Phase II Dual-Cohort Study Evaluating the Effects of Pembrolizumab in the Presence of Gut Microbiota Modulation With EDP1503 in Advanced Melanoma Naïve or Refractory to Anti-PD1 Antibody
Phase: PHASE2
Conditions: Melanoma (Skin), Melanoma
Sponsor: University of Chicago

 
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TITLE: Phase II Dual-Cohort Study Evaluating the Effects of Pembrolizumab in the 
Presence of Gut Microbiota Modulation with EDP1503 in Advanced Melanoma Naïve 
or Refractory to Anti-PD1 Antibody. 
 
SPONSOR: Randy F. Sweis, MD – University of Chicago 
 
UC NUMBER: IRB17-0461 
 
IND NUMBER: 18176 
 
PRINCIPAL INVESTIGATOR: 
 
Randy F. Sweis, MD 
Instructor 
University of Chicago 
5841 S. Maryland Ave. MC2115 
Chicago, IL 60637 
Telephone: (773) 702-1152 
Fax: (773) 834-0778 
 rsweis@medicine.bsd.uchicago.edu 
 
Version Date: April 11, 2018 Initial IND submission 
                       June 11, 2018   CTRC comments addressed 
 
 
November 21, 2018 Amendment #1 
 
 
April 10, 2019 Amendment #2 
 
 
This study is being conducted by institutional members of the Personalized Cancer Care 
Consortium (PCCC), as well as additional sites.  
 
 
 

 
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TABLE OF CONTENTS 
1.0 
TRIAL SUMMARY.................................................................................................... 6 
2.0 
TRIAL DESIGN.......................................................................................................... 6 
2.1 
Trial Design ............................................................................................................. 6 
2.2 
Trial Diagram .......................................................................................................... 7 
3.0 
OBJECTIVE(S) & HYPOTHESIS(ES) .................................................................... 7 
3.1 
Primary Objective(s) & Hypothesis(es) ................................................................ 7 
3.2 
Secondary Objective(s) & Hypothesis(es)............................................................. 7 
3.3 
Exploratory Objective ............................................................................................ 8 
4.0 
BACKGROUND & RATIONALE ............................................................................ 8 
4.1 
Background ............................................................................................................. 8 
4.1.1 Pharmaceutical and Therapeutic Background ...................................................... 8 
4.1.2 Preclinical and Clinical Trial Data ...................................................................... 10 
4.2 
Rationale ................................................................................................................ 10 
4.2.1 Rationale for the Trial and Selected Subject Population .................................... 10 
4.2.2 Rationale for Dose Selection/Regimen/Modification ......................................... 12 
4.2.3 Rationale for Endpoints ...................................................................................... 14 
5.0 
METHODOLOGY ................................................................................................... 17 
5.1 
Entry Criteria ........................................................................................................ 17 
5.1.1 Diagnosis/Condition for Entry into the Trial ...................................................... 17 
5.1.2 Subject Inclusion Criteria.................................................................................... 17 
5.1.3 Subject Exclusion Criteria .................................................................................. 18 
5.2 
Trial Treatments ................................................................................................... 20 
5.2.1 Dose Selection/Modification .............................................................................. 21 
5.2.2 Timing of Dose Administration .......................................................................... 23 

 
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5.2.3 Trial Blinding/Masking ....................................................................................... 23 
5.3 
Randomization or Treatment Allocation ............................................................ 23 
5.4 
Stratification .......................................................................................................... 23 
5.5 
Concomitant Medications/Vaccinations (allowed & prohibited) ..................... 24 
5.5.1 Acceptable Concomitant Medications ................................................................ 24 
5.5.2 Prohibited Concomitant Medications.................................................................. 24 
5.6 
Rescue Medications & Supportive Care ............................................................. 25 
5.6.1 Supportive Care Guidelines ................................................................................ 25 
5.7 
Diet/Activity/Other Considerations ..................................................................... 29 
5.7.1 Diet ...................................................................................................................... 29 
5.7.2 Contraception ...................................................................................................... 29 
5.7.3 Use in Pregnancy ................................................................................................ 31 
5.7.4 Use in Nursing Women ....................................................................................... 31 
5.8 
Subject Withdrawal/Discontinuation Criteria ................................................... 31 
5.8.1 Discontinuation of Study Therapy after CR ....................................................... 32 
5.9 
Subject Replacement Strategy ............................................................................. 33 
5.10 
Clinical Criteria for Early Trial Termination ................................................... 33 
6.0 
TRIAL FLOW CHART ........................................................................................... 34 
6.1 
Study Flow Chart .................................................................................................. 34 
7.0 
Registration PROCEDURES ................................................................................... 36 
7.1 
General Guidelines ............................................................................................... 36 
7.2 
Registration Process ............................................................................................. 36 
8.0 
TRIAL PROCEDURES ........................................................................................... 37 
8.1 
Trial Procedures ................................................................................................... 37 
8.1.1 Administrative Procedures .................................................................................. 37 

 
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8.1.2 Laboratory Procedures/Assessments .................................................................. 41 
8.1.3 Other Procedures ................................................................................................. 44 
8.2 
Assessing and Recording Adverse Events .......................................................... 45 
8.2.1 Definition of an Overdose for This Protocol and Reporting of Overdose to the 
Principal Investigator, Merck and Evelo ............................................................ 46 
8.2.2 Reporting of Pregnancy and Lactation to the Principal Investigator and to 
Merck .................................................................................................................. 47 
8.2.3 Immediate Reporting of Adverse Events to the Principal Investigator and to 
Merck .................................................................................................................. 47 
8.2.4 Evaluating Adverse Events ................................................................................. 49 
8.2.5 Serious Adverse Event Reporting to the Coordinating Center ........................... 53 
8.2.6 Serious Adverse Event Reporting by the Coordinating Center .......................... 54 
8.2.7 Serious Adverse Event Reporting to Merck ....................................................... 54 
8.2.8 Serious Adverse Event Reporting to Evelo (Sarah Cannon Safety 
Department) ........................................................................................................ 54 
9.0 
DATA REPORTING ................................................................................................ 54 
10.0 
STATISTICAL ANALYSIS PLAN ........................................................................ 55 
10.1 
Statistical Analysis Plan ....................................................................................... 55 
10.2 
Sample Size and Expected Accrual ..................................................................... 59 
11.0 
LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES ................................................................................................................. 59 
11.1 
Investigational Product ........................................................................................ 59 
11.2 
Packaging and Labeling Information ................................................................. 60 
11.3 
Clinical Supplies Disclosure ................................................................................. 60 
11.4 
Storage and Handling Requirements .................................................................. 60 
11.5 
Returns and Reconciliation .................................................................................. 60 
12.0 
ADMINISTRATIVE AND REGULATORY DETAILS ....................................... 60 

 
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12.1 
Institutional Review Board (IRB) Approval and Consent ................................ 60 
12.2 
Food and Drug Administration (FDA) Approval .............................................. 61 
12.3 
Required Documentation ..................................................................................... 61 
12.4 
Data and Safety Monitoring................................................................................. 62 
12.5 
Auditing ................................................................................................................. 62 
12.6 
Amendments to the Protocol ................................................................................ 63 
12.7 
Annual IRB Renewals, Continuing Review and Final Reports ........................ 64 
12.8 
Record Retention .................................................................................................. 64 
12.9 
Obligations of Study Site Investigators ............................................................... 64 
13.0 
APPENDICES ........................................................................................................... 65 
13.1 
ECOG Performance Status .................................................................................. 65 
13.2 
Common Terminology Criteria for Adverse Events V5 (CTCAE) .................. 65 
13.3 
Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 Criteria for 
Evaluating Response in Solid Tumors ................................................................ 65 
REFERENCES: ................................................................................................................ 66 
Appendix A: Criteria for irRECIST ................................................................................... 68 
 
 

 
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1.0 TRIAL SUMMARY 
Abbreviated Title 
Phase 2 study of Pembrolizumab + EDP1503 
Trial Phase 
Phase 2 
Clinical Indication 
Melanoma  
Trial Type 
Interventional 
Type of control 
Internal 
Route of administration 
IV and oral 
Trial Blinding 
NA 
Treatment Groups  
Anti-PD1 Treatment naïve and refractory melanoma  
Number of trial subjects 
Minimum: 55, Maximum: 70 
Estimated enrollment period 
18 – 26 months 
Estimated duration of trial 
50 months 
Duration of Participation 
Up to 2 years 
Estimated average length of 
treatment per patient 
3 months 
 
 
 
 
2.0 TRIAL DESIGN 
2.1 
Trial Design 
Phase II study observing the effect of the combination of anti-Programed Death 1 (anti-
PD1) antibody (pembrolizumab) and gut microbial manipulation with EDP1503 in 
advanced melanoma. The study will include 2 cohorts of patients with melanoma 
including  
1. Naïve to anti-PD1 antibody treatment (Cohort 1) and  
2. Refractory to anti-PD1 antibody treatment (Cohort 2).   
The study will involve initial administration of EDP1503 for a run-in period followed 
thereafter by joint administration of daily EDP1503 and treatment with pembrolizumab 
every 3 weeks. The first three patients enrolled to either cohort will pursue a two week 
EDP1503 run-in period and will be closely monitored for any toxicities related to 
EDP1503.  The second, third, and fourth patients will not be enrolled until the two week 
monotherapy period of the preceding patient is complete.   The study will pursue primary 
endpoints in cohorts 1 and 2 as below including  
1. Depth of response in naïve patients (Cohort 1) as well as the  
2. RECIST response rate to pembrolizumab in PD1 previously treated patients (Cohort 
2) in the presence of gut microbiota manipulation. 

 
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Other secondary clinical parameters such as progression-free survival and safety will 
additionally be investigated. The study will also provide the opportunity to investigate 
blood, tumor and stool based factors on response as well as the effect of EDP1503 on 
the local tumor and systemic immune environment.  
 
2.2 
Trial Diagram 
 
 
 
Treatment Groups 
Cohort 1 
Melanoma 
No prior PD1 exposure 
Cohort 2 
Melanoma 
Progression with prior PD1 
antibody treatment 
 
3.0 OBJECTIVE(S) & HYPOTHESIS(ES) 
3.1 
Primary Objective(s) & Hypothesis(es) 
(1) Objective: To assess the depth of response (Cohort 1) or RECIST response rate (Cohort 
2) of pembrolizumab in the presence of gut microbial manipulation with EDP1503 in 
subjects naïve (Cohort 1) or refractory (Cohort 2) to anti-PD1 antibody in cohorts of 
melanoma. 
Hypothesis:  The administration of pembrolizumab in the presence of gut microbiota 
manipulation with EDP1503 will enhance the activity of anti-PD1 antibody treatment. 
(2) Objective:  Assessment of safety and tolerability of EDP1503 during the monotherapy run-
in phase 
Hypothesis: EDP1503 monotherapy will demonstrate a similar safety/tolerability profile 
to probiotics such as low grade nausea, vomiting, and abdominal pain.   
3.2 
Secondary Objective(s) & Hypothesis(es) 
(1) Objective:  Assessment of progression-free survival as measured by RECIST and immune-
related response criteria   
Hypothesis:  The administration of pembrolizumab in the presence of gut microbiota 
manipulation with EDP1503 will lengthen progression-free survival relative to historical 
comparison with anti-PD1/L1 antibody monotherapy 
EDP1503 
Cohort 1: 2 weeks 
Cohort 2: 2 weeks 
EDP1503 + pembrolizumab 
Primary Endpoints:  
- 
RR 
and 
safety 
of 
EDP1503 monotherapy  
Secondary Endpoint: 
- PFS, Toxicity 
Tumor biopsy 

 
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(2) Objective:  Assessment of safety and tolerability of pembrolizumab in the presence of gut 
microbiota manipulation with EDP1503. 
Hypothesis: The administration of pembrolizumab in the presence of gut microbiota 
manipulation with EDP1503 will demonstrate a similar safety/tolerability profile to 
pembrolizumab alone  
3.3 
Exploratory Objective 
(1) 
Objective:  Assessment of whether the administration of EDP1503 alters immune cell 
phenotypes in the tumor microenvironment. 
Hypothesis: Oral administration of EDP1503 will result in changes in the immune cell 
phenotypes in the tumor microenvironment 
(2) 
Objective: Assessment of fecal material for bacterial contents 
Hypothesis: Oral administration of EDP1503 will result in increased level of EDP1503 
in the fecal contents 
(3) 
Objective: Biospecimen collection throughout the study including microbiota contents, 
peripheral blood and tumor tissue. 
Hypothesis: Oral administration of EDP1503 will result in changes in immune cell 
phenotypes detectable in the systemic circulation 
4.0 BACKGROUND & RATIONALE 
4.1 
Background 
Refer to the Investigator’s Brochure (IB)/approved labeling for detailed background 
information on pembrolizumab. 
4.1.1 Pharmaceutical and Therapeutic Background 
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades.  Accumulating evidence shows a correlation 
between tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis in 
various malignancies.  In particular, the presence of CD8+ T-cells and the ratio of CD8+ 
effector T-cells / FoxP3+ regulatory T-cells seems to correlate with improved prognosis and 
long-term survival in many solid tumors. 
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress 
immune control.  The normal function of PD-1, expressed on the cell surface of activated T-
cells under healthy conditions, is to down-modulate unwanted or excessive immune responses, 
including autoimmune reactions.  PD-1 (encoded by the gene Pdcd1) is an Ig superfamily 
member related to CD28 and CTLA-4 which has been shown to negatively regulate antigen 
receptor signaling upon engagement of its ligands (PD-L1 and/or PD-L2).  The structure of 

 
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murine PD-1 has been resolved.  PD-1 and family members are type I transmembrane 
glycoproteins containing an Ig Variable-type (V-type) domain responsible for ligand binding 
and a cytoplasmic tail which is responsible for the binding of signaling molecules.  The 
cytoplasmic tail of PD-1 contains 2 tyrosine-based signaling motifs, an immunoreceptor 
tyrosine-based inhibition motif (ITIM) and an immunoreceptor tyrosine-based switch motif 
(ITSM).  Following T-cell stimulation, PD-1 recruits the tyrosine phosphatases SHP-1 and 
SHP-2 to the ITSM motif within its cytoplasmic tail, leading to the dephosphorylation of 
effector molecules such as CD3ζ, PKCθ and ZAP70 which are involved in the CD3 T-cell 
signaling cascade.  The mechanism by which PD-1 down modulates T-cell responses is similar 
to, but distinct from that of CTLA-4 as both molecules regulate an overlapping set of signaling 
proteins.  PD-1 was shown to be expressed on activated lymphocytes including peripheral 
CD4+ and CD8+ T-cells, B-cells, T regs and Natural Killer cells.  Expression has also been 
shown during thymic development on CD4-CD8- (double negative) T-cells as well as subsets 
of macrophages and dendritic cells.  The ligands for PD-1 (PD-L1 and PD-L2) are 
constitutively expressed or can be induced in a variety of cell types, including non-
hematopoietic tissues as well as in various tumors.  Both ligands are type I transmembrane 
receptors containing both IgV- and IgC-like domains in the extracellular region and contain 
short cytoplasmic regions with no known signaling motifs.  Binding of either PD-1 ligand to 
PD-1 inhibits T-cell activation triggered through the T-cell receptor.  PD-L1 is expressed at 
low levels on various non-hematopoietic tissues, most notably on vascular endothelium, 
whereas PD-L2 protein is only detectably expressed on antigen-presenting cells found in 
lymphoid tissue or chronic inflammatory environments.  PD-L2 is thought to control immune 
T-cell activation in lymphoid organs, whereas PD-L1 serves to dampen unwarranted T-cell 
function in peripheral tissues.  Although healthy organs express little (if any) PD-L1, a variety 
of cancers were demonstrated to express abundant levels of this T-cell inhibitor.  PD-1 has 
been suggested to regulate tumor-specific T-cell expansion in subjects with melanoma (MEL).  
This suggests that the PD-1/PD-L1 pathway plays a critical role in tumor immune evasion and 
should be considered as an attractive target for therapeutic intervention. 
Pembrolizumab is a potent and highly selective humanized monoclonal antibody (mAb) of the 
IgG4/kappa isotype designed to directly block the interaction between PD-1 and its ligands, 
PD-L1 and PD-L2.  KeytrudaTM (pembrolizumab) has recently been approved in the United 
States for the treatment of patients with unresectable or metastatic melanoma and disease 
progression following ipilumumab and, if BRAF V600 mutation positive, a BRAF inhibitor. 
Bifidobacteria are a gram positive, anaerobic, non-spore forming, rod shaped genus of bacteria 
(Weber et al 2015).  They are naturally found in the colon of healthy humans and animals 
throughout early life and into adulthood (O’Callaghan et al 2016).  Bifidobacterium are 
frequently used in foods and supplements in North America and Europe and these strains in 
food products have been designated ‘Generally Regarded As Safe’ (GRAS, 21 CFR 170; FDA 
GRAS Notices) or ‘Qualified Presumption of Safety’ (QPS) Status (EFSA) along with many 
other lactic acid producing bacteria.  These bacteria are found in fermented foods, yogurts, 
supplements, and other foodstuffs at levels between 1x109- 1x1011 CFU/serving (FDA GRAS 
Notices, EFSA Journal 2013).  These strains are selected to impart beneficial health effects on 
the host and positively impact the host gut microbiota composition, metabolism, and general 
health without adverse changes to the gut (O’Callaghan et al 2016).  Many of them are 
originally isolated from healthy hosts and are ubiquitous in the diet and the healthy large 

 
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intestine of humans soon after birth throughout life.  They have been evaluated in 100s of 
clinical trials (854 references on PubMed of “clinical trials Bifidobacterium”) in subjects 
ranging from preterm infants to elderly adults with minimal adverse events.   
4.1.2 Preclinical and Clinical Trial Data 
Refer to the Investigator’s Brochures for pembrolizumab and EDP1503 regarding Preclinical 
and Clinical data. 
4.2 
Rationale 
4.2.1 Rationale for the Trial and Selected Subject Population 
Blockade of the Programmed Death-1 (PD1) receptor by pembrolizumab has demonstrated 
remarkable clinical activity in patients with advanced melanoma showing a response rate in a 
randomized phase III trial of 33%1.  However, 67% of patients do not respond and 
approximately 25% have disease progression as best overall response.  Consideration then 
should be given to manipulations that would modify the immune microenvironment and 
facilitate clinical benefit for a greater fraction of patients. 
Although multiple pharmacologic approaches to augment the efficacy of pembrolizumab have 
been proposed, these have to date have focused on targeting the tumor using anti-neoplastic 
agents or other immune-modifying drugs.  We have uncovered evidence that characteristics of 
the host also are critical, including the germline genetic makeup and also a major 
environmental factor, which is the composition of the commensal microbiota. 
Cancer has at times been described as a disease of the larger meta-organism which emphasizes 
the interplay between both between cancer and the immune system but additionally between 
the microbiota that modulate the host immune response.  Commensal organisms are essential 
to the normal development of the immune system both for innate and adaptive immunity, with 
pattern recognition receptors mediating processes throughout the body including metabolism, 
morphogenesis, and homeostasis2.  Gut microbiota especially have been identified as essential 
in mucosal and tumor immunity, regulating both local and systemic inflammation responses.  
Disruption of the gut microbiota via antibiotics (or germ-free mice) has been associated with 
decreased responsiveness of murine tumors to immunotherapies and chemotherapies3.  
Regulation of tumor-infiltrating myeloid-derived cells is proposed as a potential mechanism to 
facilitate this. 
Our group has previously described the T cell-inflamed tumor microenvironment as a potential 
predictive biomarker for response to multiple immunotherapies including therapeutic vaccines, 
anti-CTLA-4, and anti-PD-1/PD-L1 antibodies4-10.  Our analysis of the tumor 
microenvironment in patients with melanoma suggests that approximately 35-50% of cases 
show evidence of spontaneous priming of anti-tumor T cells leading to migration of CD8+ 
effector T cells into tumor sites.  This phenotype has been designated the T cell-inflamed tumor 
microenvironment and is characterized by expression of T cell markers, chemokines for T cell 
recruitment, and transcripts indicative of type I IFN signaling5,6,8. 

