A Phase II Randomized Study to Evaluate the Immunologic and Antitumor Activity of Concurrent VRP-HER2 Vaccination and Pembrolizumab for Patients With Advanced HER2-overexpressing Breast Cancer
Phase: PHASE2
Conditions: Breast Cancer, HER2+ Breast Cancer
Sponsor: Herbert Lyerly

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SPONSOR: Duke University 
 
TITLE: A Phase II randomized study to evaluate the immunologic and antitumor 
activity of concurrent VRP-HER2 vaccination and Pembrolizumab for patients with 
advanced HER2-overexpressing breast cancer 
 
IND NUMBER: 14932 
 
IND Holder:  H. Kim Lyerly, MD 
 
Duke IRB# Pro00100093 
 
NCT03632941 
 
 

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CONTENTS 
1.0 
TRIAL SUMMARY ........................................................................................... 3 
2.0 
TRIAL DESIGN ................................................................................................. 3 
3.0 
OBJECTIVE(S) & HYPOTHESIS(ES) ........................................................... 4 
4.0 
BACKGROUND & RATIONALE ................................................................... 5 
5.0 
METHODOLOGY ........................................................................................... 23 
6.0 
TRIAL FLOW CHART ................................................................................... 49 
7.0 
TRIAL PROCEDURES ................................................................................... 52 
8.0 
STATISTICAL ANALYSIS PLAN ................................................................ 66 
9.0 
LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES ......................................................................................................... 67 
10.0 
ADMINISTRATIVE AND REGULATORY DETAILS .............................. 69 
11.0 
APPENDICES .................................................................................................. 73 
 
 
 

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1.0 TRIAL SUMMARY 
Abbreviated Title 
Concurrent VRP-HER2 vaccination and Pembrolizumab for patients with 
advanced HER2+ breast cancer 
Trial Phase 
Phase II 
Clinical Indication 
Advanced HER2+ breast cancer receiving Trastuzumab and Pertuzumab 
Trial Type 
Randomized Phase II Study 
Type of control 
None 
Route of administration 
VRP-HER2 vaccine– intramuscular, Pembrolizumab - intravenous 
Trial Blinding 
None 
Treatment Groups  
Safety Arm: VRP-HER2 vaccine + Pembrolizumab (n=3) 
Arm A: VRP-HER2 vaccine (n=12) 
Arm B: Pembrolizumab alone (n=12)  
Arm C: VRP-HER2 vaccine + Pembrolizumab (n=12) 
Number of trial subjects 
39 
Estimated enrollment period 
18 months 
Estimated duration of trial 
30 months 
Duration of Participation 
24 months 
Estimated average length of 
treatment per patient 
12 weeks 
 
 
 
 
2.0 TRIAL DESIGN 
2.1 
Trial Design 
There will be an initial Safety Arm (n=3) during which subjects will receive the VRP-HER2 
immunizations plus pembrolizumab and, if there is no dose limiting toxicity* in the Safety 
Arm, then subjects will be stratified by hormone receptor status (ER and/or PR + versus 
negative) and randomized 1:1:1 into 3 arms (n=12 per arm) as per the diagram in Section 2.2. 
Specifically, subjects with metastatic HER2-overexpressing breast cancer receiving 
trastuzumab and pertuzumab** will continue these antibodies. They will undergo a biopsy of 
their tumor and peripheral blood draw for immune cell analyses and be assigned to the 
applicable arm of the study. Arm A will consist of the VRP-HER2 immunizations; Arm B 
will consist of pembrolizumab; Arm C will consist of the VRP-HER2 immunizations plus 
pembrolizumab. Tumor biopsies and peripheral blood draws will be performed following the 
course of immunizations. 

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* Dose limiting toxicity is defined as any Grade 2 or higher immediate hypersensitivity 
reactions or neurological toxicity, other Grade 3 or 4 allergic or major organ toxicity, or any 
other Grade 3 or higher toxicity attributable to study treatment (VRP-HER2 vaccine or 
pembrolizumab).
** For the concurrent Trastuzumab and Pertuzumab, dosing will be at the discretion of the 
treating physician.
2.2
Trial Diagram
3.0 OBJECTIVE(S) & HYPOTHESIS(ES)
3.1
Primary Objective(s) & Hypothesis(es)
(1) Objective: To determine whether pembrolizumab increases the tumor infiltrating (T 
cell) and peripheral blood (T cell and antibody) immune response to the VRP-HER2 
vaccine.
Hypothesis: We hypothesize that HER2 specific T cell responses and anti-tumor 
immunity induced with HER2 vaccination will be augmented by concurrent anti-PD-1 
antibody therapy.

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3.2 
Secondary Objective(s) & Hypothesis(es) 
(2) Objective: To determine whether the administration of pembrolizumab is safe in patients 
with recurrent or metastatic HER2+ cancers who are receiving the anti-HER2 vaccine 
VRP-HER2. 
 Hypothesis: We hypothesize that concurrent immunization with HER2-targeting 
vaccines and anti-PD-1 antibody therapy will be well tolerated.    
3.3 
Exploratory Objective 
(3) Objective: To collect preliminary data on the clinical response rates to this concurrent 
therapy of agents in subjects with assessable disease based on RECIST 1.1 criteria. 
Hypothesis: We hypothesize that the induction of enhanced anti-tumor T cell responses 
from concurrent HER2 vaccination and anti-PD-1 antibody therapy will lead to greater 
clinical efficacy.    
 
4.0 BACKGROUND & RATIONALE 
4.1 
Background 
HER2 expressing malignancies, while initially responsive to trastuzumab and pertuzumab,  
eventually progress; yet the HER2 protein continues to be expressed on these tumors 
suggesting they may be targets for immune therapies. Indeed, it has been demonstrated that a 
higher percentage of tumor infiltrating lymphocytes (TILs) is associated with better tumor 
response to trastuzumab in both the adjuvant1 and neoadjuvant setting in HER2+ breast 
cancers.  
One strategy for increasing the T cell lymphocyte response to tumors is to use vaccines 
capable of activating T cells against tumor associated antigens such as HER2. We have 
extensive experience developing vaccines to activate HER2-specific immune responses in 
patients with HER2 overexpressing malignancies. We vaccinated patients with HER2 
overexpressing breast cancer with dendritic cells loaded with HER2 protein or peptide2 or 
vaccines based on HER2 protein plus adjuvants3 and reported the induction of anti-HER2-
specific antibodies and T cell responses. In an attempt to develop a vaccine capable of 
inducing more effective T and B cell responses, we generated alphaviruses modified to 
express tumor antigens such as HER2. These vectors have tropism for dendritic cells and 
direct high expression of the HER2 antigen within dendritic cells. In preclinical models, we 
observed that a vaccine based on an attenuated Venezuelan Equine Encephalitis alphavirus 

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encoding HER2, could induce both cellular and humoral immune responses capable of 
controlling HER2 expressing malignancies. We completed Phase I testing of this vaccine 
called VRP(HuHER2-ECD+Tm) encoding the extracellular (ECD) and transmembrane (TM) 
domains of HER2 (subsequently referred to as VRP-HER2) alone and in conjunction with 
HER2 targeted therapies (mainly trastuzumab) to patients with locally advanced or metastatic 
HER2+ cancer. Our data from this trial, presented at the 2015 annual ASCO meeting4, 
demonstrates induction of HER2 specific T cell responses and detectable anti-HER2 
antibodies in the serum. Clinically, the VRP-HER2 vaccine was well tolerated with no dose-
limiting toxicities related to the vaccine. Our clinical follow-up to date reveals a median 
overall survival (OS) that has not been reached after greater than 35 months of follow-up in 
this heavily pre-treated metastatic population4. As the results from the CLEOPATRA study 
have established trastuzumab + pertuzumab based therapy as the standard of care for first line 
treatment of metastatic HER2+ disease, demonstrating a progression free survival (PFS) of 
18.5 months5, we are seeking to augment the HER2 specific and anti-tumor immunity in these 
patients through a randomized Phase II study of VRP-HER2 vaccination with or without anti-
PD-1 therapy with pembrolizumab.  
Previous biomarker studies have demonstrated that PD-1+ TILs are associated with poor 
prognosis in HER2 positive breast cancer6. In preclinical studies, higher T cell expression of 
the checkpoint molecule PD-1 (programmed death-1), was associated with greater 
trastuzumab benefit. Combining trastuzumab with anti-PD-1 and anti-PD-L1 antibodies 
showed greater tumor regression in mouse models of HER2+ mammary tumors7. It has also 
recently been demonstrated in breast cancer bearing mice that a combination regimen with an 
anti-PD-1 antibody and a multipeptide vaccine (derived from breast cancer antigens, 
including neu (HER2)) prolonged the vaccine-induced progression-free survival period and 
increased the median survival by nearly three-fold when compared with vaccine alone. This 
research also demonstrated that PD-1 blockade enhances breast cancer vaccine efficacy by 
altering both CD8 T cell and DC components of the tumor microenvironment8. In our own 
(unpublished) preclinical data, vaccination with a viral vector against a HER family receptor 
and anti-PD-1 antibody led to tumor regression and sustained control.  
Refer to the Investigator’s Brochure (IB)/approved labeling for detailed background 
information on pembrolizumab (MK-3475). 
4.1.1 Pharmaceutical and Therapeutic Background 
4.1.1.1 The need for new therapies for HER2+ metastatic breast cancer and 
other HER2 overexpressing malignancies 
Metastatic breast cancer continues to account for more than 400,000 deaths yearly with 
HER2+ breast cancers representing a significant fraction. Significant clinical benefit has been 

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achieved with the anti-HER2 antibody trastuzumab (Herceptin), but resistance eventually 
develops1. Lapatinib (Tykerb), a small molecule inhibitor of the tyrosine kinases of HER2 and 
epidermal growth factor receptor type 1 (EGFR), enhances time to progression to 8.4 months, 
when given with the cytotoxic capecitabine, compared with 4.4 months with capecitabine 
monotherapy2.  
Since the time of the original FDA approval of our Phase I VRP-HER2 trial, the landscape of 
HER2 breast cancer management has changed due to several recently approved HER2 
targeted therapies. Currently, first line therapies for HER2+ breast cancer are regimens 
containing trastuzumab with or without pertuzumab5. In the second line setting, the current 
approved therapies are: T-DM13 and Lapatinib9. These changes in approved regimens have 
occurred within the last few years due to the results of large randomized controlled trials3,5,9. 
With the approval of these HER2 targeted therapies, many HER2+ patients will continue on 
subsequent HER2 directed therapies after progressing on trastuzumab +/- pertuzumab. 
Nonetheless, additional therapies are clearly needed because only 20% are progression-free 
at one year. Because these tumors continue to overexpress HER2, there is great interest in 
other approaches for targeting HER2 such as “cancer vaccines” that activate anti-HER2 T 
cells and antibodies.  
We propose to institute our study in the first line setting with the goal of maximizing the 
immune and clinical response to first line therapy and HER2 vaccination.  
 
4.1.1.2 Immunotherapy targeting HER2 in breast and other tumors 
Immunotherapy for malignancies such as breast cancer with cancer vaccines is a promising 
strategy10. A number of vaccine studies for breast cancer have now been reported in which 
HER2 has served as the vaccine target and where clinical and immunologic activity has been 
reported11 (reviewed in reference 10). Immunization of breast cancer patients with therapeutic 
cancer vaccines increases the frequency of breast cancer antigen-specific T cells11. HER2 is 
a tumor antigen against which antigen-specific CD8+ cytolytic and CD4+ helper T cell 
responses have been activated in breast cancer patients by vaccines utilizing various peptide 
fragments of HER212-15. In a pilot clinical trial, we tested the safety of a vaccine consisting of 
autologous dendritic cells (DC) pulsed with the HER2 extracellular domain (ECD) E75 
peptide in patients with advanced HER2 overexpressing malignancies16. This was followed 
by a Phase I clinical trial of vaccines consisting of DC loaded with E75 and the HER2 
intracellular domain protein (ICD) in 7 breast cancer patients with no evidence of disease, but 
predicted to have more than a 30-50% risk of recurrence. Cardiac function was maintained in 
all patients17. Delayed-type hypersensitivity (DTH) reactions at the injection site occurred in 
6/7 patients and HER2 specificity was detected by cytokine flow cytometry or ELISPOT in 5 
patients. At more than 5 years of follow-up, 6/7 had detectable anti-ICD antibodies. One 

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patient experienced a resectable pulmonary recurrence at 4 years from their study 
immunizations. All patients are alive and disease-free at 4.6-6.7 years of follow-up.  
More recently, we performed a clinical trial in which we immunized women (n = 12) with 
metastatic, trastuzumab-refractory HER2-overexpressing breast cancer every 2 weeks with 
dHER2, a recombinant, truncated version of the HER2 protein including the extracellular 
domain (ECD) and part of the intracellular domain (ICD) along with the adjuvant AS15, a 
liposomal formulation containing QS21, MPL and CpG, while treating with concomitant 
lapatinib (1250mg/day)18. This regimen was well tolerated, having no cardiovascular adverse 
events or significant declines in LVEF.  HER2-specific antibody responses were detected in 
all patients following immunization. Importantly, several patients had received trastuzumab 
just prior to study initiation and still had detectable anti-HER2 antibody levels for several 
weeks after initiating the vaccinations. These data suggest that administering a HER2 
targeting vaccine during anti-HER2 therapy is well tolerated. This data is consistent with the 
findings of Disis et al, that vaccinations against HER2 during trastuzumab therapy are safe 
and immunogenic19. 
 
4.1.1.3 Rationale for assessing HER2-specific antibodies 
An emerging concept about how cancer targeting vaccines may work includes consideration 
of the impact of anti-HER2 antibodies on signaling pathways critical for breast cancer growth. 
We hypothesize that, in addition to the classical immunologic mechanisms (such as antibody 
dependent cytotoxicity and complement fixation), antibodies against receptors critical to 
tumor cell viability and growth could also have clinical benefits. This concept has been 
documented in clinical trials of HER2-based peptide vaccines. Montgomery et al reported that 
antibodies induced by HER2 peptide vaccination could affect HER2 signaling in in vitro 
assays20. This work was extended by our collaborator, Neil Spector, MD who demonstrated 
that antibodies induced by experimental HER2 vaccines (VIA) could synergize with a small 
molecule inhibitor of HER2 to induce apoptosis of HER2+ cell lines in vitro18. We observed 
the ability of the antibodies, identified in the serum of patients on our own clinical trial of 
ECD and ICD loaded dendritic cells, to bind to HER2 overexpressing cells lines (data not 
shown). Importantly, the serum from the immunized patients caused growth inhibition of 
HER2-overexpressing cell lines in vitro as shown in Figure 1 below. The magnitude of the 
effect varied, but in some patients, it was similar to the effect of trastuzumab (Herceptin). 
These data suggested we should perform additional studies to document the role of HER2-
specific antibodies on HER2-overexpressing breast cancer. 

