Defining Predictors of Radiological Transmural Response to Vedolizumab in Small Bowel Crohn's Disease Through Serum Proteomic Biomarkers
Phase: PHASE4
Conditions: Crohn Disease of Small Intestine
Sponsor: Washington University School of Medicine

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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Title: Defining Predictors of Radiological Transmural Response to Vedolizumab in Small Bowel 
Crohn’s disease through Serum Proteomic Biomarkers  
Investigators: Parakkal Deepak,1 Matthew A. Ciorba,2  
1. Assistant Professor of Medicine; 
Division of Gastroenterology, 
John T. Milliken Department of Medicine, 
Washington University in Saint Louis, MO, USA. 
2. Assistant Professor of Medicine,  
Director, Inflammatory Bowel Diseases Program,  
Director of Research, Inflammatory Bowel Diseases Program,  
Associate Director, GI Fellowship (T32), 
Division of Gastroenterology, 
John T. Milliken Department of Medicine, 
Washington University in Saint Louis, MO, USA. 
www.ciorbaibdgroup.org 
 
 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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B. Background and rationale 
VEDOLIZUMAB IN CROHN’S DISEASE: Crohn’s disease (CD) is characterized by a 
dysregulation of both the innate and adaptive immunity responses.1 Vedolizumab is a novel 
therapeutic monoclonal antibody that binds to the α4β7 integrin which is expressed specifically 
by a subset of gastrointestinal-homing T lymphocytes.2 The binding of α4β7integrin to mucosal 
addressin cell adhesion molecule-1 (MAdCAM-1) expressed on the surface of mucosal 
endothelial cells is a crucial component of the gut-selective homing mechanism for lymphocytes.  
It is currently approved for both induction and maintenance of clinical response and remission in 
moderate-severe CD who have failed at least one conventional therapy.3  
FACTORS IMPACTING CLINICAL USE OF VEDOLIZUMAB IN CROHN’S DISEASE: 
Small bowel CD has no durable surgical cure and, when moderate to severe, typically requires 
long-term maintenance therapy.  Unfortunately, small bowel CD activity is poorly reflected by 
clinical symptoms indices alone.4,5 If left untreated, inflammation is primary predictor of disease 
complications. In clinical practice, the safety profile of vedolizumab makes it an appealing choice 
to both clinicians and patients for maintenance therapy. However, clinician confidence in using 
vedolizumab for small bowel CD is not as high as one may predict it would be. Several reasons 
may underlie this.   
Pivotal trials for vedolizumab demonstrated its effectiveness in CD; however, the onset of benefit 
was less robust and slower than in UC.3,6 This slower onset, combined with the clinical challenge 
of determining disease response in Crohn’s has prompted some physicians to either avoid use or 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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IRB Expired:  11/7/2025  
 
abandon vedolizumab as a therapy prematurely.  However, the trial had clinical disease activity 
indices as their primary endpoint. Clinical status and disease activity indices such as the CD 
Activity Index (CDAI) and the Harvey Bradshaw Index (HBI) correlate poorly with objective 
markers of inflammation in the small bowel, such as C-reactive protein (CRP), endoscopy, or 
radiological disease activity parameters.5  The use of imprecise and flawed clinical disease activity 
endpoints may explain the GEMINI II trial data in the subset of patients with small bowel CD 
(Supplementary Figure 2 A and B) which has led some physicians to assume that the role for 
vedolizumab is predominately for UC and colonic CD and more limited in small bowel CD.3 
ENDOSCOPIC REMISSION WITH VEDOLIZUMAB IN CD: Recently the VICTORY 
consortium reported the rates of mucosal healing (MH) across 141 patients with moderately to 
severe CD cohort.7 In this cohort, 76.4% of the patients had either ileal or ileocolonic CD.  
Despite this, 121 out of the 141 individuals had mainly endoscopic follow-up.   
CROSS-SECTIONAL IMAGING AS A PREDICTOR OF VEDOLIZUMAB RESPONSE IN 
SMALL BOWEL CD: In population-based cohorts, up to one-third of patients with CD have 
evidence of bowel damage with stricturing or penetrating complications at diagnosis, findings 
which are underdiagnosed without the aid of cross-sectional imaging.8  This bowel damage at 
diagnosis identified by cross-sectional imaging is an independent prognostic factor associated 
with 3-fold increase in intestinal surgery and a 2-fold increase in CD-related hospitalization 
during patient follow-up.9  CTE and MRE can additionally detect inflammation in regions 
inaccessible to standard endoscopy (proximal small bowel or stricturing phenotype), and those 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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CD patients with isolated intramural disease.4  Therefore, radiological response has emerged as 
an important non-invasive treatment target in small bowel CD, associated with decreased long-
term need for corticosteroid usage, hospitalization, and surgery.10-12  Additionally, the EMBARK 
study has demonstrated that a combined scoring of disease activity using ileocolonoscopy (SES-
CD) and CTE correlated much better with biomarkers of inflammation (fecal calprotectin, IL-22, 
and serum matrix metalloproteinase-9) than ileocolonoscopy alone.13  Furthermore, a recent 
multicenter study (N = 214 CD patients) by the Grupo de Estudos de Doença Inflamatόria 
Intestinal compared outcomes with a target of transmural healing (TH) on MRE compared to 
MH on colonoscopy.14  At 12 months, TH compared to MH, showed lower rates of therapy 
escalation (15.2% vs 36.5%, p=0.03) and surgery (0% vs 11.5%, p=0.047), and longer times to 
therapy escalation and surgery (p=0.046 and p=0.045, respectively.  There is an unmet need for 
assessing objective response to vedolizumab in small bowel CD using cross-sectional 
imaging that reflects transmural healing compared to detection of MH with endoscopy. 
PREDICTORS OF REMISSION AND NON-RESPONSE TO VEDOLIZUMAB IN CROHN’S 
DISEASE: Finally, while objective and complete small bowel assessment of response to therapy 
is important, the ability to predict early who is likely to achieve response to vedolizumab at 6 and 
12 months is equally critical to optimize medical therapy within the ideal window of ‘early CD’.15  
In the VICTORY consortium a week 6 clinical remission was achieved in 10.9% with a median 
time to achieve a clinical remission of 25 weeks, though this increased to 18% at 6 months and 
35% at 12 months.7  

Protocol ID: Entyvio 
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A posthoc analysis of GEMINI II trial data was undertaken to construct a predictive model for 
week 26 clinical remission using clinical predictors.16  In this model, an elevated baseline CRP 
was incrementally associated with a reduction in the probability of achieving clinical remission in 
anti-TNF-naïve participants (OR 0.94 per mg/L increase; P-value < 0.05), but not anti-TNF-
exposed/failure participants (OR 1.00; 95% CI, 0.98–1.02). The model had limited performance 
in the validation cohort for Week 26 clinical remission (AUC 0.69), which was not significantly 
improved by adding baseline CDAI into the model (AUC 0.73). This suggests that a model 
incorporating only clinical predictors is not highly discriminatory for clinical remission. Hence, 
in small bowel CD, there is a knowledge gap in the ability to predict and assess 
response/remission. This unmet need may be addressed by demonstrating the value of 
baseline radiological and endoscopic features of disease severity and burden to improve 
prediction of clinical remission with vedolizumab.  
Early identification of primary non-response (PNR) is equally critical to optimize medical therapy 
within the ideal window of ‘early CD’.15  CD patients initiated on a TNF-alpha antagonist (anti-
TNF) exhibit PNR ranging from 36–40% in clinical trials and 13–33% in clinical practice.17  There 
is an additional knowledge gap of clinically relevant serum biomarkers that can predict PNR 
with vedolizumab therapy in small bowel CD assessed by objective radiological criteria.  This 
would allow early detection of patients that are less likely to achieve long term response to 
vedolizumab. This is important given the longer time to response (median 19 weeks) observed in 
the real-world usage of vedolizumab (VICTORY consortium).7  In IBD, proteomic approaches 
have shown promise with regards to identifying active disease and predicting response to anti-

