A Phase II Trial of MK3475 in Combination With Gemcitabine and Concurrent Hypofractionated Radiation Therapy as Bladder Sparing Treatment for Muscle-Invasive Urothelial Cancer of the Bladder
Phase: PHASE2
Conditions: Muscle-invasive Urothelial Cancer of the Bladder
Sponsor: NYU Langone Health

Official Title: 
A Phase II Trial of MK3475 in Combination with Gemcitabine and 
Concurrent Hypofractionated Radiation Therapy as Bladder Sparing 
Treatment for Muscle-Invasive Urothelial Cancer of the Bladder 
NCT Number: 
NCT02621151 
Study Number: 
s15-00220 
Document Type: 
Study Protocol and Statistical Analysis Plan 
Date of the 
Document: 
•
August 16, 2023

1 
 
 
SPONSOR:  
Perlmutter Cancer Center and NYU Langone Medical Center 
New York, NY 10016 
 
TITLE:  
NYU PCC S15-00220 
A Phase II Trial of MK3475 in Combination with Gemcitabine and Concurrent 
Hypofractionated Radiation Therapy as Bladder Sparing Treatment for Muscle-
Invasive Urothelial Cancer of the Bladder 
 
Protocol Version: August 16, 2023(Amendment 5) 
IND NUMBER: 128856 
 
Principal Investigator: Minas Economides, MD 
 
 
 
    Perlmutter NYU Cancer Center 
 
 
Biostastistical Co-investigator: Judith D. Goldberg, ScD 
 
Radiation Oncology Co-Investigator: Peter Schiff MD 
 
Independent Monitor:  
Esther Aburi, MS 
Quality Assurance Specialist 
Perlmutter Cancer Center 
An NCI-Designated Comprehensive Cancer Center  
 
NYU Langone Health 
One Park Avenue 
1th floor, Room 102B 
New York, NY 10016 
 
 

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1.0 
TRIAL SUMMARY.................................................................................................... 7 
2.0 
TRIAL DESIGN.......................................................................................................... 8 
2.1 
Trial Design ............................................................................................................. 8 
2.2 
Trial Diagram ........................................................................................................ 10 
3.0 
OBJECTIVE(S) & HYPOTHESIS(ES) .................................................................. 10 
3.1 
Primary Objective(s) & Hypothesis(es) .............................................................. 10 
3.2 
Secondary Objective(s) & Hypothesis(es) ........................................................... 10 
3.3 
Exploratory/Biomarker Objectives ..................................................................... 11 
4.0 
BACKGROUND & RATIONALE .......................................................................... 11 
4.1 
Background ........................................................................................................... 11 
 Bladder Preservation Approaches ...................................................................... 12 
 Renal Dysfunction and Bladder Preservation Strategies .................................. 12 
 Gemcitabine and Radiotherapy in Bladder Cancer .......................................... 13 
 Bladder Cancer and the Older Patient ............................................................... 14 
 Gemcitabine and the Immune Microenvironment ............................................ 14 
 Radiation and Immunogenic Cell Death ............................................................ 14 
 Abscopal effect of radiotherapy ........................................................................... 15 
 Harnessing the pro-immunogenic effects of radiation in cancer treatment: 
a new paradigm ..................................................................................................... 15 
 Pharmaceutical and Therapeutic Background .................................................. 16 
 Pembrolizumab in Advanced Bladder Cancer .................................................. 17 
Additional Preclinical and Clinical Trial Data ................................................................ 17 
4.2 
Rationale ................................................................................................................ 17 
 Rationale for the Trial and Selected Subject Population .................................. 17 
 Rationale for Dose Selection/Regimen/Modification ......................................... 18 

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4.2.2.1 Rationale for Radiation Total Dose and Fractionation: .................................... 18 
4.2.2.2 Rationale for Gemcitabine Dose and Schedule: ................................................. 19 
4.2.2.3 Rationale for Pembrolizumab Dosing: ............................................................... 20 
 Rationale for Endpoints ....................................................................................... 22 
 Efficacy Endpoints ................................................................................................ 22 
4.2.4.1 Primary Objective: ............................................................................................... 22 
4.2.4.2 Secondary Objectives: .......................................................................................... 22 
4.2.4.3 Biomarker Research/Correlative Objectives ..................................................... 22 
5.0 
METHODOLOGY ................................................................................................... 23 
5.1 
Entry Criteria ........................................................................................................ 23 
 Subject Inclusion Criteria .................................................................................... 23 
 Subject Exclusion Criteria ................................................................................... 24 
5.2 
Trial Treatments ................................................................................................... 26 
 Toxicity Monitoring, Initial and Interim Safety Analysis and Decision Rule 
for Enrollment ....................................................................................................... 26 
 Lead-In Pembrolizumab and Maximal TURBT: .............................................. 28 
 Combination Chemo-Radio-Immunotherapy: ................................................... 28 
 Post-Treatment Response Assessment: ............................................................... 32 
 Dose Selection/Modification ................................................................................. 32 
5.2.5.1 Dose Selection ........................................................................................................ 32 
5.2.5.2 Dose Modification and/or interruption ............................................................... 33 
 Timing of Dose Administration ........................................................................... 40 
 Radiation Treatment Interruption ...................................................................... 40 
 Trial Blinding/Masking ........................................................................................ 41 
5.3 
Concomitant Medications/Vaccinations (allowed & prohibited) ..................... 41 

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 Acceptable Concomitant Medications ................................................................ 41 
 Prohibited Concomitant Medications ................................................................. 41 
5.4 
Rescue Medications & Supportive Care ............................................................. 42 
 Supportive Care Guidelines ................................................................................. 42 
5.5 
Diet/Activity/Other Considerations ..................................................................... 45 
 Diet ......................................................................................................................... 45 
 Contraception ........................................................................................................ 45 
 Use in Pregnancy ................................................................................................... 46 
 Use in Nursing Women ......................................................................................... 46 
5.6 
Subject Withdrawal/Discontinuation Criteria ................................................... 46 
5.7 
Subject Replacement Strategy ............................................................................. 47 
5.8 
Clinical Criteria for Early Trial Termination ................................................... 47 
6.0 
TRIAL FLOW CHART ........................................................................................... 49 
6.1 
Study Flow Chart .................................................................................................. 49 
7.0 
TRIAL PROCEDURES ........................................................................................... 53 
7.1 
Trial Procedures ................................................................................................... 53 
 Administrative Procedures .................................................................................. 53 
 Screening and Enrollment Procedures for Participating Sites. ........................ 53 
 General Informed Consent and Screening Procedures ..................................... 54 
 Clinical Procedures/Assessments During Study Treatment ............................. 55 
 Tumor Tissue and Blood Collection and Treatment-Related Immunologic 
Correlates .............................................................................................................. 57 
 Laboratory Procedures/Assessments .................................................................. 61 
 Other Procedures .................................................................................................. 63 
 Visit Requirements ............................................................................................... 63 

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7.1.8.1 Screening ................................................................................................................ 63 
7.1.8.2 Safety Follow-Up Visit .......................................................................................... 63 
7.1.8.3 Post-Treatment Follow-up for Disease Status .................................................... 64 
7.1.8.4 Survival Follow-up ................................................................................................ 64 
7.2 
Assessing and Recording Adverse Events .......................................................... 64 
 Definition of a Pembrolizumab Overdose for This Protocol and Reporting 
of Overdose to the Sponsor and to Merck .......................................................... 65 
 Reporting of Pregnancy and Lactation to the Sponsor and to Merck ............. 66 
 Immediate Reporting of Adverse Events to the Sponsor and to Merck .......... 66 
 Evaluating Adverse Events .................................................................................. 68 
 Sponsor Responsibility for Reporting Adverse Events ..................................... 71 
8.0 
STATISTICAL Considerations ............................................................................... 71 
8.1 
Definitions of Efficacy Endpoints ........................................................................ 71 
8.2 
Statistical Analysis Plan Summary ..................................................................... 72 
9.0 
LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES ................................................................................................................. 72 
9.1 
Gemcitabine ........................................................................................................... 73 
 Availability ............................................................................................................ 73 
 Storage and Stability ............................................................................................ 73 
 Administration ...................................................................................................... 73 
 Toxicities ................................................................................................................ 73 
9.2 
Pembrolizumab (MK-3475) – Investigational Product ..................................... 73 
 Packaging and Labeling Information ................................................................. 74 
 Clinical Supplies Disclosure ................................................................................. 74 
 Storage and Handling Requirements .................................................................. 74 

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 Returns and Reconciliation .................................................................................. 74 
10.0 
ADMINISTRATIVE AND REGULATORY DETAILS ....................................... 75 
10.1 
Confidentiality ....................................................................................................... 75 
10.2 
Compliance with Financial Disclosure Requirements ....................................... 75 
10.3 
Compliance with Law, Audit and Debarment ................................................... 75 
10.4 
Compliance with Trial Registration and Results Posting Requirements ........ 75 
11.0 
Data Management Issues .......................................................................................... 75 
11.1 
Data and Source Documentation for Participating Sites .................................. 75 
11.2 
Quality Assurance ................................................................................................. 76 
 Quality Assurance for Participating Sites .......................................................... 76 
11.3 
Amendments .......................................................................................................... 77 
11.4 
Additional IRB Correspondence ......................................................................... 77 
11.5 
Document Maintenance ........................................................................................ 78 
11.6 
Noncompliance ...................................................................................................... 79 
 Regulatory Documentation .................................................................................. 79 
11.7 
Response Review ................................................................................................... 79 
11.8 
Data and Safety Monitoring Plan ........................................................................ 79 
12.0 
APPENDICES ........................................................................................................... 82 
12.1 
ECOG Performance Status .................................................................................. 82 
12.2 
Common Terminology Criteria for Adverse Events V4.0 (CTCAE) ............... 82 
12.3 
Events of Clinical Interest Guidance Document ................................................ 82 
12.4 
Radiation Directives ............................................................................................. 82 
13.0 
References: ................................................................................................................. 84 
 

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1.0 TRIAL SUMMARY 
Abbreviated Title 
A phase II Trial of Pembrolizumab (MK3475) Combined with 
Chemoradiotherapy in Muscle-Invasive Bladder Cancer  
Trial Phase 
II 
Clinical Indication 
Previously untreated cT2-T4aN0 Muscle-Invasive Urothelial Bladder 
Cancer and non-surgical candidate or refusing cystectomy. 
Trial Type 
Interventional 
Type of control 
No Treatment Control 
Route of administration 
Intravenous and external beam radiotherapy 
Trial Blinding 
Unblinded, Open Label 
Treatment Groups  
Single-Arm, No Randomization 
Number of trial subjects 
Up to a total of 54 subjects will be enrolled 
Estimated enrollment period 
2-3 years 
Estimated duration of trial 
The sponsor estimates that the trial will require approximately 60 months 
from the time the first subject signs the informed consent until the last 
subject’s last visit. 
Duration of Participation 
Protocol eligible subjects with documented muscle-invasive bladder 
cancer will participate in the trial from the time the subject signs the 
Informed Consent Form (ICF) through the final contact. There will be a 
screening period of 42 days after informed consent.  Upon determination 
of eligibility and enrollment, the patient will be eligible to receive 
treatment beginning with pembrolizumab (MK-3475) followed 2-3 weeks 
later by standard maximal TURBT.  Following a rest period of 
approximately 3-5 weeks to allow healing, the patient will receive 
combination treatment with hypofractionated radiation therapy and low-
dose twice weekly Gemcitabine over 4 weeks and concurrent every 3 
weeks Pembrolizumab (MK3475) for 3 doses. Patients will undergo a 
repeat TURBT approximately 12 weeks after completion of radiation to 
assess for response.  Patients will be followed for safety/toxicity 
assessment for up to 90 days after completion of last radiation treatment.  
Subsequent to completion or discontinuation of study treatment, patients 
will also be followed by cystoscopic and imaging surveillance to monitor 
for local, regional and distant disease recurrence for up to 5 years or until 
disease progression is confirmed, consent is withdrawn, death or 
becoming lost to follow up.  
Serious adverse events and events of clinical interest will be collected for 
90 days after the end of radiation treatment or until the subject initiates 
new anticancer therapy, whichever is earlier. All subjects will be followed 
for overall survival every 3 months (± 7 days) until death, withdrawal of 
consent, or the end of the trial follow up which is defined as 5 years from 
the date of protocol treatment start. 
 
 
 
 

8 
 
 
2.0 TRIAL DESIGN 
2.1 
Trial Design 
This is an open-label single arm phase II trial of pembrolizumab (MK-3475) in combination 
with hypofractionated EBRT (external beam radiation therapy) and gemcitabine as definitive 
therapy in patients with muscle-invasive bladder cancer who are not candidates for or decline 
radical cystectomy. 
Eligible patients are those with previously untreated histologically documented clinical stage 
T2 – T4aNx/N0M0 muscle-invasive urothelial bladder cancer who are cisplatin-ineligible and 
non-surgical candidates or those who refuse cisplatin-based neoadjuvant chemotherapy and 
radical cystectomy.  All patients will be required to submit adequate pre-treatment TURBT 
tissue (FFPE tissue block or 20 unstained slides) documenting muscle-invasive urothelial 
bladder cancer.  
Eligible patients will first receive a single dose of Pembrolizumab (MK-3475) 200 mg IV 
followed 2-3 weeks later by maximal TURBT (transurethral resection of bladder tumor).  After 
3-5 weeks to allow for healing, patients will next receive gemcitabine plus Pembrolizumab 
(MK3475) with concurrent hypofractionated EBRT over 4 weeks (5 days of radiation/week x 
4 weeks = 20 total fractions).    Patients will receive low-dose gemcitabine twice per week for 
the 4 weeks of radiation.  Pembrolizumab will be administered every 3 weeks during 
combination chemoradiation beginning on Day 1 of radiation and will continue for a total of 3 
doses.  Approximately 12 weeks after completion of radiation, patients will undergo a repeat 
cystoscopy with TURBT to evaluate pathologic response.  
This study will target a total enrollment of up to 54 patients.  Due to the lack of a previous 
phase I trial establishing the safety of this combination, an initial safety lead-in cohort of 
3 to 6 patients will be enrolled after which enrollment will be halted and an interim safety 
analysis and toxicity review will be performed. Three patients will be enrolled in the initial 
safety study and will be evaluated for safety after 90 days after the end of combination 
treatment (defined as the last day of radiation). If none of these patients has a dose-limiting 
toxicity (DLT) (defined in section 5.2.1), then the trial will proceed to enroll the efficacy 
cohort. If one of these 3 initial patients has a DLT, then an additional 3 patients will be entered 
into the safety trial. If no additional patients experience a DLT, and no additional safety 
concerns are raised by the DSMC (section 11.8) the trial continues to the Phase II efficacy 
portion for an additional 48 patients. If ≥ 2 of 6 patients has a safety event, then the trial is 
discontinued and no further patients will be enrolled.  
An additional interim safety analysis will be conducted after the 20th patient enrolled to the 
phase II efficacy cohort reaches the 90 days DLT period defined in the safety lead-in.  If 4 or 
more of 20 patients have developed a protocol defined DLT (section 5.2.1), then further 
enrollment to the study will be halted.  Based on the nature and severity of the toxicities 
observed, consideration will be made to amend the study for dose and duration of radiation, 
gemcitabine and/or pembrolizumab vs terminating the study.  Enrollment will not be 
suspended during the interim safety analysis. 

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The Phase II portion of the trial is designed to test the hypothesis that the proportion of bladder-
intact disease-free survival (BIDFS) rate at 2 years is ≥80% compared to the expected rate of 
60% in patients treated with gemcitabine and radiation alone. Bladder-intact disease free 
survival is defined as time to earliest of muscle-invasive local bladder recurrence, regional 
pelvic recurrence, distant metastases, bladder cancer related death or cystectomy.  With 48 
patients entered into the Phase II efficacy trial, we can detect this difference with a 2-sided 
alpha of 0.05 and power of 85% (calculations from EAST 6.3, Cytel, Inc.)  
After completion or discontinuation of protocol therapy, patients will be followed for local-
regional and distant disease recurrence with cystoscopic surveillance and serial cross-sectional 
imaging.  As bladder-intact-disease-free-survival (BIDFS) is the primary endpoint of the trial, 
consistency in surveillance cystoscopies and imaging frequency will be required.   
From the date of last radiation treatment, patients will undergo cross-sectional surveillance 
imaging every 3 months for the first 18 months, every 6 months for the next 18 months, and 
then yearly thereafter for up to 5 years.  Patients will also be followed by cystoscopy with or 
without TURBT and urine cytology according to institutional practice approximately every 3 
months during the first year after completion of treatment; every 4 months the second year; 
every 6 months for the next 3 years; then annually. More frequent evaluations may be 
performed as clinically indicated or in accordance with institutional practice.  Any recurrence 
of a muscle-invasive tumor will be considered a local disease recurrence for the purposes of 
the primary endpoint. 
Adverse events will be monitored throughout the trial and graded in severity according to the 
guidelines outlined in the NCI Common Terminology Criteria for Adverse Events (CTCAE) 
version 4.0. Patients will receive treatment on protocol until completion of protocol therapy, 
unacceptable adverse event(s), intercurrent illness that prevents further administration of 
treatment, investigator’s decision to withdraw the subject, subject withdraws consent, 
pregnancy of the subject or noncompliance with trial treatment or procedure requirements. 
After the completion or discontinuation of study treatment each subject will be followed for 
disease recurrence every 3 months for the first 18 months, every 6 months for the next 18 
months and then yearly thereafter for up to 5 years until disease progression is confirmed, 
consent is withdrawn, death or becoming lost to follow up.  Serious adverse events and 
events of clinical interest (ECI) will be collected from date of informed consent through 90 
days after the end of radiation treatment or until the subject initiates new anticancer therapy, 
whichever is earlier. 
 
 
 
 
 
 
 

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2.2 
Trial Diagram 
 
 
Note: Chemotherapy should occur on Monday and Thursday OR Tuesday and Friday and the 
starting date of gemcitabine and MK3475 (Pembrolizumab) should correspond to the first day 
of radiation therapy 
3.0 OBJECTIVE(S) & HYPOTHESIS(ES) 
3.1 
Primary Objective(s) & Hypothesis(es) 
(1) Objective: To evaluate the anti-tumor activity of pembrolizumab (MK3475) added to 
standard chemotherapy and radiation as definitive treatment for patients with cT2-4aN0 
muscle-invasive urothelial bladder cancer who are not candidates for or refuse radical 
cystectomy.   
Hypothesis: Activity of this combination will be measured by estimating the rate of 
bladder-intact disease-free survival at 2 years.  Pembrolizumab (MK3475) added to 
standard chemoradiation will improve the rate of bladder-intact-disease-free-survival 
(BIDFS) at 2 years over that reported for chemoradiation alone based on historical controls.   
3.2 
Secondary Objective(s) & Hypothesis(es) 
(1) Objective: Safety as defined by NCI Common Toxicity Criteria for Adverse Events 
(CTCAE) version 4.0 
(2) Objective: Complete response (CR) Rate in the bladder as assessed by pathologic 
assessment of Exam Under Anesthesia and TURBT specimen obtained at the completion 
of all protocol therapy. 
(3) Objective: Metastasis-Free Survival as assessed by time to the development of 
radiographic distant metastases from beginning of protocol therapy  
(4) Objective: Overall Survival as measured by time to death from beginning of protocol 
therapy.  
Hypothesis:  Pembrolizumab (MK3475) will improve the rate of CR in the bladder, 
metastases-free survival and overall survival when added to standard chemoradiation as 

11 
 
 
definitive therapy for patients with cT2-4aN0 muscle-invasive urothelial bladder cancer 
who are not candidates for or refuse radical cystectomy.  
3.3 
Exploratory/Biomarker Objectives 
(1) 
Objective: Evaluate PD-1, PD-L1, PD-L2, TIM-3 and VISTA expression in pre and 
post-treatment tumor samples and correlate to response.   
(2) 
Objective: Evaluate the type, density and distribution of tumor infiltrating lymphocytes 
in pre- and post-treatment tumor samples and correlate to response. 
(3) 
Objective: Evaluate changes in T-cell clonal diversity via T-cell receptor next-
generation sequencing and clonotype diversity analysis. 
(4) 
Objective: Determine presence of and changes in T-cell responses to common viral and 
microbial antigens with treatment and correlate to outcomes 
(5) 
Objective: Determine the presence of and changes in antibody responses to a broad 
range of antigens with treatment. 
4.0 BACKGROUND & RATIONALE 
4.1 Background 
Bladder cancer is a common malignancy with an estimated 74,000 cases and 16,000 deaths for 
the year 2015 in the United States.1 Although the majority of patients present with superficial 
disease, approximately 20% to 40% of patients either present with more advanced disease or 
progress after treatment for superficial disease. The standard treatment for muscle-invasive 
bladder cancer is a radical cystectomy with bilateral pelvic lymphadenectomy. Prognosis 
varies inversely with higher T stage and lymph node involvement. In a series of 1,054 patients 
undergoing radical cystectomy, the overall recurrence-free survival rates at 5 and 10 years were 
68% and 66%, respectively.2 Prospective randomized trials as well as a large meta-analysis 
have demonstrated a survival benefit for the use of cisplatin combination chemotherapy in the 
neoadjuvant setting.3-5 Pathologic complete response (pT0) to neoadjuvant chemotherapy has 
been associated with improved survival. A US phase 3 intergroup trial that randomized patients 
with invasive bladder cancer to neoadjuvant M-VAC (methotrexate, vinblastine, adriamycin 
and cisplatin) plus cystectomy or to cystectomy alone, demonstrated an 85% 5-year survival 
for patients who experienced a complete pathologic response (38% in those patients who 
received M-VAC compared to 15% for those undergoing cystectomy alone).3 Numerous 
studies over the years have determined that selective bladder preservation represents a potential 
alternative to radical cystectomy.6-12 Such an approach results in approximately 50% long-term 
disease-free survival which is comparable to the results of modern cystectomy series.13 While 
the optimal bladder preservation protocol has not yet been defined, most generally include 
maximal (as complete a resection as possible) TURBT followed by chemoradiotherapy with 
cisplatin-based chemotherapy.14 The majority of bladder preservation protocols have included 
only patients who were candidates for salvage cystectomy. After combined modality therapy, 
approximately 20% to 30% of patients will have residual tumor at re-staging TURBT and an 

