Characterization of the T‐cell receptor beta chain repertoire in tumor‐infiltrating lymphocytes

Abstract

Tumor‐infiltrating lymphocytes (TILs) are direct effectors of tumor immunity, and their characterization is important for further development of immunotherapy. Recent advances in high‐throughput sequencing technologies have enabled a comprehensive analysis of T‐cell receptor (TCR) complementarity‐determining region 3 (CDR3) sequences, which may provide information of therapeutic importance. We developed a high‐fidelity target sequencing method with the ability for absolute quantitation, and performed large‐scale sequencing of TCR beta chain (TCRB) CDR3 regions in TILs and peripheral blood lymphocytes (PBLs). The estimated TCRB repertoire sizes of PBLs from four healthy individuals and TILs from four colorectal cancer tissue samples were 608,664–1,003,098 and 90,228–223,757, respectively. The usage of J‐ and V‐regions was similar in PBLs and TILs. Proportions of CDR3 amino acid (aa) sequences occupying more than 0.01% of the total molecular population were 0.33–0.43% in PBLs and 1.3–3.6% in TILs. Additional low coverage sequencing of 15 samples identified five CDR3 aa sequences that were shared by nine patients, one sequence shared by 10 patients, and one sequence shared by 12 patients. The estimated size of the TCRB repertoire in TILs was significantly smaller than that in PBLs. The proportion of abundant species (>0.01%) in TILs was larger than that in PBLs. Shared CDR3 aa sequences represent a response to common antigens, and the identification of such CDR3 sequences may be beneficial in developing clinical biomarkers.

Biophysicochemical Motifs in T-cell Receptor Sequences Distinguish Repertoires from Tumor-Infiltrating Lymphocyte and Adjacent Healthy Tissue

“…Finding biophysicochemical TCRb motifs that, within a cancer type, are shared across the TILs repertoires of all patients but are largely absent from healthy tissue repertoires is consistent with the hypothesis that we are detecting TCR with specificity for a tumorassociated antigen that is shared between patients. We are not the first to hypothesize that patients may have shared TCRs responding to a common antigen, nor are we the first to look for the corresponding TCRs in colorectal and breast cancer TILs (7,10,25,26,41,42). To address this hypothesis, other investigators have searched for CDR3 amino acid sequences that were shared between multiple patient TILs repertoires (7,10,25,26,41,42).…”

“…Therefore, we reasoned that patients with the same cancer type or subtype may have cytotoxic T-cell responses against a common set of antigens. Indeed, there is evidence for shared immunoreactivity, as well as for shared TCR sequences (4)(5)(6)(7)(8)(9)(10). We further reasoned that if these T-cell responses could be detected, particularly early in the disease course, they could serve as an important addition to the suite of methods under development for the early detection of cancer.…”

A comprehensive study of immunology repertoires in both preoperative stage and postoperative stage in patients with colorectal cancer

“…In comparison with CDR3 length distribution between preoperative colorectal patients and healthy controls showed there was significant difference between these two groups. This result again elucidated the immune repertoire effect on colorectal cancer patients which corresponds to the similar finding of previously reported CRC immune correlation study 1 (Li et al, ; Nakanishi et al, ).…”

Determination of the complexity and diversity of the TCR β‑chain CDR3 repertoire in bladder cancer using high‑throughput sequencing

“…The results suggested that the diversity of cancer tissues was lower than that of paracancerous tissues. Nakanishi et al similarly demonstrated that the proportion of CDR3 aa sequence accounting for >0.01% of the total molecular population in the TILs is significantly higher than in peripheral blood lymphocytes in colorectal cancer (15). In addition, Han et al revealed that the HEC ratio of the TCRβ chain CDR3 sequence in carcinoma tissues is significantly higher than in the adjacent tissues from patients with hepatitis B virus-associated hepatocellular carcinoma (21).…”

“…High-throughput sequencing (HTS) is a novel method that can profile the TCR repertoire and analyse the adaptive immune response; therefore allowing the study of TCR repertoire diversity at a greater depth than previously (11,12). Notably, this technology has been used to investigate and monitor the implication of TCR in tumour immunity through large-scale sequencing of CDR3 (13–15). The present study aimed to evaluate the complexity and diversity of cancer tissues compared with paracancerous tissues by amplifying the CDR3 of TCRs using multiplex polymerase chain reaction (PCR) and HTS.…”