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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TNF.18-20  A serum proteomic analysis of patients who received ustekinumab in UNITI-1, UNITI-
2 and IM-UNITI identified IFN γ as a pharmacodynamic marker, and Serum Amyloid A and IL-6 
as early biomarkers of response to ustekinumab.21,22   
SUMMARY: The overall goal of the study is to develop data that can convincingly guide 
clinicians on the use and efficacy of vedolizumab in patients with small bowel CD.  There is 
an unmet need to identify response to vedolizumab in small bowel CD using objective endpoints. 
Current data suggest that MR enterography may meet this unmet need. There is an additional 
unmet need to develop predictive models incorporating both clinical and baseline radiological and 
endoscopic variables with higher discriminatory performance in identifying longer term clinical 
remission with vedolizumab. Finally, this proposal is strengthened by the exploratory studies 
which may identify new proteomic biomarkers that correlate with longer term radiological 
response with vedolizumab reflecting its latency of response. If successful, these serum biomarkers 
may guide a personalized approach to the treatment of small bowel CD with vedolizumab, 
allowing early identification of PNR, monitoring disease activity and the pharmacodynamics of 
vedolizumab.  
C. HYPOTHESIS 
We hypothesize that radiological response to vedolizumab will predict a reduction in need for 
corticosteroids, hospitalizations and/or surgeries in small bowel CD. We also hypothesize that 
predictive models incorporating baseline radiological variables in addition to clinical variables will 
improve model performance in predicting remission with vedolizumab at 6 months.   

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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We plan to test our central hypothesis by pursuing the following specific aims:   
Aim 1: To prospectively determine if short term (4 months) radiological TR on MRE in 
small bowel CD patients starting vedolizumab predict clinically relevant outcomes at 12 
months; 
Aim 2: To prospectively determine if inflammatory severity defined by the length of active 
small bowel lesion at baseline enterography improves the performance of model 
incorporating clinical variables in predicting clinical remission at 4 months; 
Aim 3: To assess if quantitative or qualitative change in proteomic serum biomarkers 
(using SOMAscanTM assay) is a relevant surrogate biomarker for radiologic TR on MRE at 
4 months after starting vedolizumab.   
The work proposed in Aim 1 would establish radiological response as a treatment endpoint with 
vedolizumab for small bowel CD. The work proposed in Aim 2 would allow improved 
prediction of remission with vedolizumab in small bowel CD. The work proposed in Aim 3 
would allow the development of a serum biomarker that correlates with radiological response at 
4 months. After completion of the current study aims, the next step using this study cohort would 
be to compare radiological versus endoscopic response at week 52. Future directions would 
include validating the findings of this study by performing an interventional study to personalize 
the dosing of vedolizumab starting at induction (based on markers of baseline inflammatory 
severity using MRE and cytokine burden) to achieve clinical and radiological response at 4 and 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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12 months.  We would also seek to validate the proteomic biomarkers of primary non-response 
identified in the current study cohort, in the dose optimization study. 
D. Pilot Data 
Retrospective study of treating to radiological response 
Our recent retrospective study demonstrated that treating to a target of radiological transmural 
response (TR) at initial follow-up computed tomography enterography (CTE) or magnetic 
resonance enterography (MRE) in small bowel CD is associated with an improvement in relevant 
long-term outcomes.10  In this cohort of 150 small bowel CD patients who were longitudinal 
followed with serial CTE and/or MRE, radiological TR was examined as a decrease in 
radiological findings of inflammation, in up to five small bowel lesions per patient, over follow-
up CTE/MRE. In this study, 55 patients (37%) were complete radiologic responders, 39 partial 
(26%), and 56 non-responders (37%), at the 1st follow-up CTE/MRE.  
 
 
 
 
 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
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SOMAscanTM in biomarker exploration 
In multivariable Cox models, complete and 
partial response were associated with a 
decreased risk for corticosteroid usage by over 
50% (hazard ratio (HR): 0.37 (95% 
confidence interval (CI), 0.21–0.64); 0.45 
(95% CI, 0.26–0.79)), and complete response 
decreased the risk of subsequent 
hospitalizations (Figure 1) and surgery 
(Figure 2) by over two-thirds (HRs: HR, 0.28 
(95% CI, 0.15–.50); HR, 0.34 (95% CI, 0.18–
0.63)).  Prior work has demonstrated that 
small bowel CD inflammatory severity is 
highly correlated with disease length, and that 
changes in the length of small bowel CD 
inflammation itself is a highly accurate 
Figure 2: Complete response at 2nd CTE/MRE demonstrated improved survival free 
of CD-related surgeries compared to those with non-response. 
Figure 1: Patients who demonstrated partial (p =0.04) or complete response (p < 
0.001) at 2nd CTE/MRE demonstrated improved survival free of hospitalizations for 
CD, compared to those with non-response

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SOMAscanTM (SomaLogic, Inc., Boulder, CO, USA) is a novel high-throughput analysis of 
proteins through Slow Off-rate Modified DNA Aptamer (SOMAmer)-based capture array. 
SOMAscanTM has enabled the simultaneous measurement of a large number of proteins to 
identify biomarkers in lung cancer, cardiovascular disease and inflammatory arthritis.25-29  
SOMAscanTM has also previously identified 18 proteins responsive to both prednisone and 
infliximab in pediatric IBD patients, with gene promoters regulated by nuclear factor-κB.30  Of 
these, five proteins with known functions associated with inflammation, including α-1- 
antitrypsin, insulin-like growth factor binding protein 1 and 2, resistin, and C-C motif chemokine 
23, showed a significant decrease in response to treatment.  
The SOMAscanTM panel also contains serum proteins that have been identified in previous 
studies as serum biomarkers correlating with a combination of endoscopic and cross-sectional 
imaging findings of inflammation in CD including IL-22, and serum matrix metalloproteinase-
9.13  Additional proteins in the panel have been identified in prior studies as potential biomarkers 
of infliximab (platelet factor 4, soluble CD40 ligand and IL-6) and ustekinumab response (IFN γ, 
serum amyloid A, IL-6, interleukin-17A and creatine kinase M‐type: creatine kinase B‐type 
heterodimer.19,21,22   
The mechanism of action of vedolizumab involves vedolizumab selectively inhibition of 
adhesion of alpha-4 beta-7 expressing cells to MAdCAM-1 and fibronectin but not to vascular 
cell adhesion molecule 1 (VCAM-1).2  While a prior study has explored serum MAdCAM-1 as a 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
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possible marker of response to therapy, the SOMAscanTM panel contains fibronectin and VCAM-
1, which could be explored as mechanistic biomarkers of response with vedolizumab therapy.31 
 
 
E. Study design 
Total Study Duration: 
 Final protocol to IEC/IRB/HA approval: Approved 
 IEC/IRB/HA approval to First Patient, First Visit: 2 month 
 First Patient, First Visit to Last Patient, Last Visit: 48 month 
 Treatment period: 12 months 
 Final study report timing after Last Patient, Last Visit: 6 months 
 Publication submission timing after final study report:3 months                  
Primary endpoint: 
1. Radiological response at 4 months (16±2 weeks) 
Radiological TR will be defined per-lesion and per-patient (Appendix A).  Per-lesion TR will be 
defined as a decrease in the length of inflamed small bowel lesion from baseline or improvement 
in any imaging findings associated with severe mural inflammation, i.e., restricted diffusion, 

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mural thickness, intramural T2 hyperintensity, peri-enteric T2 signal, and luminal ulcerations, 
without development of a new penetrating or stricturing complication.  Worsened lesions will be 
fined as those with an increased score of any imaging parameter associated with severe mural 
inflammation.  Unchanged lesions will be defined as those with unchanged (without worsening 
or improving) inflammatory parameters associated with severe mural inflammation.  Patients 
will be then classified for TR as responders if all individual lesions improved and non-responders 
if any of the lesions worsened, a new lesion developed at the 4 month MRE and all other 
scenarios not meeting definition of response.  Illustrative example of a radiological complete 
responder is shown in Figure 3. 
 
