Phase II Feasibility Study of Fecal Microbiota Transplant (FMT) in Advanced Melanoma Patients Not Responding to PD-1 Blockade
Phase: PHASE2
Conditions: Melanoma
Sponsor: Zarour, Hassane, MD

 
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SPONSOR: Hassane Zarour 
 
TITLE: Phase II Feasibility Study of Fecal Microbiota Transplant (FMT) in Advanced 
Melanoma Patients Not Responding to PD-1 blockade 
 
 
IND NUMBER: 17603 
 
HCC Protocol Number:  17-034 
 
PI: Diwakar Davar 
 
Co-PI: Hassane M. Zarour 
 
Source of Support: Merck and National Institute of Health - UPCI Spore 
(R01CA222203) 
 
Version: 6 dated 05/12/2021 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
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SUMMARY OF CHANGES 
 
 
 
 
SUMMARY OF CHANGES TO PROTOCOL 
 
Page 1, changed from version 5 dated 06-04-2020 to version 6 dated 5-12-
2021 
 
Page 21, #4.2, changed from Determination of "SARS-CoV-2 negative" 
status will be made on nasopharyngeal, and stool specimens obtained at two 
timepoints: 1st sample collected at least 14 days before stool sample 
donation, and a 2nd sample collected at least 14 days after stool sample 
donation; changed to  Determination of "SARS-CoV-2 negative" status will 
be made on nasopharyngeal, blood and stool specimens obtained at two 
timepoints (every 2 weeks for up to 12 weeks): 1st sample collected at least 
14 days before stool sample donation, and a 2nd sample collected at least 14 
days after stool sample donation. 
 
SUMMARY OF CHANGES TO DONOR CONSENT 
 
Page 1, changed from version 06/04/2020 to version 05/06/2021 
 
Page 3, changed from You will be asked to provide a blood sample of 
90ml for testing; changed to You will be asked to provide a blood sample 
of 90ml for testing during each visit. 
 
Page 5, Section- How long will I be in this study?, 1st paragraph, 
changed from You will be in this study for the duration of your follow-up 
for your cancer diagnosis. However, the time taken for blood and stool tests 
and stool donations is only 8 weeks. It is possible that you may be asked to 
donate more stool if a recipient who responds initially progresses and is 
considered a candidate for a second transplant or if there are more than a 
few individuals who are identified as possible recipients for samples 
originating from you; changed to You will be in this study for the duration 
of your follow-up for your cancer diagnosis. However, the time taken for 
blood, nasal swabs and stool studies will be every 2 weeks for up to 12 
weeks. It is possible that you may be asked to donate more stool if a 
recipient who responds initially progresses and is considered a candidate for 
a second transplant or if there are more than a few individuals who are 
identified as possible recipients for samples originating from you. 
 
Page 6, Section- Will I be paid if I take part in this research study, 2nd 
paragraph, added You will be reimbursed monthly in the amount of 
$25.00 for travel expenses. 
 
 

 
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1.0 TRIAL SUMMARY 
Abbreviated Title 
Phase II feasibility study of fecal microbiota transplant 
(FMT) in advanced melanoma patients not responding to 
PD-1 blockade 
Trial Phase 
II 
Clinical Indication 
PD-1 refractory advanced melanoma 
Trial Type 
Phase II Simon 2-stage 
Type of control 
N/A 
Route of administration 
pembrolizumab – IV; FMT – endoscopically administered 
Trial Blinding 
N/A 
Treatment Groups  
N/A 
Number of trial subjects 
 13 (stage 1), 7 (stage 2); total 20 
 
Estimated enrollment period 
15-20 months 
Average length of treatment 
per patient 
12 weeks (minimum; FMT with 4 cycles of pembrolizumab) 
up to 24 weeks (8 cycles of pembrolizumab) 
Duration of therapy 
Up to 2 years (24 months; 35 cycles of pembrolizumab) 
Duration of Participation 
Up to 2 years (24 months) 
 
 
 
 
2.0 TRIAL DESIGN 
2.1 
Trial Design 
This is a phase II Simon two-stage single-center study of concurrent FMT with 
pembrolizumab in patients with PD-1 resistant/refractory melanoma The study will be 
conducted over a 12-week period (and up to 24-weeks in responding patients). 
Recipient eligibility is based upon prior exposure to PD-1 inhibitor therapy and response at 
1st (or subsequent) restaging scan(s) from week 12 up to week 52. Patients must have 
received a minimum of 2 cycles  to be considered eligible. Patients who have received either 
nivolumab 
or 
pembrolizumab 
are 
eligible. 
Patients 
who 
have 
received 
pembrolizumab/nivolumab in combination with other investigational agent(s) may be 
eligible at the discretion of the treating investigator. PD-1 refractory disease is defined as 
progressive disease (PD) at the first (or subsequent) radiographic evaluation while receiving 
PD-1 inhibitor treatment as assessed by RECIST v1.1 on a restaging scan. Patients with 
stable disease as their best response are eligible; but patients with complete (or partial) 
response as their best response are ineligible. Other eligibility criteria include absence of 
active CNS disease, presence of disease amenable to biopsy and lack of contra-indications to 
FMT administration. Patients will be stratified on the presence or absence of liver metastases. 

 
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Suitable patients will be identified following first (or subsequent) restaging study that 
documents progressive disease (RECIST v1.1) at any time after a minimum 2 cycles of 
pembrolizumab or nivolumab up to week 52 (17 cycles of pembrolizumab; 26 cycles of 
nivolumab). Patients will undergo a screening evaluation consisting of imaging (including 
CNS if clinically suspected), tumor biopsy, and serological/stool studies to confirm 
suitability for FMT administration. Eligible patients will receive FMT endoscopically (along 
with intestinal biopsy) with cycle 1 pembrolizumab (+/- 3 days) followed by 3 further cycles 
of pembrolizumab (cycles 2-4) following which restaging will be performed. Patients with 
stable and/or responding disease will continue to receive pembrolizumab on study for 4 
cycles. Patients with stable and/or responding disease after 8 cycles of pembrolizumab will 
continue to receive therapy off study until disease progression or up 2 years from FMT 
administration (35 cycles total). 
2.2 
Trial Diagram 
3.0 
OBJECTIVE(S) & HYPOTHESIS(ES) 
3.1 
Primary Objective(s) & Hypothesis(es) 
• Objective: To investigate whether combination of single PD-1 responder-derived FMT 
with Pembrolizumab converts PD-1 non-responders to responders. 
Hypothesis: Failure to respond to PD-1 blockade in patients with advanced melanoma is 
associated with intestinal dysbiosis and PD-1 responder-derived FMT can convert PD-1 
non-responders to responders. 

 
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3.2 
Secondary Objective(s) & Hypothesis(es) 
(1) Objective: To investigate how FMT administration affects composition and function of 
T-cells and innate/adaptive immune system subsets. 
Hypothesis: PD-1 responder-derived FMT augments tumor antigen-specific CD8+ and 
CD4+ T-cell responses, DC maturation/function and innate immune responses to 
melanoma. 
3.3 
Exploratory Objective 
(1) 
Objective: To determine whether PD-1 response in responding patients is associated 
with common gut microbiota profile. 
Hypothesis: PD-1 responders and non-responders have distinct gut commensal 
microbiota profiles; and that administration of single responder-derived FMT can 
reconstitute responder-associated microbiota profile in PD-1 non-responders. 
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). 
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 

 
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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 regulate tumor-specific T-cell expansion and function in 
vitro (Fourcade et al. 2009). In subjects with melanoma, PD-1 response appears to be 
associated with preexisting CD8+ T cell responses to melanoma (Tumeh et al. 2014). 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. Pembrolizumab was first approved in the United States by the 
Food & Drug Administration (FDA) on September 4, 2014, for the treatment of patients with 
unresectable or metastatic melanoma and disease progression following ipilimumab (IPI) 
and, if BRAF V600 mutation positive, a BRAF inhibitor. Pembrolizumab was approved for a 
broader indication as monotherapy for the treatment of unresectable or metastatic melanoma 
in adults by the FDA on December 18, 2015. 
4.1.2 Preclinical and Clinical Trial Data 
Refer to the Investigator’s Brochure for Preclinical and Clinical data. 
4.2 
Rationale 
4.2.1 Rationale for the Trial and Selected Subject Population 
Intestinal microbiome comprises entire compilation of microorganisms dwelling in the 
gastrointestinal tract. Intestinal microbiome exists in a symbiotic relationship with the host, 
actively contributing to intestinal health and disease. Intestinal dysbiosis has been implicated 
in a wide range disease states including inflammatory bowel disease (IBD), obesity, allergic 
disorders, Type 1 diabetes mellitus, autism, obesity, and cancer in both human and animal 
models. Clostridium difficile is an infectious Gram-positive spore-forming bacillus 
microorganism that is capable of causing toxin-mediated gastrointestinal illness with a wide 
spectrum of severity. C. difficile is an intestinal commensal, growth of which is normally 

 
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suppressed by more dominant anaerobes. Antibiotic use can result in loss of commensal 
microbiota barrier effect and release of previously unavailable niches; and this dysbiosis sets 
up an inflammatory cascade. Fecal microbiota transplants (FMT) are highly effective in 
treating relapsed/refractory Clostridium difficile infection - an improvement linked to the 
increased fecal bacterial diversity in recipients following donation inoculation from healthy 
volunteers (van Nood et al. 2013).  
In models of intestinal infections, microbiota-derived signals are required to sustain mucosal 
immune homeostasis; loss of which results in chronic inflammation. Specifically in cancer, 
intestinal dysbiosis has been linked to both colorectal carcinogenesis (Schneider et al. 2017) 
and response to anti-cancer therapies (Tsilimigras et al. 2017; Roy and Trinchieri 2017); 
including chemotherapy (Iida et al. 2013), radiotherapy and immunotherapy (Roy and 
Trinchieri 2017). In the setting of anti-cancer immunotherapies, intestinal dysbiosis has been 
linked to differential responses in models of adoptive T-cell therapy, intra-tumoral CpG-
oligodeoxynucleotide therapy, and CTLA-4 and PD-1/PD-L1 immune checkpoint inhibition. 
The exact mechanisms underlying the role of intestinal microbiota in modulating anti-cancer 
immune responses are complex and likely involve many interlinked pathways; published data 
suggests that commensal microbes promote crosstalk between innate myeloid/lymphoid cells 
and dendritic cells that collectively improves immune homeostasis in intestine and sensitizes 
tumor cells to anti-cancer immune therapies (Mortha et al. 2014). 
Two recent studies have shown the role of the gut microbiome in regulating clinical 
responses to CTLA-4 and PD-1/PD-L1 blockade in murine melanoma models (Vétizou et al. 
2015; Sivan et al. 2015). Vétizou et al showed that efficacy of anti–CTLA-4 therapy was 
dependent on where mice were housed and use of broad-spectrum antibiotics; although 
efficacy was restored when antibiotic-treated or germ-free–housed mice were fed 
Bacteroides isolates. Stool from melanoma patients with Bacteroidales species had a similar 
effect. Sivan et al demonstrated that mice from difference facilities (Jackson Laboratory and 
Taconic Farms) known to have distinct microbiota profiles exhibited differential tumor 
growth - a difference that disappeared upon cohousing. This difference was transmittable, 
mediated efficacy of anti-PD-1 therapy and was identified as being related to presence of 
Bifidobacterium species in the gut flora of the Jackson Laboratory mice. Although both 
groups used similar murine models of melanoma, their findings implicated different 
microbiota (CTLA-4 Bacteroidales; PD-1 Bifidobacterium).  
Two recent studies of intestinal microbiome samples from patients with NSCLC, renal 
cancers (RCC), and melanoma patients (MPs), have shown that the presence of certain 
commensals correlated with better clinical outcome upon PD1 blockade (Gopalakrishnan et 
al. 2018; Routy et al. 2018). Metagenomics studies of stools from 100 cancer patients (60 
NSCLCs and 40 RCCs) revealed correlations between better clinical outcome upon PD-1 
blockade and the relative abundance of Akkermensia muciniphila (Routy et al. 2018). Oral 
administration of Akkermensia to non-responding tumor-bearing germ-free mice restored the 
efficacy of PD-1 blockade. In addition, 16S RNA sequencing of stools obtained from a 
limited number of MPs (n=43, 30R, 13NR) showed increased alpha diversity and relative 
abundance of Ruminicoccaceae/Faecalobacterium bacteria in PD-1 responders and lower 
Bacteroidales abundance in PD-1 non-responders (Gopalakrishnan et al. 2018). Fecal 

 
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microbiota transplant (FMT) from human PD-1 responders to melanoma-bearing germ-free 
mice reduced significantly tumor growth as compared to FMT from PD-1 non-responders. 
To the best of our knowledge, the evaluation of the role of the gut microbiome in modulating 
immunological and clinical responses to anti-cancer therapy in vivo has been conducted only 
in syngeneic mice. These studies have significant limitations including the inability of 
syngeneic murine systems to completely recapitulate the features of spontaneous human 
tumors and significant differences in intestinal microbiota between mice with identical 
genetic backgrounds. Given these factors along with the significant greater complexity and 
inter-individual variability in human microbiota relative to mice, translating these findings to 
improving outcomes of patients failing PD1/PDL1 blockade is likely to involve more than 
inoculating non-responders with Bacteroidales or Bifidobacterium. Under the aegis of a 
tissue/blood banking protocol (UPCI 96-099) supported by the Skin Cancer SPORE, we have 
prospectively banked pre-treatment biopsy, pre- and on-treatment blood [serum, processed 
peripheral blood mononuclear cells (PBMC)] and stool specimens on PD1Rs – defined as 
patients who are alive and demonstrate an ongoing response (complete or partial) at 2 years 
or greater to pembrolizumab or nivolumab given as standard of care (SOC) therapy for 
advanced melanoma. As controls, we used patients with non-response to PD-1 monotherapy 
(PD1 NR). This cohort is representative of a “real-world” advanced melanoma population 
with an overall response rate of 33%. Stool specimens from these PD1 R and PD1 NR were 
banked within 4-8 hours at -800C. In order to minimize variability, stool and oral cavity 
samples were obtained from age-matched (by decade) and sex-matched PD1Rs and PD1NRs. 
Prior to sample collection, investigators ensured that patients had not had any recent 
hospitalizations (within 1 month) and/or receipt of recent antibiotic therapy (within 1 month). 
We observed increased relative abundance of Akkermensia, Collinsella and Alistipes species 
in PD1Rs as compared to PD1NRs (Figure 2), but no differences were observed in the 
 

 
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relative abundance of Bifidobacterium species and Bacteroides fragilis (data not shown). 
Because of the limited number of pre-treatment and NR samples, the significance of these 
findings still needs to be determined with sequential microbiome analysis of larger numbers 
of PD1Rs and PD1NRs.  
It is important to understand that the vast majority of the studies evaluating the role of 
intestinal dysbiosis in response to anti-cancer therapy have been conducted in mice; and the 
translation of these experimental findings to the clinic is an ongoing challenge. Mouse tumor 
models provide an excellent means by which to dissect the molecular mechanisms of 
carcinogenesis and anti-tumor treatments; but often fail to completely recapitulate the 
features of spontaneous human tumors. Further, intestinal microbiota varies even between 
mice with identical genetic backgrounds and housed in similar conditions; with profound 
physiologic effects. Separately, the physiological and immune responses of mice are similar 
but not identical to those of humans. Given these factors along with the significant greater 
complexity and inter-individual variability in human microbiota relative to mice, translating 
these findings to improving outcomes of patients failing PD-1/PD-L1 blockade is likely to 
involve more than inoculating non-responders with Bacteroidales or Bifidobacterium. 
With immune checkpoint blockade, unique response patterns have been observed in which 
both objective responses and prolonged disease stabilization can be seen after an initial 
increase in tumor size. Immune-related response criteria (irRC) have been developed to 
better characterize these atypical responses (pseudo-progression) (Wolchok et al. 2009); but 
is important to note that atypical responses only account for 3-7% of responses seen in 
Pembrolizumab treated patients (Wolchok et al. 2009; Hodi et al. 2016). Thus, 93-97% of all 
eventual responders are identified within 12 months of commencing PD-1 monotherapy. 
There is no accepted standard therapy for melanoma patients who fail PD-1 therapy.  
The above data suggest that PD-1 R and PD-1 NR have distinct intestinal microbiota; and 
that these differences are present pre-treatment and may account for the differential response 
to PD-1 therapy in PD-1 R compared to PD-1 NR. Based on this data, we propose to 
investigate whether FMT from PD-1 R patients may convert PD-1 NR patients into PD-1 R 
with evidence of anti-melanoma T cell responses. We will also investigate whether response 
to PD-1 is associated with a specific gut microbiota profile. 
4.2.2 Rationale for Dose Selection/Regimen/Modification (Pembrolizumab) 
An open-label Phase I trial (Protocol 001) was conducted to evaluate the safety and clinical 
activity of single agent pembrolizumab.  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 pembrolizumab 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 A, B, C and D of this protocol to test for initial tumor activity.  Recent data from 
other clinical studies within the pembrolizumab program has shown that a lower dose of 

 
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pembrolizumab and a less frequent schedule may be sufficient for target engagement and 
clinical activity. 
 
