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:Robinson, Dr Mark and Wilkie, Dr Gavin and Mills, Professor Peter and Hughes, Dr Joseph and Swann, Rachael and Thomson, Dr 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 > 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