The major histocompatibility complex class II alleles Mamu-DRB1*1003 and -DRB1*0306 are enriched in a cohort of simian immunodeficiency virus-infected rhesus macaque elite controllers

Abstract

The role of CD4(+) T cells in the control of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication is not well understood. Even though strong HIV- and SIV-specific CD4(+) T-cell responses have been detected in individuals that control viral replication, major histocompatibility complex class II (MHC-II) molecules have not been definitively linked with slow disease progression. In a cohort of 196 SIVmac239-infected Indian rhesus macaques, a group of macaques controlled viral replication to less than 1,000 viral RNA copies/ml. These elite controllers (ECs) mounted a broad SIV-specific CD4(+) T-cell response. Here, we describe five macaque MHC-II alleles (Mamu-DRB*w606, -DRB*w2104, -DRB1*0306, -DRB1*1003, and -DPB1*06) that restricted six SIV-specific CD4(+) T-cell epitopes in ECs and report the first association between specific MHC-II alleles and elite control. Interestingly, the macaque MHC-II alleles, Mamu-DRB1*1003 and -DRB1*0306, were enriched in this EC group (P values of 0.02 and 0.05, respectively). Additionally, Mamu-B*17-positive SIV-infected rhesus macaques that also expressed these two MHC-II alleles had significantly lower viral loads than Mamu-B*17-positive animals that did not express Mamu-DRB1*1003 and -DRB1*0306 (P value of <0.0001). The study of MHC-II alleles in macaques that control viral replication could improve our understanding of the role of CD4(+) T cells in suppressing HIV/SIV replication and further our understanding of HIV vaccine design.

FIG. 1.

SIV-specific CD4⁺ T-cell responses in EC 95061. CD8-depleted PBMCs from animal 95061 were added to ELISPOT wells with SIVmac239 peptide pools comprising 10 peptides of 15 amino acids in length overlapping by 11 amino acids spanning most of the viral proteome. An asterisk (*) indicates CD4⁺ T-cell responses subsequently mapped in panel B (A). Several positive peptide pools from animal 95061 were mapped to peptides of 15 amino acids in length (B). The IFN-γ production in panel B was normalized to the IFN-γ secretion of each SIV-specific CD4⁺ T-cell response when stimulated with the peptide pool. Peptide sequences above each mapped pool in panel B represent the peptide(s) that elicited the highest IFN-γ secretion within each pool. SFC, spot-forming cells.

FIG. 2.

Mapping of SIV-specific CD4⁺ T-cell responses. Peptides of 10 or 11 amino acids in length were used to map each SIV-specific CD4⁺ T-cell line or clone. Gag_97-111 TE15/Gag_101-115 KT15 was mapped with peptides of 10 amino acids in length (A), Gag_181-195 CD15 was mapped using peptides of 10 amino acids in length (B), Gag_197-211 QA15 was mapped using peptides of 11 amino acids in length (C), Vpx_29-43 VE15 was mapped with peptides of 10 amino acids in length (D), Rev_9-23 ET15/Rev_13-27 RY15 was mapped with peptides of 11 amino acids in length (E), and Nef_138-152 RI15 was mapped using peptides of 10 amino acids in length (F). The IFN-γ production was normalized for each SIV-specific CD4⁺ T-cell response when stimulated with the relevant peptide, shown in bold, and autologous BLCL.

FIG. 3.

Identification of the macaque MHC-II restricting allele of SIV-specific CD4⁺ T-cell responses using RM3 transferents. RM3 cell transferents expressing a single macaque MHC-II allele (one α-chain allele and one β-chain allele) were tested with SIV-specific CD4⁺ T-cell responses. Shown are the ELISPOT analyses of eight macaque MHC-II alleles tested with SIV-specific CD4⁺ T cells (A). ICS analyses of SIV-specific CD4⁺ T-cells responses stimulated with RM3 cells expressing the relevant restricting MHC-II allele found in panel A (B). The following DNA constructs encoding MHC-II α-chain alleles were used to transfect RM3 cells with their corresponding β-chain allele: Mamu-DRA1*01041 with all of the DNA constructs encoding a DRB chain (Mamu-DRB*w201, -DRB1*0306, -DRB1*1003, -DRB*w2603, -DRB*w2104, and -DRB*w606), Mamu-DQA1*09 with Mamu-DQB1*0605, and Mamu-DPA1*0202 with Mamu-DPB1*06. The IFN-γ secretion shown in panel A was normalized for each SIV-specific CD4⁺ T-cell response when stimulated with homologous BLCL and pulsed with relevant peptide. APC+peptide+CD4 T cell, autologous BLCL pulsed with a relevant peptide plus specific CD4⁺ T cells; Transferent+CD4 T cell, SIV-specific CD4⁺ T cells stimulated with RM3 cells expressing the restricting MHC-II allele specific for the response and pulsed without peptide; Transferent+peptide+CD4 T cell, SIV-specific CD4⁺ T cells stimulated with RM3 cells expressing the restricting MHC-II allele specific for the response and pulsed with a relevant peptide.