Clinical trial NCT02525523
Conditions: Pouchitis
Sponsor: Atlantic Pharmaceuticals Ltd
Start date: 2015-12-03; Completion date: 2018-10-29
Enrollment: 138 participants; Allocation: RANDOMIZED; Intervention model: PARALLEL

Brief summary:
A Phase III, multi-centre, double-blind randomised controlled trial in subjects with chronic antibiotic refractory pouchitis.

Subjects will undertake a \<2 week screening period to provide baseline data and be assessed for eligibility. At the Baseline visit (Day 1) eligible subjects will be randomised on a 1:1 basis to either a) 240 mg alicaforsen enema or b) matching placebo.

Study drug will be administered once nightly (on going to bed) up to and including week 6. Following the Day 1 Visit, subjects will return to the clinic for safety and efficacy assessments at Week 3, 6, 10, 18 and 26.

Subjects may receive certain permitted medications as per Entry Criteria, which must remain at stable doses throughout the trial. Introduction of any new medication for pouchitis, or a dose change to an existing concomitant medication for pouchitis, other than those detailed in the protocol, will not be permitted.

Clinical symptoms associated with pouchitis will be recorded daily by the patient in a diary card.

Subjects will undergo endoscopic examination of their pouch (during Screening, and at Weeks 6 and 10). Where technically feasible, each endoscopy will provide at least one biopsy sample for histopathology.

In addition to endoscopic, histopathologic and symptomatic assessments, Quality of Life will be assessed.

Bloods for routine assessment, including haematology and biochemistry will be taken. Bloods and stool samples will be collected to evaluate relevant biomarkers.

Detailed description:

Arms: arm 1: Alicaforsen enema, 240mg once daily for 6 weeks arm 2: Placebo enema, once daily for 6 weeks
Interventions: intervention 1: Alicaforsen intervention 2: Placebo
Intervention descriptions: intervention 1: None intervention 2: None

Protocol documents:
Prot_000.pdf: 
 
CLINICAL RESEARCH PROTOCOL 
ACH UCP-301 
NCT Number NCT02525523 
EudraCT Number 2013-002952-34 
IND Number 64,905 
 
A Randomised, Double-Blind, Placebo-Controlled Trial of the Safety and Efficacy of 
Topical Alicaforsen Enema in Subjects with Active, Chronic, Antibiotic Refractory 
Primary Idiopathic Pouchitis  
 
Version 
 
Protocol Date: 
Final 3.0 
 
19 August 2016 
 
Sponsor: 
Atlantic Pharmaceuticals Ltd 
 
Atlantic House 
10 Rose & Crown Walk 
Saffron Walden 
 
Essex                                
CB10 1JH, UK 
 
 
Study Director: 
Dr Chris Dunk 
 
Director Clinical Development,  
Atlantic Pharmaceuticals Ltd 
Chief Investigator: 
Dr Brian Feagan 
Professor of Medicine, Dept of Gastroenterology 
University of Western Ontario, Canada 
Medical Monitor: 
 
Dr Colin Hayward 
Medical Monitor, Promedim Ltd 
 
Mobile Telephone: +44 (0) 7810 694469 
 


PROTOCOL SYNOPSIS  
 
Title 
A Randomised, Double-Blind, Placebo-Controlled, Multi-
Centre Trial of the Safety and Efficacy of Topical 
Alicaforsen Enema in Subjects with Active, Chronic, 
Antibiotic Refractory Primary Idiopathic Pouchitis   
Study Phase 
Phase III 
Indication 
Treatment of Chronic, Antibiotic Refractory Pouchitis  
Study Population 
Subjects with pouchitis refractory to antibiotics  
Locations 
This study will be conducted at sites in North America 
and Europe, including Israel. 
Treatment Groups 
a) Alicaforsen 240mg enema, administered nightly, for 
6 weeks. 
b) Matching placebo enema, administered nightly, for 6 
weeks. 
Primary Objective 
To determine the effect of alicaforsen enema on 
endoscopic healing and symptoms associated with 
pouchitis in those subjects with active antibiotic refractory 
pouchitis  
 
Secondary Objectives 
1. To determine the ability of alicaforsen enema to 
improve the clinical symptoms associated with 
antibiotic refractory pouchitis 
2. To determine the effect of alicaforsen enema on 
health related quality of life. 
3. To evaluate duration of effect following cessation 
of therapy 
Tertiary and Exploratory 
Objectives 
1. To determine the effect of alicaforsen enema on 
reducing pouchitis “rescue” intervention;  
2. To determine the effect of alicaforsen enema on 


histological inflammation  
3. To determine the effect of alicaforsen enema on 
health outcome. 
4. To determine the effects of alicaforsen enema on 
changes in biological markers; including CRP, 
WBC, and faecal calprotectin 
Safety Objectives 
To evaluate the safety and tolerability of alicaforsen 
enema, in subjects with chronic or recurrent acute 
antibiotic refractory pouchitis.  
Pharmacokinetic Objectives 
To determine the systemic exposure of subjects to parent 
compound following single and repeated once-daily doses 
of alicaforsen. 
Study Design 
A Phase III, multi-centre, double-blind randomised 
controlled trial in subjects with chronic antibiotic 
refractory pouchitis.   
Subjects will undertake a <3 week screening period to 
provide baseline data and be assessed for eligibility. At 
the Baseline visit (Day 1) eligible subjects will be 
randomised on a 1:1 basis to either a) 240 mg alicaforsen 
enema or b) matching placebo.  
Study drug will be administered once nightly (on going to 
bed) up to and including week 6.   
Following the Day 1 Visit, subjects will return to the 
clinic for safety and efficacy assessments at Week 3, 6, 
10, 18 and 26. Subjects will be contacted by telephone 
during Week 1 to ensure adequate compliance with study 
treatment, to ensure concomitant medications are being 
used at levels consistent with those prior to 
randomisation, and to inquire about any adverse events.    
Subjects may receive certain permitted medications as per 
Entry Criteria, which must remain at stable doses 
throughout the trial.  Introduction of any new medication 
for pouchitis, or a dose change to an existing concomitant 
medication for pouchitis, other than those detailed in the 
protocol, will not be permitted. Introduction of any new 
medication, or escalation of dose of current therapy, 
primarily for the treatment of pouchitis before Week 10 


