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

IJspeert H, Wentink M, van Zessen D, Driessen GJ, Dalm VA, van Hagen MP, Pico-Knijnenburg I, Simons EJ, van Dongen JJ, Stubbs AP, van der Burg M - Front Immunol (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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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.

Mentions: The BR rearrangements can be amplified from DNA or from RNA. Rearrangements amplified from RNA are mostly functional (also called productive), which means that they code for a functional Ig protein. Amplification of rearrangements from DNA allows analysis of both productive and unproductive rearrangements, which have not been selected. The latter is interesting because analysis of productive and unproductive IGH rearrangements in naive B-cells in controls shows that the productive rearrangements in naive B-cells have a lower number of total N-nucleotides (13.8 versus 20.2 nt) consequently leading to a shorter CDR3 length (Figure 2A). This might be explained by the fact that in bone marrow only B-cells are selected with a shorter CDR3 region. This indicates that analysis of unproductive rearrangements could give additional information about the V(D)J recombination process and selection.


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

IJspeert H, Wentink M, van Zessen D, Driessen GJ, Dalm VA, van Hagen MP, Pico-Knijnenburg I, Simons EJ, van Dongen JJ, Stubbs AP, van der Burg M - Front Immunol (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4389565&req=5

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.
Mentions: The BR rearrangements can be amplified from DNA or from RNA. Rearrangements amplified from RNA are mostly functional (also called productive), which means that they code for a functional Ig protein. Amplification of rearrangements from DNA allows analysis of both productive and unproductive rearrangements, which have not been selected. The latter is interesting because analysis of productive and unproductive IGH rearrangements in naive B-cells in controls shows that the productive rearrangements in naive B-cells have a lower number of total N-nucleotides (13.8 versus 20.2 nt) consequently leading to a shorter CDR3 length (Figure 2A). This might be explained by the fact that in bone marrow only B-cells are selected with a shorter CDR3 region. This indicates that analysis of unproductive rearrangements could give additional information about the V(D)J recombination process and selection.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus