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

Abstract

Background Cryptic Epitopes (CE) are peptides derived from the translation of one or more of the five alternative reading frames (ARFs; 2 sense and 3 antisense) of genes. Here, we compared response rates to HIV-1 specific CE predicted to be restricted by HLA-I alleles associated with protection against disease progression to those without any such association. Methods Peptides (9–11mer) were designed based on HLA-I binding algorithms for B*27, B*57 or B*5801 (protective alleles) and HLA-B*5301 or B*5501 (non-protective allele) in all five ARFs of the nine HIV-1 encoded proteins. Peptides with >50% probability of being an epitope (n=231) were tested for T cell responses in an IFN-γ ELISpot assay. PBMC samples from HIV-1 seronegative donors (n=42) and HIV-1 seropositive patients with chronic clade B infections (n=129) were used. Results Overall, 16%, 2%, and 2% of CHI patients had CE responses by IFN-γ ELISpot in the protective, non-protective, and seronegative groups, respectively (p=0.009, Fischer’s exact test). Twenty novel CE specific responses were mapped (median magnitude of 95 SFC/106 PBMC) and the majority were both anti-sense derived (90%) as well as represented ARFs of accessory proteins (55%). CE-specific CD8 T cells were multifunctional and proliferated when assessed by intracellular cytokine staining. Conclusions CE responses were preferentially restricted by the protective HLA-I alleles in HIV-1 infection suggesting that they may contribute to viral control in this group of patients.

Nowhere to hide: unconventional translation yields cryptic peptides for immune surveillance

“…In a different study examining the HLA-alleles specific responses in HIV-patients, Bansal and colleagues discovered that presentation of cryptic peptides correlated with favorable clinical outcomes (36). By bioinformatic prediction of HLA-binding cryptic peptides, they identified peptides that could be presented by HLA-B*27 like protective alleles verses peptides that could be presented by HLA-B*5301 like non-protective alleles.…”

Brief Report: Should Abacavir Be a First-Line Alternative for Adults With HIV in Sub-Saharan Africa?

“…ABC and TDF-based regimens also provide the benefit of once daily dosing, as opposed to twice daily dosing for AZT. Finally, in contrast to ABC and TDF, AZT has not been studied with integrase strand transfer inhibitors (INSTIs) such as dolutegravir [34,35], which are now a preferred component of first-line regimens in the US and Europe [22]. …”

Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection

“…IFN-␥ ELISpot assay. ELISpot assays were performed as previously described by our group and others (25,26,28,37,38,45,49,50). In brief, 96-well nitrocellulose plates were first coated with anti-IFN-␥ monoclonal antibody.…”

“…Epitope-specific CD8 ϩ T cell lines were generated from patient PBMCs initially identified by a positive response to CE based on the IFN-␥ ELISpot assay. As previously described by our group, cell lines were expanded in vitro over the course of 14 days, using two rounds of irradiated monocytes pulsed with peptide as antigen-presenting cells (26,45). In brief, at the end of 2 weeks, CD8 T cell lines were restimulated with cognate antigen in the presence of costimulatory antibodies and intracellular transport inhibitors (monensin and brefeldin A) for 12 h and analyzed via flow cytometry for effector function, as described above.…”

“…These epitopes are predominantly derived from the translation of two sense and three antisense alternative open reading frames. Translation products of any of these five alternate reading frames (ARF) were found to be recognized by CD8 T cells during the acute and chronic stages of infection (6,21,(25)(26)(27)(28)(29). While CE usually induce T cell responses of lower magnitude than that of responses induced by their main reading frame counterparts, past studies have demonstrated that immune responses to these ARF epitopes are observed in many infected individuals or are immunoprevalent during the course of the disease (25,27).…”