 
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Similar features of the immune response have been proposed to impact on the management of 
infection and cancer including modulation by commensal microbiota, development of chronic 
immune responses and regulatory mechanisms to prevent collateral tissue damage11.  We and 
others have proposed that manipulation of the microbiome has the potential ability to modulate 
the anti-tumor immune response and promote the development of an inflamed tumor 
microenvironment12,13. 
To assess the effect of microbial composition on the immune response to melanoma, our group 
compared the growth of subcutaneous B16 melanoma in genetically identical C57BL/6 mice 
derived from two different facilities which have been shown to differ in their commensal 
microbes (Jackson laboratories and Taconic farms)14. We found that B16.SIY tumors exhibited 
an increased growth rate in mice derived from Taconic (p < 0.02), which was associated with 
reduced induction of tumor specific IFN-g-producing CD8+ T cells (p < 0.009). A markedly 
increased number of SIY antigen-specific CD8 + T cells was found to accumulate within the 
tumor microenvironment in Jackson versus Taconic mice (p < 0.03). Strikingly, the differences 
in tumor growth, endogenous T cell priming, and SIY antigen-specific T cell infiltration were 
ablated in animals cohoused for at least two weeks prior to injection of tumor cells, consistent 
with a microbiota-derived effect. We thus asked whether transfer of Jackson fecal material into 
Taconic mice by oral gavage prior to tumor inoculation was sufficient to confer protective anti-
tumor responses. Indeed, Taconic mice that received Jackson feces exhibit dramatically slower 
tumor growth (p < 0.015) and increased numbers of SIY antigen-specific CD8+ T cells at the 
tumor site, compared to Taconic mice that received Taconic feces.  
We additionally assessed whether transfer of microbial contents impacted on the therapeutic 
efficacy of anti-PDL1 antibody in these systems.  Similar to what was observed above, transfer 
of fecal contents from Jackson mice to Taconic mice significantly boosted the efficacy of anti-
PDL1 antibody while transfer of Taconic fecal contents to Jackson mice had no significant 
impact. 
Thereafter we have pursued a detailed investigation of the microbial contents of the fecal 
material from Jackson mice as compared with Taconic.  In concert with colleagues at the 
Argonne National Laboratory, 16S ribosomal sequencing identified a small number of 
bacterial species that were significantly different between these strains.  The top candidate was 
the genus Bifidobacterium.  Using commercial sources, we obtained a probiotic consisting of 
only Bifidobacterium species for preclinical experimentation.  In fact, administration of two 
weekly doses of Bifidobacterium was sufficient to exert anti-tumor activity in C57BL/6 mice 
from Taconic, which synergized with anti-PD-L1 mAb to cause complete tumor elimination 
in most animals.  After an intensive screening process, Evelo Biosciences identified a strain of 
Bifidobacterium animalis lactis with consistently high performance in tumor isograft assays 
including B16 melanoma, and manufactured this strain under GMP into a drug product known 
as EDP1503.  
These data provide evidence implicating the microbiota in shaping anti-tumor immunity and 
provide a rationale for a clinical trial evaluating the efficacy of pembrolizumab in the presence 
of gut microbiota manipulation with EDP1503.  

 
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In summary, our data suggest that the intestinal microbiota have a significant impact on anti-
tumor immunity and see the potential of specific microorganisms to modify the commensal 
environment of the host and enhance the anti-tumor effect of anti-PD-1.  We therefore propose 
a phase II study evaluating the efficacy of pembrolizumab in the presence of gut microbiota 
manipulation with EDP1503 in subjects with advanced melanoma who are either naïve or 
refractory to anti-PD1 antibody treatment. 
4.2.2 Rationale for Dose Selection/Regimen/Modification  
Pembrolizumab 
An open-label Phase I trial (Protocol 001) is being conducted to evaluate the safety and 
clinical activity of single agent MK-3475.  The dose escalation portion of this trial evaluated 
three dose levels, 1 mg/kg, 3 mg/kg, and 10 mg/kg, administered every 2 weeks (Q2W) in 
subjects with advanced solid tumors.  All three dose levels were well tolerated and no dose-
limiting toxicities were observed.  This first in human study of MK-3475 showed evidence of 
target engagement and objective evidence of tumor size reduction at all dose levels (1 mg/kg, 
3 mg/kg and 10 mg/kg Q2W).  No MTD has been identified to date.  10.0 mg/kg Q2W, the 
highest dose tested in PN001, will be the dose and schedule utilized in Cohorts 1 and 2 of 
this protocol to test for initial tumor activity.  Recent data from other clinical studies within 
the MK-3475 program has shown that a lower dose of MK-3475 and a less frequent schedule 
may be sufficient for target engagement and clinical activity. 
 
PK data analysis of MK-3475 administered Q2W and Q3W showed slow systemic clearance, 
limited volume of distribution, and a long half-life (refer to IB).  Pharmacodynamic data (IL-
2 release assay) suggested that peripheral target engagement is durable (>21 days).  This 
early PK and pharmacodynamic data provides scientific rationale for testing a Q2W and 
Q3W dosing schedule.   
 
A population pharmacokinetic analysis has been performed using serum concentration time 
data from 476 patients. Within the resulting population PK model, clearance and volume 
parameters of MK-3475 were found to be dependent on body weight. The relationship 
between clearance and body weight, with an allometric exponent of 0.59, is within the range 
observed for other antibodies and would support both body weight normalized dosing or a 
fixed dose across all body weights.  MK-3475 has been found to have a wide therapeutic 
range based on the melanoma indication.  The differences in exposure for a 200 mg fixed 
dose regimen relative to a 2 mg/kg Q3W body weight based regimen are anticipated to 
remain well within the established exposure margins of 0.5 – 5.0 for MK-3475 in the 
melanoma indication. The exposure margins are based on the notion of similar efficacy and 
safety in melanoma at 10 mg/kg Q3W vs. the proposed dose regimen of 2 mg/kg Q3W (i.e. 
5-fold higher dose and exposure). The population PK evaluation revealed that there was no 
significant impact of tumor burden on exposure. In addition, exposure was similar between 
the NSCLC and melanoma indications. Therefore, there are no anticipated changes in 
exposure between different indication settings. 
 
The rationale for further exploration of 2 mg/kg and comparable doses of pembrolizumab in 
solid tumors is based on: 1) similar efficacy and safety of pembrolizumab when dosed at either 
2 mg/kg or 10 mg/kg Q3W in melanoma patients, 2) the flat exposure-response relationships 

 
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of pembrolizumab for both efficacy and safety in the dose ranges of 2 mg/kg Q3W to 10 mg/kg 
Q3W, 3) the lack of effect of tumor burden or indication on distribution behavior of 
pembrolizumab (as assessed by the population PK model) and 4) the assumption that the 
dynamics of pembrolizumab target engagement will not vary meaningfully with tumor type. 
The choice of the 200 mg Q3W as an appropriate dose for the switch to fixed dosing is based 
on simulations performed using the population PK model of pembrolizumab showing that the 
fixed dose of 200 mg every 3 weeks will provide exposures that 1) are optimally consistent 
with those obtained with the 2 mg/kg dose every 3 weeks, 2) will maintain individual patient 
exposures in the exposure range established in melanoma as associated with maximal efficacy 
response and 3) will maintain individual patients exposure in the exposure range established 
in melanoma that are well tolerated and safe.  
A fixed dose regimen will simplify the dosing regimen to be more convenient for physicians 
and to reduce potential for dosing errors.  A fixed dosing scheme will also reduce complexity 
in the logistical chain at treatment facilities and reduce wastage. 
The landscape of adjuvant therapy options for high risk cutaneous melanoma is in a state of 
flux and treatments that recently formed the backbone of systemic therapy for metastatic 
disease are now being used earlier.  Whereas interferon-α and more recently ipilimumab were 
standards of care (PMID: 23042723, PMID: 27717298), patients with high risk stage III 
melanoma now have standard of care options with combination BRAF-MEK inhibition and 
anti-PD1 antibody. In a phase III study of dabrafenib and trametinib compared with placebos, 
estimated 3 year relapse-free survival was 58% in the treatment group versus 39% for placebo 
with the hazard ratio for relapse or death of 0.47 (95% confidence interval [CI], 0.39 to 0.58; 
P<0.001) (PMID: 28891408).  In a phase III study of nivolumab compared with ipilimumab 
relapse free survival at 12 months was 71% with nivolumab as compared with 61% for 
ipilimumab with a hazard ratio for relapse or death of 0.65 (97.56% CI, 0.51 to 0.83; P<0.001) 
(PMID: 28891423). Given these data many patients diagnosed with advanced disease will have 
previously been treated with PD1 based therapy and approaches that augment systemic 
immunity to facilitate clinical response in the setting of resistance are of high priority. 
 
EDP1503 
Amounts of Bifidobacterium consumed by humans in various commercially available 
Bifidobacterium-based probiotics range from 1 x109 to 3.6 x1012 CFU15,16 The Bifidobacterium 
capsule in this study will contain >7.5x1010 CFU/capsule and will be taken at an amount of  2 
capsules bid for a total of 4 capsules per day, half in the morning and half in the evening.  
Foods containing Bifidobacterium have been consumed by millions of people largely with a 
lack of side effects.  Minor adverse events include bloating, flatus, loose stool, and mild 
gastrointestinal discomfort.  In extremely rare cases, lactic acid bacteria based probiotics have 
been identified as the cause of bacteremia but generally pose far less threat than one’s own 
gastrointestinal flora17,18.  Patients who have experienced Bifidobacterium bacteremia are 
usually immunocompromised and severely sick19.  In a majority of these cases, antibiotic 

 
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administration resulted in a patient recovery owing to Bifidobacteria’s sensitivity to a broad 
panel of antibiotics19,20.  Despite the well tolerated nature of oral Bifidobacterium, to avoid 
unnecessary risk, patients who are immunocompromised will be excluded from this study. For 
subjects who develop a concomitant illness during the trial which requires antibiotic therapy 
the Bifidobacterium or placebo therapy will be halted until at least 2 days after the cessation 
of antibiotic therapy. 
EDP1503 is a cloned strain of Bifidobacterium animalis spp. lactis. The final clone was 
selected after two rounds of cloning to ensure strain purity. Bifidobacterium animalis spp. 
lactis is classified as Generally Regarded As Safe (GRAS) in the United States.   
EDP1503 drug substance (DS) is manufactured under current Good Manufacturing Practice 
(GMP) conditions by standard industrial scale fermentation, followed by centrifugation cell 
separation and freeze-drying together with cryoprotectants. The DS is then milled into a fine 
powder, packaged into heat-sealed foil pouch and stored at 2-8 oC. 
EDP1503 drug product (DP) formulation is a blend of freeze-dried powder of Bifidobacterium 
animalis spp. lactis (DS) and excipients (e.g. Avicel PH200LM, Magnesium Stearate, and 
Aerosil). 
The 
formulated 
blend 
is 
filled 
into 
size 
0 
hard 
HPMC 
(hydroxypropylmethylcellulose) capsules, banded, and enterically coated. The enteric coating 
is designed for duodenal release (pH ≥ 5.5).  The manufactured capsules are filled into an air-
tight rigid plastic pot and vacuum sealed in a foil pouch.  The finished drug product is stored 
at 2-8oC.  
4.2.3 Rationale for Endpoints 
Here we propose a clinical trial testing the hypothesis that the administration of pembrolizumab 
in the presence of gut microbiota manipulation with EDP1503 will increase the depth of 
response in patients who are naïve to PD1 antibody and may induce response in patients who 
have previously progressed on anti-PD1 antibody. In addition the trial will test the hypothesis 
that EDP1503, as monotherapy, is safe and that any adverse effects are consistent with 
historical observations of probiotic therapy, such as mild and transient GI disturbance.  
 
The rationale for the primary endpoints in each cohort stem from the intersection of trial 
feasibility, meaningful clinical patient outcomes and the early nature of investigation 
surrounding the impact of the microbiome on anti-tumor immunity.  Sample size calculations 
for analysis of a substantial improvement in the response rate in the PD1 naïve population 
make the analysis of standard RECIST response rate not feasible in a modestly sized phase II 
study.  Randomized designs were also considered though were not supported by the 
pharmaceutical sponsor in the modestly sized phase II setting. Simultaneously it has been 
recognized in the melanoma community that quality of response to treatment is particularly 
meaningful as patients who have deep responses rarely recur21-23.  In fact multiple groups are 
proposing randomized studies to investigate early discontinuation of PD1 after maximum 
response while the Canadian government has launched such a trial24.  In this context the 
primary end point for cohort 1 was chosen as deep response (> 80%) as this level of response 
has been observed consistently in approximately 40% of patients in combination clinical trials 
of the anti-PD1 antibody (nivolumab) in combination with anti-CTLA4 antibody 

 
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(ipilimumab). This deep response rate has been published in the New England Journal of 
Medicine four times across the phase I CA209-00425, phase II CHECKMATE-06926 and phase 
III CHECKMATE-067 studies27,28.  In cohort 2 the primary endpoint is improvement in 
RECIST response as is commonly used.  In this refractory cohort no responses are normally 
expected thus facilitating a straightforward Simon two-stage design. 
Prior investigations regarding the modulation of the gut flora in preclinical melanoma models 
demonstrated that this effect restored partial tumor control however the addition of PDL1 
antibody completely ablated tumors.  Through our correlative analysis, we hope to propose a 
model by which we can suggest which patients would benefit from pembrolizumab alone or 
pembrolizumab in the presence of gut microbiota manipulation with EDP1503 or other 
probiotic. 
4.2.3.1 Efficacy Endpoints 
The primary efficacy objective of this trial is to evaluate the anti-tumor activity of 
pembrolizumab in the presence of gut microbiota manipulation with EDP1503 in subjects 
with advanced melanoma who are naïve or refractory to anti-PD1 antibody.  
 
RECIST as assessed by the investigator will be used as the primary response rate efficacy 
endpoint however irRC will also be followed. RECIST will also be used by the local site to 
determine eligibility and make treatment decisions.  The primary efficacy endpoint is 
response rate based on RECIST.   Secondary endpoints are listed in section 3.2. 
 
Immunotherapeutic agents such as pembrolizumab may produce antitumor effects by 
potentiating endogenous cancer-specific immune responses which may be functionally 
anergic.   The response patterns seen with such an approach may extend beyond the typical 
time course of responses seen with cytotoxic agents, and can manifest a clinical response 
after an initial increase in tumor burden or even the appearance of new lesions.  Standard 
RECIST criteria may not provide a complete response assessment of immunotherapeutic 
agents such as pembrolizumab therefore the irRC have been developed to encompass this. 
 
Broadly, irRC includes the concept of treatment beyond progression, if radiologic imaging 
shows PD, tumor assessment should be repeated ≥ 4 weeks later in order to confirm PD 
with the option of continuing treatment per below while awaiting radiologic 
confirmation of progression.   If repeat imaging shows a reduction in the tumor burden 
compared to the initial scan demonstrating PD, treatment may be continued as per 
treatment calendar.   If repeat imaging confirms progressive disease, subjects will be 
discontinued from trial therapy.    In determining whether or not the tumor burden has 
increased or decreased, Investigators should consider all target lesions as well as non-target 
lesions. 
 
