Supplementary Methods: Omalizumab Trial This double-blind, randomized, placebo-controlled trial was conducted at the University of Utah Hospital and

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1 Supplementary Methods: Omalizumab Trial This double-blind, randomized, placebo-controlled trial was conducted at the University of Utah Hospital and Primary Children s Hospital, Salt Lake City, UT, both referral centers. Thirty outpatient subjects with active eosinophilic esophagitis, ages 15 to 60 years, were enrolled. The sample size was chosen by an a priori power analysis suggesting an 80% chance of detecting a difference between a mean initial count of 40 eosinophils/high-power field and 10 eosinophils/high-power field. Inclusion criteria were: 1) previously diagnosed eosinophilic esophagitis 15 eosinophils per high-power field in an esophageal biopsy) who had failed topical steroid therapy, 2) serum IgE IU/ ml, and 3) acceptable medical history, physical exam, and laboratory test results, specifically no history of bleeding diathesis, significant cardiopulmonary disease, or other contraindications to upper endoscopy. Exclusion criteria per protocol included: 1) treatment with omalizumab, currently or in the previous six months, 2) need for esophageal dilation at enrollment due to food impaction or inability to pass the endoscope, 3) history of esophagogastric surgery, 4) presence of other esophageal pathology that could account for the patient s symptoms, including gastroesophageal reflux disease, 5) incarceration, 6) potential pregnancy or breast-feeding, 7) current or recent use of oral or topical corticosteroids, leukotriene receptor inhibitors, cromolyn sodium, or investigational drugs, 8) severe medical conditions prohibiting participation in the study, 9) Barrett esophagus, or 10) potentially unreliable or noncompliant subjects. Patients were recruited and enrolled by Dr. Fang (27) or Dr. O Gorman (3), from July 2006 to September Last follow-up was done as the final subject completed the trial in February Simple 1 to 1 allocation ratio randomization was done by an investigational-drug pharmacist, using the randomization function in Excel. Placebo subjects were given injections of material seemingly identical to the omalizumab., clinicians, and pathologists were all blinded as to the treatment until their observations were complete. Prespecified specific endpoints were the number of eosinophils per maximal high power field and, for dysphagia, a 0 to 6 score as follows: 0=no dysphagia; 1=solid food dysphagia monthly; 2=solid food dysphagia < weekly; 3=solid food dysphagia > weekly, < daily; 4=solid food dysphagia daily; 5=solid food dysphagia with every meal; and 6=dysphagia for solid and liquid food. Therapy consisted of omalizumab subcutaneously every 2 to 4 weeks for 16 weeks, with an omalizumab dose per supplementary table 1 (about mg/kg/ige [IU/ml]), or placebo. Endoscopy with biopsy of the proximal and distal esophagus was performed at baseline and at 16 weeks. Of 46 recruited subjects, 16 did not meet criteria and were excluded from the study. Each subject excluded either lacked sufficient eosinophils in the initial biopsy or had serum IgE content <30 IU/ml. None of the subjects declined to participate or withdrew from the study. There were no significant side effects. Every subject who began therapy completed the trial. The only substantive amendment was the requirement of the subjects to be on proton pump inhibitors during the trial once the consensus criteria for eosinophilic esophagitis were published in A majority of the subjects (all but 5 in the treatment group and 4 in the control group) were treated with high dose, twice daily proton pump inhibitors for the duration of the study and for at least 8 weeks prior to the initial biopsy 1

2 and the beginning of the study. The other subjects were not proton pump inhibitortreated for the duration of the study. Each subject not proton pump inhibitor treated during the trial had a documented lack of response to high dose proton pump inhibitors before or after the study. Supplementary Figures: Supplementary Figure 1. Omalizumab trial: eosinophil content is unchanged after treatment. Representative areas of the esophageal epithelium (A) before and (B) after a 16-week course of omalizumab. There is no significant reduction in intraepithelial eosinophil content. Supplementary Figure 2. Omalizumab depletes tissue mast cell IgE. (A) is before treatment. (B) is after omalizumab. Immunostaining for IgE (red, Cy3) and mast cell tryptase (green, Alexa 488). There was a 9-fold loss (314 to 35, arbitrary units) of red IgE staining after treatment, implying reduced mast cell IgE content (P =. 008, Wilcoxon matched pairs test). There was no significant change among placebotreated controls. 2

3 Supplementary Figure 3. There is a single IgG4 plasma cell in the subepithelial lamina propria (arrow). IgG4 is red (Cy3), CD138 is green (Alexa 488), and nuclei are blue (DAPI). In this biopsy, the granular IgG4 staining is mainly in the subepithelial lamina propria. As expected, both the epithelium and plasma cells have membrane-pattern CD138. 3