12 
 
 
additional 20% to 30% will develop new or recurrent disease in the bladder.14 Salvage 
cystectomy is required for patients with muscle-invasive persistent or recurrent tumors. Since 
many patients treated for muscle-invasive bladder cancer are older with comorbidities 
including renal dysfunction, salvage cystectomy may not be possible. Based on the success of 
bladder preservation therapy, it is reasonable to consider definitive nonsurgical treatment in 
poor-risk patients who are not candidates for cystectomy and also for patients who refuse 
radical cystectomy. 
 Bladder Preservation Approaches 
The optimal combined modality bladder-sparing regimen has not been defined however a 
recently reported phase III trial demonstrated improved local-regional control with concurrent 
chemoradiotherapy with 5-FU/Mitomycin-C over radiotherapy alone, establishing 
multimodality therapy as the optimal overall strategy.15 This approach involved a maximal 
transurethral resection of tumor followed by concurrent chemoradiation with or without 
neoadjuvant/adjuvant chemotherapy.  Cisplatin is among the most active agents in transitional 
cell carcinoma of the bladder. Furthermore, multiple preclinical studies have shown that 
cisplatin can potentiate radiation-induced damage to tumors. As a result, the majority of 
chemoradiation trials in bladder cancer have utilized concurrent cisplatin with complete 
response rates in the 59 to 75% range and 5-year survival of approximately 50%13. The 
necessity of neoadjuvant chemotherapy was explored in RTOG 89-03 in which patients were 
randomized to neoadjuvant cisplatin, methotrexate, plus vinblastine (CMV) followed by 
concurrent radiation plus cisplatin versus concurrent chemoradiation alone16. There was no 
difference in survival between the two arms at a median follow-up of 5-years. There have been 
no randomized trials comparing the results of bladder sparing with radical cystectomy. 
Compared with historical controls, the use of a combined modality approach in appropriately 
selected patients has yielded similar outcomes. Five-year survival rates of 50-60% have been 
reported with approximately 70% of these patients maintaining an intact bladder14. In a recent 
analysis of urodynamic studies and quality of life in patients treated with bladder preservation, 
the majority of patients with an intact bladder preserved normal bladder function and low rates 
of bowel symptoms and urinary incontinence were reported17. 
 Renal Dysfunction and Bladder Preservation Strategies 
Poor renal function often limits the ability to use cisplatin-based regimens in patients with 
bladder cancer. The median age of patients with bladder cancer is 68 years and glomerular 
filtration rate declines as part of the normal physiology of aging. A retrospective series 
evaluating the impact of renal impairment on eligibility for adjuvant cisplatin-based 
chemotherapy in patients with bladder cancer demonstrated a high prevalence of baseline renal 
insufficiency in this population with the probability for ineligibility increasing with age18. 
Using the Cockroft-Gault equation (based on CrCl < 60 mL/min), > 40% of patients age > 70 
years would be considered ineligible for cisplatin-based chemotherapy. In addition, many of 
these patients have concomitant medical illnesses, such as cardiac and/or vascular disease and 
diabetes mellitus which further impact on renal function and cisplatin induced toxicity. 
Alternative strategies for radiosensitization have included the use of concurrent capecitabine, 
paclitaxel alone and paclitaxel with carboplatin19-21.  

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 Gemcitabine and Radiotherapy in Bladder Cancer 
The nucleoside analog, gemcitabine is an active agent in bladder cancer and a known 
radiosensitizer at doses below cytotoxic levels.13 A phase I study reported by the University of 
Michigan of combined modality therapy with gemcitabine and radiotherapy in patients with 
muscle-invasive TCC demonstrated a high rate of bladder preservation.22 In 23 patients 
assessable for toxicity and response, the MTD of gemcitabine was 27 mg/m2 twice-weekly 
with concurrent radiotherapy a using CT-planned 3D-conformal techniques to gross tumor 
with a 1 cm expansion using an empty bladder technique for 60 Gy total, 2 Gy/d, for a total of 
6 weeks. The DLT manifested as an elevation in liver function tests, malaise, and edema. 
Complete response was seen in 21 of 23 patients (91%). The series was updated in 2009 with 
median follow up of 5.6 years, local failure occurred in 7 patients (30%), all of which were 
salvaged with cystectomy.23 The 5-year estimate of overall survival was 76%. 
There was no statistical difference in quality-of-life data collected (FACT-BL and FACT-G) 
before, during, or after concurrent gemcitabine and radiotherapy aside from those patients who 
received higher gemcitabine doses with dose-limiting toxicities24. A second phase I study led 
by investigators in the UK evaluated the MTD of gemcitabine given once weekly for four 
cycles during hypofractionated conformal radiotherapy (52.5 Gy in 20 fractions) in patients 
with locally advanced bladder cancer.25 Among the 8 patients in the study, the MTD was 150 
mg/m2 with a maximal recommended dose of 100 mg/m2. DLT consisted of one patient with 
grade 3 diarrhea and one patient with grade 3 urinary symptoms.  A complete response was 
seen in 7 of 8 patients (87.5%), all disease free at a median follow-up of 19.5 months (range, 
14-23 months).  These data led to a phase II trial that tested hypofractionated RT with 
Gemcitabine 100mg/m2 on days 1, 8, 15, and 22 in 50 patients.26 Three dimensional conformal 
RT was used to deliver 52.5 Gy in 20 fractions to the whole bladder plus a 1.5 cm margin. 
Nodal basins were not treated in an interest to minimize bowel toxicity. With a median follow 
up of 36 months, 3 year overall survival was 75%. Of note, one patient had bowel resection 
due to late toxicity and 2 died of treatment related complications. 
The most recent study reported by De Santis et al was a phase I study of radiation using 1.85 
Gy per day to 55.5 Gy with escalating doses of twice weekly gemcitabine including 20, 27, 30, 
33, 50 and 40 mg/m2 in 44 patients.   No DLTs were observed in dose levels 1–4 (20, 27, 30, 
33 mg/m2) and the MTD was defined at dose level 5 (50 mg/m2 gemcitabine twice a week) 
with two grade 3 adverse events (liver enzyme elevation and fatigue in one patient each). At 
the additional dose level of 40 mg/m2, grade 3 fatigue and diarrhea (both DLTs) occurred in 
only one of six patients and therefore 40 mg/m2 was considered the recommended dose for 
phase II testing.   In this study, 3-D conformal techniques were also used, but in this series the 
full bladder and regional lymph nodes were treated to 46.25 Gy followed by a boost to the 
partial bladder to 55.5 Gy. The 2-year local failure rate was 32%. 
The combination of gemcitabine with concurrent radiotherapy in patients with invasive bladder 
cancer is well-tolerated with substantial activity seen in the phase I setting worthy of further 
exploration in a phase II clinical trial. The tolerability of the combination is especially notable 
for use in an elderly cancer patient population with existing co-morbidities including renal 
insufficiency that limit surgery and cisplatin-based bladder preservation strategies. 

14 
 
 
 Bladder Cancer and the Older Patient 
Bladder cancer is typically a disease of elderly patients (median age, 68 years) with co-
morbidities receiving multimodality therapy and therefore represents an excellent disease 
model to incorporate a comprehensive geriatric assessment (CGA) tool. For patients, with 
localized muscle-invasive disease, standard management in the United States includes 
neoadjuvant chemotherapy followed by radical cystectomy. However, combined modality 
bladder preservation strategies have been increasingly explored as: 1) a subset of patients with 
clinical stage T2-3 disease which can be completely (or near completely) resected 
transurethrally may have comparable survival outcomes with such approaches as compared to 
surgery; 2) many older patients are poor candidates for surgery secondary to existing co-
morbid conditions; and 3) many patients simply refuse cystectomy. 
 Gemcitabine and the Immune Microenvironment 
The tumor immune microenvironment contains various elements that may work to promote or 
inhibit anti-tumor immunity.27 During periods of sustained immune activation such as cancer, 
immature myeloid cells (IMCs) are released into the peripheral circulation through the 
influence of various cytokines and soluble factors, undergo partial block of differentiation into 
myeloid derived suppressor cells (MDSCs), a heterogeneous population of cells comprised of 
myeloid cell progenitors and precursors of granulocytes, macrophages and dendritic cells with 
specific immunosuppressive functions. These cells then migrate to secondary lymphoid organs 
and tissues (such as the tumour site), where they exert their effects on other cell populations, 
such as CD8+ T-Cells.   
Gemcitabine has been shown in a tumor mouse model to dramatically and specifically reduce 
the number of CD11b/GR-1+ MDSCs in spleens of tumor-bearing mouse without significant 
reductions in CD4+ T cells, CD8+ T cells, NK cells, macrophages, or B cells. The loss of 
myeloid suppressor cells was accompanied by an increase in the antitumor activity of CD8+ T 
cells and activated NK cells.28 In a 4T1 mammary carcinoma model, gemcitabine treatment in 
tumor-bearing mice significantly inhibited tumor growth, reduced splenomegaly, and 
significantly decreased MDSC proportion in the spleen. Further, treatment of tumor-bearing 
mice with gemcitabine augmented in vitro expansion of splenic T cells and boosted IFN-
gamma secretion in response to stimulation by tumor antigen.29 
While the mechanism for selective depletion of MDSCs in preclinical models is not yet fully 
understood, these data suggest an additional role for gemcitabine combined with radiation and 
immune-checkpoint inhibition with Pembrolizumab (MK-3475).   
 Radiation and Immunogenic Cell Death 
Ionizing radiation therapy has been shown to alter the tumor milieu by enhancing trafficking 
of immune cells, induction of cytokines and co-stimulatory molecules and promotion of T-cell 
priming.  Pre-clinical cancer models have demonstrated a synergistic effect between immune 
checkpoint inhibitors and radiation, suggesting radiation may induce potent in vivo 
vaccination. Further, ionizing radiation has been shown to alter the tumor milieu by enhancing 

15 
 
 
trafficking of immune cells, induction of cytokines and co-stimulatory molecules and 
promotion of cross-priming.30  
At NYU, we have shown in the poorly immunogenic 4T1 mouse mammary carcinoma model 
that local radiation therapy to established primary tumors elicits effective CD8+ T cell 
mediated anti-tumor responses when combined with CTLA-4 blockade.31 The elicited immune 
response was effective against spontaneous lung metastases as well as the primary tumor. 
Regressing primary tumors had increased infiltration by activated CD8+ T-cells, and an 
expanded pool of tumor-specific memory CD8+ T-cells could be demonstrated in cured mice. 
These results demonstrate that RT to the primary tumor in combination with CTLA-4 blockade 
induces a therapeutically effective anti-tumor response, and it may provide antigenic 
stimulation similar to vaccination with irradiated autologous tumor cells. 
 Abscopal effect of radiotherapy 
Originally described by R.H. Mole in 1953, the abscopal effect of radiotherapy is a remote 
effect of ionizing radiation on malignancy outside the radiation field.32 The phenomenon was 
named the abscopal effect, from the Latin ab (position away from) and scopus (mark or target). 
Other investigators, over the years, have reported findings consistent with the abscopal effect 
definition, possibly as an occasional result of recovered anti-tumor immunity after 
radiotherapy.33-35 The mechanism remains unexplained, although a variety of mechanisms can 
be hypothesized,36 and recent research has re-focused on the immunological effects mediated 
by radiation.36-38 
 Harnessing the pro-immunogenic effects of radiation in cancer treatment: a new 
paradigm 
Experimental work done in two syngeneic mouse models of Lewis lung tumors and mammary 
carcinoma, testing radiotherapy with FLT-3 ligand (a growth factor for dendritic cells), 
demonstrated the induction of an immune response that reduced tumor growth outside the field 
of radiation.37, 39 The findings inspired a trial testing the combination of subcutaneous GM-
CSF (125 μg/m2) with radiotherapy to a metastatic site in patients with metastatic solid tumors. 
GM-CSF increases the percentage of dendritic cells and their maturation, facilitating cross-
presentation of newly released antigens after cell death at the site of radiotherapy. With a 
standard radiation fractionation of 3.5 Gy x 10 fractions, an abscopal response was detected in 
27% of the patients accrued to the trial.40 
Another combination strategy to overcome immune tolerance consists of the blockade of 
CTLA-4, an immune checkpoint that is a negative regulator of T-cell activation during 
priming. Prolonged survival and some cures occurred in a syngeneic model of poorly 
immunogenic, metastatic breast carcinoma, a process requiring CD8+ T-cells. Postow et al. 
recently reported a clinical case report with the same combination.41 A melanoma patient with 
disease progression while receiving ipilimumab, a monoclonal antibody that targets CTLA-4, 
was treated with hypo-fractionated radiotherapy to a pleural-based paraspinal metastasis; 
several other pre–existing metastases in the spleen and in the right lung hilum, (outside the 
radiation field) completely regressed, and remained controlled for an additional eight months. 

16 
 
 
Importantly, peripheral blood monitoring of several markers, including antibody response to 
NY-ESO-1 mirrored the clinical course. Serum analysis detected 10 antigenic targets with 
enhanced antibody responses after radiotherapy. A similar effect was previously reported in a 
study of radiation with a recombinant cancer vaccine to prostate cancer.42 These results, 
although still anecdotal, support the concept that local radiotherapy and immunotherapy can 
synergize to produce a therapeutically effective anti-tumor immune response. 
Combining radiotherapy with immunotherapy presents considerable advantages. Because of 
its localized nature, radiotherapy is devoid of most systemic effects commonly encountered 
with chemotherapy, and it limits interference with systemic immunotherapy. Moreover, a 
radiotherapy-focused intervention on the tumor may selectively subvert its microenvironment 
and in combination with the optimal immune intervention, may ideally render the cancer an in 
situ, individualized, vaccine.   
In muscle-invasive bladder cancer, up to 50% of patients will succumb to metastatic bladder 
cancer despite definitive local therapy.  Therefore, the addition of immune checkpoint 
inhibition with pembrolizumab, an anti-PD-1 inhibitor, to definitive radiation therapy to the 
bladder may work to both increase eradication of local tumor as well as distant 
micrometastases through heightened immune surveillance.  
 Pharmaceutical and Therapeutic Background 
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades.  Accumulating evidence shows a correlation 
between tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis in 
various malignancies.  In particular, the presence of CD8+ T-cells and the ratio of CD8+ 
effector T-cells / FoxP3+ regulatory T-cells seems to correlate with improved prognosis and 
long-term survival in many solid tumors. 
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress 
immune control.  The normal function of PD-1, expressed on the cell surface of activated T-
cells under healthy conditions, is to down-modulate unwanted or excessive immune responses, 
including autoimmune reactions.  PD-1 (encoded by the gene Pdcd1) is an Ig superfamily 
member related to CD28 and CTLA-4 which has been shown to negatively regulate antigen 
receptor signaling upon engagement of its ligands (PD-L1 and/or PD-L2).  The structure of 
murine PD-1 has been resolved.  PD-1 and family members are type I transmembrane 
glycoproteins containing an Ig Variable-type (V-type) domain responsible for ligand binding 
and a cytoplasmic tail which is responsible for the binding of signaling molecules.  The 
cytoplasmic tail of PD-1 contains 2 tyrosine-based signaling motifs, an immunoreceptor 
tyrosine-based inhibition motif (ITIM) and an immunoreceptor tyrosine-based switch motif 
(ITSM).  Following T-cell stimulation, PD-1 recruits the tyrosine phosphatases SHP-1 and 
SHP-2 to the ITSM motif within its cytoplasmic tail, leading to the dephosphorylation of 
effector molecules such as CD3ζ, PKCθ and ZAP70 which are involved in the CD3 T-cell 
signaling cascade.  The mechanism by which PD-1 down modulates T-cell responses is similar 
to, but distinct from that of CTLA-4 as both molecules regulate an overlapping set of signaling 
proteins.  PD-1 was shown to be expressed on activated lymphocytes including peripheral 

17 
 
 
CD4+ and CD8+ T-cells, B-cells, T regs and Natural Killer cells.  Expression has also been 
shown during thymic development on CD4-CD8- (double negative) T-cells as well as subsets 
of macrophages and dendritic cells.  The ligands for PD-1 (PD-L1 and PD-L2) are 
constitutively expressed or can be induced in a variety of cell types, including non-
hematopoietic tissues as well as in various tumors .  Both ligands are type I transmembrane 
receptors containing both IgV- and IgC-like domains in the extracellular region and contain 
short cytoplasmic regions with no known signaling motifs.  Binding of either PD-1 ligand to 
PD-1 inhibits T-cell activation triggered through the T-cell receptor.  PD-L1 is expressed at 
low levels on various non-hematopoietic tissues, most notably on vascular endothelium, 
whereas PD-L2 protein is only detectably expressed on antigen-presenting cells found in 
lymphoid tissue or chronic inflammatory environments.  PD-L2 is thought to control immune 
T-cell activation in lymphoid organs, whereas PD-L1 serves to dampen unwarranted T-cell 
function in peripheral tissues.  Although healthy organs express little (if any) PD-L1, a variety 
of cancers were demonstrated to express abundant levels of this T-cell inhibitor.  PD-1 has 
been suggested to regulate tumor-specific T-cell expansion in subjects with melanoma (MEL).  
This suggests that the PD-1/PD-L1 pathway plays a critical role in tumor immune evasion and 
should be considered as an attractive target for therapeutic intervention. 
Pembrolizumab is a potent and highly selective humanized monoclonal antibody (mAb) of the 
IgG4/kappa isotype designed to directly block the interaction between PD-1 and its ligands, 
PD-L1 and PD-L2.  KeytrudaTM (pembrolizumab) has recently been approved in the United 
Stated for the treatment of patients with unresectable or metastatic melanoma and disease 
progression following ipilumumab and, if BRAF V600 mutation positive, a BRAF inhibitor. 
 Pembrolizumab in Advanced Bladder Cancer 
A phase Ib trial of pembrolizumab in 33 advanced bladder cancer patients was recently 
presented at the 2014 European Society of Medical Oncology (ESMO) Annual Meeting and 
demonstrated rapid and durable responses in 24% of patients. Sixty-four percent experienced 
at least some decrease in their target lesions.  Therapy was well tolerated with the majority of 
adverse events being grade 1 or 2, approximately 10% rate of grade 3 or 4 adverse events and 
only 1 patient who discontinued treatment due to a treatment-related adverse event.   
A large phase II trial in untreated cisplatin-ineligible patients as well as a phase III randomized 
trial versus standard chemotherapy in the second-line setting are currently underway and 
should further define the role for pembrolizumab in advanced bladder cancer.   
Additional Preclinical and Clinical Trial Data 
Refer to the Investigator’s Brochure for additional Preclinical and Clinical data. 
4.2 
Rationale 
 Rationale for the Trial and Selected Subject Population 
Patients with localized muscle-invasive bladder cancer who are not candidates for radical 
cystectomy or those who refuse radical cystectomy are best managed with trimodality bladder 

