A Phase I Study with a Personalized Neoantigen Cancer Vaccine in Melanoma

Effective anti-tumor immunity in humans has been associated with presence of T cells targeting neoantigens that arise from non-silent tumor-specific mutations. Here we conducted whole-exome sequencing of tumor and normal cells from individual patients to identify mutations. We assessed the expression of mutated alleles by RNA-sequencing of tumor. We demonstrated the feasibility, safety and immunogenicity of a vaccine that targets up to 20 personal neoantigens predicted to be presented by the autologous patient tumor.Antigen-specific CD8+ T cells that can recognize and eliminate cancer cells play a crucial role in anti-tumor immune responses. Here we conducted single-cell sequencing of cells infiltrating melanoma specimens originating from 4 patients and determine the TCR clonality of the CD8+ tumor infiltrating cells. We investigated the relationship between T cell clonality and phenotypic cell states coupling single-cell transcriptome to single-cell TCR seq. The surface expression of a panel of protein was detected in parallel using CITE-Seq antibodies. Sorted tumor and peripheral blood specimens were processed in parallel.In order to discover cancer antigens derived from annotated and unannotated protein-coding regions of the genome, we carried out matched ribosome profiling (Ribo-seq), RNA-sequencing, and whole genome sequencing on one of the patients, as well as Ribo-seq on an additional patient. We used it to discover novel or unannotated open reading frames (nuORFs), their expression levels, as well as somatic mutations within them to predict potential neoantigens. ]]>
Key eligibility criteria were clinically or radiographically evident, pathologically confirmed stage IIIB/C and IVM1a/b melanoma deemed amenable to complete surgical resection and an ECOG performance status of 0 or 1. Other requirements included absolute lymphocyte count = 800/mcL, absolute neutrophil count = 1,500/mcL, hemoglobin count = 10g/dL, platelet count = 100,000/mcL, aminotransferases = 2 x upper limit of the normal range, total serum bilirubin = 1 x upper limit of the normal range, and serum creatinine = 1.5 x upper limit of the normal range. Patients with uveal or mucosal melanoma, prior immune modulating or other cancer directed therapies (except for IFN-alpha given as systemic adjuvant therapy for a prior melanoma or melanoma recurrence), active autoimmune disease or an immunosuppressive condition were excluded.Sample size of patients was determined by the availability of tumor specimens and reliable patient-derived melanoma cell lines. We focused our investigations on 4 melanoma patients whose tumors were previously genomically characterized (Ott et al, Nature, 2017 PMID: 28678778) and from which subsequent serial blood draws were also collected. Only for these subjects a sufficient amount of cells were available for single-cell characterization of the intratumoral microenvironment. ]]>