Secondary endpoint: 
Figure 3: Illustrative 
example of a radiological 
complete responder where 
colored arrows indicate 
corresponding bowel loops 
on follow-up CTE or MRE.  
(a) CTE 7/26/04 
demonstrating multifocal 
jejunal CD with rectovaginal 
and transsphincteric fistulae. 
(b) CTE 10/30/2006 
demonstrating radiological 
response in the jejunal and 
pelvic CD after starting on 
combination therapy with 
anti-TNF along with 
azathioprine.  
(c) MRE 10/19/2007 
demonstrating healed 
jejunal and pelvic fistulizing 
CD

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1. Clinical response (compared to baseline) at 6 weeks (±1 week), 4 months (16±2 weeks) study 
visit, clinical visit prior to 3rd cycle of 4 weekly dosing of vedolizumab among patients who 
dose-escalated after week 14 dose, and 1 year (52±4 weeks) 
 100 points reduction in CDAI or 
 ≥3 point decrease in HBI or 
 ≥5 point reduction in Patient reported outcome - 2 (PRO-2) 
2. Clinical response (compared to baseline) at 6 weeks (±1 week), 4 months (16±2 weeks) study 
visit, clinical visit prior to 3rd cycle of 4 weekly dosing of vedolizumab among patients who 
dose-escalated after week 14 dose, and 1 year (52±4 weeks) 
 CDAI score ≤150 points or 
 HBI ≤ 4 points or 
 PRO-2 ≤8 points 
3. Endoscopic disease activity at 1 year (52±4 weeks): SES-CD. 
4. Endoscopic remission at 1 year (52±4 weeks): SES-CD 0 to 2.  
Other endpoints: 
5. EQ 5-D: EuroQol instrument for recording self-reported health status 
6. Disease progression including: 
 Internal penetrating disease at MRE at 1 year (52±4 weeks) 
 Stricturing disease at MRE at 1 year (52±4 weeks) 

Protocol ID: Entyvio 
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 Hospitalization for flares or complications of the disease after  MRE at 4 months (16±2 
weeks) and till MRE at 1 year (52±4 weeks) 
 Need for surgery related to CD after  MRE at 4 months (16±2 weeks) and till MRE at 1 year 
(52±4 weeks) 
 Need for rescue corticosteroids after  MRE at 4 months (16±2 weeks) and till MRE at 1 year 
(52±4 weeks) 
 
Study population: 
Patients with known or suspected CD identified at the IBD Clinic in the Division of 
Gastroenterology and Hepatology at Washington University, St. Louis, MO will be recruited if 
they meet inclusion/exclusion criteria. Please see Appendix B for details on the study visits.  
Patient who have had a standard of care ileocolonoscopy and MRE will be recruited if they meet 
the following: 
Key inclusion criteria: 
 Moderate to severe disease activity small bowel CD (small bowel only or ileocecal only) 
visible on MRE 
 Initiated on Vedolizumab with/without thiopurines or methotrexate 
 ≥18 years old 
Key exclusion criteria: 

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 Known pregnancy on study entry.  Subjects will not be tested for pregnancy on protocol 
outside of standard of care, and is usually done prior to clinical radiological and endoscopic 
testing for patients of childbearing potential per standard of care standard operating 
procedures.  If any subject is found to be pregnant during the study they will be discontinued 
from the study visit protocol and followed per the pregnancy follow up, as outlined below 
under “Procedures for Reporting Drug Exposure during pregnancy and Birth Events”.  Any 
pregnant partner of study subjects reported during this study will be followed also as below. 
 Age <18 years old 
 Planned surgery prior to the first follow-up MRE 
 Inability to provide informed consent. 
 Perianal CD, since assessment requires performance of additional MRI of the pelvis. 
 Individuals with colonic involvement other than involvement of the ascending colon and 
cecum.   
 Inpatient scans will only be included if this is an MRE and adequate small bowel distension 
with appropriate contrast has been achieved, in the opinion of the radiology co-investigator.  
 Contraindications for MRE, including chronic kidney disease that precludes contrast 
administration, and implanted medical devices that are contraindicated for MRE. 
 Any subject condition or situation which, in the opinion of the Investigator or regulatory 
authorities, interferes with optimal study participation of the participant or produces/could 
produce significant risk to the subject. 
Treatment regimen: 

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Vedolizumab will be initiated at 300 mg intravenous (IV) dosing at 0, 2 and 6 weeks followed by 
the 1st maintenance with 300 mg IV at week 14.  Patients who have not achieved clinical 
response at week 14 will be eligible to undergo dose escalation to 4 weekly dosing of 
vedolizumab depending on the judgement of the treating gastroenterologist.  The precedent for 
this is observations from the open-label GEIMINI long-term safety (LTS) trial where patients 
who received vedolizumab every 8 weeks during GEMINI 2 maintenance were escalated to 
every 4 weeks during GEMINI LTS.32  Specifically, among the 57 patients receiving 
vedolizumab every 8 weeks during GEMINI 2 and withdrew from the study early (sustained 
non-response, disease worsening, or need for rescue medication), clinical response increased 
from 39% (22/57) at the onset of LTS trial to 54% (n=31/57) at week 28 and 35% (20/57) at 
week 100. Similar trends were seen in clinical remission, with increase from 4% (2/57) at the 
LTS trial onset to 23% (13/57) at week 28 and 19% (11/57) at week 100. A similar trend in 
efficacy was observed with increased dosing frequency regardless of prior TNF antagonist 
exposure.  Similar data was shown in the study by Wiliet et al. with dose escalation at week 10 in 
patients without clinical remission at week 6.33   
Study Visits: 
Patients entering the study will be evaluated by the investigator for all inclusion and exclusion 
criteria.  Once inclusion and exclusion criteria have been determined, all subjects will sign an 
IRB/IEC approved consent document, which complies with regulatory requirements, prior to any 
study activities.  Subjects will be given adequate time to read and consider the consent document 

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and all study information.  They will have the opportunity to ask questions of the investigator(s) 
and the study team about the study, as well as risks and benefits, prior to signing the document.   
Baseline Visit 
Baseline assessments will be collected from the clinical care record from the standard of care 
visit(s) done most prior to the subject receiving their first dose of vedolizumab.  All assessments 
will be done/collected prior to the subject’s first does of vedolizumab.  The baseline visit will 
consist of the following: 
- 
Demographic information: Date of birth, gender, and race will be collected. 
- 
Clinical assessment:  These assessments will be done by the study team prior to the 
subject receiving the first dose of vedolizumab.  
o CDAI 
o Harvey Bradshaw Index 
o PRO-2/3 
o EQ-5D 
o IBD Disability Index 
- 
Physical Exam Findings: Physical exam findings will be taken from the patient’s clinical 
care record from the standard of care visit most recently preceding the initial dose of 
vedolizumab.  If this data is not available from the visit, the information will be obtained 
from the subject during a separate visit to the clinic by the study team, and prior to the 
first dose of vedolizumab.   