18 
 
 
preservation therapy.  This treatment approach entails maximal tumor reduction in the bladder 
with TURBT, followed by combined chemoradiation.  Although a randomized trial 
demonstrated the superiority of chemoradiation vs radiation alone, the optimal radio-
sensitizing chemotherapy regimen is not yet been determined and still a significant proportion 
of patients will succumb to local-regional recurrence and also distant metastases.   
Gemcitabine combined with radiation has been demonstrated to be a well-tolerated regimen in 
multiple phase I and II trials and is an effective option for patients who cannot tolerate more 
aggressive chemoradiation regimens, such as those that contain cisplatin or 5-FU and 
mitomycin-C.  Further, gemcitabine has been shown to deplete specific immunosuppressive 
cells such as MDSCs in the tumor microenvironment, which lends strong rationale for a 
bladder preservation approach that includes immunotherapy with immune checkpoint 
inhibition.  This trial aims to test combined hypofractionated radiation therapy, added to low-
dose twice-weekly gemcitabine and pembrolizumab in patients with muscle-invasive bladder 
cancer who are not candidates for radical cystectomy or those who refuse cystectomy.  
 Rationale for Dose Selection/Regimen/Modification 
4.2.2.1 Rationale for Radiation Total Dose and Fractionation: 
Data from pre-clinical models suggest a relationship between radiation dose (fractionation) 
and ability to induce immunogenic cell death in tumors.  In humans, radiation to generate an 
in vivo tumor vaccine in combination with immune checkpoint inhibitors has only been tested 
in the context of short course focal radiotherapy to a single metastatic site in patients with 
metastatic cancer.  These data suggest higher dose (hypofractionation) elicits the greatest 
potential for immunogenic cell death.  
At NYU, we have shown in two syngeneic murine tumor models from mice of different genetic 
background, mammary carcinoma TSA (BALB/c) and colorectal carcinoma MCA38 
(C57BL/6), that fractionated RT regimens (6 Gy x5 and 8 Gy x3) were able to convert these 
unresponsive tumors into tumor responsive to anti-CTLA-4 mAb. Conversely a single RT dose 
of 20 Gy failed to show efficacy.43 In collaboration with Drs. MJ Aryankalayil and CN 
Coleman (NCI Experimental Therapeutics Section, Radiation Oncology Branch), we have 
analyzed the gene expression profiles in TSA tumors in vivo immediately after RT. Data show 
the rapid induction of immune response genes by the fractionated but not single dose RT 
regimen with a dominant type I IFN response emerging, which was confirmed by qRT-PCR. 
Data suggest that fractionated RT can convert an unresponsive tumor into one  
 
 
Table1: Biological Effective Doses of Regimens  
Biological effective doses (BED) of regimens used in case 
reports of abscopal responses from RT and ipilimumab, 
compare to RTOG-defined ablative dose  
References  
RT regimen 
BED10  

19 
 
 
responsive to anti-CTLA-4 at least in 
part by inducing an active immune 
microenvironment, a hypothesis that 
will be tested in the proposed studies. 
While the pre-clinical data support 
the choice of fractionated radiotherapy for the proposed combination with immune checkpoint 
inhibition, the optimal radiation dose per fraction remains undetermined. Table 1 reports the 
currently available clinical data. Based on the linear-quadratic model46 and with the assumption 
of α/β = 10 Gy for tumor, none of the regimens used in the 2 published clinical reports of 
abscopal effects during CTLA-4 blockade in melanoma and in our case of NSCLC, used 
biological effective doses (BEDs) for tumor control comparable to those attributed to an 
ablative regimen of 20 Gy x3 (equivalent to BED10=180).47 Despite a much lower BED than 
that predicted to result in tumor ablation, in each of the examples quoted in Table 1 a complete 
remission was observed at the irradiated site, supporting a direct contribution of the immune 
system. Interestingly, the BEDs for the regimens used in the cases of abscopal responses were 
within a close range. In the NSCLC case report summarized above the regimen used (6 Gy x5, 
BED10=48) successfully and persistently eliminated the liver metastasis in the field, 
suggesting a contribution of the immunotherapy with anti-CTLA-4. Importantly, no 
complications associated with the combination in this dose range of RT and ipilimumab were 
reported. This limited but relevant information has informed the design of the proposed trial.  
The optimal dose/fractionation schedule for radiation in the context of definitive therapy has 
not been determined.  However, data from a phase I and II trial of hypofractionated radiation 
with gemcitabine have demonstrated both safety and efficacy for this approach in patients with 
muscle-invasive bladder cancer.  Therefore, we propose a total dose of 52 Gy in 20 fractions 
as this has been validated in Phase I and II studies.25, 26  
The clinical tumor volume (CTV) will include the entire bladder and any extravesical extension 
seen on imaging plus a 1 cm expansion. . The planning target volume (PTV) will include an 
additional 0.5 cm for daily setup variation. Patients will undergo CT simulation and treatment 
will be delivered with image-guided radiation therapy with either intensity modulated radiaton 
therapy or volumetric modulated radiation therapy. . An empty bladder technique will be 
employed, as this is most reproducible. Patients will undergo cone beam CT (CBCT) since 
accurate targeting, while always important, is even more critical when hypofractionation is 
used. It is recommended that subjects undergo CBCT daily; however, a minimum of once per 
week is acceptable for this study as daily CBCT may be cumbersome from a practical 
standpoint at some centers. Treatment will be delivered 5 days per week for a total of 4 weeks 
(20 treatments). 
4.2.2.2 Rationale for Gemcitabine Dose and Schedule: 
Multiple studies have evaluated the combination of radiation and gemcitabine chemotherapy 
as definitive treatment in muscle-invasive bladder cancer.   
used  
Postow et al41 
9.5 Gy x3  
55.57  
Stamell et al44 
8 Gy x3  
43.2  
Golden et al45  
6 Gy x5  
48  
RTOG ablative 
dose  
20 Gy x3  
180 

20 
 
 
The first was a phase I trial led by the University of Michigan enrolled 23 patients with muscle-
invasive bladder to cancer to receive 60 Gy of EBRT with escalating doses of Gemcitabine. 
The starting dose of gemcitabine was 10 mg/m2 with subsequent dose levels of 20, 27, 30, and 
33 mg/m2.  No significant toxicity was demonstrated at the 10 or 20 mg/m2 twice-weekly 
doses. Dose-limiting toxicity (DLT) occurred in two of three patients treated at 33 mg/m2. 
Intermediate dose levels of 27 and 30 mg/m2 were then evaluated. The MTD of gemcitabine 
was 27 mg/m2. The DLT was systemic, manifested as an elevation in liver function tests, 
malaise, and edema. 
Another phase I study of radiation using 1.85 Gy/day to 55.5 Gy with escalating doses of 
gemcitabine administered twice weekly enrolled 44 patients with cT2-T4N0-1 urothelial 
cancer who were ineligible for surgery due to local tumor extension, performance status, age 
or co-morbidities or who refused surgery were included. After maximal transurethral resection 
patients received twice-weekly Gemcitabine at 20 mg/m2 (level 1), 27 mg/m2 (level 2), 30 
mg/m2 (level 3), 33 mg/m2 (level 4), 50 mg/m2 (level 5) and 40 mg/m2 (level 6). The primary 
end point was to determine the maximum-tolerated dose (MTD) and the dose recommended 
(RD) for further studies of this gemcitabine schedule.  MTD was defined by dose-limiting 
toxicity (DLT) in 2 or more of 6 patients, discontinuation of RT and/or gemcitabine for >1 
week in 2 or more of 6 patients due to grade (G) 3/4 acute and/or late toxicity in more than 2 
of 18 patients.  In this study, 35 of 44 patients were assessable for toxicity and thus the primary 
end point. DLTs occurred in two of five patients at dose level 5: one Grade 3 alanine 
aminotransferase elevation and one Grade 3 fatigue. The MTD, therefore, was 50 mg/m2 
gemcitabine twice weekly and 40 mg/m2 (level 6) was determined to be the RD for future 
testing (only one of six patients developed Grade 3 fatigue and diarrhea) Late toxicity was rare 
and of low grade (only G1-2). The 2-year locoregional failure rate was 32% (9/28); 10 of 28 
patients (38%) were alive with an intact bladder and no evidence of recurrent disease, 9 patients 
developed distant metastases and 6 died of their disease. 
Differences in patient populations and radiation technique may account for differences 
observed in the safety of the various dose levels of gemcitabine tested in these phase I trials.  
As the Michigan phase I trial demonstrated tolerable safety up to the 27 mg/m2 dose level but 
not above, and given the lack of prior safety data for the combination of radiation, gemcitabine 
and MK-3475 in cancer patients, proceeding with twice weekly gemcitabine 27 mg/m2 in this 
study is justified.   
4.2.2.3 Rationale for Pembrolizumab Dosing: 
An open-label Phase I trial (Protocol 001) is being conducted to evaluate the safety and 
clinical activity of single agent MK-3475.  The dose escalation portion of this trial evaluated 
three dose levels, 1 mg/kg, 3 mg/kg, and 10 mg/kg, administered every 2 weeks (Q2W) in 
subjects with advanced solid tumors.  All three dose levels were well tolerated and no dose-
limiting toxicities were observed.  This first in human study of MK-3475 showed evidence of 
target engagement and objective evidence of tumor size reduction at all dose levels (1 mg/kg, 
3 mg/kg and 10 mg/kg Q2W).  No MTD has been identified to date.  10.0 mg/kg Q2W, the 
highest dose tested in PN001, will be the dose and schedule utilized in Cohorts A, B, C and 
D of this protocol to test for initial tumor activity.  Recent data from other clinical studies 

21 
 
 
within the MK-3475 program has shown that a lower dose of MK-3475 and a less frequent 
schedule may be sufficient for target engagement and clinical activity. 
 
PK data analysis of MK-3475 administered Q2W and Q3W showed slow systemic clearance, 
limited volume of distribution, and a long half-life (refer to IB).  Pharmacodynamic data (IL-
2 release assay) suggested that peripheral target engagement is durable (>21 days).  This 
early PK and pharmacodynamic data provides scientific rationale for testing a Q2W and 
Q3W dosing schedule.   
 
A population pharmacokinetic analysis has been performed using serum concentration time 
data from 476 patients. Within the resulting population PK model, clearance and volume 
parameters of MK-3475 were found to be dependent on body weight. The relationship 
between clearance and body weight, with an allometric exponent of 0.59, is within the range 
observed for other antibodies and would support both body weight normalized dosing or a 
fixed dose across all body weights.  MK-3475 has been found to have a wide therapeutic 
range based on the melanoma indication.  The differences in exposure for a 200 mg fixed 
dose regimen relative to a 2 mg/kg Q3W body weight based regimen are anticipated to 
remain well within the established exposure margins of 0.5 – 5.0 for MK-3475 in the 
melanoma indication. The exposure margins are based on the notion of similar efficacy and 
safety in melanoma at 10 mg/kg Q3W vs. the proposed dose regimen of 2 mg/kg Q3W (i.e. 
5-fold higher dose and exposure). The population PK evaluation revealed that there was no 
significant impact of tumor burden on exposure. In addition, exposure was similar between 
the NSCLC and melanoma indications. Therefore, there are no anticipated changes in 
exposure between different indication settings. 
 
The rationale for further exploration of 2 mg/kg and comparable doses of pembrolizumab in 
solid tumors is based on: 1) similar efficacy and safety of pembrolizumab when dosed at either 
2 mg/kg or 10 mg/kg Q3W in melanoma patients, 2) the flat exposure-response relationships 
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. 

22 
 
 
 Rationale for Endpoints 
Common primary endpoints of trials investigating combined chemoradiation in bladder cancer 
include bladder intact survival and local-regional tumor control at a pre-specified time point, 
most commonly 2 or 3 years.  In the 4 published studies of radiation with gemcitabine in 
muscle-invasive bladder cancer, the rate of local-regional failure (i.e. recurrence of tumor in 
bladder or pelvis) is approximately 30-40% at two-years.  Similarly, in a pooled analysis of 6 
trials of combination chemotherapy and radiation for bladder preservation in muscle-invasive 
bladder cancer reported an endpoint of bladder-intact disease-free survival which is 
approximately 60% at 2-years.48  Bladder-intact disease free survival is defined as time to 
earliest of muscle-invasive local bladder recurrence, regional pelvic recurrence, distant 
metastases, bladder cancer related death or cystectomy. Therefore, in this study that aims to 
test the addition of pembrolizumab to standard chemoradiation in bladder preservation as well 
as in the immune surveillance of local and distant metastases,, bladder-intact disease-free 
survival at 2 years is the most appropriate and comprehensive primary endpoint.  Safety, 
complete response (CR) rate in the bladder, metastases-free survival and overall survival are 
also secondary endpoints.   
 Efficacy Endpoints 
4.2.4.1 Primary Objective:  
1. Assess the efficacy of MK3475 added to concurrent radiation and gemcitabine in the 
management of patients with MIBC who are not candidates for or decline radical 
cystectomy. The efficacy of this combination will be measured by estimating the rate 
of bladder-intact disease-free survival at 2 years. 
4.2.4.2 Secondary Objectives: 
1. Safety as defined by CTCAE v4.0 
2. Complete response (CR) rate in the bladder 
3. Metastasis-Free Survival 
4. Overall survival 
4.2.4.3 Biomarker Research/Correlative Objectives 
1. Evaluate PD-1, PD-L1, PD-L2, TIM-3 and VISTA expression in pre and post-
treatment tumor samples and correlate to response.   
2. Evaluate the type, density and distribution of tumor infiltrating lymphocytes in pre- 
and post-treatment tumor samples and correlate to response. 
3. Evaluate changes in T-cell clonal diversity via T-cell Receptor next-generation 
sequencing and clonotype diversity analysis. 

23 
 
 
4. Determine presence of and changes in T-cell responses to common viral and 
microbial antigens with treatment and correlate to outcomes 
5. Determine presence of and changes in antibody response to a broad range of antigens 
with treatment. 
5.0 METHODOLOGY 
5.1 
Entry Criteria 
 Subject Inclusion Criteria 
In order to be eligible for participation in this trial, the subject must: 
1. Histologically confirmed muscle-invasive urothelial cancer of the bladder within 60 
days of study enrollment. 
a. Patients must be willing to provide a TURBT specimen during screening and 
prior to enrollment if adequate specimen (FFPE tissue block or 20 unstained 
slides) from initial TURBT documenting muscle-invasive urothelial bladder 
cancer is not available. 
2. Clinical stage T2-T4a, N0, M0 urothelial bladder cancer. 
3. Deemed to not be a candidate for radical cystectomy by attending urologic oncologist 
or refuse radical cystectomy.  
4. Be willing and able to provide written informed consent/assent for the trial. 
5. Be ≥ 18 years of age on day of signing informed consent. 
6. Have a performance status of 0 or 1 on the ECOG Performance Scale. 
7. Demonstrate adequate organ function as defined in Table 1, all screening labs should 
be performed within 10 days of protocol enrollment.   
Table 1 Adequate Organ Function Laboratory Values 
System 
Laboratory Value 
Hematological 
 
Absolute neutrophil count (ANC) 
≥1,500 /mcL 
Platelets 
≥100,000 / mcL 
Hemoglobin 
≥9.0 g/dL  
Renal 
 
Serum creatinine OR 
 
Calculated creatinine clearance 
≤1.5 X upper limit of normal (ULN) OR 
 
≥30 mL/min as calculated by Cockcroft-Gault formula or by 24 
hour urine collection 
Hepatic 
 
Serum total bilirubin 
≤ 1.5 X ULN OR 

24 
 
 
 
Direct bilirubin ≤ ULN for subjects with total bilirubin levels > 
1.5 ULN 
AST (SGOT) and ALT (SGPT) 
≤ 1.5 X ULN  
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 
≤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 
 
 
8. 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.   
9. Female subjects 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 childbearing potential are those who have not been surgically 
sterilized or have not been free from menses for > 1 year.  
10. Male subjects 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. 
 Subject Exclusion Criteria 
The subject must be excluded from participating in the trial if the subject: 
1. Has received prior targeted small molecule therapy, radiation therapy or systemic 
chemotherapy for urothelial bladder cancer including neoadjuvant chemotherapy.  
- 
Prior intravesical chemotherapy or intravesical immunotherapy is permissible, 
however, no prior intravesical therapy is permitted within 4 weeks of study 
enrollment; adjuvant therapy is not permitted 
2. Has received prior pelvic radiation therapy. 
3. Has a history of inflammatory bowel disease or history of scleroderma. 
4. 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. 

25 
 
 
5. Has a diagnosis of immunodeficiency or is receiving systemic steroid therapy or any 
other form of immunosuppressive therapy within 7 days prior to the first dose of trial 
treatment. 
 
6. Has a known history of active TB (Bacillus Tuberculosis) 
 
7. Hypersensitivity to pembrolizumab or any of its excipients. 
8. Has had a prior anti-cancer monoclonal antibody (mAb) within 4 weeks prior to study 
Day 1 or who has not recovered (i.e., ≤ Grade 1 or at baseline) from adverse events due 
to agents administered more than 4 weeks earlier. 
9. If subject received major surgery, they must have recovered adequately from the 
toxicity and/or complications from the intervention prior to starting therapy.   
10. Any prior history of invasive malignancy within the past 5 years except non-melanoma 
skin cancer, carcinoma in-situ, localized prostate cancer without biochemical 
recurrence following definitive treatment.   
11. Has other active autoimmune disease that has required systemic treatment in the past 2 
years (i.e. with use of disease modifying agents, corticosteroids or immunosuppressive 
drugs). Replacement therapy (eg., thyroxine, insulin, or physiologic corticosteroid 
replacement therapy for adrenal or pituitary insufficiency, etc.) is not considered a form 
of systemic treatment.  
12. History of Guillain-Barre Syndrome or Stevens-Johnson Syndrome 
13. Has known history of, or any evidence of active, non-infectious pneumonitis. 
14. Has an active infection requiring systemic therapy. 
15. 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.   
16. Has known psychiatric or substance abuse disorders that would interfere with 
cooperation with the requirements of the trial. 
17. 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. 
18. Has received prior therapy with an anti-PD-1, anti-PD-L1, or anti-PD-L2 agent. 
19. Has a known history of Human Immunodeficiency Virus (HIV) (HIV 1/2 antibodies). 

26 
 
 
20. Has known active Hepatitis B (e.g., HBsAg reactive) or Hepatitis C (e.g., HCV RNA 
[qualitative] is detected). 
21. Has received a live vaccine within 30 days of planned start of study therapy. 
Note:  Seasonal influenza vaccines for injection are generally inactivated flu vaccines 
and are allowed; however intranasal influenza vaccines (e.g., Flu-Mist®) are live 
attenuated vaccines, and are not allowed. 
5.2 
Trial Treatments 
 Toxicity Monitoring, Initial and Interim Safety Analysis and Decision Rule for 
Enrollment 
As the safety of pembrolizumab added to radiation and low-dose gemcitabine is unknown, this 
study will be monitored for dose-limiting toxicity during an initial safety cohort of up to 6 
patients as well as during an interim safety analysis after 20 patients are enrolled to the phase 
II efficacy cohort. Dose-Limiting Toxicity (DLT) will be defined as:  
o Any Grade 3 or 4 non-hematologic toxicity with the specific exclusion of: 
 Grade 3 ALT that returns to levels that meet initial eligibility criteria or baseline 
within 7 days and does not require systemic immunosuppression. 
 Grade 3 liver enzyme elevation, including AST/GGT that returns to baseline 
within 7 days and does not require systemic immunosuppression 
 Grade 3 or 4 serum electrolyte or mineral abnormalities responsive to 
supplementation and that do not result in hospitalization. 
 Grade 3 or 4 amylase or lipase abnormalities that are not associated with diabetes 
mellitus (DM), associated liver or gall bladder inflammation, clinical 
manifestations of pancreatitis, and which decrease to ≤ Grade 2 within 7 days.  
 Grade 3 rash that resolves to Grade ≤ 1 within 7 days.  
 Grade 3 fever that resolves to Grade ≤ 1 within 7 days.  
 Grade 3 fatigue that resolves to Grade ≤ 2 within 7 days.  
o Grade 2 uveitis, eye pain, or blurred vision that does not respond to topical therapy and 
does not improve to Grade 1 prior to next scheduled dose. 
o Grade 2 non-hematological toxicity requiring systemic immunosuppressive therapy. 
This includes, but is not limited to, autoimmunity of the lung, heart, kidney, bowel, 
CNS, pituitary or eye. 
o Grade 2 endocrine toxicity requiring hormone replacement, with the exception of 
Grade 2 thyroiditis and thyroid dysfunction. 
o Grade 2 adrenal insufficiency. 
o Any non-hematological toxicity requiring > 14 days delay in therapy will be 
considered a DLT. 
o Note: Allergic reactions that necessitate discontinuation of study drug will not be 
considered a dose-limiting toxicity. 
o Any of the following hematologic events: 

27 
 
 
 Febrile neutropenia defined as Grade 3 or 4 neutropenia with fever ≥ 38.5 degrees 
C and/or infection.   
 Any Grade 4 neutropenia lasting 5 days or more 
 Any incident of grade 4 thrombocytopenia (platelet count <25x109/L) or grade 3 
thrombocytopenia with bleeding 
 Failure of the absolute neutrophil count (ANC) to recover to ≥1000/µL or platelets 
to recover to ≥ 50,000/µL within 14 days  
 Any incident of grade 4 anemia 
 
As the safety of single agent Pembrolizumab (MK-3475) is well known in patients with cancer, 
the DLT monitoring period will be between Day 1 of combination chemoimmunoradiotherapy 
and up to 90 days after completion of radiation.  
The first 3 subjects will be enrolled and if no subjects develop a DLT event within the DLT 
period, then the study will proceed to full enrollment of the phase II efficacy cohort of 48 
patients.  If 1 of 3 subjects develops a DLT event during the DLT period, then 3 additional 
subjects will be enrolled into the safety cohort.  If no further DLT events occur, then the study 
will proceed to full enrollment.  If 1 or more additional DLT events occur, then the trial will 
be terminated.  If 2 or more DLT events occur in the first 3 subjects enrolled, then the trial will 
be terminated.  The maximum number of patients who will be enrolled in the safety cohort is 
6 subjects.  The schema for this decision rule will be the follows: 
 
An additional interim safety analysis will be conducted after the 20th patient enrolled to the 
phase II efficacy cohort reaches the 90 days DLT period defined in the initial safety lead-in.  
If 4 or more of 20 patients have developed a protocol defined DLT, then further enrollment to 
First 3 patients 
enrolled
0 of 3 develop DLT
Proceed to full 
enrollment
1 of 3 develop DLT 
1 of 6 develop DLT
Proceed to Full 
Enrollment
≥ 2 of 6 develop DLT
Trial Terminated
≥ 2 of 3 develop DLT
Trial Terminated
3 additional 
patients

28 
 
 
the study will be halted.  Based on the nature and severity of the toxicities observed, 
consideration will be made to amend the study for dose, schedule and duration of radiation, 
gemcitabine and/or pembrolizumab vs terminating the study in consultation with the IRB, 
DSMC and the FDA.  Enrollment will not be suspended during the interim safety analysis.   
 Lead-In Pembrolizumab and Maximal TURBT: 
Protocol therapy should begin within 14 days of trial enrollment and will proceed only if the 
following laboratory indices are met within 3 days of treatment initiation (see section 6.0 
TRIAL FLOW CHART) with lead-in pembrolizumab (MK-3475): 
Hematologic 
 
Absolute neutrophil count (ANC) 
≥1,500 /mcL 
Platelets 
≥100,000 / mcL 
Hemoglobin 
≥9 g/dL  
Renal 
 
Serum creatinine OR 
Calculated creatinine clearance 
≤1.5 OR 
≥30 mL/min (calculated by Cockcroft-Gault formula or 24 hour 
urine collection) 
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) 
≤ 1.5 X ULN 
 
Patients will first receive a single dose of Pembrolizumab (MK3475) 200 mg IV followed 2-3 
weeks later by maximal TURBT (transurethral resection of bladder tumor) of any visible 
residual tumor.  Maximal TURBT is performed for maximal tumor debulking prior to initiation 
of combined chemoradiotherapy for bladder preservation in muscle-invasive bladder cancer 
and represents the standard of care. As tumor tissue from this procedure is not required for 
diagnosis, it will be collected in toto for biomarker analysis. Sites with institutional 
requirement for submission of tumor tissue specimens to pathology first may do so after 
consultation with the study sponsor/principal investigator.  As specimen obtained during 
maximal TURBT is not required for either diagnosis or treatment planning, only the minimum 
quantity required should be retained by site pathology department. Tissue collection 
procedures are outlined in section 7.1.3 and in the accompanied laboratory manual. 
 
