Dataset Information

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling

ABSTRACT: Defining the repertoire of peptides presented by the major histocompatibility complex class I (MHC I) is a key step towards the identification of relevant antigens for cancer immunotherapy. However, the identification of the cancer-specific antigens is a significant analytical challenge in view of their low abundance and low mutational load found in primary cancer specimens. Here, we describe the application of isobaric peptide labeling with tandem mass tag (TMT) to improve the detection of the MHC I peptides. Isobaric peptide labeling was found to promote the formation of multiply-charged ions and to enhance the formation of b-type fragment ions, thus resulting in a 50% improvement of MHC I peptide identification. The gain in sensitivity obtained using TMT labeling enabled the detection of low abundance MHC I peptides including tumor-specific antigens (TSAs) and minor histocompatibility antigens (MiHAs). We further demonstrate the application of this approach to quantify MiHAs presented by B-cell lymphocytes and determined their expression levels by LC-MS/MS using both synchronous precursor selection (SPS) and high field asymmetric waveform ion mobility spectrometry (FAIMS).

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Cell Culture

SUBMITTER: Eric Bonneil

LAB HEAD: Pierre Thibault

PROVIDER: PXD017918 | Pride | 2020-11-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	100Mio_BALL_TMT_nonFAIMS_Rep1.mgf	Mgf
	100Mio_BALL_TMT_nonFAIMS_Rep1.mzid.gz	Mzid
	100Mio_BALL_TMT_nonFAIMS_Rep1.pride.mgf.gz	Mgf
	100Mio_BALL_TMT_nonFAIMS_Rep1.pride.mztab.gz	Mztab
	100Mio_BALL_TMT_nonFAIMS_Rep1.raw	Raw

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Publications

Extending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling.

Pfammatter Sibylle S Bonneil Eric E Lanoix Joel J Vincent Krystel K Hardy Marie-Pierre MP Courcelles Mathieu M Perreault Claude C Thibault Pierre P

Analytical chemistry 20200623 13

Defining the repertoire of peptides presented by the major histocompatibility complex class I (MHC I) is a key step toward the identification of relevant antigens for cancer immunotherapy. However, the identification of cancer-specific antigens is a significant analytical challenge in view of their low abundance and low mutational load found in most primary cancer specimens. Here, we describe the application of isobaric peptide labeling with tandem mass tag (TMT) to improve the detection of the ...[more]

PMID: 32502341

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Project description:All nucleated mammalian cells express major histocompatibility complex (MHC) proteins that present peptides on cell surfaces for immune surveillance. These MHC-presented peptides (pMHC) can convey non-self antigens derived from pathogens or mutations to amount T-cell responses. Alterations in tumor-specific antigens – particularly mutation-bearing peptides (neoantigens) presented by MHC — can serve as potent substrates for anti-tumor immune responses. Here we employed an integrated genomic and proteomic antigen discovery strategy aimed at measuring interferon gamma (IFN-γ) induced alterations to antigen presentation, using a lymphoma cell line. IFN-γ treatment resulted in a set of differentially expressed proteins (2 % of all quantified proteins) including components of antigen presentation machinery or interferon signaling pathways. In addition, several proteasome subunits were found to be modulated, consistent with previous reports of immunoproteasome induction by IFN-γ exposure. This finding suggests that a modest proteomic response to IFN-γ could create larger alteration to cells antigen repertoires. Accordingly, by surveying immunopeptides, distinct peptide repertoires were exclusively observed in the IFN-γ induced samples. Furthermore, an additional set of presented peptides distinguished control and the IFN-γ samples by their altered relative abundances including neoantigens. Accordingly, we developed a classification system to distinguish peptides which are differentially presented due to altered expression from novel peptides resulting from changes in antigen processing. Taken together, these data demonstrate that IFN-γ can re-shape antigen repertoires by identity and by abundance. Extending this approach to models with greater clinical relevance should help develop strategies by which immunopeptide repertoires are intentionally reshaped to improve endogenous or vaccine-induced anti-tumor immune responses and potentially anti-viral immune responses.