Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells

Jane C. Yaciuk, Matthew Skaley, Wilfried Bardet, Fredda Schafer, Danijela Mojsilovic, Steven Cate, Christopher J. Stewart, Curtis McMurtrey, Kenneth W. Jackson, Rico Buchli, Alex Olvera, Samandhy Cedeño, Montserrat Plana, Beatriz Mothe, Christian Brander, John T. West, William H. Hildebrand

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Identification of CD8+ cytotoxic T lymphocyte (CTL) epitopes has traditionally relied upon testing of overlapping peptide libraries for their reactivity with T cells in vitro. Here, we pursued deep ligand sequencing (DLS) as an alternative method of directly identifying those ligands that are epitopes presented to CTLs by the class I human leukocyte antigens (HLA) of infected cells. Soluble class I HLA-A*11:01 (sHLA) was gathered from HIV-1 NL4-3-infected human CD4+ SUP-T1 cells. HLA-A*11:01 harvested from infected cells was immunoaffinity purified and acid boiled to release heavy and light chains from peptide ligands that were then recovered by size-exclusion filtration. The ligands were first fractionated by high-pH high-pressure liquid chromatography and then subjected to separation by nano-liquid chromatography (nano-LC)-mass spectrometry (MS) at low pH. Approximately 10 million ions were selected for sequencing by tandem mass spectrometry (MS/MS). HLA-A*11:01 ligand sequences were determined with PEAKS software and confirmed by comparison to spectra generated from synthetic peptides. DLS identified 42 viral ligands presented by HLA-A*11:01, and 37 of these were previously undetected. These data demonstrate that (i) HIV-1 Gag and Nef are extensively sampled, (ii) ligand length variants are prevalent, particularly within Gag and Nef hot spots where ligand sequences overlap, (iii) noncanonical ligands are T cell reactive, and (iv) HIV-1 ligands are derived from de novo synthesis rather than endocytic sampling. Next-generation immunotherapies must factor these nascent HIV-1 ligand length variants and the finding that CTL-reactive epitopes may be absent during infection of CD4+ T cells into strategies designed to enhance T cell immunity.

Original languageEnglish (US)
Pages (from-to)12992-13004
Number of pages13
JournalJournal of virology
Volume88
Issue number22
DOIs
StatePublished - Jan 1 2014

Fingerprint

HLA Antigens
T-lymphocytes
HIV
peptides
Ligands
T-Lymphocytes
Peptides
Tandem Mass Spectrometry
Human immunodeficiency virus 1
HIV-1
epitopes
High-Throughput Nucleotide Sequencing
cytotoxic T-lymphocytes
T-Lymphocyte Epitopes
Cytotoxic T-Lymphocytes
HLA antigens
ligands
peptide libraries
Peptide Library
synthetic peptides

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

Yaciuk, J. C., Skaley, M., Bardet, W., Schafer, F., Mojsilovic, D., Cate, S., ... Hildebrand, W. H. (2014). Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. Journal of virology, 88(22), 12992-13004. https://doi.org/10.1128/JVI.01914-14

Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. / Yaciuk, Jane C.; Skaley, Matthew; Bardet, Wilfried; Schafer, Fredda; Mojsilovic, Danijela; Cate, Steven; Stewart, Christopher J.; McMurtrey, Curtis; Jackson, Kenneth W.; Buchli, Rico; Olvera, Alex; Cedeño, Samandhy; Plana, Montserrat; Mothe, Beatriz; Brander, Christian; West, John T.; Hildebrand, William H.

In: Journal of virology, Vol. 88, No. 22, 01.01.2014, p. 12992-13004.

Research output: Contribution to journalArticle

Yaciuk, JC, Skaley, M, Bardet, W, Schafer, F, Mojsilovic, D, Cate, S, Stewart, CJ, McMurtrey, C, Jackson, KW, Buchli, R, Olvera, A, Cedeño, S, Plana, M, Mothe, B, Brander, C, West, JT & Hildebrand, WH 2014, 'Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells', Journal of virology, vol. 88, no. 22, pp. 12992-13004. https://doi.org/10.1128/JVI.01914-14
Yaciuk JC, Skaley M, Bardet W, Schafer F, Mojsilovic D, Cate S et al. Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. Journal of virology. 2014 Jan 1;88(22):12992-13004. https://doi.org/10.1128/JVI.01914-14
Yaciuk, Jane C. ; Skaley, Matthew ; Bardet, Wilfried ; Schafer, Fredda ; Mojsilovic, Danijela ; Cate, Steven ; Stewart, Christopher J. ; McMurtrey, Curtis ; Jackson, Kenneth W. ; Buchli, Rico ; Olvera, Alex ; Cedeño, Samandhy ; Plana, Montserrat ; Mothe, Beatriz ; Brander, Christian ; West, John T. ; Hildebrand, William H. / Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells. In: Journal of virology. 2014 ; Vol. 88, No. 22. pp. 12992-13004.
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