 Combination Chemo-Radio-Immunotherapy: 
Approximately 3 to 5 weeks after maximal TURBT to allow for healing, patients will next 
receive gemcitabine plus Pembrolizumab (MK3475) with concurrent hypofractionated EBRT 
over 4 weeks (5 days of radiation/week x 4 weeks = 20 total fractions).  Ideally radiation 
therapy should begin on a Monday for convenience, but is not required.  Radiation, 
pembrolizumab and gemcitabine must all begin on the same day. 
Combination Chemoradioimmunotherapy should begin only if the following laboratory 
parameters are met on Day 1: 
Hematologic 
 

29 
 
 
Absolute neutrophil count (ANC) 
≥1,500 /mcL 
Platelets 
≥100,000 / mcL 
Hemoglobin 
≥9 g/dL 
Renal 
 
Serum creatinine OR 
Calculated creatinine clearance 
≤1.5 OR 
≥30 mL/min (calculated by Cockcroft-Gault Formula or by 24 
hour urine collection) 
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) 
≤ 1.5 X ULN 
 
Chemotherapy: 
Gemcitabine 27mg/m2 IV (intravenous) over approximately 30 minutes (or according to 
institutional guidelines) should be administered ideally on a Monday and Thursday OR 
Tuesday and Friday schedule for 4 consecutive weeks.  Gemcitabine must be administered on 
Day 1 of radiation.  Patients who complete all doses of gemcitabine will receive a maximum 
of two doses per week during the 4 weeks of radiation therapy for a maximum of 8 doses total.   
Immunotherapy: 
Pembrolizumab 200 mg IV (intravenous) will be administered every 3 weeks during 
combination chemo-radio-immunotherapy beginning on Day 1 of radiation for a total of 3 
doses.  Pembrolizumab infusion is to be administered over 30 minutes. Every effort should be 
made 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).  
Radiation: 
Simulation and Treatment Planning 
All patients will undergo simulation in the supine position with an empty bladder. A CT scan 
will be performed in the treatment planning position without intravenous/oral contrast. The 
superior and inferior scan borders will be the top of the iliac crests and bottom of ischial 
tuberosities. Scan slice thickness should be <5 mm. Rectal and bladder contrast materials are 
not recommended as this additional volume can distort organ volumes. The rectum should be 
as empty as possible for simulation. Target tissue and normal tissue contours including the 
bladder, small bowel, colon, rectum and femoral heads should be delineated on treatment 
planning software. 
Targets and normal organs should be contoured as follows: 
Clinical Target Volume (CTV): Entire bladder and any gross extravesical disease as seen on 
imaging plus a 1 cm margin. 
Planning Target Volume (PTV): CTV plus a uniform 0.5 cm margin 

30 
 
 
Rectum: Contouring should begin at recto-sigmoid junction and end at the beginning of the 
anal canal and will include the rectal lumen. 
Femoral head/neck: Right and left femoral head and neck are to be contoured separately 
Bowel bag: Small bowel and colon are to be contoured as one contiguous structure from the 
top of the iliac crests and to include any visible small or large bowel inferiorly. This structure 
does not include the rectum, which is contoured separately. 
There is no cone down or boost dose of radiation. Treatment will be delivered with multi-field 
intensity modulated radiation therapy (IMRT) or Volumetric Modulated Arc Therapy (VMAT) 
with customized dynamic multileaf collimator (DMLC) blocking. 
Dose Prescription and Normal Tissue Constraints 
The radiation dose will be 5200 cGy in 20 fractions (260 cGy per fraction). The minimum dose 
to the PTV (Dmin) will be defined as the dose to 99% of the PTV volume. Thus, for this study 
Dmin=D(99%). The Dmin should be >95% of the prescription dose. The maximum dose 
within the PTV (Dmax) is defined as a dose to 0.035 cc volume and should be <115% of the 
prescription dose. 
Normal organ dose constraints are as follows: 
Rectum: The median dose (D50%) should be less than 4500 cGy. The maximum dose (Dmax) 
should be less than 5500 cGy. Dmax is defined as a dose to 0.035 cc. 
Femoral head/neck: The maximum dose should be less than 4500 cGy. 
Bowel bag: The maximum dose (Dmax) should not exceed 5350 cGy and median dose (D50%) 
should not exceed 4000 cGy. Dmax is defined as a dose to 0.035 cc. 
Dose volume histograms (DVH) for PTV and normal organs must be submitted for review and 
QA. A bladder DVH is not necessary as it is included in the PTV. 
Section 12.4 Radiation Directives lists the dose and volume parameters for PTV and normal 
organs. This may be used by investigators as a dose directive for IMRT/VMAT treatment 
planning. 
Technical Factors 
Linear accelerators with beam energy of ≥ 6 MV must be used. Orthogonal verification films 
are required on day 1. In addition, localization with CBCT imaging is required at least once 
per week. As noted previously, daily CBCT is highly recommended. Investigators should 
adjust the table when the tumor position deviates more than 5 mm on the cone beam CT when 
compared to the initial planning CT. 
Documentation Requirements 

31 
 
 
The CT isodose plan with dose volume histograms must be submitted to NYU within 7 
working days of initiation of treatment.  
Compliance Criteria 
Compliance will be scored in relation to target and normal organ volumes, radiation dose, 
fractionation, and elapsed days. Each parameter will be scored as being per protocol, a 
variation (acceptable), or a deviation (unacceptable). Treatment plans illustrating the isodose 
distributions through the central plane of each site should be submitted to the study sponsor. 
The DVH for the rectum, bladder, small bowel, and femoral head should also be submitted for 
review and QA. 
Volumes (CTV, PTV, small bowel, rectum): 
Per Protocol:  volumes either within  1 cm of the protocol definition 
Variation: volumes are within 1- 2 cm of the protocol definition 
Deviation: volumes  are > 2 cm of the protocol definition. 
Radiation Dose: 
Per Protocol: The dose within the PTV is 95% - 115% of the dose prescription. 
Acceptable Variation: The minimum dose within the PTV is 90-95% of the dose prescription 
or the maximum dose within the PTV is 115-120% of the dose prescription. 
Deviation: The minimum dose within the PTV is less than 90% of the dose prescription or the 
maximum dose within the PTV is greater than 120% of the dose prescription. 
Total elapsed days: 
Per Protocol: up to 3 break days 
Variation: 4 – 7 break days 
Deviation: 8 or more break days 
Radiation Toxicity 
Potential toxicities associated with radiation therapy to the pelvis include loss of pubic hair, 
cutaneous erythema in the treated area, increased urinary frequency (which could be 
permanent), fatigue, nausea, vomiting, rectal irritation, dyspareunia, ovarian failure in women, 
and sterility. Less likely but potentially serious toxicities include weight loss, rectal ulcers, 
hematochezia, bowel obstruction, ureteral obstruction, and fistula formation. Bleeding from 
the bladder mucosal surface is potentially both an acute and chronic complication. 
Radiation Therapy Quality Assurance Reviews 

32 
 
 
The NYU Radiation Oncology Co-Chair, Nicholas Sanfilippo, M.D., will perform RT Quality 
Assurance Review on an ongoing basis. 
 Post-Treatment Response Assessment: 
Approximately 12 weeks after completion of radiation, patients will undergo standard 
repeat cystoscopy with TUR of residual tumor and/or sampling of tumor bed and exam under 
anesthesia to document pathologic response (see section 8.1 for definitions of efficacy 
endpoints).  A sample of tissue will be sent for pathologic diagnosis and additional sample 
must be collected for biomarker analysis. 
Table 2.  Systemic Treatment on Trial 
Drug 
Dose/Potency 
Dose 
Frequency 
Route 
Regimen/Treatment 
Period 
Use 
Gemcitabine 
27 mg/m2a 
Twice 
per week 
IV infusion 
30 minutes 
Twice per week on 
M/Th or T/F only 
beginning on day 1 of 
radiation. 
Standard 
Pembrolizumab 
(MK-3475) 
200 mg X 
mg/kg 
Q3W 
IV infusion 
 
Every 3 weeks x 3 
doses beginning day 1 
of radiation. 
Experimental 
a. Dosing for gemcitabine during the combination chemo-radio-immunotherapy treatment should be based on the patient’s Week 1 Day 1 
calculated BSA using the actual (unadjusted) body weight.  This dosing is to be used during the complete chemo-radio-immunotherapy 
treatment for all treatment days and should only be adjusted if there is a ≥ 10% change in body weight.     
Table 3.  Radiation Treatment on Trial 
Dose/Fraction 
Number 
of 
Fractions 
Total 
Radiation 
Dose 
Technique 
Use 
2.6 Gy 
20 
52 Gy 
Multi-field intensity modulated radiation 
therapy 
(IMRT) 
planning 
with 
customized dynamic multileaf collimator 
(DMLC) blocking. 
Standard 
 
 Dose Selection/Modification 
5.2.5.1 Dose Selection 
The rationale for selection of doses to be used in this trial is provided in Section 4.0 – 
Background and Rationale.   

33 
 
 
Details on preparation and administration of pembrolizumab (MK-3475) are provided in the 
Pharmacy Manual.   
5.2.5.2 Dose Modification and/or interruption 
All patients will receive lead-in dose of pembrolizumab 200 mg IV prior to maximal TURBT 
for which no dose modifications/interruptions are permitted.  The following dose modification 
rules apply to toxicity during combination treatment considered possibly, probably, or 
definitely related to gemcitabine, pembrolizumab, radiation therapy or the combination.  
Dose modifications for hematologic toxicity will occur only on day of gemcitabine infusion 
and will be based on ANC (absolute neutrophil count) and platelet counts taken on the day of 
gemcitabine infusion.  Dose modifications for clinical assessment of non-hematologic toxicity 
will occur days of gemcitabine and/or pembrolizumab and will vary depending on the nature 
of the toxicity. 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 4 below. 
See Section 5.4.1 and Events of Clinical Interest Guidance Document for supportive care 
guidelines, including use of corticosteroids. 
Hematologic: Dose modifications for hematologic toxicity will be for gemcitabine only and 
will be made for blood counts obtained on the day of treatment with gemcitabine. Prophylactic 
granulocyte growth factor support is permitted and may be used at the discretion of the treating 
physician.  
Dose modification of Gemcitabine 
Blood counts must be obtained on each day of treatment with gemcitabine. Patients must have 
an ANC ≥ 1,500/μl and Platelet Count ≥ 100,000/μl to proceed with gemcitabine treatment. 
Patients who do not have ANC ≥ 1,500/ μl and platelet count ≥ 100,000/μl will have 
gemcitabine held for that day.  Missed gemcitabine doses will not be made up.  CBC will be 
rechecked at next scheduled treatment day until recovery to ANC ≥ 1,500/μl and platelet count 
≥ 100,000/μl at which time gemcitabine will be reinitiated at a reduced dose as described in 
the table below for up to two dose reductions. If further hematologic toxicity occurs, 
gemcitabine treatment will be permanently discontinued.  Radiation therapy will continue 
without interruption or modification. For any dose level, if after 3 weeks, the ANC has not 
recovered, all protocol treatment should be discontinued and the patients should be treated on 
an individual basis.  
Gemcitabine Dose Modification Table for Hematologic Toxicity 
ANC (cells/μL) 
 
Platelets (per μL) If Previous Dose of 
Gemcitabine was: 
Subsequent Gemcitabine 
dose upon count recovery 
<1,500 
or < 100 
27 mg/m2 (level 0) 
20 mg/m2 (level -1) 
<1,500 
or < 100 
20 mg/m2 (level -1) 16 mg/m2 (level -2) 

34 
 
 
<1,500 
or < 100 
16 mg/m2 (level -2) Discontinue Gemcitabine 
 
Febrile Neutropenia and/or Grade 4 Neutropenia and/or Grade 4 Thrombocytopenia 
For patients with grade 4 neutropenia (ANC < 500/μl) and/or febrile neutropenia (defined as 
temperature ≥ 38.5° C [101° F] sustained for more than one hour concomitant with an ANC < 
500/μl) and/or grade 4 thrombocytopenia (platelets < 25,000/μl), gemcitabine should be 
discontinued permanently and radiation therapy and pembrolizumab should be held. Radiation 
therapy and pembrolizumab may be resumed when the neutropenia resolves to < grade 2. If 
this has not been achieved after a one week delay, weekly blood counts should be checked 
until they become acceptable. If after 3 weeks, the ANC has not recovered, all protocol 
treatment should be discontinued and the patients should be treated on an individual basis.  
Grade 3 Neutropenia and/or Grade 3 Thrombocytopenia 
For patients with grade 3 neutropenia (< 1000-500/μl) and/or grade 3 thrombocytopenia (< 
50,000-25,000/μl), radiation and gemcitabine will be stopped for a minimum of one week and 
CBC with differential will be repeated weekly. Radiation and gemcitabine may be resumed 
once hematologic toxicity recovers to < grade 1. If after 3 weeks, the ANC has not recovered, 
all protocol treatment should be discontinued and the patient should be treated on an individual 
basis.  
Upon resumption, the gemcitabine will be dose reduced as outlined in the table above for up 
to 2 dose reductions. If a patient experiences grade ≥3 neutropenia and/or grade ≥3 
thrombocytopenia after any prior gemcitabine dose reduction, gemcitabine should be 
discontinued permanently.  
Renal Dysfunction: If grade 4 elevation of serum creatinine or worsening renal function 
requiring hemodialysis occurs during chemoradiotherapy, a thorough investigation of cause 
must be pursued and protocol treatment should be discontinued and the patient should be 
treated on an individual basis. 
Mucositis:  Grade 2 or greater mucositis will require withholding gemcitabine dose until 
recovery to ≤ grade 1, followed by a reduction in gemcitabine dose by 1 level for up to 2 dose 
reductions.  For grade 2 or greater mucositis despite 2 dose reductions in gemcitabine, 
gemcitabine should be discontinued.  Radiation therapy and pembrolizumab may continue.  
Cystitis 
If grade 3 or 4 cystitis toxicity occurs, treatment must be held until recovery to < grade 2 or 
baseline.  Gemcitabine will be dose reduced to dose level -2 (16 mg/m2) for all subsequent 
treatments. If after 3 weeks, the toxicity has not resolved, all protocol treatment should be 
discontinued and the patient should be treated on an individual basis.  

35 
 
 
Hepatic Dysfunction:  Hepatic dysfunction is a known potential toxicity of both 
pembrolizumab and gemcitabine and has been observed in trials of gemcitabine with radiation 
in muscle-invasive bladder cancer.   
Liver function tests will be checked on the first gemcitabine treatment day of each week 
of combination therapy.  If the bilirubin is > 1.5 x ULN (or Direct bilirubin > ULN for 
subjects with baseline total bilirubin levels > 1.5 ULN) and/or AST/ALT are > 1.5 x ULN, 
gemcitabine will be held until bilirubin is ≤ 1.5 x ULN (or Direct bilirubin ≤ ULN for subjects 
with baseline total bilirubin levels > 1.5 ULN) and AST/ALT ≤ 1.5 x ULN before resuming 
gemcitabine. In the event of a delay in treatment > 3 weeks, the patient will be removed from 
gemcitabine and pembrolizumab therapy but will continue radiation as scheduled.   
For grade 3 or 4 hepatic toxicity, gemcitabine will be held until recovery, at which time it will 
be resumed with dose reduction 1 level up to 2 reductions, after which gemcitabine will be 
discontinued.   
Dose adjustment of pembrolizumab for hepatotoxicity is outlined in table 4 and will occur on 
the scheduled days of pembrolizumab infusion only.  
Gastrointestinal Toxicity 
If grade 3 or 4 nausea/vomiting (in spite of administration of a prophylactic antiemetic 
regimen), or ileus toxicity occurs, the toxicity must resolve before treatment is resumed. 
Gemcitabine will be dose reduced 1 level for up to two dose reductions. For any dose level, if 
after 3 weeks the toxicity has not resolved, all protocol treatment should be discontinued and 
the patient should be treated on an individual basis.  
Both bladder chemoradiation and pembrolizumab may induce diarrhea with or without colitis 
and through disparate mechanisms.  Grade 1 diarrhea should be treated promptly with 
appropriate supportive care, including loperamide and gemcitabine will be dose reduced 1 level 
until resolution or return to baseline for up to 2 dose reductions. If grade 2 or 3 diarrhea occurs 
in spite of administration of prophylactic antimotility agents, all protocol therapy should be 
discontinued and appropriate investigation to underlying cause should be pursued including 
referral to gastroenterology.  If pembrolizumab induced diarrhea/colitis is presumed, then 
initiation of corticosteroids should be considered as per Table 4. Dose Modification and 
Toxicity Management Guidelines for Immune-related AEs Associated with Pembrolizumab. 
Toxicity must resolve to grade 1 or less before protocol therapy is resumed. If after 3 weeks, 
the toxicity has not resolved, all protocol treatment should be discontinued and the patient 
should be treated on an individual basis.  
Pulmonary Toxicity 
Interstitial pneumonia and pneumonitis are uncommon but known adverse events of both 
gemcitabine and pembrolizumab. Patients with worsening pulmonary symptoms including 
new onset of or worsening dyspnea, cough, or fever should promptly be evaluated for 
interstitial pneumonitis and treated as clinically indicated in section 5.4.1. Gemcitabine and 

36 
 
 
pembrolizumab should be temporarily discontinued pending diagnosis and treatment of the 
pulmonary disorder.  If immune related pneumonitis from pembrolizumab is suspected, 
treatment with pembrolizumab therapy should be held until symptoms improve to grade 1 or 
less.  Gemcitabine may be resumed as per investigator discretion.  Management guidelines for 
suspected immune related pneumonitis are outlined in Table 4 and in section 5.4.1.    
Other Non-hematologic Toxicity 
In the event of grade 3 or 4 non-hematologic toxicity not otherwise specified in the preceding 
sections felt to be at least possibly related to study treatment, hold all treatment and wait up to 
3 weeks for resolution to ≤ grade 1 or baseline. Then resume treatment with gemcitabine dose 
reduction 1 level up to a maximum of 2 dose reductions after which any subsequent event of 
similar grade 3 or 4 toxicity will lead to permanent discontinuation of all protocol therapy. 
Patients with suspected pembrolizumab toxicity should be managed as per Table 4.  
Gemcitabine Dose Modification for Obese Patients 
There is no clear documented adverse impact of treatment of obese patients when dosing is 
performed according to actual body weight. Therefore, all dosing is to be determined solely by 
(1) the patient’s BSA as calculated from actual weight or (2) actual weight without any 
modification unless explicitly described in the protocol. This will eliminate the risk of 
calculation error and the possible introduction of variability in dose administration. Failure to 
use actual body weight in the calculation of drug dosages will be considered a major protocol 
violation.  
 

