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Front. Immunol. | doi: 10.3389/fimmu.2018.00912

Discrimination between HLA class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows

  • 1Nuffield Department of Medicine, University of Oxford, United Kingdom
  • 2Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom
  • 3The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, United Kingdom

Elucidation of novel peptides presented by human leukocyte antigen (HLA) class I alleles by immunopeptidomics constitutes a powerful approach that can inform the rational design of CD8+ T cell inducing vaccines to control infection with pathogens such as human immunodeficiency virus type 1 (HIV-1) or to combat tumours. Recent advances in the sensitivity of liquid chromatography tandem mass spectrometry instrumentation have facilitated the discovery of thousands of naturally-presented HLA-restricted peptides in a single measurement. However, the extent of contamination of class I-bound peptides identified using HLA immunoprecipitation (IP)-based immunopeptidomics approaches with peptides from other sources has not previously been evaluated in depth. Here, we investigated the specificity of the IP-based immunopeptidomics methodology using HLA class I- or II-deficient cell lines and membrane protein-specific antibody IPs. We demonstrate that the 721.221 B lymphoblastoid cell line, widely regarded to be HLA class Ia-deficient, actually expresses and presents peptides on HLA-C*01:02. Using this cell line and the C8166 (HLA class I- and II-expressing) cell line, we show that some HLA class II-bound peptides were co-purified non-specifically during HLA class I and membrane protein IPs. Furthermore, IPs of “irrelevant” membrane proteins from HIV-1-infected HLA class I- and/or II-expressing cells revealed that unusually long HIV-1-derived peptides previously reported by us and other immunopeptidomics studies as potentially novel CD8+ T cell epitopes were non-specifically co-isolated, so constitute a source of contamination in HLA class I IPs. For example, a 16-mer (FLGKIWPSYKGRPGNF) which was detected in all samples studied represents the full p1 segment of the abundant intracellular or virion-associated proteolytically-processed HIV-1 Gag protein. This result is of importance, as these long co-purified HIV-1 Gag peptides may not elicit CD8+ T cell responses when incorporated into candidate vaccines. These results have wider implications for HLA epitope discovery from abundant or membrane-associated antigens by immunopeptidomics in the context of infectious diseases, cancer and autoimmunity.

Keywords: HIV, Major Histocompatibility Complex, human leukocyte antigen, epitope, Antigen Presentation, immunopeptidomics, Mass Spectrometry

Received: 12 Jan 2018; Accepted: 12 Apr 2018.

Edited by:

Shokrollah Elahi, University of Alberta, Canada

Reviewed by:

Keith R. Fowke, University of Manitoba, Canada
Lucia Lopalco, San Raffaele Hospital (IRCCS), Italy  

Copyright: © 2018 Partridge, Nicastri, Kliszczak, Yindom, Kessler, Ternette and Borrow. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Thomas Partridge, University of Oxford, Nuffield Department of Medicine, Oxford, United Kingdom,
Dr. Nicola Ternette, University of Oxford, Target Discovery Institute, Nuffield Department of Medicine, Oxford, United Kingdom,
Prof. Persephone Borrow, University of Oxford, Nuffield Department of Medicine, Oxford, United Kingdom,