Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

Jennifer G. Abelin; Dewi Harjanto; Matthew Malloy; Prerna Suri; Tyler Colson; Scott P. Goulding; Amanda L. Creech; Lia R. Serrano; Gibran Nasir; Yusuf Nasrullah; Christopher D. McGann; Diana Velez; Ying S. Ting; Asaf Poran; Daniel A. Rothenberg; Sagar Chhangawala; Alex Rubinsteyn; Jeff Hammerbacher; Richard B. Gaynor; Edward F. Fritsch; Joel Greshock; Rob C. Oslund; Dominik Barthelme; Terri A. Addona; Christina M. Arieta; Michael S. Rooney

doi:10.1016/j.immuni.2019.08.012

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

Jennifer G. Abelin
, Dewi Harjanto
, Matthew Malloy
, Prerna Suri
, Tyler Colson
, Scott P. Goulding
, Amanda L. Creech
, Lia R. Serrano
, Gibran Nasir
, Yusuf Nasrullah
, Christopher D. McGann
, Diana Velez
, Ying S. Ting
, Asaf Poran
, Daniel A. Rothenberg
, Sagar Chhangawala
, Alex Rubinsteyn
, Jeff Hammerbacher
, Richard B. Gaynor
, Edward F. Fritsch

Joel Greshock, Rob C. Oslund, Dominik Barthelme, Terri A. Addona, Christina M. Arieta, Michael S. Rooney

Research output: Contribution to journal › Article › peer-review

187 Scopus citations

Abstract

Despite their role in directing T cell responses, HLA-II epitopes remain difficult to predict, hindering their therapeutic potential. Abelin et al. develop proteomic strategies that resolve diverse HLA-II motifs and pinpoint tumor epitopes that are presented by professional APCs. These data enable improved HLA-II epitope prediction and therapeutic targeting.

Original language	English
Pages (from-to)	766-779.e17
Journal	Immunity
Volume	51
Issue number	4
DOIs	https://doi.org/10.1016/j.immuni.2019.08.012
State	Published - 15 Oct 2019

Keywords

HLA class II
HLA ligandomics
HLA-II
MHC
RNA-Seq
SILAC
antigen
autophagy
cancer
epitope prediction
isotope labeling
machine learning
mass spectrometry
neoantigen
peptide processing
phagocytosis
proteomics

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10.1016/j.immuni.2019.08.012

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Abelin, J. G., Harjanto, D., Malloy, M., Suri, P., Colson, T., Goulding, S. P., Creech, A. L., Serrano, L. R., Nasir, G., Nasrullah, Y., McGann, C. D., Velez, D., Ting, Y. S., Poran, A., Rothenberg, D. A., Chhangawala, S., Rubinsteyn, A., Hammerbacher, J., Gaynor, R. B., ... Rooney, M. S. (2019). Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction. Immunity, 51(4), 766-779.e17. https://doi.org/10.1016/j.immuni.2019.08.012

@article{5f97888ba47e4c9cad49d49baca0157c,

title = "Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction",

abstract = "Despite their role in directing T cell responses, HLA-II epitopes remain difficult to predict, hindering their therapeutic potential. Abelin et al. develop proteomic strategies that resolve diverse HLA-II motifs and pinpoint tumor epitopes that are presented by professional APCs. These data enable improved HLA-II epitope prediction and therapeutic targeting.",

keywords = "HLA class II, HLA ligandomics, HLA-II, MHC, RNA-Seq, SILAC, antigen, autophagy, cancer, epitope prediction, isotope labeling, machine learning, mass spectrometry, neoantigen, peptide processing, phagocytosis, proteomics",

