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CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription.

Bansal A, Carlson J, Yan J, Akinsiku OT, Schaefer M, Sabbaj S, Bet A, Levy DN, Heath S, Tang J, Kaslow RA, Walker BD, Ndung'u T, Goulder PJ, Heckerman D, Hunter E, Goepfert PA - J. Exp. Med. (2010)

Bottom Line: Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs).In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts.These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA. ABansal@uab.edu

ABSTRACT
Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I-associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity.

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Related in: MedlinePlus

Evolution of predicted CEs after primary HIV-1 infection. Sequencing of gag, nef, and pol was performed in 37 epidemiologically linked recipients from Zambia at the time of identified infection and every 3 mo for the first year. The number of observed mutations during this time that matched the predicted HLA-I–associated HIV-1 polymorphisms in the chronic cohort (Fig. 1) as a percentage of the total observed mutations (those not predicted in the chronic cohort) is shown. The total number of predicted mutations is shown above each bar. Symbols next to the number of predicted mutations designate the reading frames where mutations, predicted from the chronic cohort, were not caused by chance alone (*, P < 0.04; †, P < 0.01; ‡, P < 0.0001).
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fig5: Evolution of predicted CEs after primary HIV-1 infection. Sequencing of gag, nef, and pol was performed in 37 epidemiologically linked recipients from Zambia at the time of identified infection and every 3 mo for the first year. The number of observed mutations during this time that matched the predicted HLA-I–associated HIV-1 polymorphisms in the chronic cohort (Fig. 1) as a percentage of the total observed mutations (those not predicted in the chronic cohort) is shown. The total number of predicted mutations is shown above each bar. Symbols next to the number of predicted mutations designate the reading frames where mutations, predicted from the chronic cohort, were not caused by chance alone (*, P < 0.04; †, P < 0.01; ‡, P < 0.0001).

Mentions: Perhaps the best indicator of immune potency is viral escape in response to immune pressure and reversion when the pressure no longer exists. Although we predicted the presence of CD8 T cell targeting based on evidence of escape and reversion, these data were obtained cross-sectionally in a chronically infected cohort and, hence, provide indirect evidence of selection. Therefore, we sought direct evidence of selection by determining if CEs (predicted in the chronic cohort) mutate during the first year of HIV-1 infection, similar to what has been observed for conventional epitopes (Brumme et al., 2008). In 37 epidemiologically linked transmission pairs (LTPs) from Zambia, we sequenced HIV-1 gag, nef, and pol at baseline and every 3 mo for 1 yr. We hypothesized that mutations in the main reading frame, especially the synonymous mutations, may actually reflect CD8 T cell escape mutations in CEs derived from overlapping ARFs. Therefore, we analyzed the number of nonsynonymous mutations (those that result in amino acid changes in the protein) as well as the number of synonymous mutations in the main reading frame of Gag, Pol, and Nef proteins that resulted in amino acid changes in one or more of the five ARFs during the first year of infection. This analysis enabled us to determine if any of the HLA-I–associated HIV-1 polymorphisms predicted in the chronic cohort (in all six reading frames) were observed to mutate in these linked recipients. As expected from previous studies (Brumme et al., 2008), several nonsynonymous mutations (RF 1) occurring in the Gag, Nef, and Pol proteins during the first year of infection matched the predicted conventional epitope escape mutations in the chronic South African cohort (Fig. 5). Additionally, for all of the antisense reading frames (ARFs 4–6, occurring within gag, nef, and pol), several synonymous mutations in the main reading frame corresponded to amino acid changes in predicted CEs that are likely caused by immune pressure (escape or reversion) and not to chance alone (P < 0.01). Predicted CE mutations were also significantly observed in the sense reading frames (ARFs 2 and 3) of gag and pol (P < 0.04) but not nef. Similar to what has been observed previously for conventional epitopes (Li et al., 2007), the majority of CE changes occurring during the first year of infection were predicted to be reversions, although some CD8 T cell escapes were also noted.


CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription.