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4.1.1.4 Rationale for targeting PD-1/PD-L1 signaling 
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades. Accumulating evidence shows a correlation 
between tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis in 
various malignancies. In particular, the presence of CD8+ T-cells and the ratio of CD8+ 
effector T-cells / FoxP3+ regulatory T-cells seems to correlate with improved prognosis and 
long-term survival in many solid tumors. 
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress 
immune control. The normal function of PD-1, expressed on the cell surface of activated T-
cells under healthy conditions, is to down-modulate unwanted or excessive immune 
responses, including autoimmune reactions. PD-1 (encoded by the gene Pdcd1) is an Ig 
superfamily member related to CD28 and CTLA-4 which has been shown to negatively 
regulate antigen receptor signaling upon engagement of its ligands (PD-L1 and/or PD-L2). 
The structure of murine PD-1 has been resolved. PD-1 and family members are type I 
transmembrane glycoproteins containing an Ig Variable-type (V-type) domain responsible for 
ligand binding and a cytoplasmic tail which is responsible for the binding of signaling 
molecules. The cytoplasmic tail of PD-1 contains 2 tyrosine-based signaling motifs, an 
immunoreceptor tyrosine-based inhibition motif (ITIM) and an immunoreceptor tyrosine-
based switch motif (ITSM). Following T-cell stimulation, PD-1 recruits the tyrosine 
phosphatases SHP-1 and SHP-2 to the ITSM motif within its cytoplasmic tail, leading to the 
dephosphorylation of effector molecules such as CD3ζ, PKCθ and ZAP70 which are involved 
in the CD3 T-cell signaling cascade. The mechanism by which PD-1 down modulates T-cell 
responses is similar to, but distinct from that of CTLA-4 as both molecules regulate an 
FIGURE 1. Proliferation of tumor cells expressing HER2 
is inhibited by serum from patients vaccinated with a 
HER2-pulsed DC vaccine: BT474 (HER2+; solid bars) 
or MDA-MB-231 (HER2-; open bars) tumor cells were 
cultured 
with 
patients’ 
serum 
(1:20 
dilution). 
Trastuzumab (1 µg/ml) was used as a positive control and 
normal donor serum as a negative control. An MTT assay 
was performed on day 6 by adding MTT and incubating 
for 3 h at 37°C followed by lysing cells with DMSO at 
37°C for 5 minutes. Proliferation (Absorbance at 562nm) 
was measured and ratios to negative control are shown. 

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overlapping set of signaling proteins. PD-1 was shown to be expressed on activated 
lymphocytes including peripheral CD4+ and CD8+ T-cells, B-cells, T regs and Natural Killer 
cells. Expression has also been shown during thymic development on CD4-CD8- (double 
negative) T-cells as well as subsets of macrophages and dendritic cells. The ligands for PD-1 
(PD-L1 and PD-L2) are constitutively expressed or can be induced in a variety of cell types, 
including non-hematopoietic tissues as well as in various tumors. Both ligands are type I 
transmembrane receptors containing both IgV- and IgC-like domains in the extracellular 
region and contain short cytoplasmic regions with no known signaling motifs. Binding of 
either PD-1 ligand to PD-1 inhibits T-cell activation triggered through the T-cell receptor. 
PD-L1 is expressed at low levels on various non-hematopoietic tissues, most notably on 
vascular endothelium, whereas PD-L2 protein is only detectably expressed on antigen-
presenting cells found in lymphoid tissue or chronic inflammatory environments. PD-L2 is 
thought to control immune T-cell activation in lymphoid organs, whereas PD-L1 serves to 
dampen unwarranted T-cell function in peripheral tissues. Although healthy organs express 
little (if any) PD-L1, a variety of cancers were demonstrated to express abundant levels of this 
T-cell inhibitor. PD-1 has been suggested to regulate tumor-specific T-cell expansion in 
subjects with melanoma (MEL).  This suggests that the PD-1/PD-L1 pathway plays a critical 
role in tumor immune evasion and should be considered as an attractive target for therapeutic 
intervention. 
Pembrolizumab is a potent and highly selective humanized monoclonal antibody (mAb) of 
the IgG4/kappa isotype designed to directly block the interaction between PD-1 and its 
ligands, PD-L1 and PD-L2. KeytrudaTM (pembrolizumab) is now approved in the US in 
melanoma, non-small cell lung cancer, head and neck squamous cell carcinoma, classical 
Hodgkin Lymphoma, urothelial carcinoma, microsatellite instability high cancer, and gastric 
cancer. Refer to the Investigator’s Brochure for Preclinical and Clinical data. 
4.1.2 Preclinical and Clinical Trial Data 
4.1.2.1 Development of recombinant vectors that induce HER2-specific 
antibodies (HER2-VIA).   
In order to further study the role of antibodies induced against HER2, we first sought to 
improve our ability to activate anti-HER2 immune responses. Because the proteins used in 
our dendritic cell (DC) vaccine study are no longer available, and because autologous DC 
vaccines are complicated to generate, we have been developing novel recombinant adenoviral 
vectors and alphavirus replicon particles expressing HER2 for our next studies. One 
disadvantage of adenovirus is the frequent development of neutralizing antibodies that limit 
repeated immunizations. One solution is to use alphavirus-like replicon particles (VRP)21, 
based on attenuated Venezuelan equine encephalitis (VEE) virus, which are especially 
attractive because they highly express heterologous proteins, target expression to dendritic 

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cells, and induce robust humoral and cellular immune responses to the vectored gene products
22-33. Foreign genes can be inserted in place of the VEE structural protein gene region in the 
cDNA plasmid, and an RNA transcript from such a plasmid, when introduced into cells, will 
replicate and express the heterologous genes as shown schematically in Figure 2. This 
self-amplifying replicon RNA will direct the synthesis of large amounts of the foreign gene 
product within the cell, typically reaching levels of 15-20% of total cell protein22. The replicon 
RNA can be packaged into VRP by supplying the structural protein genes of VEE in trans 
(Figure 3).
Figure 2. VEE Genome Organization and Replication 
Strategy
Figure 3. Replicon Particle Vaccine and Packaging 
System
Regarding their efficacy, VRP confer protection in animal models against a variety of diseases 
that require humoral and/or cellular responses for protection (including viral infections and 
breast cancer) 21-44. 
Regarding the safety of VRP, because the replicon RNA does not contain the structural genes 
for VEE, it is a single-cycle, propagation-defective RNA and replicates only within the cell into 
which it is introduced. The “split helper” system greatly reduces the chance of an intact genome 
being regenerated by RNA-RNA recombination and, as an independent and additional layer of 
safety, two attenuating mutations are incorporated in the glycoprotein helper. In addition, 
because alphaviruses and alphavirus replicons replicate in the cytoplasm without any DNA 
intermediate forms, the VRP vaccine vector system avoids the concerns of chromosomal 
integration. The safety of the VRP system has been studied with a variety of vaccines, at doses 
up to 1 x 109 IU, in many thousands of rodents (including immunocompromised mice) and over 
100 nonhuman primates (rhesus and cynomolgus macaques), with no evidence of acute or 
chronic illness. GLP Toxicology studies in rabbits using doses of at least 1 x 108 IU and up to 
1 x 109 IU of VRP, showed only local inflammatory reactions and local reactogenicity was 
nsP1-4
C-E3-E2-6K-E1
5’
Nonstructural proteins
3’
26S promoter
+ sense
+ se
3’
26S mRNA
Structural protein genes (virus) or foreign 
antigen (replicon)
Structural proteins (or 
foreign antigen)
5’  
5’– sense
3’ + sense
Structural p
Nonstructural protein genes

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negligible in rabbits after intramuscular injection. There was no evidence of systemic, 
hematopoietic, immune system or other organ toxicity related to the vaccine.   
In regards to the clinical safety and efficacy of VRP based vectors, we performed a phase I 
clinical trial of a novel alphavirus vector encoding the tumor-associated antigen CEA (VRP-
CEA(6D), AVx701) in metastatic cancer patients44. Cohorts of 3-6 patients with advanced 
CEA- expressing malignancies who had progressed on prior therapies were enrolled at 
successive dosage levels (4x107, 1x108, 4x108 IU) of VRP-CEA(6D) given as 4 IM injections 
every 3 weeks. Dose escalation occurred if DLT occurred in <33% of patients in a given 
dosage level. Following establishment of safety, an additional cohort of 14 patients received 
VRP-CEA(6D) at the maximum tolerated dose (MTD). Treg levels and CEA-specific T cell 
and antibody responses were measured before and after immunization. Patients had colorectal 
cancer (n=23), appendiceal (1), pancreas (n=1), lung (n=2), and breast (n=1) cancer, a 
performance status of 80-100%, and had failed a median of 4 prior chemotherapeutic 
regimens. DLT was not reached and the highest dose tested (4x108 IU) was determined to be 
the maximal feasible dose. Immunizations were well tolerated with 6 grade 3 events, all related 
to tumor progression, and no grade 4 events. Patients generally possessed higher blood 
CD4posCD25highFoxP3pos Treg cells compared to normal donors. CEA-specific T cell and 
antibody responses following VRP-CEA(6D) vaccination were observed regardless of 
patients' Treg level. There were two patients with stable disease and one with a CR of a small 
liver lesion. With a median follow-up of 13 months among surviving patients, 2 of 4 patients 
without immune response and 9 of 11 patients with immune response are alive. We concluded 
that activation of CEA-specific T cells and functional antibodies is possible using VRP-
CEA(6D) despite high Treg levels in this heavily pre-treated patient population.  In this study, 
the most consistent activation of T cell and antibody responses was reported at dose level of 
4 x 108 IU.   
Regarding construction of the vector for the current proposal, we have previously generated 
a replicon construct containing the full length human HER2. In a preclinical study using mice 
transgenic for the HER2-neu protein (in which mice develop spontaneous breast tumors that 
are uniformly lethal), a group of 10 mice were vaccinated 3 times with VRP expressing HER2 
prior to tumor development. Control animals vaccinated with VRP expressing the influenza 
HA antigen (as a control) were not protected and succumbed to lethal tumor burden between 
130-200 days. In contrast, mice vaccinated with the VRP expressing HER2 were completely 
protected. No tumor masses were detected in these animals for the entirety of the study (data 
not shown). 
In order to address potential concerns about oncogenicity of the full length HER2 protein, we 
generated a similar VRP construct consisting of the extracellular (ECD) and transmembrane 
(TM) domains of HER2. This VRP, AVX901 or VRP-HER2, was used to immunize C57BL/6 
mice and demonstrated activation of HER2 ECD-specific T cells and antibodies (Figure 4). 

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Figure 4. HER2 ECD and ICD-
specific T cell and antibody 
responses of C57BL/6 mice 
vaccinated with VRP-HER2 full 
length, VRP-HER2 ECD-
TM(VRP-HER2) and VRP-HER2 
ICD.  Mice received 2 
vaccinations of 1x10^7 particles 
into the bilateral footpads on d0 
and d21.  Splenocytes and serum 
were harvested from euthanized 
mice on d35 for analysis in 
Interferon-gamma ELISPOT and 
anti-HER2 ELISA assays.   
We demonstrated that the antibodies present in sera after immunization with VRP-HER2 
possessed complement dependent cytotoxicity (Figure 5), but also had antiproliferative 
activities (Figure 6) against a HER2-expressing cell line. 
 
Figure 5.  Vaccine induced antibodies from the serum 
of mice vaccinated with VRP-HER2 full length (FL) 
and VRP-HER2 ECD/TM (VRP-HER2) mediate 
complement dependent lysis of the HER2+ human 
breast tumor line BT474, but not a HER2 neg. control 
cell line (data not shown).  Serum was diluted 1:100 
and coincubated with target cells at 37°C for 1h; rabbit 
serum (source of complement) was added. After 2.5 h, 
cytotoxicity was measured using the CytoTox 96 Non 
Radioactive Cytotoxicity Assay.  Percent lysis is 
shown.  Errors bars represent standard deviation. 
 
Figure 6.  Vaccine induced antibodies (VIA) from the 
serum of mice vaccinated with VRP-HER2 full length 
(FL) and VRP-HER2 ECD/TM (VRP-HER2) inhibit 
proliferation of HER2+ human breast tumor line 
SKBR3, but not a HER2 neg. control cell line (data not 
shown). Cells were plated in 96-well plates and 
allowed to adhere overnight at 37oC. 1:20 VIA were 
added to the cultured cells and incubated for at 37°C 
for 72 hr. Cell proliferation was measured by MTT 
assay.  
We have now completed the enrollment on the Phase 1 clinical trial of VRP-HER2 in 22 
patients with advanced HER2+ disease. Patients enrolled on this trial primarily had metastatic 
0
200
400
600
800
ELISPOT (sfc/mill)
100
1000
10000
100000
ELISA (GMT)
ECD ELISPOT
ICD ELISPOT
ELISA
ECD ELISPOT
144
340
0
ICD ELISPOT
12
7
130
ELISA
18549
18549
131
HER2 full length
HER2 ECD/TM
HER2 ICD
0
5
10
15
20
25
30
control serum
VRP-HER2 FL
VRP-HER2
ECD/TM
VRP-HER2 ICD
Vaccine induced antibodies
Pecent lysis
0
20
40
60
80
100
120
140
Saline control
VRP-HER2 FL
VRP-HER2
ECD/TM
VRP-HER2
ICD
Vaccine induced antibodies
Percent proliferation compared to 
untreated cells

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HER2+ breast cancer and were heavily pretreated, with an average of 4.5 prior lines of 
therapy. Vaccination with VRP-HER2 was well tolerated in both cohorts. There were no dose-
limiting toxicities in either cohort. The majority of the adverse events (AEs) were either Grade 
1 or 2. There were no grade 4 or greater AEs in either cohort. There were four Grade 3 AEs 
recorded consisting of hyponatremia and increased LFTs, though these were felt unrelated to 
VRP-HER2 vaccination. There was no decrease in cardiac ejection fractions of any enrolled 
patients after completing the VRP-HER2 vaccination course. Initial immune analysis of 
cohort 1, T cell responses specific for HER2 were detected by ELISPOT. Also, cohort 1 
demonstrated that the VRP-HER2 vaccine induced anti-HER2 antibodies that were detected 
by ELISA.  In cohort 1 (n=4), the median PFS was 1.9 months and the median OS has not 
been reached after a median of 35 months of follow-up. In cohort 2 (n=18), there has been 
one partial response (PR) and there are seven patients with continued stable disease (SD) at 
time of manuscript submission. The median PFS for cohort 2 is 2.0 months and the median 
OS has not been reached after a median follow-up of 6.5 months. In cohort 2, concurrent anti-
HER2 
therapies 
included: 
TDM-1 
(6/18), 
trastuzumab/ 
pertuzumab 
(5/18), 
trastuzumab/lapatinib (3/18), single agent trastuzumab (2/18) and single agent lapatinib 
(1/18). 
4.2 
Rationale 
4.2.1 Rationale for the Trial and Selected Subject Population 
HER2 expressing malignancies, while initially responsive to trastuzumab, pertuzumab, and 
TD-M1, eventually progress; yet the HER2 protein continues to be expressed on these tumors 
suggesting they may be targets for immune therapies. Indeed, It has been demonstrated that a 
higher percentage of tumor infiltrating lymphocytes (TILs) is associated with better tumor 
response to trastuzumab in both the adjuvant1 and neoadjuvant setting in HER2+ breast 
cancers.  
One strategy for increasing the T cell lymphocyte response to tumors is to use vaccines 
capable of activating T cells against tumor associated antigens such as HER2. We have had 
extensive experience developing vaccines to activate HER2-specific immune responses in 
patients with HER2 overexpressing malignancies. We vaccinated patients with HER2 
overexpressing breast cancer with dendritic cells loaded with HER2 protein or peptide2 or 
vaccines based on HER2 protein plus adjuvants3 and reported the induction of anti-HER2-
specific antibodies and T cell responses. In an attempt to develop a vaccine capable of 
inducing more effective T and B cell responses, we generated alphaviruses modified to 
express tumor antigens such as HER2. These vectors have tropism for dendritic cells and 
direct high expression of the HER2 antigen within dendritic cells. In preclinical models, we 
observed that a vaccine based on an attenuated Venezuelan Equine Encephalitis alphavirus 
encoding HER2, could induce both cellular and humoral immune responses capable of 
controlling HER2 expressing malignancies.  We completed phase I dose escalation testing of 

