Background: Various T cell subsets take part in mediating mucosal damage in IBD patients. The antigenic specificity of these cells occurs via generation and rearrangement of a functional T cell receptor (TCR), in a process involving complex recombination of different genes. High throughput sequencing platforms allow detailed assessment of TCR repertoire patterns in different diseases. There is very limited data whether TCR repertoires are altered in IBD patients and whether common clones are shared between the blood and the gut. We hypothesized that pediatric UC patients possess unique TCR repertoires resulting from clonotypic expansions in the inflamed tissue.
Methods: Peripheral blood mononuclear cells (PBMCs) and rectal biopsies were collected from newly diagnosed treatment-naïve pediatric UC patients and healthy control aged-matched subjects, without signs of intestinal inflammation. DNA was isolated and sent for high throughput sequencing to determine the TCRβ repertoire. Such a strategy, which employs massive parallel sequencing to process millions of rearranged TCR products simultaneously, permits an in-depth analysis of individual TCRs at a nucleotide level while expanding coverage of the total lymphocyte repertoire. ImmunoSeq analysis software was used for analysis.
Results: Paired PBMCs and rectal biopsies were collected from 4 control subjects and 6 UC patients (4 moderate activity, 2 severe activity). In both patients and controls, the TCR repertoire was more clonal in the tissue, compared to the blood. Moreover, the repertoire was further restricted in both PBMCs and tissue of UC patients vs. controls, and in several patients, specific clones were highly expressed in the inflamed rectum (>5% of total clones). Despite a similar clinical phenotype, the frequency of shared common clones between patients was very low. However, several unique clones were upregluated only among UC patients and vice versa. Finally, in a single patient with limited distal disease, the TCR repertoire was significantly different between inflamed and non-inflamed areas.
Conclusions: High throughput sequencing of the TCR is a powerful tool for studying adaptive immune cell function in the gut. The oligoclonality observed among UC patients suggests specialization of unique mucosal T cell clones, that likely have a role in mediating tissue damage. Additional studies are required to characterize which antigens interact with these clones.