In subjects who have initial evidence of radiological PD, it is at the discretion of the treating 
physician whether to continue a subject on study treatment until repeat imaging is obtained 
a minimum of 4 weeks later.  This decision should be based on the clinical judgment of 
the subject’s overall clinical condition, including performance status, clinical symptoms, 
and laboratory data. Subjects may receive treatment while waiting for confirmation of PD 
if they are clinically stable as defined by the following criteria: 
 
• Absence of signs and symptoms indicating disease progression 

 
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• No decline in ECOG performance status 
 
• Absence of rapid progression of disease 
 
• Absence of progressive tumor at critical anatomical sites (e.g., cord compression) 
requiring urgent alternative medical intervention 
 
When feasible, subjects should not be discontinued until progression is confirmed.  This 
allowance to continue treatment despite initial radiologic progression takes into account the 
observation that some subjects can have a transient tumor flare in the first few months after 
the start of immunotherapy, but with subsequent disease response.  Subjects that are deemed 
clinically unstable are not required to have repeat imaging for confirmation of progressive 
disease. 
4.2.3.2 Biomarker Research 
Our group has previously described the T cell-inflamed tumor microenvironment as a potential 
predictive biomarker for response to multiple immunotherapies including therapeutic vaccines, 
anti-CTLA-4, and anti-PD-1/PD-L1 antibodies4-10.  Our analysis of the tumor 
microenvironment in patients with melanoma suggests that approximately 35-50% of cases 
show evidence of spontaneous priming of anti-tumor T cells leading to migration of CD8+ 
effector T cells into tumor sites.  This phenotype has been designated the T cell-inflamed tumor 
microenvironment and is characterized by expression of T cell markers, chemokines for T cell 
recruitment, and transcripts indicative of type I IFN signaling5,6,8. 
In addition to response prediction, this gene signature is also potentially useful in identifying 
those that will not respond.  Patients harboring non-inflamed tumors therefore require 
treatment strategies which may modulate the immune response to facilitate the influx of tumor 
infiltrating lymphocytes (TIL) and conversion from a non-inflamed to an inflamed tumor.   
Beyond the tumor microenvironment, aspects of the host (patient) and commensal environment 
may also have an essential impact on immunity in response to both radiation and anti-PD1 
antibody.  Host factors of interest regarding the immune response include circulating immune 
subsets as well as germline DNA sequence and polymorphisms.  Further, a growing literature 
supports a role for commensal microbiota in the immune response to infection and cancer 
including development of acute versus chronic immune responses and regulatory mechanisms 
to prevent collateral tissue damage11.  We and others have proposed that manipulation of the 
microbiome has the potential ability to modulate the anti-tumor immune response and promote 
the development of an inflamed tumor microenvironment12,13. 
Considering this background, we propose to collect peripheral blood for serum, peripheral 
blood mononuclear cells, germline DNA, as well as fecal samples throughout treatment.  
Baseline tumor tissue prior to treatment and/or fresh tumor biopsy at baseline and at 
after EDP1503 run-in are required on all patients.  Diagnostic tissue from prior biopsy is 
allowed if the tissue was obtained by core or surgical biopsy (FNA is not acceptable) and no 
intervening systemic treatment has been administered. Peripheral blood for serum and blood 
mononuclear cells will be taken at the beginning and end of the run in period when subjects 
are only taking EDP1503 to evaluate any immediate effects on these biomarkers.  Tumor 

 
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biopsy will be required at the end of the second week of EDP1503 run-in (prior to starting 
pembrolizumab) in patient’s naïve to anti-PD1 (cohort 1) unless considered not clinically 
feasible.  These biopsies will be analyzed to evaluate the effect of the EDP1503 on the tumor 
microenvironment.   
Fecal samples will be analyzed by a variety of methods to determine quantitatively if there is 
a correlation between specific features of the host microbiome and/ or its manipulation with 
the effect on the systemic and tumor biomarkers.  Analysis may include microbial culturing 
and nucleic acid based evaluation.  Micro-organisms cultured from patient fecal samples may 
be stored and studied in preclinical models with the intent of learning more about the 
interaction between the microbiome and host immune responses.  
Additionally, it is requested that any patients who undergo tumor biopsy as part of their 
standard care during the study have any available tissue forwarded for analysis in comparison 
of pre-administration and on-/post-treatment tumor microenvironmental factors.   
5.0 METHODOLOGY 
5.1 
Entry Criteria 
5.1.1 Diagnosis/Condition for Entry into the Trial 
1. Advanced, unresectable or metastatic melanoma 
5.1.2 Subject Inclusion Criteria 
In order to be eligible for participation in this trial, the subject must: 
1. Be willing and able to provide written informed consent/assent for the trial. 
2. Be ≥ 18 years of age on day of signing informed consent. 
3. Have measurable disease based on RECIST 1.1.   
4. Be naïve to exposure in the metastatic setting to PD1/L1 antibody for cohort 1 but have 
had exposure to PD1/L1 (or PD1/L1 combination therapy) in cohort 2. Prior exposure 
to CTLA4 antibody in the metastatic setting is not allowed for cohort 1 though exposure 
in the adjuvant setting is allowed for either cohort. To be eligible for cohort 2, and 
considered refractory to PD1/L1, a patient must have had a restaging exam showing 
progressive disease at least 90 days following initiation of anti-PD1/L1 as prior therapy.  
a. Adjuvant therapy with BRAF-MEK, PD1 or CTLA4 based therapy is allowed.  
Prior adjuvant BRAF-MEK therapy will fulfill treatment requirement in the 
metastatic setting.  Patients who experience progression of disease during 
adjuvant PD1 therapy or within 6 months of completing adjuvant PD1 therapy 
will be considered refractory and thus eligible for cohort 1.  Patients with 
progression to active metastatic disease more than 6 months following 
completion of adjuvant PD1 therapy will be eligible for cohort 1. 

 
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5. Have a performance status of 0 or 1 on the ECOG Performance Scale. 
6. Demonstrate adequate organ function as defined in Table 1, all screening labs should 
be performed within 14 days of study initiation.   
Table 1  Adequate Organ Function Laboratory Values 
System 
Laboratory Value 
Hematological 
 
Absolute neutrophil count (ANC) 
≥1,500 /mcL 
Platelets 
≥100,000 / mcL 
Hemoglobin 
≥9 g/dL or ≥5.6 mmol/L without transfusion or EPO dependency 
(within 7 days of assessment) 
Renal 
 
Serum creatinine OR 
Measured or calculateda creatinine 
clearance 
(GFR can also be used in place of 
creatinine or CrCl) 
≤1.5 X upper limit of normal (ULN) OR 
 
≥60 mL/min for subject with creatinine levels > 1.5 X 
institutional ULN 
Hepatic 
 
Serum total bilirubin 
≤ 1.5 X ULN OR 
 
Direct bilirubin ≤ ULN for subjects with total bilirubin levels > 
1.5 ULN 
AST (SGOT) and ALT (SGPT) 
≤ 2.5 X ULN  OR 
≤ 5 X ULN for subjects with liver metastases 
Albumin 
>2.5 mg/dL 
aCreatinine clearance should be calculated per institutional standard. 
 
7. Female subject of childbearing potential should have a negative urine or serum 
pregnancy within 72 hours prior to receiving the first dose of study medication.  If the 
urine test is positive or cannot be confirmed as negative, a serum pregnancy test will 
be required.   
8. Female subjects of childbearing potential (Section 5.7.2) must be willing to use an 
adequate method of contraception as outlined in Section 5.7.2 – Contraception,  for the 
course of the study through 120 days after the last dose of study medication. 
Note: Abstinence is acceptable if this is the usual lifestyle and preferred contraception for 
the subject. 
9. Male subjects of childbearing potential (Section 5.7.1) must agree to use an adequate 
method of contraception as outlined in Section 5.7.1- Contraception, starting with the 
first dose of study therapy through 120 days after the last dose of study therapy. 
Note: Abstinence is acceptable if this is the usual lifestyle and preferred contraception for 
the subject. 
5.1.3 Subject Exclusion Criteria 
The subject must be excluded from participating in the trial if the subject: 

 
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1. For cohort 2: Has BRAF mutant disease but has not yet received treatment with 
RAF/MEK inhibitors. 
- 
This criteria can be met via adjuvant treatment with BRAF-MEK inhibitors 
2. Is currently participating and receiving study therapy or has participated in a study of 
an investigational agent and received study therapy or used an investigational device 
within 2 weeks of the first dose. 
3. Is currently taking Bifidobacterium based probiotics or is taking pre/pro-biotics 
regularly.     
4. Has a diagnosis of immunodeficiency or is receiving systemic steroid therapy or any 
other form of immunosuppressive therapy within 7 days prior to the first dose. 
 
5. Has a known history of active TB (Bacillus Tuberculosis) 
 
6. Hypersensitivity to pembrolizumab or any of its excipients. 
7. Has had a prior anti-cancer monoclonal antibody (mAb) within 3 weeks prior to study 
Day 1 (excluding anti-PD1 antibodies such as pembrolizumab or nivolumab in cohort 
2) or who has not recovered (i.e., ≤ Grade 1 or at baseline) from adverse events due to 
agents administered more than 4 weeks earlier. 
8. Has had prior chemotherapy, targeted small molecule therapy, or radiation therapy 
within 2 weeks prior to study Day 1 or who has not recovered (i.e., ≤ Grade 1 or at 
baseline) from adverse events due to a previously administered agent. 
- 
Note:  Subjects with ≤ Grade 2 neuropathy are an exception to this criterion and 
may qualify for the study. 
- 
Note:  If subject received major surgery, they must have recovered adequately 
from the toxicity and/or complications from the intervention prior to starting 
therapy.   
9. Has a known additional malignancy that is progressing or requires active treatment.  
Exceptions include basal cell carcinoma of the skin or squamous cell carcinoma of the 
skin that has undergone potentially curative therapy or in situ cervical cancer. 
10. Has known active central nervous system (CNS) metastases and/or carcinomatous 
meningitis.  Subjects with previously treated brain metastases may participate provided 
they are stable (without evidence of progression by imaging for at least four weeks 
prior to the first dose and any neurologic symptoms have returned to baseline), have no 
evidence of new or enlarging brain metastases, and are not using steroids for at least 7 
days prior to start of study.  This exception does not include carcinomatous meningitis 
which is excluded regardless of clinical stability.   

 
Protocol Version: 04/10/2019 
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11. Has active autoimmune disease that has required systemic treatment in the past 2 years 
(i.e. with use of disease modifying agents, corticosteroids or immunosuppressive 
drugs). Replacement therapy (eg., thyroxine, insulin, or physiologic corticosteroid 
replacement therapy for adrenal or pituitary insufficiency, etc.) is not considered a form 
of systemic treatment.  
12. Has known history of, or any evidence of active, non-infectious pneumonitis. 
13. Has an active infection requiring antibiotic therapy or has received a course of 
antibiotics within the previous 2 weeks of starting study treatment. 
14. Has a history or current evidence of any condition, therapy, or laboratory abnormality 
that might confound the results of the trial, interfere with the subject’s participation for 
the full duration of the trial, or is not in the best interest of the subject to participate, in 
the opinion of the treating investigator.   
15. Has known psychiatric or substance abuse disorders that would interfere with 
cooperation with the requirements of the trial. 
16. Is pregnant or breastfeeding, or expecting to conceive or father children within the 
projected duration of the trial, starting with the screening visit through 120 days after 
the last dose of trial treatment. 
17. Has a known history of Human Immunodeficiency Virus (HIV) (HIV 1/2 antibodies). 
18. Has known active Hepatitis B (e.g., HBsAg reactive) or Hepatitis C (e.g., HCV RNA 
[qualitative] is detected). 
19. Has received a live vaccine within 30 days of planned start of study therapy. 
Note:  Seasonal influenza vaccines for injection are generally inactivated flu vaccines 
and are allowed; however intranasal influenza vaccines (e.g., Flu-Mist®) are live 
attenuated vaccines, and are not allowed. 
 
5.2 
Trial Treatments 
The treatment to be used in this trial is outlined below in Table 2 
Table 2  Trial Treatment 
Drug 
Dose/Potency 
Dose 
Frequency 
Route of 
Administration 
Regimen/Treatment 
Period 
Pembrolizumab 200 mg 
Q3W 
IV infusion 
Day 1 of each 3 week 
cycle 
 
 
 
 
 

 
Protocol Version: 04/10/2019 
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Drug 
Dose/Potency 
Dose 
Frequency 
Route of 
Administration 
Regimen/Treatment 
Period 
Dietary 
Supplement 
Amount 
Frequency Route 
Consumption 
period 
EDP1503 
>7.5x1010 
CFU/capsule 
2 capsules 
BID 
Oral 
Daily through the 
protocol study period 
 
5.2.1 Dose Selection/Modification 
5.2.1.1 Dose Selection 
The rationale for selection of doses to be used in this trial is provided in Section 4.0 – 
Background and Rationale.   
Details on preparation and administration of pembrolizumab (MK-3475) are provided in the 
Pharmacy Manual.   
5.2.1.2 Dose Modification (Escalation/Titration/Other) 
Adverse events (both non-serious and serious) associated with pembrolizumab (or in 
combination with EDP1503) exposure may represent an immunologic etiology.  These adverse 
events may occur shortly after the first dose or several months after the last dose of treatment. 
Pembrolizumab and EDP1503 must be withheld for drug-related toxicities and severe or life-
threatening AEs. Supportive care guidelines, including use of corticosteroids are described 
below. 
All Grade 3-5 adverse events considered possibly, probably or definitely related to study 
agent(s) must be discussed with the Lead Principal Investigator.  All treating clinicians 
involved in the protocol are welcomed to discuss complicated cases at any time with the Lead 
Principal Investigator:  
Randy Sweis, MD 
University of Chicago Comprehensive Cancer Center 
 rsweis@medicine.bsd.uchicago.edu 
 
 
 

 
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Table 3 Dose Modification Guidelines (for both Pembrolizumab and EDP1503) for Drug-
Related Adverse Events 
Toxicity 
Hold 
Treatment 
For Grade 
Timing for Restarting Treatment 
Treatment Discontinuation 
Diarrhea/Colitis 
2-3 
 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
4 
Permanently discontinue 
Permanently discontinue 
AST, ALT, or 
Increased Bilirubin 
2 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose 
3-4 
Permanently discontinue 
(see exception below)a 
Permanently discontinue 
Type 1 diabetes 
mellitus (if new 
onset) or 
Hyperglycemia 
T1DM or  
3-4 
Hold pembrolizumab for new onset Type 
1 diabetes mellitus or Grade 3-4 
hyperglycemia associated with evidence of 
beta cell failure 
Resume pembrolizumab when patients are clinically and 
metabolically stable 
Hypophysitis 
2-4 
Toxicity resolves to Grade 0-1. Therapy 
with pembrolizumab can be continued 
while endocrine replacement therapy is 
instituted 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
Hyperthyroidism  
3 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
4 
Permanently discontinue 
Permanently discontinue 
Hypothyroidism 
 
Therapy with pembrolizumab can be 
continued while thyroid replacement 
therapy is instituted 
Therapy with pembrolizumab can be continued while thyroid 
replacement therapy is instituted 
 
Infusion Reaction 
2b 
Toxicity resolves to Grade 0-1  
Permanently discontinue if toxicity develops despite adequate 
premedication  
3-4 
Permanently discontinue 
Permanently discontinue 
Pneumonitis 
2 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
3-4 
Permanently discontinue 
Permanently discontinue 
Renal Failure or 
Nephritis 
2 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
3-4 
Permanently discontinue 
Permanently discontinue 
All Other Drug-
Related Toxicityc 
3 or Severe 
Toxicity resolves to Grade 0-1 
Toxicity does not resolve within 12 weeks of last dose or inability 
to reduce corticosteroid to 10 mg or less of prednisone or equivalent 
per day within 12 weeks 
4 
Permanently discontinue 
Permanently discontinue 
Note: Permanently discontinue for any severe or Grade 3 drug-related AE that recurs or any life-threatening event. 
a For patients with liver metastasis who begin treatment with Grade 2 AST or ALT, if AST or ALT increases by greater than or equal to 50% relative to baseline 
and lasts for at least 1 week then patients should be discontinued. 
b If symptoms resolve within one hour of stopping drug infusion, the infusion may be restarted at 50% of the original infusion rate   (e.g., from 100 mL/hr to 50 
mL/hr).  Otherwise dosing will be held until symptoms resolve and the subject should be premedicated  for the next scheduled dose.verse reactions for which 
treatment with study drug has been held, that do not recover to Grade 0-1 within 12 weeks of the last dose. 
 
Dosing interruptions are permitted in the case of medical / surgical events or logistical reasons 
not related to study therapy (e.g., elective surgery, unrelated medical events, patient vacation, 
and/or holidays). Subjects should be placed back on study therapy within 3 weeks of the 
scheduled interruption, unless otherwise discussed with the Lead Principal Investigator. The 
reason for interruption should be documented in the patient's study record. 

 
Protocol Version: 04/10/2019 
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If a subject’s study treatment has been interrupted for more than 2 doses of pembrolizumab, 
the investigator must contact the Lead Principal Investigator to review the subject’s condition 
in order to resume the treatment.  
 
If toxicities develop requiring treatment hold of pembrolizumab then EDP1503 supplement 
should be held as well. If toxicities not characteristic to pembrolizumab are present and the 
treating investigator believes the patient is deriving clinical benefit, pembrolizumab can be 
continued while holding EDP1503. 
 
5.2.2 Timing of Dose Administration 
All trial treatments and dietary supplements will be administered on an outpatient basis. 
An initial EDP1503 administration period of two weeks in cohort 1 and one week in cohort 2 
will precede dosing with pembrolizumab and will continue to be administered orally daily for 
the duration of the study. An exception to this for cohort 2 patients will include any patient 
who is among the first three patients enrolled who will have a 2 week run in to monitor for 
EDP1503 toxicities especially. 
Pembrolizumab 
should 
be 
administered 
on 
Day 
1 
of 
each 
cycle 
after 
all 
procedures/assessments have been completed as detailed on the Trial Flow Chart (Section 6.0) 
and may be administered up to 3 days before or after the scheduled Day 1 of each cycle due to 
administrative reasons. 
Pembrolizumab 200 mg will be administered as a 30 minute IV infusion every 3 weeks.  Sites 
should make every effort to target infusion timing to be as close to 30 minutes as possible.  
However, given the variability of infusion pumps from site to site, a window of -5 minutes and 
+10 minutes is permitted (i.e., infusion time is 30 minutes: -5 min/+10 min). 
The Pharmacy Manual contains specific instructions for the preparation of the pembrolizumab 
infusion fluid and administration of infusion solution. The Pharmacy Manual provides 
instruction for storage of EDP1503. 
5.2.3 Trial Blinding/Masking 
This is an open-label trial; therefore, the investigators and subject will know the treatment 
administered. 
5.3 
Randomization or Treatment Allocation 
There is no randomization. 
5.4 
Stratification 
There is no stratification. 

