Distinct recognition of non-clade B human immunodeficiency virus type 1 epitopes by cytotoxic T lymphocytes generated from donors infected in Africa

Abstract

We present detailed studies of human immunodeficiency virus (HIV)-specific cytotoxic T-lymphocyte (CTL) responses to clade A or C HIV type 1 in three donors infected in East Africa. We define several novel non-clade B CTL epitopes, including some restricted by HLA alleles common in Africans. Although cross-clade CTL recognition of these epitopes does occur, recognition can also be highly clade specific.

FIG. 1

Recognition of an HLA-A2-restricted peptide in A clade p17 by patient 1 CTLs. (a) Gag-specific CTLs from donor 1 specifically lysed HLA-A2-matched target cells pulsed with multiple variants of the A clade version of the previously defined HLA-A2-restricted peptide in p17, but not the B clade index version (all peptides were prepulsed for 1 h at 10 μM). (b) p17-specific CTLs from patient 1 were stained with the HLA-A*0201 tetramer complexed with either the B clade version (Y3; shown as 3Y) of the known p17 epitope peptide or the A clade version (F3; shown as 3F). The plots show the mononuclear cell population costained with tetramer (phycoerythrin [PE]) and anti-CD8 (fluorescein isothiocyanate). A double-positive population is seen only with the F3 tetramer.

FIG. 2

Recognition of A clade Gag peptides through HLA-A24 and -Cw4 by patient 2 CTLs. (a) Bulk CTL cultures from donor 2 were tested for recognition of autologous and target cell lines matched through a single class I HLA molecule presenting two 20-mer A clade Gag peptides (used at 10 μM; E/T ratio, 50:1). (b) Patient 2 bulk CTL cultures were tested for recognition of target cells matched through HLA-A24 pulsed with peptides representing truncations of the B clade version of the epitope containing residues 295 to 314 (used at 10 μM; E/T ratio, 36:1). (c) A CTL line from donor 2 specific for the HLA-A24-restricted peptide was tested for recognition of HLA-A24-matched targets with various concentrations of the A and B clade peptides in the assay (E/T ratio, 25:1). (d) A CTL line from donor 2 specific for the HLA-Cw-4-restricted p17 peptide was tested for recognition of autologous targets presenting either the A clade 20-mer or the equivalent B clade 20-mer (peptides used at 10 μM). (e) The same p17-specific CTL line from donor 2 was used to study recognition of target cells presenting either the A or B clade 20-mers at different concentrations in the assay.

FIG. 2

Recognition of A clade Gag peptides through HLA-A24 and -Cw4 by patient 2 CTLs. (a) Bulk CTL cultures from donor 2 were tested for recognition of autologous and target cell lines matched through a single class I HLA molecule presenting two 20-mer A clade Gag peptides (used at 10 μM; E/T ratio, 50:1). (b) Patient 2 bulk CTL cultures were tested for recognition of target cells matched through HLA-A24 pulsed with peptides representing truncations of the B clade version of the epitope containing residues 295 to 314 (used at 10 μM; E/T ratio, 36:1). (c) A CTL line from donor 2 specific for the HLA-A24-restricted peptide was tested for recognition of HLA-A24-matched targets with various concentrations of the A and B clade peptides in the assay (E/T ratio, 25:1). (d) A CTL line from donor 2 specific for the HLA-Cw-4-restricted p17 peptide was tested for recognition of autologous targets presenting either the A clade 20-mer or the equivalent B clade 20-mer (peptides used at 10 μM). (e) The same p17-specific CTL line from donor 2 was used to study recognition of target cells presenting either the A or B clade 20-mers at different concentrations in the assay.

