Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows
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) o...
Main Authors: | , , , , , , |
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Format: | Journal article |
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Frontiers Media
2018
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author | Partridge, T Nicastri, A Kliszczak, A Yindom, L Kessler, B Ternette, N Borrow, P |
author_facet | Partridge, T Nicastri, A Kliszczak, A Yindom, L Kessler, B Ternette, N Borrow, P |
author_sort | Partridge, T |
collection | OXFORD |
description | 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 tumors. Recent advances in the sensitivity of liquid chromatography tandem mass spectrometry instrumentation have facilitated the discovery of thousands of natural 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, and 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. |
first_indexed | 2024-03-06T19:18:44Z |
format | Journal article |
id | oxford-uuid:19527e66-55a0-4412-bb31-eeccac7f1802 |
institution | University of Oxford |
last_indexed | 2024-03-06T19:18:44Z |
publishDate | 2018 |
publisher | Frontiers Media |
record_format | dspace |
spelling | oxford-uuid:19527e66-55a0-4412-bb31-eeccac7f18022022-03-26T10:48:25ZDiscrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflowsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:19527e66-55a0-4412-bb31-eeccac7f1802Symplectic Elements at OxfordFrontiers Media2018Partridge, TNicastri, AKliszczak, AYindom, LKessler, BTernette, NBorrow, PElucidation 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 tumors. Recent advances in the sensitivity of liquid chromatography tandem mass spectrometry instrumentation have facilitated the discovery of thousands of natural 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, and 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. |
spellingShingle | Partridge, T Nicastri, A Kliszczak, A Yindom, L Kessler, B Ternette, N Borrow, P Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title | Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title_full | Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title_fullStr | Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title_full_unstemmed | Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title_short | Discrimination between human leukocyte antigen class I-bound and co-purified HIV-derived peptides in immunopeptidomics workflows |
title_sort | discrimination between human leukocyte antigen class i bound and co purified hiv derived peptides in immunopeptidomics workflows |
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