4 Supplementary Figure 4. Electron microscopy of esophageal stroma from an eosinophilic esophagitis subject. The density (arrow) represent a possible immune complex. Supplementary Figure 5. Esophagectomy IgG4 immunostain at low power, showing that the majority of the plasma cells are in the deep lamina propria at top left and bottom right. A few IgG4 plasma cells are just under the surface epithelium (top left) and in the muscularis mucosae (bottom right). The paucity of immediately subepithelial IgG4 plasma cells explains why IgG4 plasma cells are sparse in mucosal biopsies. From case 1. 4

5 Supplementary Figure 6. In full-thickness esophageal sections from 47 autopsy controls without known esophageal disease, there were 0 to 25 IgG4 plasma cells / maximal high-power field. Most IgG4 plasma cells were in the deep lamina propria. There were a mean of 4.6 (median of 1) IgG4 plasma cells/maximal high-power field; 55% of the controls had 1 or more IgG4 plasma cells. Supplementary Figure 7. IgG4 plasma cells, in red, in esophagectomy lymph node. DAPI, a nuclear counterstain, is blue. There are up to 50 IgG4 plasma cells per high-power field. From case 1. 5

6 Supplementary Tables: Supplementary Table 1. Antibodies used. Purpose Antibody Vendor Serum IgG capture antibody Serum IgG4 detection antibody IgG4 IgE mast cell plasma cell marker complement Tissue immunoperoxidase IgG4 Immunofluorescent antirabbit, secondary Immunofluorescent antimouse, secondary Negative control rabbit antibody Negative control mouse antibody anti IgG, mouse monoclonal Biotin anti IgG4, mouse monoclonal anti IgG4, rabbit monoclonal anti IgE, rabbit polyclonal anti mast cell tryptase, mouse monoclonal anticd138, mouse monoclonal anti complement 9, mouse monoclonal anti IgG4, mouse monoclonal Goat anti-rabbit, Cy3 conjugated Goat anti-mouse, Alexa 488 conjugated Nonspecific rabbit IgG Nonspecific mouse IgG1 kappa BD Biosciences Pharmingen, San Diego CA BD Biosciences Pharmingen, San Diego CA Abcam, Boston MA Dako, Carpinteria CA Dako, Carpinteria CA AbD Serotec, Raleigh, NC Vector Labs, Burlingame, CA Cell Marque, Rocklin CA Jackson Immunoresearch, West Grove, PA Jackson Immunoresearch, West Grove, PA Santa Cruz Biotechnology, Dallas, TX Santa Cruz Biotechnology, Dallas, TX 6

7 Supplementary Table 2. Omalizumab Dosing Schedule. Milligrams (mg) Per Dose Body weight (kg) Baseline IgE (IU/mL) >60-70 >70-80 >80-90 > Frequency of Dosing Q4wk > Q2wk > > > Not Dosed > > Supplementary Table 3. Demographics and Serum IgE results for omalizumab study. subjects & % male (range) in years Serum IgE before study mean ± 95% confidence interval Serum IgE after study mean ± 95% confidence interval Omalizumab 16 (81%) 32 (16 to 52) 129 ± ± 50* Placebo controls 14 (78%) 28 (15 to 39) 150 ± ± 43 Omalizumab depletion of tissue IgE causes an increase in serum IgE. The 2.8-fold (2.3 to % confidence interval) increase in serum IgE after omalizumab therapy (*, P <. 001) confirms treatment effect. 7

8 Supplementary Table 4. Demographics for Tissue Immunoglobulin Assay. subjects (% male) (range, years) Eosinophilic esophagitis 11 (45%) 39 (28 to 58) Controls 8 (37.5%) 44 (25 to 60) Supplementary Table 5. Demographics for Esophageal Biopsy Immunostaining. subjects (% male) (range, years) Eosinophilic esophagitis 24 (71%) 33 (21 to 56) Controls 9 (67%) 31 (22 to 60) Supplementary Table 6. Demographics for Autopsy IgG4 series. subjects (% male) (range, years) Autopsy controls 47 (62%) 39 (21 to 84) Supplementary Table 7. Demographics for Serum IgG4 Assay. subjects (% male) (range, years) Eosinophilic esophagitis 15 (73%) 39 (23 to 60) Controls 41 (68%) 41 (27 to 61) 8

9 CONSORT 2010 Flow Diagram Enrollment Assessed for eligibility (n=46) Excluded (n=16) Not meeting inclusion criteria (n=16) Declined to participate (n=0) Other reasons (n=0) Randomized (n=30) Allocated to intervention (n=16) Received allocated intervention (n=16) Did not receive allocated intervention (n=0) Allocation Allocated to intervention (n=14) Received allocated intervention (n=14) Did not receive allocated intervention (n=0) Lost to follow-up (n=0) Discontinued intervention (n=0) Follow-Up Lost to follow-up (n=0) Discontinued intervention (n=0) Analysed (n=16) Excluded from analysis (n=0) Analysis Analysed (n=14) Excluded from analysis (n=0)