PK data analysis of pembrolizumab 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 pembrolizumab 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.  Pembrolizumab 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 
pembrolizumab 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 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. 

 
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4.2.3 Rationale for Dose Selection/Regimen/Modification (FMT) 
FMT as defined in this study is derived from PD-1 responders (PD-1 R), hereafter termed 
“PD-1 R FMT” and administered under IND 17063. PD-1 R donor selection is detailed in 
Section 4.2.3.1. 
PD-1 R FMT samples are collected and stored in a -80°C freezer. Each FMT unit is marked 
with an expiration date of 6 months after collection, assuming storage in a -80°C freezer. 
Normal temperature fluctuations in freezer temperature of up to 5°C are acceptable. Upon 
opening, standard protocols for handling biohazardous material will be followed at all times. 
Sterile microbiological technique will be followed when handling material to avoid 
contamination. If treatments need to be destroyed, internal protocols for disposal of human 
stool should be followed. All FMT storage units are cleaned with a sporicidal disinfectant 
prior to freezing. 
FMT samples from suitable donors (PD-1 R FMT) will be obtained and screened. FMT will 
undergo processing to produce PD-1 R FMT infusate (see Appendix: FMT infusate – 
thawing and infusate preparation). Generally 30g of PD-1 R stool will be used to generate 
1 PD-1 R FMT infusate. Upon initial collection and processing, PD-1 R FMT infusate will 
be passed through a 330-micron filter to exclude particulate matter. Given the complexities 
of bacterial composition, the exact quantities of various bacteria may differ from batch to 
batch and an exact “FMT dose” cannot be calculated. 
PD-1 R FMT will be administered colonoscopically. PD-1 R FMT infusate will be thawed 
prior to administration according to prepared guidelines (see Appendix: FMT infusate – 
thawing and infusate preparation). Using universal precautions, PD-1 R FMT infusate will 
be pre-loaded into standard 50cc syringes that have a tip compatible with the endoscope port 
for direct delivery of material through channel. 
4.2.3.1 
Donor Selection 
PD-1 R are defined as patients with advanced unresectable stage IIIB/IIIC or metastatic 
melanoma treated with PD-1 checkpoint inhibitors (either nivolumab or pembrolizumab) 
who have experienced a durable partial or complete response. Median duration of follow up 
should be ≥24 months (for partial responders) or ≥12 months (for complete responders). 
Published data indicates that the likelihood of relapse in melanoma patients following this 
duration of follow up is negligible (Ribas et al. 2016; Robert et al. 2015). 
PD-1 R identified as being suitable donors – designated as “PD-1R - donors” - will be 
separately consented under a donor-specific consent form (see Appendix: Donor ICF). PD-
1 R donor inclusion and exclusion criteria are enumerated below. 
Patients with classical Hodgkin lymphoma (Ansell et al. 2015), gastric cancer (Muro et al. 
2016), hepatocellular carcinoma (Feng et al. 2017), head and neck squamous cell carcinoma 
(Ferris et al. 2016), Merkel cell carcinoma (Kaufman et al. 2016; Nghiem et al. 2016), 
microsatellite instable (MSI-H) tumors (Le et al. 2015), non-small cell lung cancer (NSCLC) 
(Gettinger et al. 2015; Garon et al. 2015), renal cell carcinoma (RCC) (Motzer et al. 2015), 
and urothelial carcinoma (UC) (Balar et al. 2017; Plimack et al. 2017) have all experienced 

 
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durable responses to PD-1/PD-L1 therapy. However, the durability of responses in this 
patient population is unknown. Study investigators will also collect samples from PD-1 R 
patients with these histologies – designated as “PD-1R– at interest population”. 
Inclusion criteria “PD-1R - donors: 
1. Documented history of metastatic melanoma (excluding uveal melanoma) treated with 
pembrolizumab or nivolumab administered singly or in combination. 
2. Currently in remission from melanoma with median duration of remission lasting ≥12 
months (for complete responders) or ≥24 months (for partial responders) measured since 
initiation of therapy. 
3. Willingness to complete donor-specific questionnaire (Appendix 1) to assess exposure to 
infectious agents including but not limited to SARS-CoV-2.  
3.1. Questionnaire (Appendix 1) will include an assessment of whether donor was 
diagnosed with laboratory-confirmed SARS-CoV-2 infection, experienced symptoms 
of COVID-19 (e.g., fever, cough, shortness of breath) not explained adequately by 
another diagnosis, or was exposed to a suspected or confirmed case of COVID-19 or 
SARS-CoV-2 infection. 
4. Willingness to complete donor-specific serologic testing to evaluate infectious agents 
including SARS-CoV-2. 
4.1. To evaluate for the possibility of SARS-CoV-2 exposure and/or infection, all 
candidate donors will undergo nasopharyngeal (NP) and stool testing for SARS-
CoV-2 using a RT-PCR intended for qualitative detection of SARS-CoV-2 nucleic 
acids. RT-PCR assay is composed  of  two  principal  steps:  (1)  extraction  of  
nucleic  from  patient  NP and stool specimens,  (2)  one-step  reverse  transcription  
and  PCR  amplification  with  SARS-CoV-2  specific  primers  and  real-time  
detection  with  2019-nCoV  specific  probes. Test will be performed by Diagnostic 
Solutions Laboratory, located at 5895 Shiloh Rd Ste 101, Alpharetta, GA.  
4.1.1. NP test: DSL COVID-19 NP assay evaluates for the presence of two 
coronavirus genes, the nucleocapsid and the spike gene. A total of three 
primer/probe sets were designed to detect nucleocapsid and spike RNA. A total 
of two primer/probe sets (CDC’s N1 and N3 primers) were designed to detect 
the viral nucleocapsid gene; 1) N1 is SARS-CoV-19 specific, 2) N3 is a 
coronavirus generic primer and  probe  set  that can  also  detect   other 
coronaviruses. The third primer/probe set was designed by Diagnostic Solutions 
Laboratory using  the  published  SARS-CoV-2  reference genome to detect 
SARS-CoV-2  specific  sequence  of  the  spike  gene. Blasting the spike primer 
and probe set indicated 100% homology with SARS-CoV-2 but no homology 
with any other nucleotide sequence present  in  the  database,  including  both  
SARS-CoV (taxonomy ID 694009) and MERS-CoV (taxonomy ID 1335626).  
Each primer and probe sets are tested in individual reactions.In addition, the test 
also detects the human RNase P gene as a sample internal extraction and  

 
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amplification  control  using  primers and  probe  sequences published by CDC. 
In addition, the test utilizes external controls as described below (low titer  
positive  control  and a negative control). 
4.1.1.1. 
A Negative Template Control (NTC) serves as a negative process 
control to monitor for any reagent contamination and  sample  carryover  
that  could  occur  during the extraction and amplification process. The NC 
consists of elution buffer and is run once for every batch of extracted 
specimens. 
4.1.1.2. 
A Positive Control (PC) is used to verify that the assay run is 
performing as intended. The PC is based on genomic RNA from SARS-
Related Coronavirus 2and will be positive for N1, N3, and S. The positive 
control is used once for each batch of extracted specimens. 
4.1.1.3. 
An Internal Control will be performed on every clinical sample as an 
endogenous control. The internal control is the human Ribonuclease P 
(RNase P) gene isolated with the sample RNA of each specimen. It will be 
used to confirm isolation efficiency as well as amplification. 
Interpretation of DSL COVID-19 Assay 
Interpretation 
RNaseP 
SARS-CoV-2 
N1 
SARS-CoV-2 
N3 
SARS-CoV-2 
spike 
Action 
COVID 
Negative 
+ 
- 
- 
- 
Report result 
COVID 
Positive 
+ 
+ 
+ 
+ 
Report result 
+ 
+ 
- 
+ 
+ 
+ 
- 
- 
+ 
- 
- 
+ 
+ 
- 
+ 
+ 
+ 
+ 
+ 
- 
COVID 
Inconclusive 
+ 
- 
+ 
- 
 
Repeat testing 
- 
+/- 
+/- 
+/- 
 
*For samples with a repeat inconclusive result, additional confirmatory testing may be conducted, if it is 
necessary to differentiate between SARS-CoV-2 and SARS-CoV-1 or other Sarbecoviruses currently unknown 
to infect humans, for epidemiological purposes or clinical management. 
 

 
14 
 
 
4.1.2. Stool test: DSL COVID-19 stool assay evaluates for the presence of three 
coronavirus genes: SARS-CoV-2 membrane (M), SARS-CoV-2 spike (S) and 
SARS-CoV-2 nucleocapsid (N). Following adequate detection of RNaseP in a 
test sample, detection of 1 of the viral genes is sufficient for a positive test 
result. Due to the discontinuous transcription of all coronaviruses that results in 
the presence of the capsid gene in a vast majority of the mRNA populations as 
well as in the full-length viral genome, detection of the capsid gene in the 
absence of additional genes is expected. The lower limit of detection (LLoD) for 
each viral gene target was determined by testing serial dilutions of the SARS-
CoV-2 genomic isolate in triplicate and is summarized in the DSL COVID-19 
validation summary. These data indicate that the LLoD for viral spike (S) and 
membrane (M) detection is 104 genomic equivalents/mL while the LLoD for 
viral capsid (N) detection is 103 genomic equivalents/mL. In addition, the 
observation that the mean CT value for each of the determined LLoDs are very 
low (close to 40 cycles), it is likely that any signal obtained below a CT of 38 is 
below the LLoD for the viral target genes and should be disregarded for analytic 
purposes. 
4.2. Determination of "SARS-CoV-2 negative" status will be made on nasopharyngeal, 
blood and stool specimens obtained at two timepoints (every 2 weeks for up to 12 
weeks): 1st sample collected at least 14 days before stool sample donation, and a 2nd 
sample collected at least 14 days after stool sample donation. 
4.3. As the turnaround of the test is 48-72 hours, the stool sample will be released for 
FMT use no sooner than 48-72 hours after 2nd test results and donor is deemed 
"SARS-CoV-2 negative". 
4.4. Candidate donors with discordant stool and NP SARS-CoV-2 results will be 
excluded. 
4.5. Candidate donors excluded based on based on screening and/or testing as described 
in 3.1 and 4.1.1-4.1.2 above will not be allowed to donate stool specimens for use in 
this study at this time. This is subject to subsequent revision should stool-specific 
SARS-CoV-2 testing become available. 
Inclusion criteria “PD-1R– at interest population”: 
1. Documented history of metastatic melanoma (or other malignancies) treated with 
pembrolizumab or nivolumab or other PD-1/PD-L1 inhibitors. 
2. Currently in complete/partial remission with duration of complete/partial remission ≥6 
months since initiation of therapy. 
Exclusion criteria: 
1. History of suspected/confirmed SARS-CoV-2/COVID infection/exposure. 

 
15 
 
1.1. Any instances of suspected/confirmed SARS-CoV-2/COVID infection/exposure will 
result in exclusion of candidate donor from further donations and exclusion from 
clinical use of any FMT manufactured from stool donated by candidate donor 
beginning 4 weeks prior to the suspected/confirmed SARS-CoV-2/COVID 
infection/exposure 
2. History of antibiotic treatment during the 1 month preceding donation. 
3. History of intrinsic gastrointestinal illnesses, including inflammatory bowel disease, 
irritable bowel syndrome, chronic diarrheal disorder (celiac disease), active primary 
gastrointestinal malignancies or major gastrointestinal surgical procedures. 
4. History of symptomatic autoimmune  illness. 
5. History of documented chronic pain syndromes (fibromyalgia, chronic fatigue) or 
neurologic, neurodevelopmental disorders. 
6. History of metabolic syndrome, obesity (BMI of >35), or moderate-to-severe 
malnutrition (as assessed clinically). 
7. Documented pregnancy (serum/urine pregnancy test to be performed on women of 
childbearing potential within 1 week of donation for transplant). 
PD-1 R FMT donors will undergo extensive screening including a detailed questionnaire and 
serological/stool/nasal swab tests (see Appendices: FMT Donor Screening Questionnaire 
and FMT Donor Lab Testing) to eliminate possibility of transmitting infectious agents prior 
to FMT sampling. Only patients deemed suitable by screening questionnaire and 
serological/stool/nasal swab tests are deemed suitable for FMT donation (see Figure below). 

 
16 
 
 
PD-1 R donors will be divided into patients with and patients without liver metastases based 
on initial staging imaging obtained immediately prior to initiation of PD-1 therapy.  
PD-1 R who agree to be donors will donate stool samples which will undergo sample 
processing and administration as detailed in Section 4.2.3. Serial serological testing will be 
performed and repeated (see figure below). 

 
17 
 
 
4.2.4 Rationale for Endpoints 
4.2.4.1 Efficacy Endpoints 
Primary efficacy endpoint: safety/toxicity and objective response rate (ORR) by RECIST 
1.1. 
Secondary efficacy endpoints: include incidence of grade III/IV toxicities, safety of FMT 
administration endoscopically, progression-free survival (PFS), and overall survival (OS). 
4.2.4.2 Biomarker Research 
Biomarker endpoints include: 
Analysis of bacterial taxa occurrence (within-sample and between-sample differences) in 
PD-1 responders, FMT responders and FMT non-responders. 
Evaluation of anti-tumor T-cell responses, DC function/maturity by multi-parameter flow 
cytometry, multiplex immunohistochemistry, analysis of T-cell receptor (TCR) 
clonality/diversity and genetic mutation/expression studies (RNAseq, exome sequencing). 

 
18 
 
5.0 METHODOLOGY 
5.1 
FMT Recipient Entry Criteria 
PD-1 resistant/refractory melanoma (excluding uveal melanoma) as defined as progressive 
disease (PD) at first (or subsequent) radiographic evaluation that demonstrates disease 
progression while receiving PD-1 inhibitor treatment. Other eligibility criteria include 
presence of disease amenable to biopsy and lack of contra-indications to FMT 
administration. 
5.1.1 Subject Inclusion Criteria 
A patient must meet all of the following criteria to be eligible to participate in this study: 
1. Have a histologically or cytologically confirmed diagnosis of unresectable stage III or 
IV melanoma. Patient may not have a diagnosis of uveal melanoma. 
 
2. Have received any number of prior systemic therapies for metastatic disease. Prior 
radiation therapy (any number) and interferon use (any formulation and/or duration) 
in the adjuvant or metastatic disease settings is permitted. Vaccine therapy will be 
counted as systemic therapy.  
 
3. Patient must currently be receiving systemic PD-1 immunotherapy with 
pembrolizumab or nivolumab to be eligible. Patients who have received PD-1 
immunotherapy in the adjuvant setting and then relapsed are eligible.  
 
4. Must be PD-1 inhibitor refractory/resistant – defined as having received at least 2 
doses of pembrolizumab with documented systemic disease progression on staging 
imaging.  
a. PD is defined as increase in tumor burden > 20% relative to nadir (minimum 
recorded tumor burden) by RECIST v1.1. 
b. Once PD is confirmed, initial date of PD documentation will be considered as 
the date of disease progression.  
c. Patients can be enrolled at any time following initiation of PD-1 therapy  
assuming patients have not had (at any time) a record of response to PD-1 
therapy (prior best response of stable disease – acceptable; prior best response 
of complete/partial response – unacceptable). 
d. For patients receiving adjuvant PD-1 inhibitor therapy, initial date of PD 
documentation will be considered as the date of disease progression. 
5. Patients with CNS disease (parenchymal but not leptomeningeal) are eligible if CNS 
metastases are treated and deemed stable (with a repeat CT/MRI imaging study) prior 
to the enrollment date. If radiation is used to treat CNS parenchymal disease, a 2 
week washout period will apply (counted from D1 treatment). 