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this vaccine called VRP(HuHER2-ECD+Tm) encoding the extracellular (ECD) and 
transmembrane (TM) domains of HER2 (subsequently referred to as VRP-HER2) alone and 
in conjunction with HER2 targeted therapies (mainly trastuzumab) to patients with locally 
advanced or metastatic HER2+ cancer. Our data from this trial, presented at the 2015 annual 
ASCO meeting4, demonstrates the induction of HER2 specific T cell responses and detectable 
anti-HER2 antibodies in the serum. Additionally, the magnitude of immune response was not 
impaired by prior anti-HER2 therapy. Clinically, the VRP-HER2 vaccine was well tolerated 
with no dose-limiting toxicities related to the vaccine. Our clinical follow-up to date of greater 
than 26 months in this heavily pre-treated metastatic population has still not met median OS4. 
As the results from the CLEOPATRA study have established that trastuzumab + pertuzumab 
based therapy as the standard of care for first line therapy for metastatic HER2+ disease, 
demonstrating a PFS of 18.5 months5. Based on these results we plan to open a Phase II study 
of VRP-HER2 vaccine given concurrently with pembrolizumab in patients receiving first line 
trastuzumab and pertuzumab for metastatic HER2+ breast cancer. 
Previous biomarker studies have shown that PD-1+ TILs are associated with poor prognosis 
in HER2 positive breast cancer6. In correlative preclinical studies, higher T cell expression of 
the checkpoint molecule PD-1 (programmed death-1), was associated with greater 
trastuzumab benefit. Combining trastuzumab with anti-PD-1 and anti-PD-L1 antibodies 
showed greater tumor regression in mouse models of HER2+ mammary tumors7. It has also 
recently been demonstrated in breast cancer bearing mice that a combination regimen with an 
anti-PD-1 antibody and a multipeptide vaccine (derived from breast cancer antigens, 
including neu (HER2)) prolonged the vaccine-induced progression-free survival period and 
increased the median survival by nearly three-fold when compared with vaccine alone. This 
research also demonstrated that PD-1 blockade enhances breast cancer vaccine efficacy by 
altering both CD8 T cell and DC components of the tumor microenvironment8. In our own 
(unpublished) preclinical data, vaccination with a viral vector against a HER family molecule 
followed by anti-PD-1 antibody led to tumor regression and sustained control. 
4.2.2 Rationale for Dose Selection/Regimen/Modification  
In our previously discussed Phase I clinical trial of the novel alphavirus vector encoding the 
tumor-associated antigen CEA (VRP-CEA(6D), AVx701) in metastatic cancer patients (44). 
DLT was not reached and the highest dose tested (4x108 IU) was determined to be the maximal 
feasible dose. Immunizations were well tolerated with 6 grade 3 events, all related to tumor 
progression, and no grade 4 events. Patients generally possessed higher blood 
CD4posCD25highFoxP3pos Treg cells compared to normal donors. CEA-specific T cell and 
antibody responses following VRP-CEA(6D) vaccination were observed regardless of 
patients' Treg level. There were two patients with stable disease and one with a CR of a small 
liver lesion. With a median follow-up of 13 months among surviving patients, 2 of 4 patients 
without immune response and 9 of 11 patients with immune response are alive. We concluded 

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that activation of CEA-specific T cells and functional antibodies is possible using VRP-
CEA(6D) despite high Treg levels in this heavily pre-treated patient population.  Because in 
this previous study, the most consistent activation of T cell and antibody responses was 
reported at dose level of 4 x 108 IU, we plan to use the same dose in this current study.   
In our recently completed study of VRP-HER2 in advanced HER2+ breast cancer patients, 
vaccination with VRP-HER2 4 x 108 IU was well tolerated by all enrolled patients. There 
were no dose-limiting toxicities in either cohort (cohort 1: VRP-HER2 vaccine alone, cohort 
2L VRP-HER2 vaccine + anti-HER2 therapy) in this study. The majority of the adverse events 
(AEs) were either Grade 1 or 2. There were no grade 4 or greater AEs in either cohort. There 
were four Grade 3 AEs recorded consisting of hyponatremia and increased LFTs, though these 
were felt unrelated to VRP-HER2 treatment. There was no decrease in cardiac ejection 
fractions of any enrolled patients after completing the VRP-HER2 vaccination course. In 
cohort 1, T cell responses specific for HER2 were detected by ELISPOT. Also in cohort 1, 
vaccine induced anti-HER2 antibodies were detected by ELISA.  In cohort 1 (n=4), the 
median PFS was 1.9 months and the median OS has not been reached after a median of 35 
months of follow-up. In cohort 2 (n=18), there has been one partial response (PR) and there 
are seven patients with continued stable disease (SD) at last data collection. The median PFS 
for cohort 2 is 2.0 months and the median OS has not been reached after a median follow-up 
of 6.5 months. In cohort 2, concurrent anti-HER2 therapy was well tolerated and concurrent 
anti-HER2 therapies included trastuzumab/ pertuzumab in five of the enrolled patients. 
 
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.   
 

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A population pharmacokinetic analysis has been performed using serum concentration time 
data from 476 patients. Within the resulting population PK model, clearance and volume 
parameters of MK-3475 were found to be dependent on body weight. The relationship 
between clearance and body weight, with an allometric exponent of 0.59, is within the range 
observed for other antibodies and would support both body weight normalized dosing or a 
fixed dose across all body weights. MK-3475 has been found to have a wide therapeutic range 
based on the melanoma indication. The differences in exposure for a 200 mg fixed dose 
regimen relative to a 2 mg/kg Q3W body weight based regimen are anticipated to remain well 
within the established exposure margins of 0.5 – 5.0 for MK-3475 in the melanoma indication. 
The exposure margins are based on the notion of similar efficacy and safety in melanoma at 
10 mg/kg Q3W vs. the proposed dose regimen of 2 mg/kg Q3W (i.e. 5-fold higher dose and 
exposure). The population PK evaluation revealed that there was no significant impact of 
tumor burden on exposure. In addition, exposure was similar between the NSCLC and 
melanoma indications. Therefore, there are no anticipated changes in exposure between 
different indication settings. 
 
The rationale for further exploration of 2 mg/kg and comparable doses of pembrolizumab in 
solid tumors is based on: 1) similar efficacy and safety of pembrolizumab when dosed at either 
2 mg/kg or 10 mg/kg Q3W in melanoma patients, 2) the flat exposure-response relationships 
of pembrolizumab for both efficacy and safety in the dose ranges of 2 mg/kg Q3W to 10 
mg/kg Q3W, 3) the lack of effect of tumor burden or indication on distribution behavior of 
pembrolizumab (as assessed by the population PK model) and 4) the assumption that the 
dynamics of pembrolizumab target engagement will not vary meaningfully with tumor type. 
The choice of the 200 mg Q3W as an appropriate dose for the switch to fixed dosing is based 
on simulations performed using the population PK model of pembrolizumab showing that the 
fixed dose of 200 mg every 3 weeks will provide exposures that 1) are optimally consistent 
with those obtained with the 2 mg/kg dose every 3 weeks, 2) will maintain individual patient 
exposures in the exposure range established in melanoma as associated with maximal efficacy 
response and 3) will maintain individual patients exposure in the exposure range established 
in melanoma that are well tolerated and safe.  
A fixed dose regimen will simplify the dosing regimen to be more convenient for physicians 
and to reduce potential for dosing errors. A fixed dosing scheme will also reduce complexity 
in the logistical chain at treatment facilities and reduce wastage. 
We therefore hypothesize that HER2 specific T cell responses and anti-tumor immunity 
induced with HER2 vaccination will be augmented by concurrent anti-PD-1 antibody therapy 
and will lead to greater clinical efficacy. We propose a randomized clinical trial with a safety 
run in to evaluate the immunologic and clinical activity of concurrent VRP-HER2 
vaccination with pembrolizumab administration to patients with HER2-overexpressing 

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breast cancer. As patients with advanced HER2+ tumors typically remain on trastuzumab + 
pertuzumab therapy, this study will enroll patients who have been stable on trastuzumab + 
pertuzumab and plan to continue this therapy during the trial. 
4.2.3 Rationale for Endpoints 
4.2.3.1 Efficacy Endpoints 
(1) Primary Objective: To determine whether pembrolizumab increases the tumor 
infiltrating (T cell) and peripheral blood (T cell and antibody) immune response to the 
VRP-HER2 vaccine.  
Hypothesis: We hypothesize that HER2 specific T cell responses and anti-tumor 
immunity induced with HER2 vaccination will be augmented by concurrent anti-PD-1 
antibody therapy. 
(2) Secondary Objective: To determine whether the administration of pembrolizumab is 
safe in patients with recurrent or metastatic HER2+ cancers who are receiving the anti-
HER2 vaccine VRP-HER2. 
 Hypothesis: We hypothesize that concurrent immunization with HER2-targeting 
vaccines and anti-PD-1 antibody therapy will be well tolerated.    
(3) Objective: To collect preliminary data on the clinical response rates to this concurrent 
therapy of agents in subjects with assessable disease based on RECIST 1.1 criteria. 
Hypothesis: We hypothesize that the induction of enhanced HER2-specific T cell 
responses from concurrent HER2 vaccination and anti-PD-1 antibody therapy will lead 
to greater clinical efficacy.    
 
4.2.3.2 Biomarker Research 
Primary Translational Objectives: 
(1) To determine whether concurrent anti-PD1 therapy (pembrolizumab) and VRP-HER2 
vaccination increases circulating and tumor infiltrating, HER2 specific T cells. 
(2) To determine whether anti-PD1 therapy (pembrolizumab) increases the percent of TIL 
density (intra-tumoral and at the advancing tumor edge) between pre- and post-
pembrolizumab.  

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Secondary Translational Objectives: 
(1) To determine whether concurrent anti-PD1 therapy (pembrolizumab) and VRP-HER2   
vaccination increases the evenness and richness of T-cell receptor clonality between 
Pre-Pembrolizumab and post-Pembrolizumab. 
(2) To determine whether concurrent anti-PD1 therapy (pembrolizumab) and VRP-HER2 
vaccination results in generalized activation of intra-tumoral CD8+ and Th1 T cell 
responses in enrolled patients 
Translational Hypothesis: 
We hypothesize that: 
(1) Administration of concurrent anti-PD1 therapy (pembrolizumab) and VRP-HER2 
vaccination will result in activation of a more potent HER2-specific T cell response in 
peripheral blood and in tumor infiltrating T cells than vaccination alone. 
(2) Administration of concurrent anti-PD1 therapy (pembrolizumab) and VRP-HER2 
vaccination will enhance the antitumor activity of vaccine activated HER2-specific T 
cells.  
1. ELISPOT: Peripheral blood for immune analysis will be drawn at screening/baseline, 
cycle 1 Day 1 (C1D1), C3D1, C5D1, week 24, and 6 months post-study completion. The 
PBMC will then be cryopreserved, and batched for subsequent immune analysis including 
ELISPOT and/or multi-parameter flow cytometric analysis. For planned ELISPOT 
analysis, PBMCs will be stimulated with peptide pools of the HER2 antigen (ICD and 
ECD peptides) as well as positive and negative controls. In the ELISPOT assay, a T-cell 
response (against HER2) will be considered positive if the mean number of spots in six 
wells with antigen exceeds the number of spots in six control wells by a magnitude of 10 
and the difference between single values of the six wells containing antigen and the six 
control wells is statistically significant at a level of p=0.05 by the t-test. In this trial of 
HER2-positive (either Stage IV or locally recurrent Stage III) invasive breast cancer 
patients, anti-HER2 INFg ELISPOT responses in Arm 1 patients receiving the VRP-
HER2 vaccine, trastuzumab, pertuzumab, and pembrolizumab will be compared with the 
anti-HER2 INFg ELISPOT responses in Arm 2 patients who are receiving 
Pembrolizumab, trastuzumab, and pertuzumab but not VRP-HER2 vaccine. Post-study 
analysis will evaluate for changes in the HER2-specific T cell responses Selected from 
the post-immunization time point that yields the largest magnitude of HER2 specific T 
cells and compare this peak level of HER2 specific T cells with the baseline magnitude of 
HER2 specific T cells. Univariate analysis will compared the difference in this maximal 
difference anti-HER2 INFg ELISPOT response between the Arm 1 patients and the Arm 

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2 patients. Differences between study arms will be evaluated by Student t-test with 
significant difference defined with a p-value ≤ 0.05. Exploratory analyses will evaluate 
the association between the induction of HER2 specific T cell responses and the clinical 
endpoints of progression free survival and overall survival. 
 
2. Serum will be collected at screening/baseline, C1D1, C3D1, C5D1, week 24, and 6 
months post-study completion. Collected serum will be analyzed for HER2-specific 
antibodies and used for immune studies. Antibody responses to HER2 will be measured 
by ELISA. Absorbance will be read at 450 nM, and control signal will be subtracted from 
protein signal. HER2 antibody titer will be defined as the serum dilution that has an 
absorbance that is twice the negative control value for the same dilution. Positive results 
may be confirmed by Western blot analysis and additional immune assays. The presence 
of anti-HER2 antibody responses detected by ELISA in Arm 1 patients receiving VRP-
HER2 vaccine, trastuzumab, pertuzumab, and pembrolizumab will be compared with the 
anti-HER2 antibody responses in Arm 2 patients receiving Pembrolizumab, trastuzumab, 
and pertuzumab but not VRP-HER2 vaccine. It is recognized that Trastuzumab binds to 
domain IV on the HER2 molecule, while Pertuzumab binds to domain II. As such, for our 
ELISA testing we will perform ELISA evaluation against multiple peptides sequences 
derived from previously recognized HER2 epitopes that will include but will not be 
limited to HER2 domains II and IV. Post-study analysis will compare the change in anti-
HER2 antibody responses from baseline, through study treatment, and post-study 
treatment in each arm. Univariate analysis will compare the difference in anti-HER2 
antibody responses at each time point between Arm 1 patients and the Arm 2 patients. 
Differences between study arms will be evaluated by Student t-test with significance 
defined as a p-value ≤ 0.05. Exploratory analyses will evaluate the association between 
the anti-HER2 antibody responses and clinical survival endpoints of PFS and OS.   
 
