Phase II Study Of Single-dose Cyclophosphamide +Pembrolizumab In Patients With Metastatic Triple Negative Breast Cancer
Phase: PHASE2
Conditions: Triple Negative Breast Cancer
Sponsor: UNC Lineberger Comprehensive Cancer Center

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
 
 
PROTOCOL AMENDMENT # 6 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
AMENDMENT INCORPORATES: 
__  Editorial, administrative changes 
_X  Scientific changes  
__  Therapy changes  
__   Eligibility Changes  
 
 
Rationale for amendment: The purpose of this amendment is to decrease the duration of 
subject follow up after treatment has ended. Currently the protocol states that subjects will 
be followed for up to 3 years, this time will be changed to reflect that subjects will be 
followed for up to 2 years.  Given that the primary objective has been met, the decrease in 
subject follow up will allow for subsequent study closure.  
 
 
Therapy changes: 
Section 4.6 
 
 
T&E Table 
 
Section 6.4 
Duration of Follow up: Follow up changed from ‘up to 3 years’ to ‘up 
to 2 years’, subsequent follow up changed to ‘up to 2 years’ 
 
Footnote 3 changed to reflect follow up for up to 2 years.  
 
Long Term Follow up: Subsequent follow up changed from ‘up to 3 
years’ to ‘up to 2 years’ 
 
 
 
 
 
 
 
 
 
 
 
 
 
THE ATTACHED VERSION DATED February 22, 2022 INCORPORATES THE 
ABOVE REVISIONS  

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
 
 
PROTOCOL AMENDMENT # 5 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
AMENDMENT #5 INCORPORATES ( Check all that apply): 
    X Editorial, Administrative Changes 
        Scientific Changes 
        Therapy Changes 
        Eligibility Changes 
 
AMENDMENT RATIONALE AND SUMMARY 
A Principal Investigator change from Dr. Benjamin Vincent to Dr. E. Claire Dees. 
 
Historically, amendments were first submitted to the UNC IRB, and then after approval, 
submitted to the site IRBs. The change is to submit amendments to the UNC IRB and to 
site IRBs at the same time. Changes in informed consent documents must be submitted to 
the Multicenter Regulatory Associate prior to submission to the site IRB.   
 
SUMMARY OF CHANGES 
1. The protocol has been revised throughout to reflect the PI change 
2. Correction of version date error in page header that was released as part of 
Amendment 5 version 1.0. 
3. Section 9.6 - Amendments to the Protocol now reads: 
For Institutions Relying on Their Own IRB: 
Investigators must submit the amendment to their institution's IRB for approval. 
For multicenter studies, any multicenter site must submit their informed consent 
revisions to the Multicenter Regulatory Associate prior to submission to their 
IRB. 
 
 
 
 
 
 
 
 
The attached version dated May 24, 2019 incorporates the above revisions 

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
 
PROTOCOL AMENDMENT # 4 
 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
AMENDMENT #4 INCORPORATES ( Check all that apply): 
    X Editorial, Administrative Changes 
        Scientific Changes 
        Therapy Changes 
        Eligibility Changes 
 
AMENDMENT RATIONALE AND SUMMARY 
A Principal Investigator change from Dr. Carey Anders to Dr. Benjamin Vincent.  Also, 
the role of Co-Principal Investigator changed from Dr. Jonathan Serody to Dr. Lisa 
Carey.   
 
The protocol has been revised throughout to reflect these changes.   
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
The attached version dated December 5, 2018 incorporates the above revisions  
 

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
 
PROTOCOL AMENDMENT # 3 
 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
AMENDMENT #3 INCORPORATES ( Check all that apply): 
    X Editorial, Administrative Changes 
    X Scientific Changes 
        Therapy Changes 
        Eligibility Changes 
 
AMENDMENT RATIONALE AND SUMMARY 
This protocol amendment changes the frequency of tumor assessments from every 9 
weeks to 12 weeks after the subject has been on treatment for at least 1 year.  This change 
allows for reduced radiation exposure to the subject. 
 
The single subject exception language was updated to align with the Sponsor’s updated 
policy of no single subject exceptions will not be granted for eligibility.  This is to 
incorporate the administrative letter dated December 1, 2017 
 
SUMMARY OF CHANGES 
1. Section 6.1, footnote 5: tumor assessment intervals increased to every 12 weeks 
after one year of study treatment.   
2. Section 6.3.7: After the first year, tumor imaging will be performed every 12 
weeks, at the end of cycles 22, 26, 30, etc 
3. Section 9.5.2:  Guidance updated to:  Eligibility single subject exceptions are not 
permitted for Lineberger Comprehensive Cancer Center Investigator Initiated 
Trials under any circumstances.  Other types of single subject exceptions may be 
allowed if proper regulatory review has been completed in accordance with 
Lineberger Comprehensive Cancer Center’s Single Subject Exception Policy. 
 
 
 
 
 
 
The attached version dated February 8, 2018 incorporates the above revisions  

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
 
PROTOCOL AMENDMENT # 2 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
AMENDMENT #2 INCORPORATES ( Check all that apply): 
    X Editorial, Administrative Changes 
    X Scientific Changes 
        Therapy Changes 
        Eligibility Changes 
 
AMENDMENT RATIONALE AND SUMMARY 
This protocol amendment defines disease progression to correspond with the clinical 
assessments appropriate for the subject population. Disease progression can be 
determined by: (1) RECIST 1.1 criteria; (2) Clinical deterioration (3) Clinical progression 
(i.e. worsening of chest wall lesion). This allows for appropriate documentation of 
disease progression for subjects who end treatment and continue onto palliative care or 
hospice.  
In addition to other administrative changes, an administrative letter from January 3, 2017, 
which defines the timeframe for ECHO or MUGO assessments as part of eligibility has 
been incorporated into this amendment.  
 
SUMMARY OF CHANGES 
1. Defined disease progression as: (1) RECIST 1.1 criteria; (2) Clinical deterioration 
(3) Clinical progression in Section 2.4.1.1 
2. Section 4.4 edited to include definition of disease progression 
3. Section 4.5 edited to ensure end of treatment time frame (+/- 10 days) is 
congruent with time and events table in 6.0 
4. Time and Events Table 6.0: 
a. 1Editotial change and clarification of ECHO/MUGO timeline 
b. 5Language added to allow for CT from PET scan to be used in tumor 
imaging 
c. 10Adjusted to correlate with correct assessments in table 
5. Language added to allow for CT from PET scan to be used for tumor imaging was 
added to section 6.2 
6. Section 6.4.1 was modified to correspond with definition of disease progression. 
This indicates subjects do not need imaging to confirm disease progression.  
 
The attached version dated October 17, 2017 incorporates the above revisions 
 

LINEBERGER COMPREHENSIVE CANCER CENTER 
 
CLINICAL ONCOLOGY RESEARCH PROGRAM 
 
 
UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL 
 
PROTOCOL AMENDMENT # 1 
 
LCCC 1525: Phase II Study Of Pembrolizumab Therapy Following a Single Priming 
Dose of Cyclophosphamide in Patients With Metastatic Triple Negative Breast Cancer 
(TNBC) 
 
 
AMENDMENT #1 INCORPORATES ( Check all that apply): 
X   Editorial, Administrative Changes 
X   Scientific Changes 
      Therapy Changes 
      Eligibility Changes 
 
AMENDMENT RATIONALE AND SUMMARY 
1. The primary purpose of this amendment is to update safety language for 
pembrolizumab that MERCK provides for investigator initiated trial protocols. 
2. Minor editorial changes were made to Inclusion criteria 9 and 10  
3. The dose modification section 4.2.2.2 was updated to include the most recent dose 
modification guidelines for pembrolizumab  
4. The Time and Events Table in Section 6.0 was updated to ensure that LFTs are 
collected at the beginning of every cycle of pembrolizumab. 
5. Footnote 3 of the Time and Events table was updated to increase the 30-day follow-
up period from a 7 day window to a 10 day window.   
6. Additional safety data clarifications were incorporated into sections 7.1.1, 7.1.4, 
7.3.3.3 
7. A new section 7.3.3.2. was added providing protocol-specific exceptions to AE 
reporting 
8. Clarified the use of irRECIST for assessment of immune-related response as 
described in section 6.7.5.1.   
 
 
 
The attached version dated October 27, 2016 incorporates the above revisions 
 
 
 
 
 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
i 
TABLE OF CONTENTS 
1.0 
BACKGROUND AND RATIONALE ..................................................................4 
1.1 
Study Synopsis ......................................................................................................4 
1.2 
Disease and Study Background .............................................................................4 
1.3 
Pembrolizumab......................................................................................................6 
1.4 
Correlative Studies ................................................................................................8 
2.0 
STUDY OBJECTIVES ...........................................................................................9 
2.4 
Endpoints .............................................................................................................10 
3.0 
PATIENT ELIGIBILITY ....................................................................................11 
3.1 
Inclusion Criteria .................................................................................................11 
3.2 
Exclusion Criteria ................................................................................................14 
4.0 
TREATMENT PLAN ...........................................................................................16 
4.1 
Schema ................................................................................................................17 
4.2 
Treatment Dosage and Administration ...............................................................17 
4.3 
Concomitant Medications/Treatments ................................................................23 
4.4 
Duration of Therapy ............................................................................................24 
4.5 
End of Treatment .................................................................................................25 
4.6 
Duration of Follow Up ........................................................................................25 
4.7 
Removal of Patients from Protocol Therapy .......................................................25 
4.8 
Study Withdrawal ................................................................................................26 
5.0 
DRUG INFORMATION ......................................................................................26 
5.1 
Cyclophosphamide ..............................................................................................26 
5.2 
Pembrolizumab....................................................................................................27 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
ii 
6.0 
EVALUATIONS AND ASSESSMENTS ............................................................34 
6.1 
Time and Events Table ........................................................................................34 
6.2 
Pre-Study Assessments .......................................................................................37 
6.3 
Treatment Assessments .......................................................................................38 
6.4 
Post-Treatment/Follow-up Assessments .............................................................40 
6.5 
Correlative Studies Procedures ...........................................................................41 
6.6 
Assessment of Safety ..........................................................................................42 
6.7 
Assessment of Efficacy .......................................................................................42 
7.0 
ADVERSE EVENTS ............................................................................................46 
7.1 
Definitions ...........................................................................................................46 
7.2 
Documentation of non-serious AEs or SARs ......................................................48 
7.3 
SAEs, Serious SARs or Events of Clinical Interest ............................................48 
7.4 
Data and Safety Monitoring Plan ........................................................................53 
8.0 
STATISTICAL CONSIDERATIONS ................................................................53 
8.1 
Study Design/Study Endpoints ...........................................................................54 
8.2 
Sample Size and Accrual.....................................................................................54 
8.3 
Toxicity Monitoring ............................................................................................55 
8.4 
Data Analysis Plans .............................................................................................55 
9.0 
STUDY MANAGEMENT ....................................................................................56 
9.1 
Institutional Review Board (IRB) Approval and Consent ..................................57 
9.2 
Required Documentation.....................................................................................57 
9.3 
Registration Procedures.......................................................................................58 
9.4 
Data Management and Monitoring/Auditing ......................................................58 
9.5 
Adherence to the Protocol ...................................................................................58 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
iii 
9.6 
Amendments to the Protocol ...............................................................................60 
9.7 
Record Retention .................................................................................................61 
9.8 
Obligations of Investigators ................................................................................61 
10.0 REFERENCES ......................................................................................................61 
11.0 APPENDICES .......................................................................................................64 
11.1 
Appendix A ECOG Performance Status .............................................................64 
11.2 
Appendix B Cockcroft-Gault Formula ................................................................65 
11.3 
Appendix C:  Prohibited Medications .................................................................66 
11.4 
Appendix D Patient Handout: Prohibited Medications .......................................67 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
4 
1.0 
BACKGROUND AND RATIONALE 
1.1 
Study Synopsis 
This phase II, single-arm, multicenter study will evaluate pembrolizumab therapy 
200 mg IV given every 3 weeks (Q3W), following a single priming dose of 
cyclophosphamide 300 mg/m2 IV in patients with advanced triple-negative breast 
cancer (TNBC) who have received at least one prior line of therapy. The primary 
objective is to estimate progression-free survival (PFS) for cyclophosphamide + 
pembrolizumab in advanced TNBC patients compared to pembrolizumab alone 
(historical PFS = 1.9 months) [1].  A biologically-focused primary objective is to 
describe the reduction in regulatory T cells (Tregs) in TNBC patients receiving 
this combination. Secondary objectives include assessments of overall response 
rate (ORR) per RECIST1.1, duration of response (DOR), disease control rate  
(DCR) and overall survival (OS) in this population receiving a single dose 
cyclophosphamide + pembrolizumab.  Determination of response to study 
treatment based on immune-related response criteria (irRECIST) is an exploratory 
objective of this trial.  Patients will continue study therapy until disease 
progression and toxicity will be assessed during treatment via NCI-CTCAE 
criteria v4. In addition, tumor samples from archival diagnostic tissue or fresh 
biopsy material (optional pre and post dose biopsy) and serial blood draws will be 
obtained for correlative biomarker studies.   
 
