Linking Pig-Tailed Macaque Major Histocompatibility Complex Class I Haplotypes and Cytotoxic T Lymphocyte Escape Mutations in Simian Immunodeficiency Virus Infection

Abstract

The influence of major histocompatibility complex class I (MHC-I) alleles on human immunodeficiency virus (HIV) diversity in humans has been well characterized at the population level. MHC-I alleles likely affect viral diversity in the simian immunodeficiency virus (SIV)-infected pig-tailed macaque (Macaca nemestrina) model, but this is poorly characterized. We studied the evolution of SIV in pig-tailed macaques with a range of MHC-I haplotypes. SIV mac251 genomes were amplified from the plasma of 44 pig-tailed macaques infected with SIV mac251 at 4 to 10 months after infection and characterized by Illumina deep sequencing. MHC-I typing was performed on cellular RNA using Roche/454 pyrosequencing. MHC-I haplotypes and viral sequence polymorphisms at both individual mutations and groups of mutations spanning 10-amino-acid segments were linked using in-house bioinformatics pipelines, since cytotoxic T lymphocyte (CTL) escape can occur at different amino acids within the same epitope in different animals. The approach successfully identified 6 known CTL escape mutations within 3 Mane-A1*084-restricted epitopes. The approach also identified over 70 new SIV polymorphisms linked to a variety of MHC-I haplotypes. Using functional CD8 T cell assays, we confirmed that one of these associations, a Mane-B028 haplotype-linked mutation in Nef, corresponded to a CTL epitope. We also identified mutations associated with the Mane-B017 haplotype that were previously described to be CTL epitopes restricted by Mamu-B*017:01 in rhesus macaques. This detailed study of pig-tailed macaque MHC-I genetics and SIV polymorphisms will enable a refined level of analysis for future vaccine design and strategies for treatment of HIV infection. IMPORTANCECytotoxic T lymphocytes select for virus escape mutants of HIV and SIV, and this limits the effectiveness of vaccines and immunotherapies against these viruses. Patterns of immune escape variants are similar in HIV type 1-infected human subjects that share the same MHC-I genes, but this has not been studied for SIV infection of macaques. By studying SIV sequence diversity in 44 MHC-typed SIV-infected pigtail macaques, we defined over 70 sites within SIV where mutations were common in macaques sharing particular MHC-I genes. Further, pigtail macaques sharing nearly identical MHC-I genes with rhesus macaques responded to the same CTL epitope and forced immune escape. This allows many reagents developed to study rhesus macaques to also be used to study pigtail macaques. Overall, our study defines sites of immune escape in SIV in pigtailed macaques, and this enables a more refined level of analysis of future vaccine design and strategies for treatment of HIV infection.

Comparative genomics of the human, macaque and mouse major histocompatibility complex

“…Ancestral‐like MHC haplotypes also appear to exist in mice and macaques . The macaque MHC class I, class II and/or entire MHC haplotypes were estimated using the MHC allele and/or pedigree information in each species such as Mafa , Mamu and Mane . Copy number variations of the MHC‐A , MHC‐E , MHC‐B , MHC‐I and MHC‐DRB loci were observed in the different macaque species, similar to the HLA‐DR haplotype .…”

Novel full-length major histocompatibility complex class I allele discovery and haplotype definition in pig-tailed macaques

“…Another advantage of defining full-length ORF sequences is in regards to restriction of infectious diseases. Previous studies have identified multiple MHC-I variants that bind to specific epitopes of SIV (Gooneratne et al 2014). In this study, we identified multiple closely related allelic variants of these MHC-I gene products that have been documented to restrict SIV epitopes.…”

Elite Control, Gut CD4 T Cell Sparing, and Enhanced Mucosal T Cell Responses in Macaca nemestrina Infected by a Simian Immunodeficiency Virus Lacking a gp41 Trafficking Motif

“…MHC class I genotyping was carried out as described previously (41)(42)(43). Total cellular RNA was isolated from whole blood or PBMCs, and first-strand cDNA was synthesized by reverse transcription with SuperScript III (Life Technologies, USA).…”

“…Of these 19 controlling animals, 15 exhibited levels below detection (Յ15 or 50 copies/ml using a standard assay or a more sensitive assay), with the other 4 animals showing persisting but low level viremia with intermittent RNA increases of 10 2 to 10 3 copies/ml. Deep-sequencing analysis showed that animals in both the ⌬GY and SIVmac239 challenge groups carried a diverse array of MHC haplotypes ( Table 1), indicating that differences in control of chronic-phase viral replication were unlikely to be associated with MHC class I genetics, including the Mane-A084 allele (formerly Mane-A*10), which has been implicated as an SIVmaccontrolling allele in pig-tailed macaques in early (54) although not more recent (41,55) studies. Viral set points for ⌬GY-controlling pig-tailed macaques were also reduced compared to those in 4 previously described ⌬GY-infected rhesus macaques (P Ͻ 0.01), which had RNA levels of 3.8 ϫ 10 4 Ϯ 1.4 ϫ 10 4 copies/ml and progressed to disease (Fig.…”