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

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.

Keywords: CVID; V(D)J recombination; immunodeficiency; next generation sequencing; repertoire.

Figure 1

V(D)J recombination and B-cell development. (A) Schematic overview of V(D)J recombination. DNA double strand breaks are introduced by the RAG proteins, subsequently the DNA is processed and ligated by DNA repair proteins from the NHEJ pathway. (B) Examples of V(D)J junctions showing junctional diversity by nucleotides that are removed, non-templated (N) nucleotides (blue) that are added, or presence of palindromic (P) nucleotides (red). (C) The B-cell repertoire in peripheral blood can be divided into the naive repertoire and the antigen-selected repertoire.

Figure 2

Naive B-cell repertoire in control and CVID patients. The naive B-cell repertoire was measured in 10 controls (C) and 18 CVID patients, resulting in total 293,216 unique productive rearrangements for control and 539,220 for CVID, and 127,261 unique unproductive rearrangements for control and 305,402 for CVID. (A) Junction characteristics of CVID patients are similar to controls. Average number of total number of deletions, N-nucleotides, and P-nucleotides are indicted per patient. (B) Similarly, the CDR3 length distribution (mean with SEM) of IGH rearrangements is comparable to controls. In addition, the frequency of amino acids in the CDR3 (median with range) is also comparable. The positively charged amino acids are indicated in red and the negatively charged in blue. (D) The diversity of the naive B-cell repertoire in CVID patients is comparable to controls, however one patient has a very restricted repertoire similar to patients with Nijmegen breakage syndrome (NBS) and ataxia telangiectasia (AT). Data are shown in box and whiskers (10–90 percentile). (E) The repertoire of this patient remains very restricted over time. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.