Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics Workflows

Frontiers in Immunology
Thomas PartridgePersephone Borrow

Abstract

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 durin...Continue Reading

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Citations

May 17, 2019·Nature Protocols·Anthony W PurcellNicola Ternette
Nov 22, 2019·Proceedings of the National Academy of Sciences of the United States of America·Wayne PaesPersephone Borrow
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Aug 4, 2021·MSystems·Owen K LeddyBryan D Bryson

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Datasets Mentioned

BETA
KJ925006

Methods Mentioned

BETA
immunoprecipitation
PCR
Pull-Down
Flow cytometry

Software Mentioned

GibbsCluster
GibbsCluster2
NetMHC4
CyAn ADP Analyzer
NetMHCcons
NetMHC
GraphPad
QuickAlign Tool
GraphPad Prism
QuickAlign

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