author = "Abelin, \{Jennifer G.\} and Dewi Harjanto and Matthew Malloy and Prerna Suri and Tyler Colson and Goulding, \{Scott P.\} and Creech, \{Amanda L.\} and Serrano, \{Lia R.\} and Gibran Nasir and Yusuf Nasrullah and McGann, \{Christopher D.\} and Diana Velez and Ting, \{Ying S.\} and Asaf Poran and Rothenberg, \{Daniel A.\} and Sagar Chhangawala and Alex Rubinsteyn and Jeff Hammerbacher and Gaynor, \{Richard B.\} and Fritsch, \{Edward F.\} and Joel Greshock and Oslund, \{Rob C.\} and Dominik Barthelme and Addona, \{Terri A.\} and Arieta, \{Christina M.\} and Rooney, \{Michael S.\}",

note = "Publisher Copyright: {\textcopyright} 2019 Elsevier Inc.",

year = "2019",

month = oct,

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doi = "10.1016/j.immuni.2019.08.012",

language = "English",

volume = "51",

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Abelin, JG, Harjanto, D, Malloy, M, Suri, P, Colson, T, Goulding, SP, Creech, AL, Serrano, LR, Nasir, G, Nasrullah, Y, McGann, CD, Velez, D, Ting, YS, Poran, A, Rothenberg, DA, Chhangawala, S, Rubinsteyn, A, Hammerbacher, J, Gaynor, RB, Fritsch, EF, Greshock, J, Oslund, RC, Barthelme, D, Addona, TA, Arieta, CM & Rooney, MS 2019, 'Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction', Immunity, vol. 51, no. 4, pp. 766-779.e17. https://doi.org/10.1016/j.immuni.2019.08.012

TY - JOUR

T1 - Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

AU - Abelin, Jennifer G.

AU - Harjanto, Dewi

AU - Malloy, Matthew

AU - Suri, Prerna

AU - Colson, Tyler

AU - Goulding, Scott P.

AU - Creech, Amanda L.

AU - Serrano, Lia R.

AU - Nasir, Gibran

AU - Nasrullah, Yusuf

AU - McGann, Christopher D.

AU - Velez, Diana

AU - Ting, Ying S.

AU - Poran, Asaf

AU - Rothenberg, Daniel A.

AU - Chhangawala, Sagar

AU - Rubinsteyn, Alex

AU - Hammerbacher, Jeff

AU - Gaynor, Richard B.

AU - Fritsch, Edward F.

AU - Greshock, Joel

AU - Oslund, Rob C.

AU - Barthelme, Dominik

AU - Addona, Terri A.

AU - Arieta, Christina M.

AU - Rooney, Michael S.

PY - 2019/10/15

Y1 - 2019/10/15

N2 - Despite their role in directing T cell responses, HLA-II epitopes remain difficult to predict, hindering their therapeutic potential. Abelin et al. develop proteomic strategies that resolve diverse HLA-II motifs and pinpoint tumor epitopes that are presented by professional APCs. These data enable improved HLA-II epitope prediction and therapeutic targeting.

AB - Despite their role in directing T cell responses, HLA-II epitopes remain difficult to predict, hindering their therapeutic potential. Abelin et al. develop proteomic strategies that resolve diverse HLA-II motifs and pinpoint tumor epitopes that are presented by professional APCs. These data enable improved HLA-II epitope prediction and therapeutic targeting.

KW - HLA class II

KW - HLA ligandomics

KW - HLA-II

KW - MHC

KW - RNA-Seq

KW - SILAC

KW - antigen

KW - autophagy

KW - cancer

KW - epitope prediction

KW - isotope labeling

KW - machine learning

KW - mass spectrometry

KW - neoantigen

KW - peptide processing

KW - phagocytosis

KW - proteomics

UR - https://www.scopus.com/pages/publications/85073037953

U2 - 10.1016/j.immuni.2019.08.012

DO - 10.1016/j.immuni.2019.08.012

M3 - Article

C2 - 31495665

AN - SCOPUS:85073037953

SN - 1074-7613

VL - 51

SP - 766-779.e17

JO - Immunity

JF - Immunity

IS - 4

ER -

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

Abstract

Keywords

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