Stanford neoantigen pipeline finds Ig targets in lymphoma

In a study published Wednesday in Nature, a Stanford University team's neoantigen identification pipeline showed patient-specific, or "idiotypic," immunoglobulin peptides were presented on human leukocyte antigen (HLA) class II molecules in mantle cell lymphoma (MCL) patients. The authors said the neoantigens could serve as a starting point for personalized cancer vaccines or T cell therapies.

The pipeline involved collecting pre-treatment tumor and non-tumor tissue samples from each patient, then using mass spectrometry to identify peptides bound to all HLA class I alleles and major histocompatibility complex class II DR (HLA-DR) from the tumor samples. Those peptides were cross-referenced to a list of mutant tumor epitopes identified via DNA sequencing of tumor and non-tumor samples, resulting in a list of neoantigens -- mutant epitopes presented to T cells on HLA molecules. ...