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@ARTICLE{Bertrand:298964,
      author       = {L. Bertrand and A. Nelde and B. C. Ramirez and I. Hatin and
                      H. Arbes and P. François and S. Demais and E. Labaronne and
                      D. Decimo and L. Guiguettaz and S. Grégoire and A. Bet and
                      G. Beauclair and A. Gross and M. C. Ziegler and M. Pereira
                      and R. Jeger-Madiot and Y. Verdier and J. Vinh and S.
                      Cardinaud and S. Graff-Dubois and A. Esclatine and C.
                      Gouttefangeas$^*$ and M. Altfeld and L. Hocqueloux and A.
                      Samri and B. Autran and O. Lambotte and H.-G. Rammensee$^*$
                      and E. P. Ricci and J. Walz$^*$ and O. Namy and A. Moris},
      title        = {{U}nveiling conserved {HIV}-1 open reading frames encoding
                      {T} cell antigens using ribosome profiling.},
      journal      = {Nature Communications},
      volume       = {16},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Springer Nature},
      reportid     = {DKFZ-2025-00393},
      pages        = {1707},
      year         = {2025},
      abstract     = {The development of ribosomal profiling (Riboseq) revealed
                      the immense coding capacity of human and viral genomes.
                      Here, we used Riboseq to delineate the translatome of HIV-1
                      in infected CD4+ T cells. In addition to canonical viral
                      protein coding sequences (CDSs), we identify 98 alternative
                      open reading frames (ARFs), corresponding to small Open
                      Reading Frames (sORFs) that are distributed across the HIV
                      genome including the UTR regions. Using a database of HIV
                      genomes, we observe that most ARF amino-acid sequences are
                      likely conserved among clade B and C of HIV-1, with 8
                      ARF-encoded amino-acid sequences being more conserved than
                      the overlapping CDSs. Using T cell-based assays and mass
                      spectrometry-based immunopeptidomics, we demonstrate that
                      ARFs encode viral polypeptides. In the blood of people
                      living with HIV, ARF-derived peptides elicit potent
                      poly-functional T cell responses mediated by both CD4+ and
                      CD8+ T cells. Our discovery expands the list of conserved
                      viral polypeptides that are targets for vaccination
                      strategies and might reveal the existence of viral
                      microproteins or pseudogenes.},
      keywords     = {HIV-1: genetics / HIV-1: immunology / Humans / Open Reading
                      Frames: genetics / CD4-Positive T-Lymphocytes: immunology /
                      Ribosomes: metabolism / HIV Infections: immunology / HIV
                      Infections: virology / HIV Infections: genetics /
                      CD8-Positive T-Lymphocytes: immunology / Genome, Viral /
                      Amino Acid Sequence / Conserved Sequence / Male / Peptides:
                      immunology / Peptides: chemistry / Peptides: genetics /
                      Ribosome Profiling / Peptides (NLM Chemicals)},
      cin          = {TU01},
      ddc          = {500},
      cid          = {I:(DE-He78)TU01-20160331},
      pnm          = {899 - ohne Topic (POF4-899)},
      pid          = {G:(DE-HGF)POF4-899},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:39966340},
      doi          = {10.1038/s41467-025-56773-2},
      url          = {https://inrepo02.dkfz.de/record/298964},
}