Additional materials and methods. Figure S1. CD4+ T cells responded to USP9X-Y2009C minimal epitope. Figure S2. CD4+ T cells recognized INPP5K-L272V neoantigen. Figure S3. T cells transduced with TCRs recognize Histone H1.5-A71D neoantigen. Figure S4. CD4+ T cells responded to RAPTOR-D654G minimal neoepitope. Figure S5. The p53-G245S minimal neoepitope was mapped to the N-terminus of the 25 amino acid neoantigen. Figure S6. Peptide parsing from Patient 7 demonstrated CTAGE5-E576V, p53-Y220C and HUWE1-F4353S responses.
Funding
National Natural Science Foundation of China
Key Clinical Specialty Discipline Construction Program
National Key Research and Development Program of China
Natural Science Foundation of Guangdong Province
Science and Technology Planning Project of Guangzhou
Director's Foundation of Nanfang Hospital
ARTICLE ABSTRACT
Purpose: This was a study prospectively evaluating intratumoral T-cell responses to autologous somatic mutated neoepitopes expressed by human metastatic ovarian cancers.Patients and Methods: Tumor-infiltrating lymphocytes (TIL) were expanded from resected ovarian cancer metastases, which were analyzed by whole-exome and transcriptome sequencing to identify autologous somatic mutations. All mutated neoepitopes, independent of prediction algorithms, were expressed in autologous antigen-presenting cells and then cocultured with TIL fragment cultures. Secretion of IFNγ or upregulation of 41BB indicated a T-cell response.Results: Seven women with metastatic ovarian cancer were evaluated, and 5 patients had clear, dominant T-cell responses to mutated neoantigens, which were corroborated by comparison with the wild-type sequence, identification of the minimal epitope, human leukocyte antigen (HLA) restriction element(s), and neoantigen-specific T-cell receptor(s). Mutated neoantigens were restricted by HLA-B, -C, -DP, -DQ, and/or -DR alleles and appeared to principally arise from random, somatic mutations unique to each patient. We established that TP53 “hotspot” mutations (c.659A>G; p.Y220C and c.733G>A; p.G245S) expressed by two different patients' tumors were both immunogenic in the context of HLA-DRB3*02:02.Conclusions: Mutation-reactive T cells infiltrated ovarian cancer metastases at sufficient frequencies to warrant their investigation as adoptive cell therapy. In addition, transfer of TP53 “hotspot” mutation-reactive T-cell receptors into peripheral blood T cells could be evaluated as a gene therapy for a diverse range of tumor histologies. Clin Cancer Res; 24(22); 5562–73. ©2018 AACR.See related commentary by McNeish, p. 5493
