Spatiotemporal homogeneity and distinctness of the T‐cell receptor β‐chain repertoires in Epstein–Barr virus‐associated primary and metastatic nasopharyngeal carcinomas

Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV)‐associated lymphoepithelioma. The aim of this study was to characterize the homogeneity and distinctness of the T‐cell repertoires within and between primary and metastatic NPCs. We used ultra‐deep sequencing of the hypervariably rearranged antigen‐binding CDR3 regions of T‐cell receptor beta (TCRbeta) to comprehensively profile the T‐cell repertoires in NPC patients receiving definitive chemoradiotherapy with long‐term follow‐up. We observed not only various spatially heterogeneous patient‐specific TCRbeta clone compositions that changed with time but also several commonly enriched TCRbeta subclones that were constantly shared between primary NPCs in the head and neck regions, locally recurrent tumors after treatment and later‐developed distant metastatic tumors in the liver, lung and bone. Comparison of the overlap frequency of the T‐cell clonality between TCRbeta repertoires enabled us to calculate the pairwise genetic distance between primary NPCs of different patients and different sites of metastatic or recurrent NPCs. The constructed NPC phylogeny clearly differentiated the low‐risk patients without relapse from the high‐risk patients with distant metastasis after chemoradiotherapy. In contrast to the rather low frequency of nonsilent somatic mutations in NPC cells, the degrees of similarity and divergence of NPC‐infiltrating lymphocyte TCRbeta repertoires among different patients showed prognostication. Moreover, the persistent presence of commonly NPC‐shared in‐frame TCRbeta CDR3 gene sequences spatiotemporally identified in the NPC‐infiltrating lymphocytes within varied EBV‐positive NPCs and their metastases suggest the existence of frequently shared epitopes of neoantigens virally or nonvirally displayed on cancer cells, thereby providing opportunities for the development of precisely tumor‐targeted immunotherapy for distant metastasis. What's new? Epstein–Barr virus‐associated nasopharyngeal carcinoma (NPC) shows marked infiltration of T lymphocytes around and within the tumors, but the relevance of this infiltration to disease outcome is not clear. Here the authors profiled the T‐cell receptor β‐chain (TCRbeta) repertoires from different patients with NPCs and show that their phylogeny clearly differentiated low‐risk patients without relapse from high‐risk metastatic patients. The authors propose that the persistent presence of the TCRbeta subclones found in primary and later‐develo