Exome Sequencing to Predict Neoantigens in Melanoma

Abstract

The ability to use circulating peripheral blood cells and matched tumor sequencing data as a basis for neoantigen prediction has exciting possibilities for application in the personalized treatment of cancer patients. We have used a high-throughput screening approach, combining whole-exome sequence data, mRNA microarrays, and publicly available epitope prediction algorithm output to identify mutated proteins processed and displayed by patient tumors and recognized by circulating immune cells. Matched autologous melanoma cell lines and peripheral blood mononuclear cells were used to create mixed lymphocyte tumor cell cultures, resulting in an expansion of tumor-reactive T cells to use for mutated peptide screening. Five patients were investigated, three of whom had a durable complete response (CR; 15þ years) in an autologous melanoma-pulsed dendritic cell clinical trial. We identified seven mutated antigens in total that stimulated T-effector memory cells in two of the five patients. While the procedure did not result in clinically applicable neoantigens for all patients, those identified were likely important in tumor clearance, leading to durable CR. The nature of the screening process allows results to be obtained rapidly and is easily applicable to a wide variety of different tumor types.

Twelve-year survival and immune correlates in dendritic cell–vaccinated melanoma patients

“…This then results in epitope spreading to other antigens, including mutated ones, which are currently considered critical rejection antigens. Interestingly, the standard DC vaccine as used in our study (i.e., cocktail-matured monocytederived DCs), but loaded with dying autologous tumor cells in 2 small trials (70,71), also resulted in longterm survival and, as recently shown in neo-epitope-specific T cells (81), underscoring the immunogenicity of this simple yet highly standardized nontoxic DC vaccine.…”

The Prediction and Function of Neoantigen in Oncobiology

“…To identify neoantigens, sequencing only the exome can dramatically reduce the cost and minimize the complexity of data analysis [19]. Now, whole-exome sequencing (WES) combined with RNA sequencing (RNA-Seq) and epitope prediction method was proved to be an efficient approach [3,20].…”

“…So identification of neoantigen is a pivotal work in both fundamental studies and clinical immunotherapies. With the fast development of next generation sequencing (NGS) and mass spectrometry technology, neoantigens can be indirectly predicted from genome research by generating high-throughput sequencing data or directly identified by LC-MS/MS in an unbiased manner [3,4].…”

CIMT 2016: Mechanisms of efficacy in cancer immunotherapy — Report on the 14th Annual Meeting of the Association for Cancer Immunotherapy May 10–12 2016, Mainz, Germany

“…Immunogenicity of the DC vaccine was shown for shared antigens as well as neoepitopes. Despite the current dogma that a high mutational load enhances the chances for a good prognosis, in patients vaccinated with DCs loaded with autologous tumor, melanoma-reactive T cells recognized not only neoantigens 18,19 . In order to not restrict immune responses to next generation sequencing (NGS)-predicted neoepitopes or defined shared tumor antigens but take advantage of the total antigenic repertoire, DCs were transfected by the Erlangen group with PCR-amplified autologous total tumor RNA and are currently being tested in a randomized, multicenter phase III clinical trial of monosomy 3-positive uveal melanoma (NCT01983748), a highly metastatic disease with no effective standard therapy, few mutations and high resistance to checkpoint blockade.…”