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An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes.

作者信息

Bjerregaard Anne-Mette, Nielsen Morten, Jurtz Vanessa, Barra Carolina M, Hadrup Sine Reker, Szallasi Zoltan, Eklund Aron Charles

机构信息

Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.

Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.

出版信息

Front Immunol. 2017 Nov 15;8:1566. doi: 10.3389/fimmu.2017.01566. eCollection 2017.


DOI:10.3389/fimmu.2017.01566
PMID:29187854
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5694748/
Abstract

Personalization of cancer immunotherapies such as therapeutic vaccines and adoptive T-cell therapy may benefit from efficient identification and targeting of patient-specific neoepitopes. However, current neoepitope prediction methods based on sequencing and predictions of epitope processing and presentation result in a low rate of validation, suggesting that the determinants of peptide immunogenicity are not well understood. We gathered published data on human neopeptides originating from single amino acid substitutions for which T cell reactivity had been experimentally tested, including both immunogenic and non-immunogenic neopeptides. Out of 1,948 neopeptide-HLA (human leukocyte antigen) combinations from 13 publications, 53 were reported to elicit a T cell response. From these data, we found an enrichment for responses among peptides of length 9. Even though the peptides had been pre-selected based on presumed likelihood of being immunogenic, we found using NetMHCpan-4.0 that immunogenic neopeptides were predicted to bind significantly more strongly to HLA compared to non-immunogenic peptides. Investigation of the HLA binding strength of the immunogenic peptides revealed that the vast majority (96%) shared very strong predicted binding to HLA and that the binding strength was comparable to that observed for pathogen-derived epitopes. Finally, we found that neopeptide dissimilarity to self is a predictor of immunogenicity in situations where neo- and normal peptides share comparable predicted binding strength. In conclusion, these results suggest new strategies for prioritization of mutated peptides, but new data will be needed to confirm their value.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/b9ea716f5cad/fimmu-08-01566-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/d5e79e74aeb7/fimmu-08-01566-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/a8c7b281b1d1/fimmu-08-01566-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/b9ea716f5cad/fimmu-08-01566-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/d5e79e74aeb7/fimmu-08-01566-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/a8c7b281b1d1/fimmu-08-01566-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4502/5694748/b9ea716f5cad/fimmu-08-01566-g003.jpg

相似文献

[1]
An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes.

Front Immunol. 2017-11-15

[2]
Population-level distribution and putative immunogenicity of cancer neoepitopes.

BMC Cancer. 2018-4-13

[3]
Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations.

Front Immunol. 2020

[4]
Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics.

J Immunother Cancer. 2023-9

[5]
Predicting T cell recognition of MHC class I restricted neoepitopes.

Oncoimmunology. 2018-8-27

[6]
Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy.

J Immunother Cancer. 2021-6

[7]
Personalized identification of tumor-associated immunogenic neoepitopes in hepatocellular carcinoma in complete remission after sorafenib treatment.

Oncotarget. 2018-10-23

[8]
'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.

Front Immunol. 2017-10-20

[9]
Sequence conservation analysis and in silico human leukocyte antigen-peptide binding predictions for the Mtb72F and M72 tuberculosis candidate vaccine antigens.

BMC Immunol. 2015-10-22

[10]
Pan-cancer analysis of neoepitopes.

Sci Rep. 2018-8-24

引用本文的文献

[1]
Properties of CD8 T-cell-recognized neoantigens in different tumor types.

Immunooncol Technol. 2025-6-13

[2]
Development of therapeutic cancer vaccines based on cancer immunity cycle.

Front Med. 2025-7-14

[3]
CTG-Initiated Cryptic Peptide Translation Up- and Downstream of a Canonical ATG Start Codon Is Enhanced by TLR Stimulation and Induces Tumor Regression in Mice.

Cancer Immunol Res. 2025-8-1

[4]
Strategies for neoantigen screening and immunogenicity validation in cancer immunotherapy (Review).

Int J Oncol. 2025-6

[5]
Shared neoantigens for cancer immunotherapy.

Mol Ther Oncol. 2025-3-28

[6]
Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.

Front Immunol. 2025-1-29

[7]
Leveraging mRNA technology for antigen based immuno-oncology therapies.

J Immunother Cancer. 2025-1-22

[8]
The transformative potential of mRNA vaccines for glioblastoma and human cancer: technological advances and translation to clinical trials.

Front Oncol. 2024-9-27

[9]
Neoantigen immunogenicity landscapes and evolution of tumor ecosystems during immunotherapy with nivolumab.

Nat Med. 2024-11

[10]
Revamping Hepatocellular Carcinoma Immunotherapy: The Advent of Microbial Neoantigen Vaccines.

Vaccines (Basel). 2024-8-21

本文引用的文献

[1]
NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.

J Immunol. 2017-11-1

[2]
Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer.

Nature. 2017-7-5

[3]
An immunogenic personal neoantigen vaccine for patients with melanoma.

Nature. 2017-7-13

[4]
MuPeXI: prediction of neo-epitopes from tumor sequencing data.

Cancer Immunol Immunother. 2017-9

[5]
Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.

Immunity. 2017-2-21

[6]
Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.

Nat Commun. 2016-11-21

[7]
Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

Nat Biotechnol. 2016-8-29

[8]
Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity.

J Immunol. 2016-8-15

[9]
Targeting of cancer neoantigens with donor-derived T cell receptor repertoires.

Science. 2016-5-19

[10]
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets.

Genome Med. 2016-3-30

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