Our hypothesis is that a single dose of cyclophosphamide given the day before 
initiation of pembrolizumab every 3 weeks will improve PFS in advanced TNBC 
patients by 1 month and that a total of 36 evaluable patients will be needed to 
detect a clinically-meaningful change in median PFS from 1.9 to 2.9 months. The 
goal of the proposed collateral biomarker research is to discover immunologic 
determinants of response to single-dose cyclophosphamide + pembrolizumab in 
this population. Our group has found that the basal-like and claudin-low 
molecular subtypes (the two subtypes that comprise virtually all TNBC) are 
enriched in tumor-infiltrating immune cells with gene-expression patterns 
consistent with active immunosuppression ([2] and unpublished data]).  We 
anticipate that clinical response to programmed cell death protein 1 and ligand 
(PD-1/PD-L1) axis inhibition by pembrolizumab will be most pronounced in 
TNBC patients whose tumors have elicited an immune response that is actively 
suppressed through PD-1/PD-L1 interaction. 
1.2 
Disease and Study Background   
It is estimated that 200,000 women world-wide are diagnosed annually with 
TNBC [3].  TNBC lacks expression of the estrogen and progesterone receptors 
(ER/PR) and the HER2 protein, and is associated with early and visceral 
recurrences, despite sensitivity to cytotoxics [4, 5]. In particular, TNBC can 
respond well to anthracyclines in combination with taxanes [6] or to taxanes or 
platinums as monotherapy [7], but the risks of relapse/recurrence remain quite 
high. In the metastatic TNBC population and from first presentation of advanced 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
5 
disease, median PFS with chemotherapy alone is ~5-8 months with an OS of ~18 
months [8, 9]. Novel approaches are clearly needed. One exciting area worthy of 
further exploration is immunotherapy, and in particular agents that inhibit the PD-
1 and PD-L1. 
1.2.1 Anti-PD1 and PD-L1 Agents in TNBC 
Anti-PD1 and PD-L1 agents have demonstrated exciting activity in several human 
cancers with an ORR of just over 20% [10, 11]. Breast cancer has only recently 
been included in trials of immunomodulating agents, as this cancer has not been 
typically viewed as immunosensitive.  In fact, intra-tumoral expression of PD1 
and PD-L1 has been shown to be associated with decreased survival in basal-like 
breast cancer [12, 13] and preliminary data in TNBC with immune checkpoint 
inhibitors have generated enthusiasm for this approach.  In the early-phase 
KEYNOTE-012 trial, treatment with the PD-1 inhibitor pembrolizumab 
demonstrated an ORR of 18.5%, including one complete response (CR) in 32 
heavily pretreated patients with PD-L1-positive recurrent metastatic TNBC [1].  
The rate of stable disease (SD) among 27 evaluable patients (median follow-up < 
10 months) was 25.9%, and median PFS was 1.9 months. Grade 3/4 adverse 
events (AEs) occurred in 15.6% of patients, and the most common AEs were 
arthralgia (18.8%), fatigue (18.8%), myalgia (15.6%), and nausea (15.6%). 
Clearly this agent is worthy of further study in TNBC. 
 
While promising the overall response rate (ORR) of 18.5% reported in TNBC is 
modest [1] .  This may be due to the presence of intra-tumoral regulatory T cells 
(Tregs), potent suppressors of the immune response [14]. In vitro, basal-like 
breast cancer cells induce Treg polarization of undifferentiated CD4+ T cells [15].  
Increased ratio of Treg to cytotoxic T lymphocytes (Treg/CTL ratio) in breast 
tumors has been associated with decreased survival in multiple studies [16].   
1.2.2 Modulation of the immune microenvironment by cyclophosphamide  
The importance of intact immune surveillance in controlling outgrowth of 
neoplastic transformation has been known for decades.  Accumulating evidence 
shows a correlation between certain subsets of 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 capacity of cyclophosphamide to deplete Tregs is long-established [17].  It is 
important to note, however, that cyclophosphamide in combination with 
immunotherapy is not without risk.  A recent study showed that repeated doses of 
cyclophosphamide may worsen outcomes when combined with other 
immunomodulating agents. Compared to the clinical profile of the CTLA-4 
inhibitor ipilimumab when administered as monotherapy, investigators reported 
reduced efficacy coupled with a doubling of toxicities when cyclophosphamide 
(300 mg/m2 IV) was given on D1 followed by ipilimumab on D3 for each of 4 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
6 
cycles in patients with metastatic melanoma.  In addition to depleting Tregs, 
cyclophosphamide may induce myeloid-derived suppressor cells and thereby 
promote tumor growth [18].  These effects have not been reported with 
cyclophosphamide given as a single dose prior to immunotherapy. Further, a 
single low dose of cyclophosphamide 300 mg/m2 prior to a novel multi-epitope 
renal cancer vaccine markedly enhanced the clinical vaccine response in patients 
who developed an active epitope-specific T cell response to vaccination [19].   
 
While multiple dosing strategies have been shown to diminish circulating Treg 
numbers, a proper dosing strategy that does not 1) yield depletion of activated 
cytotoxic T cells and/or 2) cause unacceptable drug-related toxicity is important 
to define.  In one study of an allogeneic HER2-positive GM-CSF–secreting breast 
tumor vaccine, addition of 200 mg/m2 cyclophosphamide had no impact on the 
rate of development of delayed-type hypersensitivity (a measure of effector T cell 
response), whereas a dose of 450mg/m2 was associated with diminished effector 
responses [20].  Anti-HER2 humoral immunity following vaccination was best 
enhanced with the lower cyclophosphamide dose.  In light of these data, we have 
chosen a one-time immune-priming dose of 300 mg/m2 to be given prior to the 
first cycle of pembrolizumab in this study. 
 
We have found in preclinical studies that depletion of Tregs by a drug-dependent 
genetic method or by a single infusion with low-dose cyclophosphamide results in 
improved survival and impaired tumor growth in a T11 murine model of TNBC 
of the claudin-low molecular subtype [Vincent and Serody, unpublished data].  
When Treg were depleted using a single administration of low-dose 
cyclophosphamide or using a genetic depletion method, tumor growth was 
impaired; however, all mice eventually succumbed to tumor.  Treg depletion with 
low-dose cyclophosphamide was markedly enhanced by concurrent treatment 
with anti-CTLA4 and anti-PD1 inhibitory antibodies; moreover, tumor 
impairment was pronounced and a small number of mice failed to develop tumor 
(3/20 in the combination treatment arm vs. 0/10 mice in the cyclophosphamide-
only are and 0/6 mice in the untreated arm). Thus, we hypothesize that Treg 
depletion with a single priming dose of low-dose cyclophosphamide at 300 mg/m2 
IV given prior to the first cycle of pembrolizumab (200 mg q3W) will provide 
additional therapeutic benefit in TNBC compared to pembrolizumab alone. 
1.3 
Pembrolizumab 
Pembrolizumab (MK-3475) is a potent and highly selective intravenous 
humanized mAb of the immunoglobulin (Ig) G4/kappa isotype that directly 
blocks the interaction between PD-1 and its ligands, PD-L1 and PD-L2. This 
blockade enhances functional activity of the target lymphocytes to facilitate an 
antitumor immune response, leading to tumor regression and immune rejection of 
the tumor.  KeytrudaTM (Pembrolizumab) has recently been approved at a dose of 
2 mg/kg IV every 3 weeks in the United States for the treatment of patients with 
unresectable or metastatic melanoma with disease progression following 
ipilumumab and, if BRAF V600 mutation positive, a BRAF inhibitor.  Indications 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
7 
currently under investigation by the manufacturer of pembrolizumab include non-
small cell lung cancer and glioblastoma. In addition, preliminary data from the 
KEYNOTE-012 study of pembrolizumab has generated enthusiasm for further 
investigation of immune checkpoint inhibition as a treatment strategy for TNBC.  
1.3.1 Rationale for Dose Selection/Regimen/Modification 
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 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 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
8 
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. 
1.4 
Correlative Studies 
Basal-like and claudin-low molecular subtypes of breast cancer are enriched in 
tumor-infiltrating immune cells with gene-expression patterns consistent with 
active immunosuppression ([2] and unpublished data]).  A single priming dose of 
cyclophosphamide + pembrolizumab therapy may counteract the 
immunosuppressive microenvironment of TNBC and initiate a substantive 
antitumor response. The efficacy of this combination will likely correlate with the 
presence of a substantial, but suppressed, tumor immune infiltrate. Correlative 
biomarker studies in this trial will investigate this hypothesis.  
 
Exploratory objectives based on serial blood collections and tumor samples will 
investigate whether the phenotype of tumor-infiltrating lymphocytes, including 
delineation of effector and regulatory T cells, from the diagnostic biopsy will 
correlate with clinical benefit. An evaluation of the predictive capacity of PD-L1 
expression, immune gene signatures, and a characterization of the change in 
phenotype in tumor-infiltrating lymphocytes (TILs) before and after therapy will 
be explored.  In addition, we hope to define T cell receptor (TCR) and B cell 
receptor (BCR) repertoire profiles associated with clinical benefit. We 
hypothesize that each of the following: increased PD-L1 mRNA expression, 
effector immune infiltrate, clonality in TILs and decreased regulatory cell 
populations, will be associated with clinical benefit (eg, ORR, PFS, DOR, CBR 
and OS).  
 
Some or all of these correlative studies may be conducted under the auspices of 
the Merck sponsored UNC Immunotherapy PAtient Centered Translational 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
12 
• ER- and PR-negative: defined as < 1% staining by immunohistochemistry 
(IHC) 
• HER2-negative disease, defined as IHC 0-1+ or fluorescence in situ 
hybridization (FISH) ratio < 2.0 
 
6. Patients with stable brain metastases will be allowed provided the following 
criteria are met: 
• Brain radiation was already provided at least 4 weeks prior to initiating 
study treatment    
• The subject has no new or progressive neurologic symptoms AND 
neurological symptom stability for the last 4 weeks prior to the study 
• The subject has been off of corticosteroids for at least 7 days prior to trial 
treatment 
• The subject does not have carcinomatous meningitis    
 
7. Demonstrate adequate organ function as defined in the table below; all screening 
labs to be obtained within 72 h of initiating study treatment. 
 
 

LCCC 1525 
 
CONFIDENTIAL 
PI: Dees 
 
UNIVERSITY OF NORTH CAROLINA 
February 22, 2022 
 
 
 
 
14 
 
 
10. Male subjects of childbearing potential must agree to use an adequate method 
of contraception as outlined in Section 5.2.8 or abstain from heterosexual 
activity, starting with the first dose of study therapy through 120 days after the 
last dose of study therapy. 
11. Consent for the use of any residual material from biopsy (archival tissue) and 
serial blood draws will be required for enrollment; fresh biopsy (pre and post 
dose) of tumor tissue will be optional. NOTE: Patients without adequate tissue 
for bio correlates will not be excluded or required to have a repeat biopsy.   
 
12. As determined by the enrolling physician or protocol designee, the subject 
should be able to understand and comply with study procedures for the entire 
length of the study. 
 
13. Has a LVEF within the normal institutional range (or ≥ 50%) based on an 
ECHO or MUGA, completed within 4 weeks prior to day one of treatment.  
3.2 
Exclusion Criteria 
A subject will be excluded from this study for the following reasons: 
 
1. Active infection requiring systemic therapy 
 
2. Pregnant or breastfeeding (NOTE: breast milk cannot be stored for future use 
while the mother is being treated on study). 
 
3. Has a known history of active TB (Bacillus Tuberculosis) 
 
4. Hypersensitivity to pembrolizumab or any of its excipients. 
 
5. Has a known additional malignancy that is active and/or progressive requiring 
treatment; exceptions include basal cell or squamous cell skin cancer, in situ 
cervical or bladder cancer, or other cancer for which the subject has been disease-
free for at least five years. 
 
6. Has had prior chemotherapy, targeted small molecule therapy, or radiation 
therapy within 2 weeks prior to receipt of study medication or who has not 
recovered (i.e., ≤ Grade 1 or at baseline; excludes alopecia and Grade 2 
neuropathy) from adverse events due to a previously administered agent. 
• If subject had major surgery, they must have recovered adequately from 
the toxicity and complications from the intervention prior to starting 
therapy   
 
7. Has a known additional malignancy that is progressing or requires active 
treatment.  Exceptions include basal cell carcinoma of the skin or squamous cell 

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carcinoma of the skin that has undergone potentially curative therapy or in situ 
cervical cancer. 
 
8. Has had monoclonal antibody therapy within 4 weeks prior to study Day 1 or who 
has not recovered (ie, ≤ Grade 1 at baseline; excludes alopecia and Grade 2 
neuropathy) from adverse events due to agent(s) administered more than 4 weeks 
earlier.  
 
9. Treatment with any investigational drug within 4 weeks or 5 half-lives, whichever 
is shorter, prior to the first dose of study medication. 
 
10. Used an investigational device within 4 weeks of the first dose of treatment. 
 
11. 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. 
 
12. Has active autoimmune disease that has required systemic treatment in the past 2 
years (i.e. with use of disease modifying agents, corticosteroids or 
immunosuppressive drugs). Replacement therapy (eg, thyroxine, insulin, or 
physiologic corticosteroid replacement therapy for adrenal or pituitary 
insufficiency, etc.) is not considered a form of systemic treatment.  
 
13. Has known history of (non-infectious) pneumonitis that required steroids, or 
current pneumonitis. 
 
14. Has received prior therapy with an anti-PD-1, anti-PD-L1, or anti-PD-L2 agent. 
 
15. 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. 
 
16. 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.   
17. Has known psychiatric or substance abuse disorders that would interfere with 
cooperation with the requirements of the trial. 
18. Has a known history of Human Immunodeficiency Virus (HIV) (HIV 1/2 
antibodies). 
 
19. Has participated in a previous trial and received pembrolizumab therapy 
 
20. Has known active Hepatitis B (e.g., HBsAg reactive) or Hepatitis C (e.g., HCV 
RNA [qualitative] is detected). 

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21. Has received a live vaccine within 30 days prior to the first dose of trial treatment. 
• 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 
 
22. Cyclophosphamide is a substrate for cytochromes 2B6, 2C9, 3A4 and 2C19. 
Patients must not have received any drug that is a moderate or strong inhibitor of 
2B6, 2C9, 3A4, and 2C19 within 1 week prior to receiving cyclophosphamide 
dosing through 72 hours after cyclophosphamide dosing.  Patients must not have 
received any drug that is a moderate or strong inducer of 3A4 within 2 weeks 
prior to cyclophosphamide dosing.   
 