Bansal A, Carlson J, Yan J, Akinsiku OT, Schaefer M, Sabbaj S, Bet A, Levy DN, Heath S, Tang J, Kaslow RA, Walker BD, Ndung'u T, Goulder PJ, Heckerman D, Hunter E, Goepfert PA - J. Exp. Med. (2010)

Evolution of predicted CEs after primary HIV-1 infection. Sequencing of gag, nef, and pol was performed in 37 epidemiologically linked recipients from Zambia at the time of identified infection and every 3 mo for the first year. The number of observed mutations during this time that matched the predicted HLA-I–associated HIV-1 polymorphisms in the chronic cohort (Fig. 1) as a percentage of the total observed mutations (those not predicted in the chronic cohort) is shown. The total number of predicted mutations is shown above each bar. Symbols next to the number of predicted mutations designate the reading frames where mutations, predicted from the chronic cohort, were not caused by chance alone (*, P < 0.04; †, P < 0.01; ‡, P < 0.0001).
© Copyright Policy - openaccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2812545&req=5

fig5: Evolution of predicted CEs after primary HIV-1 infection. Sequencing of gag, nef, and pol was performed in 37 epidemiologically linked recipients from Zambia at the time of identified infection and every 3 mo for the first year. The number of observed mutations during this time that matched the predicted HLA-I–associated HIV-1 polymorphisms in the chronic cohort (Fig. 1) as a percentage of the total observed mutations (those not predicted in the chronic cohort) is shown. The total number of predicted mutations is shown above each bar. Symbols next to the number of predicted mutations designate the reading frames where mutations, predicted from the chronic cohort, were not caused by chance alone (*, P < 0.04; †, P < 0.01; ‡, P < 0.0001).
Mentions: Perhaps the best indicator of immune potency is viral escape in response to immune pressure and reversion when the pressure no longer exists. Although we predicted the presence of CD8 T cell targeting based on evidence of escape and reversion, these data were obtained cross-sectionally in a chronically infected cohort and, hence, provide indirect evidence of selection. Therefore, we sought direct evidence of selection by determining if CEs (predicted in the chronic cohort) mutate during the first year of HIV-1 infection, similar to what has been observed for conventional epitopes (Brumme et al., 2008). In 37 epidemiologically linked transmission pairs (LTPs) from Zambia, we sequenced HIV-1 gag, nef, and pol at baseline and every 3 mo for 1 yr. We hypothesized that mutations in the main reading frame, especially the synonymous mutations, may actually reflect CD8 T cell escape mutations in CEs derived from overlapping ARFs. Therefore, we analyzed the number of nonsynonymous mutations (those that result in amino acid changes in the protein) as well as the number of synonymous mutations in the main reading frame of Gag, Pol, and Nef proteins that resulted in amino acid changes in one or more of the five ARFs during the first year of infection. This analysis enabled us to determine if any of the HLA-I–associated HIV-1 polymorphisms predicted in the chronic cohort (in all six reading frames) were observed to mutate in these linked recipients. As expected from previous studies (Brumme et al., 2008), several nonsynonymous mutations (RF 1) occurring in the Gag, Nef, and Pol proteins during the first year of infection matched the predicted conventional epitope escape mutations in the chronic South African cohort (Fig. 5). Additionally, for all of the antisense reading frames (ARFs 4–6, occurring within gag, nef, and pol), several synonymous mutations in the main reading frame corresponded to amino acid changes in predicted CEs that are likely caused by immune pressure (escape or reversion) and not to chance alone (P < 0.01). Predicted CE mutations were also significantly observed in the sense reading frames (ARFs 2 and 3) of gag and pol (P < 0.04) but not nef. Similar to what has been observed previously for conventional epitopes (Li et al., 2007), the majority of CE changes occurring during the first year of infection were predicted to be reversions, although some CD8 T cell escapes were also noted.

Bottom Line: Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs).In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts.These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA. ABansal@uab.edu

ABSTRACT
Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I-associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity.

Show MeSH
Related in: MedlinePlus