3. T cell receptor sequencing will be performed on the tumor tissue collected pre- and post- 
trial therapy. TCR sequencing will also be performed on blood collected prior to initiating 
pembrolizumab treatment and at C5D1 and week 24 of study and out to 6 months post-
study to assess for changes in clonality of the T cell response. In this TCR analysis, we 
will evaluate only the AA sequences for the CDR3 regions of each TCR Beta chain, as 
our prior experience suggests that small DNA sequencing errors can lead to challenges in 
DNA data alignment. To evaluate TCR clonality we will utilize Shannon entropy for each 
sample. Shannon entropy will be calculated on the clonal abundance of all productive 
TCR sequences in the dataset. Shannon entropy will then be normalized to the range [0–
1] by dividing Shannon entropy by the logarithm of the number of unique productive TCR 
sequences in the dataset. This normalized entropy value will then be inverted (1 − 
normalized entropy) to produce our clonality metric. In addition, as this is a fairly 
homogenous population we will also evaluate for the presence of induced unique 
consensus T cell populations resulting from this therapy identified from very high-level 

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summaries of clone populations in both treatment arms, and compare differences in these 
T cell populations between Arm 1 and Arm 2. In our interrogation of these dominant TCR 
clones we will specifically evaluate for changes in the TCR clones that make up the top 
5% most common clones. As an exploratory evaluation to identify HER2 specific TCR 
we will select the patients with the highest HER2 ELIspot response to VRP-HER2 
vaccination. In these patients, cytokine flow cytometry will be used to separate HER2 
responsive T-cells. We will then collect these HER2 responsive T cells and perform TCR 
sequencing. The TCR sequencing will be performed in conjunction with Adaptive 
Biotech. The second correlative analysis evaluating for HER2 specific T-cells was not 
included in the original proposal and budget and as such we will be pursuing additional 
funding mechanisms to support this work. 
 
4. Tumor biopsies collected pre- and post- trial therapy will be analyzed by IHC for PD-1, 
PD-L1, and PD-L2 expression as well as changes in expression between these time points. 
CD3+ TIL infiltration of the biopsied tumors will be assessed at these time points as well 
evaluating for changes in TIL content with vaccination with or without pembrolizumab. 
Analysis will be performed for changes in Th1, Th2, and Treg immune response through 
evaluation of changes in CD4+, CD8+, and FOXP3+ T cell subtypes. Exploratory 
analyses will evaluate the differences in TIL content between study arms to assess the 
influence of pembrolizumab on the overall TIL populations.  
 
5. Tumor Biopsies collected pre- and post- trial therapy will also be processed and evaluated 
by flow cytometry for differences and changes in T cell content and T cell subtype. 
Specifically, we will evaluate the differences in the presence of INFg+T-bet+CD4+ T 
cells and INFg+GATA+CD4+ T cells, T cell subtypes recently recognized to influence 
both the induced HER2- specific cellular immunity and clinical outcomes. In additional, 
intracellular cytokine staining will be performed to evaluate for changes in Type 1 
immunity (INFg, TNFa, and IL-2) versus Type 2 immunity (IL-4, IL-6, and IL-10) in each 
study arm. Changes in the tumor content of T-bet+ and GATA+ CD4+ T cells between 
the pre- and post- trial therapy time points will be evaluated in each arm and how the 
presence or absence of pembrolizumab influences this important population. Exploratory 
analyses will evaluate for a relationship between difference in the T-bet+ and GATA+ 
CD4+ T cell populations between the study arms and PFS and OS differences. In 
additional we will evaluate for the presence of immunosuppressive cell popualtions 
including regulatory T cells (Treg) and myeloid derived suppressor cells (MDSCs). We 
will identify Tregs based on CD4+, FOXP3+, CD25+, CD127- staining and identify 
MDSCs with staining for HLA-DR+, CD11b+ and CD33+. Exploratory analysis will 
evaluate the correlation between the tumor content of these immunosuppressive immune 
cell populations and the clinical outcomes observed in each of the arms of this study. 
These studies were not included in the original proposal and budget and as such we will 
be pursuing additional funding mechanisms to support the work detailed in #5. 

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6. Gene-expression analysis of RNA isolated from tumor biopsies collected at pre- and post-
trial therapy will be performed by real-time PCR for changes in the expression of the 
following: Granzyme A, Granzyme B, Perforin, EOMES, CXCL9, CXCL10, CD8A, 
CD4, FOXP3, ICOS, PD-1, PD-L1, PD-L2, and CTLA4. Correlation of these cytokines 
and surface proteins and induction of HER2-specific immune response in this trial will be 
exploratory. We have previously created a clinical database for the collection and 
documentation of prior lines of systemic therapy as well as the duration of such therapy. 
We will enter the enrolled patients prior lines of therapy into this database for analysis 
with planned exome sequencing results. Next generation sequencing will be performed by 
the Duke Sequencing Core. These studies were not included in the now approved budget 
and we will pursue additional funding mechanisms to support this work.  
 
7. Tumor biopsies collected pre- trial therapy will processed for Next-generation sequencing 
in order to evaluate for the presence of neoantigens. The presence and amount of 
neoantigens in tumor biopsies will be compared between both study arms to evaluate for 
equal distribution. Exploratory analyses will then evaluate the relationship between the 
presence of neoantigens and clinical response as measured by RECIST criteria to 
pembrolizumab in this study. These studies were not included in the now approved budget 
and we will pursue additional funding mechanisms to support this work.  
 
8. CTCs will be collected from peripheral blood collections at screening/baseline, C1D1, 
C3D1, C5D1, week 24, and 6 months post-study completion and analyzed for changes in 
CTC number correlating with treatment response by study arm. In an exploratory analysis 
CTCs will also be evaluated for surface expression of PD-L1, PD-L2, and CTLA-4 and 
whether changes in these surface proteins predict response to the pembrolizumab with or 
without VRP-HER2 vaccination as measured by RECIST criteria on radiographic 
imaging. These studies were not included in the now approved budget and we will pursue 
additional funding mechanisms to support this work.  
 
9. cfDNA will be collected from peripheral blood collections at screening/baseline, week 24, 
and 6 months post-study completion and analyzed in all patients for presence of known 
HER2 mutations. In additional, at these time points in patients who also have HR+ disease, 
cfDNA will be evaluated for the presence of ESR1 mutations. Exploratory analysis will 
evaluate if the presence of these mutations significantly affects the clinical response to 
pembrolizumab with or without VRP-HER2 vaccination as measured by RECIST criteria 
on radiographic imaging. These studies were not included in the now approved budget 
and we will pursue additional funding mechanisms to support this work.  
 
10. cfRNA will be collected from peripheral blood collections at screening/baseline, week 24, 
and 6 months post-study completion and analyzed from the peripheral blood of all study 

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patients and analyzed for the presence of Bmi-1 as a marker of poor prognosis in breast 
cancer. In addition from the patients with HER2+HR+ breast cancer the presence of cyclin 
D1 as a marker of endocrine resistance in HR+ patients will be evaluated for. Exploratory 
analysis will evaluate if the presence of Bmi-1 and cycle D1 affect the clinical response 
to VRP-HER2 vaccination with or without pembrolizumab as measured by RECIST 
criteria on radiographic imaging. These studies were not included in the now approved 
budget and we will pursue additional funding mechanisms to support this work. 
 
11. Multiplex array analysis using an “immunosignature” antibody based assay will be 
performed on a limited number of pre-therapy samples from this randomized trial. Serum 
obtained at baseline screening will be applied to this “immunosignature” array of 10,000 
peptides for the detection of each patient’s individual immunosignature. We will perform 
an exploratory analysis to evaluate if there is a predictive immunosignature for clinical 
response to the VRP-HER2 vaccine +/- pembrolizumab as determined by RECIST 
criteria. These studies were not included in the original proposal and budget and as such 
we will be pursuing additional funding mechanisms to support the work detailed in #11. 
 
12. Multicolor IHC analysis will be performed by a collaborator, who has developed this 
assay. This spatial image analysis approach will be performed on a limited number of pre- 
and post-therapy tumor tissue samples and can be performed on both frozen and FFPE 
tissues. For the purposes of this study, paired tumor tissue specimen slides from pre- and 
post-therapy tumor biopsies will be collected, assigned a study number, and then 
deidentified.  The deidentified paired slides will be sent to our collaborator for formal 
analysis by 10-color IHC. This analysis will evaluate the immunologic changes in three 
dimensions in the tumor microenvironment between the pre- and post-therapy samples. In 
an exploratory analysis, we will evaluate if specific immunologic changes in the tumor 
microenvironment correlate with clinical response in the selected patients, as determined 
by RECIST criteria. These studies were not included in the original proposal and budget 
and as such we will be pursuing additional funding mechanisms to support the work 
detailed in #12. 
 
5.0 METHODOLOGY 
5.1 
Entry Criteria 
5.1.1 Diagnosis/Condition for Entry into the Trial 
Histologically-confirmed breast cancer that is metastatic or locally recurrent (7th Edition of 
the AJCC TNM System) with HER2/neu overexpression by immunohistochemistry (2+,3+) 
or FISH+ per ASCO CAP guidelines and receiving trastuzumab plus pertuzumab (determined 

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by their physician). Patients who are hormone receptor (ER, PR) positive or negative are 
permitted. 
 
5.1.2 Subject Inclusion Criteria 
In order to be eligible for participation in this trial, the subject must: 
1. Have undergone treatment with trastuzumab plus pertuzumab (as selected by their 
attending physician) for at least 3 weeks prior to initiation on this study. 
2. Be willing and able to provide written informed consent/assent for the trial. Informed 
consent will be obtained from the patient prior to performing any study-related 
procedures, including screening visits. Available CT scans and bone scans performed 
as standard of care prior to signing consent can be used to fulfill eligibility 
requirements if they were performed within 4 weeks of the first dose of study drug(s). 
Available MUGA, Echocardiogram, and EKG performed as standard of care prior to 
signing consent can be used to fulfill eligibility requirements if they were performed 
within 8 weeks of the first dose of study drug(s).  
3. Resolution of all toxic side effects of prior chemotherapy, radiotherapy or surgical 
procedures to NCI CTCAE (version 5.0) Grade ≤ 1 (with the exception of grade 2 
alopecia, grade 2 neuropathy and grade 2 fatigue); 
4. Be ≥ 18 years of age on day of signing informed consent. 
5. Be willing to provide tissue from a newly obtained core or excisional biopsy of a tumor 
lesion.  Newly-obtained is defined as a specimen obtained up to 6 weeks (42 days) 
prior to initiation of treatment on Day 1.  Subjects for whom newly-obtained samples 
cannot be provided (e.g. inaccessible or subject safety concern) may submit an 
archived specimen only upon agreement from the Sponsor. 
6. Have a performance status of 0 or 1 on the ECOG Performance Scale. 
7. Normal cardiac function defined as either a MUGA or ECHO with LVEF in normal 
institutional range (MUGA 50%; ECHO 55%) 
8. Demonstrate adequate organ function as defined in Table 1, all screening labs should 
be performed within 7 days of treatment initiation.   
 
 

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Table 1  Adequate Organ Function Laboratory Values 
System 
Laboratory Value 
Hematological 
 
Absolute neutrophil count (ANC) 
≥1,500 /mcL 
Platelets 
≥100,000 / mcL 
Hemoglobin 
≥9 g/dL or ≥5.6 mmol/L without transfusion or EPO dependency 
(within 7 days of assessment) 
Renal 
 
Serum creatinine OR 
Measured 
or 
calculateda 
creatinine 
clearance 
(GFR can also be used in place of creatinine 
or CrCl) 
≤1.5 X upper limit of normal (ULN) OR 
 
≥60 mL/min for subject with creatinine levels > 1.5 X institutional 
ULN 
Hepatic 
 
Serum total bilirubin 
≤ 1.5 X ULN OR 
 
Direct bilirubin ≤ ULN for subjects with total bilirubin levels > 
1.5 ULN 
AST (SGOT) and ALT (SGPT) 
≤ 2.5 X ULN  OR 
≤ 5 X ULN for subjects with liver metastases 
Albumin 
>2.5 mg/dL 
Coagulation 
International Normalized Ratio (INR) or 
Prothrombin Time (PT) 
 
Activated Partial Thromboplastin Time 
(aPTT) 
≤1.5 X ULN unless subject is receiving anticoagulant therapy 
as long as PT or PTT is within therapeutic range of intended use 
of anticoagulants 
≤1.5 X ULN unless subject is receiving anticoagulant therapy 
as long as PT or PTT is within therapeutic range of intended use 
of anticoagulants 
aCreatinine clearance should be calculated per institutional standard. 
 
9. Female subject of childbearing potential should have a negative urine or serum 
pregnancy within 72 hours prior to receiving the first dose of study medication.  If the 
urine test is positive or cannot be confirmed as negative, a serum pregnancy test will 
be required.   
10. Female subjects of childbearing potential (Section 5.6.2) must be willing to use an 
adequate method of contraception as outlined in Section 5.6.2 – Contraception,  for 
the course of the study through 120 days after the last dose of study medication. 
Note: Abstinence is acceptable if this is the usual lifestyle and preferred contraception for 
the subject. 
11. Male subjects of childbearing potential (Section 5.6.2) must agree to use an adequate 
method of contraception as outlined in Section 5.6.2- Contraception, starting with the 
first dose of study therapy through 120 days after the last dose of study therapy. 

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Note: Abstinence is acceptable if this is the usual lifestyle and preferred contraception for 
the subject. 
12. Ability to return to Duke University Medical Center for adequate follow-up as 
required by this protocol.  
 
5.1.3 Subject Exclusion Criteria 
The subject must be excluded from participating in the trial if any of the following criteria are 
met: 
1. Patients in this study, may not receive cytotoxic chemotherapy targeted small 
molecule therapy, or radiation therapy in the 3 weeks before the first infusion of 
Pembrolizumab, during the injection period for VRP-HER2 and infusion period for 
Pembrolizumab or for at least 2 weeks after booster immunization with VRP-HER2 
(Arm 1) or who has not recovered (i.e., ≤ Grade 1 or at baseline) from adverse events 
due to a previously administered agent. 
- 
Note:  Subjects with ≤ Grade 2 neuropathy are an exception to this criterion 
and may qualify for the study. 
- 
Note:  If subject received major surgery, they must have recovered adequately 
from the toxicity and/or complications from the intervention prior to starting 
therapy.   
2. Patients may have received prior radiation including for brain metastases. 
3. Is currently participating and receiving study therapy or has participated in a study of 
an investigational agent and received study therapy or used an investigational device 
within 4 weeks of the first dose of treatment. 
4. 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. Prior history of autoimmune thyroiditis or vitiligo is permitted. 
5. Has a known history of active TB   (Bacillus Tuberculosis) 
6. Hypersensitivity to pembrolizumab or any of its excipients. 

