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

Abstract

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 TCRβ 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 TCRβ 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)

T cell receptor repertoire profiling predicts the prognosis of HBV‐associated hepatocellular carcinoma

“…We calculated the Clonality index (1‐ (Shannon's entropy)/log2 (number of productive aa unique sequences)) and the U/T index (the number of productive unique aa sequences/the number of total productive aa sequences) to estimate the diversity of T cell clones in each sample, which were independent of sample sequencing depth 13, 22, 23…”

“…Firstly, we performed the TCR sequencing using increased sequencing reads and read length, which could contribute to obtaining a more reliable data and conclusion. Secondly, we used the U/T index and the Clonality index rather than the number of productive unique aa sequences or Shannon diversity index to assess the diversity of TCR repertoire, as the former 2 indexes could better correct the impact of uneven reads amount 13, 22, 24. Using the different sequencing depth or the different diversity indicators might be another reason for the inconsistent results.…”

“…By high throughput TCR sequencing of T‐cell repertoires, differential TCR signatures had been identified in primary biliary cirrhosis, primary sclerosing cholangitis, and alcoholic liver disease, which represented an imprint of distinctive antigenic repertoires in these chronic liver diseases 13. Similarly, significant differences of T‐cell repertoires among HCC, intrahepatic cholangiocarcinoma, and mixed hepatocellular and cholangiocellular carcinoma have also been demonstrated 14.…”

Clonal Characteristics of Circulating B Lymphocyte Repertoire in Primary Biliary Cholangitis

“…The function of B lymphocytes is regulated by T cells in T-dependent responses. Recently, Liaskou et al (8) sequenced the TCR genes of 10 PBC patients and revealed 42 disease-associated T lymphocyte clones. Further characterization of these clones and extensive functional studies are required to pinpoint disease-specific B and T cell clones that could potentially be used as diagnostic markers and therapeutic targets.…”

Targeting inflammation for the treatment of alcoholic liver disease

“…malondialdehyde and 4-hydroxynonenal) (Albano & Vidali, 2010; Thiele et al, 2004, 2010). These products then interact with many proteins to form protein adducts that can act as antigens to activate the adaptive immune response (Albano & Vidali, 2010; Liaskou et al, 2016; Thiele et al, 2004, 2010). However, the exact roles of adaptive immunity and T cells in the pathogenesis of ALD remain to be elusive.…”