Neoantigen identification for 1956 and F244 murine MCA-sarcomas

This study was to predict neoantigens in 1956 and F244 murine MCA-sarcomas (female C57BL/6N and male 129S6 lines, respectively). Mutations were called by comparing tumor versus normal whole exome sequencing (WES) data, and filtered for expressing mutations using RNA-seq data. Out of expressing mutations, MHC class I or II neoantigens were predicted and screened by T cell reactivities (IFN-gamma ELISPOT and tetramer staining). Therapeutic vaccine confirmed an M50I mutation in Psmd6 and an R144S mutation in Cs to be the major MHC class I (H-2Kb) and II (I-Ab) neoantigens for 1956; and a G122A in Pex14 and a D2944Y mutation in Plec to be the major class I (H-2Kb) and class II (I-Ab) neoantigens for F244. Overall design: WES was performed for DNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line); or a tail of a female C57BL/6N or male 129S6 mouse (normal controls for 1956 and F244, respectively; n=1 per strain). RNA-seq was performed for RNA extracted from in vitro cultured 1956 or F244 cells (n=1 per line).