Note: A frequently updated P450 drug interaction table can be found at 
http://medicine.iupui.edu/clinpharm/ddis/.  Refer to Appendix C: Prohibited 
Medications for additional information.  A patient handout is provided in 
Appendix D Patient Handout: Prohibited Medications. 
4.0 
 TREATMENT PLAN 
This is a phase II, single-arm, multicenter study of a single dose (300 mg/m2) of 
cyclophosphamide given the day before cycle 1 of pembrolizumab (200 mg), 
which will administered every 3 weeks in patients with metastatic TNBC who 
have failed at least one prior line of therapy. Toxicity will be assessed during 
treatment via NCI CTCAEv4.  Archival tissue (or tissue from an optional fresh 
biopsy taken at baseline and at the end of treatment), and serial blood draws will 
be used for correlative studies. 
 
 

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4.1 
Schema 
 
 
4.2 
Treatment Dosage and Administration 
After screening and enrollment, treatment will consist of the following: 
 
A single dose of cyclophosphamide 300 mg/m2 IV (30 min – 60 min infusion) 
administered the day before cycle 1 of pembrolizumab therapy, followed by 
pembrolizumab 200 mg IV over 30 minutes on Day 2; Pembrolizumab will be 
repeated every 3 weeks until progression. 
 
Agent 
Dose 
Route 
Schedule 
Cyclophosphamide 300 mg/m2 IV over 30 - 60 
minutes  
Single dose on D1 of study 
Pembrolizumab 
200 mg 
IV over 30 minutes 
Starting on D2 of study; 
Every 3 weeks (21 days) 
until disease progression 
4.2.1 Cyclophosphamide Administration 
A single 300 mg/m2 dose of cyclophosphamide IV over 30-60 minutes will be 
administered on Day 1 (D1) of this study.  This is considered a low dose of 
cyclophosphamide compared to other regimens typically used to treat 
malignancies.  

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4.2.2 Pembrolizumab Administration 
Pembrolizumab 200 mg will be administered as a 30 minute IV infusion starting 
on Day 2 (D2) of the study (hematology labs must meet inclusion criteria to 
initiate therapy with pembrolizumab).  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). The 
Pharmacy Manual contains specific instructions for the preparation of the 
pembrolizumab infusion fluid and administration of infusion solution. This 
manual is provided as a document separate from the protocol. 
4.2.2.1 Management of Infusion Reactions for Pembrolizumab 
Signs and symptoms usually develop during or shortly after drug infusion and 
generally resolve completely within 24 hours of completion of infusion.  Refer to 
the table below for infusion reaction treatment guidelines: 
 
NCI CTCAE 
Grade 
Treatment 
Premedication at 
subsequent dosing 
Grade 1 
Mild reaction; infusion 
interruption not 
indicated; intervention 
not indicated 
Increase monitoring of vital 
signs as medically indicated 
until the subject is deemed 
medically stable in the 
opinion of the investigator. 
None 
Grade 2 
Requires infusion 
interruption but 
responds promptly to 
symptomatic 
treatment (e.g., 
antihistamines, 
NSAIDS, narcotics, 
IV fluids); 
prophylactic 
medications indicated 
for ≤24 hrs 
Stop Infusion and monitor 
symptoms. 
Additional appropriate 
medical therapy may include 
but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Increase monitoring of vital 
signs as medically indicated 
until the subject is deemed 
medically stable in the 
opinion of the investigator. If 
symptoms resolve within one 
hour of stopping drug 
infusion, the infusion may be 
restarted at 50% of the 
original infusion rate (e.g., 
from 100 mL/hr to 50 
mL/hr).  Otherwise dosing 
will be held until symptoms 
Subject may be 
premedicated 1.5hr 
(± 30 minutes) prior 
to infusion of 
pembrolizumab 
with: 
 
Diphenhydramine 
50 mg po (or 
equivalent dose of 
antihistamine). 
 
 
Acetaminophen 
500-1000 mg po (or 
equivalent dose of 
antipyretic). 

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NCI CTCAE 
Grade 
Treatment 
Premedication at 
subsequent dosing 
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. 
 
 
4.2.2.2 Other Dose Modifications for Pembrolizumab 
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 below.  See section 4.2.2.3 for supportive care 
guidelines, including use of corticosteroids. 
  

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

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If a dose of pembrolizumab is delayed, then the subsequent dose should be 
administered when symptoms have resolved to a level permissive for re-initiation 
of therapy. 
 
4.2.2.3 Rescue Medications and Supportive Care for Pembrolizumab 
Supportive Care Guidelines 
Patients 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 l. Where appropriate, these guidelines include the use of oral or intravenous 
treatment with corticosteroids as well as additional anti-inflammatory agents if 
symptoms do not improve with administration of corticosteroids.   Note that 
several courses of steroid tapering may be necessary as symptoms may worsen 
when the steroid dose is decreased. For each disorder, attempts should be made to 
rule out other causes such as metastatic disease or bacterial or viral infection, 
which might require additional supportive care. The treatment guidelines are 
intended to be applied when the investigator determines the events to be related to 
pembrolizumab.  
 
Note: if after the evaluation the event is determined not to be related, the 
investigator does not need to follow the treatment guidance (as outlined below). 
Refer to Section 4.2.2.2 for dose modifications.  
 
It may be necessary to perform conditional procedures such as bronchoscopy, 
endoscopy, or skin photography as part of evaluation of the event.  
 
• Pneumonitis:  
o For Grade 2 events, treat with systemic corticosteroids. When symptoms 
improve to Grade 1 or less, steroid taper should be started and continued 
over no less than 4 weeks. 
o For Grade 3-4 events, immediately treat with intravenous steroids.  
Administer additional anti-inflammatory measures, as needed. 
o Add prophylactic antibiotics for opportunistic infections in the case of 
prolonged steroid administration. 
 
 
 
 
• Diarrhea/Colitis:  
Subjects should be carefully monitored for signs and symptoms of enterocolitis 
(such as diarrhea, abdominal pain, blood or mucus in stool, with or without fever) 
and of bowel perforation (such as peritoneal signs and ileus).   
 
o All subjects who experience diarrhea/colitis should be advised to drink 
liberal quantities of clear fluids.  If sufficient oral fluid intake is not feasible, 

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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. Patients should be 
monitored for changes in thyroid function (at the start of treatment, periodically 
during treatment, and as indicated based on clinical evaluation) and for clinical 
signs and symptoms of thyroid disorders. 
 
o Grade 2 hyperthyroidism events (and Grade 2-4 hypothyroidism): 
 In hyperthyroidism, non-selective beta-blockers (e.g. propranolol) 
are suggested as initial therapy. 
 In hypothyroidism, thyroid hormone replacement therapy, with 
levothyroxine or liothyroinine, is indicated per standard of care. 
o Grade 3-4 hyperthyroidism  

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 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.  
 
• Infusion Reaction: 
See section 4.2.2.1 
4.3 
Concomitant Medications/Treatments 
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.   
4.3.1 Acceptable Concomitant Medications 
All treatments that the investigator considers necessary for a subject’s welfare 
may be administered at the discretion of the investigator in keeping with the 
community standards of medical care.   
4.3.2 Prohibited Concomitant Medications 
Subjects are prohibited from receiving the following therapies during the 
Screening and Treatment Phase  
 
• Anti-cancer systemic chemotherapy or biological therapy  
• Immunotherapy not specified in this protocol 

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• 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, chicken pox, yellow fever, rabies, 
BCG, and typhoid (oral) vaccine. Seasonal influenza vaccines for injection are 
generally killed virus vaccines and are allowed; however intranasal influenza 
vaccines (e.g. Flu-Mist®) are live attenuated vaccines, and are not allowed 
• Glucocorticoids may be used to modulate symptoms from an ECI of suspected 
immunologic etiology, to prevent allergic reactions, and in supportive care of 
other adverse events.  The use of physiologic doses of corticosteroids may be 
approved after consultation with the Sponsor  
Subjects who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the 
trial.  Subjects may receive other medications that the investigator deems to be 
medically necessary. 
 
Subjects are prohibited from receiving the following therapies prior to and during 
the Screening Phase  
 
• Cyclophosphamide is a substrate for cytochromes 2B6, 2C9, 2C19 and 3A4. 
Patients must not have received any drug that is a moderate or strong inhibitor 
of 3A4, 2B6, 2C9 and 2C19 within 1 week prior to cyclophosphamide dosing 
through 72 hours post cyclophosphamide dosing. Patients must not have 
received any drug that is a moderate or strong inducer of 3A4 within 2 weeks 
prior to cyclophosphamide dosing through 72 hours post cyclophosphamide 
dosing.  A frequently updated P450 drug interaction table can be found at 
http://medicine.iupui.edu/clinpharm/ddis/.  Refer to Appendix C:  Prohibited 
Medications or Those to be used with Caution for additional information. A 
patient handout is provided in Appendix D Patient Handout: Prohibited 
Medications. 
Subjects who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the 
trial.  Subjects may receive other medications that the investigator deems to be 
medically necessary. 
4.4 
Duration of Therapy 
Treatment may continue until one of the following occurs: 
• Disease progression 
Note: For unconfirmed radiographic disease progression, please see 
Sections 6.7.3 and 6.7.4 
Note: A subject may be granted an exception to continue on treatment 
with confirmed radiographic progression if clinically stable or 
clinically improved, please see Sections 6.7.3 and 6.7.4 

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Note: Disease progression can be determined by: (1) RECIST 1.1 
criteria; (2) Clinical deterioration (3) Clinical progression (i.e. 
worsening of chest wall lesion). 
• Inter-current illness that prevents further administration of treatment 
• Unacceptable adverse event(s) 
• Pregnancy 
• Patient decides to withdraw from study treatment, OR 
• General or specific changes in the patient’s condition render the 
patient unacceptable for further treatment in the judgment of the 
investigator 
• Completed 24 months of uninterrupted treatment with pembrolizumab 
or 35 administrations of study medication, whichever is later 
4.5 
End of Treatment  
The end of treatment visit should only occur when patients permanently stop 
study treatment and should be performed 30 days (+/-10 days) after the last dose 
of study medication. Patients who have an ongoing ≥grade 2 or serious AE (SAE) 
at this visit will continue to be followed until the event is resolved or deemed 
irreversible by the investigator.   
4.6 
Duration of Follow Up 
Subjects will be followed for up to 2 years after removal from study treatment or 
until death, whichever occurs first.  Patients removed from study for unacceptable 
adverse events (AEs) will be followed until resolution or stabilization of the 
event(s).   
 
The long-term follow-up visit is defined as 90 days (+/- 15 days) after the last 
dose of treatment (see Section 6.1).  All adverse events and concomitant 
medications should be followed up until this initial long-term follow-up visit (90 
days after last pembrolizumab dose). Subsequent follow-up visits, defined as 
every 60 days thereafter (+/- 15 days) for up to 2 years or until death (whichever 
is first) may be conducted via telephone.  These visits will be limited to history of 
any subsequent cancer treatments, an assessment of any SAE’s considered to be 
possibly or probably related to study treatment until resolution, and survival 
status. 
4.7 
Removal of Patients from Protocol Therapy 
Patients will be removed from protocol therapy and the PI notified when any of 
the criteria listed in section 4.4 apply.  The reason for discontinuation of protocol 
therapy will be documented on the eCRF.   
 
In case a patient decides to prematurely discontinue protocol therapy (“refuses 
treatment”), the patient should be asked if she or he may still be contacted for 
further scheduled study assessments. The outcome of that discussion should be 
documented in both the medical records and in the eCRF. 
 

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Excessive patient withdrawals from protocol therapy or from the study can render 
the study un-interpretable; therefore, unnecessary withdrawal of patients should 
be avoided. 
4.8 
Study Withdrawal 
If a subject decides to withdraw from the study (and not just from protocol 
therapy) all efforts should be made to complete and report study assessments as 
thoroughly as possible. The investigator should contact the subject or a 
responsible relative by telephone or through a personal visit to establish as 
completely as possible the reason for the study withdrawal. A complete final 
evaluation at the time of the subject’s study withdrawal should be made with an 
explanation of why the patient is withdrawing from the study. If the reason for 
removal of a subject from the study is an adverse event, the principal specific 
event will be recorded on the eCRF. 
 
5.0 
DRUG INFORMATION 
5.1 
Cyclophosphamide 
Indications: Cyclophosphamide is an alkylating agent indicated for treatment of 
malignant diseases including malignant lymphomas, Hodgkin’s disease, 
lymphocytic lymphoma, mixed-cell type lymphoma, histiocytic lymphoma, 
Burkitt’s lymphoma, multiple myeloma, leukemias, mycosis fungiodes, 
neuroblastoma, adenocarcinoma of the ovary, retinoblastoma and breast 
carcinoma. 
 
Mechanism of action: Cyclophosphamide is an alkylating agent that has 
anticancer activity. It is converted in the liver to active alkylating metabolites 
such as phosphoramide mustard by cytochrome-P450 enzymes. These alkylating 
metabolites interfere with the growth of susceptible rapidly proliferating 
malignant cells. Alkyl radicals intercalate into DNA strands and interfere with 
DNA replication. 
 
Product description: Cyclophosphamide is supplied as 500 mg, 1 gm and 2 gm 
vials containing white powder for IV administration. Store vials at or below 250C 
(770F). Cyclophosphamide does not contain any antimicrobial preservative and 
care must be taken to assure the sterility of prepared solutions. USE ASEPTIC 
TECHNIQUE. 
 
Solution preparation: Cyclophosphamide should be reconstituted in 25 mL (500 
mg), 50 mL (1 gm) or 100 mL (2 gm) sterile water for injection, USP, for IV 
infusion. Shake vigorously to dissolve the drug. To minimize risk of dermal 
exposure, always wear gloves when handling vials containing cyclophosphamide 
sterile powder for injection. 
 

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Dose and Route of administration: A single IV dose of cyclophosphamide at 300 
mg/m2 over 30-60 min will be administered on D1 of this study.  
 
