Research ArticleADAPTIVE IMMUNITY

Shaping of infant B cell receptor repertoires by environmental factors and infectious disease

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Science Translational Medicine  27 Feb 2019:
Vol. 11, Issue 481, eaat2004
DOI: 10.1126/scitranslmed.aat2004
  • Fig. 1 In years 1 to 3 of life, antibody SHM increases, but IgE shows high interindividual variation.

    (A) Data from 51 STORK children were collected with weekly phone surveys of parents, medical chart reviews every 6 months, household visits every 4 months, and venipuncture blood collection at approximately annual intervals. (B) Average SHM percentage for the IgH variable gene segment (IGHV) of expressed antibodies of the indicated isotype for each individual. Second and third samples from each subject are indicated by data point color. SHM ranges from 114 healthy adults are shown as box-whisker plots. The minimum, maximum, and median ages of the healthy adults are 17, 87, and 52 years, respectively. Blue lines show linear regression for SHM frequencies and age, and the shaded region indicates the 95% confidence interval. (C) Longitudinal SHM data from the 10 children who were sampled at three time points. Data for each individual are shown as dots of the same color, connected by lines. For both (B) and (C), SHM data for each isotype in each subject are summarized as the median SHM of reads for each isotype within each clone, then taking the mean SHM frequency over all clones. (D) B cell clonality for 38 children and 114 adult samples shown as a box-whisker. For the subset of children with sampling at two or more time points, second and third samples are indicated by color of the data point.

  • Fig. 2 Children and adults differ in IgG and IgA subclass usage but show comparable IGHV gene selection correlated with isotype switching.

    (A) The fraction of each IgG or IgA subclass used is shown. STORK specimen samples (n = 89) are indicated as points in the age 1 to 3 year category, and the 114 healthy adults (age 17 to 87 years) are the same as those in Fig. 1. The sum of the subclass fractions is more than 1.0 because a clone can contain members expressing different subclasses. P values were determined by two-sided Wilcoxon–Mann-Whitney tests: ***P < 0.001. IGHV gene usage is shown as the average for clones within each (B) child or (C) adult. Isotypes are plotted in their chromosomal ordering from upstream isotypes IgM and IgD to the most downstream isotype IgA2. IGHV ordering is based on the 20 most common IGHV genes in IgM in the STORK subjects. IgG4 and IgE are excluded because of low frequency. Dots represent outliers beyond 1.5-fold of the interquartile range. The plot axes were chosen to show the box-whiskers on a readable scale; rare outlier points with extreme values are not shown but were included in all analyses.

  • Fig. 3 SHM frequencies in B cell clones with members that bind TT in antibody phage display.

    scFv antibody phage display libraries were generated from IgH, Igκ, and Igλ transcripts from subjects 2072 and 2074. Members of the TT-specific clonal lineages were identified from phage clones in the total IgH repertoire sequence datasets generated for each antibody isotype from the PBMCs of the children, and the isotype and SHM percentages in the IGHV gene of all clone members were plotted. Each dot represents a read from a TT-binding clone member, with each clone plotted in a different color.

  • Fig. 4 IgM and IgD SHM are correlated with days of URI.

    Each point represents a STORK subject (n = 51) and shows the average SHM percentage for the IGHV gene segment of expressed antibodies of the indicated isotype as a function of the proportion of (A) FDV and (B) URI sick days. SHM data were from each subject’s final blood draw. SHM for each isotype in each subject was summarized as the median SHM of reads expressed as the indicated isotype within each clone, then taking the mean SHM percentage over all clones. Linear regression lines were plotted with 95% confidence intervals.

  • Fig. 5 Household cleanliness and TC usage show differing associations with IGH SHM.