 
19 
 
a. Stability must be confirmed with a repeat CT/MRI imaging study performed 
as part of the screening evaluation (at least 2 weeks after radiation). 
b. Patients with new CNS metastases identified during screening are ineligible. 
6. Willingness to receive FMT administered endoscopically (colonoscopically) and 
undergo necessary bowel preparation pre-procedure. 
a. Understand infectious risks associated with FMT administration. Although 
FMT infusate has been screened for bacteria, viruses, fungi and parasites there 
is a risk of transmission of known and unknown infectious organisms 
contained in the donor stool. Post-FMT bacteremia (e.g. E. coli), sepsis and 
fatal events may rarely occur. 
b. Understand non-infectious risks associated with FMT administration. 
i. Possible allergy and/or anaphylaxis to antigens in donor stool. 
ii. Theoretical risk of developing disease possibly related to donor gut 
microbiota including but not limited to: obesity, metabolic syndrome, 
cardiovascular 
disease, 
autoimmune 
conditions, 
allergic/atopic 
disorders, 
neurologic 
disorders, 
psychiatric 
conditions 
and 
malignancy. 
c. Understand risks associated with colonoscopy including risk of infection 
transmission, colonic perforation, aspiration pneumonia, and death. 
d. Understand that data regarding the long-term safety risk of FMT are lacking. 
7. Amenable to participate in the correlative studies and should have available tumor 
tissue for tumor biopsies. Acceptable biopsies include surgical biopsy, core biopsy or 
punch/surgical tumor biopsies (of accessible lesions). 
8. Have measurable disease as per RECIST version 1.1. At least 1 of the tumor sites 
must be amenable to biopsy and this may not be the site of disease used to measure 
antitumor response. 
9. Be willing and able to provide written informed consent for the trial. 
10. Be  18 years of age on day of signing informed consent. 
11. Have a performance status of 0 or 1 on the ECOG Performance Scale. 
12. Demonstrate adequate organ function as defined in Table 5.1.1, all screening labs 
should be performed within 14 days of treatment initiation.   
Table 5.1.1-1  Adequate Organ Function Laboratory Values 
System 
Laboratory Value 

 
20 
 
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 
Coagulation 
International 
Normalized 
Ratio (INR) 
or 
Prothrombin Time (PT) 
Activated Partial Thromboplastin Time (aPTT) 
≤1.5 X ULN unless subject is receiving anticoagulant therapy 
as long as PT or PTT is within therapeutic range of intended use of 
anticoagulants 
 
aCreatinine clearance should be calculated per institutional standard. 
 
13. 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.   
14. 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. 
15. 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. 
5.1.2 Subject Exclusion Criteria 
A patient meeting any of the following criteria is not eligible to participate in this study: 
1. Presence of absolute contra-indications to FMT administration 
1.1. Toxic megacolon 
1.2. Severe dietary allergies (e.g. shellfish, nuts, seafood) 
1.3. Inflammatory bowel disease 

 
21 
 
1.4. Anatomic contra-indications to colonoscopy 
2. Patients receiving PD-1 therapy whose disease is responding (as defined by RECIST 
v1.1). 
3. 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 
4 weeks of the first dose of treatment. 
4. Highly symptomatic patients (e.g., declining ECOG performance status; rapidly 
worsening symptoms; rapid progression of disease; progression of tumor at critical 
anatomical sites (e.g., spinal cord compression) requiring urgent alternative medical 
intervention) are not eligible.  
5. Expected to require any other form of systemic or localized antineoplastic therapy while 
on study. 
6. Has a diagnosis of immunodeficiency or is receiving systemic steroid therapy (> 10 mg 
prednisone daily or equivalent) or any other form of immunosuppressive therapy prior to 
trial treatment. Patients receiving systemic steroids at physiologic doses are permitted to 
enroll assuming steroid dose is not above the acceptable threshold (> 10 mg prednisone 
daily or equivalent). 
7. Has a known history of a hematologic malignancy, primary brain tumor or sarcoma, or of 
another primary solid tumor, unless the patient has undergone potentially curative therapy 
with no evidence of that disease for five years.  
 
7.1. Note: The time requirement also does not apply to patients who underwent 
successful definitive resection of basal or squamous cell carcinoma of the skin, 
superficial bladder cancer, in situ cancers including cervical cancer, breast cancer, 
melanoma, or other in situ cancers. 
 
8. Active central nervous system (CNS) metastases and/or leptomeningeal involvement.  
8.1. Note: Patients with treated brain metastases will need repeat CNS  imaging (MRI 
brain or CT head with IV contrast) to document stability. Patients with previously 
treated brain metastases may participate provided they are stable (without evidence 
of progression by MRI/CT brain imaging performed during screening period), have 
no evidence of new or enlarging brain metastases and are off systemic steroids (≤ 10 
mg/day prednisone or equivalent) for at least one week prior to enrollment. 
8.2. Note: Patients with leptomeningeal disease (leptomeningeal enhancement on 
MRI/CT imaging and/or positive CSF cytology) are not eligible to enroll. 
8.3. Note: Patients with no history of CNS disease will not require staging MRI brain 
unless they have symptoms to suggest new brain metastases. 
 
9. Had a severe hypersensitivity reaction to treatment with pembrolizumab or any of its 
excipients. 

 
22 
 
10. Has an active autoimmune disease or a documented history of autoimmune disease or 
syndrome that requires systemic steroids or immunosuppressive agents. Patients with 
vitiligo, type I diabetes, resolved childhood asthma/atopy are exceptions to this rule. 
Patients who require intermittent use of bronchodilators or local steroid injections are not 
excluded from the study. Patients with hypothyroidism stable on hormone replacement 
are not excluded from the study. 
 
11. Has a history of (non-infectious) pneumonitis that was life-threatening and/or required 
invasive support (CTCAE grade 4 or greater) or current pneumonitis. 
 
12. Has serious concomitant illnesses, such as: cardiovascular disease (uncontrolled 
congestive heart failure, uncontrolled hypertension, recent myocardial infarction within 
prior month, and severe cardiac arrhythmia), bleeding disorders, symptomatic 
autoimmune diseases, severe obstructive or restrictive pulmonary diseases, active 
systemic infections, and inflammatory bowel disorders. This includes HIV or AIDS-
related illness, or active HBV and HCV. 
 
13. Has an active infection requiring systemic therapy. 
 
14. Has active COVID-19 infection and/or exposure to SARS-CoV-2 as defined below: 
 
14.1. 
Positive SARS-CoV-2 result on nasopharyngeal and/or stool specimens (by 
RT-PCR test) 
14.2. 
Active COVID-19 infection (per CDC guidelines) 
14.3. 
Exposure to active COVID-19 infected patient (as confirmed using SARS-
CoV-2 RT-PCR test or other approved test) as defined per CDC guidelines. 
 
15. Has active human immunodeficiency virus (HIV) infection (as manifested by presence of 
HIV 1/2 antibodies and/or positive HIV ELISA/Western Blot assays). 
 
16. Has active Hepatitis B or Hepatitis C infection. Patients with a history of Hepatitis B/C 
infection who have received anti-viral therapy and are disease free (Hep B - negative 
HBsAg and HBV DNA; Hep C – negative HCV RNA) may be considered for enrollment 
after discussion with Principal Investigator. 
 
17. Has a known history of active TB (Bacillus Tuberculosis). 
18. Patient has received a live vaccine within 4 weeks prior to the first dose of treatment. 
18.1. 
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. 
19. Has not recovered (i.e., ≤ Grade 1 or at baseline) from adverse events due to agents 
administered more than 4 weeks earlier. Patients with prior adverse events on 
replacement therapy who are asymptomatic or minimally symptomatic are not excluded 
from the study (i.e. hypothyroidism, hypopituitarism, adrenal insufficiency). 

 
23 
 
20. 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.   
21. Has known psychiatric or substance abuse disorders that would interfere with cooperation 
with the requirements of the trial. 
22. Is pregnant or breastfeeding, or expecting to conceive or father children within the 
projected duration of the trial, starting with the pre-screening or screening visit through 
120 days after the last dose of trial treatment. 
5.2 
Trial Treatments 
The treatment to be used in this trial is outlined below in Table 5.2. 
Table 5.2-1 Trial Treatment 
Drug 
Dose/Potency 
Dose 
Frequency 
Route of 
Administration 
Regimen/Treatment 
Period 
Use 
Pembrolizumab 
200 mg 
Q3W 
IV infusion 
Day 1 (+/- 3 days) of each 
3-week cycle for 8 cycles 
(Cycles 1 to 8) 
Standard 
FMT 
Single 
administration 
Once 
Endoscopically 
administered 
Cycle 1 day 1 (+/- 3 days) 
Experimental 
 
5.2.1 Dose Selection/Modification (Pembrolizumab) 
5.2.1.1 Dose Selection 
Pembrolizumab will be dosed at a fixed dose of 200mg every 3 weeks. Rationale for 
selection of doses to be used in this trial is provided in Section 4.0 – Background and 
Rationale.   
5.2.1.2 Dose Modification (Escalation/Titration/Other) 
Adverse events (both non-serious and serious) associated with pembrolizumab 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 must be withheld for 
drug-related toxicities and severe or life-threatening AEs as per Table 7-1 (see Appendix 5: 
Dose Modifications for Pembrolizumab). 
In case toxicity does not resolve to Grade 0-1 within 12 weeks after last infusion, trial 
treatment should be discontinued after consultation with the Principle Investigator. With 
investigator and Sponsor agreement, subjects with a laboratory adverse event still at Grade 2 
after 12 weeks may continue treatment in the trial only if asymptomatic and controlled. For 
information on the management of adverse events, see Section 5.6.1. 

 
24 
 
Subjects who experience a recurrence of the same severe or life-threatening event at the same 
grade or greater with re-challenge of pembrolizumab should be discontinued from trial 
treatment. 
5.2.2 Timing of Dose Administration (Pembrolizumab) 
Trial treatment 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).  Trial treatment may be administered up to 3 days before or after the scheduled Day 1 of 
each cycle due to administrative reasons. Pembrolizumab will be given on study for 4 cycles 
(minimum) and up to 8 cycles in patients who are responding (or receiving clinical benefit as 
assessed by Principle Investigator). In patients who continue to respond (or receive clinical 
benefit), pembrolizumab will be administered by treating investigator(s) until disease 
progression or up to 2 years from FMT administration (35 cycles total). 
All trial treatments will be administered on an outpatient basis. 
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). 
5.2.3 Dose Selection/Modification (FMT) 
Rationale for FMT as defined and used in this trial is provided in Section 4.2.3. – Rationale 
for Dose Selection/Regimen/Modification (FMT). 
5.2.4 Timing of Dose Administration (FMT) 
FMT will be administered on cycle 1, day 1 (+/-3 days). 
5.2.5 Trial Blinding/Masking 
This is an open-label trial; therefore, the Sponsor, investigator and subject will know the 
treatment administered. 
5.3 
Randomization or Treatment Allocation 
Not applicable. 
5.4 
Stratification 
N/A 
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 

 
25 
 
vaccination may be required.  The investigator should discuss any questions regarding this 
with the Principle 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 investigator in keeping with the community standards of 
medical care.  All concomitant medication will be recorded on the case report form (CRF) 
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 included on the CRF. 
All concomitant medications received within 28 days before the first dose of trial treatment 
and 30 days after the last dose of trial treatment should be recorded.  Concomitant 
medications administered after 30 days after the last dose of trial treatment should be 
recorded for SAEs and Events of Clinical Interest (ECI) as defined in Section 7.2. 
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 
• Investigational agents other than PD-1 R FMT 
• Radiation therapy  
o Note:  Radiation therapy to a symptomatic solitary lesion or to the brain may 
be allowed at the investigator’s discretion.   
• 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 Sponsor. 
Subjects who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the trial.  
Subjects may receive other medications that the investigator deems to be medically 
necessary. 
The Exclusion Criteria describes other medications which are prohibited in this trial. 

 
26 
 
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 immune 
related adverse events (irAE) are outlined (see Appendix 5, Table 5-1). 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 
the investigator determines the events to be related to pembrolizumab. 
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 in Appendix 5, Table 5-1). Refer to 
Section 5.2.1 for dose modification. 
Note: Although FMT administration has not previously been associated with irAEs, given 
the novel combination, treating investigator(s) should attempt to delineate whether AEs that 
occur within a reasonable duration of FMT administration could have an underlying immune-
related etiology. If so determined, criteria for managing irAE (see Appendix 5, Table 5-1) 
should be extended to managing these irAEs. Occurrence of these novel irAEs should be 
reported to the Principal Investigator. 
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or 
skin photography as part of evaluation of the event.  
5.6.2 Management of Infusion Reactions  
Pembrolizumab may cause severe or life-threatening infusion reactions, including severe 
hypersensitivity or anaphylaxis. Signs and symptoms usually develop during or shortly after 
drug infusion and generally resolve completely within 24 hours of completion of infusion. 
Dose modification and toxicity management guidelines to treat pembrolizumab-associated 
infusion reactions are provided in Appendix 6 (see Appendix 6). 
5.7 
Diet/Activity/Other Considerations 
5.7.1 Diet 
Subjects should maintain a high fiber diet (daily dietary fiber intake >30 grams) unless 
modifications are required to manage an AE such as diarrhea, nausea or vomiting. To assess 
this, patients will formally be assessed by a dietician at study entry.  To accurately assess 
effect of FMT, enrolled patients are required to maintain a dietary log (see Appendix 3: 
Dietary Intake Questionnaire) to track dietary intake including supplements, probiotics. 
Treating physicians are required to minimize prescribing oral antibiotic(s) unless absolutely 

 
27 
 
required while patients are required to report antibiotic treatment anytime for the duration of 
the study.  
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.);  
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 

 
28 
 
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.  
‡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 Sponsor and to Merck 
without delay and within 24 hours to the Sponsor 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 study 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 Sponsor.   If a male 
subject impregnates his female partner the study personnel at the site must be informed 

 
29 
 
immediately and the pregnancy reported to the Sponsor 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 
Duration of Therapy 
Patients who are responding or deriving clinical benefit (at the determination of the Principal 
Investigator) at the first restaging interval (after Cycle 4 pembrolizumab) will stay on study. 
Patients who continue to respond or derive clinical benefit (at the determination of the 
Principal Investigator) at the second restaging interval (after Cycle 8 pembrolizumab) will 
continue to receive pembrolizumab on study for 2 years (or 35 cycles total), counted from the 
time of FMT initiation. Patients who development a confirmed CR will be allowed to 
discontinue therapy after a minimum of 6 months since confirmation of CR in discussion 
with Principal Investigator. 
▪ Discontinuation of Study Therapy after CR  
Discontinuation of treatment may be considered for subjects who have attained a confirmed 
CR and have treated for at least 24 weeks with pembrolizumab (from time of FMT 
administration) and had at least two treatments with pembrolizumab beyond the date when 
the initial CR was declared.  
5.8.1 2nd FMT Administration 
Patients who initially respond to but subsequently progress will be offered a second FMT 
administration at the time of confirmed progression (RECIST v1.1) at the discretion of the 
Principal Investigator if no cancer treatment was administered since the last dose of 
pembrolizumab, the subject meets the safety parameters listed in the Inclusion/Exclusion 
criteria, and the trial is open. Patients will be required to resign informed consent. 
5.9 
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 Sponsor 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. 
A subject must be discontinued from the trial for any of the following reasons: 
• The subject or legal representative withdraws consent. 
• Confirmed radiographic disease progression 

 
30 
 
• 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 
• Repeated or serious 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. 
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 detailed in Section 7.1.5.5 
• Administrative reasons 
The End of Treatment and Follow-up visit procedures are listed in Section 6 (Protocol Flow 
Chart) and Section 7.1.5 (Visit Requirements).  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 as described in Section 7.2.3.1).  Subjects 
who discontinue for reasons other than PD 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 for overall survival until death, withdrawal of consent, or the end of the study, 
whichever occurs first. 
5.10 
Subject Replacement Strategy 
Patients are deemed evaluable for safety if they were screened and received FMT and at least 
one dose of pembrolizumab.  Patients are deemed evaluable for efficacy if they completed 
screening and received FMT/pembrolizumab and 1st re-staging scan.  Patients who drop out 
of the study for reasons related to disease progression prior to 1st re-staging scan  may be 
replaced. 
5.11 
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 

 
31 
 
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 FMT infusate 
 

Product:  Pembrolizumab 
 
Protocol/Amendment No.:   
 
 
 
 
 
 
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 
(Visit 1) 
1* 2*  
3* 
4* 
To be repeated beyond 4 
cycles 
Disconti
nuation 
Safety 
Follow-upA 
Follow 
Up 
VisitsB 
Survival 
Follow-
UpC 
5* 
6* 
7* 
8+* 
Scheduling Window (Days): 
-28 to -1 
± 
3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
At time 
of 
discontin
uation 
30 
days 
post 
discontinua
tion 
Every 12 
weeks 
Every 
12 
weeks  
Administrative Procedures 
Informed Consent 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion Criteria 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Demographics and Medical History 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Prior and Concomitant Medication 
Review 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Pembrolizumab administration 
 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Post-study anticancer therapy status 
 
