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Title: Structure Based Prediction of Neoantigen Immunogenicity

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1577151
Resource Type:
Journal Article
Journal Name:
Frontiers in Immunology
Additional Journal Information:
Journal Volume: 10; Journal Issue: 08, 2019; Journal ID: ISSN 1664-3224
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
ENGLISH

Citation Formats

Riley, Timothy P., Keller, Grant L. J., Smith, Angela R., Davancaze, Lauren M., Arbuiso, Alyssa G., Devlin, Jason R., and Baker, Brian M. Structure Based Prediction of Neoantigen Immunogenicity. United States: N. p., 2019. Web. doi:10.3389/fimmu.2019.02047.
Riley, Timothy P., Keller, Grant L. J., Smith, Angela R., Davancaze, Lauren M., Arbuiso, Alyssa G., Devlin, Jason R., & Baker, Brian M. Structure Based Prediction of Neoantigen Immunogenicity. United States. doi:10.3389/fimmu.2019.02047.
Riley, Timothy P., Keller, Grant L. J., Smith, Angela R., Davancaze, Lauren M., Arbuiso, Alyssa G., Devlin, Jason R., and Baker, Brian M. Wed . "Structure Based Prediction of Neoantigen Immunogenicity". United States. doi:10.3389/fimmu.2019.02047.
@article{osti_1577151,
title = {Structure Based Prediction of Neoantigen Immunogenicity},
author = {Riley, Timothy P. and Keller, Grant L. J. and Smith, Angela R. and Davancaze, Lauren M. and Arbuiso, Alyssa G. and Devlin, Jason R. and Baker, Brian M.},
abstractNote = {},
doi = {10.3389/fimmu.2019.02047},
journal = {Frontiers in Immunology},
issn = {1664-3224},
number = 08, 2019,
volume = 10,
place = {United States},
year = {2019},
month = {8}
}

Works referenced in this record:

Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta
journal, January 2015

  • O’Meara, Matthew J.; Leaver-Fay, Andrew; Tyka, Michael D.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 2
  • DOI: 10.1021/ct500864r

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells
journal, May 2013

  • Robbins, Paul F.; Lu, Yong-Chen; El-Gamil, Mona
  • Nature Medicine, Vol. 19, Issue 6
  • DOI: 10.1038/nm.3161

HLA-Binding Properties of Tumor Neoepitopes in Humans
journal, March 2014


Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
journal, October 2013


Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings
journal, January 2004

  • Bosshard, Hans Rudolf; Marti, Daniel N.; Jelesarov, Ilian
  • Journal of Molecular Recognition, Vol. 17, Issue 1
  • DOI: 10.1002/jmr.657

Identification and Characterization of Neoantigens As Well As Respective Immune Responses in Cancer Patients
journal, November 2017


TCR contact residue hydrophobicity is a hallmark of immunogenic CD8 + T cell epitopes
journal, March 2015

  • Chowell, Diego; Krishna, Sri; Becker, Pablo D.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 14
  • DOI: 10.1073/pnas.1500973112

Structural Prediction of Peptides Bound to MHC Class I
journal, February 2006

  • Fagerberg, Theres; Cerottini, Jean-Charles; Michielin, Olivier
  • Journal of Molecular Biology, Vol. 356, Issue 2
  • DOI: 10.1016/j.jmb.2005.11.059

Sub-angstrom modeling of complexes between flexible peptides and globular proteins
journal, January 2010

  • Raveh, Barak; London, Nir; Schueler-Furman, Ora
  • Proteins: Structure, Function, and Bioinformatics
  • DOI: 10.1002/prot.22716

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry
journal, November 2016

  • Bassani-Sternberg, Michal; Bräunlein, Eva; Klar, Richard
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13404

Anatomy of hot spots in protein interfaces
journal, July 1998

  • Bogan, Andrew A.; Thorn, Kurt S.
  • Journal of Molecular Biology, Vol. 280, Issue 1
  • DOI: 10.1006/jmbi.1998.1843

DIALS : implementation and evaluation of a new integration package
journal, February 2018

  • Winter, Graeme; Waterman, David G.; Parkhurst, James M.
  • Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2
  • DOI: 10.1107/S2059798317017235

Structural basis for ineffective T-cell responses to MHC anchor residue-improved “heteroclitic” peptides: Molecular immunology
journal, December 2014

  • Madura, Florian; Rizkallah, Pierre J.; Holland, Christopher J.
  • European Journal of Immunology, Vol. 45, Issue 2
  • DOI: 10.1002/eji.201445114

Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens
journal, November 2013


Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012

  • Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
  • DOI: 10.1107/S0907444912001308

An immunogenic personal neoantigen vaccine for patients with melanoma
journal, July 2017

  • Ott, Patrick A.; Hu, Zhuting; Keskin, Derin B.
  • Nature, Vol. 547, Issue 7662
  • DOI: 10.1038/nature22991

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models
journal, October 1991

  • Sharp, Kim A.; Nicholls, Anthony; Friedman, Richard
  • Biochemistry, Vol. 30, Issue 40
  • DOI: 10.1021/bi00104a017

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer
journal, July 2017

  • Sahin, Ugur; Derhovanessian, Evelyna; Miller, Matthias
  • Nature, Vol. 547, Issue 7662
  • DOI: 10.1038/nature23003

Most viral peptides displayed by class I MHC on infected cells are immunogenic
journal, February 2019

  • Croft, Nathan P.; Smith, Stewart A.; Pickering, Jana
  • Proceedings of the National Academy of Sciences, Vol. 116, Issue 8
  • DOI: 10.1073/pnas.1815239116

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes
journal, September 2017

  • Singh, Nishant K.; Riley, Timothy P.; Baker, Sarah Catherine B.
  • The Journal of Immunology, Vol. 199, Issue 7
  • DOI: 10.4049/jimmunol.1700744

Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition
journal, October 2007

  • Borbulevych, Oleg Y.; Insaidoo, Francis K.; Baxter, Tiffany K.
  • Journal of Molecular Biology, Vol. 372, Issue 5
  • DOI: 10.1016/j.jmb.2007.07.025

MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles
journal, June 1999


A View of the Hydrophobic Effect
journal, January 2002

  • Southall, Noel T.; Dill, Ken A.; Haymet, A. D. J.
  • The Journal of Physical Chemistry B, Vol. 106, Issue 3
  • DOI: 10.1021/jp015514e

Structural prediction of peptides binding to MHC class I molecules
journal, January 2006

  • Bui, Huynh-Hoa; Schiewe, Alexandra J.; von Grafenstein, Hermann
  • Proteins: Structure, Function, and Bioinformatics, Vol. 63, Issue 1
  • DOI: 10.1002/prot.20870

Gapped sequence alignment using artificial neural networks: application to the MHC class I system
journal, October 2015


Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT
journal, February 2017

  • Remesh, Soumya G.; Andreatta, Massimo; Ying, Ge
  • Journal of Biological Chemistry, Vol. 292, Issue 13
  • DOI: 10.1074/jbc.M117.776542

Engineering the binding properties of the T cell receptor:peptide:MHC ternary complex that governs T cell activity
journal, September 2009


The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
journal, May 2017

  • Alford, Rebecca F.; Leaver-Fay, Andrew; Jeliazkov, Jeliazko R.
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 6
  • DOI: 10.1021/acs.jctc.7b00125

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
journal, October 2011


Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes
journal, September 2015

  • Cohen, Cyrille J.; Gartner, Jared J.; Horovitz-Fried, Miryam
  • Journal of Clinical Investigation, Vol. 125, Issue 10
  • DOI: 10.1172/JCI82416

Dominant forces in protein folding
journal, August 1990


Free energy mapping of class I MHC molecules and structural determination of bound peptides
journal, July 1996


Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction
journal, February 2017


Computing the Structure of Bound Peptides
journal, December 1993

  • Rosenfeld, Rakefet; Zheng, Qiang; Vajda, Sandor
  • Journal of Molecular Biology, Vol. 234, Issue 3
  • DOI: 10.1006/jmbi.1993.1607

Cancer immunotherapy: moving beyond current vaccines
journal, September 2004

  • Rosenberg, Steven A.; Yang, James C.; Restifo, Nicholas P.
  • Nature Medicine, Vol. 10, Issue 9
  • DOI: 10.1038/nm1100

SYFPEITHI: database for MHC ligands and peptide motifs
journal, November 1999

  • Rammensee, H. -G.; Bachmann, J.; Emmerich, N. P. N.
  • Immunogenetics, Vol. 50, Issue 3-4
  • DOI: 10.1007/s002510050595

Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models:  Application to Peptide Binding to Class I Major Histocompatibility Proteins
journal, November 1999

  • Rognan, Didier; Lauemøller, Sanne Lise; Holm, Arne
  • Journal of Medicinal Chemistry, Vol. 42, Issue 22
  • DOI: 10.1021/jm9910775