37 
 
 
Table 4 
Dose Modification and Toxicity Management Guidelines for Immune-related AEs Associated with 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. 
 
Immune-related 
AEs 
Toxicity grade or 
conditions 
(CTCAEv4.0) 
Action taken to 
pembrolizumab 
irAE management with 
corticosteroid and/or other 
therapies  
Monitor and follow-up  
Pneumonitis  
Grade 2 
Withhold  
• Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper 
 
• 
Monitor participants for signs and 
symptoms of pneumonitis 
• 
Evaluate participants with suspected 
pneumonitis with radiographic imaging and 
initiate corticosteroid treatment 
• 
Add prophylactic antibiotics for 
opportunistic infections 
Grade 3 or 4, or 
recurrent Grade 2 
Permanently 
discontinue 
Diarrhea / Colitis  Grade 2 or 3 
Withhold 
• Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper 
 
• 
Monitor participants 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). 

38 
 
 
Grade 4 
Permanently 
discontinue 
• 
Participants with ≥ Grade 2 diarrhea 
suspecting colitis should consider GI 
consultation and performing endoscopy to 
rule out colitis.  
• 
Participants 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. 
AST / ALT 
elevation or 
Increased 
bilirubin 
Grade 2 
Withhold 
• Administer corticosteroids (initial 
dose of 0.5- 1 mg/kg prednisone or 
equivalent) followed by taper 
• 
Monitor with liver function tests (consider 
weekly or more frequently until liver 
enzyme value returned to baseline or is 
stable 
Grade 3 or 4  
Permanently 
discontinue 
• Administer corticosteroids (initial 
dose of 1-2 mg/kg prednisone or 
equivalent) followed by taper 
Type 1 diabetes 
mellitus (T1DM) 
or 
Hyperglycemia 
 
Newly onset 
T1DM or  
Grade 3 or 4 
hyperglycemia 
associated with 
evidence of β-cell 
failure 
Withhold 
• Initiate insulin replacement 
therapy for participants with 
T1DM  
• Administer anti-hyperglycemic in 
participants with hyperglycemia  
 
• 
Monitor participants 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 
discontinue1  
Hyperthyroidism  
Grade 2 
Continue  
• Treat with non-selective beta-
blockers (eg, propranolol) or 
thionamides as appropriate  
• 
Monitor for signs and symptoms of thyroid 
disorders.  
 
Grade 3 or 4  
Withhold or  
permanently 
discontinue1 
Hypothyroidism 
Grade 2-4 
Continue  
• Initiate thyroid replacement 
hormones (eg, levothyroxine or 
liothyroinine) per standard of care 
• 
Monitor for signs and symptoms of thyroid 
disorders.  
 

39 
 
 
Nephritis and 
Renal 
dysfunction 
Grade 2 
Withhold  
• Administer corticosteroids 
(prednisone 1-2 mg/kg or 
equivalent) followed by taper. 
• 
Monitor changes of renal function 
 
Grade 3 or 4  
Permanently 
discontinue 
Myocarditis 
Grade 1 or 2 
Withhold 
• Based on severity of AE 
administer corticosteroids 
• 
Ensure adequate evaluation to confirm 
etiology and/or exclude other causes 
 
Grade 3 or 4 
Permanently 
discontinue 
All other 
immune-related 
AEs 
Intolerable/ 
persistent Grade 2 
Withhold 
• Based on type and severity of AE 
administer corticosteroids  
• 
Ensure adequate evaluation to confirm 
etiology and/or exclude other causes 
 
Grade 3 
Withhold or 
discontinue based 
on the type of 
event.  Events that 
require 
discontinuation 
include and not 
limited to:  
Gullain-Barre 
Syndrome, 
encephalitis 
Grade 4 or 
recurrent Grade 3  
Permanently 
discontinue 
1. Withhold or permanently discontinue pembrolizumab is at the discretion of the investigator or treating physician.   
NOTE:  
For participants with Grade 3 or 4 immune-related endocrinopathy where withhold of pembrolizumab is required, 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).   

40 
 
 
 
 
Dosing interruptions are permitted in the case of medical / surgical events or logistical reasons 
not related to study therapy but only after discussion with the principle investigator (e.g., 
elective surgery, unrelated medical events, patient vacation, and/or holidays). Subjects should 
be placed back on study therapy within 3 weeks of the scheduled interruption, unless otherwise 
discussed with the principle investigator. The reason for interruption should be documented in 
the patient's study record. 
 Timing of Dose Administration 
Trial treatment should be administered according to the schedule of protocol therapy 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 of each 
treatment to administrative reasons although there must always be a minimum of two days 
between gemcitabine administrations. 
All trial treatments will be administered on an outpatient basis. 
Gemcitabine 27 mg/m2 IV infusion should be administered by institutional standards and 
should occur over approximately 30 minutes. 
Pembrolizumab 200 mg will be administered as a 30 minute IV infusion every 3 weeks as 
scheduled in the trial flow chart and protocol schema.  Sites should make every effort to target 
infusion timing to be as close to 30 minutes as possible.  However, given the variability of 
infusion pumps from site to site, a window of -5 minutes and +10 minutes is permitted (i.e., 
infusion time is 30 minutes: -5 min/+10 min). 
The Pharmacy Manual contains specific instructions for the preparation of the pembrolizumab 
infusion fluid and administration of infusion solution. 
 Radiation Treatment Interruption 
No treatment interruptions will be planned. If a grade 3 hematologic toxicity (ANC, platelets) 
develops, radiation and gemcitabine should be discontinued for a minimum of one week. 
Radiation and gemcitabine may be resumed when the hematologic toxicity resolves to < grade 
1. If these laboratory values have not been reached after a one week delay, they should be 
checked weekly until they become acceptable. If after 3 weeks the blood counts have not 
recovered, all protocol treatment should be discontinued and appropriate off-protocol treatment 
should be administered. 
For a grade ≥ 3 acute colitis, cystitis or any other in field radiation-related toxicity ≥ grade 3, 
all protocol treatment should be delayed until the toxicity resolves. The treatment should be 
restarted with gemcitabine dose reduced to level -2 (16 mg/m2).  If the delay is greater than 3 
weeks, then the patient should be considered intolerant of protocol therapy and appropriate off-
protocol therapy given. 

41 
 
 
 Trial Blinding/Masking 
This is an open-label trial; therefore, the Sponsor, investigator and subject will know the 
treatment administered. 
5.3 
Concomitant Medications/Vaccinations (allowed & prohibited) 
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed 
during the ongoing trial.  If there is a clinical indication for one of these or other medications 
or vaccinations specifically prohibited during the trial, discontinuation from trial therapy or 
vaccination may be required.  The investigator should discuss any questions regarding this 
with the Merck Clinical team.  The final decision on any supportive therapy or vaccination 
rests with the investigator and/or the subject's primary physician.  
 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 ECIs as defined in Section 7.2. 
 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 therapy not specified in this protocol.  
• Immunotherapy not specified in this protocol 
• Chemotherapy not specified in this protocol 
• Investigational agents other than pembrolizumab 
• 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, shingles, yellow fever, rabies, 
BCG, and typhoid vaccine.  
• Systemic corticosteroids equivalent to > 10 mg prednisone daily for any purpose other 
than to modulate symptoms from an adverse event of clinical interest of suspected 

42 
 
 
immunologic etiology.  The use of physiologic doses of corticosteroids may be 
approved after consultation with the principle investigator. 
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 after 
consultation with the principle investigator.  Subjects may receive other medications that the 
investigator deems to be medically necessary.  Growth factors such as EPO and G-CSF are 
permitted. 
The Exclusion Criteria describes other medications that are prohibited in this trial. 
There are no prohibited therapies during the Post-Treatment Follow-up Phase. 
5.4 
Rescue Medications & Supportive Care 
 Supportive Care Guidelines 
Subjects should receive appropriate supportive care measures as deemed necessary by the 
treating investigator.  Suggested supportive care measures for the management of adverse 
events with potential immunologic etiology are outlined below and in greater detail in the ECI 
guidance document. 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 is 
instructed to follow the ECI reporting guidance but does not need to follow the treatment 
guidance (as outlined in the ECI guidance document). Refer to Section 5.2.5 for dose 
modification guidelines.  
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or 
skin photography as part of evaluation of the event. Suggested conditional procedures, as 
appropriate, can be found in the ECI guidance document. 
• Pneumonitis:  
o For Grade 2 events, treat with systemic corticosteroids. When symptoms 
improve to Grade 1 or less, steroid taper should be started and continued over 
no less than 4 weeks. 
o For Grade 3-4 events, immediately treat with intravenous steroids.  
Administer additional anti-inflammatory measures, as needed. 
o Add prophylactic antibiotics for opportunistic infections in the case of 
prolonged steroid administration. 

43 
 
 
• Diarrhea/Colitis:  
Subjects should be carefully monitored for signs and symptoms of enterocolitis (such 
as diarrhea, abdominal pain, blood or mucus in stool, with or without fever) and of 
bowel perforation (such as peritoneal signs and ileus).   
 
o All subjects who experience diarrhea/colitis should be advised to drink liberal 
quantities of clear fluids.  If sufficient oral fluid intake is not feasible, fluid and 
electrolytes should be substituted via IV infusion.  For Grade 2 or higher 
diarrhea, consider GI consultation and endoscopy to confirm or rule out colitis. 
o For Grade 2 diarrhea/colitis that persists greater than 3 days, administer oral 
corticosteroids.  
o For Grade 3 or 4 diarrhea/colitis that persists > 1 week, treat with intravenous 
steroids followed by high dose oral steroids.   
o When symptoms improve to Grade 1 or less, steroid taper should be started and 
continued over no less than 4 weeks. 
 
• Type 1 diabetes mellitus (if new onset, including diabetic ketoacidosis [DKA]) or 
≥ Grade 3 Hyperglycemia, if associated with ketosis (ketonuria) or metabolic 
acidosis (DKA) 
 
o For T1DM or Grade 3-4 Hyperglycemia 
 Insulin replacement therapy is recommended for Type I diabetes 
mellitus and for Grade 3-4 hyperglycemia associated with metabolic 
acidosis or ketonuria.  
 Evaluate patients with serum glucose and a metabolic panel, urine 
ketones, glycosylated hemoglobin, and C-peptide.  
 
• Hypophysitis: 
 
o For Grade 2 events, treat with corticosteroids. When symptoms improve to 
Grade 1 or less, steroid taper should be started and continued over no less than 
4 weeks. Replacement of appropriate hormones may be required as the steroid 
dose is tapered. 
o For Grade 3-4 events, treat with an initial dose of IV corticosteroids followed 
by oral corticosteroids. When symptoms improve to Grade 1 or less, steroid 
taper should be started and continued over no less than 4 weeks. Replacement 
of appropriate hormones may be required as the steroid dose is tapered. 
 
• Hyperthyroidism or Hypothyroidism:  
Thyroid disorders can occur at any time during treatment. Monitor patients for changes 
in thyroid function (at the start of treatment, periodically during treatment, and as 
indicated based on clinical evaluation) and for clinical signs and symptoms of thyroid 
disorders. 
 
o Grade 2 hyperthyroidism events (and Grade 3-4 hypothyroidism): 

44 
 
 
 In hyperthyroidism, non-selective beta-blockers (e.g. propranolol) are 
suggested as initial therapy. 
 In hypothyroidism, thyroid hormone replacement therapy, with 
levothyroxine or liothyroinine, is indicated per standard of care. 
o Grade 3-4 hyperthyroidism  
 Treat with an initial dose of IV corticosteroid followed by oral 
corticosteroids. When symptoms improve to Grade 1 or less, steroid 
taper should be started and continued over no less than 4 weeks. 
Replacement of appropriate hormones may be required as the steroid 
dose is tapered. 
 
• Hepatic: 
o For Grade 2 events, monitor liver function tests more frequently until returned 
to baseline values (consider weekly). 
 Treat with IV or oral corticosteroids 
o For Grade 3-4 events, treat with intravenous corticosteroids for 24 to 48 hours.  
o When symptoms improve to Grade 1 or less, a steroid taper should be started 
and continued over no less than 4 weeks. 
 
• Renal Failure or Nephritis: 
o For Grade 2 events, treat with corticosteroids. 
o For Grade 3-4 events, treat with systemic corticosteroids. 
o When symptoms improve to Grade 1 or less, steroid taper should be started and 
continued over no less than 4 weeks.  
 
Management of Infusion Reactions: Signs and symptoms usually develop during or 
shortly after drug infusion and generally resolve completely within 24 hours of 
completion of infusion.  
Table 5 below shows treatment guidelines for subjects who experience an infusion 
reaction associated with administration of pembrolizumab (MK-3475). 
Table 5 Infusion Reaction Treatment Guidelines for Pembrolizumab (MK-3475) 
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 
Subject may be premedicated 1.5h 
(± 30 minutes) prior to infusion of 
pembrolizumab (MK-3475) with: 
 
Diphenhydramine 50 mg po (or 
equivalent dose of antihistamine). 
 
Acetaminophen 500-1000 mg po 
(or equivalent dose of antipyretic). 

45 
 
 
NCI CTCAE Grade 
Treatment 
Premedication at subsequent 
dosing 
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. 
Grades 3 or 4 
Grade 3: 
Prolonged (i.e., not rapidly responsive 
to symptomatic medication and/or 
brief interruption of infusion); 
recurrence of symptoms following 
initial improvement; hospitalization 
indicated for other clinical sequelae 
(e.g., renal impairment, pulmonary 
infiltrates) 
Grade 4: 
Life-threatening; pressor or ventilatory 
support indicated 
Stop Infusion. 
Additional appropriate medical therapy may 
include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Epinephrine 
 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
Hospitalization may be indicated. 
Subject is permanently discontinued from 
further trial treatment administration. 
No subsequent dosing 
Appropriate resuscitation equipment should be available in the room and a physician readily available during the period of drug 
administration. 
 
 
5.5 
Diet/Activity/Other Considerations 
 Diet 
Subjects should maintain a normal diet unless modifications are required to manage an AE 
such as diarrhea, nausea or vomiting. 
 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.  Non-pregnant, non-
breast-feeding women may be enrolled if they are willing to use 2 methods of birth control or 
are considered highly unlikely to conceive.  Highly unlikely to conceive is defined as 1) 
surgically sterilized, or 2) postmenopausal (a woman who is ≥45 years of age and has not had 
menses for greater than 1 year will be considered postmenopausal), or 3) not heterosexually 
active for the duration of the study.  The two birth control methods can be either two barrier 
methods or a barrier method plus a hormonal method to prevent pregnancy. Subjects should 
start using birth control from study Visit 1 throughout the study period up to 120 days after the 
last dose of study therapy.  

46 
 
 
The following are considered adequate barrier methods of contraception: diaphragm, condom 
(by the partner), copper intrauterine device, sponge, or spermicide.  Appropriate hormonal 
contraceptives will include any registered and marketed contraceptive agent that contains an 
estrogen and/or a progestational agent (including oral, subcutaneous, intrauterine, or 
intramuscular agents). 
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 they must adhere to the contraception requirement (described above) for the duration 
of the study and during the follow-up period defined in section 7.2.2-Reporting of Pregnancy 
and Lactation to the Sponsor and to Merck.  If there is any question that a subject will not 
reliably comply with the requirements for contraception, that subject should not be entered into 
the study. 
 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 
immediately and the pregnancy reported to the Sponsor and to Merck and followed as 
described above and in Section 7.2.2. 
 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. 
5.6 
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: 

47 
 
 
• The subject or legal representative (such as a parent or legal guardian) withdraws 
consent. 
• Confirmed radiographic or pathologic disease progression 
• Unacceptable toxicity as described in Section 5.2.1 
• Intercurrent illness that prevents further administration of treatment 
• Investigator’s decision to withdraw the subject 
• The subject has a confirmed positive serum pregnancy test 
• Noncompliance with trial treatment or procedure requirements 
• The subject is lost to follow-up 
• 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 last day of radiation treatment, each 
subject will be followed for 90 days for adverse event monitoring.  After completion or 
discontinuation of protocol therapy, patients will undergo post-treatment follow-up for disease 
status until disease progression, withdrawing consent or becoming lost to follow-up.  After 
documented disease progression each subject will be followed by telephone for overall survival 
until death, withdrawal of consent, or the end of the study whichever occurs first. 
5.7 
Subject Replacement Strategy 
Subjects will not be replaced.  
5.8 
Clinical Criteria for Early Trial Termination 
Early trial termination will be the result of the criteria specified below: 
1. Quality or quantity of data recording is inaccurate or incomplete 
2. Poor adherence to protocol and regulatory requirements 
3. Incidence or severity of adverse drug reaction in this or other studies indicates a potential 
health hazard to subjects 
4. Plans to modify or discontinue the development of the study drug 
In the event of Merck decision to no longer supply study drug, ample notification will be 
provided so that appropriate adjustments to subject treatment can be made. 

48 
 
 
 

Product:  Pembrolizumab 
49 
Protocol/Amendment No.:   
 
 
 
 
 
 
6.0 TRIAL FLOW CHART 
6.1 
Study Flow Chart 
Trial Period: 
Screening 
Phase 
Treatmenta 
Post-
Treatment 
Assessment 
Post-Treatment Completion or 
Discontinuation 
Treatment Cycle/Title: 
Main Study 
Screening  
Lead-In 
Combination Therapy 
 
Approx 12 
Weeks Post 
Last RT  
Safety 
Follow-
upo 
Follow Up 
Visitsb 
Survival 
Follow-
Upc 
Week 1d 
Week 2d 
Week 3d 
Week 4d 
Week 7d 
Scheduling Window (Days): 
-42 
to -1 
-28 
to -1 
Weekq 
-(5-8) 
Week 
-(3-5) 
± 3d 
± 3d 
± 3d 
± 3d 
± 5d 
± 7d 
30 (±7) 
days 
post 
discon 
 
Every 12 
weeks  
W1
T1 
W1
T2 
W2
T1 
W2 
T2 
W3 
T1 
W3 
T2 
W4 
T1 
W4 
T2 
 
Administrative Procedures 
Informed Consent 
X 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/Exclusion Criteria 
 
X 
 
 
 
 
 
 
 
 
 
 
 
Demographics and Medical History 
 
X 
 
 
 
 
 
 
 
 
 
 
 
Prior and Concomitant Medication 
Reviewe 
 
X 
X 
 
X 
 
X 
 
X 
 
X 
 
X 
 
 
 
 
Post-study anticancer therapy status 
 
 
 
 
 
 
 
 
 
 
 
X 
 
Survival Status 
 
 
 
 
 
 
 
 
 
 
 
 
X 
Trial Treatment Administration 
Radiation 
 
 
 
 
M-F Daily for 20 Fractions 
 
 
 
 
 
Gemcitabines 
 
 
 
 
X 
X 
X 
X 
X 
X 
X 
X 
 
 
 
 
 
MK3475 (Pembrolizumab) 
 
 
Xq 
 
X 
 
 
 
 
 
X 
 
X 
 
 
 
 
Clinical Procedures/Assessments 
Review Adverse Eventsf 
 
 
X 
X 
X 
 
X 
 
X 
 
X 
 
X 
X 
Xg 
Xg 
 
Full Physical Examination 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Directed Physical Examination 
 
 
X 
 
X 
 
X 
 
X 
 
X 
 
X 
X 
 
 
 
Vital Signs and Weighth 
 
X 
X 
 
X 
 
X 
 
X 
 
X 
 
X 
X 
 
X 
 
ECOG Performance Statusi 
 
X 
X 
 
X 
 
X 
 
X 
 
X 
 
X 
X 
 
X 
 
Cystoscopy/TURBT/EUA 
Xj 
 
 
Xj 
 
 
 
 
 
 
 
 
 
Xj 
 
   Xb 
 

Product:  Pembrolizumab 
50 
Protocol/Amendment No.:   
 
 
 
 
 
 
Trial Period: 
Screening 
Phase 
Treatmenta 
Post-
Treatment 
Assessment 
Post-Treatment Completion or 
Discontinuation 
Treatment Cycle/Title: 
Main Study 
Screening  
Lead-In 
Combination Therapy 
 
Approx 12 
Weeks Post 
Last RT  
Safety 
Follow-
upo 
Follow Up 
Visitsb 
Survival 
Follow-
Upc 
Week 1d 
Week 2d 
Week 3d 
Week 4d 
Week 7d 
Scheduling Window (Days): 
-42 
to -1 
-28 
to -1 
Weekq 
-(5-8) 
Week 
-(3-5) 
± 3d 
± 3d 
± 3d 
± 3d 
± 5d 
± 7d 
30 (±7) 
days 
post 
discon 
 
