Direct identification of T cell epitopes in cancer tissues

Abstract

Prediction of tumor-specific T cell epitopes is an important part of cancer immunotherapies. In the past, tumor-specific T cell epitopes were identified by mapping the epitopes on the known cancer-testis antigens and tumor-associated antigens or antigens that react to the T cells induced by the cancer vaccine therapy. More recently, in silico prediction of mutation-associated neoepitopes from the whole-exome sequencing (WES) results has become another approach. However, although this approach often identifies many predicted peptides, only few have been shown to be immunogenic. Mass spectrometry (MS) has also been used to directly identify the T cell epitopes presented on tumor cell by eluting the peptides from human leukocyte antigens (HLA) class I and class II molecules. This approach of identifying neoepitopes was demonstrated to be feasible in high tumor mutation burden (TMB) tumors such as melanoma. However, identifying low-TMB-tumor-specific T cell epitopes has been challenging. Recently, Fujiwara et al. reported their successful result in identifying T cell epitopes in a low TMB tumor, namely pancreatic ductal adenocarcinoma (PDAC). Using the MS approach, they identified T cell epitopes shared by multiple pancreatic cancer patients with different HLA types. Moreover, they demonstrated that the identified epitopes bound non-matched HLA molecules and induced T cell response in peripheral T cells from non-HLA-type matched patients. Their study has opened a new venue for identifying T cell epitopes in a non-immunogenic tumor such as PDAC for the design and development of vaccine and T cell therapy.