 
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5.5 
Concomitant Medications/Vaccinations (allowed & prohibited) 
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed 
during the ongoing trial.  If there is a clinical indication for one of these or other medications 
or vaccinations specifically prohibited during the trial, discontinuation from trial therapy or 
vaccination may be required.  The treating investigator should discuss any questions regarding 
this with the Lead Principal Investigator.  The final decision on any supportive therapy or 
vaccination rests with the investigator and/or the subject's primary physician.  
5.5.1 Acceptable Concomitant Medications 
All treatments that the investigator considers necessary for a subject’s welfare may be 
administered at the discretion of the treating investigator in keeping with the community 
standards of medical care.  All concomitant medication will be recorded including all 
prescription, over-the-counter (OTC), herbal supplements, and IV medications and fluids.  If 
changes occur during the trial period, documentation of drug dosage, frequency, route, and 
date may also be recorded. 
5.5.2 Prohibited Concomitant Medications 
Subjects are prohibited from receiving the following therapies during the Screening and 
Treatment Phase (including retreatment for post-complete response relapse) of this trial: 
• Antineoplastic systemic chemotherapy or biological therapy  
• Immunotherapy not specified in this protocol 
• Chemotherapy not specified in this protocol 
• Other dietary probiotics and prebiotics 
• Investigational agents other than pembrolizumab  
• Radiation therapy  
o Note:  Radiation therapy to a symptomatic solitary lesion or to the brain may 
be allowed after discussion between the investigator and Principal Investigator.   
o Live vaccines within 30 days prior to the first dose of trial treatment and while 
participating in the trial.  Examples of live vaccines include, but are not limited 
to, the following: measles, mumps, rubella, varicella/zoster, yellow fever, 
rabies, BCG, and typhoid vaccine.  
• Systemic glucocorticoids for any purpose other than to modulate symptoms from an 
event of clinical interest of suspected immunologic etiology.  The use of physiologic 
doses of corticosteroids may be approved after consultation with the Lead Principal 
Investigator. 
• Antibiotic therapies may be required by some participants during the study.  EDP1503 
should not be held during antibiotic therapy unless deemed necessary by the treating 
investigator. If there are continued gastrointestinal symptoms or the treating 

 
Protocol Version: 04/10/2019 
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investigator feels the subject is not fully recovered then the restart can be delayed for a 
maximum of 2 weeks. 
o Antibiotic choice: Different classes of antibiotics have been shown to disrupt 
the microbiome and potentially interfere with normal host immune function to 
varying degrees.  If equally indicated amoxicillin is the preferred antibiotic as 
it minimally alters gut flora.  Clindamycin is the most detrimental antibiotic and 
should be avoided if possible (Zaura et al 2015).  Beta-lactams (other than 
amoxicillin) and fluoroquinolones broadly should be avoided if possible as well 
(Derosa et al 2017). 
Citations 
- 
Zaura E, Brandt BW, Teixeira de Mattos MJ, Buijs MJ, Caspers MPM, Rashid 
MU, Weintraub A, Nord CE, Savell A, Hu Y, Coates AR, Hubank M, Spratt 
DA, Wilson M, Keijser BJF, Crielaard W. 2015. Same exposure but two 
radically different responses to antibiotics: resilience of the salivary 
microbiome versus long-term microbial shifts in feces. mBio6(6):e01693-15. 
- 
Derosa et al 2017.  Impact of antibiotics on outcome in patients with metastatic 
renal cell carcinoma treated with immune checkpoint inhibitors. Poster Abstract 
462. J Clin Oncol 35, 2017 
 
Subjects who, in the assessment by the treating investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the trial or in the 
case of antibiotics the Bifidobacteria components of the study should be temporarily stopped.  
Subjects may receive other medications that the treating investigator deems to be medically 
necessary. 
The Exclusion Criteria describes other medications which are prohibited in this trial. 
There are no prohibited therapies during the Post-Treatment Follow-up Phase. 
5.6 
Rescue Medications & Supportive Care 
5.6.1 Supportive Care Guidelines 
Subjects should receive appropriate supportive care measures as deemed necessary by the 
treating investigator.  Suggested supportive care measures for the management of adverse 
events with potential immunologic etiology are outlined below. Where appropriate, these 
guidelines include the use of oral or intravenous treatment with corticosteroids as well as 
additional anti-inflammatory agents if symptoms do not improve with administration of 
corticosteroids.   Note that several courses of steroid tapering may be necessary as symptoms 
may worsen when the steroid dose is decreased. For each disorder, attempts should be made to 
rule out other causes such as metastatic disease or bacterial or viral infection, which might 
require additional supportive care. The treatment guidelines are intended to be applied when 

 
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the treating investigator determines the events to be related to pembrolizumab and/or 
EDP1503.  
Note: if after the evaluation the event is determined not to be related, the investigator does not 
need to follow the treatment guidance (as outlined below). Refer to Section 5.2.1 for dose 
modification.  
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or 
skin photography as part of evaluation of the event.  
• Pneumonitis:  
o For Grade 2 events, treat with systemic corticosteroids. When symptoms 
improve to Grade 1 or less, steroid taper should be started and continued over 
no less than 4 weeks. 
o For Grade 3-4 events, immediately treat with intravenous steroids.  
Administer additional anti-inflammatory measures, as needed. 
o Add prophylactic antibiotics for opportunistic infections in the case of 
prolonged steroid administration. 
• Diarrhea/Colitis:  
Subjects should be carefully monitored for signs and symptoms of enterocolitis (such 
as diarrhea, abdominal pain, blood or mucus in stool, with or without fever) and of 
bowel perforation (such as peritoneal signs and ileus).   
o All subjects who experience diarrhea/colitis should be advised to drink liberal 
quantities of clear fluids.  If sufficient oral fluid intake is not feasible, fluid and 
electrolytes should be substituted via IV infusion.  For Grade 2 or higher 
diarrhea, consider GI consultation and endoscopy to confirm or rule out colitis. 
o For Grade 2 diarrhea/colitis, that persists greater than 3 days, administer oral 
corticosteroids. 
o For Grade 3 or 4 diarrhea/colitis, that persists > 1 week, treat with intravenous 
steroids followed by high dose oral steroids.   
o When symptoms improve to Grade 1 or less, steroid taper should be started and 
continued over no less than 4 weeks. 
• Type 1 diabetes mellitus (if new onset, including diabetic ketoacidosis [DKA]) or 
≥ Grade 3 Hyperglycemia, if associated with ketosis (ketonuria) or metabolic 
acidosis (DKA) 
o For T1DM or Grade 3-4 Hyperglycemia 
 Insulin replacement therapy is recommended for Type I diabetes 
mellitus and for Grade 3-4 hyperglycemia associated with metabolic 
acidosis or ketonuria.  
 Evaluate patients with serum glucose and a metabolic panel, urine 
ketones, glycosylated hemoglobin, and C-peptide.  

 
Protocol Version: 04/10/2019 
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• Hypophysitis: 
o For Grade 2 events, treat with corticosteroids. When symptoms improve to 
Grade 1 or less, steroid taper should be started and continued over no less than 
4 weeks. Replacement of appropriate hormones may be required as the steroid 
dose is tapered. 
o For Grade 3-4 events, treat with an initial dose of IV corticosteroids followed 
by oral corticosteroids. When symptoms improve to Grade 1 or less, steroid 
taper should be started and continued over no less than 4 weeks. Replacement 
of appropriate hormones may be required as the steroid dose is tapered. 
• Hyperthyroidism or Hypothyroidism:  
Thyroid disorders can occur at any time during treatment. Monitor patients for changes 
in thyroid function (at the start of treatment, periodically during treatment, and as 
indicated based on clinical evaluation) and for clinical signs and symptoms of thyroid 
disorders. 
o Grade 2 hyperthyroidism events (and Grade 2-4 hypothyroidism): 
 In hyperthyroidism, non-selective beta-blockers (e.g. propranolol) are 
suggested as initial therapy. 
 In hypothyroidism, thyroid hormone replacement therapy, with 
levothyroxine or liothyroinine, is indicated per standard of care. 
o Grade 3-4 hyperthyroidism  
 Treat with an initial dose of IV corticosteroid followed by oral 
corticosteroids. When symptoms improve to Grade 1 or less, steroid 
taper should be started and continued over no less than 4 weeks. 
Replacement of appropriate hormones may be required as the steroid 
dose is tapered. 
• Hepatic: 
o For Grade 2 events, monitor liver function tests more frequently until returned 
to baseline values (consider weekly). 
 Treat with IV or oral corticosteroids 
o For Grade 3-4 events, treat with intravenous corticosteroids for 24 to 48 hours.  
o When symptoms improve to Grade 1 or less, a steroid taper should be started 
and continued over no less than 4 weeks. 
• Renal Failure or Nephritis: 
o For Grade 2 events, treat with corticosteroids. 
o For Grade 3-4 events, treat with systemic corticosteroids. 
o When symptoms improve to Grade 1 or less, steroid taper should be started and 
continued over no less than 4 weeks.  

 
Protocol Version: 04/10/2019 
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• Management of Infusion Reactions: Signs and symptoms usually develop during or 
shortly after drug infusion and generally resolve completely within 24 hours of 
completion of infusion.  
Table 3 below shows treatment guidelines for subjects who experience an infusion 
reaction associated with administration of pembrolizumab. 
Table 3 Infusion Reaction Treatment Guidelines 
 
NCI CTCAE Grade 
Treatment 
Premedication at subsequent 
dosing 
Grade 1 
Mild reaction; infusion interruption 
not indicated; intervention not 
indicated 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
None 
Grade 2 
Requires infusion interruption but 
responds promptly to symptomatic 
treatment (e.g., antihistamines, 
NSAIDS, narcotics, IV fluids); 
prophylactic medications indicated for 
< =24 hrs 
Stop Infusion and monitor symptoms. 
Additional appropriate medical therapy may 
include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
If symptoms resolve within one hour of stopping 
drug infusion, the infusion may be restarted at 
50% of the original infusion rate (e.g., from 100 
mL/hr to 50 mL/hr).  Otherwise dosing will be 
held until symptoms resolve and the subject 
should be premedicated for the next scheduled 
dose. 
Subjects who develop Grade 2 toxicity despite 
adequate premedication should be 
permanently discontinued from further trial 
treatment administration. 
Subject may be premedicated 1.5h 
(± 30 minutes) prior to infusion of 
pembrolizumab (MK-3475) with: 
 
Diphenhydramine 50 mg po (or 
equivalent dose of antihistamine). 
 
Acetaminophen 500-1000 mg po 
(or equivalent dose of antipyretic). 
Grades 3 or 4 
Grade 3: 
Prolonged (i.e., not rapidly responsive 
to symptomatic medication and/or 
brief interruption of infusion); 
recurrence of symptoms following 
initial improvement; hospitalization 
indicated for other clinical sequelae 
(e.g., renal impairment, pulmonary 
infiltrates) 
Grade 4: 
Life-threatening; pressor or ventilatory 
support indicated 
Stop Infusion. 
Additional appropriate medical therapy may 
include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Epinephrine 
 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
Hospitalization may be indicated. 
Subject is permanently discontinued from 
further trial treatment administration. 
No subsequent dosing 
Appropriate resuscitation equipment should be available in the room and a physician readily available during the period of drug 
administration. 
 
 

 
Protocol Version: 04/10/2019 
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• Management of Stevens-Johnson syndrome and Toxic Epidermal Necrolysis: 
To date, approximately 11,000 patients in clinical trials and 27,000 patients in the 
post-marketing setting have been treated with KEYTRUDA®. One fatal case of SJS 
in a clinical trial and one fatal case of TEN in the post-marketing setting have been 
reported in patients treated with KEYTRUDA®. Including these cases, there have 
been 8 cases of SJS (6 in clinical trials, and 2 post-marketing) and 2 cases of TEN 
(both post-marketing) all of which were serious. 
 
o For signs or symptoms of SJS or TEN, withhold KEYTRUDA® and refer 
the patient for specialized care for assessment and treatment.  
 
o If SJS or TEN is confirmed, permanently discontinue KEYTRUDA®.  
 
• Management of Immune-mediated myocarditis: 
A total of 6 cases of myocarditis have been reported in patients treated with 
KEYTRUDA® in clinical trials or in an expanded access program. There was 1 fatal 
case reported in a clinical trial. 
 
o For suspected immune-mediated myocarditis, ensure adequate evaluation to 
exclude other etiologies, and administer corticosteroids as appropriate.  
 
 
5.7 
Diet/Activity/Other Considerations 
5.7.1 Diet 
Subjects should maintain a normal diet unless modifications are required to manage an AE 
such as diarrhea, nausea or vomiting. 
5.7.2 Contraception 
Pembrolizumab may have adverse effects on a fetus in utero.  Furthermore, it is not known if 
pembrolizumab has transient adverse effects on the composition of sperm.   
For this trial, male subjects will be considered to be of non-reproductive potential if they have 
azoospermia (whether due to having had a vasectomy or due to an underlying medical 
condition).   
Female subjects will be considered of non-reproductive potential if they are either:  
(1) postmenopausal (defined as at least 12 months with no menses without an alternative 
medical cause; in women < 45 years of age a high follicle stimulating hormone (FSH) level 
in the postmenopausal range may be used to confirm a post-menopausal state in women 
not using hormonal contraception or hormonal replacement therapy. In the absence of 12 
months of amenorrhea, a single FSH measurement is insufficient.);  

 
Protocol Version: 04/10/2019 
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OR  
(2) have had a hysterectomy and/or bilateral oophorectomy, bilateral salpingectomy or bilateral 
tubal ligation/occlusion, at least 6 weeks prior to screening;  
OR  
(3) has a congenital or acquired condition that prevents childbearing. 
Female and male subjects of reproductive potential must agree to avoid becoming pregnant or 
impregnating a partner, respectively, while receiving study drug and for 120 days after the last 
dose of study drug by complying with one of the following:   
(1) practice abstinence† from heterosexual activity;  
OR  
(2) use (or have their partner use) acceptable contraception during heterosexual activity.   
Acceptable methods of contraception are‡: 
Single method (one of the following is acceptable): 
• 
intrauterine device (IUD) 
• 
vasectomy of a female subject’s male partner  
• 
contraceptive rod implanted into the skin 
Combination method (requires use of two of the following): 
• 
diaphragm with spermicide (cannot be used in conjunction with cervical 
cap/spermicide) 
• 
cervical cap with spermicide (nulliparous women only)   
• 
contraceptive sponge (nulliparous women only)  
• 
male condom or female condom (cannot be used together) 
• 
hormonal contraceptive: oral contraceptive pill (estrogen/progestin pill or progestin-
only pill), contraceptive skin patch, vaginal contraceptive ring, or subcutaneous 
contraceptive injection 
†Abstinence (relative to heterosexual activity) can be used as the sole method of 
contraception if it is consistently employed as the subject’s preferred and usual 
lifestyle and if considered acceptable by local regulatory agencies and ERCs/IRBs.  
Periodic abstinence (e.g., calendar, ovulation, sympto-thermal, post-ovulation 
methods, etc.) and withdrawal are not acceptable methods of contraception.  

 
Protocol Version: 04/10/2019 
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‡If a contraceptive method listed above is restricted by local regulations/guidelines, 
then it does not qualify as an acceptable method of contraception for subjects 
participating at sites in this country/region. 
 
Subjects should be informed that taking the study medication may involve unknown risks to 
the fetus (unborn baby) if pregnancy were to occur during the study.  In order to participate in 
the study subjects of childbearing potential must adhere to the contraception requirement 
(described above) from the day of study medication initiation (or 14 days prior to the initiation 
of study medication for oral contraception) throughout the study period up to 120 days after 
the last dose of trial therapy.  If there is any question that a subject of childbearing potential 
will not reliably comply with the requirements for contraception, that subject should not be 
entered into the study. 
5.7.3 Use in Pregnancy 
If a subject inadvertently becomes pregnant while on treatment with pembrolizumab, the 
subject will immediately be removed from the study.  The site will contact the subject at least 
monthly and document the subject’s status until the pregnancy has been completed or 
terminated.  The outcome of the pregnancy will be reported to the Principal Investigator and 
to Merck without delay and within 24 hours to the Principal Investigator and within 2 working 
days to Merck if the outcome is a serious adverse experience (e.g., death, abortion, congenital 
anomaly, or other disabling or life-threatening complication to the mother or newborn).   
The treating investigator will make every effort to obtain permission to follow the outcome of 
the pregnancy and report the condition of the fetus or newborn to the Lead Principal 
Investigator.   If a male subject impregnates his female partner the study personnel at the site 
must be informed immediately and the pregnancy reported to the Lead Principal Investigator 
and to Merck and followed as described above and in Section 7.2.2. 
5.7.4 Use in Nursing Women 
It is unknown whether pembrolizumab is excreted in human milk.  Since many drugs are 
excreted in human milk, and because of the potential for serious adverse reactions in the 
nursing infant, subjects who are breast-feeding are not eligible for enrollment. 
5.8 
Subject Withdrawal/Discontinuation Criteria 
Subjects may withdraw consent at any time for any reason or be dropped from the trial at the 
discretion of the investigator should any untoward effect occur.  In addition, a subject may be 
withdrawn by the investigator or the Principal Investigator if enrollment into the trial is 
inappropriate, the trial plan is violated, or for administrative and/or other safety reasons.  
Specific details regarding discontinuation or withdrawal are provided in Section 7.1.4 – Other 
Procedures. 
Definition of Dose Limiting Toxicity: Any toxicity of >=Grade 3, any autoimmune toxicity 
>CTCAE Gr 2; DLT observation period is for the length of monotherapy for each cohort.  