 
 
 
 
 
 
 
 
 
+ 
+ 
+ 
Survival Status 
 
 
 
 
 
 
 
 
 
+ 
+ 
+ 
+ 
Administration of Investigational Agents 
FMT administration (colonoscopic) 
 
+ 
 
 
 
 
 
 
 
 
 
 
 
Clinical Procedures/Assessments 
Review Adverse Events 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Full Physical Examination 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Vital Signs and Weight 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
ECOG Performance Status 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Patient self-monitoringD 
 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Screening questionnaire prior to FMT 
administration (see Appendix 1) 
+ 
 
 
 
 
 
 
 
 
 
 
 
 

Product:  Pembrolizumab 
 
Protocol/Amendment No.:   
 
 
 
 
 
 
Trial Period: 
Screening 
Phase 
Treatment Cyclesa 
End 
of 
Treatment Post-Treatment 
Treatment Cycle/Title: 
Study 
Screening 
(Visit 1) 
1* 2*  
3* 
4* 
To be repeated beyond 4 
cycles 
Disconti
nuation 
Safety 
Follow-upA 
Follow 
Up 
VisitsB 
Survival 
Follow-
UpC 
5* 
6* 
7* 
8+* 
Scheduling Window (Days): 
-28 to -1 
± 
3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
± 3 
At time 
of 
discontin
uation 
30 
days 
post 
discontinua
tion 
Every 12 
weeks 
Every 
12 
weeks  
Screening labs prior to FMT 
administration (see Appendix 2) 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Laboratory Procedures/Assessments: analysis performed by LOCAL laboratory 
Hematology and serum chemistryE 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
 
 
 
 
Coagulation studies and urinalysisF 
+ 
 
 
 
 
 
 
 
 
 
 
 
 
Thyroid studiesG 
+ 
+ 
 
+ 
 
+ 
 
+ 
 
 
 
 
 
Efficacy Measurements 
Tumor Imaging H 
+ 
 
 
 
+ 
 
 
 
+ 
 
 
 
 
CNS Imaging (if not previously 
performed) *CNS imaging will be 
incorporated into restaging assessments if 
prior CNS disease is known/stableH 
+* 
 
 
 
+* 
 
 
 
+* 
 
 
 
 
Tumor Biopsies; Archival Tissue Collection; Correlative Studies Blood/Stool 
Tissue Collection (pre-treatment and 
C4; biopsy at progression is optional) 
+ 
 
 
 
+ 
 
 
 
 
 
 
 
 
Correlative studies (blood)I  
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
(q12) 
 
 
+ 
 
Correlative studies (stool)J 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ (q6)  
 
+ 
 
Dietary questionnaire (Appendix 3)K 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
+ 
(q12) 
 
 
 
 
 
 
 

Product:  Pembrolizumab 
 
Protocol/Amendment No.:   
 
 
 
 
 
 
 
Study Calendar Notes: 
A Safety follow up: For all patients (responders and non-responders) at 30 days (+/- 10 days) following cycle 8 pembrolizumab on study. 
B Follow up visits: For all responder patients only every 12 weeks (+/- 14 days) following cycle 4 pembrolizumab on study. Will include correlative stool sampling. 
C Survival follow up visits: For all patients (responders and non-responders) every 12 weeks (+/- 14 days) following cycle 8 pembrolizumab on study 
D Patients self-monitoring: while on study, patients will be provided a memory card and digital thermometer to facilitate the standardized collection of AEs particularly AEs 
commonly associated with FMT including fever, diarrhea, vomiting, abdominal discomfort, constipation, and flatulence. 
E CBC w/diff, Comprehensive Serum Chemistry Panel (allowed within 28 days) 
F PT/INR and aPTT; urinalysis; Pregnancy Test; Stool and Blood Screening (allowed within 28 days) 
G FT4 and TSH (allowed within 28 days)  To be repeated at every odd cycle. 
HRestaging imaging will be obtained after 4 cycles of therapy (12 weeks) comprising of CT or PET/CT imaging. Scans will be repeated every 12 weeks.  If CNS lesions were 
present at staging, restaging imaging should include MRI brain or CT head with contrast. If CNS lesions were not present at staging scans, this need not be repeated.  
ICorrelative laboratory studies will be performed at Screening, during each cycle (Cycles 1-8) and q12 weekly afterwards till EOT. 
JCorrelative stool studies will be performed at Screening, weekly (Cycles 1-8), and q6 weekly afterwards till EOT. 
KFollowing FMT, dietary history questionnaire (Appendix 3) will be monitored q12 weekly afterwards till EOT. 
 
 
 

 
35 
 
 
7.0 TRIAL PROCEDURES 
7.1 
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 
investigator. 
Furthermore, additional evaluations/testing may be deemed necessary by the Principal 
Investigator  and/or Sponsor and/or Merck 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. 
7.1.1 Administrative Procedures 
7.1.1.1 Informed Consent 
The Investigator must obtain documented consent from each potential subject prior to 
participating in a clinical trial. 
7.1.1.1.1  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  approval  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  requirements, applicable laws and regulations and 
Sponsor requirements. 

 
36 
 
 
7.1.1.2 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.  
7.1.1.3 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.   
7.1.1.4 Prior and Concomitant Medications Review 
7.1.1.4.1 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.  
7.1.1.4.2 Concomitant Medications 
The investigator or qualified designee will record medication, if any, taken by the subject 
during the trial.  This will include the intake of any oral antibiotic(s) for any indication. All 
medications related to reportable SAEs and ECIs should be recorded as defined in Section 
7.2. 
7.1.1.5 Disease Details and Treatments 
7.1.1.5.1 Disease Details 
The investigator or qualified designee will obtain prior and current details regarding disease 
status.  
7.1.1.5.2 Prior Treatment Details 
The investigator or qualified designee will review all prior cancer treatments including 
systemic treatments, radiation and surgeries. 
7.1.1.5.3 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 

 
37 
 
the first dose of the new therapy.  Once new anti-cancer therapy has been initiated the subject 
will move into survival follow-up.  
7.1.1.6 Assignment of Screening Number 
Not applicable. 
7.1.1.7 Assignment of Randomization Number 
Not applicable. 
7.1.1.8 Trial Compliance (Medication/Diet/Activity/Other) 
Antibiotic use and/or intake of probiotics is discouraged. Use will be recorded. 
7.1.2 Clinical Procedures/Assessments 
7.1.2.1 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 5.0 (see Section 11.2).  Toxicities 
will be characterized in terms regarding seriousness, causality, toxicity grading, and action 
taken with regard to trial treatment.  
Please refer to section 7.2 for detailed information regarding the assessment and recording of 
AEs.   
7.1.2.2 Full Physical Exam 
The investigator or qualified designee will perform a complete physical exam during the 
screening period.  Clinically significant abnormal findings should be recorded as medical 
history.  A full physical exam should be performed during screening,  
7.1.2.3 Directed Physical Exam 
For cycles that do not require a full physical exam per the Trial Flow Chart, the investigator 
or qualified designee will perform a full physical exam as clinically indicated prior to trial 
treatment administration.   
7.1.2.4 Vital Signs 
Vital signs will be taken 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. 

 
38 
 
7.1.2.5 Eastern Cooperative Oncology Group (ECOG) Performance Scale 
The investigator or qualified designee will assess ECOG status (see Section 11.1) at 
screening, prior to the administration of each dose of trial treatment and discontinuation of 
trial treatment as specified in the Trial Flow Chart.   
7.1.2.6 Tumor Imaging and Assessment of Disease 
On this study, response will be first assessed after FMT administration and 4 cycles of 
pembrolizumab (cycle 4; week 21-22) and after cycle 8 (week 33-34). Assessment of 
antitumor response will be based on RECIST 1.1. Because tumor pseudo-progression is a 
well-recognized consequence of PD-1 based immunotherapies and use of FMT as a 
therapeutic agent in cancer is highly novel, confirmation of PD requires continued 
presence of PD on 2 consecutive assessments of response done at least 4 weeks apart during 
which pembrolizumab will be continued. 
Computed tomography (CT) of chest, abdomen, pelvis and CT/MRI brain scans (if clinically 
indicated) will be performed at screening and after cycle 4 (Day 1 ± 7 days). Following cycle 
4, reimaging will occur every 4 cycles (12 weeks) starting with cycle 8 (cycles 12, 16, 20 
etc.). 
PD documented at any evaluation time point will be followed with a repeated radiographic 
evaluation at the Principal Investigator’s discretion to rule out tumor pseudo-progression. 
7.1.2.7 Tumor Tissue Collection and Correlative Studies Blood/Stool Sampling 
Tumor biopsies will be performed at screening (Day -21 to -1) and at cycle 4 (Day 1 ± 7 
days). Surgical, core, or punch biopsies are permitted. Post-progression tumor biopsy is 
recommended but not required. 
Correlative blood samples will be obtained as directed in Table 6.1 (Screening, cycles 1-8 
and every 12 weeks starting after cycle 9 (Day 1 ± 3 days). 
Correlative stool samples along with dietary history questionnaire will be obtained as 
directed in Table 6.1 (Screening, weekly cycles 1-8 and every 6 weeks starting after cycle 9 
(Day 1 ± 3 days). 
7.1.3 Laboratory Procedures/Assessments 
Details regarding specific laboratory procedures/assessments to be performed in this trial are 
provided below. 
Laboratory tests for hematology, chemistry, urinalysis, and others are specified in Table 
7.1.3.  
 
Prior to receiving FMT, specific laboratory tests to screen for infectious etiologies will be 
performed as listed in Appendix 2. Results of this must be available prior to FMT 
administration.

 
39 
 
Table 7.1.3-1  Laboratory Tests 
7.1.3.1 Pharmacokinetic/Pharmacodynamic Evaluations 
7.1.3.1.1 Blood Collection for Serum Pembrolizumab 
Not applicable. No pembrolizumab pharmacokinetic sampling will be performed. 
7.1.3.1.2 Blood Collection for Anti-Pembrolizumab Antibodies  
Not applicable. No pembrolizumab pharmacokinetic sampling will be performed. 
7.1.4 Other Procedures 
7.1.4.1 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 outlined in Section 7.2 - Assessing and 
Recording Adverse Events.   
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 
specified in Section 7.1.5.5.  After discontinuing treatment following assessment of CR, 
these subjects should return to the site for a Safety Follow-up Visit (described in Section 
Hematology 
Chemistry 
Urinalysis 
Other 
Hematocrit 
Albumin 
Blood 
Serum β-human chorionic gonadot
Hemoglobin 
Alkaline phosphatase 
Glucose 
(β-hCG)† 
Platelet count 
Alanine aminotransferase (ALT) 
Protein 
PT (INR) 
WBC (total and differential) 
Aspartate aminotransferase (AST) 
Specific gravity  
aPTT 
Red Blood Cell Count 
Lactate dehydrogenase (LDH) 
Microscopic exam (If abnormal)  
Free tyroxine (T4) 
Absolute Neutrophil Count 
Carbon Dioxide ‡ 
results are noted 
Thyroid stimulating hormone (TSH
Absolute Lymphocyte Count 
Creatinine 
 
†Serum pregnancy test 
 
Uric Acid 
 
 
 
Calcium 
 
 
 
Chloride 
 
Blood for correlative studies (at sp
 
Glucose 
 
  
 
Phosphorus 
 
  
 
Potassium   
 
  
 
Sodium 
 
  
 
Magnesium 
 
  
 
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 considered standard of care in your region. 

 
40 
 
7.1.5.4.1) and then proceed to the Follow-Up Period of the study (described in Section 
7.1.5.6). 
7.1.4.2 Blinding/Unblinding 
Not applicable. This is an open-label study, neither the patients nor the treating physicians 
are blinded. 
7.1.5 Visit Requirements 
Visit requirements are outlined in Section 6.0 - Trial Flow Chart.   Specific procedure-related 
details are provided above in Section 7.1 - Trial Procedures. 
7.1.5.1 Screening: Donor 
Donor screening will commence upon signing ICF. Donor screening will consist of stool 
sampling and FMT Recipient (or Donor) Laboratory Testing (as delineated in Appendix 
2). Once collected, donor sample will be treated as outlined in Section 4.2.3.1. 
7.1.5.2 Screening: Recipient 
Screening will commence once screen-eligible patients are found to have PD on first 
restaging scan following 2 cycles of pembrolizumab (or nivolumab). Screening procedures 
are outlined in Section 6.1: Study Flow Chart. Screening procedures include: administrative 
procedures (particularly informed consent wherein patients are only considered enrolled 
after protocol-specific informed consent is signed), clinical assessments and laboratory 
assessments (particularly Appendix 1: FMT Recipient (or Donor) Screening 
Questionnaire and Appendix 2: FMT Recipient (or Donor) Laboratory Testing). There 
is a 4-week (day -28 to day -1) window during which screening will take place. 
7.1.5.3 Treatment Period 
Treatment period will commence once eligible patients have signed informed consent and 
have completed all administrative procedures including clinical assessments and laboratory 
assessments as outlined above and have been deemed eligible by Principal Investigator. 
Treatment period will commence with colonoscopic administration of FMT by 
gastroenterologists. Following FMT, pembrolizumab (cycle 1) will be administered. There is 
a 3-day window (+/- 3 days) for administration of pembrolizumab. Prior to restaging, 3 
further cycles will be administered. Schedule of activities during each treatment visit will be 
as outlined in Section 6.1: Study Flow Chart. 
Patients will be restaged after 4 cycles of pembrolizumab. Patients with stable or responding 
disease will continue to receive pembrolizumab for an additional 4 cycles. Patients with 
stable or responding disease will continue to be followed by study team until completion of 
cycle 8 pembrolizumab and 2nd restaging study. Pembrolizumab will be administered for up 
to 24 months, progression or response (as outlined in Section 5.8.). Patients who have an 
initial response but develop subsequent PD, a 2nd administration of FMT (same or different 

 
41 
 
donor) will be considered at the discretion of the investigator and sponsor if the study 
remains open (as outlined in section 7.1.5.4.). 
7.1.5.4 Post-Treatment Visits 
End of treatment (EOT) is defined as the visit where the decision is made to discontinue the 
participant from treatment. Evaluations will be performed prior to study discharge, or for 
participants who are prematurely discontinued. or participants who complete all scheduled 
cycles of therapy, the EOT visit will be the same as the last scheduled and completed on-
treatment visit. 
For participants who complete all scheduled cycles of therapy, the EOT visit will be the same 
as the last scheduled and completed on-treatment visit (eg, Cycle 9 Day 1) and the start of the 
safety follow-up period. For participants that do not complete all scheduled cycles of therapy, 
the EOT visit will be the most recent on-treatment visit (with all available safety and 
response data), does not need to be repeated and will be considered the start of the safety 
follow-up period. 
7.1.5.4.1  Safety Follow-Up Visit 
The mandatory Safety Follow-Up Visit should be conducted approximately 30 days (+/- 10 
days) after the last dose of trial treatment or before the initiation of a new anti-cancer 
treatment, whichever comes first.  All AEs that occur prior to the Safety Follow-Up Visit 
should be recorded.  Subjects with an AE of Grade > 1 will be followed until the resolution 
of the AE to Grade 0-1 (or baseline) or until the beginning of a new anti-neoplastic therapy, 
whichever occurs first.  SAEs that occur within 90 days of the end of treatment or before 
initiation of a new anti-cancer treatment should also be followed and recorded.  Subjects who 
are eligible for retreatment with pembrolizumab (as described in Section 7.1.5.5) may have 
up to two safety follow-up visits, one after the Treatment Period and one after the Second 
Course Phase. 
7.1.5.5 Re-Treatment Following Initial Response  
Following initial FMT with cycle 1 pembrolizumab, all patients will continue to receive 
further cycles of pembrolizumab as outlined in Section 5.8 and undergo periodic tumor 
assessment(s) as outlined in Section 7.1.2.6. 
Re-treatment with FMT in patients who initially respond (RECIST v1.1-defined response) 
may be allowed in selected participants with disease progression during the safety, response 
or survival follow-up period. Eligibility will be dependent upon participants having 
confirmed disease progression and will be considered on a case by case basis following 
discussion with Principal Investigator. 
Participants who meeting criteria for retreatment will be required to reconsent to study. 
Patients will be treated with a second course of FMT along with pembrolizumab. No more 
than 2 (two) FMT treatments will be permitted. Participants entering retreatment will follow 

 
42 
 
the same treatment schedule as outlined in Section 6.1. Biopsy and correlative analyses 
requirements will follow same schedule as well. 
7.1.5.6 Follow-up Visits 
Subjects who discontinue trial treatment for a reason other than disease progression will 
move into the Follow-Up Phase and be treated per standard-of-care. Patients should be 
assessed every 12 weeks by radiologic imaging to monitor disease status.  After 1 year, the 
imaging time point will occur every 12 weeks (± 7 days). 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 as detailed in Section 7.1.5.5. Information regarding post-study anti-
neoplastic treatment will be collected if new treatment is initiated. 
7.1.5.6.1 Survival Follow-up 
Once a subject experiences confirmed disease progression or starts a new anti-cancer 
therapy, the subject moves into the survival follow-up phase and should be followed every 12 
weeks to assess for survival status until death, withdrawal of consent, or the end of the study, 
whichever occurs first.  
7.1.5.7 Second Course Phase  
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: 
1. 
Either  
a. Stopped initial treatment with pembrolizumab after attaining an investigator-
determined confirmed CR according to RECIST 1.1, and 
i. 
Was treated for at least 24 weeks with pembrolizumab before 
discontinuing therapy 
ii. 
Received at least two treatments with pembrolizumab beyond the date 
when the initial CR was declared 
 
 
OR 
b. Had SD, PR or CR and stopped pembrolizumab treatment after 24 months for 
reasons other than disease progression or intolerability. 
AND 
2. 
Experienced an investigator-determined confirmed radiographic disease 
progression after stopping their initial treatment with pembrolizumab 

 
43 
 
3. 
Did not receive any anti-cancer treatment since the last dose of 
pembrolizumab 
4. 
Has a performance status of 0 or 1 on the ECOG Performance Scale 
5. 
Demonstrates adequate organ function as detailed in Section 5.1.2 
6. 
Female subject of childbearing potential should have a negative serum or 
urine pregnancy test within 72 hours prior to receiving retreatment with study 
medication.   
7. 
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.  
8. 
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.   
9. 
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 retreated at the same dose and dose interval as when 
they last received pembrolizumab.  Treatment will be administered for up to one additional 
year. 
Visit requirements are outlined in Section 6.0 – Trial Flow Chart. 
7.2 
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 
frequency and/or intensity) of a preexisting condition that is temporally associated with the 
use pembrolizumab and/or FMT 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. 

