60. Panning for neoantigens to demonstrate feasibility of neoantigen vaccines in canine melanoma

Aly Abdelkareem

Jeffrey Bryan

Dr. Jeffrey Bryan earned a Bachelor of Science degree in veterinary science from the University of California – Davis in 1991.  He received his D.V.M. from the University of California – Davis in 1993. He worked as an Associate Veterinarian from 1993-1995 and served as Medical Director from 1995-2002 of the Irving Street Veterinary Hospital in San Francisco, CA.  Bryan then completed a medical oncology residency, a Masters of Biomedical Sciences, and a PhD in Pathobiology at the University of Missouri.  He received certification by the American College of Veterinary Internal Medicine in Oncology 2005.  He is the Director of the Tom and Betty Scott Endowed Program in Veterinary Oncology, the Director of PET Imaging Center of the University of Missouri, Associate Department Chair for Research, and the Associate Director of Comparative Oncology for Ellis Fischel Cancer Center. Dr. Bryan’s research focuses on comparative examination of cancers in companion animals to better understand cancers in all species. His particular areas of interest are targeted imaging and therapy, epigenetics, and immunotherapy of cancers.  He directs the PET Imaging Center, which seeks to develop novel PET imaging agents for cancer diagnosis, localization, and prognostication.  He studies DNA methylation of canine non-Hodgkin lymphoma.  He studies immunotherapy in companion dogs including investigating fetal microchimerism.


Jeffrey Bryana, Zachary Skidmoreb, Hansjorg Rindta, Shirley Chuc, Brian Fiskb, Catrina Fronickd, Robert Fultond, Mingyi Zhoue, Nathan Bivense, Brian Mooneyf, Pei Liuf, Carol Reineroa, Malachi Griffithb, Obi L. Griffithb

aUniversity of MO, Columbia, MO, USA; bWashington University School of Medicine, St. Louis, MO, USA; cUniversity of MO, Wentzville, MO, USA; dMcDonnell Genome Institute, St. Louis, MO, USA; eDNA Core, University of MO, Columbia, MO, USA; fProteomics Core, University of MO, Columbia, MO, USA

Canine malignant melanoma (CMM) mimics human melanoma in invasiveness, metastatic behavior, and limited survival. Novel immunotherapies could target CMM neoantigen expression to dissect mechanisms of success and failure in a naturally occurring model of cancer. Tools to predict and validate canine MHC I presentation of neoantigens must be optimized to select candidate vaccine peptides.

Tissues and a cell line from a dog responding in a trial of an autologous deglycosylated melanoma vaccine were selected. Nucleic acids were extracted for WES and RNAseq. Expressed protein-coding sequence mutations were identified by strelka, varscan, mutect, and pindel. DLA allele was inferred by pseudo-alignment of RNA against known sequences and confirmed by clinical assay. Candidate neoantigens were identified with pVACtools. Membrane-bound MHC I was purified using mAb H58A. Weak acid-eluted MHC I- bound peptides were analyzed with mass spectrometry, and peptide sequences inferred by MSGFplus.

Neoantigens were predicted with strong binding affinity to DLA 88*002:01. Peptides eluted ranged from 7-16 AA with nonamers being the mode and the vast majority ranging from 9-12 AA. Candidate neoantigen sequences were compared to eluted peptides and vaccine candidates selected with highest predicted binding affinity and strongest support in the MS data.

Human MHC I typing and binding affinity software tools can be modified to predict canine MHC I binding affinity. Predicted neoantigens were confirmed by presence in peptides eluted from cells derived from the patient’s tumor. These tools will be used in future immunotherapy studies in companion dogs with melanoma as a model for humans.