    (A) Data show results for 48 households. Household cleanliness was assessed on four axes with scores given from 0 (clean) to 3 (very dirty). Linear regression lines are shown with 95% confidence intervals in gray. (B) Forty-nine households were randomized to TC usage (n = 27) or avoidance (n = 22). For both (A) and (B), SHM for each isotype in each subject was summarized as the median SHM of reads expressed as the indicated isotype within each clone, then taking the mean SHM frequency over all clones. (C) Children randomized to TC and non-TC groups, and the effect on FDV and URI sick day proportions. Wilcoxon–Mann-Whitney was used to test for significance.

  • Fig. 6 STORK subjects with eczema and other allergies show increased IgE SHM.

    IgH repertoires from children with known allergy (asthma, hives, food allergy, and/or eczema; table S2) were analyzed. In (A), subjects with and without eczema were compared (n = 14 and n = 37, respectively). In (B), subjects with any allergy (n = 17) were grouped as having allergy symptoms and compared to subjects with no allergic symptoms (n = 34). SHM for each isotype in each subject was summarized as the median SHM of reads expressed as the indicated isotype within each clone, then taking the mean SHM percentage over all clones. P values were determined using Wilcoxon–Mann-Whitney test.

  • Fig. 7 B cell clones from healthy subjects most commonly coexpress IgE and IgM, whereas allergic subjects coexpress IgE and IgA.

    UpSet plot showing the size of set intersections for clones expressing IgM, IgD, IgA, IgG, and IgE. Bars indicate the number of clones that express the given isotype(s). The vertical lines that connect the points represent set intersections. Analyses were performed on (A) 34 healthy subjects and (B) 17 subjects with eczema or allergies. Clones expressing only a single isotype are shown: IgM, IgD, IgA, or IgG (purple boxes) and IgE-only clones (dark blue boxes). The green box shows clones in healthy children that contain IgE+ and IgM+ members, whereas the gray box shows B cell clones from children with eczema or allergies that contain both IgE+ and IgA+ members. The 20 most frequent intersections are shown for both healthy and allergic children.

  • Table 1 Demographic and clinical characteristics of the STORK study sample.

    STORK study
    sample (n = 51)
    Age in weeks at first time point, median (range)81 (49–126)
    Sex
      Female24
      Male27
    Clinically diagnosed allergy/eczema
      Yes17
      No34
    Randomization arm of triclosan/triclocarban study
      Exposed27
      Unexposed22
      Not randomized2
    Household pets
      Yes16
      No35

Supplementary Materials

  • www.sciencetranslationalmedicine.org/cgi/content/full/11/481/eaat2004/DC1

    Materials and Methods

    Fig. S1. TT-binding scFvs confirmed by ELISA.

    Fig. S2. Clonal lineages of TT-binding B cells.

    Fig. S3. Proportion of IgG+ clone members that show evidence of antigen selection.

    Fig. S4. Proportion of IgE+ clone members that show evidence of antigen selection.

    Fig. S5. Household pet exposure and antibody SHM percentages.

    Fig. S6. Clonal lineage trees with IgE-containing members.

    Table S1. Demographic and household characteristics in this subcohort (n = 51) and the full cohort (n = 136).

    Table S2. Clinical and household information for STORK children in this study.

    Table S3. Primer sequences for heavy and light chain V(D)J amplicon generation for phage display.

    Data file S1. Primary data

    References (4860)

  • The PDF file includes:

    • Materials and Methods
    • Fig. S1. TT-binding scFvs confirmed by ELISA.
    • Fig. S2. Clonal lineages of TT-binding B cells.
    • Fig. S3. Proportion of IgG+ clone members that show evidence of antigen selection.
    • Fig. S4. Proportion of IgE+ clone members that show evidence of antigen selection.
    • Fig. S5. Household pet exposure and antibody SHM percentages.
    • Fig. S6. Clonal lineage trees with IgE-containing members.
    • Table S1. Demographic and household characteristics in this subcohort (n = 51) and the full cohort (n = 136).
    • Table S2. Clinical and household information for STORK children in this study.
    • Table S3. Primer sequences for heavy and light chain V(D)J amplicon generation for phage display.
    • References (4860)

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    Other Supplementary Material for this manuscript includes the following:

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