Possible side effects: 
• Nausea, vomiting, diarrhea 
• Urinary bladder toxicity 
• Bone marrow suppression 
• Gonadal suppression 
• Myelodysplasia 
• Alopecia 
• Immunosuppression 
• Hyperpigmentation of the skin 
Full prescribing information on cyclophosphamide is available at: 
http://medlibrary.org/lib/rx/meds/cyclophosphamide-1/  
 
Handling and Disposal: Please see policy on hazardous drugs:  
http://news.unchealthcare.org/empnews/att/2011/nov/admin0188/.  
 
Local requirements for disposal of hazardous drugs should be followed at each 
participating clinical site. 
 
Precautions: 
See section 4.3.2 
5.2 
Pembrolizumab 
 
5.2.1 Description 
Clinical Supplies will be provided by Merck as summarized in the table below. 
 
Product Name & Potency 
Dosage Form 
pembrolizumab 50 mg 
Lyophilized Powder for 
Injection 
pembrolizumab 100 mg/4mL 
Solution for Injection 
 
5.2.2 Supplier/How Supplied 
Pembrolizumab will be provided at no cost to the study patient by Merck, the 
manufacturer of the drug. Clinical supplies will be affixed with a clinical label in 
accordance with regulatory requirements. 
 
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. 

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5.2.3 Handling and Dispensing 
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. 
 
5.2.4 Storage and Stability 
As per the pharmacy manual, provided as a document separate from the protocol. 
 
 

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5.2.5 Return and Retention 
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 (eg, 
UNC IDS drug destruction 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. 
 
5.2.6 Adverse Events Associated with Pembrolizumab 
The most common adverse reactions (reported in ≥20% of patients in clinical 
trials of pembrolizumab) included fatigue, cough, nausea, pruritus, rash, 
decreased appetite, constipation, arthralgia, and diarrhea. The following warnings 
are associated with the use of pembrolizumab:  
 
 
 
Immune-Mediated Pneumonitis 
Pneumonitis occurred in ~3% of melanoma patients treated in clinical trials of 
pembrolizumab. The median time to development of pneumonitis was 5 months 
with a median duration of 4.9 months.  The one patient with Grade 3 pneumonitis 
required initial treatment with high-dose systemic corticosteroids (greater than or 
equal to 40 mg prednisone or equivalent per day) followed by a corticosteroid 
taper. Pneumonitis completely resolved in seven of the nine patients with 
Grade 2-3 pneumonitis. 
 
Immune-Mediated Colitis 
Colitis (including microscopic colitis) occurred 1% of melanoma patients treated 
in clinical trials of pembrolizumab. The median time to onset of was 6.5 months 
with a median duration of 2.6 months. All three patients with Grade 2 or 3 colitis 
were treated with high-dose corticosteroids (greater than or equal to 40 mg 
prednisone or equivalent per day). 
 
Immune-Mediated Hepatitis  
Hepatitis (including autoimmune hepatitis) occurred in 0.5% of melanoma 
patients treated in clinical trials of pembrolizumab. The time to onset was 22 days 
for the case of Grade 4 hepatitis which lasted 1.1 months. The patient with Grade 
4 hepatitis permanently discontinued pembrolizumab and was treated with high-
dose (greater than or equal to 40 mg prednisone or equivalent per day) systemic 
corticosteroids followed by a corticosteroid taper. Both patients with hepatitis 
experienced complete resolution of the event.  
 
Immune-Mediated Hypophysitis  

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Hypophysitis occurred in 0.5% of melanoma patients treated in clinical trials of 
pembrolizumab. The time to onset was 1.7 months for the patient with Grade 4 
hypophysitis and 1.3 months for the patient with Grade 2 hypophysitis. Both 
patients were treated with high-dose (greater than or equal to 40 mg prednisone or 
equivalent per day) corticosteroids followed by a corticosteroid taper and 
remained on a physiologic replacement dose.  
 
Renal Failure and Immune-Mediated Nephritis  
Nephritis occurred in 3 (0.7%) patients of melanoma patients treated in clinical 
trials of pembrolizumab, consisting of one case of Grade 2 autoimmune nephritis 
(0.2%) and two cases of interstitial nephritis with renal failure (0.5%), one Grade 
3 and one Grade 4. The time to onset of autoimmune nephritis was 11.6 months 
after the first dose of pembrolizumab (5 months after the last dose) and lasted 3.2 
months; this patient did not have a biopsy. Acute interstitial nephritis was 
confirmed by renal biopsy in two patients with Grades 3-4 renal failure. All three 
patients fully recovered renal function with treatment with high-dose 
corticosteroids (greater than or equal to 40 mg prednisone or equivalent per day) 
followed by a corticosteroid taper. 
 
Immune-Mediated Hyperthyroidism  
Hyperthyroidism occurred in 5 (1.2%) of 411 melanoma patients treated in 
clinical trials of pembrolizumab. The median time to onset was 1.5 months and 
the median duration was 2.8 months (range 0.9 to 6.1). One of two patients 
with Grade 2 and the one patient with Grade 3 hyperthyroidism required initial 
treatment with high-dose corticosteroids (greater than or equal to 40 mg 
prednisone or equivalent per day) followed by a corticosteroid taper. One patient 
(0.2%) required permanent discontinuation of pembrolizumab due to 
hyperthyroidism. All five patients with hyperthyroidism experienced complete 
resolution of the event. 
 
Immune-Mediated Hypothyroidism  
Hypothyroidism occurred in 34 (8.3%) of 411 melanoma patients treated in 
clinical trials of pembrolizumab. The median time to onset of hypothyroidism was 
3.5 months. All but two of the patients with hypothyroidism were treated with 
long-term thyroid hormone replacement therapy. The other two patients only 
required short-term thyroid hormone replacement therapy. No patient received 
corticosteroids or discontinued pembrolizumab for management of 
hypothyroidism. Thyroid disorders can occur at any time during treatment.  
 
Other Immune-Mediated Adverse Reactions 
Other clinically important immune-mediated adverse reactions can occur. The 
following clinically significant, immune-mediated adverse reactions occurred in 
less than 1% of patients treated with pembrolizumab, including exfoliative 
dermatitis, uveitis, arthritis, myositis, pancreatitis, hemolytic anemia, partial 
seizures arising in a patient with inflammatory foci in brain parenchyma, and 
adrenal insufficiency. 

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Across clinical studies with pembrolizumab in approximately 2000 patients, the 
following additional clinically significant, immune-mediated adverse reactions 
were reported in less than 1% of patients: myasthenic syndrome, optic neuritis, 
and rhabdomyolysis. 
 
Embryofetal Toxicity 
Based on its mechanism of action, pembrolizumab may cause fetal harm when 
administered to a pregnant woman. Animal models link the PD-1/PD-L1 
signaling pathway with maintenance of pregnancy through induction of maternal 
immune tolerance to fetal tissue.  
 
5.2.7 Contraindications 
There are no reported contraindications associated with the use of 
pembrolizumab. 
 
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.   
 
5.2.8 Contraception 
Female and male subjects of reproductive potential must agree to avoid becoming 
pregnant or impregnating a partner, respectively, while receiving study drug and 
for 120 days after the last dose of study drug by complying with one of the 
following:   
(1) practice abstinence† from heterosexual activity;  
OR 
(2) use (or have their partner use) acceptable contraception during heterosexual 
activity.   
 
Acceptable methods of contraception are‡: 
 
Single method (one of the following is acceptable): 
• 
intrauterine device (IUD) 
• 
vasectomy of a female subject’s male partner  
• 
contraceptive rod implanted into the skin 
  
Combination method (requires use of two of the following): 
• 
diaphragm with spermicide (cannot be used in conjunction with cervical 
cap/spermicide) 
• 
cervical cap with spermicide (nulliparous women only)   
• 
contraceptive sponge (nulliparous women only)  
• 
male condom or female condom (cannot be used together) 
• 
hormonal contraceptive: oral contraceptive pill (estrogen/progestin pill or 
progestin-only pill), contraceptive skin patch, vaginal contraceptive ring, 
or subcutaneous contraceptive injection 

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†Abstinence (relative to heterosexual activity) can be used as the sole method of 
contraception if it is consistently employed as the subject’s preferred and usual 
lifestyle and if considered acceptable by local regulatory agencies and 
ERCs/IRBs.  Periodic abstinence (e.g., calendar, ovulation, sympto-thermal, 
post-ovulation methods, etc.) and withdrawal are not acceptable methods of 
contraception.  
  
‡If a contraceptive method listed above is restricted by local 
regulations/guidelines, then it does not qualify as an acceptable method of 
contraception for subjects participating at sites in this country/region. 
 
Subjects should be informed that taking the study medication may involve 
unknown risks to the fetus (unborn baby) if pregnancy were to occur during the 
study.  In order to participate in the study subjects of childbearing potential must 
adhere to the contraception requirement (described above) from the day of study 
medication initiation (or 14 days prior to the initiation of study medication for 
oral contraception) throughout the study period up to 120 days after the last dose 
of trial therapy.  If there is any question that a subject of childbearing potential 
will not reliably comply with the requirements for contraception, that subject 
should not be entered into the study. 
 
5.2.9 Use in Pregnancy 
If a patient inadvertently becomes pregnant while on treatment with 
pembrolizumab, the patient will immediately be removed from the study.  The site 
will contact the patient at least monthly and document the patient’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 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 patient 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 7.3.3. 
 
5.2.10 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, patients who are breast-feeding are not eligible for 
enrollment. 
 
5.2.11 Overdose 
For purposes of this trial, an overdose will be defined as any dose exceeding the 
prescribed dose for pembrolizumab by 20% over the prescribed dose. No specific 

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information is available on the treatment of overdose of pembrolizumab. In the 
event of overdose, pembrolizumab should be discontinued and the patient should 
be observed closely for signs of toxicity.  Appropriate supportive treatment should 
be provided if clinically indicated. 
 
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) (see section 7.3.3) 

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Survival analysis 
 
 
 
 
 
 
 
 
 
X 

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Key to Time and Events Table Footnotes  
 
1Radiological assessments, ECHO or MUGA, and physical exam may be performed up to 4 
weeks prior to day 1 of treatment.  Other evaluations except for pregnancy must be performed 
within 2 weeks prior to Cycle 1 Day 1 of treatment. Serum B-HCG must be performed within 72 
hours prior to first dose of study medication for women of child-bearing potential.  Screening labs 
performed within 72 hours prior to Cycle 1 Day 1 do not need to be repeated on C1D1.  
2 On Study D1 a single priming dose of cyclophosphamide will be given the day before initiating 
treatment with pembrolizumab on Day 2 of the study. Pembrolizumab cycles are to be repeated 
every 3 weeks (21 days) until progression.  A window of +/- 3 days applies to all study visits. 
3The end of treatment visit should be performed 30 days (+/-10 days) after the last dose of study 
medication. Patients who have on ongoing ≥grade 2 or serious AE (SAE) at this visit will 
continue to be followed until the event is resolved or deemed irreversible by the investigator.  The 
first long-term follow-up visit is defined as 90 days (+/- 15 days) after the last dose of treatment.  
Serious adverse events (SAEs; or follow-up to any SAEs) that occur within 90 days of the end of 
pembrolizumab (or prior to start of new anti-cancer therapy, whichever is earlier) or any grade of 
Events of Clinical Interest (see section 7.3 and the ECI Guidance Document that is provided as a 
document separate from this protocol) that occur within 90 days of the end of pembrolizumab or 
30 days after the initiation of a new anti-cancer therapy (whichever is earlier) must be 
recorded. Subsequent follow-up visits, defined as every 60 days thereafter (+/- 15 days) for up to 
2 years or until death (whichever is first) may be conducted via telephone.  These visits will be 
limited to history of any subsequent cancer treatments, an assessment of any SAE’s considered to 
be possibly or probably related to study treatment until resolution, and survival status.   
4Perform a complete history at baseline only, thereafter focused history on symptoms/toxicity; 
physical exam to include height (baseline only), examination of the skin, weight, and vital signs. 
5Tumor imaging should remain consistent throughout study, and should include contrasted 
computed tomography (CT) of the chest, abdomen and pelvis, bone scan and, if clinically 
indicated, brain MRI. CT Scan from PET scan can also be used instead of contrast CT. The scans 
should be performed every 9 weeks at the end of cycles 3, 6, 9, etc., in the first year and every 12 
weeks after one year until progression. EOT scan will not be performed if subject cannot 
withstand scan due to clinical deterioration, or if progression can be determined clinically (i.e. 
worsening of chest wall lesion).  
6Serum B-HCG must be performed within 72 hours prior to first dose of study medication for 
women of child-bearing potential.  
 7Hematology: CBC with differential, Hgb, and platelet count; Liver function tests: total bilirubin, 
AST (SGOT) and ALT (SGPT). Serum chemistry: potassium, sodium, calcium, creatinine, 
magnesium, phosphorus, BUN, albumin, and total protein.  
8Thyroid panel includes TSH, T3 and free T4.  If consistent with institutional standard of care, it 
is acceptable to obtain TSH alone and only obtain T3 and free T4 if clinically useful. This test 
should be performed at screening and then every 6 weeks during pembrolizumab therapy (D1 of 
odd numbered cycles of pembrolizumab) and at the end of treatment visit. 

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9Coagulation profile includes prothrombin time or INR, and activated partial thromboplastin time. 
Patient entering the study while receiving anti-coagulation therapy or those who have the 
initiation of an anti-coagulation therapy should have their coagulation test performed per the 
investigator’s discretion. 
10Fixed paraffin-embedded blocks or slides from the original diagnostic specimen or from a 
recurrence must be requested for patients at baseline.  We will collect fresh biopsies (optional) in 
consenting patients for correlative studies at baseline (predose) and end of treatment (post dose). 
Additional details are provided in section 6.5 and in the study procedures laboratory manual 
11Blood samples (taken predose) will be collected for correlative studies. Additional details are 
provided in section 6.5 and in the study procedures laboratory manual. 
 
