The isolation and characterisation of MHC-presented peptides from CML-derived cell-lines, with a focus on post-translational modification

Phosphorylation is a key regulator of protein function and activity, and aberrant kinase activity is implicated in a wide range of malignancies, of which the bcr:abl fusion kinase found in chronic myeloid leukaemia is a classic example. As phosphopeptides are known to be presented by both the MHC class-I and class- II pathways, against which specific CD4+ and CD8+ T cell responses may be generated, study of MHC-presented phosphopeptides may reveal unique cancer antigens with direct links to the neoplastic state. Mild acid cell-surface elution is a rapid and effective method for MHC class-I peptide capture, though complicated by contamination with non-MHC peptides and poor downstream compatibility, especially with IMAC, a popular method for phosphopeptide enrichment. As an alternative to the citrate-phosphate elution buffer, a TMA-formate elution buffer is proposed. This was developed for IMAC compatibility, and osmotically balanced and supplemented to minimise cell lysis, (assessed by several assays) and used with a pH 5.5 prewash to reduce non- MHC peptide contamination. MALDI-MS/MS of MHC class-I peptides from K562- A3 cells found a sequence with high homology to a known cancer antigen as the common peak for both citrate-phosphate and TMA-formate eluted cells.