Identifying a minor histocompatibility antigen in mauritian cynomolgus macaques encoded by APOBEC3C

Allogeneic hematopoietic stem cell transplants can lead to dramatic reductions in human immunodeficiency virus (HIV) reservoirs. This effect is partially mediated by donor T cells recognizing lymphocyte-expressed minor histocompatibility antigens (mHAgs). The potential to mark malignant and latently infected cells for destruction makes mHAgs attractive targets for cellular immunotherapies. However, testing such HIV reservoir reduction strategies will likely require preclinical studies in non-human primates (NHPs). In this study, we used a combination of alloimmunization, whole exome sequencing, and bioinformatics to identify an mHAg in Mauritian cynomolgus macaques (MCMs). We mapped the minimal optimal epitope to a 10-mer peptide (SW10) in apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3C (APOBEC3C) and determined the major histocompatibility complex class I restriction element as Mafa-A1∗063, which is expressed in almost 90% of MCMs. APOBEC3C SW10-specific CD8+ T cells recognized immortalized B cells but not fibroblasts from an mHAg-positive MCM. These results provide a framework for identifying mHAgs in a non-transplant setting and suggest that APOBEC3C SW10 could be used as a model antigen to test mHAg-targeted therapies in NHPs

Specific CD8+ T cell responses correlate with control of simian immunodeficiency virus replication in Mauritian cynomolgus macaques

Specific major histocompatibility complex (MHC) class I alleles are associated with an increased frequency of spontaneous control of human and simian immunodeficiency viruses (HIV and SIV). The mechanism of control is thought to involve MHC class I-restricted CD8+ T cells, but it is not clear whether particular CD8+ T cell responses or a broad repertoire of epitope-specific CD8+ T cell populations (termed T cell breadth) are principally responsible for mediating immunologic control. To test the hypothesis that heterozygous macaques control SIV replication as a function of superior T cell breadth, we infected MHC-homozygous and MHC-heterozygous cynomolgus macaques with the pathogenic virus SIVmac239. As measured by a gamma interferon enzyme-linked immunosorbent spot assay (IFN-γ ELISPOT) using blood, T cell breadth did not differ significantly between homozygotes and heterozygotes. Surprisingly, macaques that controlled SIV replication, regardless of their MHC zygosity, shared durable T cell responses against similar regions of Nef. While the limited genetic variability in these animals prevents us from making generalizations about the importance of Nef-specific T cell responses in controlling HIV, these results suggest that the T cell-mediated control of virus replication that we observed is more likely the consequence of targeting specificity rather than T cell breadth

Reduction of CD4+ T Cells In Vivo Does Not Affect Virus Load in Macaque Elite Controllers ▿

A small percentage of human immunodeficiency virus (HIV)- and simian immunodeficiency virus (SIV)-infected individuals spontaneously control virus replication. The majority of these elite controllers mount high-frequency virus-specific CD4+ T cell responses. To evaluate the role these responses might play in viral control, we depleted two elite controller macaques of CD4+ cells. SIV-specific CD4+ T cell responses did not return to baseline levels until 8 weeks postdepletion. Viral loads remained stable throughout the experiment, suggesting that SIV-specific CD4+ T cell responses may not play a direct role in controlling chronic viral replication in these elite controllers

Escape from CD8 +

A small number of HIV-infected individuals known as elite controllers experience low levels of chronic phase viral replication and delayed progression to AIDS. Specific HLA class I alleles are associated with elite control, implicating CD8(+) T lymphocytes in the establishment of these low levels of viral replication. Most HIV-infected individuals that express protective HLA class I alleles, however, do not control viral replication. Approximately 50% of Mamu-B*00801(+) Indian rhesus macaques control SIVmac239 replication in the chronic phase in a manner that resembles elite control in humans. We followed both the immune response and viral evolution in SIV-infected Mamu-B*00801(+) animals to better understand the role of CD8(+) T lymphocytes during the acute phase of viral infection, when viral control status is determined. The virus escaped from immunodominant Vif and Nef Mamu-B*00801–restricted CD8(+) T lymphocyte responses during the critical early weeks of acute infection only in progressor animals that did not control viral replication. Thus, early CD8(+) T lymphocyte escape is a hallmark of Mamu-B*00801(+) macaques who do not control viral replication. By contrast, virus in elite controller macaques showed little evidence of variation in epitopes recognized by immunodominant CD8(+) T lymphocytes, implying that these cells play a role in viral control

