Numerous neoepitope-based vaccination strategies are in testing for clinical use in the treatment of cancer. Rapid identification of immunostimulatory neoantigen targets hastens neoantigen vaccine development. Papers recently published in Nature Biotechnology describe two independent machine-learning-based algorithms that demonstrate improved identification of MHC class II-binding peptides. Herein, we outline the benefits of these algorithms and their implications for future immunotherapies.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Keenan, T. E., Burke, K. P. & Van Allen, E. M. Genomic correlates of response to immune checkpoint blockade. Nat. Med. 25, 389–402 (2019).
Ott, P. A. et al. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547, 217–221 (2017).
Alspach, E. et al. MHC-II neoantigens shape tumour immunity and response to immunotherapy. Nature 574, 696–701 (2019).
Bassani-Sternberg, M. et al. Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry. Nat. Commun. 7, 13404 (2016).
Racle, J. et al. Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes. Nat. Biotechnol. 37, 1283–1286 (2019).
Chen, B. et al. Predicting HLA class II antigen presentation through integrated deep learning. Nat. Biotechnol. 37, 1332–1343 (2019).
Zhang, X. et al. Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy. Biomed. Pharmacother. 120, 109542 (2019).
Karpanen, T. & Olweus, J. The potential of donor T-cell repertoires in neoantigen-targeted cancer immunotherapy. Front. Immunol. 8, 1718 (2017).
Arstila, T. P. et al. A direct estimate of the human alphabeta T cell receptor diversity. Science 286, 958–961 (1999).
Kudela, P. et al. Cross-reactive CD4+T cells against one immunodominant tumor-derived epitope in melanoma patients. J. Immunol. 179, 7932–7940 (2007).
Ahmadzadeh, M. et al. Tumor-infiltrating human CD4+ regulatory T cells display a distinct TCR repertoire and exhibit tumor and neoantigen reactivity. Sci. Immunol. 4, eaao4310 (2019).
Tondini, E. et al. A poly-neoantigen DNA vaccine synergizes with PD-1 blockade to induce T cell-mediated tumor control. Oncoimmunology 8, 1652539 (2019).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Rights and permissions
About this article
Cite this article
Moore, T.V., Nishimura, M.I. Improved MHC II epitope prediction — a step towards personalized medicine. Nat Rev Clin Oncol 17, 71–72 (2020). https://doi.org/10.1038/s41571-019-0315-0
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41571-019-0315-0