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7. Has had a prior anti-cancer monoclonal antibody (mAb) within 3 weeks prior to study 
Day 1 or who has not recovered (i.e., ≤ Grade 1 or at baseline) from adverse events 
due to agents administered more than 3 weeks earlier.  Exceptions include 
trastuzumab, pertuzumab.  
8. Has a known additional malignancy that is progressing or requires active treatment.  
Exceptions include basal cell carcinoma of the skin or squamous cell carcinoma of the 
skin that has undergone potentially curative therapy or in situ cervical cancer. 
9. Has known active CNS metastases and/or carcinomatous meningitis. Participants with 
previously treated brain metastases may participate provided they are radiologically 
stable, i.e. without evidence of progression for at least 4 weeks by repeat imaging (note 
that the repeat imaging should be performed during study screening), clinically stable 
and without requirements of steroid treatment for at least 14 days prior to the first dose 
of study treatment.   
10. 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.  
11. Has history of (non-infectious) pneumonitis that required steroids or active, non-
infectious pneumonitis. 
12. Has an active infection requiring systemic therapy or systemic use of antimicrobials 
within 72 hours prior to the first study treatment 
13. 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.   
14. Has known psychiatric or substance abuse disorders that would interfere with 
cooperation with the requirements of the trial. 
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 received prior therapy with an anti-PD-1, anti-PD-L1, or anti-PD-L2 agent. 

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17. Hypersensitivity to pembrolizumab or any of its excipients. 
 
18. Has a known history of Human Immunodeficiency Virus (HIV) (HIV 1/2 antibodies). 
19. Has known active Hepatitis B (e.g., HBsAg reactive) or Hepatitis C (e.g., HCV RNA 
[qualitative] is detected). 
20. Has received a live vaccine within 30 days of planned start of study therapy. 
Note:  Seasonal influenza vaccines for injection are generally inactivated flu vaccines 
and are allowed; however intranasal influenza vaccines (e.g., Flu-Mist®) are live 
attenuated vaccines, and are not allowed. 
5.2 
Trial Treatments 
The treatment to be used in this trial is outlined below: 
Table 2. Trial Treatment – Safety Arm, Arm A, Arm B, and ARM C 
Drug 
Dose/Potency 
Dose 
Frequen
cy 
Route of 
Administration 
Regimen/Treat-
ment Period 
Use 
Safety Arm  
Pembrolizumab 
200 mg 
Q3W 
IV infusion 
Day 1 of each 3 
week cycle x 5 
cycles 
Experimental 
VRP-HER2 
4 x 108 IU 
Q2W 
IM injection 
Cycle 1: Day 1 
and Day 15  
Cycle 2: Day 8 
Booster –  
Cycle 5, Day 1  
Experimental 
Arm A 
 
 
 
 
 
VRP-HER2 
4 x 108 IU 
Q2W 
IM injection 
Cycle 1: Day 1 
and Day 15  
Cycle 2: Day 8 
Booster –  
Cycle 5, Day 1  
Experimental 
Arm B 
Pembrolizumab 
200 mg 
Q3W 
IV infusion 
Day 1 of each 3 
week cycle x 5 
cycles 
Experimental 

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Drug 
Dose/Potency 
Dose 
Frequen
cy 
Route of 
Administration 
Regimen/Treat-
ment Period 
Use 
Arm C 
Pembrolizumab 
200 mg 
Q3W 
IV infusion 
Day 1 of each 3 
week cycle x 5 
cycles 
Experimental 
VRP-HER2 
4 x 108 IU 
Q2W 
IM injection 
Cycle 1: Day 1 
and Day 15  
Cycle 2: Day 8 
Booster –  
Cycle 5, Day 1  
Experimental 
 
Trial treatment should begin on the day of randomization or as close as possible to the date 
on which treatment is allocated/assigned. 
5.2.1 Dose Selection/Modification 
5.2.1.1 Dose Selection – VRP-HER2 
Because 4 x 108 IU VRP was previously given in our prior vaccine study of VRP-HER2, and 
because of manufacturing considerations, we will use 4 x 108 IU VRP-HER2 for the present 
study. 
VRP-HER2 is formulated at a concentration of 5.2 x 108 IU/mL (2.6 x 108 IU per 0.5 mL). 
Two vials will be needed for each injection for 4 x 108 IU dose.  Prior to injection, the 
appropriate vials should be removed from the freezer and allowed to thaw at controlled room 
temperature (20-25°C, 68-77°F) for at least 20 minutes and not more than 30 minutes, after 
which it should be kept at 2-8°C (35-46°F). The vaccine is stable for at least 4 hours after 
removal from the freezer when kept refrigerated at 2-8°C (35-46°F). The thawed vial should 
be swirled and then, using aseptic technique, the pharmacist should withdraw the appropriate 
volume from the appropriate vial using a 1-mL syringe. 
The vaccine should be injected as soon as possible (but within 2 hrs of preparation) using a 1 
to 1/2 inch, 20 to 25 gauge needle. If the vaccine cannot be injected immediately, the syringe 
should be stored at 2-8°C (35-46°F) for up to 2 hours.  
All injections of vaccine should be given as a volume of 0.77 mL by intramuscular injection 
in the upper arm after preparation of the site with alcohol. Either arm may be used for the 
initial injection. Subsequent vaccinations should be rotated between arms (e.g., injections 1 
and 3 in right arm, then injections 2 in left arm). If for any reason a patient is not able to 

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receive one of the scheduled vaccinations in their upper arm, the vaccination may be 
administered by intramuscular injection in the subject’s thigh at the discretion of the 
investigator.  This change in administration will be noted in the CRF.  When preparing a dose 
in a syringe and administering the dose, consideration should be given to the volume of 
solution that may remain in the needle after the dose is administered, to ensure that the full 
dose specified in the protocol is administered. 
5.2.1.2 Dose Selection – Pembrolizumab 
The rationale for selection of doses to be used in this trial is provided in Section 4.0 – 
Background and Rationale.   
Details on preparation and administration of pembrolizumab (MK-3475) are provided in the 
Pharmacy Manual.  
5.2.1.3 Dose Modification (Escalation/Titration/Other) – VRP-HER2 
In the prior Phase I study of VRP-HER2 vaccination in advanced HER2+ malignancies, the 
vaccination was well tolerated with no dose limiting toxicities (Table 3). 
Table 3 Adverse events – possibly, probably, and definitely related to VRP-HER2 from Phase 
1 protocol. 
Grade of Adverse Event - VRP-HER2 
 
Arm 
1- Mild 
2- Mod  
3-Severe  
4-LifeThr 
5-Lethal 
Total 
 
n 
n  
(%)  
n  
(%)  
n  
(%)  
n  
(%)  
n  
(%)  
N  
Non-Hematologic Adverse Events 
General disorders and administration site conditions  
Fatigue  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
0  
(0%)  
1  
(6%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Fever  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
2  
(11%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Injection site 
reaction  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
2  
(11%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Malaise  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
1  
(6%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Infections and 
infestations 
 
 
 
 
 
 
 
 
 
 
 
 
Rash pustular  
1  
1  
(20%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  

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2  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Musculoskeletal and connective tissue disorders 
Musculoskeletal 
and connective 
tissue disorder - 
Other, specify  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
1  
(6%)  
1  
(6%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Pain in 
extremity  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
5  
(28%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Renal and urinary disorders 
Urinary 
retention  
1  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
1  
(6%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
Summary 
Maximum 
Non-
Hematologic 
AE  
1  
1  
(20%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
7  
(39%)  2  
(11%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
All Adverse Events 
Summary 
Maximum 
Overall AE  
1  
1  
(20%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
0  
(0%)  
5  
 
2  
7  
(39%)  2  
(11%)  0  
(0%)  
0  
(0%)  
0  
(0%)  
18  
 
Dose modifications: 
Any subject that experiences a Dose Limiting Toxicities (DLT) related to the VRP-HER2 
immunization will not receive any further injections of study drug. (See section below for the 
definition of a DLT)  
For grade 2 toxicity (other than fever, myalgias, arthalgias, or fatigue) related to the VRP-
HER2 immunizations, dosing in an individual patient must be held until toxicity resolves to 
grade 1 or less, but no dose adjustments will be made. 
For grade 1 or less toxicity, no modifications are required.   
• If 0 or 1 Dose Limiting Toxicities (DLT) occur in the Safety Arm, this dose of 
VRP-HER2 will be used in the randomized portion of the study.  
• If 2 or more DLT occur in the Safety Arm, then 6 more patients will be accrued 
into the safety cohort at dose level -1 consisting of VRP-HER2 at dose 
2 x 108 IU intramuscularly, given every 2 weeks for a total of three doses and 
one additional booster dose at C5D1.   
• If 0 or 1 patients experience DLT at dose level -1, then this dose will be chosen 
for the randomized portion of the study. 

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• If 2 or more subjects experience DLT at dose level -1 in either cohort, the study 
will be held and redesigned. 
 
DLTs will be collected and reviewed by the PI as they occur and entered into the study 
database for assessment at Day 42. 
Dosing: 
Dose level 
Dose of VRP-HER2 
Dose level 1 
4 x 108 IU 
Dose level -1 
2 x 108 IU 
 
Any occurrence of a grade 4 or greater toxicity will prompt the study sponsor and investigator 
to conduct a thorough evaluation of the available safety information to justify a decision to 
continue enrolling new subjects into the study. 
 
Definition of Dose-limiting Toxicity (DLT) 
Dose limiting toxicity is defined as any Grade 2 or higher immediate hypersensitivity 
reactions or neurological toxicity, other Grade 3 or 4 allergic or major organ toxicity, or any 
other Grade 3 or higher toxicity attributable to study treatment (VRP-HER2 vaccine or 
pembrolizumab). 
 
 
 
 
 

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5.2.1.4 Dose Modification (Escalation/Titration/Other) – Pembrolizumab 
Table 4: Dose Modification and Toxicity Management Guidelines for Immune-related 
AEs Associated with Pembrolizumab  
General instructions: 
1. Corticosteroid taper should be initiated upon AE improving to Grade 1 or less and continue to taper over at 
least 4 weeks. 
2. For situations where pembrolizumab has been withheld, pembrolizumab can be resumed after AE has been 
reduced to Grade 1 or 0 and corticosteroid has been tapered. Pembrolizumab should be permanently 
discontinued if AE does not resolve within 12 weeks of last dose or corticosteroids cannot be reduced to 
≤10 mg prednisone or equivalent per day within 12 weeks.  
3. For severe and life-threatening irAEs, IV corticosteroid should be initiated first followed by oral steroid. 
Other immunosuppressive treatment should be initiated if irAEs cannot be controlled by corticosteroids. 
 
Immune-
related AEs 
Toxicity grade 
or conditions 
(CTCAEv5.0) 
Action taken to 
pembrolizuma
b 
irAE management with 
corticosteroid and/or 
other therapies  
Monitor and follow-up  
Pneumonitis  
Grade 2 
Withhold  
• Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed by 
taper 
 
• 
Monitor participants for 
signs and symptoms of 
pneumonitis 
• 
Evaluate participants 
with suspected 
pneumonitis with 
radiographic imaging 
and initiate 
corticosteroid treatment 
• 
Add prophylactic 
antibiotics for 
opportunistic infections 
Grade 3 or 4, 
or recurrent 
Grade 2 
Permanently 
discontinue 
Diarrhea / 
Colitis  
Grade 2 or 3 
Withhold 
• Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed by 
taper 
 
• 
Monitor participants for 
signs and symptoms of 
enterocolitis (ie, 
diarrhea, abdominal pain, 
blood or mucus in stool 
with or without fever) 
and of bowel perforation 
(ie, peritoneal signs and 
ileus). 
• 
Participants with ≥ Grade 
2 diarrhea suspecting 
colitis should consider 
GI consultation and 
performing endoscopy to 
rule out colitis.  
Grade 4 
Permanently 
discontinue 

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• 
Participants with 
diarrhea/colitis should be 
advised to drink liberal 
quantities of clear fluids.  
If sufficient oral fluid 
intake is not feasible, 
fluid and electrolytes 
should be substituted via 
IV infusion. 
AST / ALT 
elevation or 
Increased 
bilirubin 
Grade 2 
Withhold 
• Administer 
corticosteroids (initial 
dose of 0.5- 1 mg/kg 
prednisone or 
equivalent) followed by 
taper 
• 
Monitor with liver 
function tests (consider 
weekly or more 
frequently until liver 
enzyme value returned to 
baseline or is stable 
Grade 3 or 4  
Permanently 
discontinue 
• Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed by 
taper 
Type 1 
diabetes 
mellitus 
(T1DM) or 
Hyperglycemi
a 
 
Newly onset 
T1DM or  
Grade 3 or 4 
hyperglycemia 
associated with 
evidence of β-
cell failure 
Withhold 
• Initiate insulin 
replacement therapy for 
participants with T1DM  
• Administer anti-
hyperglycemic in 
participants with 
hyperglycemia  
 
• 
Monitor participants for 
hyperglycemia or other 
signs and symptoms of 
diabetes. 
Hypophysitis 
Grade 2 
Withhold 
• Administer 
corticosteroids and 
initiate hormonal 
replacements as 
clinically indicated.   
 
• 
Monitor for signs and 
symptoms of 
hypophysitis (including 
hypopituitarism and 
adrenal insufficiency)  
Grade 3 or 4  
Withhold or 
permanently 
discontinue1  
Hyperthyroidi
sm  
Grade 2 
Continue  
• Treat with non-selective 
beta-blockers (eg, 
propranolol) or 
thionamides as 
appropriate  
• 
Monitor for signs and 
symptoms of thyroid 
disorders.  
 
Grade 3 or 4  
Withhold or  
permanently 
discontinue1 
Hypothyroidis
m 
Grade 2-4 
Continue  
• Initiate thyroid 
replacement hormones 
(eg, levothyroxine or 
liothyroinine) per 
standard of care 
• 
Monitor for signs and 
symptoms of thyroid 
disorders.  
 

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Nephritis and 
Renal 
dysfunction 
Grade 2 
Withhold  
• Administer 
corticosteroids 
(prednisone 1-2 mg/kg 
or equivalent) followed 
by taper. 
• 
Monitor changes of renal 
function 
 
Grade 3 or 4  
Permanently 
discontinue 
Myocarditis 
Grade 1 or 2 
Withhold 
• Based on severity of AE 
administer 
corticosteroids 
• 
Ensure adequate 
evaluation to confirm 
etiology and/or exclude 
other causes 
 
Grade 3 or 4 
Permanently 
discontinue 
All other 
immune-
related AEs 
Intolerable/ 
persistent 
Grade 2 
Withhold 
• Based on type and 
severity of AE 
administer 
corticosteroids  
• 
Ensure adequate 
evaluation to confirm 
etiology and/or exclude 
other causes 
 
Grade 3 
Withhold or 
discontinue 
based on the 
type of event.  
Events that 
require 
discontinuation 
include and not 
limited to:  
Gullain-Barre 
Syndrome, 
encephalitis 
Grade 4 or 
recurrent 
Grade 3  
Permanently 
discontinue 
1. Withhold or permanently discontinue pembrolizumab is at the discretion of the investigator or treating 
physician.   
NOTE:  
For participants with Grade 3 or 4 immune-related endocrinopathy where withhold of pembrolizumab is 
required, pembrolizumab may be resumed when AE resolves to ≤ Grade 2 and is controlled with hormonal 
replacement therapy or achieved metabolic control (in case of T1DM).   
 
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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5.2.2 Timing of Dose Administration 
Trial treatment with pembrolizumab and/or VRP-HER2 vaccine should be administered  
according to the study calendar after all procedures/assessments have been completed as 
detailed on the Trial Flow Chart (Section 6.0).   
In the Safety Arm and in Arms A and C, timing of VRP-HER2 vaccine doses will be on Cycle 
1 - Day 1, Cycle 1 - Day 15, and Cycle 2 – Day 8. A VRP-HER2 booster vaccination will be 
given on Cycle 5, Day 1. This timing for VRP-HER2 is based on a Q2 weekly schedule 
established in our recently completed trial.  
In the Safety Arm and Arms B and C, pembrolizumab 200 mg will be administered as a 30 
minute IV infusion every 3 weeks. Although every effort should be made to target infusion 
timing to be as close to 30 minutes as possible, given the variability of infusion pumps, a 
window of -5 minutes and +10 minutes is permitted (i.e., infusion time is 30 minutes: -5 
min/+10 min). 
Trial treatment may be administered up to 3 days before or after the scheduled Day 1 of each 
cycle due to administrative reasons. 
All trial treatments will be administered on an outpatient basis. 
The Pharmacy Manual contains specific instructions for the preparation of the pembrolizumab 
infusion fluid and administration of infusion solution. 
5.2.3 Concurrent HER2 targeted therapy: trastuzumab plus pertuzumab 
Patients receiving concurrent trastuzumab plus pertuzumab will receive the same doses of 
their concurrent treatment. Trastuzumab and Pertuzumab will be administered under the 
direction of the patients attending physician. VRP-HER2 vaccinations will be given on the 
same day as trastuzumab plus pertuzumab if possible, but may be given between trastuzumab 
plus pertuzumab doses. Pembrolizumab infusions will be given on the same day as 
trastuzumab plus pertuzumab if possible, but may be given between trastuzumab plus 
pertuzumab doses. 
5.2.4 Trial Blinding/Masking 
This is an open-label trial; therefore, the Sponsor, investigator, and subject will know the 
treatment administered. 

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5.3 
Randomization or Treatment Allocation 
There will be an initial safety arm (n=3), and if this combination therapy is without DLT, then 
patients will be stratified by hormone receptor status (ER and/or PR + (defined as >1%) versus 
negative) and randomized 1:1:1 into 3 arms (up to N=12 in each arm (ARM A, B, C) by the 
study statistician using a random number generator or table.  
5.4 
Concomitant Medications/Vaccinations (allowed & prohibited) 
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed 
during the ongoing trial. If there is a clinical indication for one of these or other medications 
or vaccinations specifically prohibited during the trial, discontinuation from trial therapy or 
vaccination may be required. The investigator should discuss any questions regarding this 
with the Merck Clinical team. The final decision on any supportive therapy or vaccination 
rests with the investigator and/or the subject's primary physician.  
5.4.1 Acceptable Concomitant Medications 
All treatments that the investigator considers necessary for a subject’s welfare may be 
administered at the discretion of the investigator in keeping with the community standards of 
medical care. All concomitant medication will be recorded on the case report form (CRF) 
including all prescription, over-the-counter (OTC), herbal supplements, and IV medications 
and fluids. If changes occur during the trial period, documentation of drug dosage, frequency, 
route, and date may also be included on the CRF. 
All concomitant medications received within 28 days before the first dose of trial treatment 
and 30 days after the last dose of trial treatment should be recorded. Concomitant medications 
administered after 30 days after the last dose of trial treatment should be recorded for SAEs 
and ECIs as defined in Section 7.9. 
5.4.2 Prohibited Concomitant Medications 
Subjects are prohibited from receiving the following therapies during the Screening and 
Treatment Phase of this trial: 
• Antineoplastic systemic chemotherapy or biological therapy. Endocrine therapy and 
anti-HER2 therapies are permitted. 
• Immunotherapy not specified in this protocol 
• Chemotherapy not specified in this protocol 
• Investigational agents other than pembrolizumab 

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• Radiation therapy  
o Note:  Radiation therapy to a symptomatic solitary lesion or to the brain may 
be allowed at the investigator’s discretion.   
• Live vaccines within 30 days prior to the first dose of trial treatment and while 
participating in the trial. Examples of live vaccines include, but are not limited to, the 
following: measles, mumps, rubella, varicella/zoster, yellow fever, rabies, BCG, and 
typhoid vaccine.  
• Systemic glucocorticoids for any purpose other than to modulate symptoms from an 
event of clinical interest of suspected immunologic etiology. The use of physiologic 
doses of corticosteroids may be approved after consultation with the Sponsor. 
Subjects who, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the trial.  
Subjects may receive other medications that the investigator deems to be medically necessary. 
The Exclusion Criteria describes other medications which are prohibited in this trial. 
There are no prohibited therapies during the Post-Treatment Follow-up Phase. 
5.5 
Rescue Medications & Supportive Care 
5.5.1 Supportive Care Guidelines 
Subjects should receive appropriate supportive care measures as deemed necessary by the 
treating investigator. Suggested supportive care measures for the management of adverse 
events with potential immunologic etiology are outlined below. Where appropriate, these 
guidelines include the use of oral or intravenous treatment with corticosteroids as well as 
additional anti-inflammatory agents if symptoms do not improve with administration of 
corticosteroids. Note that several courses of steroid tapering may be necessary as symptoms 
may worsen when the steroid dose is decreased. For each disorder, attempts should be made 
to rule out other causes such as metastatic disease or bacterial or viral infection, which might 
require additional supportive care. The treatment guidelines are intended to be applied when 
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 5.2.1 for dose 
modification.  
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or 
skin photography as part of evaluation of the event.  

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• Pneumonitis:  
o For Grade 2 events, treat with systemic corticosteroids. When symptoms 
improve to Grade 1 or less, steroid taper should be started and continued over 
no less than 4 weeks. 
o For Grade 3-4 events, immediately treat with intravenous steroids. 
Administer additional anti-inflammatory measures, as needed. 
o Add prophylactic antibiotics for opportunistic infections in the case of 
prolonged steroid administration. 
• Diarrhea/Colitis:  
Subjects should be carefully monitored for signs and symptoms of enterocolitis (such 
as diarrhea, abdominal pain, blood or mucus in stool, with or without fever) and of 
bowel perforation (such as peritoneal signs and ileus).   
o All subjects who experience diarrhea/colitis should be advised to drink liberal 
quantities of clear fluids. If sufficient oral fluid intake is not feasible, fluid and 
electrolytes should be substituted via IV infusion. For Grade 2 or higher 
diarrhea, consider GI consultation and endoscopy to confirm or rule out colitis. 
o For Grade 2 diarrhea/colitis,  administer oral corticosteroids.  
o For Grade 3 or 4 diarrhea/colitis, 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 

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

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o When symptoms improve to Grade 1 or less, steroid taper should be started 
and continued over no less than 4 weeks.  
• Management of Infusion Reactions: Signs and symptoms usually develop during or 
shortly after drug infusion and generally resolve completely within 24 hours of 
completion of infusion.  
The Table below shows treatment guidelines for subjects who experience an infusion 
reaction associated with administration of pembrolizumab (MK-3475). 
Table 5 Infusion Reaction Treatment Guidelines 
NCI CTCAE Grade 
Treatment 
Premedication at subsequent 
dosing 
Grade 1 
Mild reaction; infusion interruption 
not indicated; intervention not 
indicated 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
None 
Grade 2 
Requires infusion interruption but 
responds promptly to symptomatic 
treatment (e.g., antihistamines, 
NSAIDS, narcotics, IV fluids); 
prophylactic medications indicated for 
< =24 hrs 
Stop Infusion and monitor symptoms. 
Additional appropriate medical therapy may 
include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
If symptoms resolve within one hour of stopping 
drug infusion, the infusion may be restarted at 
50% of the original infusion rate (e.g., from 100 
mL/hr to 50 mL/hr).  Otherwise dosing will be 
held until symptoms resolve and the subject 
should be premedicated for the next scheduled 
dose. 
Subjects who develop Grade 2 toxicity despite 
adequate premedication should be 
permanently discontinued from further trial 
treatment administration. 
Subject may be premedicated 1.5h 
(± 30 minutes) prior to infusion of 
pembrolizumab (MK-3475) with: 
 
Diphenhydramine 50 mg po (or 
equivalent dose of antihistamine). 
 
Acetaminophen 500-1000 mg po 
(or equivalent dose of antipyretic). 
Grades 3 or 4 
Grade 3: 
Prolonged (i.e., not rapidly responsive 
to symptomatic medication and/or 
brief interruption of infusion); 
recurrence of symptoms following 
initial improvement; hospitalization 
indicated for other clinical sequelae 
(e.g., renal impairment, pulmonary 
infiltrates) 
Grade 4: 
Life-threatening; pressor or ventilatory 
support indicated 
Stop Infusion. 
Additional appropriate medical therapy may 
include but is not limited to: 
IV fluids 
Antihistamines 
NSAIDS 
Acetaminophen 
Narcotics 
Oxygen 
Pressors 
Corticosteroids 
Epinephrine 
 
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator. 
Hospitalization may be indicated. 
No subsequent dosing 

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NCI CTCAE Grade 
Treatment 
Premedication at subsequent 
dosing 
Subject is permanently discontinued from 
further trial treatment administration. 
Appropriate resuscitation equipment should be available in the room and a physician readily available during the period of drug 
administration. 
 
 
• Management of VRP-HER2 Vaccine Reactions: Reactions have not been observed 
in prior study; however, like other vaccines, they could theoretically occur within 
minutes to as long as a day after an injection. 
Treatment of Toxicity for VRP-HER2 vaccine: Bronchospasm, stridor, wheezing, 
respiratory depression (Respiratory Rate < 8), cardiac arrhythmia, generalized 
urticaria, systolic Blood Pressure ≤ 80mm Hg, angioedema, shock, or loss of 
consciousness  
1. Remain at patient bedside  
2. Have another nurse notify physician 
3. Administer Normal Saline (NS) at KVO, if hypotensive then give NS 500ml 
bolus  
4. Start oxygen for dyspnea, stridor, wheezing or respiratory depression at 2 
liters/nasal cannula, initiate continuous pulse oximetry and call respiratory 
therapist (RT)  
5. Give diphenhydramine 50 mg IVP** x 1 (Intravenous Push) 
6. Give methylprednisolone 125mg IV** x 1 (Intravenous Infusion) 
7. Give epinephrine 0.3mg (auto-injector) x 1 IM (Intramuscular) x OR 
epinephrine 0.3mg (1:1000) SQ (Subcutaneous) x 1 (may repeat x 1 in 5 
minutes)  
8. If no response to above interventions within 5 minutes or patient condition 
worsens, call a code 911 or: 
 
At Duke: x115 (Duke) 
  
9. Vital signs with pulse oximetry every 2 minutes  until patient is stable, then 
every 5 minutes for 30 minutes and then every 15 minutes for 1 hr or as the 
patient’s condition requires  
 
**If no IV access or IV access lost, may give these agents IM as appropriate. 
• Discontinuation of VRP-HER2 injections Required for: 
(1) Life threatening anaphylactic reactions or Grade 4 toxicity attributed to the 
injections.  

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(2) Patients with an NCI CTCAE (version 5.0) ≥ Grade 2  decrease in ejection 
fraction, during the vaccination period may not receive any further vaccine 
(VRP-HER2).  
Patients with a ≥ Grade 2 decrease in ejection fraction in the period thirty days 
after the last vaccination should continue to be monitored every 4 weeks for at 
least 16 weeks. 
(3) Initiation of radiotherapy or chemotherapy or new hormonal therapy. 
Note: If patients experience progression prior to receiving all 3 immunizations 
and the booster, they may continue to receive VRP-HER2 at their physician’s 
discretion.  
Note: If a subject in the safety cohort becomes safety non-evaluable (i.e., is 
removed prior to completion of the assigned vaccine schedule for the following 
reasons: refusal of therapy, noncompliance, intercurrent illness and physician 
discretion), the subject will be replaced. 
• Criteria for Evaluating Cardiac Adverse Events in Patient receiving concurrent 
trastuzumab 
(1) Patients with an NCI CTCAE (version 5.0) Grade 2 or greater LVEF decrease, 
during the vaccination period may not receive any further vaccine (VRP-HER2). 
Patients with a Grade 2 or greater LVEF decrease in the period thirty days after 
the last vaccination should continue to be monitored every 4 weeks for at least 16 
weeks. 
(2) Patients will be assessed for left ventricular ejection fraction (LVEF) within 8 
weeks prior to initiation of study drug and will receive a MUGA or ECHO at 
week 8 of the study. If a patient has completed their vaccinations and has a 
clinical or standard of care indication for an ECHO/MUGA before week 8 and 
there is a Grade 2 or greater LVEF decrease, we will stop their HER2 targeted 
therapy. Any patient found to have a Grade 2 or greater LVEF decrease while 
still within the 8 weeks of this study should continue to be monitored every 4 
weeks for at least 16 weeks. After the cardiac echo/MUGA follow-up as directed 
above, patients further cardiac monitoring will be at the discretion of their 
attending physician. We will collect the LVEF data, obtained by the patients 
attending physician, for up to 6 months after completion of vaccination.  
 
Patients on study will be monitored by their treating clinical team for cardiac 
adverse events every 3 months according to labeling recommendations in patients 
that continue to receive trastuzumab (including after completion or discontinuation 
of vaccine injections and/or pembrolizumab infusions). 

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5.6 
Diet/Activity/Other Considerations 
5.6.1 Diet 
Subjects should maintain a normal diet unless modifications are required to manage an AE 
such as diarrhea, nausea or vomiting. 
5.6.2 Contraception 
Pembrolizumab may have adverse effects on a fetus in utero. Furthermore, it is not known if 
pembrolizumab has transient adverse effects on the composition of sperm.   
For this trial, male subjects will be considered to be of non-reproductive potential if they have 
azoospermia (whether due to having had a vasectomy or due to an underlying medical 
condition).   
Female subjects will be considered of non-reproductive potential if they are either:  
(1) postmenopausal (defined as at least 12 months with no menses without an alternative 
medical cause; in women < 45 years of age a high follicle stimulating hormone (FSH) 
level in the postmenopausal range may be used to confirm a post-menopausal state in 
women not using hormonal contraception or hormonal replacement therapy. In the 
absence of 12 months of amenorrhea, a single FSH measurement is insufficient.);  
OR  
(2) have had a hysterectomy and/or bilateral oophorectomy, bilateral salpingectomy or 
bilateral tubal ligation/occlusion, at least 6 weeks prior to screening;  
OR  
(3) has a congenital or acquired condition that prevents childbearing. 
Female and male subjects of reproductive potential must agree to avoid becoming pregnant 
or impregnating a partner, respectively, while receiving study drug and for 120 days after the 
last dose of study drug by complying with one of the following:   
(1) practice abstinence† from heterosexual activity;  
OR  
(2) use (or have their partner use) acceptable contraception during heterosexual activity.   

