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Deep TCR repertoire sequencing reveals relative change in peanut specific clonotype in subjects undergoing rush oral immunotherapy


Oral immunotherapy is an emerging therapy currently under investigation for the treatment of food allergy [1]. Underlying mechanisms are thought to involve a switch in the food specific T cell response from Th2 to either Th1, Tr1 and/or Treg. It is unknown whether this change in response results from re-education of existing pathological food-specific T cells or from their replacement by new healthy T cells (change of guard hypothesis).


The objective was to evaluate the clonal distribution of peanut specific T cell in subjects with peanut allergy and follow changes in clonotype with treatment using a high-throughput T cell receptor (TCR) sequencing platform. Peripheral blood mononuclear cells (PBMCs) from three subjects undergoing rush oral immunotherapy in a previous trial [2] and three control subjects on avoidance diet were cultured with peanut extract at baseline and at 9 and 18 months. Carboxyfluorescein succinimidyl ester (CFSE)-low peanut proliferating T cells were then isolated by fluorescence-activated cell sorting (FACS) and TCR analysis was performed.


The CFSE-low proliferating fraction was found to be comprised of between 2000 and 12,000 different T cell clones. However, only between 15 and 25% of proliferating T cells (from 100-400 different clones) were consistently found at all three time points and probably represented true peanut-specific T cells. While the relative frequency of these peanut-specific clones was stable over time in subjects on avoidance diet (R=0.633 to 0.760), it was found to change in subjects undergoing oral immunotherapy (R= 0.123 to 0.350), following two characteristic patterns.


Using a deep TCR sequencing platform, we found that only a fraction of CFSE-low peanut proliferating T cells were consistent in time and likely to represent true peanut specific T cells. Oral immunotherapy was associated with changes in relative frequency of clones within this fraction, which would support the change of guard hypothesis.


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    Bégin P, Chinthrajah RS, Nadeau KC: Oral immunotherapy for the treatment of food allergy. Hum Vaccin Immunother. 2014, 10: 8-

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    Bégin P, Dominguez T, Wilson SP, Bacal L, Mehrotra A, Kausch B, Trela A, Tavassoli M, Hoyte E, O’Riordan G, Blakemore A, Seki S, Hamilton RG, Nadeau KC: Phase 1 results of safety and tolerability in a rush oral immunotherapy protocol to multiple foods using Omalizumab. Allergy, Asthma & Clinical Immunology. 2014, 10: 7-10.1186/1710-1492-10-S1-A7.

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P. Bégin was supported by AllerGen NCE Inc. (the Allergy, Gene and Environment Network), a member of the Networks of Centre of Excellence Canada program.

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Correspondence to Philippe Bégin.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

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Bégin, P., Nadeau, K.C. Deep TCR repertoire sequencing reveals relative change in peanut specific clonotype in subjects undergoing rush oral immunotherapy. All Asth Clin Immun 10, A53 (2014).

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  • Peripheral Blood Mononuclear Cell
  • Relative Frequency
  • Food Allergy
  • Sequencing Platform
  • Response Result