High-throughput T-cell receptor sequencing across chronic liver diseases reveals distinct disease-associated repertoires

摘要

Hepatic T-cell infiltrates and a strong genetic human leukocyte antigen association represent characteristic features of various immune-mediated liver diseases. Conceptually the presence of disease-associated antigens is predicted to be reflected in T-cell receptor (TCR) repertoires. Here, we aimed to determine if disease-associated TCRs could be identified in the nonviral chronic liver diseases primary biliary cirrhosis (PBC), primary sclerosing cholangitis (PSC), and alcoholic liver disease (ALD). We performed high-throughput sequencing of the TCR chain complementarity-determining region 3 of liver-infiltrating T cells from PSC (n=20), PBC (n=10), and ALD (n=10) patients, alongside genomic human leukocyte antigen typing. The frequency of TCR nucleotide sequences was significantly higher in PSC samples (2.53 +/- 0.80, mean +/- standard error of the mean) compared to PBC samples (1.13 +/- 0.17, P<0.0001) and ALD samples (0.62 +/- 0.10, P<0.0001). An average clonotype overlap of 0.85% was detected among PSC samples, significantly higher compared to the average overlap of 0.77% seen within the PBC (P=0.024) and ALD groups (0.40%, P<0.0001). From eight to 42 clonotypes were uniquely detected in each of the three disease groups (30% of the respective patient samples). Multiple, unique sequences using different variable family genes encoded the same amino acid clonotypes, providing additional support for antigen-driven selection. In PSC and PBC, disease-associated clonotypes were detected among patients with human leukocyte antigen susceptibility alleles. Conclusion: We demonstrate liver-infiltrating disease-associated clonotypes in all three diseases evaluated, and evidence for antigen-driven clonal expansions. Our findings indicate that differential TCR signatures, as determined by high-throughput sequencing, may represent an imprint of distinctive antigenic repertoires present in the different chronic liver diseases; this thereby opens up the prospect of studying disease-relevant T cells in order to better understand and treat liver disease. (Hepatology 2016;63:1608-1619)