No abstract

BackgroundTumors acquire numerous mutations during development and progression. These mutations give rise to neoantigens that can be recognized by T cells and generate antibodies. Tumor mutational burden (TMB) is correlated with, and has often been used as a surrogate of, neoantigen load, although that relationship is different depending on cancer types. Recent studies reported correlations between higher TMB and better overall survival after immune checkpoint blockade therapies in bladder, colorectal, head and neck, and lung cancers but not in breast cancer. On the other hand, the relationship between neoantigen load and survival has been controversial in literature. Higher neoantigen load has been linked to better overall survival in ovarian cancer and melanoma, but worse survival in multiple myeloma. Recently, no clear associations were found between neoantigen load and survival in 33 cancer types although only class-I restricted neoantigens were included.Materials and MethodsWe developed a bioinformatics workflow, REAL-neo, for identification, quality control (QC), and prioritization of both class-I and class-II human leukocyte antigen (HLA) bound neoantigens that arise from tumor somatic single nucleotide mutations (SNM), small insertions and deletions (INDEL), and gene fusions. The correlations between TMB and neoantigen load per sample were calculated using Pearson Correlation Coefficient. TMB and neoantigen load comparisons between various groups were performed using Student’s t-test. The survival analyses were performed using the Cox proportional hazards models while correcting for covariates.ResultsWe applied REAL-neo to 835 primary breast tumors in the Cancer Genome Atlas (TCGA) and performed comprehensive profiling and characterization of the predicted neoantigens. SNMs contributed to only 6.25% of the total neoantigens (# of class-I vs. class-II neoantigens = 1: 3.5); INDELs accounted for 57.17% of the total (class-I : class-II= 1:2), and gene fusions were responsible for 36.58% of the total (class-I : class-II = 1:2.2). TMB were positively correlated with total and each sub-categories of neoantigen load (class I: SNM: r = 0.59, p < 2.2E-16; INDEL: r = 0.28, p < 2.2E-16; gene fusion: r = 0.26, p = 2.01E-11; class II: SNM: r = 0.47, p < 2.2E-16; INDEL: r = 0.16, p = 1.7E-05; gene fusion: r = 0.31, p = 4.37E-13). The vast majority (99.75%) of the predicted neoantigens occurred in ≤1% of the cases and 83.76% were patient-specific found in one patient only. Tumors with somatic and germline functional mutations in BRCA1 or BRCA2 genes had higher TMB (p = 2.76E-06) and overall neoantigen load (p = 0.009). Lower HLA class-I and class-II restricted neoantigen loads from SNM and INDEL were found to predict worse overall survival independent of TMB, breast cancer subtypes, tumor infiltrating lymphocyte (TIL) levels, tumor stage, and age at diagnosis (class-I: HR = 1.81, p = 0.04; class-II: HR = 1.89, p = 0.042).ConclusionsOur study highlighted the importance of accurate and comprehensive neoantigen profiling and QC, and is the first to report the predictive value of neoantigen load for overall survival in breast cancer. This work was support by the State of Florida Cancer Center Grant, the bioinformatics program of Mayo Clinic Center for Individualized Medicine, and the Mayo Clinic inter-SPORE development grant.Disclosure InformationY.W. Asmann: None. Y. Ren: None. D.P. Wickland: None. V. Sarangi: None. S. Tian: None. J.M. Carter: None. A.S. Mansfield: None. M.S. Block: None. M.E. Sherman: None. K.L. Knutson: None. Y. Lin: None.

Background: Recent studies have indicated that vaccination can protect against cancer development. One key aspect of developing vaccines is circumventing peripheral tolerance by identifying subdominant epitopes that are unique to the deregulated tumor microenvironment. While existing subdominant epitope vaccines are showing efficacy in preventing cancer, these vaccines are applicable only for subsets of patients with specific HLA subtypes. Therefore, we recently developed a degenerate HER2 subdominant epitope-based vaccine that should be useful in approximately 85% of all patients. The vaccine consists of a pool of four HLA-DR-restricted 15-amino acid epitopes (p59, p88, p422, and p885) that are naturally processed and are designed to elicit helper T cell immunity, the cornerstone of immune surveillance. Here we present Phase I trial results of this multi-peptide HER2 vaccine. Methods: Eligible women had HER2+ breast cancer (Stages II-III) and had completed standard treatment (i.e. surgery, chemotherapy, and trastuzumab) at least 90 days prior to enrollment and were rendered disease free. Vaccine included the above epitope pool along with adjuvant GM-CSF. Patients were vaccinated six times over six months and were monitored for toxicity at each visit. Peripheral blood samples were collected for immune responses evaluating for T cell and antibody immunity. Endpoints were safety and immunogenicity leading to the development CD4 helper T cells that recognized naturally-processed HER2. Results: Twenty-two subjects (age 33 to 69 years) were enrolled. At the present analysis, 21 have completed all 6 vaccination cycles; one patient withdrew after developing a grade 1 injection site reaction during the first vaccination cycle. Twenty patients have had LVEF measured after vaccination; only 2 patients had an LVEF drop of 10% or more but remained in the normal LEVF range. One severe toxicity was reported: a grade 3 INR increase considered unrelated to treatment. Mild to moderate (grade 1-2) toxicities included injection site reactions, fatigue, and white blood cell count decreases. All patients were alive at analysis and only one experienced a recurrence (median follow-up 507 days, range 22 – 844). Twenty patients have had immune response assessments. Vaccine induced T cell immunity was observed in 94% of patients to p59, in 94% of patients to p88, in 82% of patients to p422, and in 74% of patients to p885. Importantly, T cell immunity to naturally processed HER2 proteins occurred in 94% of patients. The mean number of T cells specific for each peptide, post vaccination, ranged from 349–528 T cells per million peripheral blood mononuclear cells (PBMCs). The mean number of T cells specific for whole HER2 protein was 783 T cells per million PBMCs compared to a mean of 898 T cells/million PBMCs specific for the foreign tetanus toxin. In contrast to T cell responses, modestly increased antibody immunity to HER2 occurred in 35% of patients, consistent with the T cell-inducing design of the vaccine. Conclusion: Our results show that it is possible to develop vaccines with broad HLA coverage that circumvent natural tolerance and induce tumor antigen-specific immunity in the vast majority of patients. Citation Format: Knutson KL, Kalli KR, Block MS, Hobday TJ, Padley DJ, Erskine CL, Dockter T, Suman VJ, Wilson G, Degnim AC. Robust generation of T cell immunity to HER2 in HER2+ breast cancer patients with a degenerate subdominant HLA-DR epitope vaccine. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-11-02.

No abstract