 
Protocol Version: 04/10/2019 
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A subject must be discontinued from the trial for any of the following reasons: 
• The subject or legal representative (such as a parent or legal guardian) withdraws 
consent. 
• Confirmed radiographic disease progression 
Note: A subject may be granted an exception to continue on treatment with 
confirmed radiographic progression if clinically stable or clinically improved. 
• Unacceptable adverse experiences as described in Section 5.2.1.2 
• Intercurrent illness that prevents further administration of treatment 
• Investigator’s decision to withdraw the subject 
• The subject has a confirmed positive serum pregnancy test 
• Noncompliance with trial treatment or procedure requirements 
• The subject is lost to follow-up 
• Completed 24 months of uninterrupted treatment with pembrolizumab or 35 
administrations of study medication, whichever is later. 
Note: 24 months of study medication is calculated from the date of first dose. Subjects 
who stop pembrolizumab after 24 months may be eligible for up to one year of 
additional study treatment if they progress after stopping study treatment provided they 
meet the requirements. 
• Administrative reasons 
After the end of treatment, each subject will be followed for 30 days for adverse event 
monitoring (serious adverse events will be collected for 90 days after the end of treatment).  
Subjects who discontinue for reasons other than progressive disease will have post-treatment 
follow-up for disease status until disease progression, initiating a non-study cancer treatment, 
withdrawing consent or becoming lost to follow-up.  After documented disease progression 
each subject will be followed by telephone for overall survival until death, withdrawal of 
consent, or the end of the study, whichever occurs first. 
5.8.1 Discontinuation of Study Therapy after CR  
Discontinuation of treatment may be considered for subjects who have attained a confirmed 
CR that have been treated for at least 24 weeks with pembrolizumab and had at least two 
treatments with pembrolizumab beyond the date when the initial CR was declared.  Subjects 
who then experience radiographic disease progression may be eligible for up to one year of 
additional treatment with pembrolizumab via the Second Course Phase at the discretion of the 
investigator if no cancer treatment was administered since the last dose of pembrolizumab, the 

 
Protocol Version: 04/10/2019 
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subject meets the safety parameters listed in the Inclusion/Exclusion criteria, and the trial is 
open.  Subjects will resume therapy at the same dose and schedule at the time of initial 
discontinuation.   
5.9 
Subject Replacement Strategy 
5.10 Clinical Criteria for Early Trial Termination 
Early trial termination will be the result of the criteria specified below: 
1. Quality or quantity of data recording is inaccurate or incomplete 
2. Poor adherence to protocol and regulatory requirements 
3. Incidence or severity of adverse drug reaction in this or other studies indicates a potential 
health hazard to subjects 
4. Plans to modify or discontinue the development of the study drug 
In the event of Merck or Evelo decision to no longer supply study drug, ample notification will 
be provided so that appropriate adjustments to subject treatment can be made. 
 

 
Protocol Version: 04/10/2019 
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6.0 TRIAL FLOW CHART 
6.1 
Study Flow Chart 
Trial Period: 
Screening 
Phase 
Treatment Cyclesa 
End of 
Treatment 
Post-Treatment 
Treatment Cycle/Title: 
Study 
Screening 
EDP1503 
run-inb  
1 
2  
3 
4 
To be repeated beyond 8 
cycles 
Discon 
Safety 
Follow-up 
Follow Up Visits In 
Absence of 
Progressionc 
Every 12 weeks post 
discon 
5 
6 
7 
8 
Scheduling Window (Days): 
-21 to -1 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
At time of 
Discon 
30 days 
post 
discon 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion Criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
Demographics and Medical History 
X 
 
 
 
 
 
 
 
 
 
 
 
 
Prior and Concomitant Medication Review 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Pembrolizumab Administration 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
 
 
 
Review Adverse Events 
X 
Xg 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Physical Examination 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Vital Signs and Weight 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
ECOG Performance Status 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Pregnancy Test – Urine or Serum β-HCG 
X 
 
 
 
 
 
 
 
 
 
 
 
 
CBC with Differential 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Comprehensive Serum Chemistry Panel 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
Urinalysis 
X 
 
 
 
 
 
 
 
 
 
 
 
 
TSH (with reflexive T3, FT4 as indicated) 
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 

 
Protocol Version: 04/10/2019 
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Trial Period: 
Screening 
Phase 
Treatment Cyclesa 
End of 
Treatment 
Post-Treatment 
Treatment Cycle/Title: 
Study 
Screening 
EDP1503 
run-inb  
1 
2  
3 
4 
To be repeated beyond 8 
cycles 
Discon 
Safety 
Follow-up 
Follow Up Visits In 
Absence of 
Progressionc 
Every 12 weeks post 
discon 
5 
6 
7 
8 
Scheduling Window (Days): 
-21 to -1 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
At time of 
Discon 
30 days 
post 
discon 
Tumor Imaging (window includes all of 
cycle following drug administration) 
X 
 
 
 
 
X 
 
 
 
X 
 
 
 
Archival or Newly Obtained Tissue 
Collectiond 
Xd 
 
Xd 
 
 
 
 
 
 
 
 
 
 
Correlative Studies Blood Collectione 
X 
Xh 
Xf 
 
 
X 
 
 
 
 
X 
 
 
Fecal Sample 
X 
 
X 
 
 
X 
 
 
 
 
X 
X 
 
a – Treatment cycles = 21 days 
b – EDP1503 alone run-in for two weeks (14 days)  in cohort 1 and one week (7 days) in cohort two and continuous thereafter with pembrolizumab. An exception to this for 
cohort 2 patients will include any patient who is among the first three patients enrolled who will have a 2 week run in to monitor for EDP1503 toxicities especially. Cohort 
2 cannot initiate the one week run-in until 3 patients have cleared two week EDP1503 run. Pembrolizumab will be administered on D1 of every cycle. EDP1503 will be 
taken po (2 capsules bid) for all 21 days of every cycle. 
c – Patients who discontinue treatment without progression will have follow up visits for up to 2 years following drug discontinuation 
d – Archival tissue for newly diagnosed metastatic melanoma is allowed in cohort 1.  Fresh biopsies are otherwise required. Second biopsy at the end of the EDP1503 run-in 
period after at least 10 days in cohort 1 and at least 4 days in cohort 2. 
e – Samples to be collected for correlative blood analysis are detailed in section 8.1.1.11 
f – Sample to be taken prior to the initiation of pembrolizumab therapy 
g - Nursing assessment for adverse events at 48 hours which can be completed by telephone. 
h – Research cytokines, blood culture, whole blood 
 
 

 
Protocol Version: 04/10/2019 
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7.0 REGISTRATION PROCEDURES 
7.1 
General Guidelines 
Prior to registration and any study-specific evaluations being performed, all patients must have 
given written informed consent for the study and must have completed the pre-treatment 
evaluations.  Patients must meet all of the eligibility requirements listed in Section 3. Eligible 
patients will be entered on study centrally by the University of Chicago multi-site coordinator. 
All 
sites 
should 
call 
the 
coordinator 
at 
(773) 
834-1746 
or 
PhaseIICRA@medicine.bsd.uchicago.edu to verify availability of a slot. 
7.2 
Registration Process 
When a potential patient has been identified, notify the CRA via phone or email to ensure a 
reservation on the study ((773) 834-1746 or PhaseIICRA@medicine.bsd.uchicago.edu). 
Reservations for potential subjects will only be held for subjects who have signed consent for 
that particular study. 
When registering a subject, the following must occur:  
• Confirm that the institution has a current IRB approval letter for the correct version of 
protocol/consent and has an annual update on file, if appropriate.  
• Submit all required materials (Eligibility Checklist, Source documentation, & signed 
consent form) to confirm eligibility and required pre-study procedures to the CRA a 
minimum of 48 hours prior to the subject’s scheduled therapy start date.  
• Source documentation includes copies of all original documents that support each 
inclusion/exclusion criteria.  The eligibility checklist does not serve as source 
documentation but rather as a checklist that original source documentation exists for 
each criterion. 
• Communicate with the CRA to ensure all necessary supporting source documents are 
received and the potential subject is eligible to start treatment on schedule. If there are 
questions about eligibility, the CRA will discuss it with the PI. PI may clarify, but not 
overturn, eligibility criteria.  
• Affiliate sites must confirm registration of subjects by obtaining a subject study ID 
number from the CRA via phone, fax or email.  
• If a subject does not start on the scheduled day 1 treatment date, promptly inform the 
CRA as the delay in start may deem the subject ineligible and/or require further or 
repeat testing to ensure eligibility.  
• The date the patient receives treatment for the first time will be considered the patient’s 
“OnStudy Date.” The patient’s subject ID will be assigned and a confirmation of 
registration will be issued by the CRA on this date. Subjects that sign consent and do 
not go “OnStudy” will be recorded in the database with the date they signed consent 

 
Protocol Version: 04/10/2019 
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and the reason for not going “OnStudy” (e.g., Ineligible, Screen Failure or Withdrawn 
Consent).    
8.0 TRIAL PROCEDURES 
8.1 
Trial Procedures 
The Trial Flow Chart - Section 6.0 summarizes the trial procedures to be performed at each 
visit.  Individual trial procedures are described in detail below.  It may be necessary to perform 
these procedures at unscheduled time points if deemed clinically necessary by the treating 
investigator. 
Furthermore, additional evaluations/testing may be deemed necessary by the investigator for 
reasons related to subject safety. In some cases, such evaluation/testing may be potentially 
sensitive in nature (e.g., HIV, Hepatitis C, etc.), and thus local regulations may require that 
additional informed consent be obtained from the subject.  In these cases, such 
evaluations/testing will be performed in accordance with those regulations. 
8.1.1 Administrative Procedures 
8.1.1.1 Informed Consent 
The Investigator must obtain documented consent from each potential subject prior to 
participating in a clinical trial. 
8.1.1.1.1  General Informed Consent 
Consent must be documented by the subject’s dated signature or by the subject’s legally 
acceptable representative’s dated signature on a consent form along with the dated signature 
of the person conducting the consent discussion.  
A copy of the signed and dated consent form should be given to the subject before participation 
in the trial. 
The initial informed consent form, any subsequent revised written informed consent form and 
any written information provided to the subject must receive the IRB/ERC’s 
approval/favorable opinion in advance of use.  The subject or his/her legally acceptable 
representative should be informed in a timely manner if new information becomes available 
that may be relevant to the subject’s willingness to continue participation in the trial.  The 
communication of this information will be provided and documented via a revised consent 
form or addendum to the original consent form that captures the subject’s dated signature or 
by the subject’s legally acceptable representative’s dated signature. 
Specifics about a trial and the trial population will be added to the consent form template at 
the protocol level.   
The informed consent will adhere to IRB/ERC requirements, applicable laws and local 
regulations. 

 
Protocol Version: 04/10/2019 
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8.1.1.2 Inclusion/Exclusion Criteria 
All inclusion and exclusion criteria will be reviewed by the investigator or qualified designee 
to ensure that the subject qualifies for the trial.  
8.1.1.3 Medical History 
A medical history will be obtained by the investigator or qualified designee.  Medical history 
will include all active conditions, and any condition diagnosed within the prior 10 years that 
are considered to be clinically significant by the Investigator.  Details regarding the disease for 
which the subject has enrolled in this study will be recorded separately and not listed as medical 
history.   
8.1.1.4 Prior and Concomitant Medications Review 
8.1.1.4.1 Prior Medications 
The investigator or qualified designee will review prior medication use, including any 
protocol-specified washout requirement, and record prior medication taken by the subject 
within 28 days before starting the trial.  Treatment for the disease for which the subject has 
enrolled in this study will be recorded separately and not listed as a prior medication.  
8.1.1.4.2 Concomitant Medications 
The investigator or qualified designee will record medication, if any, taken by the subject 
during the trial.  All medications related to reportable SAEs and ECIs should be recorded. 
8.1.1.5 Disease Details and Treatments 
8.1.1.5.1 Disease Details 
The investigator or qualified designee will obtain prior and current details regarding disease 
status.  
8.1.1.5.2 Prior Treatment Details 
The investigator or qualified designee will review all prior cancer treatments including 
systemic treatments, radiation and surgeries. 
8.1.1.5.3 Subsequent Anti-Cancer Therapy Status 
The investigator or qualified designee will review all new anti-neoplastic therapy initiated after 
the last dose of trial treatment.  If a subject initiates a new anti-cancer therapy within 30 days 
after the last dose of trial treatment, the 30 day Safety Follow-up visit must occur before the 
first dose of the new therapy.  Once new anti-cancer therapy has been initiated the subject will 
move into survival follow-up.  

 
Protocol Version: 04/10/2019 
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8.1.1.6 Adverse Event (AE) Monitoring 
The investigator or qualified designee will assess each subject to evaluate for potential new or 
worsening AEs as specified in the Trial Flow Chart and more frequently if clinically indicated.  
Adverse experiences will be graded and recorded throughout the study and during the follow-
up period according to NCI CTCAE Version 5 (see Section 11.2).  Toxicities will be 
characterized in terms regarding seriousness, causality, toxicity grading, and action taken with 
regard to trial treatment.  
8.1.1.7 Physical Exam 
The investigator or qualified designee will perform a physical exam at protocol specified time 
points as per the Trial Flow Chart (Section 6.0).  Clinically significant abnormal findings 
should be recorded as medical history.  A full physical exam should be performed during 
screening.  
8.1.1.8 Vital Signs 
The investigator or qualified designee will take vital signs at screening, prior to the 
administration of each dose of trial treatment and at treatment discontinuation as specified in 
the Trial Flow Chart (Section 6.0).  Vital signs should include temperature, pulse, respiratory 
rate, weight and blood pressure.  Height will be measured at screening only. 
8.1.1.9 Eastern Cooperative Oncology Group (ECOG) Performance Scale 
The investigator or qualified designee will assess ECOG status at screening, prior to the 
administration of each dose of trial treatment and discontinuation of trial treatment as specified 
in the Trial Flow Chart.   
8.1.1.10 Tumor Imaging and Assessment of Disease 
Baseline and restaging radiologic imaging will be performed to encompass all sites of 
metastatic disease. This will generally include at least CT CAP though the specific imaging 
study can be changed by the treating investigator depending on patient circumstances.  
Radiologic imaging modality should be consistent throughout the study for response 
assessment.  For patients who have known bone metastases at baseline, bone scan should 
additionally be pursued as standard of care for disease assessment. 
8.1.1.11 Tumor Tissue Collection and Correlative Studies Blood Sampling 
 The following tables outline the requirements for tissue and blood banking. These will be 
collected and stored for batched future analysis. 
Biospecimen type 
Collection Time Point 
Number of 
samples per 
patient 

 
Protocol Version: 04/10/2019 
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Fecal sample 
Pre administration of EDP1503  
Following run in of EDP1503 
At dose 4 of treatment with 
pembrolizumab 
At discontinuation visit 
30 days after cessation of 
EDP1503 
10 samples (2 
samples each from 
5 time points) 
A paraffin-embedded tissue block of 
metastatic tumor taken before 
initiation of treatment. 
Pre-treatment:  obtained prior 
treatment on protocol 
1 historical sample 
Paraffin-embedded tissue block of 
metastatic tumor taken before 
initiation of treatment (if available). 
Pre-treatment:  obtained prior 
treatment on protocol 
1 sample 
Paraffin-embedded tissue block of 
metastatic tumor taken after 
EDP1503 run in.  Where feasible 
this should be taken from the same 
metastatic or primary site as the 
initial biopsy.   
Pre-treatment:  obtained after 
the EDP1503 run in  
1 sample 
Peripheral Blood Mononuclear 
Cells: ~60 ml of anti-coagulated 
whole blood in green top tube  
Pre-administration of 
EDP1503: 8-10 tubes taken 
within 21 days prior to 
EDP1503 administration. 
8-10 tubes taken at the 
following time points:  
 (1) at day of dose 1 pre-
administration of 
pembrolizumab  
(2) dose 4 pembrolizumab  
(3) at time of progressive 
disease. 
Up to 40 samples 
total over 4 time 
points 
Whole blood for germline DNA: 8-
10 mL of whole blood in PAXgene 
tube 
Within 21 days prior to 
administration of EDP1503  
1 sample 
Cytokines 
Pre administration of EDP1503  
4 samples 

 
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Following approximately 48 
hours of EDP1503 
Following run in of EDP1503 
At dose 4 of treatment with 
pembrolizumab 
Blood Culture 
Pre administration of EDP1503  
Following run in of EDP1503 
2 samples 
EDP1503 PCR 
Pre administration of EDP1503  
Following run in of EDP1503 
2 samples 
 
Biospecimens will be shipped and stored in the University of Chicago Human Immune 
Monitoring Core Facility as below with the exception of one stool sample from each time point 
which will be sent to Evelo Biosciences. 
Human Immune Monitoring Core: 
Contact: Yuanyuan Zha 
University of Chicago - Human Immune Monitoring Core 
910 E. 58th St. MKL057 
Chicago, IL 60637 
yzha1@bsd.uchicago.edu 
Phone: 773-702-4812 
 
Ship human microbiome sample kits to*: 
Evelo Biosciences 
Contact: Dr Maria Sizova 
620 Memorial Drive, 5th Floor  
Cambridge, MA 02139 
maria@evelobio.com 
 
*A pre-labeled box and shipping label will be provided.  
8.1.2 Laboratory Procedures/Assessments 
Laboratory tests for hematology, chemistry, urinalysis, and others are specified in Table 5.   
 
Laboratory tests for screening or entry into the Second Course Phase should be performed 
within 14 days prior to EDP1503 administration.  After Cycle 1, pre-dose laboratory 
procedures can be conducted up to 72 hours prior to dosing.  Results must be reviewed by the 
investigator or qualified designee and found to be acceptable prior to each dose of trial 
treatment.  