will be determined as “rescue” intervention.  Once 
rescued, a subject will complete an early termination visit 
and will be considered a treatment failure.  Surgical 
procedures targeted to pouchitis before Week 10 will also 
be considered as “rescue” interventions. 
Clinical symptoms associated with pouchitis will be 
recorded daily by the subject in an electronic diary card 
and elements recorded in the eCRF up to Week 10.  
Subjects will undergo endoscopic examination of their 
pouch (during Screening, and at Weeks 6 and 10). 
Subjects may receive an additional endoscopic 
examination later during the study if clinically indicated. 
Indications for repeated endoscopy might include 
confirmation of sustained response to treatment, or 
recurrent disease (following initially successful response). 
The purpose of the additional endoscopy is to document 
duration of effect and / or time-to-next-flare, hence the 
timing of any additional endoscopic procedure will vary 
from subject to subject. For this reason, this procedure 
will be undertaken at the investigator’s discretion 
following discussion with the Sponsor’s Medical Monitor. 
Where technically feasible, each endoscopy will provide 
at least one biopsy sample for histopathology. 
To assess Quality of Life, subjects will complete: the EQ-
5D, the Cleveland Global Quality of Life score [CGQL] 
and the Work Productivity Activity Impairment index 
[WPAI]. These assessments will be made during the 
treatment period, and the follow-up phase of the study. 
Bloods for routine assessment, including haematology and 
biochemistry will be taken. Bloods will also be taken for 
biomarkers, including CRP. In addition, stool samples 
will be collected to evaluate faecal calprotectin levels. 
Blood samples for routine haematology and biochemistry, 
as well as faecal calprotectin, will be collected during the 
screening period and results should be available to the 
investigator at the Baseline visit. Following the Baseline 
visit the investigator will be blinded to CRP, WBC, and 
lab faecal calprotectin levels (which will be collected 
again at Weeks 3 and 6, and for calprotectin specifically 


during the follow-up period of the trial).   
Additional blood samples will be collected for 
pharmacokinetic determinations. 
Any subjects who withdraw consent to participate in the 
study after receiving study medication, for any reason, 
will be asked to complete the Early Discontinuation Visit. 
The overall study design is described by a study flowchart 
at the end of the protocol synopsis section. 
Number of Subjects 
This study will randomise 138 subjects.  
69 subjects will receive 240 mg alicaforsen enema, once 
nightly; 69 subjects will receive matching placebo enema.   
Estimated Study Duration 
A subject’s participation in this study will last for up to 29 
weeks (including the <3 week screening phase, 6 week 
treatment phase and 20 week follow up phase). 
Summary of Subject 
Eligibility Criteria 
Inclusion Criteria: 
1. Written informed consent; 
2. Male or female subjects, ≥18 years of age who 
have undergone an IPAA for UC 
3. History of pouchitis 
Documented evidence of active pouchitis, based on 
endoscopy, symptoms and histopathology, as follows: 
4. Endoscopic score >2 on the endoscopic 
component of a modified MAYO score (where 
friability is scored as >2) 
Note: the area within 1 cm of the pouch staple, or 
pouch suture line, is not considered evaluable 
5. Symptomatic disease (stool frequency):  
Subjects must demonstrate increased stool 
frequency compared to what is considered 
“normal” after their IPAA operation 
(“baseline”). Stool frequency must be an 
absolute value of > 6 stools per day, and > 3 


stools per day above the post-IPAA “baseline”.  
Note: The measurement of stool frequency will be a 
7-day average rounded to the nearest integer. The 
most recent 7 days of data will be used to calculate the 
average.    
6. Inclusion criteria removed   
7. Overall PDAI score > 7 
8. Must have Chronic Antibiotic Refractory 
Pouchitis 
Chronic Antibiotic Refractory Pouchitis is defined as 
remaining in active disease despite antibiotic therapy 
for at least 2 continuous weeks.  There is no 
requirement for antibiotic use to be current, or within 
a defined time-window.  Antibiotics must be stopped 
4 weeks before the Randomisation Visit, which is 
effectively 2 weeks before the Screening Visit. As a 
minimum the antibiotic regime will comprise 
ciprofloxacin 1g/day, or metronidazole 15 – 20 
mg/kg/day. Subjects must have been in active disease 
for a minimum of 4 weeks at the point of 
randomisation.  
 
