Influence of HAART on Alternative Reading Frame Immune Responses over the Course of HIV-1 Infection

Abstract

Background Translational errors can result in bypassing of the main viral protein reading frames and the production of alternate reading frame (ARF) or cryptic peptides. Within HIV, there are many such ARFs in both sense and the antisense directions of transcription. These ARFs have the potential to generate immunogenic peptides called cryptic epitopes (CE). Both antiretroviral drug therapy and the immune system exert a mutational pressure on HIV-1. Immune pressure exerted by ARF CD8 + T cells on the virus has already been observed in vitro . HAART has also been described to select HIV-1 variants for drug escape mutations. Since the mutational pressure exerted on one location of the HIV-1 genome can potentially affect the 3 reading frames, we hypothesized that ARF responses would be affected by this drug pressure in vivo . Methodology/Principal findings In this study we identified new ARFs derived from sense and antisense transcription of HIV-1. Many of these ARFs are detectable in circulating viral proteins. They are predominantly found in the HIV-1 env nucleotide region. We measured T cell responses to 199 HIV-1 CE encoded within 13 sense and 34 antisense HIV-1 ARFs. We were able to observe that these ARF responses are more frequent and of greater magnitude in chronically infected individuals compared to acutely infected patients, and in patients on HAART, the breadth of ARF responses increased. Conclusions/Significance These results have implications for vaccine design and unveil the existence of potential new epitopes that could be included as vaccine targets.

Immune Screening Identifies Novel T Cell Targets Encoded by Antisense Reading Frames of HIV-1

“…Relative to their length and the frequency whereby they are targeted, responses to these ASPs compare well with observed reactivities to epitopes encoded in forward cryptic HIV reading frames (4) and response rates to well-studied regulatory HIV proteins, such as Tat, Vif, and Rev (19). The response rates are also comparable to activities reported by Champiat et al, who identified responses to ASPs that partially overlapped with four of our ASP sequences (6). Together, the present study corroborates earlier reports of responses to epitopes in alternative HIV reading frames and suggests that HIV may express several additional, relatively conserved proteins that may be under evolutionary constraints and thus exert hitherto-unknown functions.…”

“…Accumulating evidence indicates that in addition to CTL responses targeting known structural and nonstructural HIV proteins, CTL responses to epitopes in alternative reading frames (ARFs) of HIV can contribute to in vivo immune selection pressure (4)(5)(6). Importantly, these CTL responses are not limited to ARFs in the sense direction, but may also target antisense-encoded ARFs (5,6).…”

“…Accumulating evidence indicates that in addition to CTL responses targeting known structural and nonstructural HIV proteins, CTL responses to epitopes in alternative reading frames (ARFs) of HIV can contribute to in vivo immune selection pressure (4)(5)(6). Importantly, these CTL responses are not limited to ARFs in the sense direction, but may also target antisense-encoded ARFs (5,6). Antisense transcription of known host genes in human and rodent cells has been extensively described (7)(8)(9)(10), and the existence of an antisense protein (ASP) in HIV was first proposed more than 20 years ago (10)(11)(12).…”

Enhanced Recognition of HIV-1 Cryptic Epitopes Restricted by HLA Class I Alleles Associated With a Favorable Clinical Outcome

“…Using a selected set of CE (9–11 mers) based on HLA-I associated HIV-1 polymorphisms; we and others have previously shown that CE are frequently targeted during HIV-1 infection 39,40 . A recent paper illustrated enhanced ARF encoded immune responses in HIV infected patients receiving antiretroviral therapy (ART) 44 . Similar to our prior work 39 most of the peptides used in this study were derived from reverse frames.…”

“…Similar to our prior work 39 most of the peptides used in this study were derived from reverse frames. The T-cell responses in this study were examined in a small subset of HIV-1 infected individuals expressing HLA A*02, B*07 and B*58 alleles 44 . However, no study to date has assessed the frequency, functionality and biological significance of CE in context of specific HLA class I alleles associated with differential disease outcome.…”