Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

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)

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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:Swann, Rachael and Robinson, Dr Mark and Wilkie, Dr Gavin and Thomson, Dr Emma and Hughes, Dr Joseph and Patel, Professor Arvind and Mills, Professor Peter 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 > Institute of Infection Immunity and Inflammation
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
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

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
645101T-cell mediated evolution of hepatitis C virus during acute infectionEmma ThomsonWellcome Trust (WELLCOME)102789/Z/13/ZMVLS III - CENTRE FOR VIRUS RESEARCH
656491Basis of the host range and tissue tropism for hepatitis C virusArvind PatelMedical Research Council (MRC)MC_UU_12014/2MVLS III - CENTRE FOR VIRUS RESEARCH