Exclusion Criteria: 
1. Lack of effective contraception 
Women of childbearing potential may not participate 
unless they are surgically sterile or are using adequate 
contraception. 
The following contraceptive methods are acceptable: 
hormonal (eg oral, injection, transdermal patch, 
implant, cervical ring), barrier (eg condom or 
diaphragm with spermicidal agent), intrauterine 
system or intrauterine device. If hormonal 
contraceptives are used by female subjects, they must 
be established for 6 weeks before the first 
administration of test product. Male sterilization is 
considered an acceptable form of contraception if the 


appropriate post-vasectomy documentation (absence 
of sperm) is provided in the subject’s medical notes. 
Sexual abstinence is considered acceptable if this is in 
line with the preferred and usual lifestyle of the 
subject; periodic abstinence (eg calendar, ovulation, 
symptothermal, post-ovulation methods) and 
withdrawal are not acceptable methods of 
contraception.  
Male subjects with female partners of child-bearing 
potential and female subjects who are neither 
surgically sterilized nor post-menopausal (defined as 
no menses for one year or an FSH value > 40 IU/L) 
will be required to use effective contraception 
throughout the study and for 30 days after. 
2. Women who are pregnant or breastfeeding; 
3. History of allergy or adverse event to 
oligonucleotides including alicaforsen, 
hydroxymethylcellulose, methyl or 
propylparabens.  
Stable use of concomitant medications for pouchitis is 
generally permitted, doses of concomitant medication, 
where taken, should be optimised in accordance with 
local/national practice guidelines, and dose levels and 
types of baseline medications for pouchitis will be 
documented and any changes during the study will be 
recorded. Changes in use of medications for pouchitis 
and high doses of oral steroids are not permitted. It is 
particularly important to maintain stable medication 
through to measurement of the primary end-point at 
Week 10. Criteria which would lead to exclusion of 
subjects from the study are described below: 
4. Changes in dose to strong analgesia, such as 
opioid containing compounds within 4 weeks of 
the Screening Visit.  
5. History of regular NSAID use. 
6. Oral 5-aminosalicylate (5-ASA) compounds; 
exclude subjects who have discontinued or 
changed doses of oral 5-ASA within 4 weeks of 


the Screening Visit. 
7. Oral budesonide > 6.0 mg / day is not permitted; 
exclude subjects who have received budesonide 
for < 6 weeks, or who have changed doses of 
budesonide within 4 weeks of the Screening 
Visit.   
8. Oral steroids other than budesonide; exclude 
subjects who exceed a daily dose of 15 mg 
prednisolone or equivalent, who have received 
oral steroids for < 6 weeks, or who have 
changed dose within 4 weeks of the Screening 
Visit.  
9. Use of rectal compounds is not permitted; these 
agents must be discontinued at the Screening 
Visit.  
10. Immunosuppressant therapy (azathioprine, 6-
mercaptopurine, methotrexate, cyclosporin); 
exclude subjects who have received treatment 
for < 12 weeks, or who have changed doses 
within 8 weeks of the Screening Visit.  
11. Biological agents: Anti-tumour necrosis factor 
(anti – TNF) therapy and / or vedolizumab; are 
not permitted within 8 weeks of the Screening 
Visit. 
12. Previous use of alicaforsen is permitted: 
treatment course must have completed at least 
12 weeks prior to the Screening Visit. 
(Alicaforsen pre-treated subjects may not 
contribute to the primary efficacy analysis.) 
13. All other agents targeted to pouchitis, including 
experimental agents, must have been 
discontinued at least 8 weeks prior to the 
Screening Visit, or for a period equivalent to 5 
half-lives (t½) of the agent (whichever is 
longer)  
It is acceptable to recruit subjects who remain on 
optimised, stable doses of oral 5-ASA, oral steroids 
(below the doses stipulated above) and 


immunosuppressants.  
It is acceptable to recruit subjects who terminated 
treatment with oral 5-ASA or oral steroids 4 weeks 
before the Screening Visit, or immunosuppressants 
8 weeks before the Screening Visit. 
Note: Analgesic use should remain stable throughout 
the trial where possible. Paracetamol is the analgesic 
of choice. 
Note: VSL3 treatment (and other probiotic treatments) 
will be permitted as long as maintained stable for 4 
weeks prior to the Screening Visit, and maintained at a 
stable dose throughout the trial 
Also excluded are subjects with: 
14. Anastomotic stricture which precludes 
evaluation of the pouch and terminal ileum.   
15. Unable to undertake endoscopic evaluation 
16. Faecal incontinence due to anal sphincter 
dysfunction 
17. Infections to cytomegalovirus or Clostridium 
Difficile 
18. Faecal transplantation within 12 weeks of 
screening 
19. Intestinal malabsorption 
20. Pancreatic maldigestion 
21. Suspected irritable pouch syndrome 
22. Cuffitis (inflammation of the anal mucosa). 
Subjects with active antibiotic refractory 
pouchitis as the predominant condition, but who 
also have cuffitis, may be enrolled   
23. Crohn’s disease of the pouch; defined as either: 
a) complex perianal or pouch fistula and/or  
b) extensive pre-pouch ileitis with deep 
ulceration 
 
24. Subjects with a history of malignancy, except 


for basal cell carcinoma or non-metastatic 
squamous cell carcinoma of the skin and ductal 
carcinoma in situ breast cancer. Subjects who 
have a history of malignancy with >5 years 
since completion of curative therapy, without 
recurrence, may be screened. 
25. Subjects who are receiving or have received 
nasogastric/nasoenteric bottle feeding, an 
elemental diet, or total parenteral nutrition 
within the 2 weeks prior to Day 1 
26. Subjects with a history of clinically significant 
and/or persistent haematologic (including 
coagulation disorders), renal, hepatic, 
metabolic, psychiatric, CNS, pulmonary or 
cardiovascular disease; which in the 
investigators opinion, would exclude entry into 
the study  
27. Subjects with any laboratory tests considered 
clinically significant at screening  
28. Subjects who may be unavailable for the 
duration of the trial, likely to be noncompliant 
with the protocol, or who are felt to be 
unsuitable by the Investigator for any other 
reason including, for example, inability to retain 
an enema formulation 
29. Pelvic sepsis should be excluded as a 
differential diagnosis within 12 months of 
randomisation. 
Concomitant Medications 
During the course of their participation in the study, all 
subjects will be required to remain on stable doses of their 
existing concomitant medications for pouchitis, neither 
increasing nor decreasing the dose.  
Introduction of a new medication for pouchitis, or an 
increase in the dose of an existing pouchitis medication, 
should be avoided throughout the study. This will be 
regarded as “rescue” intervention if it occurs prior to 
Week 10 and lead to the early termination of the subject. 
Loperamide and other anti-diarrhoeal medication should 


