Strategies for B-cell receptor repertoire analysis in primary immunodeficiencies: from severe combined immunodeficiency to common variable immunodeficiency.

Hanna Ijspeert,David Van Zessen,Marjolein Wentink,Erik J Simons,Virgil A S H Dalm,Martin P Van Hagen,Jacques J M Van Dongen,Mirjam Van Der Burg,Andrew P Stubbs,Gertjan J Driessen,Ingrid Pico-Knijnenburg

doi:10.3389/fimmu.2015.00157

Hanna Ijspeert, David Van Zessen + Show 9 more

Open Access

https://doi.org/10.3389/fimmu.2015.00157

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Journal: Frontiers in Immunologie	Publication Date: Apr 8, 2015
Citations: 17	License type: cc-by

Affiliation: Erasmus MC

Abstract

The antigen receptor repertoires of B- and T-cells form the basis of the adaptive immune response. The repertoires should be sufficiently diverse to recognize all possible pathogens. However, careful selection is needed to prevent responses to self or harmless antigens. Limited antigen receptor repertoire diversity leads to immunodeficiency, whereas unselected or misdirected repertoires can result in autoimmunity. The antigen receptor repertoire harbors information about abnormalities in many immunological disorders. Recent developments in next generation sequencing allow the analysis of the antigen receptor repertoire in much greater detail than ever before. Analyzing the antigen receptor repertoire in patients with mutations in genes responsible for the generation of the antigen receptor repertoire will give new insights into repertoire formation and selection. In this perspective, we describe strategies and considerations for analysis of the naive and antigen-selected B-cell repertoires in primary immunodeficiency patients with a focus on severe combined immunodeficiency and common variable immunodeficiency.

Highlights

V(D)J RECOMBINATION OF IMMUNOGLOBULIN AND T-CELL RECEPTOR LOCI The antigen receptor repertoire is defined as the total set of different B-cell (BR) or T-cell receptors (TRs)
Extensive analysis of double strand breaks (DSBs) repair kinetics revealed that these DSBs are mainly localized to heterochromatin and require opening of the closed chromatin structure in order to be repaired by non-homologous end joining pathway (NHEJ) during the G1 phase of the cell cycle or HR in the G2 phase
ANTIGEN RECEPTOR REPERTOIRE DIVERSITY The total diversity of the unique TRs and BRs is the sum of combinational diversity based on the usage of different combinations of V, (D), and J genes and junctional diversity due to nucleotide deletions by exonuclease activity, non-templated (N) nucleotide insertions that are introduced by the enzyme terminal deoxynucleotidyl transferase (TdT), and the presence of palindromic (P) nucleotides that arise due to asymmetric hairpin opening by Artemis (Figure 1B)

Summary

Introduction

V(D)J RECOMBINATION OF IMMUNOGLOBULIN AND T-CELL RECEPTOR LOCI The antigen receptor repertoire is defined as the total set of different B-cell (BR) or T-cell receptors (TRs). ANTIGEN RECEPTOR REPERTOIRE DIVERSITY The total diversity of the unique TRs and BRs is the sum of combinational diversity based on the usage of different combinations of V, (D), and J genes and junctional diversity due to nucleotide deletions by exonuclease activity, non-templated (N) nucleotide insertions that are introduced by the enzyme TdT, and the presence of palindromic (P) nucleotides that arise due to asymmetric hairpin opening by Artemis (Figure 1B). The antigen-selected repertoire can be analyzed in sorted memory B-cells or by sequencing of IGG and IGA transcripts from RNA isolated from peripheral blood mononuclear cells.

Results

Conclusion