A new clustering approach identifies tumor-specific common TCRs with pan-cancer reactivity

Abstract

Tumor-specific T-cells are key in combating cancer as shown in adoptive cell therapy with tumor infiltrating lymphocytes (TILs) and checkpoint inhibitor therapy. Studies in many types of cancer have shown that preexisting tumor reactive T-cells are not only tumor-but typically also patient-specific, requiring personalized treatment options. For viral infections, public T-cell receptors (TCRs) with substantial sequence homologies suggest shared immune-dominant targets in human leucocyte antigen (HLA)-matched individuals. We hypothesized that also in the complex TCR repertoires of tumors subsets of tumor-specific TCRs exist that can be found in different patients with identical or near identical TCRs. This paper presents a TCR-V(D)J-sequence clustering approach identifying clusters of tumor-specific common TCRs mainly from TILs of non-small cell lung cancer (NSCLC) patients. Using two TCR-clusters as examples, we show that T-cells engineered genetically to only express those common TCRs recognized HLA-matched allogeneic tumor cell lines in a cluster typical manner. Recognition of allogeneic tumors was dependent on the HLA allele inferred by the cluster and could be blocked by HLA antibodies. In addition to NSCLC, TCR repertoire analyses in pancreatic ductal adenocarcinoma and a smaller number of breast and colorectal cancer samples revealed TCRs highly homologous or even identical to NSCLC cluster TCRs. TCR-T cells expressing TCRs from these tumors assigned to a specific cluster recognized allogeneic tumor lines in the expected cluster-typical manner. These findings suggest a pan-cancer therapeutic potential of tumor-specific common TCRs.