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Acceptable methods of contraception are‡: 
Single method (one of the following is acceptable): 
• 
intrauterine device (IUD) 
• 
vasectomy of a female subject’s male partner  
• 
contraceptive rod implanted into the skin 
 
Combination method (requires use of two of the following): 
• 
diaphragm with spermicide (cannot be used in conjunction with cervical 
cap/spermicide) 
• 
cervical cap with spermicide (nulliparous women only)   
• 
contraceptive sponge (nulliparous women only)  
• 
male condom or female condom (cannot be used together) 
• 
hormonal contraceptive: oral contraceptive pill (estrogen/progestin pill or progestin-
only pill), contraceptive skin patch, vaginal contraceptive ring, or subcutaneous 
contraceptive injection 
†Abstinence (relative to heterosexual activity) can be used as the sole method of 
contraception if it is consistently employed as the subject’s preferred and usual 
lifestyle and if considered acceptable by local regulatory agencies and ERCs/IRBs.  
Periodic abstinence (e.g., calendar, ovulation, sympto-thermal, post-ovulation 
methods, etc.) and withdrawal are not acceptable methods of contraception.  
‡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 

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will not reliably comply with the requirements for contraception, that subject should not be 
entered into the study. 
5.6.3 Use in Pregnancy 
If a subject inadvertently becomes pregnant while on treatment with pembrolizumab, the 
subject will immediately be removed from the study. The site will contact the subject at least 
monthly and document the subject’s status until the pregnancy has been completed or 
terminated. The outcome of the pregnancy will be reported to the Sponsor and to Merck 
without delay and within 24 hours to the Sponsor and within 2 working days to Merck if the 
outcome is a serious adverse experience (e.g., death, abortion, congenital anomaly, or other 
disabling or life-threatening complication to the mother or newborn).   
The study investigator will make every effort to obtain permission to follow the outcome of 
the pregnancy and report the condition of the fetus or newborn to the Sponsor. If a male 
subject impregnates his female partner the study personnel at the site must be informed 
immediately and the pregnancy reported to the Sponsor and to Merck and followed as 
described above and in Section 7.9.2. 
5.6.4 Use in Nursing Women 
It is unknown whether pembrolizumab is excreted in human milk. Since many drugs are 
excreted in human milk, and because of the potential for serious adverse reactions in the 
nursing infant, subjects who are breast-feeding are not eligible for enrollment. 
5.7 
Subject Withdrawal/Discontinuation Criteria 
Subjects may withdraw consent at any time for any reason or be dropped from the trial at the 
discretion of the investigator should any untoward effect occur. In addition, a subject may be 
withdrawn by the investigator or the Sponsor if enrollment into the trial is inappropriate, the 
trial plan is violated, or for administrative and/or other safety reasons. Specific details 
regarding discontinuation or withdrawal are provided in Section 7.5 – Other Procedures. 
A subject must be discontinued from the trial for any of the following reasons: 
• The subject or legal representative (such as a parent or legal guardian) withdraws 
consent. 
• Confirmed radiographic disease progression 
  

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Note: A subject may be granted an exception to continue on treatment with 
confirmed radiographic progression if clinically stable or clinically improved. 
• Adverse experience that is determined by the principal investigator or the patients 
physician to warrant study discontinuation for safety reasons 
• Intercurrent illness that prevents further administration of treatment 
• Investigator’s decision to withdraw the subject 
• The subject has a confirmed positive serum pregnancy test 
• Noncompliance with trial treatment or procedure requirements 
• The subject is lost to follow-up 
• Administrative reasons 
The End of Treatment and Follow-up visit procedures are listed in Section 6 (Protocol Flow 
Chart). After the end of treatment, each subject will be followed for 30 days for adverse event 
monitoring (serious adverse events will be collected for 90 days after the end of treatment as 
described in Section 7.6). Subjects who discontinue for reasons other than progressive disease 
will have post-treatment follow-up for disease status until disease progression, initiating a 
non-study cancer treatment, withdrawing consent or becoming lost to follow-up. After 
documented disease progression each subject will be followed by telephone for overall 
survival until death, withdrawal of consent, or the end of the study, whichever occurs first. 
5.7.1 Discontinuation of Study Therapy after CR  
Discontinuation of treatment may be considered for subjects who have attained a confirmed 
CR and had at least two treatments with pembrolizumab beyond the date when the initial CR 
was declared.  
5.8 
Subject Replacement Strategy 
If any patient in the safety cohort is inevaluable for toxicity (for example, does not complete 
all study therapy and 30 day follow-up), then they will be replaced. No study replacements 
are planned during the randomization phase. 
5.9 
Clinical Criteria for Early Trial Termination 
Early trial termination will be the result of the criteria specified below: 

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1. Quality or quantity of data recording is inaccurate or incomplete 
2. Poor adherence to protocol and regulatory requirements 
3. Incidence or severity of adverse drug reaction in this or other studies indicates a potential 
health hazard to subjects 
4. Plans to modify or discontinue the development of the study drug 
In the event of Merck decision to no longer supply study drug, ample notification will be 
provided so that appropriate adjustments to subject treatment can be made. 
 

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6.0 TRIAL FLOW CHART 
6.1 
Study Flow Chart 
Cycle Days → 
Screen3 
Cycle 1 
Cycle 2 
Cycle 3 
Cycle 4 
Cycle 5 
30-Day 
Safety 
Visit 
Week 24 
and 6-Mo. 
Follow-up11 
Procedure / Test ↓ 
D1 
D8 
D15 
D1 
D8 
D15 D1 
D8 
D15 
D1 
D8 D15 
D1 
D8 
D15 
Informed Consent 
X 
History / Physical / 
ECOG 
X 
X 
X1 
X2 X1 
X 
X2 
X 
X 
Collection of AEs 
X 
X 
 
X1 
X2 X1 
 
X 
 
 
X2 
 
 
X 
 
 
X10 
X 
Serum Pregnancy (HCG) 
X4 
CBC with diff 
X5 
X 
X2 
X 
X2 
X 
X 
Chemistries, LFTs, TSH 
X5 
X 
X2 
X 
X2 
X 
X 
Coags (PT/INR, aPTT) 
X 
X 
EKG 
X6 
MUGA or ECHO 
X6 
X7 
Tumor biopsy 
X 
X 
Blood draw for Immune 
Monitoring 
X 
X 
X 
X8 
X12 

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Cycle Days → 
Screen 
Cycle 1 
Cycle 2 
Cycle 3 
Cycle 4 
Cycle 5 
30-Day 
Safety 
Visit 
Week 24 and 
6-Mo. Follow-
upI 
Procedure / Test ↓ 
D1 
D8 D15 D1 
D8 D15 D1 
D8 D15 D1 
D8 D15 D1 
D8 D15 
CT Scan of C/A/P; Bone 
scan if needed 
X6 
X9 
X9 
VRP-HER21 
X 
X1 
X1 
X 
Pembrolizumab1 
X 
X2 
X 
X2 
X 
 
Note: Study activities may be performed +/-3 days from designated day. 
1VRP-HER2 is to be administered only to subjects in Arms A, C, and the Safety Arm; Subjects in Arm B (pembrolizumab alone) do not 
need to return to clinic for assessments on C1D15 or C2D8. Subjects in Arm C and the Safety Arm will return for all study visits. 
2Pembrolizumab is to be administered only to subjects in Arms B, C, and the Safety Arm; Subjects in Arm A (VRP-HER2 alone) do not 
need to return to clinic for assessments on C2D1 or C4D1. Subjects in Arm C and the Safety Arm will return for all study visits. 
3Unless otherwise noted below, screening assessments are to take place within 28 days prior to C1D1. Refer to Section 7.1.1 for all 
screening assessment timelines. 
4Serum pregnancy test must be performed and determined negative within 72 hours of the first dose of study drug(s). 
5CBC with differential, Chemistries including LFTs tests are to be completed within 7 days of the first dose of study drug(s). (Refer to 
Table 6 of Section 7.4 for the complete list of labs to be assessed for screening) 
6Available CT scans and bone scans performed as standard of care prior to signing consent can be used to fulfill eligibility requirements 
if they were performed within 4 weeks of the first dose of study drug(s). Available MUGA, Echocardiogram (ECHO), and EKG 
performed as standard of care prior to signing consent can be used to fulfill eligibility requirements if they were performed within 8 
weeks of the first dose of study drug(s). 
7The second ECHO or MUGA Scan will be performed at week cycle 5 day 1 or at end of study visit, whichever is completed first. The 
same cardiac imaging modality should be used consistently for an individual patient throughout the study. 

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8Treatment phase concludes at week 14. However, if subjects go off study before week 14 a blood draw for immune monitoring will be 
performed. A research biopsy will be performed at the discretion of the investigator. 
9The results of available CT scans and bone scans performed as standard of care will be obtained at approximately cycle 5 day 1 +/- 7 
days and then during follow-up every 6 weeks for 1 year, followed by every 9 weeks. 
10AE assessments will be conducted in person or by phone approximately 30 days after the last dose of trial treatment or before the 
initiation of a new anti-cancer treatment, whichever comes first. Subjects with an AE of Grade > 1 will be followed until the resolution 
of the AE to Grade 0-1 or until the beginning of a new anti-neoplastic therapy, whichever occurs first. SAEs that occur within 90 days 
of the end of treatment or before initiation of a new anti-cancer treatment should be followed and recorded. 
11During the follow-up phase, we will collect survival data every 12 weeks through contacting the patients (in person, by email, or phone 
call), chart review, and/or by contacting their local oncologist to determine when subjects have any late toxicities, have progression of 
disease, or are no longer living. If the subject has progressive disease they do not need to be followed after the time of progression.  
12At investigators discretion, peripheral blood (up to 90 ml) for immune monitoring will be obtained every three months for one year. 
 
 
 
 
 

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7.0 TRIAL PROCEDURES/ASSESSMENTS 
The Trial Flow Chart - Section 6.0 summarizes the trial procedures to be performed at each 
visit.  Individual trial procedures are described in detail below.  It may be necessary to perform 
these procedures at unscheduled time points if deemed clinically necessary by the investigator. 
Furthermore, additional evaluations/testing may be deemed necessary by the Sponsor and/or 
Merck for reasons related to subject safety. In some cases, such evaluation/testing may be 
potentially sensitive in nature (e.g., HIV, Hepatitis C, etc.), and thus local regulations may 
require that additional informed consent be obtained from the subject.  In these cases, such 
evaluations/testing will be performed in accordance with those regulations. 
7.1 
Screening period 
During the Screening Period, subjects are consented and screened for the study. Informed 
consent must be obtained before initiation of any screening procedure that is performed 
solely for the purpose of determining eligibility for this study. Evaluations performed as part 
of routine care before informed consent can be considered as screening evaluations if done 
within the defined screening period, and if permitted by the local Institutional Review Board 
(IRB)/ Independent Ethics Committee (IEC) policies. Study eligibility is based on meeting 
all of the inclusion criteria and none of the exclusion criteria before the first dose of study 
drug on Cycle 1 Day 1. 
 
7.1.1 Screening Procedures 
The following study procedures must be done within 28 days prior to Cycle 1 Day 1: 
• Demographics 
• Medical and cancer history 
• Physical examination including Height, Vital signs and weight 
• Concomitant medications 
• ECOG performance status 
• EKG (assessment performed up to 8 weeks prior to C1D1 for SOC can be used) 
• TSH 
• Adverse event assessment (review of baseline symptoms) 
• Tumor assessment (CT and/or bone scans performed up to 4 weeks prior to C1D1 for 
SOC can be used) 
• MUGA or echocardiogram (assessments performed up to 8 weeks prior to C1D1 for 
SOC can be used) 
• Blood draw for immune monitoring 
• Tumor biopsy will be performed following informed consent and screening procedures 
and within 6 weeks prior to Cycle 1 Day 1. 
 
The following study procedures must be done within 7 days prior to Cycle 1 Day 1: 

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• CBC with differential 
• Chemistries including liver function tests (LFTs)* 
 
The serum pregnancy test for women of childbearing potential must be completed (and result 
must be negative) within 72 hours of the first dose of study drug(s). 
 
Subject eligibility is determined using lab results obtained up to 7 days prior to Cycle 1 Day 
1. Any laboratory assessments repeated on Cycle 1 Day 1 must meet eligibility requirements. 
The Screening Period ends upon receipt of the first dose of study drug or final determination 
that the subject is ineligible for the study. 
*See 7.4 Laboratory Procedures/Assessments 
 
7.1.2 Assignment of Subject ID Number 
Patients will be identified with the following code system:   
Safety Arm: VRP-HER2-0S1-001, -002, -003…-00x 
Arm A: VRP-HER2-A-001, -002, -003…-00x  
Arm B: VRP-HER2-B-001, -002, -003…-00x 
Arm C: VRP-HER2-C-001, -002, -003…-00x 
7.2 
 Treatment Period 
During the Treatment Period, subjects will receive the assigned study treatment as per section 
5.2. Dose modification guidelines are described in 5.2.1.  
 
