Robinson, M. W., Hughes, J. , Wilkie, G. S., Swann, R. , Barclay, S. T., Mills, P. R., Patel, A. H. , Thomson, E. C. and McLauchlan, J. (2016) Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region. Frontiers in Immunology, 7, 131. (doi: 10.3389/fimmu.2016.00131) (PMID:27092143) (PMCID:PMC4820669)
|
Text
117788.pdf - Published Version Available under License Creative Commons Attribution. 1MB |
Abstract
To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future experiments to accurately address the question of whether T cell responses contribute to SVR upon antiviral therapy. This pipeline represents a novel technique to analyze T cell dynamics in situations where conventional antigen-dependent methods are limited due to suppression of T cell functions and highly diverse antigenic sequences.
Item Type: | Articles |
---|---|
Additional Information: | Funding information: Medical Research Council (Award number(s): MRC Centenary Award (MR), Intramural Programme Grants (JM, AP)); Wellcome Trust (Award number(s): 102789/Z/13/Z (ET)). |
Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Robinson, Dr Mark and Wilkie, Dr Gavin and Mills, Professor Peter and Hughes, Dr Joseph and Swann, Dr Rachael and Thomson, Professor Emma and Patel, Professor Arvind and McLauchlan, Professor John |
Authors: | Robinson, M. W., Hughes, J., Wilkie, G. S., Swann, R., Barclay, S. T., Mills, P. R., Patel, A. H., Thomson, E. C., and McLauchlan, J. |
College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
Journal Name: | Frontiers in Immunology |
Publisher: | Frontiers |
ISSN: | 1664-3224 |
ISSN (Online): | 1664-3224 |
Copyright Holders: | Copyright © 2016 The Authors |
First Published: | First published in Frontiers in Immunology 7:131 |
Publisher Policy: | Reproduced under a Creative Commons License |
University Staff: Request a correction | Enlighten Editors: Update this record