 
44 
 
Adverse events may occur any time during the course of the clinical trial.  Progression of the 
cancer under study is not considered an adverse event. 
All adverse events that occur after the consent form is signed but before treatment initiation 
must be reported by the investigator if they cause the subject to be excluded from the trial, or 
are the result of a protocol-specified intervention, including but not limited to washout or 
discontinuation of usual therapy, diet, placebo treatment or a procedure. 
From the time of treatment initiation through 30 days following cessation of treatment, all 
adverse events must be reported by the investigator. Such events will be recorded at each 
examination on the Adverse Event case report forms/worksheets.  The reporting timeframe 
for adverse events meeting any serious criteria is described in section 7.2.3.1. The 
investigator will make every attempt to follow all subjects with non-serious adverse events 
for outcome. 
Adverse events will not be collected for subjects during the screening period as long as that 
subject has not undergone any protocol-specified procedure or intervention.  If the subject 
requires a blood draw, fresh tumor biopsy etc., the subject is first required to provide consent 
to the main study and AEs will be captured according to guidelines for standard AE 
reporting. 
7.2.1 Definition of an Overdose for This Protocol and Reporting of Overdose to the 
Sponsor and to Merck 
For purposes of this study, reporting of adverse events will commence after administration of 
study agents (day +1 and onwards). Adverse events occurring prior to this including those 
during pre-screening period, screening period and during prior pembrolizumab (or 
nivolumab) administration will be captured as part of the medical record but will not be 
submitted. 
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); while an overdose of FMT will be defined as any 
dose exceeding 3 administrations at a given time (dose ≥3 times the indicated dose). No 
specific information is available on the treatment of overdose of pembrolizumab. No specific 
information is available on the treatment of overdose of FMT. 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. 
If an adverse event(s) is associated with (“results from”) pembrolizumab and/or FMT, the 
adverse event(s) is reported as a serious adverse event, even if no other seriousness criteria 
are met. 
If a dose of pembrolizumab and/or FMT 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.” 

 
45 
 
All reports of overdose with and without an adverse event must be reported within 24 hours 
to the Sponsor and within 2 working days hours to Merck Global Safety. (Attn: Worldwide 
Product Safety; FAX 215-993-1220). 
7.2.2 Reporting of Pregnancy and Lactation to the Sponsor 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) that occurs during the trial. 
Pregnancies and lactations that occur after the consent form is signed but before treatment 
allocation/randomization must be reported by the investigator if they cause the subject to be 
excluded from the trial, or are the result of a protocol-specified intervention, including but 
not limited to washout or discontinuation of usual therapy, diet, placebo treatment or a 
procedure.   
Pregnancies and lactations that occur from the time of treatment allocation/randomization 
through 120 days following cessation of Sponsor’s product, or 30 days following cessation 
of treatment if the subject initiates new anticancer therapy, whichever is earlier, must be 
reported by the investigator.  All reported pregnancies 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 to the Sponsor and within 2 working days to 
Merck Global Safety. (Attn: Worldwide Product Safety; FAX 215-993-1220) 
7.2.3 Immediate Reporting of Adverse Events to the Sponsor and to Merck 
7.2.3.1 Serious Adverse Events 
An SAE is any AE that fulfills one of the criteria outlined in Table 6. 
Examples of such “important medical events” include allergic bronchospasm requiring 
intensive treatment in an emergency room or at home, blood dyscrasias or convulsions that 
do not result in inpatient hospitalization, or the development of drug dependency or drug 
abuse.  
Medical and scientific judgment should be exercised in deciding whether expedited reporting 
is appropriate in other situations, such as with important medical events described above.  
Events that meet SAE criteria must be recorded and reported regardless of expectedness or 
assessed association with study drug.  
Note: Planned hospital admissions or surgical procedures for elective procedures or for an 
illness or disease that existed before the signing of the ICF or before the subject was enrolled 
in the study will not be captured as SAEs. If planned admissions or procedures occur at a 

 
46 
 
time other than what was planned (i.e., due to an exacerbation in the preexisting illness or 
disease), they should be reported as SAEs. 
For the time period beginning when study drugs (FMT and pembrolizumab combination on 
day +1) are administered, 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 (reference 
Section 7.2.3.3 for additional details) that occurs to any subject must be reported within 24 
hours to the Principal Investigator and within 2 working days to Merck Global Safety if it 
causes the subject to be excluded from the trial, or is the result of a protocol-specified 
intervention, including but not limited to washout or discontinuation of usual therapy, diet, 
placebo treatment or a procedure. 
For the time period beginning study drugs (FMT and pembrolizumab combination on day 
+1) are administered through 90 days following cessation of treatment, or 30 days following 
cessation of treatment if the subject initiates new anticancer therapy, whichever is earlier, 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 (reference Section 7.2.3.3 for 
additional details), whether or not related to the pembrolizumab and/or FMT, must be 
reported within 24 hours to the Principal Investigator and within 2 working days to Merck 
Global Safety. 
Additionally, any serious adverse event, considered by an investigator to be related to 
pembrolizumab and/or FMT that is brought to the attention of the investigator at any time 
following C1D1 through the end of the specified safety follow-up period specified in the 
paragraph above, or at any time outside of the time period specified in the previous paragraph 
also must be reported immediately to the Principal Investigator and to Merck Global Safety. 
All subjects with serious adverse events must be followed up for outcome. 
The causal relationship to study drugs is determined by a physician and should be used to 
assess all adverse events (AE). The causal relationship can be one of the following: 
• Unrelated: 
o Exposure to investigational agents (FMT and/or pembrolizumab) has not 
occurred; or 
o Administration of investigational agents (FMT and/or pembrolizumab) and 
occurrence of AE are not reasonably related in time; or 
o AE is considered likely to be related to an etiology other than the use of the 
investigational agents (FMT and/or pembrolizumab); and there are no facts or 
arguments to suggest a causal relationship to the investigational agents (FMT 
and/or pembrolizumab). 
• Possibly related:  
o Administration of the investigational agents (FMT and/or pembrolizumab) are 
reasonably related in time; and  

 
47 
 
o AE could not be explained equally well by factors or causes other than 
exposure to investigational agents (FMT and/or pembrolizumab). 
• Probably related: 
o Administration of investigational agents (FMT and/or pembrolizumab) and 
occurrence of AE are reasonably related in time; and 
o AE is more likely explained by exposure to the investigational agents (FMT 
and/or pembrolizumab) than by other factors or causes. 
Every effort should be made to discern whether any reported AE/SAE are related to either 
pembrolizumab or FMT. If it is deemed equally likely for AE/SAE to be related to both, that 
should be reflected as well. 
SAE reports and any other relevant safety information are to be forwarded to the Merck 
Global Safety facsimile number:  +1-215-993-1220 
A copy of all 15 Day Reports and Annual Progress Reports is submitted as required by FDA, 
European Union (EU), Pharmaceutical and Medical Devices agency (PMDA) or other local 
regulators. Investigators will cross reference this submission according to local regulations to 
the Merck Investigational Compound Number (IND, CSA, etc.) at the time of submission.  
Additionally investigators will submit a copy of these reports to Merck & Co., Inc. (Attn: 
Worldwide Product Safety; FAX 215-993-1220) at the time of submission to FDA. 
7.2.3.2 Events of Clinical Interest 
Selected non-serious and serious adverse events are also known as Events of Clinical Interest 
(ECI) and must be reported within 24 hours to the Sponsor and within 2 working days to 
Merck Global Safety. (Attn: Worldwide Product Safety; FAX 215-993-1220). 
For the time period beginning when the consent form is signed until treatment 
allocation/randomization, any ECI, or follow up to an ECI, that occurs to any subject must be 
reported within 24 hours to the Sponsor and within 2 working days to Merck Global Safety if 
it causes the subject to be excluded from the trial, or is the result of a protocol-specified 
intervention, including but not limited to washout or discontinuation of usual therapy, diet, 
placebo treatment or a procedure. 
For the time period beginning at treatment allocation/randomization through 90 days 
following cessation of treatment, or 30 days following cessation of treatment if the subject 
initiates new anticancer therapy, whichever is earlier, any ECI, or follow up to an ECI, 
whether or not related to pembrolizumab, must be reported within 24 hours to the Sponsor 
and within 24 hours to Merck Global Safety. 
Events of clinical interest for this trial include: 
1. Any use of oral and/or intravenous antibiotics for any duration/indication must be reported 
within 24 hours to the Principal Investigator. Reporting should include the name, dose and 
duration of antibiotic prescribed and the indication(s) it was prescribed for. 

 
48 
 
 
2. Any use of oral and/or intravenous steroids for any duration/indication must be reported 
within 24 hours to the Principal Investigator. Reporting should include the name, dose and 
duration of steroid prescribed and the indication(s) it was prescribed for. 
 
3. An overdose of pembrolizumab and/or FMT, as defined in Section 7.2.1 - Definition of an 
Overdose for This Protocol and Reporting of Overdose to the Principlal Investigator, that is 
not associated with clinical symptoms or abnormal laboratory results. 
 
4. 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.  
7.2.3.3 Protocol-Specific Exceptions to Serious Adverse Event Reporting  
Suspected/actual events as outlined in this section will not be reported to Merck as described 
in Section 7.2.3.- Immediate Reporting of Adverse Events to the Sponsor and to Merck, 
unless there is evidence suggesting a causal relationship between the drug and the event. Any 
such event will be submitted to the Principal Investigator within 24 hours and to Merck 
Global Safety within 2 working days either by electronic or paper media. 
Specifically, the suspected/actual events covered in this exception include any event that is 
disease progression of the cancer under study. 
The Principal Investigator will monitor unblinded aggregated efficacy endpoint events and 
safety data to ensure the safety of the subjects in the trial. Any suspected endpoint which 
upon review is not progression of the cancer under study will be forwarded to Merck Global 
Safety as a SAE within 2 working days of determination that the event is not progression of 
the cancer under study 
Hospitalization related to convenience (e.g.transportation issues etc.) will not be considered a 
SAE. 
 
7.2.4 Evaluating Adverse Events 
An investigator who is a qualified physician will evaluate all adverse events according to the 
NCI Common Terminology for Adverse Events (CTCAE), version 5.0. 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 and 
attribution to pembrolizumab and/or FMT. 

 
49 
 
Table 7.2.4-1  Evaluating Adverse Events 
An investigator who is a qualified physician or qualified designee, will evaluate all adverse events as to: 
V5.0 
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 pembrolizumab and/or FMT 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 pembrolizumab 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 Sponsor within 24 hours and to Merck 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 to the Sponsor and to 
Merck within 2 working days.. 
 
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 

 
50 
 
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 pembrolizumab and/or FMT to be discontinued? 
Relationship to 
pembrolizumab  
Did pembrolizumab and/or FMT cause the adverse event? The determination of the likelihood that pembrolizumab and/or FMT 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 pembrolizumab and/or FMT and the AE; the greater the correlation with the 
components and their respective elements (in number and/or intensity), the more likely pembrolizumab and/or FMT caused the adverse event (AE): 
 
Exposure 
Is there evidence that the subject was actually exposed to pembrolizumab and/or FMT 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 pembrolizumab and/or FMT?  
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 
 

 
51 
 
Relationship 
The following components are to be used to assess the relationship between the test drug and the AE: (continued) 
to 
pembrolizumab 
and/or FMT 
(continued)  
Dechallenge 
Was pembrolizumab 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 
the Sponsor’s product; or (3) the trial is a single-dose drug trial); or (4) Sponsor’s product(s) is/are only used one time.) 
 
Rechallenge 
Was the subject re-exposed to pembrolizumab 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) Sponsor’s product(s) is/are used only one time). 
NOTE: IF A RECHALLENGE IS PLANNED FOR AN ADVERSE EVENT WHICH WAS SERIOUS AND WHICH MAY HAVE BEEN 
CAUSED BY pembrolizumab , OR IF REEXPOSURE TO pembrolizumab POSES ADDITIONAL POTENTIAL SIGNIFICANT RISK TO THE 
SUBJECT, THEN THE RECHALLENGE MUST BE APPROVED IN ADVANCE BY THE SPONSOR 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 pembrolizumab or drug class pharmacology or 
toxicology? 
The assessment of relationship will be reported on the case report forms /worksheets by an investigator who is a qualified physician 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 pembrolizumab and/or FMT 
relationship). 
Yes, 
there 
is 
a 
reasonable 
possibility 
of 
pembrolizumab 
and/or FMT relationship. 
There is evidence of exposure to pembrolizumab and/or FMT.  The temporal sequence of the AE onset relative to the administration of 
pembrolizumab is reasonable.  The AE is more likely explained by pembrolizumab than by another cause. 
No, there is not a reasonable 
possibility 
of 
pembrolizumab 
and/or FMT relationship 
Subject did not receive the pembrolizumab and/or FMT OR temporal sequence of the AE onset relative to administration of pembrolizumab is not 
reasonable OR the AE is more likely explained by another cause than the pembrolizumab .  (Also entered for a subject with overdose without an 

 
52 
 
associated AE.) 

 
53 
 
 
 
7.2.5 Sponsor Responsibility for Reporting Adverse Events 
All Adverse Events will be reported to regulatory authorities, IRB/IECs and investigators in 
accordance with all applicable global laws and regulations.  
8.0 STATISTICAL ANALYSIS PLAN 
8.1. 
Overview of the Study 
This study is designed to assess the objective response rate (ORR) and toxicity of the 
addition of FMT to PD-1/PD-L1 treated patients. The patients will be evaluated for response 
and toxicity using the Simon’s two-stage phase II design. 
 
