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Population-based case-control association studies are often utilized for the identification of common variants in genes causing common disease such as TB. Some of the major genes identified by this approach and validated in several populations including our work, include the chemokine (C-C motif) ligand 2 (CCL2), human leukocyte antigen (HLA), interferon-γ (IFNG), mannose-binding lectin (MBL), nitric oxide synthase 2, inducible (NOS2A), solute carrier family 11A member 1 (SLC11A1), SP110, and the toll-like receptor (TLR) genes. The large numbers we use mean that these studies are well-powered. 

We have also done linkage studies which in one case identified the variations located in cathepsin Z (CTSZ), melanocortin 3 receptor (MC3R), which were then validated by us in a case-control design. In another linkage project, we found two loci influencing reaction to the tuberculin skin test, which implies a degree of protection from TB.

Genome-wide association studies (GWAS) are also free of assumptions of involvement in a disease, and employment of this recent methodology is underway to find novel loci involved in TB.?

Functional Studies

Autophagy

Autophagy is a process that allows eukaryotic cells to generate nutrients under conditions of starvation by degrading damaged or obsolete organelles and proteins. In addition to this, autophagy has also been found to play a role in a number of physiological and pathophysiological processes which include regulation of the innate immune system where it aids in the clearance of intracellular pathogens such as Mtb.

Research has begun to focus on association between variations in genes encoding proteins involved in autophagy and increased susceptibility to TB. We are currently evaluating a number of autophagy-related genes for association with increased TB susceptibility in our large cohort of TB infected and control individuals.

While the identification of gene variants associated with increased susceptibility to TB is crucial, it is also important to understand the functional role these gene variants play in the disease progression. We aim to unravel the molecular determinants of impaired autophagy in TB infection. These studies include gene expression analysis of autophagy-related genes, protein-protein interaction analysis and live cell imaging using fluorescence and super resolution confocal microscopy.

Gene-Gene Interactions

Increasing evidence show that host genetic factors determine susceptibility to developing disease. These factors are complex, and examining them in isolation may result in missing the effect of factors that do not act independently, i.e. when the effect of one gene on disease outcome is modified by the variant of another gene.

It is therefore important to understand the role of gene-gene interactions, commonly referred to as epistasis, in susceptibility to tuberculosis infection.

The statistical tools and methods we use to find interactions in our large tuberculosis case-control sample bank are also relevant to other complex diseases with multiple underlying genetic causes.

Human Genetic Diversity

Genetic variation between humans can be ascribed to differences between individuals within populations (85-90%) and to differences between populations (10-15%). As humans migrated out of Africa, they adapted to new environments and groups became isolated from one another. This resulted in different frequencies of genetic variants in the resultant populations.

Evidence from mitochondrial DNA and Y-chromosome studies shows that the San of Southern Africa are likely to be the oldest human population group. We have participated in a collaboration with researchers from the USA to collect samples from this population group for genome-wide analysis, which will be an important resource for gaining insight into the genetic history of humans.

Admixture occurs when two or more previously separated population groups produce offspring. The predominant population group in the Western Cape, South Africa, is the admixed group known officially as the South African Coloured (SAC). The SAC had their origins in the diverse groups in the early days of Cape history, including Europeans settlers, the slaves they brought in from Indonesia, India and other parts of Africa, local Bantu-speakers, and the indigenous Khoe-San. They therefore constitute a complex combination of continental populations.

We are using the powerful technique of admixture mapping to find genetic variants that differ in frequency between source populations of the SAC and may have a role in susceptibility to tuberculosis.

In addition, proportions of ancestry received from source populations vary between individuals in the population and this may have a confounding effect in genetic association studies if the differences are not homogeneous between case and control groups. We have therefore also developed a small panel of ancestry informative markers (AIMs) that can be used to adjust for admixture in candidate gene association studies of the SAC – see Software.

Pharmacogenetics

Primary Immuno-Deficiency

Primary immunodeficiencies (PIDs) are a group of more than 130 disorders affecting the development and function of the immune system. Generally, PIDs are monogenic disorders with a Mendelian pattern of inheritance. Of particular interest to our research are PIDs that are known to cause increased susceptibility to mycobacteria. These include Mendelian Susceptibility to Mycobacterial Disease (MSMD), Chronic Granulomatous Disease (CGD) and Severe Combined Immunodeficiency (SCID).

We believe that genes that are mutated to cause these PIDs would be plausible candidate genes for increased susceptibility to tuberculosis in the general population. Several MSMD, CGD and SCID-causing genes have been identified and our research team will assess these genes for increased susceptibility to tuberculosis in our large panel of TB patients.

While many mutations for MSMD, CGD and SCID have previously been identified, a large number of affected individuals exists for whom no gene mutation has been found. In collaboration with the National Health Laboratory Service’s Immunological Unit as well as the Department of Clinical Genetics and Genetic Counselling, we are using next generation exome sequencing to identify novel MSMD, CGD and SCID-causing mutations.

The novel mutations will inform treatment for these patients, and will also be assessed for their role in increased TB susceptibility in the general population.?

Wildlife Genetics