also be maintained at a stable dose where possible. 
Drugs, Drug Dosages and 
Formulations 
Alicaforsen enema will be administered at a dose of 
240mg of alicaforsen per 60ml enema. Applications will 
be made once daily, at night time.  
Study drug will be produced in a hydroxypropyl 
methylcellulose enema formulation, and will be provided 
for the trial in sealed, plastic enema bottles. This may be 
lubricated with petroleum jelly as required. 
Control Groups 
Placebo will be provided in matching bottles and consist 
of hydroxypropylmethylcellulose base plus methyl and 
propyl parabens preservatives. 
Route of Administration 
Study medication will be administered by the subject, at 
bedtime, while the subject is lying down. Subjects will be 
instructed to remain in this position until they no longer 
have the urge to evacuate the enema. The enema should 
be retained for as long as possible, ideally until the 
following morning. 
Procedures 
At each study visit, some or all of the following 
procedures will be conducted: 
Medical history taken (including smoking history), 
physical examination, vital signs, bodyweight, blood 
samples for, haematology, biochemistry and CRP. Urine 
samples will be collected for urinalysis. A serum 
pregnancy test will be performed. Stool samples for faecal 
calprotectin will be collected. The PDAI score will also be 
calculated.  
Subjects will complete the EQ-5D, the CGQL quality of 
life questionnaire, and a health outcome questionnaire 
(WPAI).  
Electronic diary cards will be utilised daily to record 
subjects’ symptoms (bowel frequency, degree of urgency, 
incontinence, abdominal pain/cramps, rectal bleeding). In 
addition, they will confirm administration of study 


medication and record enema retention time. 
The subjects will complete the diary daily from Screening 
until Week 10. 
Study bottles (unused) will be collected for assessment of 
compliance at each visit and subjects re-educated about 
administration if compliance is low.  
Please see Schedule of Events at the end of this synopsis 
for additional details. 
 
Co-Primary Endpoint 
Co-Primary Endpoints:  
 
1. Proportion of subjects with endoscopic remission; 
defined as absence of friability and ulceration, represented 
by a score of <1 (endoscopy component of a modified 
MAYO score) at Week 10. 
Note : the area within 1 cm of the pouch suture line will 
not be included in the endoscopic evaluation.   
 
2. Proportion of subjects with a stool frequency 
represented by a MAYO subscore of <1 at Week 10. 
 
Secondary Endpoints 
Secondary Endpoints: 
1. Percentage change in stool frequency from 
baseline compared to placebo; Week 6 and Week 
10.  
2. Change in urgency score from baseline compared 
to placebo; Week 6. 
3. Change in rectal bleeding score from baseline 
compared to placebo; Week 6. 
4. Proportion of subjects who achieve overall PDAI 
<5 at both Week 6 and Week 10.  


5. Mean change from baseline in CGQL at Week 6. 
6. Proportion of subjects by Week 26, who have not 
received additional treatment for pouchitis flares, 
since commencing study. 
Tertiary and Exploratory 
Endpoints 
Tertiary Endpoints 
1. Time to first use of “rescue” intervention  
2. Proportion of subjects who achieve histological 
response; response = PDAI subscore 1 (for 
subjects with baseline score >1), or >2 point 
reduction; remission = PDAI subscore 0 for 
subjects who had a baseline subscore above 0. 
3. Proportion of subjects achieving endoscopic 
response, as defined by improvement of >1 
point on the endoscopic component of the 
modified MAYO score, by the central reader; 
Week 10 
4. Change from baseline in PDAI score, at Week 6 
and Week 10 
5. Change from baseline in PDAI clinical 
symptoms score (at Weeks 6 and 10) 
6. Proportion of subjects who achieve overall 
PDAI <3 at both Week 6 and Week 10  
7. Change from baseline in PDAI endoscopy 
score; at Week 6 and Week 10 
8. Change from baseline in Quality of Life 
measured by the EQ-5D at Week 6 and Week 
10 
9. Mean change from baseline in CGQL at Week 
10 
10. Proportion of subjects who achieve post surgery 
stool frequency at both Week 6 and Week 10 
11. Time to clinical “remission” (defined as 
achieving post surgery stool frequency)  
12. Change from baseline in faecal incontinence 
episodes 


