A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes

Renata Blatnik, Nitya Mohan, Maria Bonsack, Lasse G. Falkenby, Stephanie Hoppe, Kathrin Josef, Alina Steinbach, Sara Becker, Wiebke M. Nadler, Marijana Rucevic, Martin R. Larsen, Mogjiborahman Salek, Angelika B. Riemer*

*Kontaktforfatter for dette arbejde

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

223 Downloads (Pure)

Resumé

For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3-based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711–19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.

OriginalsprogEngelsk
Artikelnummer1700390
TidsskriftProteomics
Vol/bind18
Udgave nummer11
Antal sider9
ISSN1615-9853
DOI
StatusUdgivet - jun. 2018

Fingeraftryk

T-Lymphocyte Epitopes
HLA Antigens
Peptides
Epitopes
Assays
T-cells
Oncogene Proteins
varespladib methyl
Computer Simulation
Purification
Vaccines
Impurities
Antigens
Mutation

Bibliografisk note

© 2018 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Citer dette

Blatnik, R., Mohan, N., Bonsack, M., Falkenby, L. G., Hoppe, S., Josef, K., ... Riemer, A. B. (2018). A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics, 18(11), [1700390]. https://doi.org/10.1002/pmic.201700390
Blatnik, Renata ; Mohan, Nitya ; Bonsack, Maria ; Falkenby, Lasse G. ; Hoppe, Stephanie ; Josef, Kathrin ; Steinbach, Alina ; Becker, Sara ; Nadler, Wiebke M. ; Rucevic, Marijana ; Larsen, Martin R. ; Salek, Mogjiborahman ; Riemer, Angelika B. / A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. I: Proteomics. 2018 ; Bind 18, Nr. 11.
@article{ea393e7110b545c08104111288bbdb57,
title = "A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes",
abstract = "For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3-based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711–19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.",
keywords = "human papillomavirus (HPV), immunopeptidomics, immunotherapy, neoepitopes, targeted mass spectrometry (MS)",
author = "Renata Blatnik and Nitya Mohan and Maria Bonsack and Falkenby, {Lasse G.} and Stephanie Hoppe and Kathrin Josef and Alina Steinbach and Sara Becker and Nadler, {Wiebke M.} and Marijana Rucevic and Larsen, {Martin R.} and Mogjiborahman Salek and Riemer, {Angelika B.}",
note = "{\circledC} 2018 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA.",
year = "2018",
month = "6",
doi = "10.1002/pmic.201700390",
language = "English",
volume = "18",
journal = "Proteomics",
issn = "1615-9853",
publisher = "Wiley - V C H Verlag GmbH & Co. KGaA",
number = "11",

}

Blatnik, R, Mohan, N, Bonsack, M, Falkenby, LG, Hoppe, S, Josef, K, Steinbach, A, Becker, S, Nadler, WM, Rucevic, M, Larsen, MR, Salek, M & Riemer, AB 2018, 'A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes', Proteomics, bind 18, nr. 11, 1700390. https://doi.org/10.1002/pmic.201700390

A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. / Blatnik, Renata; Mohan, Nitya; Bonsack, Maria; Falkenby, Lasse G.; Hoppe, Stephanie; Josef, Kathrin; Steinbach, Alina; Becker, Sara; Nadler, Wiebke M.; Rucevic, Marijana; Larsen, Martin R.; Salek, Mogjiborahman; Riemer, Angelika B.

I: Proteomics, Bind 18, Nr. 11, 1700390, 06.2018.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes

AU - Blatnik, Renata

AU - Mohan, Nitya

AU - Bonsack, Maria

AU - Falkenby, Lasse G.

AU - Hoppe, Stephanie

AU - Josef, Kathrin

AU - Steinbach, Alina

AU - Becker, Sara

AU - Nadler, Wiebke M.

AU - Rucevic, Marijana

AU - Larsen, Martin R.

AU - Salek, Mogjiborahman

AU - Riemer, Angelika B.

N1 - © 2018 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA.

PY - 2018/6

Y1 - 2018/6

N2 - For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3-based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711–19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.

AB - For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3-based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711–19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.

KW - human papillomavirus (HPV)

KW - immunopeptidomics

KW - immunotherapy

KW - neoepitopes

KW - targeted mass spectrometry (MS)

U2 - 10.1002/pmic.201700390

DO - 10.1002/pmic.201700390

M3 - Journal article

C2 - 29603667

AN - SCOPUS:85046158445

VL - 18

JO - Proteomics

JF - Proteomics

SN - 1615-9853

IS - 11

M1 - 1700390

ER -