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o Height/Weight 
o Waist/Hip Ratio 
- 
Blood Tests:  
o C-reactive Protein (taken from the clinical care record as described below) 
o Albumin (taken from the clinical care record as described below) 
o Hematocrit (taken from the clinical care record as described below for assessment 
of CDAI) 
o SOMAscan panel (drawn for protocol as described below) 
- 
 
- 
Stool Collection:  At the time of consent, participants will be provided a stool collection 
kit and asked to collect a small amount of stool when they have a bowel movement, prior 
to their first dose of vedolizumab, for genetic, microbiome, or biomarker analysis. If the 
patient is unable to provide a stool sample, permission may be asked to obtain a rectal 
swab, or a sample collection kit will be mailed to them and asked to mail the stool sample 
back to us in a prepaid envelope. If the patient is in the hospital and tests have been 
ordered on their stool, stool may be collected from what is left over after the tests have 
been completed. The stool will be assigned a unique specimen code. The mRNA in the 
stool would be extracted and the genetic expression profile of this sample would be 
determined. All participants consent to having details from their medical records (age, 
ethnicity, medications, surgery, tobacco use, family history, disease activity, disease 
history) at the Washington University Medical Center, and entered into a database 

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associated with a patient code. If the patient's records do not include all relevant 
information, a study team member may obtain this information directly from the patient.  
The specimen(s) will not have the participant name or address on it; it will be labeled 
with a code in order to protect the patient's health information and identity. The 
specimen(s) will be stored in locked freezers in a locked laboratory at WUSM. All coded 
specimens will be linked to study participants on a separate master list, which will be 
stored in a locked cabinet (the study coordinators have the only key) or a password 
protected file. This information will be kept separate from the clinical data. 
- 
Endoscopic Assessment: Subjects will have endoscopic assessment as baseline prior to 
initiation of vedolizumab, as a part of their standard of care treatment.  Subjects who 
have had endoscopic assessment with biopsies from the ileum confirming small bowel 
Crohn’s disease as a part of their standard of care treatment in the six (6) months prior to 
study enrollment may be used for the baseline study assessment, at the investigator’s 
discretion.  If a more recent endoscopic assessment is done with this reporting, the more 
recent assessment will be used. 
- 
Radiological Assessment: Radiological assessment will be performed on all patients as a 
part of their clinical standard of care prior to initiating vedolizumab.  Clinical read will be 
evaluated using the assessment tool in Appendix B and guidance from Appendix A. 
o MR Enterography 
Week 6 Visit (+/- 1 week)  

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Week 6 Visit assessment will be done 6 weeks (+/- 1 week) after initiating vedolizumab as a part 
of clinical standard of care treatment as described in this protocol.  The visit will consist of the 
following: 
- 
Clinical assessment:   
o CDAI 
o Harvey Bradshaw Index 
o PRO-2/3 
o EQ-5D 
o IBD Disability Index 
- 
Blood Tests:  
o C-reactive Protein (taken from the clinical care record as described below) 
o Albumin (taken from the clinical care record as described below) 
o Hematocrit (taken from the clinical care record as described below for assessment 
of CDAI) 
o SOMAscan panel (drawn for protocol as described below) 
Week 16 Visit (+/- 2 weeks)  
Week 16 Visit assessment will be done 16 weeks (+/- 2 weeks) after initiating vedolizumab as a 
part of clinical standard of care treatment as described in this protocol.  The visit will consist of 
the following: 

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- 
Clinical assessment:   
o CDAI 
o Harvey Bradshaw Index 
o PRO-2/3 
o EQ-5D  
o IBD Disability Index 
- 
Physical Exam Findings: Physical exam findings will be taken from the patient’s clinical 
care record from the most recent standard of care visit.  If this data is not available from 
the visit, the information will be obtained from the subject during a separate visit to the 
clinic by the study team.   
o Height/Weight 
o Waist/Hip Ratio 
- 
Blood Tests:  
o C-reactive Protein (taken from the clinical care record as described below) 
o Albumin (taken from the clinical care record as described below) 
o Hematocrit (taken from the clinical care record as described below for assessment 
of CDAI) 
- 
Stool Collection:  As above referenced in the Baseline Visit. 
- 
Radiological Assessment:  
o MR Enterography 
Clinical Visit 

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The Clinical Visit assessment will only be done if a dose escalation is needed for vedolizumab 
treatment in patients who do not achieve clinical response at week 14, per investigator discretion.  
- 
Clinical assessment:   
o CDAI 
o Harvey Bradshaw Index 
o PRO-2/3 
o EQ-5D 
o IBD Disability Index 
- 
Blood Tests:  
o C-reactive Protein (taken from the clinical care record as described below) 
o Albumin (taken from the clinical care record as described below) 
o Hematocrit (taken from the clinical care record as described below for assessment 
of CDAI) 
 
Week 52 Visit (+/- 4 weeks) 
Week 52 assessments will be done 52 weeks (+/- 4 weeks) after initiating vedolizumab as a part 
of clinical standard of care treatment as described in this protocol.  The visit will consist of the 
following: 
- 
Clinical assessment:   

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o CDAI 
o Harvey Bradshaw Index 
o PRO-2/3 
o EQ-5D 
o IBD Disability Index 
- 
Physical Exam Findings:  Physical exam findings will be taken from the patient’s clinical 
care record from the most recent standard of care visit.  If this data is not available from 
the visit, the information will be obtained from the subject during a separate visit to the 
clinic by the study team.   
o Height/Weight 
o Waist/Hip Ratio 
- 
Blood Tests:  
o C-reactive Protein (taken from the clinical care record as described below) 
o Albumin (taken from the clinical care record as described below) 
o Hematocrit (taken from the clinical care record as described below for assessment 
of CDAI) 
- 
Endoscopic Assessment: Subjects will have endoscopic assessment as a part of their 
standard of care treatment, and this report may be used for the study assessment. 
o SES-CD 

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- 
Radiological Assessment: Radiological assessment will be performed on all patients as a 
part of their clinical standard of care.  Clinical read will be evaluated using the 
assessment tool in Appendix B and guidance from Appendix A. 
o MR Enterography 
- 
Disease Progression Assessment: In order to assess the Disease Progression endpoint the 
following will be assessed for the time point between the Week 16 Visit MRE and the 
Week 52 Visit MRE: 
o Any hospitalization for disease flare or complications of the disease 
o Need for surgery related to CD 
o Need for rescue corticosteroids 
Withdrawal Criteria: 
Subjects are free to withdraw their consent from study participation at any time, for any reason, 
without interference to their continued standard medical care.  Subjects will be withdrawn should 
the any of the following occur: 
- 
The subject develops, or has an exacerbation of, any medical condition, which the 
investigator believes would preclude, interfere, or otherwise make the subject’s continued 
participation in the study unsafe. 
- 
The subject withdraws consent. 
- 
Any confirmation of pregnancy. 
- 
Any regulatory request of subject withdrawal 

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- 
Any subject non-compliance with study procedures in the opinion of the investigator. 
- 
The subject experiences a severe or serious adverse event which would, in the opinion of 
the investigator, preclude the subject from continued participation. 
Safety Reporting  
Institution/Investigator is solely responsible for reporting all Adverse Events and Serious 
Adverse Events to regulatory authorities, investigators, IRBs or IECs and Takeda, as applicable, 
in accordance with national regulations in the countries where the study is conducted.  
Regardless of expectedness or causality, all SAEs and pregnancy reports must also be reported 
in English by facsimile to Takeda Pharmacovigilance or designee: 
Fatal and Life Threatening SAEs within 24 hours of the sponsor-investigator’s observation or 
awareness of the event 
All other serious (non-fatal/non-life threatening) events within 4 calendar days of the sponsor-
investigator’s observation or awareness of the event 
Takeda Safety Reporting Contact Information 
Takeda requires that all information be communicated to Takeda’s Pharmacovigilance 
Department as outlined in the study contract. 