6.2 
Pre-Study Assessments 
Clinical evaluation:  complete history; physical exam to include height (baseline 
only) and weight, examination of skin and vital signs; ECOG performance status 
(see Appendix A) 
Laboratory studies:   
 Pregnancy Test: A serum pregnancy test (β-HCG) is required for all 
women of childbearing potential at screening within 72 hours prior to 
the first dose of study treatment under this protocol.  
 Hematology: CBC with differential,  Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein (or calculate creatinine clearance via 
Cockcroft-Gault (see Appendix B) as noted in inclusion criterion #7) 
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
 Coagulation Studies: PT or INR and PTT (Note: Patient entering the 
study while receiving anti-coagulation therapy or those who have the 
initiation of an anti-coagulation therapy should have their coagulation 
test performed per investigator’s discretion) 
 Thyroid panel: TSH, T3 and free T4 (see footnote 8 in Time and 
Events table) 
Archival tissue: Request access to archival tissue to support correlative studies. 
(see section 6.5.1); consent for the use of any residual material from biopsy will 
be required for enrollment.  Patients without adequate tissue for bio correlates will 
not be excluded or required to have a repeat biopsy. 
Optional tumor biopsy: Collect a fresh biopsy in consenting subjects for 
correlative studies. 
Blood sample for biomarkers: See section 6.5.2 and refer to the Study Procedures 
Laboratory Manual for sample collection details. 
Concomitant Medications: Review (see section 4.3, Appendix C:  Prohibited 
Medications and exclusion criterion #21) 
Toxicity Assessment: Perform per NCI CTCAEv4 

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Tumor imaging: Baseline tumor imaging should include computed tomography 
(CT) of the chest, abdomen and pelvis, bone scan and, if clinically indicated, 
brain MRI. CT Scan from PET scan can also be used instead of contrast CT. 
6.3 
Treatment Assessments 
6.3.1 Study D1 (perform all assessments prior to cyclophosphamide 
administration) 
Clinical evaluation:  focused history on symptoms/toxicity; physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A) 
Laboratory studies: (need not be repeated if performed < 72 hours prior to first 
dose) 
 Hematology: CBC with differential,  Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4 
Cyclophosphamide administration: 300 mg/m2 IV over 30-60 min 
Blood sample for biomarkers: (see section 6.5.2) Taken predose: 3x 8mLs whole 
blood in ACD tubes required at each scheduled draw (Required) 
6.3.2 Study Day 2 (D1 Cycle 1 pembrolizumab) 
Clinical evaluation:  focused history on symptoms/toxicity 
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4 
Pembrolizumab administration: 200 mg IV over 30 min 
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
6.3.3 D1 Cycle 2 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)  
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4 

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Pembrolizumab administration: 200 mg IV over 30 min  
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
6.3.4 D1 Cycle 3 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)  
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
 Thyroid panel: TSH, T3 and free T4 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4 
Pembrolizumab administration: 200 mg IV over 30 min 
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
6.3.5 D1 Cycle 4 
Clinical evaluation:  focused history on symptoms/toxicity.  Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)  
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4) 
Pembrolizumab administration: 200 mg IV over 30 min 
Tumor Imaging: repeat assessments performed at baseline  
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
6.3.6 D1 Cycle 5 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)  
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 

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 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
 Thyroid panel: TSH, T3 and free T4 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4) 
Pembrolizumab administration: 200 mg IV over 30 min 
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
6.3.7 D1 Cycle 6-n 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)   
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 
 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
 Thyroid panel: TSH, T3 and free T4 (D1 of cycles 7, 9, 11, etc.)* 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4; Patients who have on ongoing ≥grade 2 or serious 
AE (SAE) at this visit will continue to be followed until the event is resolved or 
deemed irreversible by the investigator.   
Pembrolizumab administration: 200 mg IV over 30 min 
Tumor Imaging: repeat assessments performed at baseline at the end of cycles 6, 
9, 12, etc., for the first year.  After the first year, tumor imaging will be performed 
every 12 weeks, at the end of cycles 22, 26, 30, etc until disease progression/end 
of treatment. 
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
 
*Note: Thyroid panel should be performed every 6 weeks during treatment with 
pembrolizumab i.e., D1 of odd numbered cycles 7, 9, 11, etc.  
6.4 
Post-Treatment/Follow-up Assessments 
6.4.1 End of Treatment 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, vital signs and ECOG performance status 
(see Appendix A)   
Laboratory studies:   
 Hematology: CBC with differential, Hgb, and platelet count 

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 Serum Chemistries: These include the following parameters: 
potassium, sodium, calcium, creatinine, magnesium, phosphorus, 
BUN, albumin, and total protein  
 LFTs: These include total bilirubin, AST (SGOT), ALT (SGPT) 
 Thyroid panel: TSH, T3, free T4 
Concomitant Medications: Review (see section 4.3) 
Toxicity: Per NCI CTCAEv4) 
Tumor Imaging: repeat assessments performed at baseline. Tumor imaging is not 
required to assess progression. If subject cannot withstand tumor imaging due to 
clinical deterioration, imaging will not be required.  
Blood sample for biomarkers: (see section 6.5.2); 3x 8mLs whole blood in ACD 
tubes required at each scheduled draw (Required) 
Optional tumor biopsy: Collect a fresh post dose biopsy in consenting subjects for 
correlative studies. 
 
6.4.2 Long-term follow up (90 days after last dose of pembrolizumab) 
Clinical evaluation:  focused history on symptoms/toxicity. Physical exam to 
include weight, examination of skin, and vital signs 
Toxicity: Per NCI CTCAEv4; Serious adverse events (SAEs; or follow-up to any 
SAEs) that occur within 90 days of the end of pembrolizumab (or prior to start of 
new anti-cancer therapy, whichever is earlier) or any grade of Events of Clinical 
Interest (see section 7.3 and the ECI Guidance Document that is provided as a 
document separate from this protocol) that occur within 90 days of the end of 
pembrolizumab or 30 days after the initiation of a new anti-cancer therapy 
(whichever is earlier) must be recorded.    
Survival analysis: 
 
Note: Subsequent follow-up visits to occur every 60 days (+/- 15 days) for up to 2 
years or until death (whichever is first) may be conducted via telephone, and will 
be limited to history of any subsequent cancer treatments, an assessment of any 
SAE’s considered to be possibly or probably related to study treatment until 
resolution, and survival status.   
6.5 
Correlative Studies Procedures 
These are described in more detail in the study procedures laboratory manual.  
6.5.1 Archival Tissue 
Archival tumor tissue (paraffin-embedded blocks/slides) from the patient’s 
original diagnostic biopsy will be requested and collected from all enrolled 
patients.  See accompanying laboratory manual for additional details, including 
details on shipping and storage.  

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6.5.2 Fresh Biopsy (optional) 
All patients will also be asked if a fresh biopsy is possible prior to initiation of 
therapy and at the end of treatment but these biopsies are not required (this is 
optional). See accompanying laboratory manual for additional details, including 
details on shipping and storage.  
6.5.3 Blood samples 
Patients will have a three ACD tubes (whole blood, 3 x 8mL) collected at the 
times as noted in the Time and Event table (sample should be collected predose). 
Sample collection, storage, and shipment instructions for serum samples will be 
provided in the Laboratory Manual. 
6.6 
Assessment of Safety  
Any patient who receives treatment on this protocol will be evaluable for toxicity.  
Each patient will be assessed periodically for the development of any toxicity 
according to the Time and Events table (section 6.0).  Toxicity will be assessed 
according to the NCI CTCAE v4. 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 adverse events (AEs) of 
unknown etiology associated with pembrolizumab exposure should be evaluated 
to determine if it is an Event of Clinical Importance (ECI) with a potential 
immunologic etiology (termed immune-related adverse events, or irAEs); see the 
separate ECI guidance document (provided as a document separate from this 
protocol) regarding the identification, evaluation and management of potential 
irAEs.   
 
Progression of the cancer under study is not considered an adverse event unless it 
is considered to be drug related by the investigator. 
 
Please refer to section 7.0 for detailed information regarding the assessment of 
toxicity and recording of AEs.   
6.7 
Assessment of Efficacy 
Subjects who have received at least 1 dose of pembrolizumab will be evaluable 
for assessment of response and progression.  Progression can be documented: (1) 
according to RECIST 1.1 criteria per tumor imaging; (2) as Clinical deterioration; 
or (3) Clinical Progression. Subjects whose cancer growth is documented by 
physical examination without imaging confirmation will count as progression (i.e. 
worsening of chest wall lesions).  Patients who drop out of the study for any 
reason (eg. toxicity of treatment, decide to withdraw) will still be followed for 
PFS and OS.    

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6.7.1 Assessment of Disease-Tumor Measurement Based on RECIST 1.1 
Disease assessment according to RECIST 1.1 criteria will include imaging and 
physical examination. Refer to the Response Evaluation Criteria in Solid Tumors 
(RECIST) Committee, version 1.1 (Eur J Cancer 45;2009:228-247) for additional 
details on RECIST 1.1. To ensure comparability between baseline and subsequent 
disease assessments, the same method(s) of assessment (eg, CT scan, MRI, etc) 
will be used throughout the study for determining response. Tumor assessment 
will be completed as outlined in the Time and Events table in section 6.1. 
6.7.2 Baseline Documentation of Target and Non-Target Lesions 
All measurable lesions up to a maximum of 5 lesions total (and a maximum of 
two lesions per organ) representative of all involved organs should be identified 
as target lesions and will be recorded and measured at baseline.   
 
Target lesions should be selected on the basis of their size (lesions with the longer 
diameter), be representative of all involved organs, but in addition should be those 
that lend themselves to reproducible repeated measurements.  
 
A sum of the diameters (longest for non-nodal lesions, short axis for nodal 
lesions) for all target lesions will be calculated and reported as the baseline sum 
diameters. If lymph nodes are to be included in the sum, only the short axis is 
added into the sum.  The baseline sum diameters will be used as reference to 
further characterize the objective tumor response of the measurable dimension of 
the disease. 
 
All other lesions (or sites of disease) including pathological lymph nodes should 
be identified as non-target lesions and should also be recorded at baseline. 
Measurements are not required and these lesions should be followed as “present” 
or “absent”, or in rare cases “unequivocal progression”.   
6.7.3 Evaluation of Target Lesions using RECIST 1.1 Criteria 
NOTE: In addition to the information below, also see section 4.3.2 in the 
international criteria proposed by the Response Evaluation Criteria in Solid 
Tumors (RECIST) Committee, version 1.1 (Eur J Cancer 45;2009:228-247) for 
special notes on the assessment of target lesions.  
 
Complete response (CR)−Disappearance of all target lesions.  Any pathological 
lymph node (LN) (whether target or non-target) must have decreased in short axis 
to <10mm. 
 
Partial response (PR)−At least a 30% decrease in the sum of the longest diameter 
LD of the target lesions taking as reference the baseline sum LD. 
 
Progressive Disease (PD)−At least a 20% increase in the sum of the LD of the 
target lesions taking as reference the smallest sum LD recorded since the 

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treatment started including baseline if that is the smallest on study.  In addition to 
the relative increase of 20%, the sum must also demonstrate an absolute increase 
of at least 5mm.  The appearance of one or more new lesions also constitutes PD. 
  
Note: Any progressive disease as defined by RECIST1.1 in patients that are 
asymptomatic without signs or symptoms of impending visceral crisis SHOULD 
be confirmed by a repeat scan to rule out "tumor flare". In these patients and per 
MD discretion, pembrolizumab therapy should be continued in these patients until 
the repeat scan is performed≥ 4 weeks and no more than 6 weeks from the time 
the initial scan indicated PD. If PD is confirmed, patients will be withdrawn from 
study. If tumor flare confirmed, patients may continue therapy as per protocol. 
Subjects that have clear progressive disease as defined by RECIST 1.1 should be 
withdrawn from treatment and a repeat scan is not necessary. 
 
Stable disease (SD)−Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD taking as references the smallest sum LD since the 
treatment started. 
6.7.4 Evaluation of Non-Target Lesions using RECIST 1.1 Criteria 
Complete response (CR)−Disappearance of all non-target lesions and 
normalization of tumor marker levels.  All LN must be non-pathological in size 
(<10mm short axis).   
 
Non-complete response (non-CR)/non-progression (non-PD)−Persistence of one 
or more non-target lesion(s) or/and maintenance of tumor marker level above the 
normal limits. 
 
Progressive disease (PD)−Appearance of one or more new lesions and/or 
unequivocal progression of existing non-target lesions. 
 
Note: Any progressive disease as defined by RECIST1.1 in patients that are 
asymptomatic without signs or symptoms of impending visceral crisis SHOULD 
be confirmed by repeat scan to rule out "tumor flare". In these patients and per 
MD discretion, pembrolizumab therapy should be continued in these patients until 
the repeat scan is performed ≥ 4 weeks but no more than 6 weeks later. If PD is 
confirmed, patients will be withdrawn from study. If tumor flare confirmed, 
patients may continue therapy as per protocol. Subjects that have clear 
progressive disease as defined by RECIST 1.1 should be withdrawn from 
treatment and a repeat scan is not necessary. 
 
6.7.5 Other Efficacy Parameters 
6.7.5.1 Evaluation of Response by irRECIST 
An exploratory objective of this study involves assessment of ORR, DCR, PFS 
and DOR based in immune response criteria as outlined below (see Guidelines for 

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the evaluation of immune therapy activity in solid tumors: immune-related 
response criteria. Wolchok JD et al. Clin Cancer Res 2009;15(23):7412-20, 
Nishino et al. Clin Cancer Res 19(14):3936-43, and Bohnsack O. et al., 
Adaptation of the immune related response criteria: irRECIST. Annals of 
Oncology (2014) 25 (suppl_4): iv361-iv372. 10.1093/annonc/mdu342, 2014). 
 
irRECIST criteria are based on irRC criteria (Wolchok et al) adapted for 
unidimensional measurement as outlined by Nishino et al. The adaptation 
described by Bohnsack et al. further aligns irRECIST to allow for assessment of 
baseline non-target lesions and new non-measurable lesions, and discusses the 
impact of those lesions on the overall tumor response assessment. The adaptation 
by Bohnsack et al. allows for evaluation of patients with non-target disease only 
and patients in the adjuvant setting (not applicable for this study in subjects with 
metastatic disease). 
  