8.2. 
Sample Size 
13 patients will be accrued in the first stage. If the study continues to the second stage, an 
additional 7 patients will be accrued. The detailed decision rule and sample size justification 
are in the following Section 8.5.1. 
8.3. 
Dose Limiting Toxicity (DLT) Definition and Monitoring 
Dose limiting toxicity (DLT) will be defined based on incidence of AEs 
considered possibly related to pembrolizumab and/or FMT that occur any time from the 
initial dose of study treatment of FMT in combination with pembrolizumab, with severity 
graded according to the NCI Common Terminology Criteria for Adverse Events (CTCAE), 
Version 5.0. Any occurrence of CTCAE grade 3 or greater adverse event in four weeks 
following the administration of the FMT will be considered a DLT. 
DLT will be monitored during DLT monitoring period, latter defined as 4-week period 
following administration of FMT/pembrolizumab. During DLT monitoring period, no further 
patient enrollment will occur. DLTs will be monitored for the first 3 patients in each cohort. 
During the DLT monitoring period, only 1 patient will be enrolled per month. 
Given that this is a novel combination study, in the event of AE, treating investigator(s) will 
make every effort to attribute AE to either pembrolizumab or FMT. In the event that AE 
attribution is “possibly” related to both pembrolizumab or FMT, this will be reflected in the 
AE attribution form. 
8.4. 
Stopping Criteria 
Occurrence of any death occurring within 30 days of receiving the investigational agent that 
is considered at least possibly related to the agent will be treated as a study stopping 
criterion. 

 
54 
 
During this period of time, the study investigators and independent DSMB will evaluate 
death to determine causality (relationship to either pembrolizumab or FMT or both). Autopsy 
will be encouraged. 
Study will not recur till after 30 day period has passed. Study will only resume if study 
investigators and independent DSMB collectively determine that death was unlikely related 
to investigational agents (FMT and/or pembrolizumab). 
8.5. 
Analysis Plan 
8.5.1. Decision Rule and Sample Size Justification 
8.5.1.1. 
Patient Evaluability and Definition of Objective Response 
All patients meeting the eligibility criteria who have signed a consent form and begun 
pembrolizumab and/or FMT will be considered evaluable for estimation of the response 
probability.  For evaluable patients, objective response will be assessed by RECIST 1.1. 
8.5.1.2. 
Decision Rule:   
Based on prior data on response rates in this patient population, the largest ORR where the 
proposed treatment would be considered unpromising in this population is 5%.  The smallest 
success proportion that would warrant further subsequent studies with the proposed treatment 
in this patient population is 25%.  The following design is based on Simon's minimax two-
stage study design and uses  to test the null hypothesis that the true success rate in each 
patient population is at most 5%.  
In Stage 1: Enter 13 evaluable patients and follow for at least 12 
weeks. If 0 patients have a confirmed response in this 
timeframe, we will consider this early evidence that this 
treatment regimen is not sufficiently active in this patient 
population. If 1 or more patients have a response, then accrual 
will continue in the second stage of this trial. 
In Stage 2: Enter an additional 7 evaluable patients to the trial. If 2 or 
fewer successes are observed in the 20 evaluable patients, we 
will consider this sufficient evidence that this treatment is not 
sufficiently effective in this patient population. If 3 or more 
successes are observed in the first 20 evaluable patients, then 
this treatment will be considered promising in this patient 
population and will be evaluated further in future studies.  
Power and Significance Level: Assuming that the number of successes is 
binomially distributed, this decision rule has a significance level of 0.07; 
i.e., there is a 7% chance of finding the drug to be effective when it truly 
is not. This decision rule has 90% power to detect an effective treatment 
given that the true response rate is at least 25% using this treatment.  
 

 
55 
 
8.5.2. Analysis of the Primary Endpoint  
The ORR in each cohort will be estimated by the number of objective responses divided by 
the total number of evaluable patients. Exact 95% confidence intervals for the true ORR will 
be calculated.  
 
Toxicity: As per NCI CTCAE Version 5.0, the term toxicity is defined as adverse events that 
are classified as either unrelated, possibly or probably related to study treatment.  The 
maximum grade for each type of toxicity will be recorded for each patient, and frequency 
tables will be reviewed to determine toxicity patterns.  Although the addition of FMT to PD-
1/PD-L1 treated patients is novel, as FMT is being administered only once, no true “dose 
escalation” design is required. However, to accurately capture toxicities for this novel 
combination, we will be monitoring toxicities closely. The detailed data and safety 
monitoring plan is in Section 10.5. 
8.5.3. Analysis of Secondary and Exploratory Endpoints 
The secondary objective is to investigate how FMT administration affects composition and 
function of T-cells and innate/adaptive immune system subsets. The pre-post difference of 
these endpoints will be compared between responders and non-responders with the two sided 
t-test or Wilcoxon rank sum test where appropriate. The exploratory objective is to determine 
whether PD-1 response in responding patients is associated with common gut microbiota 
profile. The same statistical analysis methods will be used as for the secondary endpoints. 
9.0 LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES 
9.1 
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. 
Pembrolizumab is supplied by the HCC pharmacy. FMT is manufactured as described in 
Section 4.2.3. No clinical supplies are provided by Merck. 
9.2 
Packaging and Labeling Information 
Clinical supplies will be affixed with a clinical label in accordance with regulatory 
requirements. 
9.3 
Clinical Supplies Disclosure 
This trial is open-label; therefore, the subject, the trial site personnel, the Sponsor 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. 

 
56 
 
9.4 
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. 
9.5 
Returns and Reconciliation 
The investigator is responsible for keeping accurate records of the FMT infusates generated 
during the context of this study, the amount dispensed to and returned by the subjects and the 
amount remaining at the conclusion of the trial.  
10.0 ADMINISTRATIVE AND REGULATORY DETAILS 
10.1 
Confidentiality 
The confidentiality of records that could identify subjects must be protected, respecting the 
privacy and confidentiality rules applicable to regulatory requirements, the subjects' signed 
ICF and, in the US, the subjects’ signed HIPAA Authorization. The consent form must also 
include a statement that Merck and regulatory authorities have direct access to participant 
records. The rights, safety, and well-being of the study subjects are the most important 
considerations and should prevail over interests of science and society. 
10.2 
Compliance with Financial Disclosure Requirements 
Study investigators will ensure compliance with US Food and Drug Administration (FDA) 
financial disclosure regulations as set forth in 21 CFR Part 54. 
10.3 
Compliance with Law, Audit and Debarment 
The study may be evaluated by Sponsor or designee internal auditors and government 
inspectors who must be allowed access to CRFs, source documents, other study files, and 
study facilities. All audit reports will be kept confidential. 
10.4 
Compliance with Trial Registration and Results Posting Requirement 
The data collected during this study are confidential and proprietary to Sponsor or designee. 
Any publications or abstracts arising from this study must adhere to the publication 
requirements set forth in the clinical trial agreement (CTA) governing Investigator 
participation in the study. These requirements include, but are not limited to, submitting 
proposed publications to Sponsor or designee at the earliest practicable time prior to 
submission or presentation and otherwise within the time period set forth in the CTA. 
10.5 
Data Safety Monitoring Plan 

 
57 
 
Sponsor-Investigator, sub-investigators, regulatory, CRS management, clinical research 
coordinators, clinical research associates, data managers, and clinic staff meet monthly in 
Melanoma Center Data Safety Monitoring Boards (DSMB) to review and discuss study data 
to include, but not limited to, the following: 
a. 
Serious adverse events 
b. 
Subject safety issues 
c. 
Recruitment issues 
d. 
Accrual 
e. 
Protocol deviations 
f. 
Unanticipated problems 
g. 
Breaches of confidentiality  
Under the terms of the Food and Drug Administration Modernization Act (FDAMA) and the 
Food and Drug Administration Amendments Act (FDAAA) (21 CFR 312.50, 21 CFR 
312.56), the Sponsor of the trial is solely responsible for determining whether the trial and its 
results are subject to the requirements for submission to the Clinical Trials Data Bank, 
http://www.clinicaltrials.gov.  Information posted will allow subjects to identify potentially 
appropriate trials for their disease conditions and pursue participation by calling a central 
contact number for further information on appropriate trial locations and trial site contact 
information.     
Minutes from the DSMB meetings are available to anyone unable to attend the center 
DSMB. 
All toxicities encountered during the study will be evaluated on an ongoing basis according 
to the NCI Common Toxicity Criteria version 5. All study treatment associated adverse 
events that are serious, at least possibly related and unexpected will be reported to the IRB. 
Any modifications necessary to ensure subject safety and decisions to continue, or close the 
trial to accrual are also discussed during these meetings. If any literature becomes available 
which changes the risk/benefit ratio or suggests that conducting the trial is no longer ethical, 
the IRB will be notified in the form of an Unanticipated Problem submission and the study 
may be terminated. 
All study data reviewed and discussed during these meetings will be kept confidential. Any 
breach in subject confidentiality will be reported to the IRB in the form of an Unanticipated 
Problem submission. The summaries of these meetings are forwarded to the UPCI Data 
Safety and Monitoring Committee (DSMC), which also meets monthly following a 
designated format. 
For all research protocols, there will be a commitment to comply with the IRB’s policies for 
reporting unanticipated problems involving risk to subjects or others (including adverse 

 
58 
 
events). DSMC progress reports, to include a summary of all serious adverse events and 
modifications, and approval will be submitted to the IRB at the time of renewal. 
Protocols with subjects in long-term (survival) follow-up or protocols in data analysis only, 
will be reviewed twice a year rather than monthly by the disease center DSMB. 
Both the UPCI DSMC as well as the individual disease center DSMB have the authority to 
suspend accrual or further investigate treatment on any trial based on information discussed 
at these meetings. 
All records related to this research study will be stored in a locked environment. Only the 
researchers affiliated with the research study and their staff will have access to the research 
records. 
10.6 
Quality Management System 
Independent monitoring of the clinical study for protocol and Guidelines on Good Clinical 
Practice compliance will be conducted periodically (i.e., at a minimum of annually) by 
qualified staff of the Education and Compliance Office – Human Subject Research, Research 
Conduct and Compliance Office, University of Pittsburgh. 
The Investigator (i.e., the study site principal investigator) and the University of Pittsburgh 
and University of Pittsburgh Medical Center will permit direct access of the study monitors 
and appropriate regulatory authorities to the study data and to the corresponding source data 
and documents to verify the accuracy of this data. 
10.7 
Data Management 
The Investigator (i.e., the study site principal investigator) will maintain records in 
accordance with Good Clinical Practice. 
The investigator will retain the specified records and reports for up to 2 years after the 
marketing application is approved for the investigational drug; or, if a marketing application 
is not submitted or approved for the investigational drug, until 2 years after investigations 
under the IND have been discontinued and the FDA so notified. 
10.8 
Institutional Review Board (IRB) Approval 
The investigator (i.e., the study site principal investigator) will obtain, from the University of 
Pittsburgh Institutional Review Board (IRB), prospective approval of the clinical protocol 
and corresponding informed consent form(s); modifications to the clinical protocol and 
corresponding informed consent forms, and advertisements (i.e., directed at potential 
research subjects) for study recruitment, if applicable. 
The only circumstance in which a deviation from the current IRB-approved clinical 
protocol/consent form(s) may be initiated in the absence of prospective IRB approval is to 
eliminate an apparent immediate hazard to the research subject(s). In such circumstances, the 
investigator will promptly notify the University of Pittsburgh IRB of the deviation. 

 
59 
 
The University of Pittsburgh IRB operates in compliance with FDA regulations at 21 CFR 
Parts 50 and 21 CFR 56, and in conformance with applicable International Conference on 
Harmonization (ICH) Guidelines on Good Clinical Practice. 
In the event that the University of Pittsburgh IRB requires, as a condition of approval, 
substantial changes to a clinical protocol submitted under an FDA-accepted IND application, 
or in the event of an sponsor’s decision to modify the previously accepted clinical protocol, 
the sponsor will submit (i.e., in advance of implementing the change) a Protocol Amendment 
to the IND describing any change that significantly affects the safety of subjects, the scope of 
the investigation, or the scientific quality of the study. Examples of protocol changes 
requiring the submission of a Protocol Amendment include: 
• 
Any increase in drug dosage or duration of exposure of individual subjects to the 
investigational drug beyond that described in the current protocol, or any significant 
increase in the number of subjects under study. 
• 
Any significant change in the design of the protocol (such as the addition or deletion 
of a control group). 
• 
The addition of a new test or procedure that is intended to improve monitoring for, or 
reduce the risk of, a side effect or AE; or the dropping of a test intended to monitor 
the safety of the investigational drug. 
 
10.9 
Ethical and Scientific Conduct of the Clinical Study 
The clinical study will be conducted in accordance with the current IRB-approved clinical 
protocol; ICH Guidelines on Guidelines on Good Clinical Practice; and relevant policies, 
requirements, and regulations of the University of Pittsburgh IRB, University of Pittsburgh 
and University of Pittsburgh Medical Center, Commonwealth of Pennsylvania, and 
applicable federal agencies. 
10.10 Informed Consent 
The investigator (i.e., the study site principal investigator) will make certain that an 
appropriate informed consent process is in place to ensure that potential research subjects, or 
their authorized representatives, are fully informed about the nature and objectives of the 
clinical study, the potential risks and benefits of study participation, and their rights as 
research subjects. The investigator, or a sub-investigator(s) designated by the sponsor, will 
obtain the written, signed informed consent of each subject, or the subject’s authorized 
representative, prior to performing any study-specific procedures on the subject. The date and 
time that the subject, or the subject’s authorized representative, signs the informed consent 
form and a narrative of the issues discussed during the informed consent process will be 
documented in the subject’s case history. The investigator or sub-investigator will retain the 
original copy of the signed informed consent form, and a copy will be provided to the 
subject, or to the subject’s authorized representative. 
The investigator will make certain that appropriate processes and procedures are in place to 
ensure that ongoing questions and concerns of enrolled subjects are adequately addressed and 
that the subjects are informed of any new information that may affect their decision to 
continue participation in the clinical study. In the event of substantial changes to the clinical 

 
60 
 
study or the risk-to-benefit ratio of study participation, the investigator will obtain the 
informed consent of enrolled subjects for continued participation in the clinical study. 
 
 
11.0 
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES 
11.1 
Tumor Biopsies 
Tumor biopsies from at least one accessible tumor lesion will be obtained from all patients 
during screening and after 4 doses of pembrolizumab (+/- 1 week). Where possible, tumor 
biopsies will be obtained at tumor progression. 
Punch biopsies, surgical excisional biopsies or core biopsies are acceptable. Patients with 
internal visceral disease may require image guided needle biopsies. 
11.2 
Correlative Studies 
Correlative studies will be performed using PBMCs and tumor tissues collected from the 
patients included in the study as detailed in the laboratory manual.  
These studies will include: 
• Multiparemeter flow cytometry to evaluate T cell phenotype and function 
• Nanosotring studes of tumor biopsies 
• RNAseq and exome sequencing 
• Studies of T cell repertoire 
• Stool samples will be used for genomic evaluation of microbiota 
o 16S ribosomal RNA (rRNA) and metagenomic sequencing will be used to 
characterize the complexity of the human microbiome in the stool and at 
multiple body sites. 16S rRNA gene sequencing is a well-established method 
for studying phylogeny and taxonomy of samples from complex microbiomes 
or environments that are difficult or impossible to study. 
Prior biopsy samples including primary tumor shave/excision biopsies, sentinel lymph node 
biopsies, completion lymph node dissection samples will be requested from pathology. Prior 
tissue obtained to establish metastatic disease, as part of definitive surgical management or 
as part of standard of care testing prior to current therapy will also be requested. These 
samples will be used for immunohistochemical (IHC) and RNA sequencing studies to 
evaluate immune responses and gene signatures associated with improved clinical outcome. 
 
 
 
 
 

 
61 
 
APPENDICES 
Appendix 1: FMT Recipient (or Donor) Screening Questionnaire 
Dear *** : 
 
You have been identified as a potential donor for a medical procedure called fecal microbiota transplantation 
(FMT, or stool transplantation). FMT is a relatively new medical procedure that has been used to treat patients 
with C. difficile infections (CDI) – a diarrheal illness caused by antibiotics that kill the normal stool bacteria of 
the human gastrointestinal tract. The composition of gut bacteria has been shown to mediate outcomes to PD-1 
inhibitor therapy in animal models of melanoma. You have been identified by Dr. Diwakar Davar and Dr. 
Hassane Zarour as a potential stool donor.  
 
Your doctors are conducting a study in which patients with advanced melanoma whose cancer is not 
responding to PD-1 therapy receive FMT. In this study, selected patients will receive an extract from your 
frozen stool sample. Are you interested in learning more about how you can participate as a donor for FMT?  
YES, PLEASE  / NO THANKS 
 
If no, you do not need to answer any more questions. Please return this form to the person who gave it to you or 
to the return address at the end of this form.  If yes, please continue to answer the following questions: 
 
Name (please print): 
Date of birth: 
Gender:  
MALE  /  FEMALE 
Telephone number(s):  
 
Date Completed: 
Time Completed: 
 
The answers to the following questions will be used by our stool transplant physician to determine if your feces 
can be used for a stool transplant. The answers to some but not all questions may disqualify you as a donor. 
Please answer the questions truthfully. The answers that you give will NOT be shared with the person you are 
donating to or appear in his/her chart. 
 
