die ontwikkeling van die senuweestelsel en regulasie van die aangebore immuunsisteem uitgelig. Die rol van algemene variante (> 5%) in TBM vatbaarheid was ondersoek deur 'n genoom-wye assosiasie studie (GWAS) uit te voer. 'n Totaal van 123 TBM gevalle, 400 pulmonêre TB (PTB) gevalle en 477 gesonde kontroles is genotipeer op die MEGA. Die GWAS analise, wat 114 TBM pasiënte met 395 gesonde kontroles vergelyk het, het nie enige assosiasie met TBM vatbaarheid gevind nie. 'n Tweede analise wat 114 TBM pasiënte met 382 PTB pasiënte vergelyk het was uitgevoer om assosiasie van variante met verskillende TB fenotipes te ondersoek. Geen assosiasie met progressie vanaf pTB tot TBM was gevind nie. Die huidige studie verteenwoordig die eerste eksoom volgordebepaling en GWAS van ‘n TBM groep en het ‘n enkele voorheen onbeskryfde assosiasie met TBM vatbaarheid geïdentifiseer. Hierdie resultate bevorder ons begrip van TBM in terme van ENPs sowel as gene wat siektevatbaarheid beïnvloed. Daarbenewens was 'n aantal gene betrokke by aangebore immuniteit met behulp van IPA geïdentifiseer vir verdere genotipiese en funksionele ondersoeke.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/100421
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