Every 12 
weeks  
W1
T1 
W1
T2 
W2
T1 
W2 
T2 
W3 
T1 
W3 
T2 
W4 
T1 
W4 
T2 
 
Laboratory Procedures/Assessments: analysis performed by LOCAL laboratory 
Pregnancy Test – Urine or Serum β-HCG 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
PT/INR and aPTTl 
 
Xm 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
CBC with Differential 
 
Xm 
Xq 
 
Xn,r 
Xn 
Xn 
Xn 
Xn 
Xn 
Xn 
Xn 
Xn 
X 
Xo 
 
 
Comprehensive Serum Chemistry Panel 
 
Xm 
Xq 
 
Xn,r 
 
Xn 
 
Xn 
 
Xn 
 
Xn 
X 
Xo 
 
 
Urinalysis 
 
Xm 
 
 
 
 
 
 
 
 
 
 
 
 
Xo 
 
 
T3, FT4 and TSH 
 
Xm 
 
 
Xn 
 
 
 
 
 
Xn 
 
Xn 
 
Xo 
 
 
Efficacy Measurements 
Tumor Imaging 
 
Xk 
 
 
 
 
 
 
 
 
 
 
 
X 
 
Xb 
 
Tumor Biopsies/Archival Tissue Collection/Correlative Studies Blood 
Archival or Newly Obtained Tissue 
Collection 
Xj 
 
 
Xj 
 
 
 
 
 
 
 
 
 
Xj 
 
 
 
Correlative Studies Blood Collection 
 
 
Xp 
Xp 
Xp 
 
 
 
 
 
Xp 
 
Xp 
Xp 
Xp,o 
 
 

Product:  Pembrolizumab 
51 
Protocol/Amendment No.:   
 
 
 
 
 
 
a. 
Treatment entails the period from initial lead-in dose of pembrolizumab (MK3475), followed 2-3 weeks later by maximal TURBT (transurethral resection of 
bladder tumor), followed 3-5 weeks later by combination therapy.  In general, assessments/procedures are to be performed on the first treatment day of each 
week and prior to the first dose of systemic treatment with gemcitabine and/or pembrolizumab unless otherwise specified. 
b. 
Following completion (or discontinuation if feasible) of study treatment, patients will undergo surveillance cystoscopy with urine cytology and imaging to 
monitor for local and distant disease recurrence, respectively.  Requirements for monitoring of disease status are outlined in section 7.1.8.3 
c. 
After the start of new anti-cancer treatment or documented disease progression by the investigator/site radiologist, the subject should be contacted by telephone 
or other method by institutional practice approximately every 3 months to assess for survival status for up to 5 years. 
d. 
In general, the window for each visit is ± 3 days unless otherwise noted. Treatment with gemcitabine should be on a Monday-Thursday or Tuesday-Friday 
schedule, however in the event of treatment schedule change due to scheduling/administrative reasons there must be at least 2 days between gemcitabine 
treatments.  
e. 
Prior medications – Record all medications taken within 28 days of study enrollment. Concomitant medications – Enter new medications started during the trial 
through the Safety Follow-up visit. Record all medications taken for SAEs as defined in Section 7.2. 
f. 
AEs and laboratory safety measurements will be graded per NCI CTCAE version 4.0. All AEs, whether gradable by CTCAE or not, will also be evaluated for 
seriousness. 
g. 
Record all AEs occurring within 90 days after the last day of radiation treatment. Report all SAEs (related and unrelated to trial treatment) and ECIs occurring 
up until 90 days after the last day of radiation treatment or the start of new anti-cancer treatment, whichever comes first.  
h. 
Vital signs to include temperature, pulse, respiratory rate, weight and blood pressure. Height will be measured at screening visit only. Vital signs will be 
collected at screening, prior to the administration of each dose of trial treatment at every cycle, at treatment discontinuation, and at follow-up. 
i. 
ECOG performance status at screening to be performed within 10 days prior to study enrollment. ECOG performance status will also be performed prior to the 
administration of each dose of trial treatment at every cycle, at treatment discontinuation, and at follow-up. 
j. 
Patients must have histologically documented muscle-invasive urothelial cancer of the bladder diagnosed within 60 days of enrollment from which tissue 
(described in inclusion criteria section 5.1) must be available for correlative studies.  Patients who do not have tissue available must be willing to undergo repeat 
TURBT during the screening period. Results of a test performed prior to the subject signing consent as part of routine clinical management are acceptable in 
lieu of a screening test if performed within the window specified for screening procedures (e.g., within 10 days prior to trial enrollment for required lab tests).  
As tissue collected during maximal TURBT after lead-in pembrolizumab is not required for tissue diagnosis, it will be collected in-toto for biomarker analysis.  
The tissue obtained at post-treatment TUR of residual tumor and/or tumor-bed will be submitted for diagnostic pathology, and an additional sample must be 
will be collected for biomarker analysis.  The diagnostic pathology report must accompany tissue from the post-treatment TUR.  See section 7.1.5 and the 
accompanied laboratory manual for additional tissue collection and processing requirements. 
k. 
Baseline tumor imaging should include Chest-Xray or CT Chest (preferred) and CT or MRI of the Abdomen/Pelvis.  Bone scan should be performed only if 
clinically indicated. 
l. 
Coagulation factors (PT/INR and aPTT) should be tested as part of the screening procedures for all subjects. Any subject receiving anticoagulant therapy should 
have coagulation factors monitored closely throughout the trial. 
m. 
Laboratory tests for screening are to be performed within 10 days prior to study enrollment. See Section 7.1.6 for details regarding laboratory tests. 
n. 
After Lead-in treatment, pretreatment lab samples during combination therapy can be collected up to 36 hours prior to the scheduled time point. See Section 
7.1.6 for details regarding laboratory tests. 
o. 
Unresolved abnormal labs that are pembrolizumab-related AEs should be followed until resolution. Labs do not need to be repeated after the end of treatment 
if labs are within normal range. Safety follow up will occur at 30 days (+/- 7 days) from date of last radiation, chemotherapy or pembrolizumab treatment, 
whichever is last.   

Product:  Pembrolizumab 
52 
Protocol/Amendment No.:   
 
 
 
 
 
 
Trial Period: 
Screening 
Phase 
Treatmenta 
Post-
Treatment 
Assessment 
Post-Treatment Completion or 
Discontinuation 
Treatment Cycle/Title: 
Main Study 
Screening  
Lead-In 
Combination Therapy 
 
Approx 12 
Weeks Post 
Last RT  
Safety 
Follow-
upo 
Follow Up 
Visitsb 
Survival 
Follow-
Upc 
Week 1d 
Week 2d 
Week 3d 
Week 4d 
Week 7d 
Scheduling Window (Days): 
-42 
to -1 
-28 
to -1 
Weekq 
-(5-8) 
Week 
-(3-5) 
± 3d 
± 3d 
± 3d 
± 3d 
± 5d 
± 7d 
30 (±7) 
days 
post 
discon 
 
Every 12 
weeks  
W1
T1 
W1
T2 
W2
T1 
W2 
T2 
W3 
T1 
W3 
T2 
W4 
T1 
W4 
T2 
 
p. 
Procedures for collection, handling and storage of blood specimens for correlative studies is outlined in section 7.1.5 and the accompanied laboratory manual.  
Collection of blood for correlative studies at the time of cystoscopy/TURBT procedures on study should occur ideally on the same day of the procedure, as 
feasible.  Other collections must occur as specified in the flow chart. 
q. 
Lead-in pembrolizumab (MK-3475) should begin with 14 days of study enrollment. Laboratory requirements for treatment with lead-in pembrolizumab are 
outlined in section 5.2.2.  If screening labs are completed within 3 days of Lead-In treament, labs on day of lead-in treatment do not need to be repeated.  
r. 
Laboratory requirements for treatment on day 1 of combination chemo-radio-immunotherapy are outlined in section 5.2.3. 
s. 
s. Dosing for gemcitabine during the combination chemo-radio-immunotherapy treatment should be based on the patient’s Week 1 Day 1 calculated BSA.  This 
dosing is to be used for the duration of chemo-radio-immunotherapy treatment for all treatment days and should only be adjusted if there is a ≥ 10% change in 
body weight. 
 
 
 

Product:   Pembrolizumab 
53 
Protocol/Amendment No.:  S15-00220 
 
 
 
 
 
 
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 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. 
 Administrative Procedures 
Research Subject Screening ID Assignment and General Enrollment Procedures 
Potentially eligible patients will first be approached for study participation and provided the 
opportunity to review the informed consent document for the study.   
Informed consent will be obtained from interested patients and consent documents will be 
submitted to the study sponsor and a screening ID number will be assigned.  
Only subsequent to obtaining informed consent should protocol specific screening procedures 
be performed as outlined in the Study Flow Chart in Section 6.0 within the appropriate 
timeframes. 
Following completion of screening procedures and during the enrollment process, a protocol 
specific eligibility checklist will need to be completed and signed by the investigator. 
 Screening and Enrollment Procedures for Participating Sites. 
Central registration for this study will take place at NYU Perlmutter Cancer Center.  Patients 
who have signed informed consent at a participating site will undergo screening procedures 
and the designated CRA at the participating site will contact the designated research staff at 
NYU to notify him/her of the patient consent and screening via email.  When the subject has 
completed all screening requirements, the following should be submitted for review: 
1. 
The completed or partially completed NYU Eligibility Checklist 
2. 
The signed informed consent document and HIPAA Authorization Form. 
3. 
Supporting source documentation for eligibility questions (relevant laboratory 
results, pathology report, radiology report, MD notes including documentation 
of medical history, prior treatment records, physical exam and other screening 
evaluations as noted in the Trial Flow Chart) 
Upon receipt, research staff the NYU will conduct a review of all the documents.  Once 
complete and all source documents received, if the patient meets all eligibility criteria for study 

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participation, and the site is in good standing with NYU, the NYU research staff will 
enrollment the patient onto the protocol.  Upon enrollment confirmation, a subject ID will be 
assigned to the patient and communicated to the participating site along with confirmation of 
the patient’s enrollment.  Treatment on protocol should begin within the timeline outlined in 
the Trial Flow Chart, Section 6.0.   
 General Informed Consent and Screening Procedures 
Consent must be documented by the subject’s dated signature or by the subject’s legally 
acceptable representative’s dated signature on a consent form along with the dated signature 
of the person conducting the consent discussion.  
A copy of the signed and dated consent form should be given to the subject before participation 
in the trial. 
The initial informed consent form, any subsequent revised written informed consent form and 
any written information provided to the subject must receive the IRB/ERC’s 
approval/favorable opinion in advance of use.  The subject or his/her legally acceptable 
representative should be informed in a timely manner if new information becomes available 
that may be relevant to the subject’s willingness to continue participation in the trial.  The 
communication of this information will be provided and documented via a revised consent 
form or addendum to the original consent form that captures the subject’s dated signature or 
by the subject’s legally acceptable representative’s dated signature. 
Specifics about a trial and the trial population will be added to the consent form template at 
the protocol level.   
The informed consent will adhere to IRB/ERC requirements, applicable laws and regulations 
and Sponsor requirements. 
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.  
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.   

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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,  
 
Prior and Concomitant Medications Review 
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.  
Concomitant Medications 
The investigator or qualified designee will record medication, if any, taken by the subject 
during the trial.  All medications related to reportable SAEs and ECIs should be recorded as 
defined in Section 7.2. 
Disease Details and Treatments 
Disease Details 
The investigator or qualified designee will obtain prior and current details regarding disease 
status.  
Prior Treatment Details 
The investigator or qualified designee will review all prior cancer treatments including 
systemic treatments, radiation and surgeries. 
Subsequent Anti-Cancer Therapy Status 
The investigator or qualified designee will review all new anti-neoplastic therapy initiated after 
the last dose of trial treatment.  If a subject initiates a new anti-cancer therapy within 30 days 
after the last dose of trial treatment, the 30 day Safety Follow-up visit must occur before the 
first dose of the new therapy as feasible.  Once new anti-cancer therapy has been initiated the 
subject will move into survival follow-up.  
Trial Compliance (Medication/Diet/Activity/Other) 
 Clinical Procedures/Assessments During Study Treatment 
Clinical procedures and assessments are outlined in detail in the Trial Flow Chart, in Section 
6.0.   

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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 4.0.  Toxicities will be characterized in terms 
regarding seriousness, causality, toxicity grading, and action taken with regard to trial 
treatment.  
For subjects receiving treatment with pembrolizumab all AEs of unknown etiology associated 
with pembrolizumab exposure should be evaluated to determine if it is possibly an event of 
clinical interest (ECI) of a potentially immunologic etiology (termed immune-related adverse 
events, or irAEs); see the separate ECI guidance document attached to this protocol regarding 
the identification, evaluation and management of potential irAEs.   
Please refer to section 7.2 for detailed information regarding the assessment and recording of 
AEs.   
Directed Physical Exam 
For visits that do not require a full physical exam per the Trial Flow Chart, the investigator or 
qualified designee will perform a directed physical exam as clinically indicated prior to trial 
treatment administration.   
Vital Signs 
The investigator or qualified designee will take vital signs at screening, prior to the 
administration of each dose of trial treatment and at treatment discontinuation as specified in 
the Trial Flow Chart (Section 6.0).  Vital signs should include temperature, pulse, respiratory 
rate, weight and blood pressure.  Height will be measured at screening only. 
Eastern Cooperative Oncology Group (ECOG) Performance Scale 
The investigator or qualified designee will assess ECOG status (see Section 12.0) at screening, 
prior to the administration of each dose of trial treatment and discontinuation of trial treatment 
as specified in the Trial Flow Chart.   
Tumor Imaging and Assessment of Disease 
Patients will undergo tumor imaging/assessment of disease at time points outlined in the Trial 
Flow Chart in Section 6.0 and will include imaging of the chest, abdomen and pelvis.  For 
chest imaging, either CT scan or X-ray is acceptable.  For abdomen and pelvis imaging, either 
MRI with contrast or CT scan with contrast is acceptable.  For patients who cannot receive 
contrast with either MRI or CT scan, a non-contrast imaging study may be accepted after 
discussion with the principal investigator.  

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 Tumor Tissue and Blood Collection and Treatment-Related Immunologic 
Correlates 
Tissue and blood acquisition 
To quantify the amount of treatment related immunologic alterations, tissue acquisition and 
blood sampling will occur at multiple time-points, while patients are enrolled onto the study. 
Non-surgical candidates or patients that refuse radical cystectomy with cT2-T4aN0 muscle 
invasive bladder cancer will undergo pretreatment biopsy if FFPE tissue block or 20 unstained 
slides of pre-treatment TURBT tissue is not available. This will serve as their baseline tumor-
immunologic status. Thereafter, they will receive their first infusion of pembrolizumab. A 
second tumor specimen will be acquired via a maximal TURBT 2-3 weeks afterwards, prior to 
the start of combination chemoradioimmunotherapy. This specimen will serve as an indicator 
for the capacity of pembrolizumab alone to reactivate exhausted T-cells and/or expand 
intratumoral T-cell clones. Once starting radiotherapy, patients will receive concurrent 
gemcitabine (given bi-weekly) and pembrolizumab (given every 3-weeks x3 infusions). These 
patients will be treated with a hypofractionated course of radiotherapy to 52 Gy in 20 fractions 
M-F over 4 weeks.  Approximately 12 weeks after the last day of radiation therapy, patients 
will undergo cystoscopy/TUR of any residual tumor tissue and/or resection of tumor bed for 
assessment of treatment response and post-treatment immunologic status.  A sample from this 
procedure will be sent to diagnostic pathology for tissue diagnosis and additional sample must 
be collected for biomarker analysis.  Collection of tumor tissue and blood sampling will occur 
at baseline and along the designated time-points as illustrated in the Trial Flow Chart in Section 
6.0 and processed/shipped according to the accompany laboratory manual. Approximately 40 
ml of blood will be collected from participating subjects during each visit. 
Tissue and blood storage 
All blood and tissue samples will be processed immediately and stored indefinitely for later 
analysis in a locked -80°C freezer in the NYU Biorepository Core for research purposes only. 
These specimens will not be linked to any clinical data and will be de-identified in the clinical 
research database. Only the data manager will have access to the master list with the patient 
name and an identification number. This master list will be secured in a password protected 
HIPAA compliant research database. Only the investigators listed on this protocol will have 
access to these samples. After both blood and tissue samples are analyzed at a later date, any 
unutilized samples will be preserved indefinitely in the NYU CBRD for potential future 
research. All patients enrolled will be given a unique identifier. Only the data manager will 
know the code linking patient and study ID number. Patients will be assigned a unique code 
number. All specimens collected will be deidentified and assigned the same unique study 
number of the corresponding patient and will also be marked with the collection time point. 
Clinical information regarding toxicities and response will likewise be stored in a de-identified 
database using only the unique identifier.  
For patients enrolled at a participating site, measures to assure secure and HIPAA compliant 
storage of quality biospecimens will be determined by participating site institutional protocols. 

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Patients may decide to withdraw their samples from storage or future use at any time after 
informed consent either verbally or in writing.   
Tissue and Blood Acquisition, Handling and Storage 
Transurethral resection of bladder tumor specimens will be collected at the time of biopsy 
procedure with tissue both flash frozen and fixed in formalin and paraffin embedded according 
to NYU or participating site standards.  Peripheral blood will be collected at the time points 
described in Section 6.0 Trial Flow Chart for serum and PBMCs according to NYU or 
participating site standards.   
All biospecimens collected at participating sites will be stored locally (at the respective 
participating sites core facility) and batch shipped centrally to the NYU Biorepository Core 
(CBRD) at 1/3, 2/3 and full enrollment.   
The laboratory that will performing the correlative analyses described below has not yet been 
determined.  
Storage of Samples for Future Research: 
Biospecimens collected on this study will be used for the experiments described below, which 
are focused on determining mechanisms of response and resistance to combination 
immunotherapy, chemotherapy and radiation.  No germline genetic testing will be performed 
on any specimens collected during this trial with the exception of limited germline sequencing 
performed solely for the purpose of distinguishing tumor-derived mutations from clonal 
hematopoiesis during potential circulating tumor DNA assay analysis (e.g., using the Natera 
Signatera™ assay). This germline sequencing is not used to identify inherited genetic traits, 
and no germline findings will be stored, analyzed for unrelated purposes, or returned to the 
study team or participants.".   
 
Excess biospecimens not completely utilized in these experiments will be stored indefinitely 
at the NYU CBRD for future use in experiments focused on bladder cancer that are yet to be 
determined.  As above, at no time will germline genetic testing be performed on any specimens.  
All specimens collected will maintain the assigned unique study number of the corresponding 
patient.  Deidentified samples may be shared with other research institutions.  The storage of 
biospecimens for future research on this clinical trial is not optional.  We anticipate to use most 
of the blood/ biopsy samples before the study completion. We believe that allowing for storage 
and usage of the remaining samples for future research is ethically justified and a preferred 
option to discarding these materials.  Patients will be clearly counseled on this requirement 
both verbally and in writing during informed consent. 
 
