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Front Immunol. 2018 Jan 30;9:99. doi: 10.3389/fimmu.2018.00099. eCollection 2018.

A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.

Author information

1
Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, United States.
2
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, United States.
3
Division of Oncology, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, United States.
4
Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, United States.
5
Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States.
6
Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
7
Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, United States.

Abstract

The identification of recurrent human leukocyte antigen (HLA) neoepitopes driving T cell responses against tumors poses a significant bottleneck in the development of approaches for precision cancer therapeutics. Here, we employ a bioinformatics method, Prediction of T Cell Epitopes for Cancer Therapy, to analyze sequencing data from neuroblastoma patients and identify a recurrent anaplastic lymphoma kinase mutation (ALK R1275Q) that leads to two high affinity neoepitopes when expressed in complex with common HLA alleles. Analysis of the X-ray structures of the two peptides bound to HLA-B*15:01 reveals drastically different conformations with measurable changes in the stability of the protein complexes, while the self-epitope is excluded from binding due to steric hindrance in the MHC groove. To evaluate the range of HLA alleles that could display the ALK neoepitopes, we used structure-based Rosetta comparative modeling calculations, which accurately predict several additional high affinity interactions and compare our results with commonly used prediction tools. Subsequent determination of the X-ray structure of an HLA-A*01:01 bound neoepitope validates atomic features seen in our Rosetta models with respect to key residues relevant for MHC stability and T cell receptor recognition. Finally, MHC tetramer staining of peripheral blood mononuclear cells from HLA-matched donors shows that the two neoepitopes are recognized by CD8+ T cells. This work provides a rational approach toward high-throughput identification and further optimization of putative neoantigen/HLA targets with desired recognition features for cancer immunotherapy.

KEYWORDS:

MHC class I; T cell receptor; cancer; computational biology; human leukocyte antigens; neoepitopes; structural biology

PMID:
29441070
PMCID:
PMC5797543
DOI:
10.3389/fimmu.2018.00099
[Indexed for MEDLINE]
Free PMC Article

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