Infections with HIV-1 and mycobacterium tuberculosis : the role of HLA class II alleles and HIV phenotypes

Human Immunodeficiency Virus (HIV) and Mycobacterium tuberculosis (M.tb), are the two infectious diseases causing the greatest number of deaths globally. The burden of these infections is most felt in the developing world particularly in sub-Saharan Africa. This is also a region where some of the studies in this thesis were conducted. The thesis explores both, i) host genetic factors, i.e. human leukocyte antigen (HLA) class II molecules and ii) pathogen factors in the form of HIV phenotypes in order to better understand the host-pathogen interaction in infection.

We investigated in paper I the frequency of HLA class II allele frequencies in Botswana and the association of the HLA class II alleles with susceptibility or control of HIV-1 infection. Certain HLA alleles were identified to be associated with protection from HIV infection whilst other alleles were found to be associated with better control of infection.

In paper II, we described a novel peptide array and used recombinant HLA class II monomers to identify peptides binding to different HLA class II monomers alleles. HIV-1 peptides binding to three common HLA class II alleles (HLA DRB1*0101, DRB1*1501 and DRB1*0401) were identified. Some of the HLA class II binding peptides were further explored using intracellular cytokine staining (ICS) to determine if they serve as T-cell epitopes and are able to elicit a CD4+ T-cell response.We proceeded to implement the assay described in paper II to identify peptides from sixty-one M.tb proteins for binding to the three HLA class II alleles (HLA DR1, DR2 and DR4). The 61 M.tb proteins were then ranked by epitope density which helped to identify M.tb proteins that could serve as immunogens for CD4+ T-cells and ultimately as targets for M.tb vaccine design or the development of diagnostic assays.

In paper IV, we investigated antibody responses directed against 7466 M.tb peptides derived from 61 M.tb proteins. The peptides were printed on a peptide microarray chip. Antibody responses from a group of patients with clinical tuberculosis were compared with the humoral recognition pattern in a well-defined healthy control cohort. This allowed the identification of peptides differentially recognized in the two groups. M.tb peptides which were exclusively recognized in serum from TB patients could be further explored for the use in diagnostic assays.

We investigated in Papers V and VI HIV-1 subtype C coreceptor use in HIV patients in Botswana. Whilst paper V focused on coreceptor use in treatment naïve patients, paper VI focused on coreceptor use in patients failing antiretroviral treatment. Compared to other HIV subtypes, subtype C seems to have less variants that are purely CXCR4 using although a few dual tropic (R5X4) strains have been identified. We found using single genome sequencing that population sequencing can underestimate the prevalence of dual tropic or non R5 strains. Even in HIV subtype C infections, it would be important to first evaluate the viral phenotype before treatment with HIV coreceptor inhibitors.

In conclusion, this work may advance our knowledge of host and pathogen factors that are helpful in improving or developing better interventions against HIV and M.tb.

List of scientific papers

I. Ndungu T, Gaseitsiwe S, Sepako E, Doualla-Bell F, Peter T, Kim S, Thior I, Novitsky VA, Essex M (2005). Major histocompatibility complex class II (HLA-DRB and -DQB) allele frequencies in Botswana: association with human immunodeficiency virus type 1 infection. Clin Diagn Lab Immunol. 12(9):1020-8.
https://doi.org/10.1128/CDLI.12.9.1020-1028.2005

II. Gaseitsiwe S, Valentini D, Ahmed R, Mahdavifar S, Magalhaes I, Zerweck J, Schutkowski M, Gautherot E, Montero F, Ehrnst A, Reilly M, Maeurer M (2009). Major histocompatibility complex class II molecule-human immunodeficiency virus peptide analysis using a microarray chip. Clin Vaccine Immunol. 16(4):567-73.
https://doi.org/10.1128/CVI.00441-08

III. Gaseitsiwe S, Valentine D, Mahdavifar S, Reilly M, Ehrnst A, Maeurer M (2009). Peptide microarray-based identification of Mycobacterium tuberculosis epitope binding to HLA-DRB1*0101, DRB1*1501 and DRB1*0401. Clin Vaccine Immune. [Accepted]
https://doi.org/10.1128/CVI.00208-09

IV. Gaseitsiwe S, Valentini D, Mahdavifar S, Magalhaes I, Hoft DF, Zerweck J, Schutkowski M, Andersson J, Reilly M, Maeurer MJ (2008). Pattern recognition in pulmonary tuberculosis defined by high content peptide microarray chip analysis representing 61 proteins from M. tuberculosis. PLoS One. 3(12):e3840.
https://doi.org/10.1371/journal.pone.0003840

V. Ndungu T, Sepako E, McLane MF, Chand F, Bedi K, Gaseitsiwe S, Doualla-Bell F, Peter T, Thior I, Moyo SM, Gilbert PB, Novitsky VA, Essex M (2006). HIV-1 subtype C in vitro growth and coreceptor utilization. Virology. 347(2): 247-60.
https://doi.org/10.1016/j.virol.2005.11.047

VI. Gaseitsiwe S, Pramanik L, Mine M, Essex M, Ehrnst A (2009). Coreceptor use in HIV-1 subtype C strains from patients failing antiretroviral treatment in Botswana. [Manuscript]