SHORT REPORT Open Access

Discovery and full genome characterization of a new SIV lineage infecting red-tailed guenons (Cercopithecus ascanius schmidti) in Kibal

Pegivirus avoids immune recognition but does not attenuate acute-phase disease in a macaque model of HIV infection

<div><p>Human pegivirus (HPgV) protects HIV+ people from HIV-associated disease, but the mechanism of this protective effect remains poorly understood. We sequentially infected cynomolgus macaques with simian pegivirus (SPgV) and simian immunodeficiency virus (SIV) to model HIV+HPgV co-infection. SPgV had no effect on acute-phase SIV pathogenesis–as measured by SIV viral load, CD4+ T cell destruction, immune activation, or adaptive immune responses–suggesting that HPgV’s protective effect is exerted primarily during the chronic phase of HIV infection. We also examined the immune response to SPgV in unprecedented detail, and found that this virus elicits virtually no activation of the immune system despite persistently high titers in the blood over long periods of time. Overall, this study expands our understanding of the pegiviruses–an understudied group of viruses with a high prevalence in the global human population–and suggests that the protective effect observed in HIV+HPgV co-infected people occurs primarily during the chronic phase of HIV infection.</p></div

Acute phase CTL responses against ARF-10 in two SIV-infected Rhesus macaques.

<p>A) and B) Magnitude of CTL responses against 15-mers in ARF-10 in Rhesus macaques rh2261, A, and r04028, B, as measured by IFN–γ ELISPOT using cryopreserved PBMC harvested 3 weeks after initial SIV infection. The SIV infection history of the animals is described in the text. Bars are color coded to match with remaining panels in the figure. C) and D) Peptide dilutions to fine map the minimal optimal epitopes targeted in ARF-10 by rh2261, C, and r04028, D. For rh2261, we used PBMC harvested in the acute phase of infection. For animal r04028, due to PBMC sample limitations, we expanded antigen-specific CTL by exposing PBMC to autologous irradiated BLCL pulsed with the responsive 15-mer for several weeks and used these cells in an ELISPOT. For panels A–C, we used 100,000 PBMC per well, in duplicate, in ELISPOT plates. For the epitope mapping with r04028, we used 20,000 antigen-specific cells per well combined with 10,000 autologous BLCL per well as antigen presenting cells. Peptides tested are shown at right of each mapping panel and the peptides we determined represented the minimal epitopes are shown in color to match panels A and B. E) The mapped epitopes within ARF-10 are boxed using the color scheme described above.</p

The genomic locations of ARFs -1 and -10 as well as the primers used to amplify this region for pyrosequencing, within the SIVmac239 genome.

<p>The SIVmac239 genome is 10,535 nt in length. The ORFs encoding the classical viral proteins are shown in blue and the ORFs encoding the ARFs studied in this report are shown in orange. Note that ARF-10 is depicted as separate from Rev exon 1 to emphasize its independent translation. However, ARF-10 is a composite of the first exon of Rev and the first 50 amino acids translated from the Rev intron. The relative locations of the forward and reverse primers used to amplify viral RNA for pyrosequencing are shown as labeled black arrows. This image was created using the software Geneious version 5.6.4 created by Biomatters, available from <a href="http://www.geneious.com" target="_blank">www.geneious.com</a>.</p

Acute phase CTL responses against ARF-1 in two SIV-infected Rhesus macaques.

<p>A) and B) Similar to panels A and B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061383#pone-0061383-g002" target="_blank">figure 2</a>. Here, we depict the week 3 responses to 15-mers within ARF-1 in two animals, r97111, A, and r97035. The infection history of these animals is described in the text. C) and D) The minimal epitope was mapped to the RP9 peptide in both animals using serial 10-fold dilutions of peptide in IFN–γ ELISPOT assays. The peptides used are shown at right and the RP9 peptide, which was determined to be the minimal epitope is shown in orange. E) The location of the RP9 epitope within ARF-1.</p