The translation of an RNA or DNA template into proteins is a
complex process that can produce a wide variety of functional and
non-functional protein products. Translation involves “reading” the genetic code,
and the nature of the protein produced depends on where the reading of the code
starts and stops (called the “reading frame”) and also which direction the code
is read in (forwards is called “sense” while backwards is called “antisense”). HIV’s
RNA genome contains nine reading frames encoding functional proteins, but it is
also known that alternate reading frames exist which can be translated into
proteins that are non-functional (or have unknown functions). Antisense
translation can also lead to the production of such proteins. The extent to
which these proteins are targeted by the immune system in HIV-infected people
has not been well characterized.
Two new papers in the Journal of Experimental Medicine address
this knowledge gap by evaluating CD8 T cell response to “cryptic” epitopes derived
from HIV proteins produced from both alternate reading frames and antisense
transcription. The reported results indicate that targeting of cryptic HIV
epitopes by CD8 T cells is surprisingly common. Both papers also present
evidence that CD8 T cell responses against cryptic epitopes can result in
mutations in the RNA sequences encoding these epitopes that abrogate CD8 T cell
recognition (immune escape).
The implication of these findings is that there is an
unexplored plethora of potential targets for HIV-specific T cell responses that
could conceivably be exploited to improve vaccine design. Anju Bansal and
colleagues note that the process of codon optimization, which is commonly used
to try and improve expression of HIV proteins by vaccine candidates, alters the
proteins produced from alternate reading frames so that they differ (by as much
as 80%) from those generated by natural infection. So counter-intuitively, it
is possible that codon optimization – which was used in the Merck Ad5 vaccine –
actually reduces the breadth of the resultant HIV-specific CD8 T cell response.
Bansal et al also point out that that the ALVAC-HIV vaccine used in the
recently reported RV-144 vaccine trial is not codon optimized and could
potentially induce responses to cryptic epitopes (CE); they conclude that "it may be important to take into account the contribution of CE-induced responses in the overall CD8 T cell repertoire of future vaccine constructs."
Published online January 11, 2010
doi:10.1084/jem.20092060
The Journal of Experimental Medicine
Brief Definitive Report
Anju Bansal1, Jonathan Carlson4, Jiyu Yan1, Olusimidele T.
Akinsiku2, Malinda Schaefer5,6, Steffanie Sabbaj1, Anne Bet2, David N. Levy7,
Sonya Heath1, Jianming Tang1,2, Richard A. Kaslow3, Bruce D. Walker8,9, Thumbi
Ndung’u8,9, Philip J. Goulder8,9,10, David Heckerman4, Eric Hunter5,6, and Paul
A. Goepfert1,2
1 Department of Medicine, 2 Department of Microbiology, and
3 Department of Epidemiology, University of Alabama at Birmingham, Birmingham,
AL 35294. 4 Microsoft Research, Redmond, WA 98052. 5 Emory Vaccine Center at
Yerkes National Primate Research Center and 6 Department of Pathology and
Laboratory Medicine, Emory University, Atlanta, GA 30329. 7 Department of Basic
Science, New York University College of Dentistry, New York, NY 10010. 8 Ragon
Institute of Massachusetts General Hospital, Massachusetts Institute of
Technology, and Harvard, Boston, MA 02129. 9 HIV Pathogenesis Program, Doris
Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013,
South Africa. 10 Department of Pediatrics, University of Oxford, Oxford OX1
3SY, England, UK
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.
Published online January 11, 2010
doi:10.1084/jem.20091808
The Journal of Experimental Medicine
Article
Christoph T. Berger1, Jonathan M. Carlson2, Chanson J.
Brumme1, Kari L. Hartman1, Zabrina L. Brumme1,3,4, Leah M. Henry1, Pamela C.
Rosato1, Alicja Piechocka-Trocha1, Mark A. Brockman1,3,4, P. Richard
Harrigan3,5, David Heckerman2, Daniel E. Kaufmann1, and Christian Brander1,6,7
1 Ragon Institute of Massachusetts General Hospital,
Massachusetts Institute of Technology, and Harvard, Boston, MA 02129. 2
Microsoft Research, Seattle, WA 98033. 3 British Columbia Centre for Excellence
in HIV/AIDS, Vancouver, BC V6B 5S8, Canada. 4 Simon Fraser University, Burnaby,
BC V5A 4Y7, Canada. 5 Division of AIDS, University of British Columbia,
Vancouver, BC V6Z 1Y6, Canada. 6 Institucio Catalana de Recerca i Estudis
Avancats, 08010 Barcelona, Spain. 7 Irsicaixa HIV Research Institute–HIVACAT,
Hospital Germans Trias i Pujol, Badalona, 08916 Barcelona, Spain
CD8+ cytotoxic T lymphocyte (CTL)–mediated immune responses
to HIV contribute to viral control in vivo. Epitopes encoded by alternative
reading frame (ARF) peptides may be targeted by CTLs as well, but their
frequency and in vivo relevance are unknown. Using host genetic (human
leukocyte antigen [HLA]) and plasma viral sequence information from 765
HIV-infected subjects, we identified 64 statistically significant (q < 0.2)
associations between specific HLA alleles and sequence polymorphisms in
alternate reading frames of gag, pol, and nef that did not affect the regular
frame protein sequence. Peptides spanning the top 20 HLA-associated imprints
were used to test for ex vivo immune responses in 85 HIV-infected subjects and
showed responses to 10 of these ARF peptides. The most frequent response
recognized an HLA-A*03–restricted +2 frame–encoded epitope containing a unique
A*03-associated polymorphism at position 6. Epitope-specific CTLs efficiently
inhibited viral replication in vitro when viruses containing the wild-type
sequence but not the observed polymorphism were tested. Mutating alternative
internal start codons abrogated the CTL-mediated inhibition of viral replication.
These data indicate that responses to ARF-encoded HIV epitopes are induced
during natural infection, can contribute to viral control in vivo, and drive
viral evolution on a population level.
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