1. Are you at least 18 years old? 
YES/NO 
2. Except for birth control, do you take any prescription medications? 
YES/NO 
3. What is your height in feet and inches? 
 
 
 
 
 
 
 
4. What is your weight in pounds? 
 
5. Have you ever donated blood before? 
a. 
If yes, have you even been notified by the blood bank of any positive testing for infectious 
conditions such as hepatitis C or HIV? 
b. If no, have you attempted to donate blood previously but asked not to donate for medical 
reasons ? 
 
Please answer the following YES / NO questions to the best of your ability: 
 
In the past 6 weeks 
6. Female donors: Have you been pregnant or are you pregnant now?  YES / NO / I AM MALE 
 
In the past 8 weeks have you: 
7. Donated blood, platelets or plasma?    YES  / NO 
8. Had any vaccinations or other shots?   YES  / NO 
9. Had contact with someone who had a smallpox vaccination? YES  /  NO 

 
62 
 
 
In the past 3 months have you: 
10. Used any antibiotics?  
YES  /  NO 
11. Had any diarrhea?  
YES  /  NO 
12. Had any vomiting? 
YES  /  NO 
 
13. Had any food poisoning? YES  /  NO 
14. Had any fevers?  
YES  /  NO 
15. Been hospitalized (long enough to stay overnight)? 
 
YES  /  NO 
16. Been seen in an emergency room or urgent care visit? 
YES  /  NO 
 
In the past 12 months have you 
17. Had a blood transfusion?  
 
 
 
YES  /  NO 
 
18. Had a transplant such as organ, tissue, or bone marrow? 
YES  /  NO 
 
19. Had a graft such as bone or skin? 
 
 
 
YES  /  NO 
20. Come into contact with someone else’s blood? 
 
YES  /  NO 
21. Had an accidental needle-stick? 
 
 
 
YES  /  NO 
22. Had sexual contact with anyone who has HIV/AIDS or has had a positive test for the HIV/AIDS virus?
 
 
YES  /  NO 
23. Had sexual contact with a prostitute or anyone else who takes money or drugs or other payment for 
sex? 
YES  /  NO 
 
24. Had sexual contact with anyone who has ever used needles to take drugs or steroids, or anything not 
prescribed by their doctor? YES  /  NO 
25. Had sexual contact with anyone who has hemophilia or has used clotting factor concentrates? 
 
YES  /  NO 
26. Had sexual contact with a person who has hepatitis? YES  /  NO 
27. Lived with a person who has hepatitis? 
YES  /  NO 
28. Had a tattoo? 
 
YES  /  NO 
29. Had ear or body piercing? YES  /  NO 
30. Had or been treated for syphilis or gonorrhea? 
 
YES  /  NO 
31. Been in juvenile detention, lockup, jail, or prison for more than 72 hours? 
 
YES  /  NO 
 
In the past three years have you 
32. Been outside the United States or Canada? YES  /  NO 
 
From 1980 through 1996, 
33. Did you spend time that adds up to three (3) months or more in the United Kingdom? (Northern 
Ireland, Wales, Scotland, England [sometimes called Great Britain])? YES  /  NO 
 
34. Were you a member of the U.S. military, a civilian military employee, or a dependent of a member of 
the U.S. Military? 
YES  /  NO 
 
From 1980 to the present, did you 
35. Spend time that adds up to five (5) years or more in Europe?   
YES  /  NO 
36. Receive a blood transfusion in the United Kingdom or France? 
 YES  /  NO 
 
From 1977 to the present, have you: 
37. Received money, drugs, or other payment for sex? 
 
 
YES  /  NO 
38. Male donors: had sexual contact with another male, even once? 
 YES   / NO  /  I AM 
FEMALE 
 
COVID-19 Related Exposure 
39. Have you at any time been diagnosed with laboratory-confirmed SARS-CoV-2 infection?  
40. Have you at any time experienced symptoms of COVID-19 (e.g., fever, cough, shortness of breath) not 
explained adequately by another diagnosis?  
41. Have you been exposed to a suspected or confirmed case of COVID-19 or SARS-CoV-2 infection? 
 
Have you EVER: 

 
63 
 
42. Had C. difficile infection previously?  
 
YES  /  NO 
43. Had a positive test for the HIV/AIDS virus? YES  /  NO 
44. Used needles to take drugs, steroids, or anything not prescribed by your doctor? YES  /  NO 
 
45. Used clotting factor concentrates?   
YES  /  NO 
46. Had hepatitis? 
 
 
 
 
YES  /  NO 
 
47. Had malaria? 
 
 
 
 
YES  /  NO 
48. Had Chagas’ disease? 
 
 
 
YES  /  NO 
49. Had babesiosis?  
 
 
YES  /  NO 
50. Received a dura mater (or brain covering) graft? 
YES  /  NO 
51. Had any type of cancer, including leukemia? 
YES  /  NO 
52. Had parents, brothers, sisters, or children diagnosed with cancer? 
YES  /  NO 
53. Had any problems with your heart or lungs?  
YES  /  NO 
54. Had a bleeding condition or a blood disease? 
YES  /  NO 
55. Had sexual contact with anyone who was born in or lived in Africa? 
YES  /  NO 
56. Been in Africa?  
 
 
 
 
YES  /  NO 
57. Been in the Caribbean? 
 
 
 
YES  /  NO 
58. Been in Central or South America (anywhere south of the US Border including Mexico)?  
 
 
 
 
YES  /  NO 
 
59. Been elsewhere outside the US? 
 
 
YES  /  NO 
60. Had relatives who had Creutzfeldt-Jakob disease? 
YES  /  NO 
61. Been previously tested for HIV or viral hepatitis? 
YES  /  NO 
62. Tested positive for MRSA (methicillin resistant Staphylococcus aureus), VRE (vancomycin resistant 
enterococcus) or other resistant bacteria? 
YES  /  NO 
63. Had diarrhea lasting for longer than 2 weeks? 
 
 
YES  /  NO 
 
64. Had irritable bowel syndrome? 
 
 
 
YES  /  NO 
65. Had chronic constipation?  
 
 
 
YES  /  NO 
66. Had chronic pain? 
 
 
 
 
 
YES  /  NO 
  
A physician will review this form to determine if you can be scheduled for a screening visit with an infectious 
disease physician for additional questions.  If you answer in the positive to questions 39-41, you will be referred 
to an infectious disease physician for additional evaluation.  If you are eligible based on this visit, you will be 
scheduled for laboratory testing.  If you are eligible and willing to participate as a potential stool donor, you will 
be asked to do the following: 
 
1) Schedule a screening visit with a physician in Oakland at the Falk Medical Building 
2) Have blood tests and stool tests collected for testing 
3) Donate stool either in person or off-site on the morning of the scheduled procedure. 
 
Please mail this form to: 
 
ATTN: Diwakar Davar, MD and Hassane Zarour, MD 
UPCI Fecal Transplant Program 
Hillman Cancer Center, UPCI Research Pavilion 
5117 Center Avenue 
Suite 1.32d 

 
64 
 
Appendix 2: FMT Recipient (and Donor) Laboratory Testing 
 
Required stool and serologic testing is detailed below. 
 
Both donors and recipients will provide stool samples after signing ICF. 
 
Serologic tests (blood, stool, nasal swabs) in donors will be performed per Section 4.2.3. 
(Figure 4). 

 
65 
 
 
 
 
 
 
Blood  
Stool  
Nasal 
#HIV antibody 
$Hepatitis A total Ab 
#Hepatitis B surface Ab, core Ab, 
surface Ag   
#Hepatitis C Ab 
#Syphilis screening serology 
Strongyloides stercoralis Ab 
#Entamoeba histolytica Ab 
#HTLV-1 and HTLV-2 Ab 
*CMV IgG 
*EBV AB panel 
*HSV-1 IgG 
*HSV-2 IgG 
*HHV-6 IgG 
*JC virus Ab 
@Bacteria 
• 
Campylobacter 
• 
Clostridium difficile 
• 
E.coli H7 
• 
Helicobacter pylori 
• 
Salmonella 
• 
Shigella 
• 
Vibrio 
• 
Yersinia 
@Viruses 
• 
Rotavirus 
• 
Adenovirus 
• 
Norovirus 
• 
SARS-CoV-2 
@Fungi/Parasites 
• 
Giardia 
• 
Cryptosporidia 
• 
Ova/parasites 
#MDRO 
• 
Vancomycin Resitant 
Enterococci (VRE) 
• 
Carbapenum Resitant 
Enterobacteriaceae (CRE) 
• 
Extended Spectrum Beat-
Lactamase producing bacteria 
(ESBLs) 
*MRSA 
%SARS-CoV-2 (will be 
done 2 weeks before)  
% if positive, ineligible to donate FMT and will result in reflex referral to Infectious Disease Physician. 
• 
Determination of "SARS-CoV-2 negative" status will be made on specimens obtained at two 
timepoints: 1st sample collected at least 14 days before stool sample donation, and a 2nd sample 
collected at least 14 days after stool sample donation. 
• 
As the turnaround of the test is 48-72 hours, the stool sample will be released for FMT use no 
sooner than 48-72 hours after 2nd test results and donor is deemed "SARS-CoV-2 negative". 
• 
Donors who were excluded based on based on screening and/or testing as described in 3.1 and 
4.1.1-4.1.2 above will not be allowed to donate stool specimens for use in this study at this time. 
This is subject to subsequent revision should stool-specific SARS-CoV-2 testing become 
available. 
#if positive, ineligible to donate FMT 
*if positive, eligible to receive FMT from seropositive or negative donors (i.e. donors who are similarly 
positive or who test negative). 
@if positive, must be repeated and be tested negative prior to determination of eligibility (NOTE: 
exceptions may be made in the case of asymptomatic recipients who test positive AFTER consultation 
with PI). 
$if positive, must be followed by Hepatitis A IgG and IgM.  
• 
For donors: IgM positive donors are ineligible to donate. IgG positive donors are eligible to 
donate. 
• 
For recipients: IgM/G status does not affect ability to receive FMT. 

 
66 
 
Appendix 3: Dietary History Questionnaire for Microbiome Sampling 
Version date 1/17/19 
 
Dietary History  Questionnaire 
 
This is a food frequency questionnaire (FFQ) modified for patients receiving immune 
checkpoint blockade (ICB) therapy. This FFQ is modified from the publically available Diet 
History Questionnaire (DHQ) developed by staff at the Risk Factor Assessment Branch 
(RFAB) of the National Institutes of Health. This FFQ consists of a finite list of foods and 
beverages with response categories to indicate usual frequency of consumption over the time 
period queried. 
 
This FFQ is designed to be completed every time you visit receive treatment or are in to see 
your physician. It can either be done at home or at each study visit.  
 
Demographics 
First Name __________________________________________ 
Last Name __________________________________________ 
Sex ______________ 
 
 
 
Current Medications (including supplements). 
For this question, please report the names and dosages of all prescription medications you 
take. Please include supplements and any as-needed (prescription or over the counter) 
medicines you take at least weekly. 
Current Medications (including supplements and vitamins). 
 
 
Visits 
For this question, please indicate today’s date and your weight in pounds (lbs). 
Date ________________________ 
Weight (in lbs) ________________ 
 
 
Beverages 
What beverages do you drink? 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in 8oz terms.  Please choose only one answer for each question. 
 
Do you drink beverages? 
• No 
• Yes 
 
Do you drink fruit and/or vegetable juices? 

 
67 
 
• No 
• Yes 
 
How often do you drink fruit juice? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
How often do you drink vegetable juice? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
How often do you drink other fruit/vegetable juice? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
Do you drink milk or milk-based beverages? 
• No 
• Yes 
 
How often do you drink milk including flavored milk (chocolate, strawberry etc.)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 

 
68 
 
• 4-5 times per day 
• 6 or more times per day 
 
How often do you drink milk based meal replacements (Boost, Ensure, Carnation Instant  
Breakfast)?? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
Do you drink coffee and/or tea? 
• No 
• Yes 
 
How often do you drink coffee and/or tea? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
Do you typically add sugar (or sugar equivalents such as Equal, Splenda etc.) to your coffee 
and/or tea? 
• No 
• Yes 
 
How much sugar (or sugar equivalents such as Equal, Splenda etc.) do you add? 
• 1 sachet 
• 2 sacets 
• 3 or more sachets 
 
Do you typically add milk (or milk equivalents such as half-and-half, creamer etc.) to your 
coffee and/or tea? 
• No 
• Yes 
 
How much milk (or milk equivalents such as half-and-half, creamer etc.) do you add? 
• 1 sachet 

 
69 
 
• 2 sacets 
• 3 or more sachets 
 
Do you drink soda/pop or other carbonated beverages? 
• No 
• Yes 
 
How often do you drink soda/pop or other carbonated beverages (including diet soda)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
Do you drink sports/energy drinks (including diet variety) such as Gatorade, Powerade etc.? 
• No 
• Yes 
 
How often do you drink sports/energy drinks (including diet variety) such as Gatorade, 
Powerade etc.? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
Do you drink alcohol (including beer, spirits, wine)? 
• No 
• Yes 
 
How often do you drink beer?  
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 

 
70 
 
• 6 or more times per day 
 
How often do you drink wine? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
How often do you drink mixed drinks and/or liquor? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Fruits 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
fruit: 1 piece of medium fresh fruit (apple, orange etc); OR 2 pieces of small fresh fruit 
(apricot, plum etc); 1/2 cup of tinned/frozen fruit (berries, tinned peaches etc); OR 1 handful 
of dried fruit (raisins, trail mix). 
Please choose only one answer for each question. 
 
Do you consume fruits? 
• No 
• Yes 
 
For fruit, which of the following categories of fruit do you typically consume? 
• 
Apples 
• 
Berries (raspberries, strawberries, blueberries) 
• 
Citrus fruits (orange, grapefruit, clementines) 
• 
Stone fruits (peaches, apricots) 
• 
Tropical fruits (bananas, pineapple) 
• 
Melons (watermelon, honeydew) 
• 
Grapes 

 
71 
 
 
How often do you consume a serving of fruit? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Vegetables 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
vegetables: 1 medium vegetable (potatoe, carrot, yam, etc.); OR 1/2 cup cooked vegetable 
(broccoli, peas, spinach etc.); OR 1 cup salad). 
Please choose only one answer for each question. 
 
Do you consume vegetables? 
• No 
• Yes 
 
For vegatables, which of the following categories of vegetables do you typically consume? 
• Cruciferous vegetables (broccoli, brussel sprouts) 
• Leafy greens 
• Marrow vegetables (cucumber, zucchini) 
• Root vegetables (potatoes, sweet potatoes) 
• Stem vegetables (asparagus) 
 
 
How often do you consume a serving of vegetables? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Legumes 

 
72 
 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
legumes: 3/4 cup cooked lentils (green, red lentils etc.), 3/4 cup cooked beans (kidney beans, 
white beans, chickpeas, baked beans, split beans, etc.). 
Please choose only one answer for each question. 
 
Do you consume legumes or pulses? 
• No 
• Yes 
 
How often do you consume a serving of legumes? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Cereals & Breads 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
breads and/or cereals: 1/2 cup cooked oatmeal (or porridge, cream of wheat etc); OR 1/2 cup 
cereal or muesli; OR 1 slice whole-grain bread; OR 2 slices white bread). 
Please choose only one answer for each question. 
 
Do you consume breads and cereals? 
• No 
• Yes 
 
For bread, do you typically consume white or whole-grain bread? 
• White 
• Whole grain 
 
How often do you consume a serving of breads and/or cereals? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 

 
73 
 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Rice & Pastas 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
rice or pasta: 1/2 cup cooked brown rice or whole-wheat pasta (or quinoa etc.); OR 1 cup 
cooked white rice or regular pasta). 
Please choose only one answer for each question. 
 
Do you consume rice and/or pasta? 
• No 
• Yes 
 
For rice, do you typically consume white,  brown rice or rice alternatives (quinoa etc.)? 
• White 
• Brown 
• Quinoa 
 
For pasta, do you typically consume regular or whole-wheat pasta? 
• Regular 
• Whole-wheat 
 
How often do you consume a serving of rice or pasta (including alternatives such as quinoa 
etc.)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Meat & Poultry 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  

 
74 
 
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
meat and/or poultry: 1 3-oz serving; OR 1 chicken breast; OR 1/2 cup ground meat or 
poultry). 
Please choose only one answer for each question. 
 
