Table 2.
Putative neoepitopes encoding mutations found recurrently in hematological cancers
| Protein | Mutation | Putative epitope | Peptide | HLA-Restriction | Predicted HLA binding affinity (nM) | Hematopoietic and Lymphoid Cancer Frequencies |
|---|---|---|---|---|---|---|
| CALR | K385Nfs*47 | RPRTSCREA | CALR-REA | HLA-B*07:02 | 12 | Essential thrombocythemia (31.1%), Myelofibrosis (27.3%) |
| SPARPRTSC | CALR-SPA | HLA-B*07:02 | 22 | |||
| RMRRTRRKM | CALR-RMR | HLA-B*07:02 | 56 | |||
| RPRTSCREAC | CALR-REAC | HLA-B*07:02 | 23 | |||
| RMMRTKMRMR | CALRp2 | HLA-A*03:01 | 41 | |||
| KMRMRRMRR | CALRp7 | HLA-A*03:01 | 35 | |||
| RTRRKMRRK | CALRp15 | HLA-A*03:01 | 54 | |||
| FBXW7 | R465C | TVCCMHLHEK | TVC | HLA-A*11:01 | 29 | T-ALL (15.4%), Precursor T cell lymphoblastic lymphoma (15.6%) |
| STVCCMHLHEK | STV | HLA-A*11:01 | 65 | |||
| HTSTVCCMHLH | HTS | HLA-A*11:01 | 495 | |||
| R465H | STVHCMHLH | STVH | HLA-A*11:01 | 78 | ||
| TVHCMHLHEK | TVH | HLA-A*11:01 | 43 | |||
| P53 | R248Q | SSCMGGMNQR | NQR | HLA-A*11:01 | 177 | Mantle cell lymphoma (9.1%), B-ALL (6.9%), T-ALL (8.6%), Follicular lymphoma (18.5%), AML (7%), MDS (7.3%), CLL (10.9%), T cell lymphoma (18.6%), Burkitt’s lymphoma (18%), Diffuse large B cell lymphoma (12.6%) |
| R248W | SSCMGGMNWR | NWR | HLA-A*11:01 | 320 | ||
| MyD88 | L265P | RPIPIKYKAM | RPI | HLA-B*07:02 | 20 | MGUS (46.8%), Waldenström’s macroglobulinaemia (86.3%), Diffuse large B cell lymphoma (14.4%) |
| SPGAHQKRPI | SPG | HLA-B*07:02 | 40 | |||
| IDH2 | R140Q | SPNGTIQNIL | SPN | HLA-B*07:02 | 72 | AML (9.7%), Angioimmunoblastic T cell lymphoma (24.1%) |
| DNMT3A | R882H | VSNMSHLAR | VSN | HLA-A*11:01 | 61 | AML (20.4%), MDS (9.1%), T cell lymphoma (25.7%), |
| STAT3 | Y640F | QIQSVEPFTK | QIQ | HLA-A*11:01 | 60 | T cell large granular lymphocytic leukaemia (34.3%), Adult T-cell leukemia/lymphoma (21.1%) |
The catalogue of somatic mutations in cancer (COSMIC) was used to identify mutations found recurrently in hematological cancers. The MHC binding algorithm NetMHC3.4 was utilized to identify putative neoepitopes encoding these mutations that were predicted to bind strongly to common European Caucasoid HLA class I alleles. T-ALL T cell acute lymphoblastic leukemia, B-ALL B cell acute lymphoblastic leukemia, AML acute myeloid leukemia, MDS myelodysplastic syndrome, CLL chronic lymphocytic leukemia, MGUS monoclonal gammopathy of undetermined significance