Overall response using the irRECIST is based on tumor burden as follows: 
 
irCR 
Complete disappearance of all lesions (whether measurable or 
not, and no new lesions) Lymph nodes must decrease to < 10 
mm in short axis. Confirmation of response is not mandatory. 
irPR 
Decrease in tumor burden ≥30% in TMTB relative to baseline 
confirmed by a consecutive assessment at least 4 weeks after 
first documentation, non-target lesions are irNN, and no 
equivocal progression of new non-measurable lesions. 
irSD 
Not meeting criteria for irCR, irPR, in absence of irPD 
irPD 
Increase in tumor burden ≥20% increase and minimum 5 mm 
absolute increase in TMTB compared to nadir, or irPD for non-
target or new non-measurable lesions confirmed by a repeat, 
consecutive assessment no less than 4 weeks from the date first 
documented 
irNN 
No target disease was identified at baseline and at follow-up the 
patient fails to meet criteria for irCR or irPD. 
 
 irNN = irNon-CR/Non-PD 
TMTB = Total measureable tumor burden 
 
 

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7.0 
ADVERSE EVENTS 
7.1 
Definitions  
7.1.1 Adverse Event (AE) 
An adverse event (AE) is any untoward medical occurrence (e.g., an abnormal 
laboratory finding, symptom, or disease temporally associated with the use of a 
drug) in a patient or clinical investigation subject administered a pharmaceutical 
product and which does not necessarily have a causal relationship with this 
treatment.  An AE can therefore be any unfavorable and unintended sign 
(including an abnormal laboratory finding), symptom, or disease temporally 
associated with the use of a medicinal product, whether or not related to the 
medicinal product.   
 
Hospitalization for elective surgery or routine clinical procedures that are not the 
result of an AE (e.g., surgical insertion of central line) need not be considered 
AEs and should not be recorded as an AE.  Disease progression should not be 
recorded as an AE, unless it is attributable by the investigator to the study therapy. 
 
Adverse events may occur during the course of the use of Merck product in 
clinical trials, or as prescribed in clinical practice, from overdose (whether 
accidental or intentional), from abuse and from withdrawal.  Progression of the 
cancer under study is not considered an adverse event.  
 
All adverse events that occur after the consent form is signed but before treatment 
allocation/randomization must be reported by the investigator if they cause the 
subject to be excluded from the trial, or are the result of a protocol-specified 
intervention, including but not limited to washout or discontinuation of usual 
therapy, diet, placebo treatment or a procedure. 
From the time of treatment allocation/randomization through 30 days following 
cessation of treatment, all adverse events must be reported by the investigator. 
Such events will be recorded at each examination on the Adverse Event case 
report forms/worksheets.  The reporting timeframe for adverse events meeting 
any serious criteria is described in section 7.3.3. The investigator will make every 
attempt to follow all subjects with non-serious adverse events for outcome. 
Adverse events will not be collected for subjects during the pre-screening period 
(for determination of archival tissue status) as long as that subject has not 
undergone any protocol-specified procedure or intervention.  If the subject 
requires a blood draw, fresh tumor biopsy etc., the subject is first required to 
provide consent to the main study and AEs will be captured according to 
guidelines for standard AE reporting.  
 

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7.1.2 Suspected Adverse Reaction (SAR) 
A suspected adverse reaction (SAR) is any AE for which there is a reasonable 
possibility that the drug is the cause.   Reasonable possibility means that there is 
evidence to suggest a causal relationship between the drug and the AE.  A 
suspected adverse reaction implies a lesser degree of certainty about causality 
than adverse reaction, which means any adverse event caused by a drug.   
 
Causality assessment to a study drug is a medical judgment made in consideration 
of the following factors: temporal relationship of the AE to study drug exposure, 
known mechanism of action or side effect profile of study treatment, other recent 
or concomitant drug exposures, normal clinical course of the disease under 
investigation, and any other underlying or concurrent medical conditions.  Other 
factors to consider in considering drug as the cause of the AE: 
• Single occurrence of an uncommon event known to be strongly associated 
with drug exposure (e.g., angioedema, hepatic injury, Stevens-Johnson 
Syndrome) 
• One or more occurrences of an event not commonly associated with drug 
exposure, but otherwise uncommon in the population (e.g., tendon 
rupture); often more than once occurrence from one or multiple studies 
would be needed before the sponsor could determine that there is 
reasonable possibility that the drug caused the event.   
• An aggregate analysis of specific events observed in a clinical trial that 
indicates the events occur more frequently in the drug treatment group 
than in a concurrent or historical control group 
7.1.3 Unexpected AE or SAR 
An AE or SAR is considered unexpected if the specificity or severity of it is not 
consistent with the applicable product information (e.g., Investigator’s Brochure 
(IB) for an unapproved investigational product or package insert/summary of 
product characteristics for an approved product).  Unexpected also refers to AEs 
or SARs that are mentioned in the IB as occurring with a class of drugs or as 
anticipated from the pharmacological properties of the drug, but are not 
specifically mentioned as occurring with the particular drug under investigation.   
7.1.4 Serious AE or SAR 
An AE or SAR is considered serious if, in the view of either the investigator or 
sponsor, it results in any of the following outcomes: 
• Death; 
• Is life-threatening (places the subject at immediate risk of death from 
the event as it occurred); 
• Requires inpatient hospitalization (>24 hours) or prolongation of 
existing hospitalization;* 
• Results in congenital anomaly/birth defect; 
• Results in a persistent or significant incapacity or substantial 
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• Important medical events that may not result in death, be life-
threatening, or require hospitalization may be considered a serious 
adverse drug experience when, based upon appropriate medical 
judgment, they may jeopardize the patient or subject and may require 
medical or surgical intervention to prevent one of the outcomes listed 
in the definition.  For reporting purposes, also consider the occurrences 
of pregnancy as an event which must be reported as an important 
medical event. 
 
*Hospitalization for anticipated or protocol specified procedures such as 
administration of chemotherapy, central line insertion, metastasis interventional 
therapy, resection of primary tumor, or elective surgery, will not be considered 
serious adverse events. 
 
Pregnancy that occurs during the study must also be reported as an SAE. 
 
• Note: In addition to the above criteria, adverse events meeting either of the 
below criteria, although not serious per ICH definition, are reportable to the 
Merck in the same timeframe as SAEs to meet certain local requirements. 
Therefore, these events are considered serious by Merck for collection 
purposes. 
o Is a new cancer (that is not a condition of the study); 
o Is associated with an overdose. 
 
 
7.2 
Documentation of non-serious AEs or SARs 
For non-serious AEs or SARs, documentation must begin from day 1 of study 
treatment and continue through the 30 day follow-up period after treatment is 
discontinued.   
 
Collected information should be recorded in the Case Report Forms (CRF) for 
that patient.  Please include a description of the event, its severity or toxicity 
grade, onset and resolved dates (if applicable), and the relationship to the study 
drug. Documentation should occur at least monthly.  
7.3 
SAEs, Serious SARs or Events of Clinical Interest  
7.3.1 Timing 
After informed consent but prior to initiation of study medications, only SAEs 
caused by a protocol-mandated intervention will be collected (e.g. SAEs related to 
invasive procedures such as biopsies, medication washout).  
 
For any other experience or condition that meets the definition of an SAE or a 
serious SAR, recording of the event must begin from day 1 of study treatment and 

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continue through the 90 day follow-up period after treatment is discontinued (or 
to the initiation of new anti-cancer treatment, whichever is earliest).  
7.3.2 Documentation and Notification 
These events (SAEs or Serious SARs) must be recorded in the SAE console 
within Oncore™ for that patient within 24 hours of learning of its occurrence.  
For Affiliate sites, an email must also be sent to the NCCN Project Manager 
indicating that an SAE or Serious SAR has been entered into Oncore (email 
contact will be provided at study start-up).  
7.3.3 Reporting  
IRB Reporting Requirements: 
UNC: 
• UNC will submit an aggregated list of all SAEs to the UNC IRB annually 
at the time of study renewal according to the UNC IRB policies and 
procedures. 
The UNC-IRB will be notified of all SAEs that qualify as an Unanticipated 
Problem as per the UNC IRB Policies using the IRB’s web-based reporting 
system (see section 9.5.3) within 7 days of the Investigator becoming aware of 
the problem.   
Affiliate sites:   
• For affiliate sites using a local IRB of record, please submit adverse events 
per local IRB policy. 
• For affiliate sites relying on the UNC-IRB, an aggregated list of all SAEs 
will be submitted to the UNC IRB annually at the time of study renewal 
according to the UNC IRB policies and procedures. In addition, any SAEs 
that qualify as an Unanticipated Problem will be entered into Oncore and 
reported to the UNC IRB by the UNCCN Project Manager using the IRB’s 
web-based reporting system (see section 9.5.3) within 7 days of the 
Investigator becoming aware of the problem.   
Pregnancy 
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, as a 
serious adverse event.  The patient is to be discontinued immediately from any 
protocol directed therapy. 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 adverse events (Important medical events).  
If the pregnancy continues to term, the outcome (health of infant) must also be 

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reported. Such events must be reported within 24 hours to the Sponsor and within 
2 days to the manufacturer (; see 7.3.3.1 Merck report requirements). 
 
Pregnancies and lactations that occur after the consent form is signed but before 
treatment allocation must be reported by the investigator if they cause the subject 
to be excluded from the trial, or are the result of a protocol-specified intervention, 
including but not limited to washout or discontinuation of usual therapy, diet, 
placebo treatment or a procedure.   
Pregnancies and lactations that occur from the time of treatment through 120 days 
following cessation of study medication, or 30 days following cessation of 
treatment if the subject initiates new anticancer therapy, whichever is earlier, must 
be reported by the investigator.   
 
For Affiliate sites, the pregnancy, suspected pregnancy, or positive pregnancy test 
must be reported to the UNCCN Project Manager within 24 hours via facsimile to 
919-966-4300.  The female subject should be referred to an obstetrician-
gynecologist, preferably one experienced in reproductive toxicity for further 
evaluation and counseling. 
 
 
FDA Expedited Reporting requirements: 
If an investigator deems that an event is both a serious SAR AND unexpected, it 
must also (in addition to Oncore) be recorded on the MedWatch Form 3500A as per 
21 CFR 312.32.  For Affiliate Investigators, the MedWatch form should be faxed to 
the UNCCN Project Manager at 919-966-4300 along with supporting 
documentation defining the event and causality.  The MedWatch 3500a form can be 
accessed at: 
http://www.fda.gov/Safety/MedWatch/HowToReport/DownloadForms/default.htm. 
(Please be sure and access form 3500a, and not form 3500).   UNC, as the Sponsor 
of the study, will make the final determination regarding FDA submission.   
 
Once the UNC Principal Investigator determines an event is a serious SAR AND 
unexpected, the MedWatch 3500A form will be submitted to the FDA by the 
UNCCN Project Manager.  If the event is serious, unexpected and considered to be 
possibly-, probably- or definitely-related to the study treatment, the UCCN Project 
Manager will inform the Regulatory Associate at UNC who will be responsible for 
submitting the SAR to the IND. All IND safety reports must be submitted on Form 
3500A and be accompanied by Form 1571. The FDA must be notified or any 
unexpected or life-threatening suspected adverse reactions as soon as possible, but 
no later than 7 calendar days of learning of the event. 
 
The UNCCN Project Manager will also be responsible for informing each Affiliate 
site of all serious and unexpected SARs reported to the FDA via fax as soon as 
possible.   
 

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7.3.3.1 Merck Reporting Requirements 
Any SAE, or follow up to a SAE, 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 90 days following cessation of treatment, or the 
initiation of new anti-cancer therapy, whichever is earlier, whether or not related 
to Merck product, must be reported within 24 hours to the Sponsor and within 2 
working days to Merck Global Safety. All subjects with serious adverse events 
must be followed up for outcome. 
 
Non-serious Events of Clinical Interest will be forwarded to Merck Global Safety 
and will be handled in the same manner as SAEs.  
 
Additionally, any serious adverse event, considered by an investigator who is a 
qualified physician to be related to Merck product that is brought to the attention 
of the investigator at any time outside of the time period specified in the previous 
paragraph also must be reported immediately to the 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 
 
All 15-Day Reports and Annual Progress Reports must be submitted as required 
to FDA. Investigators will cross-reference these reports 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. 
 
Events of Clinical Interest 
Selected non-serious and serious adverse events are also known as Events of 
Clinical Interest (ECI) and must be reported within 24 hours to the Sponsor and 
within 2 working days to Merck Global Safety. (Attn: Worldwide Product Safety; 
FAX 215 993-1220). 
 
For the time period beginning when the consent form is signed until treatment 
allocation/randomization, any ECI, or follow up to an ECI, that occurs to any 
subject must be reported within 24 hours to the Sponsor and within 2 working 
days to Merck Global Safety if it causes the subject to be excluded from the trial, 
or is the result of a protocol-specified intervention, including but not limited to 
washout or discontinuation of usual therapy, diet, placebo treatment or a 
procedure. 
 
For the time period beginning at treatment allocation/randomization through 90 
days following cessation of treatment, or 30 days following cessation of treatment 
if the subject initiates new anticancer therapy, whichever is earlier, any ECI, or 
follow up to an ECI, whether or not related to Merck product, must be reported 
within 24 hours to the Sponsor and within 24 hours to Merck Global Safety. 

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Events of clinical interest for this trial include: 
1.  an overdose of Merck product, as defined below under overdose.  
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.  
 
Overdose 
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) 
 
Pregnancy and Lactation 
See above in this section for additional information. Such events must be reported 
within 2 working days to Merck Global Safety. (Attn: Worldwide Product Safety; 
FAX 215 993-1220). 
 