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All reported adverse drug reactions and safety issues related to Takeda compound must be 
included in the final study report. 
Describe procedures for reporting Adverse Events and Serious Adverse Events. 
Definitions:  
Adverse event (AE) means any untoward medical occurrence in a patient or subject administered 
a medicinal product; the untoward medical occurrence does not necessarily have a causal 
relationship with this treatment.  An AE can therefore be any unfavorable and unintended sign 
(including an abnormal laboratory finding), symptom, or disease temporally associated with the 
use of a medicinal (investigational) product whether or not it is related to the medicinal product.  
This includes any newly occurring event, or a previous condition that has increased in severity 
or frequency since the administration of study drug. 
An abnormal laboratory value will not be assessed as an AE unless that value leads to 
discontinuation or delay in treatment, dose modification, therapeutic intervention, or is 
considered by the investigator to be a clinically significant change from baseline.   
An adverse drug reaction (ADR) is a response to a medicinal product which is noxious and 
unintended. Response in this context means that a causal relationship between a medicinal 
product and an adverse event is at least a reasonable possibility. This includes adverse reactions 
which arise from: use of a medicinal product within the terms of the marketing authorization; 

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use outside the terms of the marketing authorization, including overdose, misuse, abuse and 
medication errors; and occupational exposure*. 
* This corresponds to the exposure to a medicinal product for human use as a result of one’s 
occupation, such as nurses who may handle products routinely in their occupational setting. 
Serious AE (SAE) means any untoward medical occurrence that at any dose: 
1) results in death, 
2) is life-threatening, 
Note: The term “life-threatening” in the definition of “serious” refers to an event in which the 
patient was at risk of death at the time of the event; it does not refer to an event which 
hypothetically might have caused death if it were more severe. 
3) requires inpatient hospitalization or prolongation of present hospitalization, 
4) results in persistent or significant disability/incapacity, 
5) leads to a congenital anomaly/birth defect, 
6) may require intervention to prevent one of 1)-5) above or may expose the patient to danger, even 
though the event is not immediately life-threatening or fatal or does not result in hospitalization. 
 Clarification should be made between a serious AE (SAE) and an AE that is considered severe 
in intensity (Grade 3 or 4), because the terms serious and severe are NOT synonymous.  The 
general term severe is often used to describe the intensity (severity) of a specific event; the event 

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itself, however, may be of relatively minor medical significance (such as a Grade 3 headache).  
This is NOT the same as serious, which is based on patient/event outcome or action criterion 
described above, and is usually associated with events that pose a threat to a patient’s life or 
ability to function.  A severe AE (Grade 3 or 4) does not necessarily need to be considered 
serious.  For example, a white blood cell count of 1000/mm3 to less than 2000 is considered 
Grade 3 (severe) but may not be considered serious.  Seriousness (not intensity) serves as a 
guide for defining regulatory reporting obligations. 
Procedures for Reporting Drug Exposure during Pregnancy and Birth Events 
If a woman becomes pregnant or suspects that she is pregnant while participating in this study, 
she must inform the investigator immediately and permanently discontinue study drug.  The 
sponsor-investigator must fax a completed Pregnancy Form to the Takeda Pharmacovigilance or 
designee immediately.  The pregnancy must be followed for the final pregnancy outcome (i.e., 
delivery, still birth, miscarriage) and Takeda Pharmacovigilance or designee will request this 
information from the sponsor-investigator. Please refer to study contract for Takeda 
pharmacovigilance contact information. 
If a female partner of a male patient becomes pregnant during the male patient’s participation in 
this study, the sponsor-investigator must also immediately fax a completed Pregnancy Form to 
the Takeda Pharmacovigilance or designee. Every effort should be made to follow the pregnancy 
for the final pregnancy outcome. Please refer to study contract for Takeda pharmacovigilance 
contact information. 

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Product Complaints and Medication Errors  
A product complaint is a verbal, written, or electronic expression that implies dissatisfaction 
regarding the identity, strength, purity, quality, or stability of a drug product.  Individuals who 
identify a potential product complaint situation should immediately contact Takeda and report 
the event.   
A medication error is a preventable event that involves an identifiable patient and that leads to 
inappropriate medication use, which may result in patient harm.  While overdoses and 
underdoses constitute medication errors, doses missed inadvertently by a patient do not.  
Individuals who identify a potential medication error situation should immediately contact 
Takeda (see below) and report the event. 
Phone: 1-877-TAKEDA7 (1-877-825-3327) 
E-mail: medicalinformation@tpna.com 
FAX: 1-800-247-8860 
Product complaints and medication errors in and of themselves are not AEs.  If a product 
complaint or medication error results in an SAE, an SAE form should be completed and sent to 
Takeda Pharmacovigilance. 
Serum proteomic analysis with SOMAscanTM   

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Serum protein concentration in AIM 3 will be as measured using SOMAscanTM at the certified 
Genome Technology Access Center (GTAC) microarray facility at Washington University using 
Agilent microarray readout.34  This will be drawn prior to initiation of therapy and at week 6. 
This proteomic platform has enabled the simultaneous measurement of a large number of 
proteins to identify biomarkers in lung cancer, cardiovascular disease, inflammatory arthritis and 
inflammatory bowel disease.25-30,35   
The GTAC lab has been certified in SomaScanTM technology from the SomaLogics company. 
The SOMAscan assay quantitatively transforms the proteins present in a biological sample into a 
specific SOMAmer-based DNA signal. A SOMAmer-protein binding step is followed by a series 
of partitioning and wash steps that converts relative protein concentrations into measurable 
nucleic acid signals that are quantified using DNA detection technology, which for the 
SOMAscan Assay with 1,310 SOMAmer reagents is by hybridization to custom DNA 
microarrays. The assay offers exceptional dynamic range, quantifying proteins that span over 8 
logs in abundance (from femtomolar to micromolar) and excellent reproducibility (4.6% median 
%CV). Agilent SOMAScan slides will be processed through the Agilent scanner and image data 
will be extracted using Agilent Feature Extraction software. Extracted initial raw signal intensity 
data will be uploaded onto the SOMAScan server for data QC and standardization. The final data 
set will include SOMAscan generated .adat file, a reformatted text file with standardized relative 
fluorescent unit (RFU) for ~1.3K proteins, SOMAscan Quality Statements (SQS) and basic 
differential expression. The technology has been well validated by mass-spec here at Washington 
University. 

