Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C

Abstract

A systematic analysis of immune responses on a population level is critical for a human immunodeficiency virus type 1 (HIV-1) vaccine design. Our studies in Botswana on (i) molecular analysis of the HIV-1 subtype C (HIV-1C) epidemic, (ii) frequencies of major histocompatibility complex class I HLA types, and (iii) cytotoxic T-lymphocyte (CTL) responses in the course of natural infection allowed us to address HIV-1C-specific immune responses on a population level. We analyzed the magnitude and frequency of the gamma interferon ELISPOT-based CTL responses and translated them into normalized cumulative CTL responses. The introduction of population-based cumulative CTL responses reflected both (i) essentials of the predominant virus circulating locally in Botswana and (ii) specificities of the genetic background of the Botswana population, and it allowed the identification of immunodominant regions across the entire HIV-1C. The most robust and vigorous immune responses were found within the HIV-1C proteins Gag p24, Vpr, Tat, and Nef. In addition, moderately strong responses were scattered across Gag p24, Pol reverse transcriptase and integrase, Vif, Tat, Env gp120 and gp41, and Nef. Assuming that at least some of the immune responses are protective, these identified immunodominant regions could be utilized in designing an HIV vaccine candidate for the population of southern Africa. Targeting multiple immunodominant regions should improve the overall vaccine immunogenicity in the local population and minimize viral escape from immune recognition. Furthermore, the analysis of HIV-1C-specific immune responses on a population level represents a comprehensive systematic approach in HIV vaccine design and should be considered for other HIV-1 subtypes and/or different geographic areas.

FIG. 1.

Magnitude of HIV-1C-specific CTL responses. The x axis of each graph was scaled according to the number of HIV-1C synthetic peptides used for a particular viral protein, and the length of the graph does not necessarily correspond to the actual size of the viral protein because of the differences in the lengths of the synthetic peptides. The y axis was scaled equally for each viral protein. Filled dots represent individual HIV-1C-specific CTL responses to particular synthetic peptides. CTL responses were expressed as SFC per million PBMC (sfc/mln pbmc). Only responses equal to or higher than 100 SFC/10⁶ PBMC were taken into account. Open dots represent nonresponsive synthetic peptides. n represents the number of samples tested with a particular set of synthetic peptides. PR, protease; IN, integrase.

FIG. 2.

(A) Frequency of HIV-1C-specific CTL responses. The x axis of each graph was scaled according to the number of HIV-1C synthetic peptides used for a particular viral protein, and the length of the graph does not necessarily correspond to the actual size of the viral protein because of the differences in the lengths of the synthetic peptides. The y axis was scaled equally for each viral protein. Bars represent percent frequency for a particular synthetic peptide. n represents the number of samples tested with a particular set of synthetic peptides. PR, protease; IN, integrase. (B) Frequency distribution of HIV-1C-specific CTL responses to the synthetic peptides representing viral proteins. The boundary of the box closest to zero indicates the 25th percentile, a solid line within the box marks the median, a dashed line within the box shows the mean value, and the boundary of the box farthest from zero indicates the 75th percentile. Bars below and above the boxes indicate the 10th and 90th percentiles, respectively. Points below and above the bars indicate the 5th and 95th percentiles, respectively, when the sample size permitted these calculations. Pro, protease; IN, integrase.

FIG. 2.

(A) Frequency of HIV-1C-specific CTL responses. The x axis of each graph was scaled according to the number of HIV-1C synthetic peptides used for a particular viral protein, and the length of the graph does not necessarily correspond to the actual size of the viral protein because of the differences in the lengths of the synthetic peptides. The y axis was scaled equally for each viral protein. Bars represent percent frequency for a particular synthetic peptide. n represents the number of samples tested with a particular set of synthetic peptides. PR, protease; IN, integrase. (B) Frequency distribution of HIV-1C-specific CTL responses to the synthetic peptides representing viral proteins. The boundary of the box closest to zero indicates the 25th percentile, a solid line within the box marks the median, a dashed line within the box shows the mean value, and the boundary of the box farthest from zero indicates the 75th percentile. Bars below and above the boxes indicate the 10th and 90th percentiles, respectively. Points below and above the bars indicate the 5th and 95th percentiles, respectively, when the sample size permitted these calculations. Pro, protease; IN, integrase.

FIG. 3.

Normalized cumulative HIV-1C-specific CTL responses. The x axis of each graph was scaled according to the number of HIV-1C synthetic peptides used for a particular viral protein, and the length of the graph does not necessarily correspond to the actual size of the viral protein because of the differences in the lengths of the synthetic peptides. The y axis was scaled equally for each viral protein. Bars represent normalized cumulative HIV-1C-specific CTL responses to a particular synthetic peptide across the viral genome. n represents the number of samples tested with a particular set of synthetic peptides. PR, protease; IN, integrase.

FIG. 4.

Immunodominant regions in HIV-1C. Immunodominant and subdominant regions in the HIV-1C genome in the context of CTL responses are shown. The locations of immunodominant and subdominant regions are scaled to their actual position in the HIV-1C genome. For details, see Table 4. LTR, long terminal repeat; PR, protease; IN, integrase.