 
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Table 5  Laboratory Tests 
Hematology 
Chemistry 
Urinalysis 
Other 
Hematocrit 
Albumin 
Blood 
Serum β-human chorionic gonadotropin† 
Hemoglobin 
Alkaline phosphatase 
Glucose 
  (β-hCG)† 
Platelet count 
Alanine aminotransferase (ALT) 
Protein 
Thyroid stimulating hormone (TSH) 
WBC (total and differential) 
Aspartate aminotransferase (AST) 
Specific gravity  
Total thriiodothyronine (T3) (If TSH 
abnormal) 
Red Blood Cell Count 
Lactate dehydrogenase (LDH) 
Microscopic exam (If abnormal)  
Free thyroxine (T4) (If TSH abnormal) 
Absolute Neutrophil Count 
Carbon Dioxide 
results are noted 
 
Absolute Lymphocyte Count 
  (CO2 or biocarbonate) 
Urine pregnancy test † 
 
 
Uric Acid 
 
 
 
Calcium 
 
 
 
Chloride 
 
Blood for correlative studies 
 
Glucose 
 
  
 
Potassium   
 
  
 
Sodium 
 
  
 
Total Bilirubin 
 
  
 
Direct Bilirubin (If total bilirubin is 
elevated above the upper limit of 
normal) 
 
 
 
Total protein 
 
 
 
Blood Urea Nitrogen 
 
 
† Perform on women of childbearing potential only. If urine pregnancy results cannot be confirmed as negative, a serum pregnancy test will be required.   
 
 
 

 
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8.1.3 Other Procedures 
8.1.3.1 Withdrawal/Discontinuation 
When a subject discontinues/withdraws prior to trial completion, all applicable activities 
scheduled for the final trial visit should be performed at the time of discontinuation.  Any 
adverse events which are present at the time of discontinuation/withdrawal should be followed 
in accordance with the safety requirements. Subjects who a) attain a CR or b) complete 24 
months of treatment with pembrolizumab may discontinue treatment with the option of 
restarting treatment if they meet the criteria. After discontinuing treatment following 
assessment of CR, these subjects should return to the site for a Safety Follow-up Visit and then 
proceed to the Follow-Up Period of the study. 
8.1.3.2 Follow-up Visits 
Subjects who discontinue trial treatment for a reason other than disease progression will move 
into the Follow-Up Phase and should be assessed every 12 weeks (90 ± 7 days) by radiologic 
imaging to monitor disease status.  Every effort should be made to collect information 
regarding disease status until the start of new anti-neoplastic therapy, disease progression, 
death, end of the study or if the subject begins retreatment with pembrolizumab. Information 
regarding post-study anti-neoplastic treatment will be collected if new treatment is initiated. 
Subjects who are eligible to receive retreatment with pembrolizumab will move from the 
follow-up phase to the Second Course Phase when they experience disease progression.   
8.1.3.3 Second Course Phase (Retreatment Period) 
Subjects who stop pembrolizumab with SD or better may be eligible for up to one year of 
additional pembrolizumab therapy if they progress after stopping study treatment.  This 
retreatment is termed the Second Course Phase of this study and is only available if the study 
remains open and the subject meets the following conditions: 
• Either  
o Stopped initial treatment with pembrolizumab after attaining an investigator-
determined confirmed CR according to RECIST 1.1, and 
 Was treated for at least 24 weeks with pembrolizumab before discontinuing 
therapy 
 Received at least two treatments with pembrolizumab beyond the date when 
the initial CR was declared 
 
 
OR 
o Had SD, PR or CR and stopped pembrolizumab treatment after 24 months of study 
therapy for reasons other than disease progression or intolerability 

 
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AND 
• Experienced an investigator-determined confirmed radiographic disease progression 
after stopping their initial treatment with pembrolizumab 
• Did not receive any anti-cancer treatment since the last dose of pembrolizumab 
• Has a performance status of 0 or 1 on the ECOG Performance Scale 
• Demonstrates adequate organ function as detailed in Section 5.1.2 
• Female subject of childbearing potential should have a negative serum or urine 
pregnancy test within 72 hours prior to receiving retreatment with study medication.   
• Female subject of childbearing potential should be willing to use 2 methods of birth 
control or be surgically sterile, or abstain from heterosexual activity for the course of 
the study through 120 days after the last dose of study medication (Reference Section 
5.7.2).  Subjects of child bearing potential are those who have not been surgically 
sterilized or have been free from menses for > 1 year.  
• Male subject should agree to use an adequate method of contraception starting with the 
first dose of study therapy through 120 days after the last dose of study therapy.   
• Does not have a history or current evidence of any condition, therapy, or laboratory 
abnormality that might interfere with the subject’s participation for the full duration of 
the trial or is not in the best interest of the subject to participate, in the opinion of the 
treating investigator. 
 
Subjects who restart treatment will be re-treated at the same dose and dose interval as when 
they last received pembrolizumab.  Treatment will be administered for up to one additional 
year.  EDP1503 will also be restarted pending availability of supplement supply. 
Visit requirements are outlined in Section 6.0 – Trial Flow Chart. 
 
8.2 
Assessing and Recording Adverse Events 
An adverse event is defined as any untoward medical occurrence in a patient or clinical 
investigation subject administered a pharmaceutical product and which does not necessarily 
have to have a causal relationship with this treatment. An adverse event can therefore be any 
unfavorable and unintended sign (including an abnormal laboratory finding, for example), 
symptom, or disease temporally associated with the use of a medicinal product or protocol-
specified procedure, whether or not considered related to the medicinal product or protocol-
specified procedure.  Any worsening (i.e., any clinically significant adverse change in 

 
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frequency and/or intensity) of a preexisting condition that is temporally associated with the use 
of the Merck’s product, is also an adverse event. 
Changes resulting from normal growth and development that do not vary significantly in 
frequency or severity from expected levels are not to be considered adverse events.  Examples 
of this may include, but are not limited to, teething, typical crying in infants and children and 
onset of menses or menopause occurring at a physiologically appropriate time. 
Merck product includes any pharmaceutical product, biological product, device, diagnostic 
agent or protocol-specified procedure, whether investigational (including placebo or active 
comparator medication) or marketed, manufactured by, licensed by, provided by or distributed 
by Merck for human use. 
Adverse events may occur during the course of the use of Merck product in clinical trials, or 
as prescribed in clinical practice, from overdose (whether accidental or intentional), from abuse 
and from withdrawal. 
Progression of the cancer under study is not considered an adverse event.  
All adverse events will be recorded from first day of study drug administration through 30 days 
following cessation of treatment and at each examination on the Adverse Event case report 
forms/worksheets. 
 
8.2.1 Definition of an Overdose for This Protocol and Reporting of Overdose to the 
Principal Investigator, Merck and Evelo 
For purposes of this trial, an overdose of pembrolizumab will be defined as any dose of 1,000 
mg or greater (≥5 times the indicated dose).  No specific information is available on the 
treatment of overdose of pembrolizumab. Appropriate supportive treatment should be provided 
if clinically indicated. In the event of overdose, the subject should be observed closely for signs 
of toxicity.  Appropriate supportive treatment should be provided if clinically indicated. 
Overdose of EDP1503 will be defined as more than 6 capsules  in a day.  There is no known 
safety issue surrounding this however pill counts will be documented to confirm appropriate 
dosing.  Appropriate supportive treatment should be provided if clinically indicated. Overdose 
of EDP1503 does not require report as a serious adverse event but will be reported as an 
adverse event. 
If an adverse event(s) is associated with (“results from”) the overdose of a Merck product, the 
adverse event(s) is reported as a serious adverse event, even if no other seriousness criteria are 
met. 
If a dose of Merck’s product meeting the protocol definition of overdose is taken without any 
associated clinical symptoms or abnormal laboratory results, the overdose is reported as a non-
serious Event of Clinical Interest (ECI), using the terminology “accidental or intentional 
overdose without adverse effect.” 

 
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All reports of overdose with and without an adverse event must be reported within 24 hours of 
site knowledge of the event to the UC CCC Cancer Clinical Trials Office and Lead Principal 
Investigator and within 2 working days hours to Merck Global Safety. (Attn: Worldwide 
Product Safety; FAX 215 993-1220) 
8.2.2 Reporting of Pregnancy and Lactation to the Principal Investigator and to 
Merck 
Although pregnancy and lactation are not considered adverse events, it is the responsibility of 
investigators or their designees to report any pregnancy or lactation in a subject (spontaneously 
reported to them), including the pregnancy of a male subject's female partner that occurs during 
the trial or within 120 days of completing the trial completing the trial, or 30 days following 
cessation of treatment if the subject initiates new anticancer therapy, whichever is earlier.  All 
subjects and female partners of male subjects who become pregnant must be followed to the 
completion/termination of the pregnancy.  Pregnancy outcomes of spontaneous abortion, 
missed abortion, benign hydatidiform mole, blighted ovum, fetal death, intrauterine death, 
miscarriage and stillbirth must be reported as serious events (Important Medical Events).  If 
the pregnancy continues to term, the outcome (health of infant) must also be reported. 
Such events must be reported within 24 hours of site knowledge of the event to the UC CCC 
Cancer Clinical Trials Office and Lead Principal Investigator and within 2 working days to 
Merck Global Safety. (Attn: Worldwide Product Safety; FAX 215 993-1220) 
8.2.3 Immediate Reporting of Adverse Events to the Principal Investigator and to 
Merck 
8.2.3.1 Serious Adverse Events 
A serious adverse event is any adverse event occurring at any dose or during any use of 
Merck’s product that: 
• Results in death; 
• Is life threatening; 
• Results in persistent or significant disability/incapacity; 
• Results in or prolongs an existing inpatient hospitalization; 
• Is a congenital anomaly/birth defect; 
• Is a new cancer (that is not a condition of the study); 
• Is associated with an overdose; 
• Is an other important medical event  
Refer to Table 6 for additional details regarding each of the above criteria. 
Any serious adverse event, or follow up to a serious adverse event, including death due to any 
cause other than progression of the cancer under study that occurs to any subject from first day 
of study drug administration through 90 days following cessation of treatment, or the initiation 
of new anti-cancer therapy, whichever is earlier, whether or not related to Merck or Evelo 
product, must be reported within 24 hours of site knowledge of the event to the UC CCC 

 
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Cancer Clinical Trials Office and Lead Principal Investigator and within 2 working days to 
Merck and Sarah Cannon Development Innovation Safety Department who will hold the 
Global Safety Database for EDP1503. 
Non-serious Events of Clinical Interest will be forwarded to Merck and Sarah Cannon 
Development Innovation Safety Department and will be handled in the same manner as SAEs.  
Additionally, any serious adverse event, considered by an investigator to be related to Merck 
product that is brought to the attention of the investigator at any time outside of the time period 
specified in the previous paragraph also must be reported immediately to the UC CCC Cancer 
Clinical Trials Office and Principal Investigator and to Merck and Evelo. 
SAE reports and any other relevant safety information are to be forwarded to the Merck Global 
Safety facsimile number:  +1-215-993-1220 and to Sarah Cannon Development Innovation 
Safety Department facsimile number 1-866-807-4325. 
All subjects with serious adverse events must be followed up for event outcome. 
8.2.3.2 Unexpected Events 
Unexpected events are those not listed at the observed specificity or severity in the protocol, 
informed consent, investigator brochure, or FDA-approved package insert.  An event is 
considered unexpected if it is listed as occurring within the class of drugs or otherwise expected 
from the drug’s pharmacological properties but which has not been previously observed with 
this specific investigational agent. 
8.2.3.3 Adverse Reactions 
An adverse event is considered to be an adverse reaction if there is evidence to suggest a causal 
relationship to the study agent.  This may include a single occurrence of an event strongly 
associated with drug exposure (e.g. Stevens-Johnson Syndrome), one or more occurrence of 
an event otherwise uncommon is the study population, or an aggregate analysis of specific 
events occurring at greater than expected frequency. 
8.2.3.4 Events of Clinical Interest 
Selected non-serious and serious adverse events are also known as Events of Clinical Interest 
(ECI) and must be recorded as such on the Adverse Event case report forms/worksheets and 
reported within 24 hours of site knowledge of the event to the UC CCC Cancer Clinical Trials 
Office and Lead Principal Investigator and within 2 working days to Merck Global Safety. 
(Attn: Worldwide Product Safety; FAX 215 993-1220) and Sarah Cannon Development 
Innovation Safety Department. 
Events of clinical interest for this trial include: 
1.  an overdose of Merck product, as defined in Section 7.2.1, that is not associated with clinical 
symptoms or abnormal laboratory results.  

 
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2.  an elevated AST or ALT lab value that is greater than or equal to 3X the upper limit of 
normal and an elevated total bilirubin lab value that is greater than or equal to 2X the upper 
limit of normal and, at the same time, an alkaline phosphatase lab value that is less than 2X the 
upper limit of normal, as determined by way of protocol-specified laboratory testing or 
unscheduled laboratory testing.* 
*Note:  These criteria are based upon available regulatory guidance documents. The 
purpose of the criteria is to specify a threshold of abnormal hepatic tests that may require 
an additional evaluation for an underlying etiology.   
 
Subjects should be assessed for possible ECIs prior to each dose.  Lab results should be 
evaluated and subjects should be asked for signs and symptoms suggestive of an immune-
related event.  Subjects who develop an ECI thought to be immune-related should have 
additional testing to rule out other etiologic causes.  If lab results or symptoms indicate a 
possible immune-related ECI, then additional testing should be performed to rule out other 
etiologic causes.  If no other cause is found, then it is assumed to be immune-related. 
 
8.2.4 Evaluating Adverse Events 
An investigator will evaluate all adverse events according to the NCI Common Terminology 
for Adverse Events (CTCAE), version 5. Any adverse event which changes CTCAE grade 
over the course of a given episode will have each change of grade recorded on the adverse 
event case report forms/worksheets. 
All adverse events regardless of CTCAE grade must also be evaluated for seriousness. 

 
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Table 6 Evaluating Adverse Events 
An investigator, will evaluate all adverse events as to: 
v5 CTCAE 
Grading 
Grade 1 
Mild; asymptomatic or mid symptoms; clinical or diagnostic observations only; intervention not indicated. 
Grade 2 
Moderate; minimal, local or noninvasive intervention indicated; limiting age-appropriate instrumental ADL. 
 
Grade 3 
Severe or medically significant but not immediately life-threatening; hospitalization or prolongation or hospitalization indicated; 
disabling; limiting self-care ADL. 
 
Grade 4 
Life threatening consequences; urgent intervention indicated. 
 
Grade 5 
Death related to AE 
Seriousness 
A serious adverse event is any adverse event occurring at any dose or during any use of Merck product that: 
 
†Results in death; or 
 
†Is life threatening; or places the subject, in the view of the investigator, at immediate risk of death from the event as it occurred (Note: This does not include 
an adverse event that, had it occurred in a more severe form, might have caused death.); or 
 
†Results in a persistent or significant disability/incapacity (substantial disruption of one’s ability to conduct normal life functions); or 
 
†Results in or prolongs an existing inpatient hospitalization (hospitalization is defined as an inpatient admission, regardless of length of stay, even if the 
hospitalization is a precautionary measure for continued observation. (Note: Hospitalization for an elective procedure to treat a pre-existing condition that has 
not worsened is not a serious adverse event.  A pre-existing condition is a clinical condition that is diagnosed prior to the use of a Merck product and is 
documented in the patient’s medical history.); or 
 
†Is a congenital anomaly/birth defect (in offspring of subject taking the product regardless of time to diagnosis);or 
 
Is a new cancer (that is not a condition of the study) (although not serious per ICH definition, is reportable to the Lead Principal Investigator within 24 hours 
of site knowledge of the event and to Merck and Sarah Cannon Development Innovation Safety Department within 2 working days to meet certain local 
requirements); or 
 
Is an overdose (whether accidental or intentional).  Any adverse event associated with an overdose is considered a serious adverse event for collection 
purposes. An overdose that is not associated with an adverse event is considered a non-serious event of clinical interest and must be reported within 24 hours 
of site knowledge of the event to the Lead Principal Investigator and to Merck and Sarah Cannon Development Innovation Safety Department within 2 
working days. 

 
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Other important medical events that may not result in death, not be life threatening, or not require hospitalization may be considered a serious adverse event 
when, based upon appropriate medical judgment, the event may jeopardize the subject and may require medical or surgical intervention to prevent one of the 
outcomes listed previously (designated above by a †). 
Duration 
Record the start and stop dates of the adverse event. If less than 1 day, indicate the appropriate length of time and units 
Action taken  
Did the adverse event cause study agent(s) to be discontinued? 
Relationship to 
Merck or Evelo 
Product  
Did study agent(s) cause the adverse event? The determination of the likelihood that Merck  product caused the adverse event will be provided by an 
investigator who is a qualified physician. The investigator’s signed/dated initials on the source document or worksheet that supports the causality noted on 
the AE form, ensures that a medically qualified assessment of causality was done. This initialed document must be retained for the required regulatory time 
frame. The criteria below are intended as reference guidelines to assist the investigator in assessing the likelihood of a relationship between the test drug and 
the adverse event based upon the available information. 
The following components are to be used to assess the relationship between study agent(s) and the AE; the greater the correlation with the components 
and their respective elements (in number and/or intensity), the more likely study agent(s) caused the adverse event (AE): 
 
Exposure 
Is there evidence that the subject was actually exposed to study agent(s) such as: reliable history, acceptable compliance assessment (pill 
count, diary, etc.), expected pharmacologic effect, or measurement of drug/metabolite in bodily specimen? 
 
Time Course 
Did the AE follow in a reasonable temporal sequence from administration of study agent(s)?  
Is the time of onset of the AE compatible with a drug-induced effect (applies to trials with investigational medicinal product)? 
 
Likely Cause 
Is the AE not reasonably explained by another etiology such as underlying disease, other drug(s)/vaccine(s), or other host or environmental 
factors 

 
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Relationship 
The following components are to be used to assess the relationship between the study agent(s) and the AE: (continued) 
to Merck or 
Evelo Product 
(continued)  
Dechallenge 
Was study agent(s) discontinued or dose/exposure/frequency reduced? 
If yes, did the AE resolve or improve? 
If yes, this is a positive dechallenge. If no, this is a negative dechallenge. 
(Note: This criterion is not applicable if: (1) the AE resulted in death or permanent disability; (2) the AE resolved/improved despite continuation of 
pembrolizumab; or (3) the trial is a single-dose drug trial); or (4) pembrolizumab is only used one time.) 
 