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes
journal, November 2017

  • Bjerregaard, Anne-Mette; Nielsen, Morten; Jurtz, Vanessa
  • Frontiers in Immunology, Vol. 8
  • DOI: 10.3389/fimmu.2017.01566

Computational prediction of neoantigens: do we need more data or new approaches?
journal, February 2018


The Length Distribution of Class I–Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele–Specific Binding Preference
journal, January 2016

  • Trolle, Thomas; McMurtrey, Curtis P.; Sidney, John
  • The Journal of Immunology, Vol. 196, Issue 4
  • DOI: 10.4049/jimmunol.1501721

Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics
journal, January 2011

  • Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M.
  • The Journal of Immunology, Vol. 186, Issue 5
  • DOI: 10.4049/jimmunol.1003150

Breast Cancer Neoantigens Can Induce CD8 + T-Cell Responses and Antitumor Immunity
journal, June 2017


The Phenix software for automated determination of macromolecular structures
journal, September 2011


Peptide-Binding Groove Contraction Linked to the Lack of T Cell Response: Using Complex Structure and Energy To Identify Neoantigens
journal, August 2018


Targeting of cancer neoantigens with donor-derived T cell receptor repertoires
journal, May 2016


The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design
journal, March 2017


Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
journal, May 2003

  • Nielsen, Morten; Lundegaard, Claus; Worning, Peder
  • Protein Science, Vol. 12, Issue 5
  • DOI: 10.1110/ps.0239403

MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009

  • Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042073

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing
journal, November 2014

  • Yadav, Mahesh; Jhunjhunwala, Suchit; Phung, Qui T.
  • Nature, Vol. 515, Issue 7528
  • DOI: 10.1038/nature14001

NetTepi: an integrated method for the prediction of T cell epitopes
journal, May 2014


A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations
journal, January 2018


Features and development of Coot
journal, March 2010

  • Emsley, P.; Lohkamp, B.; Scott, W. G.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
  • DOI: 10.1107/S0907444910007493

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity
journal, September 2014

  • Duan, Fei; Duitama, Jorge; Al Seesi, Sahar
  • The Journal of Experimental Medicine, Vol. 211, Issue 11
  • DOI: 10.1084/jem.20141308

Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes
journal, November 1998


Recent Advances in Targeting CD8 T-Cell Immunity for More Effective Cancer Immunotherapy
journal, January 2018


Efficient MHC class I-peptide binding is required but does not ensure MHC class I-restricted immunogenicity
journal, December 1994


How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire
journal, February 2016

  • Blevins, Sydney J.; Pierce, Brian G.; Singh, Nishant K.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 9
  • DOI: 10.1073/pnas.1522069113

Electrostatic aspects of protein–protein interactions
journal, April 2000


Modeling the structure of bound peptide ligands to major histocompatibility complex
journal, September 2004

  • Tong, Joo Chuan; Tan, Tin Wee; Ranganathan, Shoba
  • Protein Science, Vol. 13, Issue 9
  • DOI: 10.1110/ps.04631204

Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove
journal, January 2016


The functional capacity of the natural amino acids for molecular recognition
journal, January 2010

  • Birtalan, Sara; Fisher, Robert D.; Sidhu, Sachdev S.
  • Molecular BioSystems, Vol. 6, Issue 7
  • DOI: 10.1039/b927393j

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
journal, October 2017

  • Jurtz, Vanessa; Paul, Sinu; Andreatta, Massimo
  • The Journal of Immunology, Vol. 199, Issue 9
  • DOI: 10.4049/jimmunol.1700893

The Structure and Stability of an HLA-A*0201/Octameric Tax Peptide Complex with an Empty Conserved Peptide-N-Terminal Binding Site
journal, June 2000


PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
journal, January 2010


Two Different T Cell Receptors use Different Thermodynamic Strategies to Recognize the Same Peptide/MHC Ligand
journal, February 2005

  • Davis-Harrison, Rebecca L.; Armstrong, Kathryn M.; Baker, Brian M.
  • Journal of Molecular Biology, Vol. 346, Issue 2
  • DOI: 10.1016/j.jmb.2004.11.063

Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
journal, April 1991


Four A6-TCR/Peptide/HLA-A2 Structures that Generate Very Different T Cell Signals Are Nearly Identical
journal, July 1999


POPISK: T-cell reactivity prediction using support vector machines and string kernels
journal, January 2011


Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
journal, December 1991

  • Nicholls, Anthony; Sharp, Kim A.; Honig, Barry
  • Proteins: Structure, Function, and Genetics, Vol. 11, Issue 4
  • DOI: 10.1002/prot.340110407