Exploratory Endpoints: 
1. Change from baseline in work productivity and 
activity as measured by the WPAI 
2. Change from baseline in histology score on 
D’Haens scale 
3. Change from baseline in inflammatory markers 
including CRP, WBC, calprotectin 
Safety and 
Pharmacokinetics 
Safety Endpoints: 
   The safety analysis will be conducted in all randomised 
subjects receiving at least a part of one dose 
1. The number and proportion of subjects with AEs; 
(worsening of pouchitis will also be evaluated 
separately) 
2. Assessment of clinical laboratory parameters 
3. Assessment of vital signs 
Pharmacokinetic Endpoints: 
   Systemic absorption of alicaforsen will be determined 
from plasma samples. Full plasma profiles will be 
determined in a cohort of approximately 12 separately 
consenting subjects. In order to obtain 12 alicaforsen 
profiles, a total of 24 subjects will be separately 
consented and bled. The blood samples obtained from 
subjects randomised to placebo will not be analysed. 
Profiles will be determined at Weeks 0 (baseline) and 6.  
Samples will be taken at the following time-points: pre-
dose, 10, 20, 30min, 1, 2, 3, 4, 6, 12 and 24h.  
In addition, single bleeds will be taken from all other 
consenting subjects, prior to enema administration, at 
Weeks 0, 3 and 6. 
Statistical Considerations 
Assuming 50% of subjects on alicaforsen and 20% on 
placebo meet the co-primary end-point a 1:1 design will 
require 69 subjects per treatment group, 138 in total to 
show a significant difference using a Z-test with 
continuity correction and pooled variance. This assumes a 
two-sided 5% statistical significance level and 90% power 
(PASS 13 Power Analysis and Sample Size Software 
(2014). NCSS, LLC. Kaysville, Utah, USA, 


ncss.com/software/pass).  
 
Open Label Access after 
Week 26 
Provision will be made for subjects who meet appropriate 
criteria to receive open-label access (OLA) to alicaforsen 
after they have completed Week 26 of the double-blind 
phase of the study. Safety and efficacy data will be 
collected in accordance with regulatory requirements 
pertaining to open label access to unlicensed medications.  
This provision of open-label access to alicaforsen through 
this clinical trial will continue until the subject no longer 
derives benefit, or until alicaforsen receives marketing 
authorisation for use in Pouchitis, or development is 
discontinued, whichever is sooner. 
Procedures: 
For each OLA alicaforsen treatment course, the following 
procedures will be conducted: 
Collection of changes in medical history or adverse events 
since last study visit, physical examination to ascertain 
changes since last study visit, vital signs, blood samples 
for haematology and biochemistry. Urine samples for 
urinalysis. A serum pregnancy test will be performed. 
Please see Schedule of Events for additional details 
Inclusion Criteria: 
1. Written informed consent; 
2. Previous participation to Week 26 of double blind 
phase; 
3. Demonstrated compliance with previous 
alicaforsen/blinded treatment; 
4. Current evidence of active disease, based on 
clinical symptoms.  
 
 
Exclusion Criteria: 
1. Lack of effective contraception; 
2. Women who are pregnant or breastfeeding; 
3. History of allergy or adverse event to 


hydroxymethylcellulose, methyl or 
propylparabens;  
4. Concurrent use of experimental agents;  
5. Subjects with any laboratory tests considered 
clinically significant; 
6. Subjects who may be unavailable for the duration 
of the treatment course, likely to be noncompliant, 
or who are felt to be unsuitable by the Investigator 
for any other reason; 
Drugs, Dosages and Formulations: 
Alicaforsen enema will be administered at a dose of 
240mg of alicaforsen per 60ml enema. Applications will 
be made once daily, at night time in the same regimen as 
the double-blind phase of the study.  
OLA alicaforsen will be produced in a hydroxypropyl 
methylcellulose enema formulation, and will be provided 
in sealed, plastic enema bottles.  
Sponsor 
This study is sponsored by Atlantic Pharmaceuticals Ltd. 
Atlantic Pharmaceuticals Ltd is responsible for all 
operational aspects of this study. 
 

SAP_001.pdf: 
 
CLINICAL RESEARCH STATISTICAL ANALYSIS PLAN 
ACH UCP-301 
NCT Number NCT02525523 
EudraCT Number 2013-002952-34 
IND Number 64,905 
 
A Randomised, Double-Blind, Placebo-Controlled Trial of the Safety and Efficacy of 
Topical Alicaforsen Enema in Subjects with Active, Chronic, Antibiotic Refractory 
Primary Idiopathic Pouchitis  
 
Protocol Date: 
19 August 2016 
 
Sponsor: 
Atlantic Pharmaceuticals Ltd 
 
Atlantic House 
10 Rose & Crown Walk 
Saffron Walden 
 
Essex                                
CB10 1JH, UK 
 
 
Study Director: 
Dr Chris Dunk 
 
Director Clinical Development,  
Atlantic Pharmaceuticals Ltd 
Chief Investigator: 
Dr Brian Feagan 
Professor of Medicine, Dept of Gastroenterology 
University of Western Ontario, Canada 
Medical Monitor: 
 
Dr Colin Hayward 
Medical Monitor, Promedim Ltd 
 
Mobile Telephone: +44 (0) 7810 694469 
 
 
 
 
1 
STATISTICAL CONSIDERATIONS 
A detailed and comprehensive Statistical Analysis Plan (SAP) will be prepared and signed-
off before database lock.  Minor changes to the statistical methods set out in this protocol 


need not be reported as a protocol amendment but must be documented in the SAP and in the 
study report. 
The statistical analysis and report will conform to the relevant ICH requirements. 
1.1 
STATISTICAL METHODS 
1.1.1 Summary Tables and Listings 
The standard summary statistics for continuous baseline and outcome variables are: N, mean, 
standard deviation, median, quartiles, minimum and maximum.  
The standard summary statistics for categorical baseline and outcome variables are: count and 
proportion (expressed as percentage of non-missing values). 
All efficacy outcomes, vital signs and laboratory assessments will be summarised by 
treatment group and timepoint.  Baseline and demographic data will be summarised by 
treatment group.  
The summary tables and figures will be supported by full subject listings. 
1.1.2 Hypothesis Testing and Confidence Intervals 
All significance probabilities will be two tailed.  Statistical tests will be at a 5% level of 
significance. 
Confidence intervals will be 95% two-sided. 
1.1.3 Randomisation and Stratification  
The center will dispense the study medication under blinded conditions according to a 
centrally administered, permuted block randomisation sequence (1:1 ratio for the treatment 
arms), managed at the study level and implemented using IWRS.    
1.1.4 Subject Population/Sets to Be Evaluated 
It is expected that there will be an average of 3 to 4 subjects recruited per site, and hence 
stratification by study site could be potentially unblinding with respect to the block size given 
the expected difference in response rates between the two study arms. In accordance with 
recommendations included in ICH E9 guidelines, the randomisation will therefore be 
stratified by region, i.e. North America (US and Canada) and Rest of World (Europe, 
including Israel). 
 
