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Supplementary table 1. Demographics, diagnostics, IgE and IgG positivity to milk allergens
and IgE and IgG4 peptide recognition for each patient and control.
Supplementary table 1 in excel file format.
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Supplementary table 2. IgG4 epitopes significantly changed (p<0.05) over the time.
D
6 months
12 months
24 months
p4-6 (10-35)
p28-33 (82-116)
p38 (112-131)
p43-50 (127-167)
p2-6 (4-35)
p30-33 (88-116)
p38 (112-131)
p43-44 (127-149)
p29-32 (85-113)
p38 (112-131)
p43-46 (127-155)
p7-10 (19-47)
p7-10 (19-47)
p7-10 (19-47)
p12-13 (34-56)
p27-28 (79-101)
p7-9 (19-44)
IgG4
α-s1-casein
α-s2-casein
β-casein
κ-casein
p43-46 (127-155)
p26-28 (76-101)
p42 (124-143)
p2-5 (4-32)
p19-20 (55-77)
p3-6 (7-35)
p8 (22-41)
p15-20 (43-77)
p25-26 (73-95)
p29-30 (85-107)
p2-6 (4-35)
p3-7 (7-38)
p18-20 (52-77)
p23 (67-86)
p16-19 (46-74)
p25-34 (73-119)
p29-34 (85-119)
p45-46 (133-155)
p50-51 (148-170)
β-lactoglobulin
p17-18 (49-71)
p23-24 (67-89)
p35 (103-122)
p44-45 (130-152)
p14-18 (40-71)
p22-24 (64-89)
p44-47 (130-158)
p14-18 (40-71)
p21-24 (61-89)
p35 (103-122)
p45 (133-152)
Statistical analysis was performed by the Wilcoxon signed-rank test comparing IgG4 signal
intensity after the achievement of oral desensitization (D) and 6, 12, and 24 months of
follow up with the initial time before CM-OIT (0).
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Supplementary table 3. IgE epitopes significantly changed (p<0.05) over the time.
D
6 months
IgE
α-s1-casein
12
months
24 months
p10 (28-47)
p27 (79-98)
α-s2-casein
β-casein
κ-casein
β-lactoglobulin
p13 (37-56)
p35 (103-122)
p49-51 (145-170)
p62 (184-203)
p23 (67-86)
Statistical analysis was performed by the Wilcoxon signed-rank test comparing IgE signal
intensity after the achievement of oral desensitization (D) and 6, 12, and 24 months of
follow up with the initial time before CM-OIT (0).
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Supplementary table 4. IgE epitopes significantly different (p<0.05) between patients groups
IgE
Low risk
vs
moderate risk
α-s1-casein
p24 (70-89)
α-s2-casein
β-casein
κ-casein
β-lactoglobulin
Low risk
vs
high risk
p7-9 (19-44)
p25-28 (73-101)
p44 (130-149)
p49 (145-164)
p60 (178-197)
p8-11 (22-50)
p32-33 (94-116)
p49-51 (145-170)
p15 (43-62)
p25 (73-92)
p54-55 (160-182)
p63-64 (187-209)
p3-6 (7-35)
Moderate risk
vs
high risk
p7-9 (19-44)
p25-28 (73-101)
p49 (145-164)
p60 (178-197)
p9-10 (25-47)
Statistical analysis was performed by One Way ANOVA followed by Bonferroni post-hoc tests
comparing each group of patients.
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Supplementary table 5. IgG4 epitopes significantly different (p<0.05) between patients groups.
IgG4
Low risk
vs
moderate risk
α-s1-casein
α-s2-casein
β-casein
κ-casein
β-lactoglobulin
Low risk
vs
high risk
Moderate risk
vs
high risk
p50-51 (148-170)
Statistical analysis was performed by One Way ANOVA followed by Bonferroni post-hoc tests
comparing each group of patients.
SUPPLEMENTARY FIGURE LEGENDS
Supplementary figure 1. Time trend evolution of IgE- and IgG4-binding epitopes in the
groups of patients. Each line represents the average number of peptides bound by IgE
and IgG4 in low (green line), moderate (blue line) and high (red line) risk patients
before CM-OIT (0), after the achievement of oral desensitization (D), and at 6, 12 and
24 months of follow-up. Results are means ± S.E.M. Statistical analysis was performed
comparing independently each group of patients by One Way ANOVA of repeated
measures followed by post-hoc analysis using the Holm-Sidak method comparing each
time with baseline (0) (*P < 0.05, **P < 0.01, and ***P < 0.001).
Supplementary figure 2. Temporal differences in IgE and IgG4 epitope binding of α-s1casein (A), α-s2-casein (B), β-casein (C), κ-casein (D) and β-lactoglobulin (E) in the
groups of patients. Overlapping peptides are represented on the x-axis. The average fold
change of fluorescent intensity of each peptide is represented on the y-axis. The lines
represent the patient’s average fold change of fluorescent intensity (weighted average Zscores) at each time of the OIT treatment (after the achievement of oral desensitization
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(D), red line; at 6 months of follow-up, green line; 12 months of follow-up, purple line;
24 months of follow-up, blue line) relative to baseline (0).
Supplementary figure 3. Scatter plot and the associated linear regression line of the
number of peptides bound by IgE for each patient before CM-OIT and the number of
reactions (A) and duration of treatment (B).
Supplementary figure 4. Machine learning bioinformatics analysis to identify the
peptide biomarkers which better correlate with the number of reactions. (A) Mean
Decrease Accuracy (%IncMSE) and Mean Decrease Gini (IncNodePurity) (sorted
decreasingly from top to bottom) of attributes as assigned by random forest. (B) Scatter
plot and the associated linear regression line of the number of peptides bound by IgE
from 5 to 16 to predict the number of reactions.
Supplementary figure 5. Machine learning bioinformatics analysis to identify the
peptide biomarkers which better correlate with the number of reactions. (A) Mean
Decrease Accuracy (%IncMSE) and Mean Decrease Gini (IncNodePurity) (sorted
decreasingly from top to bottom) of attributes as assigned by random forest. (B) Scatter
plot and the associated linear regression line of the number of peptides bound by IgE
from
5
to
16
to
predict
the
duration
of
treatment.
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