T-Cell Receptor Diversity…What Are You Missing?

Trena Cormier on November 15, 2021

The T cell receptor (TCR) is one of the distinguishing molecules of the adaptive immune system. TCRs allow mammalian immune systems to recognize and respond to foreign entities (pathogens, vaccines, and disease treatments) while preventing autoimmune & allergic responses.  How do TCRs respond both to immune challenges like infectious disease as well as treatments like cancer vaccines while recognizing the self?  The answer is T cell receptor diversity (TCR diversity).

TCR diversity happens on multiple levels. The first level of diversity is in the receptor structure itself; TCRs are transmembrane αβ or δϒ protein heterodimers.  Next, diversity is generated through genomic rearrangements of the four TCR genes, TCRα, TCRβ, TCRδ, and TRCϒ, respectively.  All TCR proteins contain Variable (V), Joining (J) and Constant (C) domains and TCRβ & TCRδ have an additional Diversity (D) domain. The Variable domain amino acid sequence of one TCR can differ from another TCR due to the many variable segments contained within the TCR gene, and that combine randomly through genomic rearrangement. A conservative estimate of the number of possible αβ T-cell receptor combinations in T cells is 1.4 million distinct molecules (1).  And that doesn’t include the possible rearrangements in the TCRδϒ molecules!

When a specific population of TCRs responds to an immune stimulus, the result is a clonal expansion of the T cells carrying the specific genomic rearrangements that generated those unique TCRs.  This increase in the RNA corresponding to the unique genomic rearrangement that generated the TCR changes the demographics of the TCR RNA population.  In other words, clonal expansion of a specific T cell lineage will lead to measurable changes in the diversity of the TCR RNA population. Therefore, TCR RNA diversity is a very informative way to measure immune system responses to disease or therapies. Basic researchers and clinical scientists may study the populations of T cells and their specific TCR RNA to identify biomarkers or perform immune profiling and cell screening (for infection, response to treatment, relapse, or further research, etc.) using T cell receptor profiling (TCR profiling).

COVID Leaves a Mark in the T Cell Receptor

Recently, Marion Moreews and colleagues (2) published a timely paper describing statistically significant differences in the TCR profile of children diagnosed with post-COVID Multisystem Inflammatory Syndrome (MIS-C) compared to the TCR profile of healthy donors & others.  This research group used different approaches and technologies: mAb T-cell Vβ repertoire staining, TCR sequencing, and direct detection of TCR variable region transcripts with a beta version of the nCounter® TCR Diversity Panel.  The researchers found that “75% of the MIS-C patients (and none of the other clinical groups) displayed T-cell receptor beta variable genes 11-2 (TRBV11-2)/Vβ21.3+ expansions”. Additionally, polyclonal Vβ21.3+ T cells were the only cells associated with the levels of Interleukin-18 (IL-18) and IL-1RA, two ILs associated with the cytokine storm that is characteristics of MIS-C and points towards a path for future studies and possible clinical interventions. The polyclonal nature of the TCR expansion identified with the TCR Diversity Panel was confirmed by TCR sequencing on an independent platform, providing a real-world, proof-of-concept of using the TCR Diversity Panel on a set of challenging, small volume pediatric samples.

T Cell Receptor Diversity and Allergies

Another study by Duncan Morgan and colleagues (3) described the use of FACS, flow cytometry, and TCR sequencing to study T cells collected from biopsies of patients with eosinophilic esophagitis (EoE). In this study, activation of allergy-specific T cells results in the upregulation of genes involved in the dysregulation of lipid metabolism, a potential mechanistic pathway across multiple allergic diseases. TCR profiling of the patient samples indicated clonal convergence of T cell lineages, and that this clonal expansion may be allergen-specific. The significance of clonal expansion is further discussed in this paper, and in another article in the same journal (4), which discusses the possibility of developing personalized allergy treatments that target the limited TCR repertoire of the pathogenic TH2 cells and their downstream activation pathways. 

The nCounter TCR Diversity Panel

There are several different TCR profiling kits and protocols available to researchers from a variety of vendors, but many of these protocols rely on enzymatic and sequencing steps which add bias, time, and expense to experiments.  The nCounter TCR Diversity Panel is unique in that it allows researchers to quickly detect shifts in TCR diversity with a simple expression assay that requires zero sequencing or enzymatic steps and can be analyzed in minutes with an automated report on the ROSALIND® platform that gives a TCR Diversity Score for each sample.

How could the TCR Diversity Panel help you distinguish between clonal and polyclonal T cell expansions?  Could you identify downstream pathways that explain disease mechanisms and provide insight into what parts of a tissue respond to a T cell stimulus?

1) Kindt TJ, Goldsby RA, Osborne BA, Kuby J. Immunology, 2007

2) Moreews M, et al,

3) Morgan D, et al,

4) Morgenstern M, et al,

For Research Use Only. Not for use in diagnostic procedures.

Post by Trena Cormier