Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data

Qiang Gong,Timothy C Greiner,Francesco Abate,Wing C Chan,Chao Wang,Jo-Heon Kim,Weiwei Zhang,Timothy W Mckeithan,Adam Cornish,Raul Rabadan,Giorgio G Inghirami,Xin Wang,Yang Hu,Javeed Iqbal

doi:10.1038/s41598-017-11310-0

Abstract

T-cell clonality of peripheral T-cell lymphoma (PTCL) is routinely evaluated with a PCR-based method using genomic DNA. However, there are limitations with this approach. The purpose of this study was to determine the utility of RNA-seq for assessing T-cell clonality and T-cell antigen receptor (TCR) repertoire of the neoplastic T-cells in 108 PTCL samples. TCR transcripts, including complementarity-determining region 3 (CDR3) sequences, were assessed. In normal T cells, the CDR3 sequences were extremely diverse, without any clonotype representing more than 2% of the overall TCR population. Dominant clones could be identified in 65 out of 76 PTCL cases (86%) with adequate TCR transcript expression. In monoclonal cases, the dominant clone varied between 11% and 99% of TCRβ transcripts. No unique Vα or Vβ usage was observed. Small T-cell clones were often observed in T- and NK-cell tumors in a percentage higher than observed in reactive conditions. γ chain expression was very low in tumors expressing TCRαβ, but its expression level was high and clonality was detected in a TCRγδ expressing tumor. NK cell lymphoma (NKCL) did not express significant levels of TCR Vβ or Vγ genes. RNA-seq is a useful tool for detecting and characterizing clonal TCR rearrangements in PTCL.

Highlights

Each mature T-cell expresses a unique T-cell antigen receptor (TCR) which is a combination of either αβ chains or γδ chains
Among the biallelic clonal TCRα or TCRβ transcripts, the ratio between the top 2 clones (C1/C2) is significantly higher when the second-largest clone contains nonproductive complementaritydetermining region 3 (CDR3) sequences (p = 0.0008, Welch two sample t-test; Figure 1), which may be due to the nonsense-mediated mRNA decay mechanism[27]
The clonal rearrangement of TCR genes is useful in supporting the diagnosis of a T-cell lymphoma

Summary

Introduction

Each mature T-cell expresses a unique T-cell antigen receptor (TCR) which is a combination of either αβ chains or γδ chains. The TCRα and β loci are too complex and cumbersome for routine DNA clonal analyses, but flow cytometry can detect TCRβ gene usage and imply clonality[9, 10]. These approaches are limited by the lack of sequence information. RNA-seq provides information about the usage of variable (V), diversity (D) if applicable, and joining (J) regions of the TCRα, β, γ, and δ chains and yields the unique sequence of the CDR3, which includes the V(D)J junctions as well as N-nucleotides added by terminal deoxynucleotidyl transferase (TdT). We report here the utility of RNA-seq in assessing T-cell clonality and in analyzing the TCR repertoire in different PTCL subtypes

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Conclusion