All Randomised Set  
The All Randomised Set comprises all subjects which have been randomised.  
Safety Set  
The safety analysis (SAF) set will consist of all randomized subjects who took at least a part 
of one dose of study drug, and will be used for all analyses of safety. 
Full Analysis Set  
The full analysis set (FAS) will consist of all randomized subjects with confirmed active 
pouchitis at baseline, and who took at least one dose of study drug and have at least one post-


baseline assessment of efficacy. The FAS will be the primary analysis set for analyses of 
efficacy. 
 
Per Protocol Set  
The per protocol set (PPS) will comprise all subjects in the FAS who have not violated any 
major entry criteria and have not deviated significantly from the protocol during the course of 
the study.  Any efficacy analyses from this population will be considered as supportive to 
those performed on the FAS.  Reasons for exclusion from the PPS will be defined 
prospectively in the statistical analysis plan. 
 
Pharmacokinetically Evaluable Analysis Set  
The Pharmacokinetically Evaluable Analysis Set (PKAS) comprises all subjects receiving 
active treatment with sufficient blood samples taken to establish a pharmacokinetic profile 
and for whom the time of last dose prior to sampling is known. 
 
The final determination of the membership of analysis sets will be made at the blinded data 
review meeting. 
1.2 
SAMPLE SIZE DETERMINATION 
The sample size is based on being able to claim superiority of alicaforsen over placebo; at 
Week 10 separately for each of the two co-primary endpoints. 
 
The primary analysis will be based on a Cochran-Mantel-Haenszel Test (CMH) stratifying by 
region. In addition, a difference in the proportion of subjects with treatment success (and the 
associated estimated 95% confidence interval) will be presented based on the Z-test. 
 
For both co-primary end-points, it is assumed in the sample size calculation that 50% of patients on 
alicaforsen and 20% on placebo will have a successful treatment outcome. Based on a 1:1 design, 63 
subjects per treatment group will be required to show superiority (alicaforsen to placebo odds ratio 
>1) using a two-sided CMH Test at the 5% significance level and with 95% power.  For the same 
design, 69 subjects per treatment group will be required to show superiority (proportion of 
successes for alicaforsen minus placebo >0) using a two-sided z-test with continuity correction and 
pooled variance at the 5% significance level and with 95% power. 
 
With 69 subjects per treatment group (138 in total), the study will therefore be powered to show 
superiority both in terms of the difference of proportions and the odds ratio (both calculations 
derived using PASS 13 Power Analysis and Sample Size Software (2014). NCSS, LLC. Kaysville, Utah, 
USA, ncss.com/software/pass). 
To demonstrate the superiority of alicaforsen over placebo, both co-primary endpoints must be 
significant using a two sided CMH test at the 5% significance level. Therefore, a total sample size of 
138 subjects will give an overall power of 90% (0.95 * 0.95) assuming independence of the two co-
primary endpoints.  
The randomization is stratified by region (North America vs Rest of World). 
 


1.3 
STATISTICAL ANALYSES 
1.3.1 Demographic and Baseline Characteristics 
Subject demographic and baseline characteristic data will be summarised using the standard 
summary statistics.  
1.3.2 Efficacy Analysis 
All efficacy analyses and summaries will be performed using the FAS. A confirmatory 
analysis of the primary efficacy parameter will be carried out using the PPS.  
All statistical tests comparing the treatment groups will be two-tailed and at the 5% level of 
significance. 
1.3.2.1 Co-Primary Efficacy Analysis 
The co-primary measures of efficacy will be: 
• The proportion of subjects who are in endoscopic remission (Endoscopic Score <1), and  
• The proportion of subjects who achieve a Stool Frequency Score <1, at Week 10.  
The proportion of subjects who achieve each of the co-primary measures of efficacy at Week 
10 will be presented and compared between treatment groups using a Cochran-Mantel-
Haenszel test accounting for region. The difference in proportions between the two groups 
and associated 95% confidence interval will also be presented. 
Subjects with a missing endoscopic assessment at week 10, or insufficient stool frequency 
data, will be declared not to have achieved the respective outcomes. 
Secondary analyses of the co-primary endpoints will include investigations of the effect of 
treatment and baseline characteristics (region, treatment, sex, age group, PDAI score) on the 
co-primary endpoints using logistic regression models.  
1.3.2.2 Secondary and Tertiary Efficacy Analyses 
Stool Frequency 
The mean daily stool frequency (frequency of bowel movement) will be evaluated from the 
data recorded in the subject’s diary using the data from the 7 days prior to each study visit.  
Mean frequency and change from baseline will be summarized. 
The change from baseline at each study visit will be analyzed using a mixed effects repeated 
measures analysis of covariance (ANCOVA) model of the change from baseline with region, 
treatment, Visit, treatment*Visit interaction, sex and age group as fixed effects and baseline 
value as covariate. 
The proportion of subjects with a Stool Frequency Score equal to 0 (‘Normal number of 
stools per day for the subject’) will be summarized and analyzed in the same way as for the 
co-primary endpoints. 
The time to clinical remission will be summarized using Kaplan-Meier methods. Subjects 
without remission, (including those who withdrew from the study without remission) will be 
censored at the time of last assessment of the Stool Frequency Score.  Kaplan-Meier curves 