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Other laboratory tests 
Serum will be collected at all 5 time points with CRP, hematocrit (as part of CBC) and serum 
albumin prior to medication initiation, week 6, 4 months (16±2 weeks), prior to the 3rd 4 weekly 
cycle of vedolizumab after dose escalation in patients who failed to achieve clinical response 
(CDAI 100 point decrease) at week 14 and at 52 ± 4 weeks.   
F. Statistical plan 
Statistical analysis 
AIM 1: Response at 4 month MRE will be categorized as non-response versus response to 
biologic.  Association between response status at 4 month MRE and clinically relevant outcomes 
will be assessed at week 52 in logistic regression model adjusting for variables include gender, 
age at disease onset/disease duration, smoking status and presence of stricturing/fistulizing 
disease at baseline MRE.  Additional time-to clinically relevant outcomes after 6 month MRE 
depending on response status will be assessed using Cox proportional hazards model adjusting 
for prior mentioned variables 
AIM 2: Multivariate logistic regression analyses and backward model selection will be 
performed for baseline clinical, radiological (length of disease) and endoscopic variables (SES-
CD score) and variable interactions that are found to be significant (P < 0.05) on the initial 
univariate analyses. Adjusted odds ratio (OR) will be presented for predictors included in the 
model, with OR > 1 indicating an increased probability of achieving clinical remission at Week 

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26. Discrimination performance of the model will be presented as area under the curve (AUC) 
from receiver operating characteristic curves. 
AIM 3: Normality of protein values will be determined by the Kolmogorov Smirnov and 
Shapiro-Wilk normality tests. Statistical techniques will include Wilcoxon signed-rank test 
(comparing baseline to posttreatment values in the same individual), Mann-Whitney U test 
(comparing change in individual proteins in SOMAscanTM between the response categories at 
week 14 MRE), linear regression analysis (SOMA scanTM vs. CRP) and logistic regression 
analysis (change in levels of identified proteins in SOMAscanTM versus response categories, 
adjusting for patient and disease characteristics). Spearman rank correlation analysis will be 
applied to assess correlations. The alpha-level will be set at 0.05 for statistical significance.  
Bonferroni correction will be applied for multiple testing. 
Sample size analysis 
We estimate 37% of CD patients with complete, 26% partial and 37% non-response at 14 week 
MRE based on prior data.10  At a power of 80% and a type-1 error (alpha) of 0.05 to detect a 
hazards ratio of 2.5 or more, we estimate that 38 or more patients will transition from 
partial/non-response to complete response based on prior data. In a year, we expect 50% of the 
patients making such a transition. Hence, we plan to recruit at least 76 patients to this cohort.  
Alternately, 130 CD patients would be estimated to detect an HR of 2.0 assuming 50% transition 
within 1 year.   

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G. Scientific team collaborators 
This project is collaboration between the Division of Gastroenterology, Mallinckrodt Institute of 
Radiology and the Biomarker core at Washington University, St. Louis, MO.  Dr. Deepak has 
joined the faculty at Washington University. He has extensive research experience in the field of 
the use of diagnostic imaging in IBD, mentored by Dr. David H. Bruining and Dr. Joel G. 
Fletcher.4,10-12,36,37 Dr. Ciorba has published extensively on biomarkers in IBD18,38-41 and on 
MRE imaging for IBD with the Mallinckrodt group.42  
H. Limitations of study design 
Our study will utilize a scoring system with MRE with components derived from previously 
validated methodology utilizing both CTE and MRE.  While several MR based scoring systems 
are currently available, these have largely been modeled after and validated against endoscopic 
scoring systems, with only a modest weight given to small bowel inflammation (eg, only 1 of 5 
bowel segments scored in the Magnetic Resonance Index of Activity Score as part of the small 
bowel). 36 These have additional limitations in describing overall disease burden and 
reproducibility. 
 
 

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J. References 
1. 
Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. 
Nature. Jul 26 2007;448(7152):427-434. 
2. 
Wyant T, Fedyk E, Abhyankar B. An Overview of the Mechanism of Action of the 
Monoclonal Antibody Vedolizumab. J Crohns Colitis. Dec 2016;10(12):1437-1444. 
3. 
Sandborn WJ, Feagan BG, Rutgeerts P, et al. Vedolizumab as induction and maintenance 
therapy for Crohn's disease. N Engl J Med. Aug 22 2013;369(8):711-721. 
4. 
Deepak P, Fletcher JG, Fidler JL, Bruining DH. Computed Tomography and Magnetic 
Resonance Enterography in Crohn's Disease: Assessment of Radiologic Criteria and 
Endpoints for Clinical Practice and Trials. Inflamm Bowel Dis. Sep 2016;22(9):2280-
2288. 
5. 
Peyrin-Biroulet L, Reinisch W, Colombel JF, et al. Clinical disease activity, C-reactive 
protein normalisation and mucosal healing in Crohn's disease in the SONIC trial. Gut. Jan 
2014;63(1):88-95. 
6. 
Feagan BG, Rutgeerts P, Sands BE, et al. Vedolizumab as induction and maintenance 
therapy for ulcerative colitis. The New England journal of medicine. Aug 22 
2013;369(8):699-710. 

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7. 
Dulai PS, Singh S, Jiang X, et al. The Real-World Effectiveness and Safety of 
Vedolizumab for Moderate-Severe Crohn's Disease: Results From the US VICTORY 
Consortium. Am J Gastroenterol. Aug 2016;111(8):1147-1155. 
8. 
Peyrin-Biroulet L, Loftus EV, Jr., Colombel JF, Sandborn WJ. The natural history of 
adult Crohn's disease in population-based cohorts. Am J Gastroenterol. Feb 
2010;105(2):289-297. 
9. 
Fiorino G, Morin M, Bonovas S, et al. Prevalence of Bowel Damage Assessed by Cross-
Sectional Imaging in Early Crohn's Disease and its Impact on Disease Outcome. J 
Crohns Colitis. Mar 01 2017;11(3):274-280. 
10. 
Deepak P, Fletcher JG, Fidler JL, et al. Radiological Response Is Associated With Better 
Long-Term Outcomes and Is a Potential Treatment Target in Patients With Small Bowel 
Crohn's Disease. Am J Gastroenterol. Jul 2016;111(7):997-1006. 
11. 
Deepak P, Fletcher JG, Fidler JL, et al. Long-Term Maintenance of Radiological 
Response Is Associated With Decreased Probability of Surgeries, Hospitalizations, and 
Corticosteroids Usage in Crohn's Disease Patients. Gastroenterology. April 
2016;150(4):S130-130. 
12. 
Deepak P, Fletcher JG, Fidler JL, et al. Natural History of Radiological Transmural 
Healing in Small Bowel Crohn's Disease Patients Undergoing Serial Enterography. 
Gastroenterology. 2016;150(4):S130-131. 

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13. 
Faubion WA, Jr., Fletcher JG, O'Byrne S, et al. EMerging BiomARKers in Inflammatory 
Bowel Disease (EMBARK) study identifies fecal calprotectin, serum MMP9, and serum 
IL-22 as a novel combination of biomarkers for Crohn's disease activity: role of cross-
sectional imaging. Am J Gastroenterol. Dec 2013;108(12):1891-1900. 
14. 
Raimumdo Fernandes S, Vale Rodrigues R, Bernardo S ea. Transmural healing is better 
than mucosal healing in Crohn's disease (abstract). J Crohns Colitis. Vol.11, Supplement 
1, pp:S33 - S34. (Feb 2017). 
15. 
Peyrin-Biroulet L, Billioud V, D'Haens G, et al. Development of the Paris definition of 
early Crohn's disease for disease-modification trials: results of an international expert 
opinion process. Am J Gastroenterol. Dec 2012;107(12):1770-1776. 
16. 
Dulai P, Boland B, Singh S, et al. P-049 Validated Prediction Model for Clinical 
Remission with Vedolizumab in Crohn's Disease: Post Hoc Analysis of GEMINI II 
Clinical Trial (abstract). Inflamm Bowel Dis. 2017;23:S21. 
17. 
Ding NS, Hart A, De Cruz P. Systematic review: predicting and optimising response to 
anti-TNF therapy in Crohn's disease - algorithm for practical management. Aliment 
Pharmacol Ther. Jan 2016;43(1):30-51. 
18. 
Iskandar HN, Ciorba MA. Biomarkers in inflammatory bowel disease: current practices 
and recent advances. Transl Res. Apr 2012;159(4):313-325. 

