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Table 2 Putative neoepitopes encoding mutations found recurrently in hematological cancers

From: Isolation of T cell receptors targeting recurrent neoantigens in hematological malignancies

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%)
  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