Assays in Tissue 
PD-1, PD-L1, and PD-L2 biomarkers in pre and post-treatment tumor samples 
Pembrolizumab specifically targets the PD-1 receptor and prevents binding with its ligands, 
PD-L1 and PD-L2. To correlate treatment response with the expression of targeted biomarkers 

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for T-cell exhaustion, formalin fixed paraffin embedded tissue will be sectioned and stained 
for PD-1, PD-L1, and PD-L2 by IHC. As previously described for metastatic bladder cancer, 
samples will be scored for each biomarker expression on tumor and tumor-infiltrating immune 
cells as IHC 0, 1, 2, or 3 if <1%, 1-5%, 6-10%, or >10%, respectively 49. However, the final 
cutoff selection for each immunostain will be based on prevalence of staining in the four IHC 
categories and the ability to reliably score tissues into each of the four categories. Tumor tissue 
for PD-L1 testing will occur at Qualtek Laboratories, and samples sent to Qualtek Laboratories 
will be de-idenitified.    
Classic immunoscore of tumor infiltrating lymphocytes 
Intratumoral lymphocyte profiles have been correlated with survival in some cancers 50. 
Radiotherapy has been shown to perturb the types and percentages of certain tumor infiltrating 
lymphocytes 51. Additionally, gemcitabine has been shown to selectively decrease the amount 
of tumor associated myeloid-derived suppressor cells52. To ascertain the types of tumor 
infiltrating lymphocytes and their abundance before and after treatment, formalin fixed 
paraffin embedded tissue will be sectioned and stained and the percentages of positive staining 
cells will be determined. Slides will be stained with H&E and CD8, CD4, CD45, Ki67, Fox-
P3, CD68, pSTAT1, Ki67, and granzyme B via immunohistochemistry (IHC).  
Assays in Blood 
Blood will be collected at various time-points and analyzed for CD3, CD8, CD68, Fox-P3, 
HLA-DR, and Ki67 using a standard protocol with an LSR II, multi-color flow cytometer. 
T-cell receptor next-generation sequencing and clonotype diversity analysis 
Radiotherapy has been shown to increase the T-cell clonality within treated tumors 53. T-cell 
receptor sequencing and clonality quantification will be performed from tumor samples 
preserved using RNA later and stored at -80˚C. DNA will be isolated by mincing, followed by 
extraction using a DNeasy kit. TCR-β CDR3 regions will be amplified and sequenced using 
the survey ImmunoSeq assay in a multiplexed PCR method using 45 primers specific to 
TCR Vβ gene segments and 13 reverse primers specific to TCR Jβ gene segments. Reads 
of 87bp in length will be obtained using Illumina HiSeq System. As previously described, 
the top 100 most frequent TCR clonotypes in the tumor will be used to examine their 
frequencies in pre and post-treatment blood specimens 53. Additional sampling of 
untreated tumors will be used to analyze the whole exome and whole transcriptome for 
outcome correlates. 
Determination of T-cell responses to a panel of common viral and microbial mimicking 
antigens 
Responses to CTLA-4 checkpoint blockade have been correlated with T-cell responses to viral 
and microbial mimicking proteins54. We anticipate similar responses for PD-1 checkpoint 
blockade with pembrolizumab. Thus, previously identified candidate viral and antimicrobial 
mimicking antigens, recognized by activated T-cells, will be cultured with autologous 

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peripheral-blood mononuclear cells and then analyzed by means of intracellular cytokine 
staining for IL-2, CD107a, MIP 1β, TNFα, and INFλ 55.  
T-cell exhaustion via non-redundant immune mechanisms: TIM-3 and VISTA immunoscoring 
in non-responders versus responders 
Recent evidence suggests non-redundant immune mechanisms that may lead to T-cell 
exhaustion 53. In addition to conducting IHC on the pembrolizumab targets, PD-1, PD-L1, and 
PD-L2, we will also test for the increased expression of TIM-3 and VISTA. Each protein has 
been shown to be expressed on the cell surface of T-cells and has been associated with 
diminished T-cell function. If TIM-3 or VISTA shows increased expression after treatment in 
non-responding patients, further exploration for dual checkpoint blockade will be sought after 
in subsequent studies.  
Induction of IgG antibody responsse 
Spotted antigen arrays will be used to detect circulating antibodies will be performed on plasma 
derived from the baseline and on treatment timepoints. After standard preprocessing of the 
protein array data, Cluster and Treeview software will be used for unsupervised clustering of 
the data with Pearson correlation and complete linkage. For each array, an antigen is identified 
as being detected if its value is above the median. To determine the number of up- and 
downmodulated antibodies, the difference in log2 intensity values of pretreatment and post-
treatment samples will be taken for each patient to identify antigens that are detected 
differentially due to treatment. Number of antibodies with at least 2- or 4-fold difference 
between pretreatment and post-treatment samples will be compared between clinical 
responders and nonresponders by performing two-sided Wilcoxon rank sum test. 
Analysis of circulating tumor DNA (ctDNA) 
Whole-exome sequencing will be performed on tumor and matched normal samples from 44 
patients to identify 16 patient-specific clonal, somatic single nucleotide variants (SNV), as 
previously described.21 These SNVs were used to design personalized multiplex PCR, NGS 
assays (SignateraTM, Natera Inc., TX, USA) which will run on cell-free DNA extracted from 
plasma samples to detect ctDNA with high sensitivity down to 0.01% variant allele 
frequency, maintaining a high analytical specificity of 99.7%.22,23 Plasma samples with at 
least two tumor-specific variants detected above a pre-defined threshold will be defined as 
ctDNA-positive.  
This exploratory analysis has the potential to determine the predictive value of ctDNA in this 
population. Ultimately, our study can lead to the use of a minimally invasive technique 
(ctDNA) to identify patients at higher risk of recurrence and be used todevelop a more 
rational biomarker for response to treatment with immunotherapy. 

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 Laboratory Procedures/Assessments 
Details regarding specific laboratory procedures/assessments to be performed in this trial are 
provided below Laboratory Safety Evaluations (Hematology, Chemistry and Urinalysis) 
Laboratory tests for hematology, chemistry, urinalysis, and others are specified in Table 6.   

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Table 6 Laboratory Tests 
Hematology (CBC) 
Chemistry (CMP) 
Urinalysis 
Other 
Hematocrit 
Albumin 
Blood 
Serum β-human chorionic gonadotropin† 
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)  
Total thriiodothyronine (T3) 
Absolute Neutrophil Count 
Carbon Dioxide 
results are noted 
Free tyroxine (T4) 
Absolute Lymphocyte Count 
  (CO2 or bicarbonate) 
Urine pregnancy test † 
Thyroid stimulating hormone (TSH) 
 
Uric Acid 
 
 
 
Calcium 
 
 
 
Chloride 
 
Blood for correlative studies 
 
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 urine pregnancy results cannot be confirmed as negative, a serum pregnancy test will be required.   
 
 
 

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 Other Procedures 
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 that 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.   
Blinding/Unblinding 
 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. 
7.1.8.1 Screening 
The screening period will begin following informed consent of a potentially eligible patient.  
Screening requirements and timelines are outlined in the Trial Flow Chart in Section 6.0 and 
must be completed within 28 days prior to enrollment unless otherwise stated in the Flow 
Chart. Potential subjects will be evaluated to determine that they fulfill the entry 
requirements as set forth in Section 5.1.  Results of a test performed prior to the subject 
signing consent as part of routine clinical management are acceptable in lieu of a screening 
test if performed within the specified time frame.  
 
Screening procedures are to be completed within 28 days prior to enrollment except for the 
following: 
• TURBT specimen may be obtained during screening and within 42 days of 
enrollment if adequate specimen is not available for correlative studies.  
• PT/PTT/INR, CBC, CMP, Urinalysis and Thyroid studies must be performed within 
14 days prior to enrollment.   
 
See Section on Tumor Tissue and Blood Collection for Treatment-Related Immunologic 
Correlates for additional details regarding tumor tissue requirements.  
Subjects may be rescreened after initially failing to meet the inclusion/exclusion criteria and 
results from assessments performed during the initial screening period are acceptable in lieu 
of a repeat screening test if performed within the specified time frame and the 
inclusion/exclusion criteria is met. 
 
7.1.8.2 Safety Follow-Up Visit 
The mandatory Safety Follow-Up Visit should be conducted approximately 30 days after the 
last day of radiation, chemotherapy or pembrolizumab treatment whichever is last or before 
the initiation of a new anti-cancer treatment. All AEs that occur prior to the Safety Follow-Up 

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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 until the beginning of a new anti-neoplastic therapy, 
whichever occurs first.  Adverse event monitoring will continue for up to 90 days from the end 
of radiation treatment or before initiation of a new anti-cancer treatment whichever occurs first.   
7.1.8.3 Post-Treatment Follow-up for Disease Status 
Monitoring for surveillance of disease recurrence will occur by two methods:  Cross-sectional 
chest, abdominal and pelvic imaging for evaluation of regional and distant disease recurrence 
and surveillance cystoscopy with or without TURBT and urine cytology for evaluation of local 
disease recurrence. 
Surveillance imaging for distant disease recurrence should be CT Chest (preferred) or chest x-
ray and CT or MRI of the A/P and should occur from date of last radiation treatment 
approximately every 3 months for the first 18 months, every 6 months for the next 18 months, 
followed by yearly for up to 5 years.  
Patients will have their first post-treatment cystoscopy/TURBT approximately 12 weeks (3 
months) after the last day of radiation therapy and preferably AFTER the first surveillance 
imaging. Subsequently, patients will be followed with cystoscopy and urine cytology 
according to institutional practice approximately every 3 months during the first year after 
completion of treatment; every 4 months the second year; every 6 months for the next 3 years; 
then annually. More frequent evaluations may be performed as clinically indicated or in 
accordance with institutional practice.  Any recurrence of a muscle-invasive tumor will be 
considered a local disease recurrence for the purposes of the primary endpoint. 
7.1.8.4 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 contacted by telephone or 
other method by institutional practice every 12 weeks to assess for survival status until death, 
withdrawal of consent, or the end of the study, whichever occurs first.  
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 
of the Merck’s product, is also an adverse event. 
Changes resulting from normal growth and development that do not vary significantly in 
frequency or severity from expected levels are not to be considered adverse events.  Examples 

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of this may include, but are not limited to, teething, typical crying in infants and children and 
onset of menses or menopause occurring at a physiologically appropriate time. 
Merck product includes any pharmaceutical product, biological product, device, diagnostic 
agent or protocol-specified procedure, whether investigational (including placebo or active 
comparator medication) or marketed, manufactured by, licensed by, provided by or distributed 
by Merck for human use. 
Adverse events may occur during the course of the use of Merck product in clinical trials or 
within the follow-up period specified by the protocol, or prescribed in clinical practice, from 
overdose (whether accidental or intentional), from abuse and from withdrawal. 
Adverse events may also occur in screened subjects during any pre-allocation baseline period 
as a result of a protocol-specified intervention, including washout or discontinuation of usual 
therapy, diet, placebo treatment or a procedure. 
Progression of the cancer under study is not considered an adverse event unless it is considered 
to be drug related by the investigator. 
All adverse events will be recorded from the time the consent form is signed through 30 days 
following cessation of treatment and 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. 
 Definition of a Pembrolizumab Overdose for This Protocol and Reporting of 
Overdose to the Sponsor and to Merck 
For purposes of this trial, an overdose of pembrolizumab will be defined as any dose of 1,000 
mg or greater (≥5 times the indicated dose).  No specific information is available on the 
treatment of overdose of pembrolizumab. Appropriate supportive treatment should be provided 
if clinically indicated. In the event of overdose, the subject should be observed closely for signs 
of toxicity.  Appropriate supportive treatment should be provided if clinically indicated. 
If an adverse event(s) is associated with (“results from”) the overdose of a Merck product, the 
adverse event(s) is reported as a serious adverse event, even if no other seriousness criteria are 
met. 
If a dose of Merck’s product meeting the protocol definition of overdose is taken without any 
associated clinical symptoms or abnormal laboratory results, the overdose is reported as a non-
serious Event of Clinical Interest (ECI), using the terminology “accidental or intentional 
overdose without adverse effect.” 
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) 

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 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), including the pregnancy of a male subject's female partner that occurs during 
the trial or within 120 days of completing the trial completing the trial, or 30 days following 
cessation of treatment if the subject initiates new anticancer therapy, whichever is earlier.  All 
subjects and female partners of male subjects who become pregnant must be followed to the 
completion/termination of the pregnancy.  Pregnancy outcomes of spontaneous abortion, 
missed abortion, benign hydatidiform mole, blighted ovum, fetal death, intrauterine death, 
miscarriage and stillbirth must be reported as serious events (Important Medical Events).  If 
the pregnancy continues to term, the outcome (health of infant) must also be reported. 
Such events must be reported within 24 hours to the Sponsor and within 2 working days to 
Merck Global Safety. (Attn: Worldwide Product Safety; FAX 215 993-1220) 
 Immediate Reporting of Adverse Events to the Sponsor and to Merck 
Serious Adverse Events 
A serious adverse event is any adverse event occurring at any dose or during any use of 
Merck’s product that: 
• Results in death; 
• Is life threatening; 
• Results in persistent or significant disability/incapacity; 
• Results in or prolongs an existing inpatient hospitalization; 
• Is a congenital anomaly/birth defect; 
• Is a new cancer (that is not a condition of the study); 
• Is associated with an overdose; 
• Is another important medical event  
Refer to Table 7 for additional details regarding each of the above criteria. 
Progression of the cancer under study is not considered an adverse event unless it results in 
hospitalization or death. 
Any serious adverse event, or follow up to a serious adverse event, including death due to any 
cause other than progression of the cancer under study that occurs to any subject from the time 
the consent is signed through 30 days following cessation of treatment, or the initiation of new 
anti-cancer therapy, whichever is earlier, whether or not related to Pembrolizumab, must be 
reported within 24 hours to the Sponsor and within 2 working days to Merck Global Safety.  
Non-serious Events of Clinical Interest will be forwarded to Merck Global Safety and will be 
handled in the same manner as SAEs.  

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Additionally, any serious adverse event, considered by an investigator who is a qualified 
physician to be related to Pembrolizumab that is brought to the attention of the investigator at 
any time outside of the time period specified in the previous paragraph also must be reported 
immediately to the Sponsor and to Merck. 
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. 
All subjects with serious adverse events must be followed up for outcome. 
Events of Clinical Interest 
Selected non-serious and serious adverse events are also known as Events of Clinical Interest 
(ECI) and must be recorded as such on the Adverse Event case report forms/worksheets and 
reported within 24 hours to the Sponsor and within 2 working days to Merck Global Safety. 
(Attn: Worldwide Product Safety; FAX 215 993-1220) Events of clinical interest for this trial 
include: 
1.  An overdose of Merck product, as defined in Section 7.2.1 - Definition of an Overdose for 
This Protocol and Reporting of Overdose to the Sponsor, that is not associated with clinical 
symptoms or abnormal laboratory results.  
2.  An elevated AST or ALT lab value that is greater than or equal to 3X the upper limit of 
normal and an elevated total bilirubin lab value that is greater than or equal to 2X the upper 
limit of normal and, at the same time, an alkaline phosphatase lab value that is less than 2X the 
upper limit of normal, as determined by way of protocol-specified laboratory testing or 
unscheduled laboratory testing.* 
*Note:  These criteria are based upon available regulatory guidance documents. The 
purpose of the criteria is to specify a threshold of abnormal hepatic tests that may require 
an additional evaluation for an underlying etiology.  The trial site guidance for assessment 
and follow up of these criteria can be found in the Investigator Trial File Binder (or 
equivalent). 
1. Additional adverse events: 
 
A separate guidance document has been provided entitled “Event of Clinical Interest 
Guidance Document” (previously entitled, “Event of Clinical Interest and Immune-Related 
Adverse Event Guidance Document”).  This document can be found in Appendix 4 and 
provides guidance regarding identification, evaluation and management of ECIs and irAEs.   

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ECIs (both non-serious and serious adverse events) identified in this guidance document 
from the date of first dose through 90 days following cessation of treatment, or 30 days 
after the initiation of a new anticancer therapy, whichever is earlier, need to 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), regardless of attribution to study 
treatment, consistent with standard SAE reporting guidelines. 
 
Subjects should be assessed for possible ECIs prior to each dose.  Lab results should be 
evaluated and subjects should be asked for signs and symptoms suggestive of an immune-
related event.  Subjects who develop an ECI thought to be immune-related should have 
additional testing to rule out other etiologic causes.  If lab results or symptoms indicate a 
possible immune-related ECI, then additional testing should be performed to rule out other 
etiologic causes.  If no other cause is found, then it is assumed to be immune-related. 
 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 4.0. 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. 

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Table 7 Evaluating Adverse Events 
An investigator who is a qualified physician, will evaluate all adverse events as to: 
V4.0 
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 Merck product that: 
 
†Results in death; or 
 
†Is life threatening; or places the subject, in the view of the investigator, at immediate risk of death from the event as it occurred (Note: This does not include an 
adverse event that, had it occurred in a more severe form, might have caused death.); or 
 
†Results in a persistent or significant disability/incapacity (substantial disruption of one’s ability to conduct normal life functions); or 
 
†Results in or prolongs an existing inpatient hospitalization (hospitalization is defined as an inpatient admission, regardless of length of stay, even if the 
hospitalization is a precautionary measure for continued observation. (Note: Hospitalization [including hospitalization for an elective procedure] for a preexisting 
condition which has not worsened does not constitute a serious adverse event.); 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) or 
 
Is an overdose (whether accidental or intentional).  Any adverse event associated with an overdose is considered a serious adverse event. 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. 
 
Other important medical events that may not result in death, not be life threatening, or not require hospitalization may be considered a serious adverse event when, 
based upon appropriate medical judgment, the event may jeopardize the subject and may require medical or surgical intervention to prevent one of the outcomes 
listed previously (designated above by a †). 
Duration 
Record the start and stop dates of the adverse event. If less than 1 day, indicate the appropriate length of time and units 
Action taken  
Did the adverse event cause the Merck product to be discontinued? 
Relationship to 
test drug  
Did the Merck product cause the adverse event? The determination of the likelihood that the Merck product caused the adverse event will be provided by an 
investigator who is a qualified physician. The investigator’s signed/dated initials on the source document or worksheet that supports the causality noted on the AE 
form, ensures that a medically qualified assessment of causality was done. This initialed document must be retained for the required regulatory time frame. The 
criteria below are intended as reference guidelines to assist the investigator in assessing the likelihood of a relationship between the test drug and the adverse event 
based upon the available information.  
The following components are to be used to assess the relationship between the Merck product and the AE; the greater the correlation with the components and 
their respective elements (in number and/or intensity), the more likely the Merck product caused the adverse event (AE): 
 
Exposure 
Is there evidence that the subject was actually exposed to the Merck product 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 the Merck product?  
Is the time of onset of the AE compatible with a drug-induced effect (applies to trials with investigational medicinal product)? 
 
Likely Cause 
Is the AE not reasonably explained by another etiology such as underlying disease, other drug(s)/vaccine(s), or other host or environmental 
factors 
 

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Relationship 
The following components are to be used to assess the relationship between the test drug and the AE: (continued) 
to Merck 
product 
(continued)  
Dechallenge 
Was the Merck product 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 Merck product; or (3) the trial is a single-dose drug trial); or (4) Merck product(s) is/are only used one time.) 
 
Rechallenge 
Was the subject re-exposed to the Merck product 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) Merck 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 THE MERCK PRODUCT, OR IF REEXPOSURE TO THE MERCK PRODUCT POSES ADDITIONAL POTENTIAL 
SIGNIFICANT RISK TO THE SUBJECT, THEN THE RECHALLENGE MUST BE APPROVED IN ADVANCE BY THE U.S. CLINICAL 
MONITOR 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 the Merck product 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 a Merck product relationship). 
Yes, there is a reasonable 
possibility of Merck product 
relationship. 
There is evidence of exposure to the Merck product.  The temporal sequence of the AE onset relative to the administration of the Merck product 
is reasonable.  The AE is more likely explained by the Merck product than by another cause. 
No, there is not a reasonable 
possibility Merck product 
relationship 
Subject did not receive the Merck product OR temporal sequence of the AE onset relative to administration of the Merck product is not reasonable 
OR there is another obvious cause of the AE.  (Also entered for a subject with overdose without an associated AE.) 

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 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 CONSIDERATIONS 
This study will target a total enrollment of up to 54 patients.  Due to the lack of a previous 
phase I trial establishing the safety of this combination, an initial safety lead-in cohort of 3 to 
6 patients will be enrolled after which enrollment will be halted and an interim safety analysis 
and toxicity review will be performed. Three patients will be enrolled in the initial safety study 
and will be evaluated for safety after 90 days after the end of treatment (defined as the last day 
of radiation). If none of these patients has a safety event (defined in section 5.2.1), then the 
trial will proceed to enroll the phase II efficacy cohort (48 patients). If one of these 3 initial 
patients has a safety event, then an additional 3 patients will be entered into the safety trial. If 
1 of 6 patients experiences a safety event, the trial continues to the Phase II efficacy cohort. If 
≥ 2 of 6 patients has a safety event, then the trial is discontinued and no further patients will 
be enrolled. An additional interim safety analysis will be conducted after the 20th patient 
enrolled in the phase II cohort reaches the 90 days DLT period as described in section 5.2.1, 
however enrollment will not be suspended during this analysis. 
The Phase II portion of the trial is designed to test the hypothesis that the proportion of bladder-
intact disease-free survival at 2 years is ≥80% compared to the expected bladder-intact disease-
free survival rate of 60% in patients treated with gemcitabine and radiation alone based on the 
landmark rate at 2 years.  Bladder-intact disease-free survival is defined in section 8.1.  For the 
purpose of sample size considerations, we use a binomial calculation. With 48 patients entered 
into the Phase II efficacy trial, we can detect this difference in rates with a 2-sided alpha of 
0.05 and power of 85% (calculations from EAST 6.3, Cytel, Inc.) If pre-defined safety stopping 
rules are met (section 5.2.1), then further enrollment will be halted and the trial will be closed.  
If stopping rules are not met and no additional safety concerns are raised by the DSMC, then 
the study will proceed to enroll an additional efficacy cohort of 48 patients. Efficacy will also 
be evaluated in the safety cohort and results will be presented separately and combined.  
8.1 
Definitions of Efficacy Endpoints 
Bladder-intact disease-free survival will be defined as time from initiation of protocol therapy 
until the development of muscle-invasive bladder cancer recurrence, regional pelvic 
recurrence, distant metastases, bladder cancer–related death, or cystectomy.  
Approximately 12 weeks after completion of last radiation treatment, patients will be required 
to undergo standard cystoscopy, exam under anesthesia and TUR of residual tumor and/or 
tumor bed to document pathologic response.  Objective response in the bladder will be defined 
as follows: 

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• 
Complete Response (CR) requires the no tumor palpable on bimanual examination 
under anesthesia, no tumor visible on cystoscopy, negative tumor site biopsy, and 
negative urine cytology. 
• 
Partial Response (PR) requires that all response criteria of a CR be met with the 
exception that the urine cytology remains positive OR CIS is seen in the biopsy. 
• 
No Response (NR) requires the continued presence of the tumor (cT ≥ 1) in the 
tumor-site biopsy specimen, or elsewhere (includes tumor growth < 50%). 
• 
Progression requires an increase of 50% or more in the largest diameter of the 
endoscopically appreciable tumor and the continued presence of tumor in the 
tumor-site biopsy specimen. Progression may also occur as a result of the 
development of metastatic disease as demonstrated on imaging studies or physical 
examination with biopsy confirmation when appropriate. 
8.2 
Statistical Analysis Plan Summary 
The primary endpoint for the efficacy analysis in phase II portion will be bladder-intact 
disease-free survival rate at two years. The rate of bladder-intact disease-free survival at 2 
years will be estimated using time to failure methods; Kaplan Meier curves will be provided 
and the rate at 2 years will be estimated using a 95% confidence interval.    Patients who do 
not experience failure of any type (defined by the events included in the bladder-intact disease-
free survival definition in section 8.1) will be censored on the date of last follow up. 
Patient characteristics at baseline will be summarized using descriptive statistics, graphical 
displays and frequency distributions. CR rates will be estimated along with exact 95% 
confidence intervals. CR rates (and 95% confidence intervals) will be estimated within strata 
defined by individual baseline disease and patient characteristics as well.  
Changes from baseline in biomarkers and other exploratory parameters will be summarized 
over time using descriptive statistics and graphical displays. Mixed effects regression models 
will be used to evaluate changes over time and Cox regression models will be used to explore 
the relationships between baseline characteristics and time dependent changes in biomarkers.  
9.0 LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES 
Qualified personnel who are familiar with procedures that minimize undue exposure to 
themselves and to the environment should undertake the preparation, handling, and safe 
disposal of chemotherapeutic agents in a self-contained, protective environment. 
Discard unused portions of injectable chemotherapeutic agents that do not contain a 
bacteriostatic agent or are prepared with unpreserved diluents (i.e., Sterile Water for Injection 
USP or 0.9% Sodium Chloride for Injection USP) within eight hours of vial entry to minimize 
the risk of bacterial contamination. 