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19. 
Meuwis MA, Fillet M, Lutteri L, et al. Proteomics for prediction and characterization of 
response to infliximab in Crohn's disease: a pilot study. Clin Biochem. Aug 
2008;41(12):960-967. 
20. 
Roda G, Caponi A, Benevento M, et al. New proteomic approaches for biomarker 
discovery in inflammatory bowel disease. Inflamm Bowel Dis. Jul 2010;16(7):1239-1246. 
21. 
Li K, Hayden K, Wadman E, et al. Dop052 Molecular response to ustekinumab in 
moderate-to-severe Crohn's disease by serum protein and biopsy gene expression 
analysis: results from Ustekinumab phase 3 studies (abstract). Journal of Crohn's & 
colitis. 2017;11(suppl_1):S57-S58. 
22. 
Li K, Hayden K, Wadman E, et al. Sa1837 Molecular Response to Ustekinumab in 
Moderate-to-Severe Crohn's Disease by Serum Protein Analysis: Results from UNITI-1 
Induction, UNITI-2 Induction, and IMUNITI Maintenance Studies (abstract). 
Gastroenterology. 2016;150(4):S377. 
23. 
Bruining DH, Loftus EV, Jr., Ehman EC, et al. Computed tomography enterography 
detects intestinal wall changes and effects of treatment in patients with Crohn's disease. 
Clin Gastroenterol Hepatol. Aug 2011;9(8):679-683 e671. 
24. 
Spilseth B, Fidler, J, Bruining, D, Hansel, S, Harmsen, W, Rimola, J, Holmes, D, Larson, 
A, Pruthi, S, Fletcher, J. Global Patient Assessment of Crohn’s Disease Severity: Is 
MaRIA Sufficient, or Does Length of Enteric Inflammation Matter? Radiological Society 

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of North America 2013 Scientific Assembly and Annual Meeting, December 1 - December 
6, 2013 ,Chicago IL.  http://archive.rsna.org/2013/13022081.html Accessed November 
18, 2016. 
25. 
Mehan MR, Ayers D, Thirstrup D, et al. Protein signature of lung cancer tissues. PLoS 
One. 2012;7(4):e35157. 
26. 
Ngo D, Sinha S, Shen D, et al. Aptamer-Based Proteomic Profiling Reveals Novel 
Candidate Biomarkers and Pathways in Cardiovascular Disease. Circulation. Jul 26 
2016;134(4):270-285. 
27. 
Ganz P, Heidecker B, Hveem K, et al. Development and Validation of a Protein-Based 
Risk Score for Cardiovascular Outcomes Among Patients With Stable Coronary Heart 
Disease. JAMA. Jun 21 2016;315(23):2532-2541. 
28. 
McArdle A, Qasim Butt A, Szentpetery A, et al. Developing clinically relevant 
biomarkers in inflammatory arthritis: A multiplatform approach for serum candidate 
protein discovery. Proteomics Clin Appl. Jun 2016;10(6):691-698. 
29. 
Murota A, Suzuki K, Kassai Y, et al. Serum proteomic analysis identifies interleukin 16 
as a biomarker for clinical response during early treatment of rheumatoid arthritis. 
Cytokine. Feb 2016;78:87-93. 

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30. 
Heier CR, Fiorillo AA, Chaisson E, et al. Identification of Pathway-Specific Serum 
Biomarkers of Response to Glucocorticoid and Infliximab Treatment in Children with 
Inflammatory Bowel Disease. Clin Transl Gastroenterol. Sep 15 2016;7(9):e192. 
31. 
Boland BS, Rivera-Nieves J, Jain A, et al. 535 Soluble MAdCAM-1: a potential 
Biomarker for response to vedolizumab (abstract). Gastroenterology. 2015;148(4):S-106-
S-107. 
32. 
Vermeire S, Loftus EV, Jr., Colombel JF, et al. Long-term Efficacy of Vedolizumab for 
Crohn's Disease. J Crohns Colitis. Sep 28 2016. 
33. 
Williet N, Boschetti G, Fovet M, et al. Association Between Low Trough Levels of 
Vedolizumab During Induction Therapy for Inflammatory Bowel DiseasesWith Need for 
Additional Doses Within 6 months. Clin Gastroenterol Hepatol. Nov 24 2016. 
34. 
Gold L, Walker JJ, Wilcox SK, Williams S. Advances in human proteomics at high scale 
with the SOMAscan proteomics platform. N Biotechnol. Jun 15 2012;29(5):543-549. 
35. 
Rohloff JC, Gelinas AD, Jarvis TC, et al. Nucleic Acid Ligands With Protein-like Side 
Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents. Mol 
Ther Nucleic Acids. Oct 07 2014;3:e201. 

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IRB Expired:  11/7/2025  
 
36. 
Deepak P, Kolbe AB, Fidler JL, Fletcher JG, Knudsen JM, Bruining DH. Update on 
Magnetic Resonance Imaging and Ultrasound Evaluation of Crohn's Disease. 
Gastroenterol Hepatol (N Y). Apr 2016;12(4):226-236. 
37. 
Deepak P, Bruining DH. Radiographical evaluation of ulcerative colitis. Gastroenterol 
Rep (Oxf). Aug 2014;2(3):169-177. 
38. 
Santhanam S, Alvarado DM, Ciorba MA. Therapeutic targeting of inflammation and 
tryptophan metabolism in colon and gastrointestinal cancer. Transl Res. Jan 
2016;167(1):67-79. 
39. 
Lee A, Kanuri N, Zhang Y, Sayuk GS, Li E, Ciorba MA. IDO1 and IDO2 non-
synonymous gene variants: correlation with crohn's disease risk and clinical phenotype. 
PLoS One. 2014;9(12):e115848. 
40. 
Ciorba MA. Indoleamine 2,3 dioxygenase in intestinal disease. Curr Opin Gastroenterol. 
Mar 2013;29(2):146-152. 
41. 
Gupta NK, Thaker AI, Kanuri N, et al. Serum analysis of tryptophan catabolism pathway: 
correlation with Crohn's disease activity. Inflamm Bowel Dis. Jul 2012;18(7):1214-1220. 
42. 
Ha CY, Kumar N, Raptis CA, Narra VR, Ciorba MA. Magnetic resonance enterography: 
safe and effective imaging for stricturing Crohn's disease. Dig Dis Sci. Oct 
2011;56(10):2906-2913. 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
Amendment 3 8Jun2021   Page 42 of 46 
Last IRB Approval: 11/8/2024 
IRB Expired:  11/7/2025  
 
43. 
Kim DH, Carucci LR, Baker ME, et al. ACR Appropriateness Criteria Crohn Disease. J 
Am Coll Radiol. Oct 2015;12(10):1048-1057 e1044. 
44. 
Fowler KJ, Dassopoulos T, Raptis C. Magnetic resonance enterography in the evaluation 
of Crohn's disease: a primer for the gastroenterologist. Inflamm Bowel Dis. Nov 
2014;20(11):2179-2188. 
 
 
 
 
 
 
 
 
 
Appendix A: Reader’s manual and sample data collection sheet for individual scan 
Overview: 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
Amendment 3 8Jun2021   Page 43 of 46 
Last IRB Approval: 11/8/2024 
IRB Expired:  11/7/2025  
 
1. Scoring to be done per patient and per lesion, of not more than 5 of the longest lesions identified 
on MR enterography (MRE). 
2. Lesion to be identified on index MRE. 
3. Skip lesion defined as two areas of active Crohn’s disease that must be separated by 
circumferential normal intestine. 
4. Location of segment involved(free text or selected): Series and image # 
5. Length of active disease segment in centimeters. 
6. Mural thickness small bowel: 
 
0 = <3 mm  
 
1 = >3–5 mm  
 
2 = >5–7 mm  
 
3 = >7 mm 
7. Mural T2 Signal: 
 
0 = Equivalent to normal bowel wall                 
 
1 = Minor increase in signal: bowel wall appears dark grey on fat-saturated images 
 
2 = Moderate increase in signal: bowel wall appears light grey on fat-saturated images 
 
3 = Marked increase in signal: bowel wall contains areas of white high signal 
approaching that of luminal content            
8. Peri-mural T2 signal: 
 
0 = Equivalent to normal mesentery  
 
1 = Increase in mesenteric signal but no fluid 
 
2 = Small fluid rim (≤2 mm)  
 
3 = Larger fluid rim (>2 mm) 
9. Presence of small bowel ulcerations: Wall defect that extends from the lumen intramurally, but 
not beyond the outside bowel wall. 
 