7.3.3.2 Protocol-Specific Exceptions to Serious Adverse Event Reporting  
Efficacy endpoints as outlined in this section will not be reported to Merck as AEs 
to the Sponsor and to Merck, unless there is evidence suggesting a causal 
relationship between the drug and the event. Any such event will be submitted to 
the Sponsor within 24 hours and to Merck Global Safety within 2 working days 
either by electronic or paper media. 

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Specifically, the suspected/actual events covered in this exception include any 
event that is disease progression of the cancer under study. 
The Sponsor will monitor aggregated efficacy endpoint events and safety data to 
ensure the safety of the subjects in the trial. Any suspected endpoint which upon 
review is not progression of the cancer under study will be forwarded to Merck 
Global Safety as a SAE within 2 working days of determination that the event is 
not progression of the cancer under study. 
Hospitalization related to convenience (e.g.transportation issues etc.) will not be 
considered a SAE. 
 
7.4 
Data and Safety Monitoring Plan 
The Principal Investigator will provide continuous monitoring of patient safety in 
this trial with periodic reporting to the Data and Safety Monitoring Committee 
(DSMC).  
 
Meetings/teleconferences will be held at a frequency dependent on study accrual, 
and in consultation with the study Biostatistician.  These meetings will include the 
investigators as well as protocol nurses, clinical research associates, regulatory 
associates, data managers, biostatisticians, and any other relevant personnel the 
principal investigators may deem appropriate.  At these meetings, the research 
team will discuss all issues relevant to study progress, including enrollment, 
safety, regulatory, data collection, etc. 
 
The team will produce summaries or minutes of these meetings. These summaries 
will be available for inspection when requested by any of the regulatory bodies 
charged with the safety of human subjects and the integrity of data including, but 
not limited to, the oversight (Office of Human Research Ethics (OHRE) 
Biomedical IRB, the Oncology Protocol Review Committee (PRC) or the North 
Carolina TraCS Institute Data and Safety Monitoring Board (DSMB).   
 
The UNC LCCC Data and Safety Monitoring Committee (DSMC) will review the 
study on a regular (quarterly to annually) basis, with the frequency of review 
based on risk and complexity as determined by the UNC Protocol Review 
Committee.  The UNC PI will be responsible for submitting the following 
information for review: 1) safety and accrual data including the number of 
patients treated; 2) significant developments reported in the literature that may 
affect the safety of participants or the ethics of the study; 3) preliminary response 
data; and 4) summaries of team meetings that have occurred since the last report.  
Findings of the DSMC review will be disseminated by memo to the UNC PI, 
PRC, and the UNC IRB and DSMB.   
8.0 
STATISTICAL CONSIDERATIONS 

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8.1 
Study Design/Study Endpoints 
This is a prospective, open-label, single arm, phase 2 trial of single-dose 
cyclophosphamide +pembrolizumab in patients with metastatic triple negative 
breast cancer (TNBC). The primary hypothesis being evaluated is that the 
addition of one dose of cyclophosphamide prior to initiation of pembrolizumab 
will result in an approximately 50% improvement in progression free survival 
(PFS) when compared to historical controls that were treated with pembrolizumab 
alone [1].  A biologically-focused primary objective is to describe the reduction in 
Tregs in patients with metastatic TNBC receiving cyclophosphamide + 
pembrolizumab. 
 
Secondary endpoints include the ORR, DCR, DOR, and OS. The tolerability and 
safety of single-dose cyclophosphamide + pembrolizumab in patients with 
metastatic TNBC will also be assessed (See section 2.4.2. for end point 
definitions and Section 8.3). 
 
Correlative studies, based on serial blood collections and tumor samples, will be 
done under a separate protocol based on availability of archival diagnostic tissue 
(see section 1.4). 
8.2 
Sample Size and Accrual 
The primary objective of this study is to estimate PFS defined as time from D1 of 
treatment until disease progression or death from any cause. Based on recent 
phase 1 data with pembrolizumab alone, we set the null hypothesis for median 
PFS at 1.9 months. The alternative hypothesis is a median PFS of 2.9 months for 
patients who receive a single dose cyclophosphamide prior to pembrolizumab. 
This approximately 50% increase in PFS would be considered clinically 
significant. 
 
Assuming that accrual occurs within a 12 month period, and all patients are 
followed for at least 6 months, 36 patients are needed to detect the change in 
median PFS from 1.9 to 2.9 months. This sample size calculation is based on a 
one-sided 0.05 significance level, 80% power, and assuming an exponential 
survival time distribution (calculated using SWOG online One Arm Survival 
calculator at https://www.swogstat.org/stat/public/one survival.html).  We will 
also assume a 10% consent and not treat or loss to follow-up rate. Therefore we 
plan to enroll 40 patients to ensure that 36 are evaluable for the primary endpoint.  
We expect accrual to take approximately 2 years  , with the rate of accrual being 1 
to 2  patients per month. 
 
While this study is not specifically powered for the assessment of Treg reduction, 
with the projected evaluable sample size, we will be able to detect an approximate 
reduction in Tregs of 67% (i.e.a3-fold reduction) using the Wilcoxon sign-rank 
test, with 80% power and a one-sided alpha=0.05. 

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8.3 
Toxicity Monitoring  
Toxicity will be assessed using NCI CTCAE version 4. Patients will be monitored for 
excessive toxicity over the duration of the study. A toxicity rate due to the study 
regimen greater than 25% would be considered unacceptable.   
 
Pocock-type boundaries will be utilized as described in Ivanova, A., et al. Biometrics. 
2005;61(2):540-5.  If a toxicity boundary is reached, accrual for the study will be 
suspended and the Data Safety and Monitoring Committee (DSMC) will be alerted. 
The DSMC (in consultation with the Principal Investigator and MERCK) will 
evaluate the toxicity events to help determine whether or not to terminate the study. 
 
Accrual to the trial is to be suspended if the number of protocol defined toxic 
events is equal to or larger than boundary in the table below. 
 
Number of Patients 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 
Boundary 
- - - 4 5 5 5 6 6 7 7 7 8 8 9 9 9 10 10 10 
Number of Patients 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 
Boundary 
11 11 11 12 12 12 13 13 14 14 14 15 15 15 16 16  
 
 
 
8.4 
Data Analysis Plans 
The primary efficacy analysis will be based on the primary objective. The primary 
objective of this study is to estimate PFS defined as time from D1 of treatment 
until documented disease progression or death from any cause. The Kaplan-Meier 
method will be used to estimate PFS and median PFS will be reported along with 
its 95% confidence interval. 
 
Also of primary interest is quantifying the expected reduction in Tregs. While this 
is listed as a co-primary objective, statistically it will be treated as an exploratory 
objective.  With the projected sample size, we will be able to detect a reduction in 
Tregs of 67% (ie, 3-fold reduction) using the Wilcoxon sign-rank test. We will 
report appropriate descriptive statistics to quantitate the number and function of 
Tregs in these patients. 
 
Secondary objectives include estimating the ORR, DCR, DOR, OS, and 
characterizing the toxicity profile and safety of this regimen.  ORR and DCR will 
be reported along with their corresponding exact two-sided 95% confidence 
intervals. The Kaplan-Meier method will be used to estimate DOR and OS. 
Median DOR and OS will be reported along with their 95% confidence intervals.  
 
The analysis of the toxicity and safety of this regimen will be based on the 
frequency of adverse events and their severity for patients who received any study 
medicine. Worst toxicity grades per patient will be tabulated for adverse events 
and laboratory measurements by using the NCI CTCAEv4 and will be reported in 
the form of frequency tables. 
 

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Demographic and baseline laboratory results will be summarized using 
descriptive statistics.  
 
Definitions 
• Progression Free Survival (PFS): A patient’s progression-free survival will be 
defined as the time from D1 of treatment until the date he or she has 
documented disease progression or dies. Any patient who has received study 
treatment but has neither experienced progression nor died will be censored 
on the date of his or her last tumor assessment  
• Overall Survival (OS): A patient’s survival time will be defined as the time 
from start of treatment to the date of his or her death. If the patient has not 
died, survival will be censored on last date the patient was known to be alive  
• Overall Response Rate (ORR): The overall response rate will be defined as 
the total number of patients whose response are either a CR or PR divided by 
the number of response evaluable patients 
• Disease Control Rate (DCR): Clinical benefit will be defined as the total 
number of patients whose responses are either a CR, PR, or SD divided by the 
number of response evaluable patients. Patients will need to be at least a SD 
for at least 6 months in order to be considered to have received clinical benefit 
from the treatment regimen 
• Duration of Overall Response (DOR): The duration of overall response will 
be computed for patients whose best response is either PR or CR. It will be 
measured from when the time measurement criteria are first met for complete 
response or partial response (whichever status is recorded first) until the first 
date of progressive disease or death. Patients who neither progress nor die will 
be censored on the date of their last tumor assessment 
 
Exploratory objectives will be evaluated when sample sizes are such to allow 
appropriate analyses. To explore possible associations of biological markers with 
ORR, logistic regression modeling will be used. To explore possible associations 
of biological markers with PFS and OS, Cox regression modeling will be used. 
Fisher’s exact tests will be used to test for differences in ORR and DCR between 
subtypes of TNBC.  For each T cell phenotype, the change in percentage of T 
cells will be calculated at the patient level, and descriptive statistics will be 
reported.  TCR and BCR repertoire profiles will be characterized as having high 
or low sequence ‘diversity’, and the possible association of these dichotomized 
variables will be explored by Fisher’s exact test with ORR, and Cox regression 
modeling with PFS and OS. The same statistical methods (outlined above) will 
used for outcomes defined using the irRECIST criteria. 
9.0 
STUDY MANAGEMENT 

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9.1 
Institutional Review Board (IRB) Approval and Consent 
It is expected that the IRB will have the proper representation and function in 
accordance with federally mandated regulations.  The IRB should approve the 
consent form and protocol. 
 
In obtaining and documenting informed consent, the investigator should comply 
with the applicable regulatory requirement(s), and should adhere to Good Clinical 
Practice (GCP) and to ethical principles that have their origin in the Declaration 
of Helsinki. 
 
 
 
Before recruitment and enrollment onto this study, the patient will be given a full 
explanation of the study and will be given the opportunity to review the consent 
form. Each consent form must include all the relevant elements currently required 
by the FDA Regulations and local or state regulations. Once this essential 
information has been provided to the patient and the investigator is assured that 
the patient understands the implications of participating in the study, the patient 
will be asked to give consent to participate in the study by signing an 
IRB-approved consent form. 
 
Prior to a patient’s participation in the trial, the written informed consent form 
should be signed and personally dated by the patient and by the person who 
conducted the informed consent discussion. 
9.2 
Required Documentation 
Before the study can be initiated at any site, the following documentation must be 
provided to the Clinical Protocol Office (CPO) at the University of North 
Carolina. 
 
• A copy of the official IRB approval letter for the protocol and 
informed consent 
• IRB membership list 
• CVs and medical licensure for the principal investigator and any sub-
investigators who will be involved in the study. 
• Form FDA 1572 appropriately filled out and signed with appropriate 
documentation (NOTE: this is required if UNC holds the IND.  
Otherwise, the Investigator’s signature documenting understanding of 
the protocol and providing commitment that this trial will be 
conducted according to all stipulations of the protocol is sufficient to 
ensure compliance) 
• CAP and CLIA Laboratory certification numbers and institution lab 
normal values 
• Executed clinical research contract 

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9.3 
Registration Procedures 
All patients must be registered with the LCCC CPO UNCCN at the University of 
North Carolina before enrollment to study.  To register a patient call the UNCCN 
at
 Monday-Friday 8:30 am – 5:00 pm EST. Fax 
 or 
email (address to be provided at SIM) registration form, signed informed consents 
and all source documents to confirm eligibility. When sending registration request 
with eligibility documentation, please allow 24 hours for source to be reviewed. 
 
For Affiliate patients, to register and confirm patient eligibility, please fax 
registration forms, informed consent, and source documents to
.  
9.4 
Data Management and Monitoring/Auditing 
The CPO UNCCN of the UNC LCCC will serve as the coordinating center for 
this trial. Data will be collected through a web based clinical research platform, 
OnCore®.  Other study institutions will be given a password to directly enter their 
own data onto the web site via electronic case report forms (eCRFs).  UNCCN 
personnel will coordinate and manage data for quality control assurance and 
integrity. 
 
All data will be collected and entered into OnCore® by Clinical Research 
Associates (CRAs) from UNC LCCC and participating institutions.  The 
investigators at each site will allow monitors to review all source documents 
supporting data entered into OnCore®. The UNCCN Data Coordinator can be 
reached at
. 
 
As an investigator initiated study, this trial will also be audited by the Lineberger 
Cancer Center audit committee every six or twelve months, depending on the 
participation of affiliate sites. 
9.5 
Adherence to the Protocol 
Except for an emergency situation in which proper care for the protection, safety, 
and well-being of the study patient requires alternative treatment, the study shall 
be conducted exactly as described in the approved protocol.   
9.5.1 Emergency Modifications 
UNC and Affiliate investigators may implement a deviation from, or a change of, 
the protocol to eliminate an immediate hazard(s) to trial subjects without prior 
UNC or their respective institution’s IRB/IEC approval/favorable opinion.   
 
For Institutions Relying on UNC’s IRB: 
For any such emergency modification implemented, a UNC IRB modification 
form must be completed by UNC Research Personnel within five (5) business 
days of making the change.   
 