will be presented with estimates of the probability of remaining remission-free at Weeks 3, 6 
and 10 together with their 95% confidence intervals.  The time to clinical remission will be 
investigated using a Cox proportional hazards regression model including terms for region, 
treatment, sex, age group, and the baseline mean number of bowel movements per day. 
Urgency 
Urgency will be recorded for each bowel movement in the subject’s diary as none (0), some 
urgency (1), great urgency (2), and subject soiled themselves, involuntarily (3). The 
frequency of each score in the 7 diary days prior to a study visit will be evaluated. 
Changes from baseline in urgency score at week 6 will be summarized and compared 
between treatments. 
The proportion of subjects recording urgency episodes with score 3 (fecal incontinence) after 
3, 6 and 10 weeks of treatment will be analysed using logistic regression models including 
terms for region, treatment, sex, age group and baseline urgency. 
Rectal Bleeding 
The frequency of rectal bleeding will be evaluated from the data recorded in the subject’s 
diary for the 7 days prior to each study visit.  
Changes from baseline in rectal bleeding at Week 6 will be summarized and compared 
between treatments.  
PDAI 
The PDAI will be assessed at Day 1 and Weeks 6 and 10. The separate domain scores and the 
overall score, together with their change from baseline, will be calculated at each visit and 
summarized by treatment group.   
The change from baseline for each PDAI domain score and for the overall score, will be 
analysed using the same repeated measures ANCOVA model as for the mean number of 
bowel movements per day. 
Estimates of the following proportions of subjects will be evaluated at Weeks 6 and Weeks 
10: 
• Those who achieve an overall PDAI score <5  
• Those who achieve an overall PDAI score <3 
• Histological Improvement, defined as a PDAI Histology Score <=1 (for subjects with 
a baseline score >1), or with at least a 2-point improvement from baseline 
• Histological Healing, defined as a PDAI Histology Score of 0 for subjects that had a 
baseline subscore above 0. 
Each of these proportions will be compared between treatment groups at each visit using a 
Cochran-Mantel-Haenszel test accounting for region. In addition, they will be analyzed using 
separate logistic regression models for Week 6 and Week 10. These models will include 
terms for region, treatment, sex, age group and the corresponding baseline PDAI score. 


Quality of Life Questionnaire 
Quality of life is assessed using the CGQL (at baseline and Weeks 6, 10, 18 and 26) and EQ-
5D-5L (at baseline, Week 6 and Week 10). 
The change from baseline for each CGQL and EQ-5D domain score, and for the overall 
scores, will be summarized by study visit.   
The Total CGQL Score and the EQ-5D Index score will be analysed using the same repeated 
measures ANCOVA model as for the mean number of bowel movements per day. 
Pouchitis intervention 
The proportion of subjects, by week 26, who have not received any additional pouchitis 
treatment will be calculated and compared between the two treatment groups. 
The time to first intervention (including POUCHITIS related surgery) will be calculated for 
each subject.  The time will be calculated in days from the start of study treatment. 
Subjects not requiring a rescue intervention during their treatment period will be censored at 
the time of stopping study treatment in the analysis.  Kaplan-Meier curves will be presented 
and estimates of the probability of no “rescue” intervention at Weeks 3, 6 and 10 will be 
provided together with their 95% confidence intervals.  
In addition, time to first “rescue intervention” will be analyzed using a Cox’s proportional 
hazards regression model including terms for region, treatment, sex, age group, and the 
baseline PDAI score.   
1.3.2.3 
Exploratory 
The exploratory analysis will include, but will not be limited to, the exploratory analyses 
specified in this protocol.  Any exploratory analyses performed which were not specified in 
the protocol or the statistical analysis plan will be clearly described as such in the clinical 
study report. 
Histology 
The change from baseline in histological score, assessed using the D’Haens score, will be 
measured at baseline, Weeks 6 and 10. Changes from baseline will be summarized. 
Inflammatory markers 
The inflammatory marker CRP and WBC will be measured at Screening, Day 1 and Weeks 3 
and 6.  The change from baseline to Weeks 3 and 6 will be analysed  
Faecal calprotectin will be measured at screening, Weeks 3, 6, 10, 18 and 26. The change 
from baseline will be summarized. 
WPAI 
Scores derived from the WPAI (i.e. the percentage of worktime missed due to health issues, 
percentage of work impairment due to health issues, percentage activity impairment due to 
health issues, and the percentage productivity loss) will be suitably summarized by treatment 
group at each study visit. 


1.3.2.4 
Subgroup analysis 
The primary endpoint will also be analysed in the following subgroups for consistency with 
the overall trial results. 
• Gender 
• Age group 
Subjects who have previously failed antibiotics will be further categorized into those who 
were “efficacy” failures (failed to respond to initial therapy, or lost response to continued 
therapy) and those who failed due to intolerance.  An appropriate summary/analysis of these 
subjects groups will be performed.  
1.3.3 
Safety Analysis 
Safety will be assessed using the SAF. 
1.3.3.1 
The number and proportion of subjects with AEs 
Adverse Events will be coded using the MedDRA classification to give a preferred term and 
primary system organ class for each event. Proportions of subjects with adverse events will 
be presented by treatment group. Tables of AEs will be presented by system organ class, and 
preferred term, and include overall totals for AEs within each system organ class. Counting 
will be done by subject and not by event. A table of counts and percentages will also be made 
of those subjects with SAEs or AEs which led to withdrawal from the study.  
Treatment-emergent AEs are defined as adverse events that had an onset day and time on or 
after the day and time of the first dose of study drug up to 30 days after the last application of 
treatment. Adverse Events having missing onset dates will be considered as treatment 
emergent. 
 