Rechallenge 
Was the subject re-exposed to study agent(s) in this study? 
If yes, did the AE recur or worsen? 
If yes, this is a positive rechallenge. If no, this is a negative rechallenge. 
(Note: This criterion is not applicable if: (1) the initial AE resulted in death or permanent disability, or (2) the trial is a single-dose drug trial); or (3) 
pembrolizumab is only used one time). 
NOTE: IF A RECHALLENGE IS PLANNED FOR AN ADVERSE EVENT WHICH WAS SERIOUS AND WHICH MAY HAVE BEEN CAUSED 
BY STUDY AGENT(S), OR IF REEXPOSURE TO STUDY AGENT(S) POSES ADDITIONAL POTENTIAL SIGNIFICANT RISK TO THE 
SUBJECT, THEN THE RECHALLENGE MUST BE APPROVED IN ADVANCE BY THE LEAD PRINCIPAL INVESTIGATOR AS PER DOSE 
MODIFICATION GUIDELINES IN THE PROTOCOL. 
 
Consistency 
with Trial 
Treatment 
Profile 
Is the clinical/pathological presentation of the AE consistent with previous knowledge regarding study agent(s) or drug class pharmacology or 
toxicology? 
The assessment of relationship will be reported on the case report forms /worksheets by an investigator according to his/her best clinical judgment, including consideration of the above 
elements. 
Record one of the following 
Use the following scale of criteria as guidance (not all criteria must be present to be indicative of study agent(s) relationship). 
Yes, there is a reasonable 
possibility of study agent(s) 
relationship. 
There is evidence of exposure to study agent(s).  The temporal sequence of the AE onset relative to the administration of study agent(s) is reasonable.  
The AE is more likely explained by study agent(s)than by another cause. 
No, there is not a reasonable 
possibility of study agent(s) 
relationship 
Subject did not receive the study agent(s) OR temporal sequence of the AE onset relative to administration of study agent(s) is not reasonable OR 
the AE is more likely explained by another cause than the study agent(s).  (Also entered for a subject with overdose without an associated AE.) 

 
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8.2.5 Serious Adverse Event Reporting to the Coordinating Center 
All Adverse Events will be reported to regulatory authorities, IRB/IECs and investigators in 
accordance with all applicable global laws and regulations.  
For reporting SUSARs, reporting will comply with CFR 312.32. 
All serious adverse events and all Events of Clinical Interest that have been specified to require 
expedited reporting occurring on this study require expedited reporting to the University of 
Chicago Comprehensive Cancer Center (UC CCC).  The responsible Research Nurse or other 
designated individual at the treating site should report the SAE to the Lead Principal 
Investigator and the Cancer Clinical Trials Office (CCTO) within 24 hours of site knowledge 
of the event.  Reports should be made using the ‘Serious Event Report’ Form. Please scan and 
send via email (preferred) or fax to the following: 
University of Chicago Phase II CRA General: 
PhaseIICRA@medicine.bsd.uchicago.edu 
Phone: 773-834-1746 
Fax: 773-702-4889 
 
UC CCC Cancer Clinical Trials Office Quality Assurance: 
qaccto@bsd.uchicago.edu 
 
All unexpected adverse reactions must be reported to the IND holder so that the University of 
Chicago CCTO can inform the FDA.  The responsible Research Nurse or other designated 
individual at the treating site should provide a complete written report using the FDA 
MedWatch 3500A form.  The completed form should be sent to the CCTO at 
qaccto@bsd.uchicago.edu 
and 
to 
the 
Phase 
II 
CRA 
at 
PhaseIICRA@medicine.bsd.uchicago.edu within the specified timelines below regardless of 
whether all information regarding the event is available.  If applicable, a follow-up report 
should be provided to the CCTO if additional information on the event becomes available. 
Participating sites should not forward any adverse event reports directly to the FDA.  The 
CCTO will report all events to the FDA as per the current FDA guidelines.   
Fatal or Life-threatening Events: within 4 calendar days from treating investigator 
knowledge of the event 
All Other Reportable Events: within 10 calendar days of treating investigator 
knowledge of the event 
All serious adverse events should also be reported to the local IRB of record according to 
their policies and procedures.   
 

 
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8.2.6 Serious Adverse Event Reporting by the Coordinating Center 
The designated UC CCC Regulatory Manager will notify all participating sites of all 
unexpected and serious adverse reactions that occur on this clinical trial and which are reported 
to the FDA and/or UC Institutional Review Board (IRB).  When reported to the FDA, a copy 
of the completed Form 3500A (MedWatch) will be provided to the responsible Regulatory 
Manager by the CCTO IND Coordinator for distribution to all participating sites. 
8.2.7 Serious Adverse Event Reporting to Merck 
Any serious adverse event reported to the UC CCC, whether or not related to Merck product, 
must also be reported within 2 working days to Merck Global Safety.   
Non-serious Events of Clinical Interest will be forwarded to Merck Global Safety and will be 
handled in the same manner as SAEs.  
SAE reports and any other relevant safety information are to be forwarded to the Merck Global 
Safety facsimile number:  +1-215-993-1220. 
The University of Chicago coordinating center staff will be responsible for reporting all events 
to Merck.   
8.2.8 Serious Adverse Event Reporting to Evelo (Sarah Cannon Safety Department) 
Any serious adverse event reported to the UC CCC, whether or not related to Evelo product, 
must also be reported within 2 working days to Sarah Cannon Development Innovation Safety 
Department.  
Non-serious Events of Clinical Interest will be forwarded to Sarah Cannon Development 
Innovation Safety Department and will be handled in the same manner as SAEs.  
SAE reports and any other relevant safety information are to be forwarded to Sarah Cannon 
Development Innovation Safety Department. 
Safety Dept. Fax #: 1-866-807-4325 
Safety Dept. Email: CANN.SAE@SCRI-Innovations.com  
The University of Chicago coordinating center staff will be responsible for reporting all events 
to Sarah Cannon Development Innovation Safety Department. 
9.0 DATA REPORTING 
Data reporting will be performed utilizing the eVelos electronic data capture system.  The 
University of Chicago CRA will provide you with the applicable user registration information.  
All required data must be recorded in the eVelos database at the completion of each cycle.  
AEs are to be entered in real time. SAEs are to be entered on the Serious Event Form within 
24 hours of the site’s knowledge of the event and sent via email (preferred) or fax to the 

 
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University 
of 
Chicago 
(PhaseIICRA@medicine.bsd.uchicago.edu 
or 
qaccto@bsd.uchicago.edu; Fax: 773-702-4889). All case report forms must be completed by 
designated study personnel. Each screened (consented) patient is to be entered into eVelos 
within 48 hours of patient registration. In addition to direct data entry, sites may be required to 
provide supporting source documentation. Source records are original documents, data, and 
records (e.g., medical records, raw data collection forms, pharmacy dispensing records, 
recorded data from automated instruments, laboratory data) that are relevant to the clinical 
trial. Each site will prepare and maintain adequate and accurate source documents. These 
documents are designed to record all observations and other pertinent data for each subject 
enrolled in this clinical trial. Source records must be adequate to reconstruct all data transcribed 
onto the case report form.   
10.0 STATISTICAL ANALYSIS PLAN 
10.1 Statistical Analysis Plan  
 
For purposes of analysis, the following populations are defined: 
Population 
Description 
Enrolled 
All participants who sign the ICF. 
Safety 
All participants who take at least 1 dose of study intervention.  
Evaluable 
All participants and who had no important protocol deviations 
affecting efficacy variables.  
 
Hypothesis: Modulation of the gut microbiota with EDP1503 will augment the depth of 
response or response rate in patients with advanced melanoma who are naïve or refractory to 
anti-PD1 antibody. 
 
The study will have two cohorts of subjects including: 
1. Subjects with advanced melanoma who are naïve to anti-PD1 antibody. 
2. Subjects with advanced melanoma who are refractory to anti-PD1 antibody. 
 
Cohort one will employ a single stage design while cohort two will employ a Simon two stage 
design in which subjects will be treated with pembrolizumab in combination with EDP1503.   
 
Cohort 1: Subjects with melanoma who are naive to anti-PD1 antibody:  
Given the robust activity of pembrolizumab in patients with melanoma naïve to anti-PD1 
monotherapy, we have proposed “deep response” (>80% tumor reduction) as the primary 
response endpoint in the frontline setting for cohort 1.  This was based on the experience 
described of anti-PD1 antibody (nivolumab) in combination with anti-CTLA4 antibody 
(ipilimumab) in which approximately 40% of patients had >80% tumor reduction as best 
overall response25,29-31.  Utilizing this response endpoint as opposed to the RECIST response 
definition of 30% tumor shrinkage will allow the sample size to be reduced and thus facilitate 
a more rapid completion of the trial.   

 
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The co-primary efficacy endpoint will be rate of deep response by RECIST.  Given the deep 
response rate of approximately 5% to monotherapy anti-PD1 antibody, we will consider a 
response rate of 0.05 as not promising, and a response rate of 0.20 as promising.  The type I 
error rate is set at 0.1 and the type II error rate at 0.1. Given that pembrolizumab is a clinical 
standard of care, a single stage accrual design will be employed including 35 patients.    If 4 or 
more deep responses are observed in 35 total subjects the combination would be deemed of 
substantial interest in patients with PD1 treatment naïve melanoma, given that the EDP1503 
safety is also established (co-primary objective). A chi-squared test will be performed for the 
responder rate, and a 95% confidence interval may be produced, if deemed appropriate.  
For the secondary efficacy objectives, progression-free survival (PFS) will be estimated by the 
Kaplan-Meier method.  PFS will be defined as the time from first dose of either drug until 
disease progression or death from any cause.  Surviving subjects without progression will be 
censored as of the date of the last negative examination.   
 
Adverse events will be tabulated by type, severity, and attribution.  Immune responses, as 
assessed at baseline, week 6, and week 12 will be analyzed by mixed effects regression for 
longitudinal data.  Baseline and post-treatment values will also be compared between 
responders and non-responders.  Microbial data will be analyzed descriptively, pooling the data 
with that from subjects in other studies. 
 
Cohort 2 For subjects with melanoma who are refractory to anti-PD1 antibody:  
The primary efficacy endpoint of cohort 2 will be RECIST response rate.  Given that 
response would not be expected in subjects with prior progression on anti-PD1, we will 
consider a response rate of 0.05 as not promising and 0.20 as promising.  The type I error rate 
is set at 0.1 and the type II error rate at 0.1. A total of 35 subjects would be proposed.  In an 
optimal Simon two stage design, 1 response in 20 subjects would be required in the first stage 
and 4 or more responses observed in 35 total subjects the combination would be deemed of 
substantial interest in the treatment of patients with PD1 refractory melanoma, given that the 
EDP1503 safety is also established (co-primary objective). A chi-squared test will be 
performed for the responder rate, and a 95% confidence interval may be produced, if deemed 
appropriate.  However if any responses are observed detailed investigation of changes in the 
microbiome and tumor microenvironment will be indicated.  The probability of stopping this 
cohort early is 42% if the true response rate is only 0.05. 
Description of secondary and correlative endpoints will be the same as cohort 1.  
Hypothesis: EDP1503 monotherapy will demonstrate a similar safety and tolerability profile 
to probiotics though may be associated with low grade nausea, vomiting, and abdominal pain.   
The study will have two cohorts of subjects with a monotherapy run-in with EDP1503 as 
described earlier. There will be 2 analyses of safety across this study: 
1. EDP1503 monotherapy run-in 
2. Overall safety for the combination of pembrolizumab and EDP1503 
 
All safety analyses will be performed on the Safety Population.  

 
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The co-primary endpoint for this study is the incidence of SAEs and AEs during the 
monotherapy run-in with ED the monotherapy period with EDP1503.  
 
All AEs will be coded using the latest available version of the Medical Dictionary for 
Regulatory Activities (MedDRA) and categorized by intensity (mild/moderate/severe).  
Treatment-emergent AEs and SAEs will be listed and summarized by treatment period and 
participant population, system organ class and preferred term.  
 
Definition of Dose Limiting Toxicity: Any toxicity of >=Grade 3, any autoimmune toxicity 
>CTCAE Gr 2; DLT observation period is for the length of monotherapy for each cohort. The 
first three patients enrolled will successively complete their 2 week DLT period prior to 
initiation of the subsequent patients.  
Safety laboratory measurements: These variables will be listed and summarized by treatment 
group and participant population.  
 
Statistical analysis of tumor biopsies 
Monotherapy with pembrolizumab is associated with an approximately 40% response rate in 
therapy naive patients. Morphologic predictors of response include expression of PDL-1, an 
interferon gamma target indicative of an active inflammatory response to tumor, and the 
presence of tumor infiltrating CD8 T cells, dendritic cells, and NK cells of particular 
phenotypes. The therapeutic hypothesis of EDP1503 is that it will either induce or augment an 
antitumor inflammatory response, and/or will induce production of neoantigen presenting 
MHC class I in the tumor.  
The primary goal of the biopsy analysis is to determine whether the tumor has sustained an 
infiltration by innate and adaptive immune cells, and/or increased tumoral expression of 
antigen expression apparatus such as components of MHC Class I, consistent with the 
therapeutic hypothesis. The secondary goal is to determine whether either the baseline level of 
inflammatory infiltrate or the level induced by EDP1503 treatment is predictive of immediate 
an extended response to the combination of EDP1503 with pembrolizumab.  
The primary assays for analysis of the paired biopsies are the Nanostring IO 360 assay, an 
extensively validated transcript profiling assay used for semi-quantitative cell enumeration and 
transcriptional response in biopsies (Danaher et al.), as well as immunofluoresence based 
direct enumeration of immune cells and their spatial co-localization.  
 
The primary hypothesis for statistical analysis of the paired biopsies is to accept or reject the 
hypothesis that the tumor inflammation signature (TIS, or T cell-inflamed GEP), a function 
calculated from the abundance of 18 transcripts detected in the sample (Table below), has 
changed in the tumor due to therapy. This function is highly correlated with pembrolizumab 
treatment outcome (Ayers et al.). 

 
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Table: 18 component transcripts of the TIS score 
TIGIT 
PD-L1 
PSMB10 
STAT1 
CD27 
CXCR6 
IDO1 
HLADRB1 
CD8A 
CMKLR1 
CXCL9 
HLAE 
PD-L2 
NKG7 
HLADQA1 
  
LAG3 
CCl5 
CD276 
  
 
The variance of baseline data due to sampling variation is provided by published studies on 
the variability of the TIS due to sampling (Walldren et al.)  From the dataset of multiple 
samplings of a baseline sample, a ratio of paired baseline TIS scores (n=85) was calculated, 
median (IQR): 0.9 (.25).  To determine whether a difference in TIS score from day 14 to 
baseline is statistically significant from replicate TIS measurements, a 95% Bca confidence 
interval was constructed from 10000 bootstrap replicates using the ratios of paired baseline 
TIS scores, (0.81,1.31).  Based on this estimate, a TIS ratio score > 1.31 would suggest a 
significant result at the 95% confidence level.  
Association of the TIS with response rate (either deep response of > 80% in Cohort 1 or 
RECIST response rate in Cohort 2) and PFS will be analyzed following the established 
methods of (Ayers et al.).  
Several outcomes may be envisaged:  
• EDP1503 causes increase in TIS in a subset of patients and that increase is associated 
with an increase in RR and PFS. 
• Baseline TIS is associated with PFS, and changes induced by EDP1503 treatment are 
not associated with changes in RR and PFS. 
• EDP1503 does not affect TIS in any patient. 
 
These hypotheses will be explored using linear mixed effects models fitted to immunological 
parameters and related composite scores to determine associations of rate of change with 
treatment outcome, following the strategy of Ribas et al. 
 
We will also perform additional exploratory analyses. 
In addition to the TIS, the IO360 panel provides for the individual semi-quantitative 
enumeration of multiple cell types including NK, DC, and T cells, which will be enumerated 
in pre and post treatment biopsies.  

 
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The immunofluorescense assays will additionally provide quantitation of immune cell types. 
The ability to sample multiple portions of each pre and post treatment sample with IF will 
allow for high-dimensional resolution of group differences determined by Wilcoxon rank-sum 
test. These results will be cross correlated with the Nanostring analysis, and the quality of the 
correlation compared to Ribas et al. 
References: 
Danaher P et al. Gene expression markers of Tumor Infiltrating Lymphocytes. JITC 5:18-33 
(2017) 
Ayers et al. IFNg related mRNA profile predicts clinical response to PD-1 blockade. JCI 
127(8):2930-2940 (2017) 
Walldren et al. Development and analytical performance of a molecular diagnostic for anti-
PD1 response on the nCounter Dx Analysis System. ASCO 2016, Abstract 3034. 
Ribas A et al. Oncolytic Virtherapy Promotes Intratumoral T Cell Infiltration and Improves 
Anti-PD-1 Immunotherapy. Cell 170, 1109-1119 (2017) 
10.2 Sample Size and Expected Accrual 
The study will be conducted through the University of Chicago Personal Cancer Care 
Consortium which includes both sophisticated private practices as well as collaborating 
academic centers.  Patient accrual through this mechanism would be projected to be 3 subjects 
per month. Cohort 1 and Cohort 2 will enroll 35 evaluable patients each. 
See section 10.1 for the description of the sample size. 
11.0 LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES 
11.1 Investigational Product  
The investigator shall take responsibility for and shall take all steps to maintain appropriate 
records and ensure appropriate supply, storage, handling, distribution and usage of 
investigational product in accordance with the protocol and any applicable laws and 
regulations. 
Clinical Supplies will be provided by Merck and Evelo as summarized in Table 7. 
Table 7 Product Descriptions 
Product Name & Potency 
Dosage Form 
Pembrolizumab 50 mg 
Lyophilized Powder for Injection 
Pembrolizumab 100 mg/ 4mL 
Solution for Injection 

 
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Product Name & Potency 
Dosage Form 
EDP1503 >7.5x1010 organisms/capsule 
Enteric capsule size 0 for oral delivery 
 
11.2 Packaging and Labeling Information 
Clinical supplies will be affixed with a clinical label in accordance with regulatory 
requirements. 
11.3 Clinical Supplies Disclosure 
This trial is open-label; therefore, the subject, the trial site personnel, the Principal Investigator 
and/or designee are not blinded to treatment. Drug identity (name, strength) is included in the 
label text; random code/disclosure envelopes or lists are not provided. 
11.4 Storage and Handling Requirements 
Clinical supplies must be stored in a secure, limited-access location under the storage 
conditions specified on the label.   
Receipt and dispensing of trial medication must be recorded by an authorized person at the 
trial site. 
Clinical supplies may not be used for any purpose other than that stated in the protocol. 
11.5 Returns and Reconciliation 
The investigator is responsible for keeping accurate records of the clinical supplies received, 
the amount dispensed to and returned by the subjects and the amount remaining at the 
conclusion of the trial.  
Upon completion or termination of the study, all unused and/or partially used investigational 
product will be destroyed at the site per institutional policy. It is the Investigator’s 
responsibility to arrange for disposal of all empty containers, provided that procedures for 
proper disposal have been established according to applicable federal, state, local and 
institutional guidelines and procedures, and provided that appropriate records of disposal are 
kept. 
12.0 ADMINISTRATIVE AND REGULATORY DETAILS 
12.1 Institutional Review Board (IRB) Approval and Consent 
Unless otherwise specified, each participating institution must obtain its own IRB approval. It 
is expected that the IRB will have the proper representation and function in accordance with 
federally mandated regulations.  The IRB should approve the consent form and protocol. 