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The total administered dose of chemotherapy may be rounded up or down within a range of 
5% of the actual calculated dose. 
9.1 
Gemcitabine  
Gemcitabine (1.1(2’deoxy-2,2’-difluorocytidine; dFDC; difluorodeoxycytidine; gemcitabine 
hydrocholoride; Gemzar®) is a nucleoside analogue in the pyrimidine antimetabolite class 
which is S-phase specific. Its phosphorylated product is incorporated into DNA and interferes 
with DNA synthesis. Gemcitabine also exhibits self-potentiation by causing an enzymatically 
mediated reduction in the intracellular nucleotide pool. Additional information regarding 
gemcitabine is available in the package information. 
 Availability 
Gemcitabine is commercially supplied as vials containing 200 mg of white lyophilized powder 
in a 10 ml size single use vial or 1 gram of lyophilized powder in a 50 ml single use vial. 
 Storage and Stability 
Intact vials containing sterile powder are stored at room temperature. When prepared as 
directed in the package insert, reconstituted and further diluted solutions of gemcitabine are 
stable for 24 hours at room temperature. 
 Administration 
In this study, gemcitabine will be given intravenously over 30 minutes in an appropriate 
volume of normal saline. 
 Toxicities 
Common toxicities include a flu-like syndrome manifested by fever, fatigue, myalgias, 
headache, cough. Myelosuppression is the usual dose limiting toxicity. Mild elevations in 
hepatic transaminase levels occur in as many as two-thirds of patients but are reversible. 
Dyspnea occurs in 10-23% and is occasionally associated with a drug-induced pneumonitis. 
More often, dyspnea is likely associated with the underlying malignancy. Nausea, vomiting 
and anorexia are common, but usually of mild to moderate severity. Stomatitis and diarrhea or 
constipation occur less often. Proteinuria  and hematuria are usually asymptomatic though 
frequent. A serious hemolytic-uremic syndrome is, however, rare (<1%). Paresthesias and 
peripheral neuropathies occur in 2-10%. Allergic reactions including bronchospasm occur 
infrequently (4%). Minimal alopecia (15%) and macular or maculopapular rashes have also 
been reported. 
9.2 
Pembrolizumab (MK-3475) – Investigational Product 
The investigator shall take responsibility for and shall take all steps to maintain appropriate 
records and ensure appropriate supply, storage, handling, distribution and usage of 
investigational product in accordance with the protocol and any applicable laws and 
regulations. 
Clinical Supplies will be provided by Merck as summarized in Table 7. 

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Table 7  Product Descriptions 
Product Name & Potency 
Dosage Form 
Pembrolizumab 50 mg 
Lyophilized Powder for Injection 
Pembrolizumab 100 mg/ 4mL 
Solution for Injection 
 
 Packaging and Labeling Information 
Clinical supplies will be affixed with a clinical label in accordance with regulatory 
requirements. 
 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. 
 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. 
 Returns and Reconciliation 
The investigator is responsible for keeping accurate records of the clinical supplies received 
from Merck or designee, the amount dispensed to and returned by the subjects and the amount 
remaining at the conclusion of the trial.  
Upon completion or termination of the study, all unused and/or partially used investigational 
product will be destroyed at the site per institutional policy. It is the Investigator’s 
responsibility to arrange for disposal of all empty containers, provided that procedures for 
proper disposal have been established according to applicable federal, state, local and 
institutional guidelines and procedures, and provided that appropriate records of disposal are 
kept. 

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10.0 ADMINISTRATIVE AND REGULATORY DETAILS 
10.1 Confidentiality 
The study team will maintain clinical and laboratory data in a designed manner to ensure 
patient confidentiality. All study personnel have passed human subject protection courses. 
Tissue and blood samples will be retained within NYU for correlative studies.   If specimens 
are sent to collaborators outside of NYU, they will only be labeled with an assigned protocol-
patient identification number without patient identifiers. Systems used for electronic data 
capture are compliant with FDA regulations in 21 CFR Part 11 and applicable local regulatory 
agency guidelines. All documents are kept in strictly confidential files and are only made 
accessible for review of sponsors, monitors and authorized representatives of regulatory 
agencies as described in the informed consent document.  
 
10.2 Compliance with Financial Disclosure Requirements 
10.3 Compliance with Law, Audit and Debarment 
10.4 Compliance with Trial Registration and Results Posting Requirements 
Under the terms of the Food and Drug Administration Modernization Act (FDAMA) and the 
Food and Drug Administration Amendments Act (FDAAA), 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.     
11.0 DATA MANAGEMENT ISSUES 
A clinical research associate (CRA) will be assigned to the study and his/her responsibilities 
will include protocol compliance, data collection, abstraction and data entry, data reporting, 
regulatory monitoring, problem resolution and prioritization, and coordination of activities of 
the protocol study team.  
The data collected for this study will be entered into a HIPAA compliant, password secured 
research database.  Source documentation will be available to support the computerized patient 
record. 
11.1 Data and Source Documentation for Participating Sites 
Data 
The participating site will enter data remotely into NYU internet-based research database.  
Designated research staff at participating sites will be provided Kerberos (NYU Medical 
Center Identification) IDs and passwords to allow entry to the database.  Standardized case 
reports forms (CRFs) and data entry guidelines have been created for this study.  The site staff 

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will receive training on the database before enrolling their first patient.  The participating site 
Principle Investigator is ultimately responsible for ensuring that these forms are completed 
accurately and in a timely manner.  
Source Documentation 
Source documentation refers to original records of observations, clinical findings and 
evaluations that are subsequently recorded as data.  Source documentation should be consistent 
with the data entered.  Relevant source documentation to be submitted throughout the study 
includes: 
• Baseline measures to assess pre-protocol disease status (CT/MRI imaging, pathology 
reports, laboratory values, clinical assessments etc). 
• Treatment records 
• Grade 3-5 toxicities/adverse events not previously submitted with SAE reports 
• Response designation 
 
Source documentation should be sent to NYU at the contact provided, attention of S15-00220 
research staff. 
11.2 Quality Assurance 
Weekly enrollment report will be generated to monitor patient accruals and completeness of 
registration data.  Routine data quality reports will be generated to assess missing data and 
inconsistencies.  Accrual rates and extent and accuracy of evaluations and follow-up will be 
monitored periodically throughout the study period and potential problems will be brought to 
the attention of the study team and principle investigator for discussion and action. 
Random-sample data quality and protocol compliance audits will be conducted by the study 
team at a minimum of two (2) times per year, or more frequently as indicated.  
 Quality Assurance for Participating Sites 
Each participating site in the accrual of subjects to this protocol will be audited by the staff of 
the NYU study team for protocol and regulatory compliance, data verification and review of 
source documentation.  Audits may be accomplished in one of two ways: 1) selected subject 
records can be audited on-site at participating sites or 2) source documents for selected subjects 
will be sent to NYU for audit.  Audits will usually be determined by subject accrual numbers 
and rate of accrual, but can also be prompted by SAEs or request of NYU Principle 
Investigator. 
Audits will be conducted at least once shortly after initiation of subject recruitment at a 
participating site, annually during the study (or more frequently if indicated), and at the end or 
closeout of the trial.  The number of subjects audited will be determined by available time and 
complexity of each subject’s treatment course.   

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The audit will include a review of source documentation to evaluate compliance for: 
• Informed consent documents and screening procedures 
• Adherence to eligibility criteria 
• Protocol defined treatment. 
• Required baseline, on study and follow-up protocol testing 
• IRB documents (submitted amendments, annual continuing review reports, SAE’s) 
• Case report form submissions to NYU, including timelines and accuracy. 
 
A wrap-up session will be conducted at the participating site and preliminary findings will be 
discussed with the participating site PI and research team.  The preliminary results will be sent 
to the NYU PI.  
 
Each audit will be summarized and a final report will be sent to the PI at the audited site within 
30 days of the audit. The report will include a summary of the findings, case by case review of 
subjects audited, specific recommendations on performance and/or shortcomings and request 
for corrective action plans, when necessary.  When corrective action is required, the 
participating site must reply within 45 days of receipt of the audit report with their corrective 
action plan.   
 
A copy of the audit report and corrective action plan (if applicable) submitted by the 
participating site must be sent to the NYU IRB, and maintained in the department’s protocol 
regulatory binder.  
 
11.3 Amendments 
Each change to the protocol document must be organized and documented by NYU and first 
approved by the NYU IRB.  Upon receipt of the NYU IRB approval, NYU will immediately 
distribute all non-expedited amendments to the participating sites for submission to their local 
IRBs. 
Participating sites must obtain approval for all non-expedited amendments from their IRB 
within 90 calendar days of NYU IRB Approval. If the amendment is the result of a safety issue 
or makes eligibility criteria more restrictive, sites will not be permitted to continue enrolling 
new subjects until the participating site IRB approval has been granted for the amended 
protocol.  
The following documents must be provided to NYU for each amendment within the stated 
timelines 
• Participating site IRB Approval 
• Participating site IRB approved informed consent form and HIPAA authorization. 
 
11.4 Additional IRB Correspondence 
Continuing review approval 

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The continuing review approval letter from the participating site’s IRB and the most current 
approved version of the informed consent document should be submitted to NYU within 14 
days of verification.  Failure to submit the re-approval in the stated timeline will result in 
suspension of study activities.  
Deviations and Violations 
A protocol deviation on this study is defined as a request to treat a research participant who 
does not meet all the eligibility criteria, pretreatment evaluation, or who requires alteration in 
their study plan. If a deviation from this protocol is proposed for a potential or existing 
participant at NYU or a participating site, approval from the NYU IRB is required prior to 
the action. Participating sites should contact the NYU PI who will in turn seek approval from 
the NYU IRB/PB. 
  
A protocol violation is anything that occurs with a participant, which deviated from the 
protocol without prior approval from the NYU IRB. For protocol violations that are 
identified after they occur, the participating site should report to NYU as soon as possible.  
The NYU PI will in turn report the violation to the NYU IRB/PB.  
 
Participating sites should report deviations and violations to their institution’s IRBs as soon 
as possible per that site’s institutional guidelines. Approvals/acknowledgments from the 
participating site IRB for protocol deviations and violations should be submitted to NYU as 
received.  
Other correspondence  
Participating sites should submit other correspondence to their institution’s IRB according to 
local guidelines, and submit copies of that correspondence to NYU. 
11.5 Document Maintenance 
The NYU PI and the Participating Site PI will maintain adequate and accurate records to 
enable the implementation of the protocol to be fully documented and the data to be 
subsequently verified.  
 
The participating sites will ensure that all participating site IRB correspondence (IRB 
approval letters referencing protocol version date and amendment number, IRB approved 
protocol, appendices, informed consent forms, deviations, violations, and approval of 
continuing reviews) is maintained in the regulatory binder on site and sent to NYU.  
 
A regulatory binder for each site will also be maintained at NYU; this binder may be paper or 
electronic.  After study closure, the participating site will maintain all source documents, 
study related documents and CRFs for 3 years.  
 

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11.6 Noncompliance  
If a participating site is noncompliant with the protocol document, accrual privileges may be 
suspended and/or contract payments may be withheld, until the outstanding issues have been 
resolved.  
 
 Regulatory Documentation 
Prior to implementing this protocol at NYU, the protocol, informed consent form, HIPAA 
authorization and any other information pertaining to participants must be approved by the 
NYU Institutional Review Board (IRB). Prior to implementing this protocol at the 
participating sites, approval for the NYU IRB approved protocol must be obtained from the 
participating site’s IRB. 
The following documents must be provided to NYU by the participating site before the 
participating site can be activated and begin consenting patients. 
• IRB approval for the protocol, appendices and informed consent form and HIPAA 
authorization 
• IRB Membership List 
• IRB’s Federal Wide Assurance Number and OHRP Registration Number 
• Curriculum Vitae and medical license for each investigator and consenting professional 
• Documentation of human subjects research certification training for investigators and 
key staff members at participating sites 
 
Upon receipt of the required documents, NYU will formally contact the site and grant 
permission to proceed with consenting and enrollment.  
 
11.7 Response Review 
Since therapeutic efficacy is a stated primary objective, all site’s participant’s outcome data 
including pathology and imaging are subject to review by NYU (study sponsor), and may need 
to be obtained from the participating sites for review by NYU (study sponsor).  These materials 
must be sent to NYU upon request.  
11.8 Data and Safety Monitoring Plan 
At the NYU Perlmutter Cancer Center, all investigator-sponsored trials are subject to 
standardized data and safety monitoring, which includes scientific peer review, IRB review, 
Phase I/II committee review and DSMC review as well as periodic and random internal 
auditing. 
 
The review of adverse events for this trial will occur at five levels: 
 
1. Principal Investigator: Adverse events are discussed at weekly research meetings led 
by the Program Leader (Minas Economides, MD) for the Genitourinary Cancers 
Program and attended by other clinical investigators, research nurses, data managers, 

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clinical nurses. Protocol monitoring, compliance and data verification, assessment of 
therapeutic responses and adverse events are evaluated by this group on a weekly 
basis.  Protocol deviations and violations are tracked at these meetings and corrective 
action plans are instituted as needed.  
2. Data and Safety Monitoring Committee (DSMC): The NYU Perlmutter Cancer Center 
DSMC reviews all data for patient safety according to the DSMC policies. This review 
includes an examination of patient accrual, adverse events and study results. For phase 
I, dose finding trials, a review of toxicity after the first defined cohort is conducted to 
assure no DLTs are found before proceeding to the next cohort, per the protocol 
definition. If additional cohorts are required to establish the recommended dose for the 
extended safety cohort, these cohorts will be evaluated in a similar manner. By 
definition, dose finding cohort data will have to be confirmed or extended, by the trial 
definition, prior to proceeding to the next treatment group. Reviews will be done within 
2-3 days of the complete cohort data set being available, even if not coinciding with a 
scheduled monthly meeting, so as to not delay study accrual. Once the recommended 
dose is established, further interim reviews will be performed at accrual points 
established by the protocol. All studies are required to be reviewed at least annually, 
regardless of their accrual status. Principal Investigators are required to attend the 
review of their studies. 
3. Institutional Review Board (IRB): An annual report to the IRB is submitted by the trial 
PI for continuation of the protocol. It includes a summary of all AEs, total enrollment 
with demographics, protocol violations, and current status of subjects as well as 
available clinical trial data. 
4. In addition, the internal audit committee will inspect the source documents, including 
consent forms for randomly selected enrolled participants at regular intervals 
throughout the trial to verify adherence to the protocol; the completeness, accuracy and 
consistency of the data; and adherence to ICH Good Clinical Practice guidelines.  
 
Ongoing monitoring for accrual, protocol conduct and compliance and safety will occur via 
regularly scheduled teleconferences between the sponsor (NYU) and participating sites.  
During the enrollment of the initial safety cohort (up to 6 patients), these teleconferences will 
occur every 2 weeks.  If the trial proceeds to full enrollment, these teleconferences will occur 
on a monthly basis.   
 
Safety concerns raised during these teleconferences and during the course of study conduct 
will be recorded and reviewed along with frequency and grade of AEs at the NYU Perlmutter 
DSMC.  This DSMC will serve as the primary independent safety committee for review of 
adverse events that occur on this study as this committee meets most frequently.  
 
The Quality Assurance Specialist at NYU Langone Health is an independent, disinterested, 
third party with the appropriate expertise who will review the enrollment of subjects at NYU 
Langone to ensure that study screening and eligibility procedures were conducted and 
documented in accordance with the IRB-approved protocol prior to publication and/or 
submission to a sponsor or regulatory authority. In addition, this third party will review and 
confirm all study data and analysis prior to publication and or submission to a sponsor or 

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regulatory authority. This third party must not have a reporting relationship to Dr. Balar. and 
must be prepared to provide information to the CIMU, upon request, relative to the monitoring 
of study documentation in this regard. 

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12.0 APPENDICES 
12.1 ECOG Performance Status 
Grade 
Description 
0 
Normal activity. Fully active, able to carry on all pre-disease 
performance without restriction. 
1 
Symptoms, but ambulatory. Restricted in physically strenuous 
activity, but ambulatory and able to carry out work of a light or 
sedentary nature (e.g., light housework, office work). 
2 
In bed <50% of the time. Ambulatory and capable of all self-care, but 
unable to carry out any work activities. Up and about more than 50% 
of waking hours. 
3 
In bed >50% of the time. Capable of only limited self-care, confined 
to bed or chair more than 50% of waking hours. 
4 
100% bedridden. Completely disabled. Cannot carry on any self-care. 
Totally confined to bed or chair. 
5 
Dead. 
* As published in Am. J. Clin. Oncol.:  Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., 
McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern Cooperative Oncology 
Group. Am J Clin Oncol 5:649-655, 1982. The Eastern Cooperative Oncology Group, Robert Comis 
M.D., Group Chair. 
 
12.2 Common Terminology Criteria for Adverse Events V4.0 (CTCAE) 
The descriptions and grading scales found in the revised NCI Common Terminology Criteria 
for Adverse Events (CTCAE) version 4.0 will be utilized for adverse event reporting. 
(http://ctep.cancer.gov/reporting/ctc.html) 
12.3 Events of Clinical Interest Guidance Document 
Attached separately to this protocol.  
12.4 Radiation Directives 
Phase II Trial of MK3475 in Combination with Gemcitabine and Concurrent 
HypoFractionated Radiation Therapy as Bladder Sparing Treatment for Muscle-
Invasive Urothelial Cancer of the Bladder 
 
PTV dose:  5200cGy;  260 cGy per fraction in 20 fractions 
 
Values in parenthesis = Acceptable Variation to protocol constraints.  
Dmax defined as dose to 0.035 cc volume 
 
 

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Structure 
Paramete
r 
Constraint 
Comments: 
Targets 
                             
 
PTV 
D99% 
> 95% (90%) of 
Rx          
IMRT/VMAT surrogate for Dmin 
Dmax 
< 115% (120%) 
 
Normal Structures 
 
 
Rectum 
D50% 
< 4500 cGy 
 
Dmax 
< 5500 cGy 
 
 
 
 
 
Right Femoral 
Head/Neck 
Dmax 
< 4500 cGy          
 
Left Femoral 
Head/Neck 
Dmax 
<4500 cGy 
 
 Bowel bag 
D50% 
< 4000 cGy              
Dmax 
< 5350 cGy         
 
 
 
 
 
 
Guide to Abbreviations:   Rx = Prescription, Dmax = maximum dose received by a structure 
[cGy or as a % of prescription], Dmean = mean dose to structure, Dx =Dose delivered to x% or 
x cc of structure volume (ie. D50% = Dmedian), Vx = Volume of structure receiving > x dose [% 
or cc]. 
 
 
 
 
 
 
 
 
 
 
  

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