T cell receptor β-chain repertoire analysis reveals intratumour heterogeneity of tumour-infiltrating lymphocytes in oesophageal squamous cell carcinoma

Abstract

Oesophageal squamous cell carcinoma (ESCC) has a generally poor prognosis, due to the lack of effective treatment methods. Immunotherapeutic approaches based on tumour-infiltrating lymphocytes (TILs) have demonstrated that durable responses are produced in some patients with solid tumours, which suggests the potential feasibility of clinical application of immunotherapy for ESCC. However, many of the basic characteristics of TILs in ESCC are poorly understood, including clonality, specificity and spatial heterogeneity of the response of TILs, which depends on the interaction between antigens and T cell receptors (TCRs). We used ultra-deep sequencing of rearranged genes in TCR β-chain (TCRβ) to profile the basic characteristics of T cells in tumour tissues (four to six regions from each tumour) as well as matched adjacent normal tissue and peripheral blood from seven patients diagnosed with primary ESCC. We found that T cell clones within ESCCs were quite different from those of the peripheral blood and even the adjacent normal tissues in general. Although there was a relatively higher degree of overlap of intratumoural TCRβ repertoires than those between the tumour and other tissues, intratumoural TCRβ repertoires were spatially heterogeneous. Due to the restricted sampling, high-throughput TCRβ sequencing could characterize the diversity and composition of a limited (compartment-dependent) fraction of the respective T cell clones in any individual ESCC, expanding our understanding of immune behaviour and immune response and shedding more light on ESCC immunotherapy. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

High-throughput T cell receptor sequencing reveals distinct repertoires between tumor and adjacent non-tumor tissues in HBV-associated HCC

“…26,27 Research on esophageal squamous cell carcinoma (ESCC) has demonstrated that the tumor tissues were not significantly more oligo-clonal than adjacent normal tissues and blood samples. 28 The discrepancies between the results of these studies and our study might be attributable to HBV infection, which might cause inflammation and necrosis in adjacent non-tumor tissues. In addition, years or decades are needed for hepatitis or cirrhosis to advance to HCC; thus, the immune environment in hepatitis B patients is not identical to that in other tumors.…”

T cell receptor repertoire profiling predicts the prognosis of HBV‐associated hepatocellular carcinoma

“…We calculated the Clonality index (1‐ (Shannon's entropy)/log2 (number of productive aa unique sequences)) and the U/T index (the number of productive unique aa sequences/the number of total productive aa sequences) to estimate the diversity of T cell clones in each sample, which were independent of sample sequencing depth 13, 22, 23…”

“…Firstly, we performed the TCR sequencing using increased sequencing reads and read length, which could contribute to obtaining a more reliable data and conclusion. Secondly, we used the U/T index and the Clonality index rather than the number of productive unique aa sequences or Shannon diversity index to assess the diversity of TCR repertoire, as the former 2 indexes could better correct the impact of uneven reads amount 13, 22, 24. Using the different sequencing depth or the different diversity indicators might be another reason for the inconsistent results.…”

T cell receptor β‐chain repertoire analysis reveals the association between neoantigens and tumour‐infiltrating lymphocytes in multifocal papillary thyroid carcinoma

“…Detailed information of TCRβ CDR3 sequencing has been described in our previous study 11 . In brief, the TCRβ CDR3 regions were amplified and sequenced using Multiplex PCR and Illumina Hiseq2500 platform (MyGenostics, Beijing, China) from 2 µg of genomic 7 DNA for each sample 12 .…”

“…To evaluate the diversity of TCRβ repertoire between any two samples, a distance metric was defined and ranged from 0 to infinity as described in our previous study 11 .…”