 
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In obtaining and documenting informed consent, the investigator should comply with the 
applicable regulatory requirement(s), and should adhere to Good Clinical Practice (GCP) and 
to ethical principles that have their origin in the Declaration of Helsinki. 
Before recruitment and enrollment onto this study, the patient will be given a full explanation 
of the study and will be given the opportunity to review the consent form. Each consent form 
must include all the relevant elements currently required by the FDA Regulations and local or 
state regulations. Once this essential information has been provided to the patient and the 
investigator is assured that the patient understands the implications of participating in the 
study, the patient will be asked to give consent to participate in the study by signing an IRB 
approved consent form. 
Prior to a patient’s participation in the trial, the written informed consent form should be signed 
and personally dated by the patient and by the person who conducted the informed consent 
discussion. 
12.2 Food and Drug Administration (FDA) Approval 
This study will be conducted under an IND held by Dr. Randy Sweis at the University of 
Chicago.  The University of Chicago CCTO will be responsible for facilitating all 
communications with the FDA on behalf of the IND holder.   Participating sites should not 
communicate directly with the FDA.     
12.3 Required Documentation 
Prior to the selection of a study site that is not a full member of the Personalized Cancer Care 
Consortium, the audit and trial oversight processes for the site must be reviewed and approved 
by the UC CCC Clinical Research Advisory Committee.   
Before the study can be initiated at any site, the following documentation must be provided to 
the Cancer Clinical Trials Office (CCTO) at the University of Chicago Comprehensive Cancer 
Center. 
• A copy of the official IRB approval letter for the protocol and informed consent 
• IRB membership list 
• CVs and medical licensure for the principal investigator and any sub-investigators who 
will be involved in the study. 
• Form FDA 1572 appropriately filled out and signed with appropriate documentation  
• CAP and CLIA Laboratory certification numbers and institution lab normal values 
• Investigational drug accountability standard operating procedures 
 
Additionally, before the study can be initiated at any site, the required executed research 
contract/subcontract must be on file with the University of Chicago. 

 
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12.4 Data and Safety Monitoring 
This study will be remotely monitored by the designated University of Chicago Clinical 
Research Associate (CRA) in accordance with the University of Chicago, Section of 
Hematology/Oncology standard operating procedure titled Monitoring of Multi-Institutional 
Investigator Initiated Clinical Trials. 
Prior to subject recruitment, and unless otherwise specified, a participating site will undergo a 
Site Initiation Teleconference to be conducted by the designated University of Chicago 
research team. The site’s principal investigator and his or her study staff must attend the site 
initiation meeting.  
Monitoring will be conducted to verify the following: 
• Adherence to the protocol 
• Completeness and accuracy of study data and samples collected 
• Compliance with regulations  
• Submission of required source documents  
 
Participating sites will also undergo a site close-out teleconference upon completion, 
termination or cancellation of a study to ensure fulfillment of study obligations during the 
conduct of the study, and to ensure that the site Investigator is aware of his/her ongoing 
responsibilities. 
Unless otherwise specified, this protocol will undergo weekly review at the multi-institutional 
data and safety monitoring teleconference as per procedures specified by the UC CCC NCI-
approved Data and Safety Monitoring Plan. The conference will review: 
• Enrollment rate relative to expectations, characteristics of participants 
• Safety of study participants (Serious Adverse Event & Adverse Event reporting) 
• Adherence to protocol (protocol deviations) 
• Completeness, validity and integrity of study data 
• Retention of study participants 
 
Protocol deviations are to be documented using the Protocol Deviation Form and sent via email 
to PhaseIICRA@medicine.bsd.uchicago.edu. Deviations that are considered major because 
they impact subject safety or alter the risk/benefit ratio, compromise the integrity of the study 
data, and/or affect subjects’ willingness to participate in the study must be reported within 7 
days. 
Please 
contact 
the 
University 
of 
Chicago 
CRA 
(PhaseIICRA@medicine.bsd.uchicago.edu) if you have questions about how to report 
deviations.  All major protocol deviations should also be reported to the local IRB of record 
according to their policies and procedures.  
12.5 Auditing 
In addition to the clinical monitoring procedures, the University of Chicago Comprehensive 
Cancer Center will perform routine Quality Assurance Audits of investigator-initiated clinical 

 
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trials as described in the NCI-approved UC CCC DSM Plan. Audits provide assurance that 
trials are conducted and study data are collected, documented and reported in compliance with 
the protocol. Further, quality assurance audits ensure that study data are collected, documented 
and reported in compliance with Good Clinical Practices (GCP) Guidelines and regulatory 
requirements. The audit will review subjects enrolled at the University of Chicago in 
accordance with audit procedures specified in the UC CCC Data and Safety Monitoring plan. 
For institutions who are formal members of the Personalized Cancer Care Consortium (PCCC), 
the UC CCC will conduct on site quality assurance audits on average every two years during 
the enrollment and treatment phase of the study.  
Auditing procedures for participating sites that are not full members of the PCCC must be 
specified and approved by the UC CCC Clinical Research Advisory Committee.  In general, 
for sites that are not full members of the PCCC, auditing responsibility will be delegated to the 
participating center, with the annual audit report forwarded to the University of Chicago for 
review.   
A regulatory authority (e.g. FDA) may also wish to conduct an inspection of the study, during 
its conduct or even after its completion. If an inspection has been requested by a regulatory 
authority, the site investigator must immediately inform the University of Chicago Cancer 
Clinical Trials Office and Regulatory Manager that such a request has been made. 
12.6 Amendments to the Protocol 
All modifications to the protocol, consent form, and/or questionnaires will be submitted to 
the University of Chicago IRB for review and approval. A list of the proposed modifications 
or amendments to the protocol and/or an explanation of the need of these modifications will 
be submitted, along with a revised protocol incorporating the modifications. Only the Study 
Lead PI can authorize any modifications, amendments, or termination of the protocol. Once 
a protocol amendment has been approved by the University of Chicago IRB, the Regulatory 
Manager will send the amended protocol and consent form (if applicable) to the affiliate 
institutions electronically. Upon receipt of the packet the affiliate institution is expected to 
do the following: 
• The affiliate must reply to the email from the Regulatory Manager indicating that the 
amendment was received by the institution and that it will be submitted to the local 
IRB.  
 
• The amendment should be submitted to the affiliate institution’s IRB as soon as 
possible after receipt. The amendment must be IRB approved by the institution 
within 3 months from the date that it was received.  
 
• The  University  of  Chicago  version  date  and/or  amendment  number  must  
appear  on  the  affiliate consent form and on the affiliate IRB approval letter.  
The version dates can be found on the footer of every page of the protocol and 
consent form.  The amendment number can be found on the University of Chicago 
IRB amendment approval letter that is sent with the protocol/amendment mailing.  
 

 
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The IRB approval for the amendment and the amended consent form (if amended consent is 
necessary) for the affiliate institution must be sent to the designated UC Regulatory Manager as 
soon as it is received. 
12.7 Annual IRB Renewals, Continuing Review and Final Reports 
A continuing review of the protocol will be completed by the University of Chicago IRB and 
the participating institutions’ IRBs at least once a year for the duration of the study. The 
annual IRB renewal approvals for participating institutions should be forwarded promptly 
to the Regulatory Manager. If the institution’s IRB requires a new version of the consent 
form with the annual renewal, the consent form should be included with the renewal letter. 
12.8 Record Retention 
Study documentation includes all CRFs, data correction forms or queries, source documents, 
Sponsor-Investigator correspondence, monitoring logs/letters, and regulatory documents (e.g., 
protocol and amendments, IRB correspondence and approval, signed patient consent forms). 
 
Source documents include all recordings of observations or notations of clinical activities and 
all reports and records necessary for the evaluation and reconstruction of the clinical research 
study. 
 
Government agency regulations and directives require that all study documentation pertaining 
to the conduct of a clinical trial must be retained by the study investigator.  In the case of a 
study with a drug seeking regulatory approval and marketing, these documents shall be 
retained for at least two years after the last approval of marketing application in an International 
Conference on Harmonization (ICH) region.  In all other cases, study documents should be 
kept on file until three years after the completion and final study report of this investigational 
study. 
 
12.9 Obligations of Study Site Investigators 
The Study Site Principal Investigator is responsible for the conduct of the clinical trial at the 
site in accordance with Title 21 of the Code of Federal Regulations and/or the Declaration of 
Helsinki.  The Study Site Principal Investigator is responsible for personally overseeing the 
treatment of all study patients.  He/she must assure that all study site personnel, including sub-
investigators and other study staff members, adhere to the study protocol and all 
FDA/GCP/NCI regulations and guidelines regarding clinical trials both during and after study 
completion. 
 
The Study Site Principal Investigator at each institution or site will be responsible for assuring 
that all the required data will be collected and entered into the CRFs. Periodically, monitoring 
visits or audits will be conducted and he/she must provide access to original records to permit 
verification of proper entry of data. 
 

 
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13.0 APPENDICES 
13.1 ECOG Performance Status 
Grade 
Description 
0 
Normal activity. Fully active, able to carry on all pre-disease 
performance without restriction. 
1 
Symptoms, but ambulatory. Restricted in physically strenuous 
activity, but ambulatory and able to carry out work of a light or 
sedentary nature (e.g., light housework, office work). 
2 
In bed <50% of the time. Ambulatory and capable of all self-care, but 
unable to carry out any work activities. Up and about more than 50% 
of waking hours. 
3 
In bed >50% of the time. Capable of only limited self-care, confined 
to bed or chair more than 50% of waking hours. 
4 
100% bedridden. Completely disabled. Cannot carry on any self-care. 
Totally confined to bed or chair. 
5 
Dead. 
* As published in Am. J. Clin. Oncol.:  Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., 
McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern Cooperative Oncology 
Group. Am J Clin Oncol 5:649-655, 1982. The Eastern Cooperative Oncology Group, Robert Comis 
M.D., Group Chair. 
 
13.2 Common Terminology Criteria for Adverse Events V5 (CTCAE) 
The descriptions and grading scales found in the revised NCI Common Terminology Criteria 
for Adverse Events (CTCAE) version 5 will be utilized for adverse event reporting. 
(http://ctep.cancer.gov/reporting/ctc.html) 
13.3 Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 Criteria for 
Evaluating Response in Solid Tumors 
RECIST version 1.1* will be used in this study for assessment of tumor response. While either 
CT or MRI may be utilized, as per RECIST 1.1, CT is the preferred imaging technique in this 
study. 
* As published in the European Journal of Cancer: 
 
E.A. Eisenhauer, P. Therasse, J. Bogaerts, L.H. Schwartz, D. Sargent, R. Ford, J. 
Dancey, S. Arbuck, S. Gwyther, M. Mooney, L. Rubinstein, L. Shankar, L. Dodd, R. Kaplan, 
D. Lacombe, J. Verweij. New response evaluation criteria in solid tumors: Revised RECIST 
guideline (version 1.1). Eur J Cancer. 2009 Jan;45(2):228-47. 
In addition, volumetric analysis will be explored by central review for response assessment. 
 
 

 
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MELANOMA (STOP-GAP): CANADIAN CLINICAL TRIALS GROUP STUDY 
(CCTG) ME.13. JOURNAL OF CLINICAL ONCOLOGY 2018;36:TPS9600-TPS. 
25. 
WOLCHOK JD, KLUGER H, CALLAHAN MK, ET AL. NIVOLUMAB PLUS 
IPILIMUMAB IN ADVANCED MELANOMA. NEW ENGLAND JOURNAL OF 
MEDICINE 2013;369:122-33. 
26. 
POSTOW MA, CHESNEY J, PAVLICK AC, ET AL. NIVOLUMAB AND 
IPILIMUMAB VERSUS IPILIMUMAB IN UNTREATED MELANOMA. NEW 
ENGLAND JOURNAL OF MEDICINE 2015;372:2006-17. 
27. 
LARKIN J, CHIARION-SILENI V, GONZALEZ R, ET AL. COMBINED 
NIVOLUMAB AND IPILIMUMAB OR MONOTHERAPY IN UNTREATED 
MELANOMA. NEW ENGLAND JOURNAL OF MEDICINE 2015;373:23-34. 
28. 
WOLCHOK JD, CHIARION-SILENI V, GONZALEZ R, ET AL. OVERALL 
SURVIVAL WITH COMBINED NIVOLUMAB AND IPILIMUMAB IN ADVANCED 
MELANOMA. NEW ENGLAND JOURNAL OF MEDICINE 2017;377:1345-56. 
29. 
LARKIN J, CHIARION-SILENI V, GONZALEZ R, ET AL. COMBINED 
NIVOLUMAB AND IPILIMUMAB OR MONOTHERAPY IN UNTREATED 
MELANOMA. THE NEW ENGLAND JOURNAL OF MEDICINE 2015;373:23-34. 
30. 
POSTOW MA, CHESNEY J, PAVLICK AC, ET AL. NIVOLUMAB AND 
IPILIMUMAB VERSUS IPILIMUMAB IN UNTREATED MELANOMA. THE NEW 
ENGLAND JOURNAL OF MEDICINE 2015;372:2006-17. 
31. 
WOLCHOK JD, ROLLIN L, LARKIN J. NIVOLUMAB AND IPILIMUMAB 
IN ADVANCED MELANOMA. THE NEW ENGLAND JOURNAL OF MEDICINE 
2017;377:2503-4. 
14.0 
CRITERIA FOR irRECIST 
Tumor Burden 
(Baseline and New) 
Non-Target Lesions 
(Baseline and New) 
Response 
Disappearance of non-nodal 
lesions. All pathologic lymph 
nodes < 10 mm (short axis) 
Disappearance of non-nodal 
lesions. All pathologic lymph 
nodes < 10 mm (short axis) 
irCRa 
≥ 30% decrease from baseline 
Any 
irPRa 
≥ 20% increase from nadir and 
at least 5 mm 
Any 
irPDa 
Neither sufficient decrease to 
qualify for PR, nor sufficient 
increase to qualify for PD 
Any 
irSD 
Disappearance of all non-nodal 
lesions. All pathologic lymph 
nodes < 10 mm 
Any other than disappearance of 
all non-nodal lesions and 
reduction of pathologic lymph 
nodes < 10 mm 
irPRa 

 
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Not all evaluatedb 
Any 
irNE 
a Selection as best response requires confirmation by 2 consecutive measurements at least 4 weeks apart. 
b If some lesions are measured, response may be inferred from available measurements. For example, growth 
in evaluated target lesions may be sufficient for irPD regardless of status of non-evaluated lesions. 
 
 

 
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MELANOMA (STOP-GAP): CANADIAN CLINICAL TRIALS GROUP STUDY 
(CCTG) ME.13. JOURNAL OF CLINICAL ONCOLOGY 2018;36:TPS9600-TPS. 
25. 
WOLCHOK JD, KLUGER H, CALLAHAN MK, ET AL. NIVOLUMAB PLUS 
IPILIMUMAB IN ADVANCED MELANOMA. NEW ENGLAND JOURNAL OF 
MEDICINE 2013;369:122-33. 
26. 
POSTOW MA, CHESNEY J, PAVLICK AC, ET AL. NIVOLUMAB AND 
IPILIMUMAB VERSUS IPILIMUMAB IN UNTREATED MELANOMA. NEW 
ENGLAND JOURNAL OF MEDICINE 2015;372:2006-17. 
27. 
LARKIN J, CHIARION-SILENI V, GONZALEZ R, ET AL. COMBINED 
NIVOLUMAB AND IPILIMUMAB OR MONOTHERAPY IN UNTREATED 
MELANOMA. NEW ENGLAND JOURNAL OF MEDICINE 2015;373:23-34. 
28. 
WOLCHOK JD, CHIARION-SILENI V, GONZALEZ R, ET AL. OVERALL 
SURVIVAL WITH COMBINED NIVOLUMAB AND IPILIMUMAB IN ADVANCED 
MELANOMA. NEW ENGLAND JOURNAL OF MEDICINE 2017;377:1345-56. 
29. 
LARKIN J, CHIARION-SILENI V, GONZALEZ R, ET AL. COMBINED 
NIVOLUMAB AND IPILIMUMAB OR MONOTHERAPY IN UNTREATED 
MELANOMA. THE NEW ENGLAND JOURNAL OF MEDICINE 2015;373:23-34. 
30. 
POSTOW MA, CHESNEY J, PAVLICK AC, ET AL. NIVOLUMAB AND 
IPILIMUMAB VERSUS IPILIMUMAB IN UNTREATED MELANOMA. THE NEW 
ENGLAND JOURNAL OF MEDICINE 2015;372:2006-17. 
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WOLCHOK JD, ROLLIN L, LARKIN J. NIVOLUMAB AND IPILIMUMAB 
IN ADVANCED MELANOMA. THE NEW ENGLAND JOURNAL OF MEDICINE 
2017;377:2503-4.