Tumor-infiltrating lymphocytes in colorectal tumors display a diversity of T cell receptor sequences that differ from the T cells in adjacent mucosal tissue

Abstract

Tumors from colorectal cancer (CRC) are generally immunogenic and commonly infiltrated with T-lymphocytes. However, the details of the adaptive immune reaction to these tumors are poorly understood. We have accrued both colon tumor samples and adjacent healthy mucosal samples from 15 CRC patients to study lymphocytes infiltrating these tissues. We apply a method for detailed sequencing of T-cell receptor (TCR) sequences from tumor infiltrating lymphocytes (TILs) in CRC tumors at high throughput to probe T-cell clones in comparison to the TCRs from adjacent healthy mucosal tissue. In parallel, we captured TIL counts using standard immunohistochemistry. The variation in diversity of the TIL repertoire was far wider than the variation of T-cell clones in the healthy mucosa, and the oligoclonality was higher on average in the tumors. However, the diversity of the T-cell repertoire in both CRC tumors and healthy mucosa was on average 100-fold lower than in peripheral blood. Using the TCR sequences to identify and track clones between mucosal and tumor samples, we determined that the immune response in the tumor is different than in the adjacent mucosal tissue, and the number of shared clones is not dependent on distance between the samples. Together, these data imply that CRC tumors induce a specific adaptive immune response, but that this response differs widely in strength and breadth between patients.

The T-cell Receptor Repertoire Influences the Tumor Microenvironment and Is Associated with Survival in Aggressive B-cell Lymphoma

“…DLBCL nodes showed reduced levels of percentage of total T-cells but a more clonal and less diverse T-cell population compared with non-diseased nodes. These findings are consistent with the differences in TCR repertoire seen between colon cancer biopsies and adjacent non-diseased mucosa (24). In diseased nodes, elevated checkpoint levels were associated with higher T-cell diversity (entropy).…”

Identification of shared TCR sequences from T cells in human breast cancer using emulsion RT-PCR

“…Comprehensive analysis of V-beta use in healthy individuals does not show dominance in TRBV7 use (26,29). Furthermore, it has been described previously that specific V-beta subsets are enriched within the tumor (29,30), and analysis of colorectal tumors has shown that only one-third of shared V-beta TCRs are from the TRBV7 family (13). However, use of V-region primers designed to bind closer to the 5′ end of the variable genes, coupled with the rapid development of sequencers delivering greater read length and depth, will be instrumental in expanding the limits and sensitivity of emulsion RT-PCR.…”

“…The alpha-and beta-chains of the TCR undergo V(D)J recombination and heterodimerize in the thymus, resulting in a diverse T-cell repertoire that specifically recognizes peptide-MHC complexes. Many studies have analyzed the alpha-and beta-chains of TIL TCRs separately using highthroughput sequencing to describe the diversity of TILs (10)(11)(12)(13). Pairs are readily identified after expansion of T-cell clones, although culture of T cells can lead to substantial skewing of the repertoire (14), which may select for T cells of varied affinity or avidity (15).…”

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

“…These values are smaller than the degree of tumor and normal tissue overlap in ESCC, which accounted for approximately 25% of samples, but similar to the degree of tumor and adjacent mucosal tissue overlap in colorectal tumors, which ranged from 0.2 to 38%. 29,30 This difference might be related to the different starting materials and approaches for TCR profiling. Although starting from genomic DNA and multiplexed PCR strategies is relatively easier for performing, these techniques are associated with significant bias.…”

“…Studies of other tumors, such as clear cell renal cell carcinomas and colorectal tumors, have indicated that TCR diversity in tumor tissues is much lower compared with adjacent non-invasive renal tissues or adjacent mucosal tissues. 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.…”