FIG. 2

Recognition of A clade Gag peptides through HLA-A24 and -Cw4 by patient 2 CTLs. (a) Bulk CTL cultures from donor 2 were tested for recognition of autologous and target cell lines matched through a single class I HLA molecule presenting two 20-mer A clade Gag peptides (used at 10 μM; E/T ratio, 50:1). (b) Patient 2 bulk CTL cultures were tested for recognition of target cells matched through HLA-A24 pulsed with peptides representing truncations of the B clade version of the epitope containing residues 295 to 314 (used at 10 μM; E/T ratio, 36:1). (c) A CTL line from donor 2 specific for the HLA-A24-restricted peptide was tested for recognition of HLA-A24-matched targets with various concentrations of the A and B clade peptides in the assay (E/T ratio, 25:1). (d) A CTL line from donor 2 specific for the HLA-Cw-4-restricted p17 peptide was tested for recognition of autologous targets presenting either the A clade 20-mer or the equivalent B clade 20-mer (peptides used at 10 μM). (e) The same p17-specific CTL line from donor 2 was used to study recognition of target cells presenting either the A or B clade 20-mers at different concentrations in the assay.

FIG. 2

Recognition of A clade Gag peptides through HLA-A24 and -Cw4 by patient 2 CTLs. (a) Bulk CTL cultures from donor 2 were tested for recognition of autologous and target cell lines matched through a single class I HLA molecule presenting two 20-mer A clade Gag peptides (used at 10 μM; E/T ratio, 50:1). (b) Patient 2 bulk CTL cultures were tested for recognition of target cells matched through HLA-A24 pulsed with peptides representing truncations of the B clade version of the epitope containing residues 295 to 314 (used at 10 μM; E/T ratio, 36:1). (c) A CTL line from donor 2 specific for the HLA-A24-restricted peptide was tested for recognition of HLA-A24-matched targets with various concentrations of the A and B clade peptides in the assay (E/T ratio, 25:1). (d) A CTL line from donor 2 specific for the HLA-Cw-4-restricted p17 peptide was tested for recognition of autologous targets presenting either the A clade 20-mer or the equivalent B clade 20-mer (peptides used at 10 μM). (e) The same p17-specific CTL line from donor 2 was used to study recognition of target cells presenting either the A or B clade 20-mers at different concentrations in the assay.

FIG. 2

Recognition of A clade Gag peptides through HLA-A24 and -Cw4 by patient 2 CTLs. (a) Bulk CTL cultures from donor 2 were tested for recognition of autologous and target cell lines matched through a single class I HLA molecule presenting two 20-mer A clade Gag peptides (used at 10 μM; E/T ratio, 50:1). (b) Patient 2 bulk CTL cultures were tested for recognition of target cells matched through HLA-A24 pulsed with peptides representing truncations of the B clade version of the epitope containing residues 295 to 314 (used at 10 μM; E/T ratio, 36:1). (c) A CTL line from donor 2 specific for the HLA-A24-restricted peptide was tested for recognition of HLA-A24-matched targets with various concentrations of the A and B clade peptides in the assay (E/T ratio, 25:1). (d) A CTL line from donor 2 specific for the HLA-Cw-4-restricted p17 peptide was tested for recognition of autologous targets presenting either the A clade 20-mer or the equivalent B clade 20-mer (peptides used at 10 μM). (e) The same p17-specific CTL line from donor 2 was used to study recognition of target cells presenting either the A or B clade 20-mers at different concentrations in the assay.

FIG. 3

Recognition of novel CTL epitopes presented by HLA-A26, -B70, and -B*8101 by CTLs from donor 3. (a) A CTL line from donor 3 was tested for recognition of autologous targets with various concentrations of the A and B clade equivalents of a Gag peptide presented by HLA-A26 and -B70 (E/T ratio, 20:1). (b) Bulk CTL cultures from donor 3 were shown to recognize a 20-mer peptide from A clade p24 only when presented by target cells matched through HLA-B*8101. (c) Peptide-specific CTLs from donor 3 recognized a 9-mer peptide from D clade Pol when presented by target cells matched through HLA-B70 (peptide used at 10 μM; E/T ratio, 20:1).