For Institutions Relying on Their Own IRB: 

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For Affiliate investigators relying on their own institution’s IRB, as soon as 
possible after the modification has been made, the implemented deviation or 
change and the reasons for it should be submitted to: 
 
• To UNC Principal Investigator for agreement  
• The Affiliate institution’s IRB for review and approval.  (Once 
IRB’s response is received, this should be forwarded to the 
UNCCN Regulatory Associate). 
9.5.2 Single Patient/Subject Exceptions 
Eligibility single subject exceptions are not permitted for Lineberger 
Comprehensive Cancer Center Investigator Initiated Trials under any 
circumstances.  Other types of single subject exceptions may be allowed if proper 
regulatory review has been completed in accordance with Lineberger 
Comprehensive Cancer Center’s Single Subject Exception Policy. 
9.5.3 Other Protocol Deviations/Violations 
According to UNC’s IRB, a protocol deviation is any unplanned variance from an 
IRB approved protocol that:  
• Is generally noted or recognized after it occurs 
• Has no substantive effect on the risks to research participants 
• Has no substantive effect on the scientific integrity of the research plan 
or the value of the data collected  
• Did not result from willful or knowing misconduct on the part of the 
investigator(s).  
 
An unplanned protocol variance is considered a violation if the variance meets 
any of the following criteria:  
• Has harmed or increased the risk of harm to one or more research 
participants. 
• Has damaged the scientific integrity of the data collected for the study. 
• Results from willful or knowing misconduct on the part of the 
investigator(s). 
• Demonstrates serious or continuing noncompliance with federal 
regulations, State laws, or University policies. 
 
If a deviation or violation occurs please follow the guidelines below: 
 
For Institutions Relying on UNC’s IRB: 
Protocol Deviations: UNC or Affiliate personnel will record the deviation in 
OnCore®, and report to any sponsor or data and safety monitoring committee in 
accordance with their policies.  Deviations should be summarized and reported to 
the IRB at the time of continuing review. 
 

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Protocol Violations: Violations should be reported by UNC personnel within one 
(1) week of the investigator becoming aware of the event using the same IRB 
online mechanism used to report Unanticipated Problems.   
 
For Institutions Relying on Their Own IRB: 
In addition to adhering to the policies regarding protocol compliance set forth by 
your institution’s IRB, the following is also required: 
 
Protocol Deviations: In the event a deviation from protocol procedures is 
identified, record the deviation in OnCore®. 
 
Protocol Violations: Any protocol violation that occurs must be reported to your 
IRB per institutional policies and reported to the UNCCN Project Manager within 
5 days. UNC-CH will determine if the violation affects the safety of the patient 
and integrity of the data.  Once your institution’s IRB response is received, please 
forward to the UNCCN Regulatory Associate. 
 
Unanticipated Problems: 
Affiliate Sites: 
Any events that meet the criteria for “Unanticipated Problems (UPs)” as defined 
by UNC’s IRB must also be reported to the UNCCN Project Manager.   The 
UNCCN Project Manager will report the event to the UNC IRB using the IRB’s 
web-based reporting system.  Examples of such UPs include a lost or stolen 
laptop computer that contains sensitive study information. 
 
UNC 
Any events that meet the criteria for “Unanticipated Problems” as defined by 
UNC’s IRB must be reported by the Study Coordinator using the IRB’s web-
based reporting system.   
9.6 
Amendments to the Protocol 
Should amendments to the protocol be required, the amendments will be 
originated and documented by the Principal Investigator at UNC.  It should also 
be noted that when an amendment to the protocol substantially alters the study 
design or the potential risk to the patient, a revised consent form might be 
required.   
 
For Institutions Relying on UNC’s IRB: 
The written amendment, and if required the amended consent form, must be sent 
to UNC’s IRB for approval prior to implementation.   
 
For Institutions Relying on Their Own IRB: 
Investigators must submit the amendment to their institution’s IRB for approval.  
For multi-center studies, any multi-center site must submit their informed consent 
revisions to the Multi-center Regulatory Associate prior to submission to their 
IRB.   

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9.7 
Record Retention 
Study documentation includes all eCRFs, data correction forms or queries, source 
documents, Sponsor-Investigator correspondence, monitoring logs/letters, and 
regulatory documents (e.g., protocol and amendments, IRB correspondence and 
approval, signed patient consent forms). 
 
Source documents include all recordings of observations or notations of clinical 
activities and all reports and records necessary for the evaluation and 
reconstruction of the clinical research study. 
 
Government agency regulations and directives require that all study 
documentation pertaining to the conduct of a clinical trial must be retained by the 
study investigator.  In the case of a study with a drug seeking regulatory approval 
and marketing, these documents shall be retained for at least two years after the 
last approval of marketing application in an International Conference on 
Harmonization (ICH) region.  In all other cases, study documents should be kept 
on file until three years after the completion and final study report of this 
investigational study. 
9.8 
Obligations of Investigators 
The Principal Investigator is responsible for the conduct of the clinical trial at the 
site in accordance with Title 21 of the Code of Federal Regulations and/or the 
Declaration of Helsinki.  The Principal Investigator is responsible for personally 
overseeing the treatment of all study patients.  The Principal Investigator must 
assure that all study site personnel, including sub-investigators and other study 
staff members, adhere to the study protocol and all FDA/GCP/NCI regulations 
and guidelines regarding clinical trials both during and after study completion. 
 
The Principal Investigator at each institution or site will be responsible for 
assuring that all the required data will be collected and entered into the eCRFs. 
Periodically, monitoring visits will be conducted and the Principal Investigator 
will provide access to his/her original records to permit verification of proper 
entry of data. At the completion of the study, all eCRFs will be reviewed by the 
Principal Investigator and will require his/her final signature to verify the 
accuracy of the data. 
10.0 REFERENCES 
               
1. 
Nanda, R., Chow L.Q., Dees, E.C. et al., Abstract S1-09: A phase Ib study of 
pembrolizumab (MK-3475) in patients with advanced triple-negative breast 
cancer. Cancer Res, 2015. 75(9 Supplement): p. S1-09. 
2. 
Iglesia, M.D., Vincent, B.G., Parker, J. S. et al., Prognostic B-cell signatures 
using mRNA-seq in patients with subtype-specific breast and ovarian cancer. Clin 
Cancer Res, 2014. 20(14): p. 3818-29. 

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3. 
Swain, S., Triple-negative breast cancer: metastatic risk and role of platinum 
agents. 44th Annual Meeting of the American Society of Clinical Oncology, 
2008. 
4. 
Anders, C. and L.A. Carey, Understanding and treating triple-negative breast 
cancer. Oncology (Williston Park, NY), 2008. 22(11): p. 1233. 
5. 
Anders, C.K. and L.A. Carey, Biology, metastatic patterns, and treatment of 
patients with triple-negative breast cancer. Clin Breast Cancer, 2009. 9: p. S73-
S81. 
6. 
Sikov, W.M., Berry, D.A., Perou, C.M. et al., Impact of the addition of 
carboplatin and/or bevacizumab to neoadjuvant once-per-week paclitaxel 
followed by dose-dense doxorubicin and cyclophosphamide on pathologic 
complete response rates in stage II to III triple-negative breast cancer: CALGB 
40603 (Alliance). J Clin Oncol, 2015. 33(1): p. 13-21. 
7. 
Tutt, A., P. Ellis, and L. Kilburn, The TNT trial: a randomized phase III trial of 
carboplatin (C) compared with docetaxel (D) for patients with metastatic or 
recurrent locally advanced triple negative or BRCA1/2 breast cancer 
(CRUK/07/012). San Antonio Breast Cancer Symposium, 2014: p. S3-01. 
8. 
Lin, N.U., Sohl, C.E., Razzak, A.R., et al., Sites of distant recurrence and clinical 
outcomes in patients with metastatic triple-negative breast cancer: high incidence 
of central nervous system metastases. Cancer, 2008. 113 (10): p. 2638-45. 
9. 
Dent, R., Trudeau, M., Pritchard, K.I., et al., Triple-negative breast cancer: 
clinical features and patterns of recurrence. Clin Cancer Res, 2007. 13(15 Pt 1): 
p. 4429-34. 
10. 
Herbst, R., Gordon M.S., Fine G.D., et al. A study of MPDL3280A, an engineered 
PD-L1 antibody in patients with locally advanced or metastatic tumors. J Clin 
Oncol, 2013. 31(suppl; abst 3000).  
11. 
Soria, J., et al., Clinical activity, safety and biomarkers of PD-L1 blockade in non-
small cell lung cancer (NSCLC): additional analyses from a clinical study of the 
engineered antibody MPDL3280A (anti-PDL1). Eur J Cancer, 2013. 49: p. S798-
S798. 
12. 
Muenst, S., Schaerli, A.R., Gao, F., et al., Expression of programmed death 
ligand 1 (PD-L1) is associated with poor prognosis in human breast cancer. 
Breast Cancer Res Treat, 2014. 146(1): p. 15-24. 
13. 
Muenst, S., Soysal, S.D., Gao, F. et al., The presence of programmed death 1 
(PD-1)-positive tumor-infiltrating lymphocytes is associated with poor prognosis 
in human breast cancer. Breast Cancer Res Treat, 2013. 139(3): p. 667-676. 
14. 
Schmidt, A., N. Oberle, and P.H. Krammer, Molecular mechanisms of treg-
mediated T cell suppression. Front Immunol, 2012. 3:51 at 
http://dx.doi.org/10.3389/fimmu.2012.00051 
15. 
Karasar, P. and G. Esendagli, T helper responses are maintained by basal-like 
breast cancer cells and confer to immune modulation via upregulation of PD-1 
ligands. Breast Cancer Res Treat, 2014. 145(3): p. 605-614. 
16. 
deLeeuw, R.J., Kost, S.E., Kakal, J.A., et al., The prognostic value of FoxP3+ 
tumor-infiltrating lymphocytes in cancer: a critical review of the literature. Clin 
Cancer Res, 2012. 18(11):p. 3022-3029. 

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17. 
Le, D.T. and E.M. Jaffee, Regulatory T-cell modulation using cyclophosphamide 
in vaccine approaches: a current perspective. Cancer Res, 2012. 72(14):p 3439-
3444. 
18. 
Becker, J.C. and D. Schrama, The dark side of cyclophosphamide: 
cyclophosphamide-mediated ablation of regulatory T cells. J Invest Dermatol, 
2013. 133(6): p. 1462-1465. 
19. 
Walter, S., et al., Multipeptide immune response to cancer vaccine IMA901 after 
single-dose cyclophosphamide associates with longer patient survival. 
NatureMed, 2012. 18(8): p. 1254-1261. 
20. 
Emens, L.A., et al., Timed sequential treatment with cyclophosphamide, 
doxorubicin, and an allogeneic granulocyte-macrophage colony-stimulating 
factor–secreting breast tumor vaccine: A chemotherapy dose-ranging factorial 
study of safety and immune activation. J Clin Oncol, 2009. 27(35): p. 5911-5918. 
21. 
Topalian, S.L., et al., Safety, activity, and immune correlates of anti-PD-1 
antibody in cancer. N Engl J Med, 2012. 366(26): p. 2443-54. 
 
 
 

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11.0 APPENDICES 
11.1 
Appendix A 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. Capable of only limited self-care, 
confined to bed or chair 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. 
 
 

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11.2 
Appendix B Cockcroft-Gault Formula 
 
Estimated creatinine clearance (mL/min) = (140-age in years) X (weight in kg) 
 
 
 
 
 
 
72 X (serum creatinine in mg/dL) 
 
For females, use 85% of calculated creatinine clearance value. 
 
 
 
 
 

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11.4 
Appendix D Patient Handout: Prohibited Medications  
 
One of the medications you are receiving during this clinical trial is 
cyclophosphamide.  Cyclophosphamide interacts with some drugs that are 
processed by your liver. Because of this, it is very important to tell your study 
doctors about all of your medicine before you start this study. It is also very 
important to tell them if you stop taking any regular medicine, or if you start 
taking a new medicine while you take part in this study. When you talk about 
your medicine with your study doctor, include medicine you buy without a 
prescription at the drug store (over-the counter remedy), or anything that you buy 
from the health food store or grocery store (herbal supplement). Many health care 
prescribers can write prescriptions. You must also tell your other prescribers 
(doctors, physicians’ assistants or nurse practitioners) that you are taking part in a 
clinical trial. Bring this paper with you.  
 
• Cyclophosphamide is processed by a certain enzyme in the liver called 
CYP450 enzymes.  Drugs that increase the activity of this enzyme are 
called “inducers”, and drugs that decrease the activity of this enzyme are 
called “inhibitors”.  Cyclophosphamide must be used very carefully with 
other medicines that are inducers or inhibitors of CYP450.   
• You and healthcare providers who prescribe drugs for you must be careful 
about adding or removing any drug in this category 
• Before you start the study, your study doctor will work with your regular 
prescriber to switch the following medications if you are taking them:  
o Ticlopidine, fluvoxamine, efavirenz, amodiarone, diosmin, 
fluconazole, miconazole, oxandrolone, ticynafen, amprenavir, 
atazanvir, clarithromycin, conivaptan, fosamprenavir, grapefruit 
juice, idinavir, itraconazole, ketoconazole, nefazodone, nelfinavir, 
ritonavir, saquinavir, telithromycin, telaprevir, troleansomycin, 
vriconazole, aprepitant, cimetidine, darunavir, diltiazem, 
erythromycin, fluconazole, imatinib, nifedipine, posaconazole, 
tofisopam, verapamil, carbamazepine, phenytoin, rifampin, 
St  John’s Wort, bosentan, etravirine, nafcillin, nevirapine, and 
phenobarbital 
• Your regular prescribers should look at this web site: 
http://medicine.iupui.edu/clinpharm/ddis/table.asp to see if any medicine 
they want to prescribe is on a list of drugs to avoid.  Your study doctor 
may also have a list of medications for you to show your regular 
prescribers instead of, or in addition to, this website.   
• If you drink grapefruit juice or eat grapefruit, you should avoid these for at 
least 1 week before receiving cyclophosphamide until 3 days after the 
dose.   
• Other medicines can be a problem with your study drugs. 

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o You should check with your doctor or pharmacist whenever you 
need to use an over-the-counter medicine or herbal supplement. 
o Your regular prescriber should check a medical reference or call 
your study doctor before prescribing any new medicine for you. 
Your study doctor’s name is _______________ and he or she can 
be contacted at _______________________.