ABSTRACTPURPOSECancer neoantigens are important targets of cancer immunotherapy. Neoantigen vaccines have the potential to induce or enhance highly specific antitumor immune responses with minimal risk of autoimmunity. We have developed a neoantigen DNA vaccine platform capable of efficiently presenting both HLA class I and II epitopes. To test the safety, feasibility and efficacy of this platform, we performed a phase 1 clinical trial in triple negative breast cancer patients with persistent disease following neoadjuvant chemotherapy, a patient population at high risk of disease recurrence.EXPERIMENTAL DESIGNExpressed somatic mutations were identified by tumor/normal exome sequencing and tumor RNA sequencing. The pVACtools software suite was used to identify and prioritize cancer neoantigens. Neoantigen DNA vaccines were designed and manufactured in an academic GMP facility at Washington University School of Medicine. Neoantigen DNA vaccines were administered via electroporation following completion of standard of care therapy. Safety was measured by clinical and laboratory evaluation. Immune responses were assessed by ELISPOT, flow cytometry and TCR sequencing.RESULTS18 subjects received three doses of a personalized neoantigen DNA vaccine encoding on average 11 neoantigens per patient (range 4-20). The vaccinations were well tolerated with limited adverse events, primarily related to injection site reactions. Neoantigen-specific immune responses were induced in 16/18 patients as measured by ELISPOT and flow cytometry. At a median follow-up of 36 months, progression-free survival was 87.5% (95% CI: 72.7-100%) in the cohort of vaccinated patients compared to 49% (95% CI: 36.4-65.9%) in a cohort of institutional historical control patients (p=0.011).CONCLUSIONSNeoantigen DNA vaccines are safe, feasible, and capable of inducing a neoantigen-specific immune response. There is preliminary evidence of improved disease-free survival compared to historical controls.

Background: Neoantigens result from somatic mutations present in cancers but not normal tissue.Neoantigens appear to play an important role in cancer immunotherapies and represent an attractive target for cancer vaccines.Methods: Following IRB and FDA approval, a phase Ib clinical trial testing the safety and immunogenicity of a neoantigen DNA vaccine in pancreatic cancer opened for enrollment (NCT03122106).Nonsynonymous mutations were identified using tumor/normal whole-exome sequencing, and gene expression in the tumor at the mRNA level was verified using cDNA-capture sequencing.Candidate neoantigens were identified and prioritized using the pVACseq suite of computational tools.Patients who underwent surgical resection and completed adjuvant chemotherapy without recurrent disease received a neoantigen vaccine at monthly

Introduction: We sought to establish the clinical relevance of metastatic disease in the axillary lymph nodes of patients with clinically node-negative breast cancer, as detected by axillary ultrasound (AUS), fine needle aspiration biopsy (FNAB), and real-time reverse transcription polymerase chain reaction (RT-PCR). Methods: Eighty patients with clinically node-negative breast cancer were enrolled in a prospective study. Patients underwent AUS to evaluate lymph node morphology as either “normal” or “suspicious” by standard criteria (generalized or focal thickening of the cortex, disparity in size of one or more lymph nodes compared with others, rounded appearance, and effacement of the lymph node fatty hilum). Patients with “normal” AUS underwent sentinel lymph node biopsy (SLNB) with FNAB intraoperatively. Patients with “suspicious” AUS underwent AUS-guided FNAB. FNAB specimens were analyzed by multimarker, real-time RT-PCR (mam, mamB, muc1, PSE, CK19, PIP, EpCAM, TFF1) and compared to final pathology. Results: In patients with a “normal” AUS (n=40), 34 were node-negative on final pathology, while 6 were node-positive. All 6 patients with node-positive disease had a positive marker profile. Of 34 patients with node-negative disease, 31 (91%) had a negative marker profile, while 3 (9%) had a positive marker profile. In patients with a “suspicious” AUS (n=40), 28 (70%) had positive cytopathology and histopathology. Twenty-three of 28 also had a positive marker profile, while 5 patients had a negative marker profile. Twelve of 40 patients with “suspicious” AUS (30%) had negative cytopathology. Five were node-positive on final pathology; 4 had a positive marker profile and 1 had a negative marker profile. Seven patients were node-negative on final pathology; 2 had a positive marker profile and 5 had a negative marker profile. Mean size of lymph node metastasis detected by the panel was 7.2 mm (range 3 mm - 1.7 cm). A positive marker profile was associated with traditional indicators of prognosis, including histologic grade, estrogen and progesterone receptor and Her2neu status, and increasing tumor size (p<0.05 for each). The overall sensitivity and specificity of AUS, FNAB, and RT-PCR in predicting the final histopathologic status of the axilla was 85% and 88%, respectively. Conclusion: This is the first report to demonstrate that real-time RT-PCR analysis of FNAB specimens is feasible in predicting the final lymph node status in patients with clinically node-negative breast cancer. Over-expression of breast-cancer associated genes correlates with traditional indicators of disease prognosis.