Activation of MCL with a TLR9 agonist alters MHC presentation of the lymphoma immunoglobulin. Equal numbers of MCL cells were incubated for 72 hours with or without cytosine guanine dinucleotide (CpG), a TLR9 agonist. (A) Flow cytometry assessment of antigen-presentation molecule expression with (orange) and without (blue) CpG treatment. Two representative cases of MCL are shown. (B) MHC-I– and MHC-II–bound ligands were purified and analyzed by LC and MS. The total number of unique MHC-I (left) and MHC-II (right) associated peptides is shown with and without CpG treatment. (C) The number of unique MHC-I– and MHC-II–bound ligands derived from the lymphoma immunoglobulin (Ig) constant and variable regions is shown. (D) Kernel density violin plots of the estimated normalized abundance of MHC-II–bound peptides recovered from unstimulated and CpG-treated MCL. (E) Mapping of MHC-I and MHC-II presentation of the MCL immunoglobulin is shown. MHC ligands recovered from CpG-treated cells and untreated cells are separated by a dashed line. ND, not detected; NPA, normalized protein abundance.