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Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells.

Ternette N, Block PD, Sánchez-Bernabéu Á, Borthwick N, Pappalardo E, Abdul-Jawad S, Ondondo B, Charles PD, Dorrell L, Kessler BM, Hanke T - J. Virol. (2015)

Bottom Line: We employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify 6,358 unique peptides associated with the class I human leukocyte antigen (HLA), of which 98 peptides were derived from the MVA vector and 7 were derived from the HIVconsv immunogen.MVA.HIVconsv infection generally altered the composition of HLA class I-associated human (self) peptides, but these changes corresponded only partially to changes in the whole cell host protein abundance.Identification and quantitation of HLA class I-associated peptides by Q-MS will not only find broad application in T-cell epitope discovery but also inform vaccine design and allow evaluation of efficient epitope presentation using different delivery strategies.

View Article: PubMed Central - PubMed

Affiliation: The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom nicola.ternette@ndm.ox.ac.uk.

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The immunopeptidome reflects changes of the cellular proteome in MVA.HIVconsv-infected cells. (A) The most relevant pathways that are affected by MVA.HIVconsv infection at 3.5 hpi, as identified by Ingenuity Pathway Analysis, for all proteins according to the abundances of the corresponding HLA-associated peptides (left) and the intracellular proteins (right), as determined by label-free quantitative LC-MS/MS. All changes in abundance were determined between the 3.5-h time point and the negative control. (B) Correlation factors between the trend of protein abundance and the trend of the HLA-associated peptide abundance at 0, 1.5, 2.5, and 3.5 hpi. A proportional correlation was assigned a value of +1, and an inverse correlation was assigned a value of −1. Factors are plotted for all proteins along the x axis, for which both protein and immunopeptide abundances were determined.
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Figure 7: The immunopeptidome reflects changes of the cellular proteome in MVA.HIVconsv-infected cells. (A) The most relevant pathways that are affected by MVA.HIVconsv infection at 3.5 hpi, as identified by Ingenuity Pathway Analysis, for all proteins according to the abundances of the corresponding HLA-associated peptides (left) and the intracellular proteins (right), as determined by label-free quantitative LC-MS/MS. All changes in abundance were determined between the 3.5-h time point and the negative control. (B) Correlation factors between the trend of protein abundance and the trend of the HLA-associated peptide abundance at 0, 1.5, 2.5, and 3.5 hpi. A proportional correlation was assigned a value of +1, and an inverse correlation was assigned a value of −1. Factors are plotted for all proteins along the x axis, for which both protein and immunopeptide abundances were determined.

Mentions: Infection of cells with viruses including MVA (40) results in a dramatic alteration of host cell protein expression. To assess the changes in the Jurkat cell proteome following MVA.HIVconsv infection and the resulting altered self-peptidome associated with the HLA class I molecules, proteomes and immunopeptidomes of uninfected and MVA.HIVconsv-infected cells were analyzed and compared by using Ingenuity Pathway Analysis (IPA) software (Fig. 7A). Generally, many similarities between protein and HLA peptide abundances were observed. The “virus entry via endocytic pathways,” “purine nucleotides de novo biosynthesis,” and “protein ubiquitination pathway” were among the most significantly affected pathways, reflected by both the cellular proteome and immunopeptidome. However, when correlating the protein abundance trend with the trend of the corresponding epitope presentation abundance throughout the analyzed time course, a range of proportional (+1 correlation factor) to antiproportional (−1 correlation factor) correlations and no correlation (0 correlation factor) were observed (Fig. 7B; see also Table S2 in the supplemental material). Interestingly, for any one protein for which multiple peptides were presented, correlation trends were not always consistent (see Table S2 in the supplemental material). These findings indicate that for each HLA-associated peptide, a specific generation-and-presentation pathway applies, and a general correlation between presentation and protein abundance is not feasible.


Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells.

Ternette N, Block PD, Sánchez-Bernabéu Á, Borthwick N, Pappalardo E, Abdul-Jawad S, Ondondo B, Charles PD, Dorrell L, Kessler BM, Hanke T - J. Virol. (2015)

The immunopeptidome reflects changes of the cellular proteome in MVA.HIVconsv-infected cells. (A) The most relevant pathways that are affected by MVA.HIVconsv infection at 3.5 hpi, as identified by Ingenuity Pathway Analysis, for all proteins according to the abundances of the corresponding HLA-associated peptides (left) and the intracellular proteins (right), as determined by label-free quantitative LC-MS/MS. All changes in abundance were determined between the 3.5-h time point and the negative control. (B) Correlation factors between the trend of protein abundance and the trend of the HLA-associated peptide abundance at 0, 1.5, 2.5, and 3.5 hpi. A proportional correlation was assigned a value of +1, and an inverse correlation was assigned a value of −1. Factors are plotted for all proteins along the x axis, for which both protein and immunopeptide abundances were determined.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4442425&req=5

Figure 7: The immunopeptidome reflects changes of the cellular proteome in MVA.HIVconsv-infected cells. (A) The most relevant pathways that are affected by MVA.HIVconsv infection at 3.5 hpi, as identified by Ingenuity Pathway Analysis, for all proteins according to the abundances of the corresponding HLA-associated peptides (left) and the intracellular proteins (right), as determined by label-free quantitative LC-MS/MS. All changes in abundance were determined between the 3.5-h time point and the negative control. (B) Correlation factors between the trend of protein abundance and the trend of the HLA-associated peptide abundance at 0, 1.5, 2.5, and 3.5 hpi. A proportional correlation was assigned a value of +1, and an inverse correlation was assigned a value of −1. Factors are plotted for all proteins along the x axis, for which both protein and immunopeptide abundances were determined.
Mentions: Infection of cells with viruses including MVA (40) results in a dramatic alteration of host cell protein expression. To assess the changes in the Jurkat cell proteome following MVA.HIVconsv infection and the resulting altered self-peptidome associated with the HLA class I molecules, proteomes and immunopeptidomes of uninfected and MVA.HIVconsv-infected cells were analyzed and compared by using Ingenuity Pathway Analysis (IPA) software (Fig. 7A). Generally, many similarities between protein and HLA peptide abundances were observed. The “virus entry via endocytic pathways,” “purine nucleotides de novo biosynthesis,” and “protein ubiquitination pathway” were among the most significantly affected pathways, reflected by both the cellular proteome and immunopeptidome. However, when correlating the protein abundance trend with the trend of the corresponding epitope presentation abundance throughout the analyzed time course, a range of proportional (+1 correlation factor) to antiproportional (−1 correlation factor) correlations and no correlation (0 correlation factor) were observed (Fig. 7B; see also Table S2 in the supplemental material). Interestingly, for any one protein for which multiple peptides were presented, correlation trends were not always consistent (see Table S2 in the supplemental material). These findings indicate that for each HLA-associated peptide, a specific generation-and-presentation pathway applies, and a general correlation between presentation and protein abundance is not feasible.

Bottom Line: We employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify 6,358 unique peptides associated with the class I human leukocyte antigen (HLA), of which 98 peptides were derived from the MVA vector and 7 were derived from the HIVconsv immunogen.MVA.HIVconsv infection generally altered the composition of HLA class I-associated human (self) peptides, but these changes corresponded only partially to changes in the whole cell host protein abundance.Identification and quantitation of HLA class I-associated peptides by Q-MS will not only find broad application in T-cell epitope discovery but also inform vaccine design and allow evaluation of efficient epitope presentation using different delivery strategies.

View Article: PubMed Central - PubMed

Affiliation: The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom nicola.ternette@ndm.ox.ac.uk.

Show MeSH
Related in: MedlinePlus