Sequence analysis of T-cell repertoires in health and disease

Abstract

T-cell antigen receptor (TCR) variability enables the cellular immune system to discriminate between self and non-self. High-throughput TCR sequencing (TCR-seq) involves the use of next generation sequencing platforms to generate large numbers of short DNA sequences covering key regions of the TCR coding sequence, which enables quantification of T-cell diversity at unprecedented resolution. TCR-seq studies have provided new insights into the healthy human T-cell repertoire, such as revised estimates of repertoire size and the understanding that TCR specificities are shared among individuals more frequently than previously anticipated. In the context of disease, TCR-seq has been instrumental in characterizing the recovery of the immune repertoire after hematopoietic stem cell transplantation, and the method has been used to develop biomarkers and diagnostics for various infectious and neoplastic diseases. However, T-cell repertoire sequencing is still in its infancy. It is expected that maturation of the field will involve the introduction of improved, standardized tools for data handling, deposition and statistical analysis, as well as the emergence of new and equivalently large-scale technologies for T-cell functional analysis and antigen discovery. In this review, we introduce this nascent field and TCR-seq methodology, we discuss recent insights into healthy and diseased TCR repertoires, and we examine the applications and challenges for TCR-seq in the clinic.

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire

“…Thus, instead of detecting the presence of tumor-reactive TCRs, our signature set reflects peripheral diversity that is depleted in glioma patients with high PBMC-TIL divergence (JSM Δ,corr ). These motifs distinguish them from the healthy and tumor-free individuals as well as low-divergence GBM patients, reminiscent of repertoire narrowing observed following strong T-cell responses to certain diseases (10,16,19). Our ability to infer high VJ-independent TIL divergence based on a repertoire-wide shift away from the properties of healthy PBMC, not on a shift toward antitumor TCRs, circumvents confounding variability in the antigenic specificities of these TCRs in GBM and other heterogeneous tumors.…”

“…Besides providing unprecedented insight into the determinants of TCR diversity in healthy individuals, previous applications of this strategy have provided new understanding of xenoreactivity in transplants, infection in human patients and animal models, and therapeutic response, residual disease, and relapse in cancer (for a review, see ref. 10). …”

αβ T-cell receptor bias in disease and therapy (Review)

“…As each CDR3 sequence represents one T cell clone, the polyclonal or oligoclonal expansion of T cells can be determined through the detection of CDR3 spectratype by various methods such as PCR DNA blotting, PCR GeneScan sequence analysis, and high throughput TCR sequencing (TCR-seq) (17). The biased TCR AV and BV gene families are considered to be antigen-specific and can be used in immunotherapy.…”

Toward effective sharing of high-dimensional immunology data

“…The initiation of collaborative and cross-laboratory research in any area inevitably lags behind the introduction and refinement of new measurement techniques because such research is largely driven by the community of users of the technique and because the requirements evolve with an improved understanding of the methods involved. For instance, in measuring antibody and T cell receptor repertoire data, the field has not coalesced around a single 'best' experimental or analytical process 18 , with experimental differences centering on the sequencing of genomic DNA or mRNA: some methods retain heavy-light chain pairing information whereas others do not, and different bioinformatics approaches are used to analyze the data. Comparative studies between laboratories will be required to identify best experimental practices 3 .…”