Worsening of pouchitis will be evaluated as a separate event. 
 
1.3.3.2 
Laboratory Parameters  
The number (%) of subjects with abnormal values post-baseline will be tabulated by 
treatment group. In addition, summary statistics (i.e., mean, minimum, maximum, standard 
deviation, and number of subjects) will be presented for each treatment group for each 
laboratory parameter at each visit. When calculating the summary statistics only, the last 
observation within a visit window will be used if there are multiple observations. Changes 
from baseline will be presented in a similar format. An additional listing will be provided of 
those subjects who have clinically significant laboratory values. The data will also be 
presented as shift tables and clinically significant abnormalities will also be examined. 
1.3.3.3 
Vital Signs  
Abnormal vital signs will be counted by treatment group. The number (%) of subjects with 
any post-baseline vital sign readings above and/or below the specified levels will be 
presented for each treatment group. In addition, summary statistics (i.e., mean, minimum, 
maximum, standard deviation, and number of subjects) will be presented for each treatment 
group for each vital sign at each visit, comparing changes from baseline. When calculating 
the summary statistics only, the last observation within a visit window will be used if there 


are multiple observations. The data will also be presented as shift tables and clinically 
significant abnormalities will also be examined.  
1.3.3.4 Withdrawals 
The number (%) of subjects who withdraw from the study and their reasons for withdrawal 
will be tabulated by treatment group. The distribution of withdrawals and reasons will also be 
displayed at each visit by treatment group 
1.3.4 OPEN LABEL ACCESS ANALYSIS 
The following safety analysis will be conducted in all subjects receiving at least a part of one 
dose 
1. The number and proportion of subjects with AEs; (worsening of disease will also be 
evaluated separately) 
2. Assessment of clinical laboratory parameters 
3. Assessment of vital signs 
 
The following efficacy analysis will be conducted in all subjects receiving at least 80% of a 
42-night treatment course 
1.  Percentage of subjects who report response to open-label access alicaforsen. 
2. Interval between previous and current treatment courses 
1.4 
BLINDED DATA REVIEW MEETING 
The Sponsor will convene a Blinded Data Review Meeting after the data has been cleaned 
but before the study is unblinded.  The review will be performed within the framework of the 
requirements of the ICH Guideline E9. 
The terms of reference for the Data Review Meeting will include, but will not be limited to: 
• the determination of whether protocol violations are 'major' or 'minor', or not a 
protocol violation at all; 
• the allocation of subjects to analysis sets; 
• a review of missing data and of outliers; 
• a review of the distribution of the efficacy variables, considering any implications for 
the proposed method of statistical analysis; 
• an assessment of the overall endoscopic remission rate; 
• a review of whether additional covariates need to be included in the analyses; 
• the finalisation of the SAP. 
If the overall endoscopic remission rate indicates that the assumptions of the sample size 
calculation were not realized during the study then the Sponsor, taking the advice of the Data 
Review Meeting, may make one or more of the following changes to the primary analysis: 


• changing the definition of the analysis set used; 
• changing the definition of the primary endpoint; 
• any other change deemed by the Sponsor as necessary to preserve the integrity of the 
study. 
All persons taking part in the Data Review Meeting and all persons taking part in any 
deliberations concerning the format of the primary analysis must remain blinded to treatment 
allocation until any changes to the protocol specified analyses are documented and signed-
off.  
Formal records shall be kept of when the statistical analysis plan was finalized as well as 
when the blind was subsequently broken. 
1.4.1 PK Parameters   
Plasma PK parameters for alicaforsen will be evaluated as follows. All consenting subjects 
will provide single time-point plasma samples at Day 1, Week 3 and Week 6.  
In addition, full plasma concentration-time curves will be generated from a subset of 
randomised subjects (24 subjects, approximately 12 on active treatment and 12 on placebo) at 
Day 1 and Week 6.   Samples from subjects in the placebo group will NOT be analyzed. 
In this subset of subjects, the following PK parameters, as a minimum, will be calculated for 
alicaforsen:  Cmax, tmax, t½, AUCt, AUC0–24, AUC0–∞, and λz . 
The following pharmacokinetic parameters will be derived: 
Cmax 
The peak plasma concentration. 
 
tmax 
The time of peak plasma concentration. 
 
t½ 
The terminal half-life calculated from the terminal slope of the log 
concentration-time curve. 
 
AUC 
The area under the concentration-time curve will be calculated using the 
trapezoid rule for the interval 0 to tn h (time tn is the time at which the last non-
zero level was recorded), plus the area under the exponential curve from tn h to 
infinity.  The linear trapezoidal method will be used up to tmax, and the 
logarithmic method will be used for the plasma concentrations declining from 
Cmax.  The area from the time of last measured concentration to infinity will be 
extrapolated using the following formula:  
z
n
t
C
AUC
n
λ
ˆ
=
∞
−
 


where λz is the elimination rate constant calculated from non-linear regression of the 
terminal portion of the plasma concentration time curve, and 
is the predicted value of 
the concentration at time tn.   
 
Alicaforsen concentration-time curves will be plotted for individual subjects and will be 
summarized at Day 1 and Week 6, with concentrations on both log and linear scales. Single 
time-point PK data will be tabulated and summarized for each subject at Day 1, Week 3 and 
Week 6.  Summary statistics for these data will also be computed across subjects.  
 
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