0 = No 
 
1 = Yes 
10. Stricture (obstruction) defined as luminal narrowing in area of Crohn’s disease with unequivocal 
proximal dilation, or that is persistent over two time points (e.g., multiple pulse sequences or delayed 
series) 
 
0 = none,                                                  
 
1 = yes without upstream dilation (< 3 cm)                   
 
2 = mild upstream dilation  3- 4 cm,                        
 
3 = moderate-severe upstream dilation > 4 cm 
11. Presence of new internal penetrating disease: Sinus, simple fistula or complex fistulae, abscess or 
phlegmon 
 
0 = None 
 
1 = Yes 
12. Qualitative diffusion weight imaging (DWI) analysis evaluated as absence or presence of 
hyperintensity suggestive of active disease on DWI with b-value of 800 s/mm2. 
13. For quantitative assessment, the apparent diffusion coefficient (ADC) will be calculated for each 
active small bowel lesion with a region of interest area between 10 and 30 mm2 was drawn in the 
area of highest signal intensity in the bowel wall. 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
Amendment 3 8Jun2021   Page 44 of 46 
Last IRB Approval: 11/8/2024 
IRB Expired:  11/7/2025  
 
Lesion Response Definition: 
Qualitative per-lesion analysis 
•       Improved lesion: Decrease in length of active segment or improvement in other morphological 
features listed below, without new internal penetrating disease. 
 Mural thickness of small bowel segment 
 Mural T2 signal  
 Perimural T2 signal  
 Qualitative or quantitative DWI analysis 
 Luminal ulceration 
 Stricture 
•       Worsened lesion: Increase in any of the above imaging parameters including new internal 
penetrating disease. 
•       Unchanged lesion:  Without worsening parameters of any of the above and not classified as an 
improved lesion. 
Per patient response definition  
• 
Response: All lesions improved. 
• 
Non-response: Existing lesion(s) worsened, new lesion was detected and all other scenarios not 
meeting definition of response. 
 
 
 
 
 
 
 
 
 
 
Sample data collection sheet for all 5 lesions per scan for the radiologist 
MRN _____________                Case Number _________________ 

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
Amendment 3 8Jun2021   Page 45 of 46 
Last IRB Approval: 11/8/2024 
IRB Expired:  11/7/2025  
 
Patient Last Name _______________        Date of study ___________________ 
Lesion
1
2
3
4
5
Location: 
1 = Distal Ileum 
2 = Proximal ileum 
3 = Jejunum 
Length (record in cm) 
Mural thickness small bowel: 
• 0 = <3 mm  
• 1 = >3–5 mm  
• 2 = >5–7 mm  
• 3 = >7 mm 
Mural T2 Signal: 
• 0 = Equivalent to normal bowel wall                 
•1 = Minor increase in signal 
•2 = Moderate increase in signal 
•3 = Marked increase in signal
Peri-mural T2 signal:  
• 0 = Equivalent to normal mesentery  
• 1 = Increase in mesenteric signal but no fluid 
• 2 = Small fluid rim (≤2 mm)  
• 3 = Larger fluid rim (>2 mm)
Small bowel ulcerations: 
• 0 = No 
• 1 = Yes
Stricture (obstruction): 
• 0 = none,                                                  
• 1 = yes without upstream dilation 
• 2 = upstream dilation  3- 4 cm                        
• 3 = upstream dilation > 4 cm
Presence of new sinus, simple fistula or complex 
fistulae, abscess or inflammatory mass 
• 0 = None 
• 1 = Yes
Qualitative DWI analysis: 
0 = No change 
1 = Improved 
2 = Worsened 
ADC value 
Radiologist impression: 
1=improved 
2=unchanged 
3=worsened 
              If 5 lesions on index, new inflammatory lesions appearing on f/u scans?  0 = no 1 = yes      

Protocol ID: Entyvio 
PI: Deepak, Parakkal 
Sponsor: Washington University School of Medicine 
 
Amendment 3 8Jun2021   Page 46 of 46 
Last IRB Approval: 11/8/2024 
IRB Expired:  11/7/2025  
 
Appendix B: Study visit with details of symptomatic, serological, endoscopic and radiological assessment at each visit. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Baseline visit 
 
Demographic 
Information 
 
Clinical assessment:  
 CDAI 
 Harvey Bradshaw 
index 
 PRO-2/3 
 EQ-5D 
 IBD Disability 
Index 
 
Physical examination:  
 Height/weight 
 Waist/hip ratio 
 
Blood tests 
 
C-reactive protein 
 
Albumin 
 
Hematocrit 
 
SOMAscanTM : 
panel~1310 
proteins € 
 
Stool Sample 
 
Endoscopic 
assessment  
 
Radiological 
assessment:  
MR enterography, see 
Appendix B 
6±1 week visit 
Clinical visit§ 
52±4 week visit 
 
Clinical assessment:  
 CDAI 
 Harvey Bradshaw 
index 
 PRO-2/3 
 EQ-5D 
 IBD Disability Index 
 
Blood tests 
 
C-reactive protein 
 
Albumin 
 
Hematocrit 
 
SOMAscanTM : 
panel~1310 proteins € 
 
Clinical assessment:  
 CDAI 
 Harvey Bradshaw 
index 
 PRO-2/3 
 EQ-5D 
 IBD Disability Index 
 
Physical examination:  
 Weight 
 Waist/hip ratio 
 
Blood tests 
 
C-reactive protein 
 
Albumin 
 
Hematocrit 
 
Stool Sample 
 
Radiological assessment: 
MR enterography, see 
Appendix B 
 
 
 
Clinical assessment:  
 CDAI 
 Harvey Bradshaw 
index 
 PRO-2/3 
 EQ-5D 
 IBD Disability 
Index 
 
Physical examination:  
 Weight 
 Waist/hip ratio 
 
Blood tests 
 
C-reactive protein 
 
Albumin 
 
Hematocrit 
 
Endoscopic 
assessment: SES-CD 
 
Radiological 
assessment: MR 
enterography, see 
Appendix B 
 
Disease Progression 
Assessment 
 
 
16±2 week visit 
 
Clinical assessment:  
 CDAI 
 Harvey Bradshaw 
index 
 PRO-2/3 
 EQ-5D 
 IBD Disability Index 
 
Blood tests 
 
C-reactive protein 
 
Albumin 
 
Hematocrit 
 
 
§ If dose escalated to q 4 weekly dosing due to lack of clinical response (CDAI-100 point decrease) at week 14. The clinical visit will coincide with trough 
measurement prior to 3rd cycle of vedolizumab after dose escalation. 
€ SOMAscanTM measures ~1310 proteins including Tumor Necrosis Factor receptor superfamily, IL-6, IL-17A, IL-22, serum amyloid A‐1 protein, chemokines, 
fibronectin, VCAM-1, platelet factor-4, CD40 ligand, creatine kinase M‐type: creatine kinase B‐type heterodimer.