Do you consume meat and/or poultry? 
• No 
• Yes 
 
If you consume meat and/or poultry, what is your primary method of cooking? 
• Grilling 
• Pan or shallow frying 
• Deep-frying 
• Baking 
• Other 
 
How often do you consume a serving of chicken or other poultry (1 chicken breast or 
equivalent)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
How often do you consume a serving of pork, beef or other meat (1 3-oz pork chop, 1 5-oz 
patty, etc.)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Fish & Shellfish 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  

 
75 
 
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
fish and/or shellfish: 1 3-oz serving of fish; OR 1 4-oz serving of shrimp; OR 3/4-lb cooked 
lobster or crab). 
Please choose only one answer for each question. 
 
Do you consume fish and/or shellfish? 
• No 
• Yes 
 
If you consume fish and/or shellfish, what is your primary method of cooking? 
• Grilling 
• Pan or shallow frying 
• Deep-frying 
• Baking 
• Other 
 
How often do you consume a serving of fish and/or shellfish? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Eggs 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
eggs: 1 egg; OR 3 egg whites; OR 1 cup egg substitute. 
Please choose only one answer for each question. 
 
Do you consume eggs? 
• No 
• Yes 
 
If you consume eggs, do you typically consume whole eggs or egg products (egg whites, and 
egg yolks in egg whites frozen, refrigerated liquid, or dried forms)? 
• Whole eggs including yolks 
• Egg whites 
• Egg substitutes 
 

 
76 
 
If you consume eggs, what is your primary method of cooking? 
• Grilling 
• Pan or shallow frying 
• Deep-frying 
• Baking 
• Other 
 
How often do you consume a serving of eggs? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Meat Alternatives 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following is an example of 1 SERVING of 
meat alternatives: 1/2 cup raw/cooked tofu (or alternative). 
Please choose only one answer for each question. 
 
Do you consume meat alternatives (tempeh, tofu, seitan, gluten, etc)? 
• No 
• Yes 
 
How often do you consume a serving of meat alternatives (tempeh, tofu, seitan, gluten, etc)? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Yoghurt & Cheese 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  

 
77 
 
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
yoghurt and/or cheese: 1 cup yoghurt/cheese; 8 fluid oz yoghurt/cheese). 
Please choose only one answer for each question. 
 
Do you consume yoghurt and/or cheese? 
• No 
• Yes 
 
If you consume yoghurt and/or cheese, what type do you typically eat? 
• Whole fat cheese or yoghurt 
• Low fat cheese or yoghurt 
• 2% cheese or yoghurt 
• Non-fat cheese or yoghurt 
• Cottage cheese 
 
How often do you consume a serving of yoghurt and/or cheese? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 
 
 
Sweets & Desserts 
For this question, please estimate the frequency and quantity of the item in question. 
Frequency is estimated as: 1-2 times per week, 3-4 times per week, 5-6 times per week, 1 
time per day, 2-3 times per day, 4-5 times per day, 6 or more times per day.  
Please quantify intake in terms of servings. The following are examples of 1 SERVING of 
dessert: 1 oz serving; OR 100g serving; OR 1 2" brownie; OR 1/2 cup ice-cream. 
Please choose only one answer for each question. 
 
Do you consume sweets, baked goods and/or desserts? 
• No 
• Yes 
 
If you consume sweets, baked goods and/or desserts, what type do you typically eat? 
• Ice-cream 
• Cakes and cookies and brownies 
• Muffins 
• Pies 
• Doughnuts 
 

 
78 
 
How often do you consume a serving of sweets, baked goods and/or desserts? 
• <1 time per week 
• 1-2 times per week 
• 3-4 times per week 
• 5-6 times per week 
• 1 time per day 
• 2-3 times per day 
• 4-5 times per day 
• 6 or more times per day 

 
79 
 
 
Appendix 4: Memory Card for Patients while on Study 
 
This is a questionnaire to facilitate self-monitoring of symptoms that may be related to the 
fecal microbiome transplant (FMT) and/or pembrolizumab therapy that you have received. 
You should review this questionnaire daily while on study. If you do develop symptoms, 
particularly if these symptoms are persistent, please bring this to the attention of the 
investigator and your study nurse. This questionnaire will be administered at each study visit.  
 
 
Memory Card 
Adverse Event 
1 
2 
3 
4 
5 
Abdominal 
discomfort 
Asymptomatic; 
clinical 
or 
diagnostic 
observations 
only; 
intervention 
not 
indicated 
Symptomatic; 
limiting 
instrumental ADL 
Severe discomfort; 
limiting self care 
ADL 
N/A 
N/A 
Constipation 
Occasional 
or 
intermittent 
symptoms; 
occasional use of 
stool 
softeners, 
laxatives, 
dietary 
modification, 
or 
enema 
Persistent symptoms 
with regular use of 
laxatives or enemas; 
limiting 
instrumental ADL 
Obstipation 
with 
manual evacuation 
indicated; limiting 
self care ADL 
Life-threatening 
consequences; 
urgent 
intervention 
indicated 
N/A 
Diarrhea 
Increase of <4 stools 
per 
day 
over 
baseline; 
mild 
increase in ostomy 
output compared to 
baseline 
Increase of 4 - 6 
stools per day over 
baseline; 
moderate 
increase in ostomy 
output compared to 
baseline 
Increase 
of 
>=7 
stools per day over 
baseline; 
incontinence; 
severe increase in 
ostomy 
output 
compared 
to 
baseline; 
limiting 
self care ADL 
Life-threatening 
consequences; 
urgent 
intervention 
indicated 
N/A 
Fever 
38.0-39.0 degrees C  
(100.4-102.2 
degrees F) 
>39.0-40.0 degrees 
C 
(102.3-104.0 
degrees F) 
>40.0 degrees C (> 
104.0degrees F) for 
≤24 hrs 
>40.0 degrees C 
(> 
104.0degrees 
F) for >24 hrs 
N/A 
Flatulence 
Asymptomatic; 
clinical 
or 
diagnostic 
observations 
only; 
intervention 
not 
indicated 
Symptomatic; 
limiting 
instrumental ADL 
Severe discomfort; 
limiting self care 
ADL 
N/A 
N/A 
Vomiting 
1 
- 
2 
episodes 
(separated 
by 
5minutes) in 24 hrs 
3 
- 
5 
episodes 
(separated 
by 
5minutes) in 24 hrs 
≥6 
episodes 
(separated 
by 
5minutes) 
in 
24 
hrs; tube feeding, 
TPN 
or 
hospitalization 
indicated 
Life-threatening 
consequences; 
urgent 
intervention 
indicated 
N/A 
 

 
80 
 
Appendix 5: Dose Modifications for Pembrolizumab for Immune-Related Adverse 
Events 
Adverse events (AEs) associated with pembrolizumab exposure may represent an 
immunologic etiology. These immune-related AEs (irAEs) may occur shortly after the first 
dose or several months after the last dose of pembrolizumab treatment and may affect more 
than one body system simultaneously. Therefore, early recognition and initiation of treatment 
is critical to reduce complications. Based on existing clinical study data, most irAEs were 
reversible and could be managed with interruptions of pembrolizumab, administration of 
corticosteroids, and/or other supportive care. For suspected irAEs, ensure adequate 
evaluation to confirm etiology or exclude other causes. Additional procedures or tests such as 
bronchoscopy, endoscopy, or skin biopsy may be included as part of the evaluation. Based on 
the severity of irAEs, withhold or permanently discontinue pembrolizumab and administer 
corticosteroids. Dose modification and toxicity management guidelines for irAEs associated 
with pembrolizumab are provided here. 
Table 5-1: Dose Modification Guidelines for Drug-related Adverse Events: Pembrolizumab 
General instructions:  
1. Corticosteroid taper should be initiated upon AE improving to Grade 1 or less and continue to 
taper over at least 4 weeks.  
2. For situations where pembrolizumab has been withheld, pembrolizumab can be resumed after 
AE has been reduced to Grade 1 or 0 and corticosteroid has been tapered. Pembrolizumab should 
be permanently discontinued if AE does not resolve within 12 weeks of last dose or 
corticosteroids cannot be reduced to ≤ 10 mg prednisone or equivalent per day within 12 weeks.  
3. For severe and life-threatening irAEs, IV corticosteroid should be initiated first followed by 
oral steroid. Other immunosuppressive treatment should be initiated if irAEs cannot be controlled 
by corticosteroids.  
irAE 
CTCAE 
Grade 
Action Taken 
with 
Pembrolizumab 
irAE 
Management 
with 
Corticosteroid 
and/or Other 
Therapies 
Monitoring and 
Follow-Up 
Pneumonitis 
Grade 2 
Withhold 
Administer 
corticosteroids 
(initial dose of 
prednisone 1-2 
mg/kg or 
equivalent) 
followed by taper.  
 
Monitor subjects for 
signs and symptoms 
of pneumonitis.  
Evaluate subjects 
with suspected 
pneumonitis with 
radiographic 
imaging and initiate 
corticosteroid 
treatment.  
Add prophylactic 
antibiotics for 
opportunistic 
Grade 3 or 4, 
or recurrent 
Grade 2 
Permanently 
discontinue 

 
81 
 
infections  
 
Diarrhea/colitis 
Grade 2 or 3 
Withhold 
Administer 
corticosteroids 
(initial dose of 
prednisone 1-2 
mg/kg or 
equivalent) 
followed by taper.  
 
Monitor subjects for 
signs and symptoms 
of enterocolitis (ie, 
diarrhea, abdominal 
pain, blood or mucus 
in stool with or 
without fever) and 
of bowel perforation 
(ie, peritoneal signs 
and ileus). 
Subjects with ≥ 
Grade 2 diarrhea 
suspecting colitis 
should consider GI 
consultation and 
performing 
endoscopy to rule 
out colitis. 
Subjects with 
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.  
Consider infliximab 
5 mg/kg for 
treatment of severe 
immune-related 
colitis that does not 
respond within 
1 week to high-dose 
steroids. 
Grade 4 
Permanently 
discontinue 
AST/ALT 
elevation or 
increased 
bilirubin  
 
Grade 2 
Withhold 
Administer 
corticosteroids 
(initial dose of 
prednisone 0.5-1 
mg/kg or 
equivalent) 
Monitor with liver 
function tests 
(consider weekly or 
more frequently 
until liver enzyme 
value returned to 

 
82 
 
followed by taper.  
 
baseline or is stable).  
 
Grade 3 or 4 
Permanently 
discontinue 
Administer 
corticosteroids 
(initial dose of 
prednisone 1-2 
mg/kg or 
equivalent) 
followed by taper.  
 
TIDM or 
hyperglycemia 
New onset 
T1DM or 
Grade 3 or 4 
hyperglycemia 
associated 
with evidence 
of β-islet 
failure 
Withhold 
Initiate insulin 
replacement 
therapy for 
subjects with 
T1DM.  
 
Administer 
antihyperglycemic 
in subjects with 
hyperglycemia.  
 
Monitor subjects for 
hyperglycemia or 
other signs and 
symptoms of 
diabetes.  
 
Hypophysitis  
Grade 2 
Withhold 
Administer 
corticosteroids and 
initiate hormonal 
replacements 
as 
clinically 
indicated. 
 
Monitor for signs 
and symptoms of 
hypophysitis 
(including 
hypopituitarism and 
adrenal 
insufficiency).  
 
Grade 3 or 4 
Withhold 
or 
permanently 
discontinue 
Hyperthyroidism  Grade 2 
Withhold 
Treat 
with 
nonselective beta-
blockers 
(eg, 
propranolol) 
or 
thionamides 
as 
appropriate. 
Monitor for signs 
and symptoms of 
thyroid disorders. 
Grade 3 or 4 
Withhold 
or 
permanently 
discontinuea, b 
Hypothyroidism  Grade 2-4 
Continue 
Initiate 
thyroid 
replacement 
hormones 
(eg, 
levothyroxine 
or 
liothyronine) 
per 
standard of care.  
 
Monitor for signs 
and symptoms of 
thyroid disorders. 

 
83 
 
Nephritis 
and 
renal 
dysfunction 
Grade 2 
Withhold 
Administer 
corticosteroids 
(initial 
dose 
of 
prednisone 
1-2 
mg/kg 
or 
equivalent) 
followed by taper. 
Monitor changes of 
renal function.  
 
Grade 3 or 4 
Permanently 
discontinue 
Rash 
Grade 1 or 2 
Continue 
Manage 
with 
topical 
steroids 
with or without 
drug interruption  
 
 
Grade 3c 
Withhold 
until 
toxicity resolves 
to Grade 0-1 
Administer 
corticosteroids 
(initial 
dose 
of 
prednisone 
1-2 
mg/kg 
or 
equivalent) 
followed by taper.  
 
Restart 
pembrolizumab 
at 
same dose if rash is 
mild and assessed as 
Grade 3 based only 
on body surface area 
and resolves without 
oral steroids. If oral 
steroids are required, 
or if rash is severe, 
decrease by 1 dose 
level once resolved 
to Grade 0-1. 
Grade 4 
Permanently 
discontinue 
Amylase and/or 
lipase increased. 
Grade 
3 
or 
less 
May 
continue 
treatment 
with 
approval of PI or 
medical monitor 
 
Permanently 
discontinue 
if 
clinical signs and 
symptoms 
of 
pancreatitis develop 
(abdominal 
pain, 
nausea, vomiting).  
 
Grade 4 
Withhold 
until 
toxicity resolves 
to Grade 0-1d. 
 
Myocarditis 
Grade 1 or 2 
Hold therapy till 
toxicity resolves 
to Grade 0 
Admit patient and 
start 
high-dose 
corticosteroids. 
Intensive care unit 
admission; consider 
other 
immunosuppressants 
if 
the 
patient's 
condition 
deteriorates. 
Grade 3 or 4 
Permanently 
discontinue 
Neuropathy 
Grade 2 
Toxicity 
resolves 
to 
≤ 
Grade 
1 
or 
 
 

 
84 
 
baseline within 4 
weeks, restart at 
same 
dose. 
Toxicity 
does 
not resolve to ≤ 
Grade 1 within 4 
weeks, 
reduce 
dose 
1 
dose 
level. 
Grade 3 or 4 
Permanently 
discontinue 
All 
other 
immune-related 
AEs 
Grade 3, or 
intolerable/ 
persistent 
Grade 2  
Withhold 
Based on severity 
of AE administer 
corticosteroids. 
Ensure 
adequate 
evaluation 
to 
confirm etiology or 
exclude 
other 
causes.  
 
Grade 
4 
or 
recurrent 
Grade 3. 
Permanently 
discontinue 
AE = adverse event; ALT = alanine aminotransferase; AST = aspartate aminotransferase; GI = gastrointestinal; 
irAE = immune-related adverse event; IV = intravenous; T1DM = Type 1 diabetes mellitus. 
aDecision to withhold or permanently discontinue pembrolizumab is at the discretion of the investigator or 
treating physician. 
bFor subjects with Grade 3 or 4 immune-related endocrinopathy where pembrolizumab must be withheld, 
pembrolizumab may be resumed when AE resolves to ≤ Grade 2 and is controlled with hormonal replacement 
therapy or achieved metabolic control (in case of T1DM). 
cParticipants with Grade 3 rash in the absence of desquamation, with no mucosal involvement, not requiring 
systemic steroids, and resolving to Grade 1 within 14 days do not have to withhold study treatment. 
dIf Grade 4 amylase and/or lipase increase is asymptomatic and abdominal imaging suggests no pathology, 
study treatment dosing may continue with medical monitor approval. 

 
85 
 
Appendix 6: Toxicity Management of Infusion Reactions Related to Pembrolizumab 
Pembrolizumab may cause severe or life-threatening infusion reactions, including severe 
hypersensitivity or anaphylaxis. Signs and symptoms usually develop during or shortly after 
drug infusion and generally resolve completely within 24 hours of completion of infusion. 
Dose modification and toxicity management guidelines on pembrolizumab-associated 
infusion reaction are provided in Table 8-1. 
Table 6-1: Infusion Reaction Management 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 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 
Stop Infusion. 
Additional appropriate medical therapy may include but 
is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
No subsequent 
dosing 

 
86 
 
NCI CTCAE Grade 
Treatment 
Premedication at 
Subsequent Dosing 
for other clinical 
sequelae (e.g., renal 
impairment, pulmonary 
infiltrates) 
Grade 4: 
Life-threatening; pressor 
or ventilatory support 
indicated 
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. 
Appropriate resuscitation equipment should be available in the room and a physician readily available during 
the period of drug administration 
 

 
87 
 
 
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