Extended Data Figure 6: MHC-I presentation of lymphoma Ig neoantigens in the Raji lymphoma cell line.

a, Top, MHC-I binding affinity predictions were performed for all potential 9-amino-acid peptides from the Raji Ig heavy chain. The best binding affinity for an endogenous class I MHC allele is shown in black. The predicted binding to an ectopically expressed HLA-B35:01 allele is shown in red. Bottom, the Raji lymphoma cell line was transfected with the HLA-B35:01 allele. MHC-I antigen presentation profiling was performed for both the parental cell line and the B35-transfected line. Recovered peptides were matched against the Raji Ig heavy- and light-chain sequences. Positions differing from the germline variable region altered by either somatic hypermutation or V(D)J recombination are shown in red. Three peptides corresponding to Raji Ig were identified, shown in boxes. All three were only found in the B35-transfected Raji cells. Asterisks indicate peptides that were identified proteomically. b, The predicted binding IC₅₀ (nM) based on netMHCpan is shown for each recovered peptide for each of the Raji HLA alleles. Red shading indicates a predicted high-affinity interaction with the corresponding HLA allele.