The following study procedures are to be completed as follows: 
• History including concomitant medications and adverse events assessment and 
Physical examination including vital signs and ECOG performance status each visit 
(C1D1, C1D15, C2D1, C2D8, C3D1, C4D1, C5D1) 
o Arm A (VRP-HER2) will require visits C1D1, C1D15, C3D1, C2D8, C5D1 
o Arm B (pembrolizumab) will require visits C1D1, C2D1, C3D1, C4D1, C5D1 
o Arm C and Safety Arm (pembrolizumab + VRP-HER2) will require all visits 
listed above 
• CBC with differential (Each cycle day 1 – excluding Arm A: C2D1, C4D1) 
• Chemistries including LFTs and TSH (Each cycle day 1 – excluding Arm A: C2D1, 
C4D1) 
• Blood draw for immune assays visit (C1D1, C3D1, C5D1) 
• MUGA scan or echocardiogram (C5D1 or at end of treatment, whichever comes first) 
• Tumor biopsy (C5D1) 

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7.3 
Post-Treatment Period (week 24 and 6-month follow-up) 
• History including concomitant medications and adverse events assessment and 
Physical examination including vital signs and ECOG performance status each visit 
• CBC with differential 
• Chemistries including LFTs and TSH 
• Blood draw for immune assays visit 
 
7.4 
Laboratory Procedures/Assessments 
Details regarding specific laboratory procedures/assessments to be performed in this trial are 
provided in the table below. 
Table 6  Laboratory Tests 
Hematology 
Chemistry 
Other 
Hematocrit 
Albumin 
Serum β-human 
chorionic gonadotropin 
(β-hCG)† 
Hemoglobin 
Alkaline phosphatase 
   
Platelet count 
Alanine aminotransferase (ALT) 
PT (INR) 
WBC (total and differential) 
Aspartate aminotransferase 
(AST) 
aPTT 
Red Blood Cell Count 
Lactate dehydrogenase (LDH) 
 
Absolute Neutrophil Count 
Carbon Dioxide ‡ 
Free tyroxine (T4) 
Absolute Lymphocyte Count 
  (CO2 or biocarbonate) 
Thyroid stimulating 
hormone (TSH) 
 
Uric Acid 
PK 
 
Calcium 
 
 
Chloride 
Blood for correlative 
studies 
 
Glucose 
  
 
Phosphorus 
  
 
Potassium   
  
 
Sodium 
  
 
Magnesium 
  
 
Total Bilirubin 
  
 
Direct Bilirubin (If total bilirubin 
is elevated above the upper limit 
of normal) 
 
 
Total protein 
 
 
Blood Urea Nitrogen 
 

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7.5 
Other Procedures 
7.5.1 Withdrawal/Discontinuation 
When a subject discontinues or is withdrawn prior to trial completion, all applicable activities 
scheduled for the final Week 24 trial visit should be performed at the time of discontinuation. 
If subject withdraws prior to cycle 5, a post-treatment research biopsy will be performed at the 
discretion of the investigator. Any adverse events which are present at the time of 
discontinuation/withdrawal should be followed in accordance with the safety requirements 
outlined in Section 7.9 - Assessing and Recording Adverse Events. After discontinuing 
treatment following assessment of CR, these subjects should return to the site for a Safety 
Follow-up Visit (described in Section 7.6) and then proceed to the Follow-Up Period of the 
study (described in Sections 7.7 and 7.8). 
7.6 
Safety Follow-Up Visit 
The mandatory Safety Follow-Up Visit should be conducted either in person or by telephone 
approximately 30 days after the last dose of trial treatment or before the initiation of a new 
anti-cancer treatment, whichever comes first. All AEs that occur prior to the Safety Follow-Up 
Visit should be recorded.  Subjects with an AE of Grade > 1 will be followed until the 
resolution of the AE to Grade 0-1 or until the beginning of a new anti-neoplastic therapy, 
whichever occurs first.  SAEs that occur within 90 days of the end of treatment or before 
initiation of a new anti-cancer treatment should also be followed and recorded. 
7.7 
Follow-up Visits 
Subjects who discontinue trial treatment for a reason other than disease progression will move 
into the Follow-Up Phase and should be assessed every 6 weeks (42 ± 7 days) by radiologic 
imaging to monitor disease status.  After 1 year, the imaging time point will occur every 9 
weeks (± 7 days). Every effort should be made to collect information regarding disease status 
until the start of new anti-neoplastic therapy, disease progression, death, end of the study. At 
investigators discretion, blood draws (up to 90 ml) for immune monitoring will be obtained 
every three months for one year.    
7.8 
Survival Follow-up 
Once a subject experiences confirmed disease progression or starts a new anti-cancer therapy, 
the subject moves into the survival follow-up phase and should be contacted by telephone 
every 12 weeks to assess for survival status until death, withdrawal of consent, or the end of 
the study, whichever occurs first.  
 

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7.9 
Assessing and Recording Adverse Events 
An adverse event is defined as any untoward medical occurrence in a patient or clinical 
investigation subject administered a pharmaceutical product and which does not necessarily 
have to have a causal relationship with this treatment. An adverse event can therefore be any 
unfavorable and unintended sign (including an abnormal laboratory finding, for example), 
symptom, or disease temporally associated with the use of a medicinal product or protocol-
specified procedure, whether or not considered related to the medicinal product or protocol-
specified procedure. Any worsening (i.e., any clinically significant adverse change in 
frequency and/or intensity) of a preexisting condition that is temporally associated with the use 
of the Merck’s product, is also an adverse event. 
Changes resulting from normal growth and development that do not vary significantly in 
frequency or severity from expected levels are not to be considered adverse events. Examples 
of this may include, but are not limited to, teething, typical crying in infants and children and 
onset of menses or menopause occurring at a physiologically appropriate time. 
Merck product includes any pharmaceutical product, biological product, device, diagnostic 
agent or protocol-specified procedure, whether investigational (including placebo or active 
comparator medication) or marketed, manufactured by, licensed by, provided by or distributed 
by Merck for human use. 
Adverse events may occur during the course of the use of Merck product in clinical trials, or 
as prescribed in clinical practice, from overdose (whether accidental or intentional), from abuse 
and from withdrawal. 
Progression of the cancer under study is not considered an adverse event.  
All adverse events 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 7.9.3.1. The 
investigator will make every attempt to follow all subjects with non-serious adverse events for 
outcome. 
Adverse events will not be collected for subjects during the 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 

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etc., the subject is first required to provide consent to the main study and AEs will be captured 
according to guidelines for standard AE reporting.  
 
7.9.1 Definition of an Overdose for This Protocol and Reporting of Overdose to the 
Sponsor and to Merck 
For purposes of this trial, an overdose of pembrolizumab will be defined as any dose of 1,000 
mg or greater (≥5 times the indicated dose). No specific information is available on the 
treatment of overdose of pembrolizumab. Appropriate supportive treatment should be provided 
if clinically indicated. In the event of overdose, the subject should be observed closely for signs 
of toxicity. Appropriate supportive treatment should be provided if clinically indicated. 
If an adverse event(s) is associated with (“results from”) the overdose of a Merck product, the 
adverse event(s) is reported as a serious adverse event, even if no other seriousness criteria are 
met. 
If a dose of Merck’s product meeting the protocol definition of overdose is taken without any 
associated clinical symptoms or abnormal laboratory results, the overdose is reported as a non-
serious Event of Clinical Interest (ECI), using the terminology “accidental or intentional 
overdose without adverse effect.” 
All reports of overdose with and without an adverse event must be reported within 24 hours to 
the Sponsor and within 2 working days hours to Merck Global Safety. (Attn: Worldwide 
Product Safety; FAX 215 993-1220) 
7.9.2 Reporting of Pregnancy and Lactation to the Sponsor and to Merck 
Although pregnancy and lactation are not considered adverse events, it is the responsibility of 
investigators or their designees to report any pregnancy or lactation in a subject 
(spontaneously reported to them) that occurs during the trial. 
Pregnancies and lactations that occur after the consent form is signed but before treatment 
allocation/randomization must be reported by the investigator if they cause the subject to be 
excluded from the trial, or are the result of a protocol-specified intervention, including but not 
limited to washout or discontinuation of usual therapy, diet, placebo treatment or a procedure.   
Pregnancies and lactations that occur from the time of treatment allocation/randomization 
through 120 days following cessation of Sponsor’s product, or 30 days following cessation of 
treatment if the subject initiates new anticancer therapy, whichever is earlier, must be reported 
by the investigator. All reported pregnancies must be followed to the completion/termination 
of the pregnancy. Pregnancy outcomes of spontaneous abortion, missed abortion, benign 
hydatidiform mole, blighted ovum, fetal death, intrauterine death, miscarriage and stillbirth 
must be reported as serious events (Important Medical Events). If the pregnancy continues to 
term, the outcome (health of infant) must also be reported. 

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Such events must be reported within 24 hours to the Sponsor and within 2 working days to 
Merck Global Safety. (Attn: Worldwide Product Safety; FAX 215 993-1220) 
7.9.3 Immediate Reporting of Adverse Events to the Sponsor and to Merck 
7.9.3.1 Serious Adverse Events 
A serious adverse event is any adverse event occurring at any dose or during any use of 
Merck’s product and/or VRP-HER2 that: 
• Results in death; 
• Is life threatening; 
• Results in persistent or significant disability/incapacity; 
• Results in or prolongs an existing inpatient hospitalization; 
• Is a congenital anomaly/birth defect; 
• Is an other important medical event  
• 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. 
● 
Is a new cancer (that is not a condition of the study); 
● 
Is associated with an overdose. 
For the time period beginning when the consent form is signed until treatment 
allocation/randomization, any serious adverse event, or follow up to a serious adverse event, 
including death due to any cause other than progression of the cancer under study (reference 
Section 7.9.3.3 for additional details), 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 serious adverse event, or follow up to a serious 
adverse event, including death due to any cause other than progression of the cancer under 
study (reference Section 7.9.3.3 for additional details), whether or not related to the Merck 
product, must be reported within 24 hours to the Sponsor and within 2 working days to Merck 
Global Safety. 
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 following consent through the end of the specified safety follow-up period specified 

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in the paragraph above, or at any time outside of the time period specified in the previous 
paragraph also must be reported immediately to the Sponsor and to Merck Global Safety. 
All subjects with serious adverse events must be followed up for outcome. 
SAE reports and any other relevant safety information are to be forwarded to the Merck 
Global Safety facsimile number:  +1-215-993-1220 
A copy of all 15 Day Reports and Annual Progress Reports is submitted as required by FDA, 
European Union (EU), Pharmaceutical and Medical Devices agency (PMDA) or other local 
regulators. Investigators will cross reference this submission according to local regulations to 
the Merck Investigational Compound Number (IND, CSA, etc.) at the time of submission.  
Additionally investigators will submit a copy of these reports to Merck & Co., Inc. (Attn: 
Worldwide Product Safety; FAX 215 993-1220) at the time of submission to FDA. 
7.9.3.2 Events of Clinical Interest 
Selected non-serious and serious adverse events are also known as Events of Clinical Interest 
(ECI) and must be reported within 24 hours to the Sponsor and within 2 working days to Merck 
Global Safety. (Attn: Worldwide Product Safety; FAX 215 993-1220). 
For the time period beginning when the consent form is signed until treatment 
allocation/randomization, any ECI, or follow up to an ECI, that occurs to any subject must be 
reported within 24 hours to the Sponsor and within 2 working days to Merck Global Safety if 
it causes the subject to be excluded from the trial, or is the result of a protocol-specified 
intervention, including but not limited to washout or discontinuation of usual therapy, diet, 
placebo treatment or a procedure. 
For the time period beginning at treatment allocation/randomization through 90 days following 
cessation of treatment, or 30 days following cessation of treatment if the subject initiates new 
anticancer therapy, whichever is earlier, any ECI, or follow up to an ECI, whether or not related 
to Merck product, must be reported within 24 hours to the Sponsor and within 24 hours to 
Merck Global Safety. 
Events of clinical interest for this trial include: 
1.  an overdose of Merck product, as defined in Section 7.9.1 - Definition of an Overdose for 
This Protocol and Reporting of Overdose to the Sponsor, that is not associated with clinical 
symptoms or abnormal laboratory results.  
2.  an elevated AST or ALT lab value that is greater than or equal to 3X the upper limit of 
normal and an elevated total bilirubin lab value that is greater than or equal to 2X the upper 
limit of normal and, at the same time, an alkaline phosphatase lab value that is less than 2X the 
upper limit of normal, as determined by way of protocol-specified laboratory testing or 
unscheduled laboratory testing.* 

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*Note:  These criteria are based upon available regulatory guidance documents. The 
purpose of the criteria is to specify a threshold of abnormal hepatic tests that may require 
an additional evaluation for an underlying etiology.  
7.9.3.3 Protocol-Specific Exceptions to Serious Adverse Event Reporting  
Efficacy endpoints as outlined in this section will not be reported to Merck as described in 
Section 7.9.3- Immediate Reporting of Adverse Events to the Sponsor and to Merck, unless 
there is evidence suggesting a causal relationship between the drug and the event. Any such 
event will be submitted to the Sponsor within 24 hours and to Merck Global Safety within 2 
working days either by electronic or paper media. 
Specifically, the suspected/actual events covered in this exception include any event that is 
disease progression of the cancer under study. 
The Sponsor will monitor unblinded aggregated efficacy endpoint events and safety data to 
ensure the safety of the subjects in the trial. Any suspected endpoint which upon review is not 
progression of the cancer under study will be forwarded to Merck Global Safety as a SAE 
within 2 working days of determination that the event is not progression of the cancer under 
study 
Hospitalization related to convenience (e.g.transportation issues etc.) will not be considered a 
SAE. 
 
7.9.4 Evaluating Adverse Events 
An investigator who is a qualified physician will evaluate all adverse events according to the 
NCI Common Terminology for Adverse Events (CTCAE), version 5.0. Any adverse event 
which changes CTCAE grade over the course of a given episode will have each change of 
grade recorded on the adverse event case report forms/worksheets. 
All adverse events regardless of CTCAE grade must also be evaluated for seriousness. 

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Table 7  Evaluating Adverse Events 
An investigator who is a qualified physician, will evaluate all adverse events as to: 
V5.0 
CTCAE 
Grading 
Grade 1 
Mild; asymptomatic or mid symptoms; clinical or diagnostic observations only; intervention not indicated. 
Grade 2 
Moderate; minimal, local or noninvasive intervention indicated; limiting age-appropriate instrumental 
ADL. 
 
Grade 3 
Severe or medically significant but not immediately life-threatening; hospitalization or prolongation or 
hospitalization indicated; disabling; limiting self-care ADL. 
 
Grade 4 
Life threatening consequences; urgent intervention indicated. 
 
Grade 5 
Death related to AE 
Seriousness 
A serious adverse event is any adverse event occurring at any dose or during any use of Merck product that: 
 
†Results in death; or 
 
†Is life threatening; or places the subject, in the view of the investigator, at immediate risk of death from the event as it 
occurred (Note: This does not include an adverse event that, had it occurred in a more severe form, might have caused death.); 
or 
 
†Results in a persistent or significant disability/incapacity (substantial disruption of one’s ability to conduct normal life 
functions); or 
 
†Results in or prolongs an existing inpatient hospitalization (hospitalization is defined as an inpatient admission, regardless 
of length of stay, even if the hospitalization is a precautionary measure for continued observation. (Note: Hospitalization for an 
elective procedure to treat a pre-existing condition that has not worsened is not a serious adverse event.  A pre-existing condition 
is a clinical condition that is diagnosed prior to the use of a Merck product and is documented in the patient’s medical history.); 
or 
 
†Is a congenital anomaly/birth defect (in offspring of subject taking the product regardless of time to diagnosis);or 
 
Is a new cancer (that is not a condition of the study) (although not serious per ICH definition, is reportable to the Sponsor 
within 24 hours and to Merck within 2 working days to meet certain local requirements); or 
 
Is an overdose (whether accidental or intentional).  Any adverse event associated with an overdose is considered a serious 
adverse event for collection purposes. An overdose that is not associated with an adverse event is considered a non-serious 
event of clinical interest and must be reported within 24 hours to the Sponsor and to Merck within 2 working days.. 
 
Other important medical events that may not result in death, not be life threatening, or not require hospitalization may be 
considered a serious adverse event when, based upon appropriate medical judgment, the event may jeopardize the subject and 
may require medical or surgical intervention to prevent one of the outcomes listed previously (designated above by a †). 
Duration 
Record the start and stop dates of the adverse event. If less than 1 day, indicate the appropriate length of time and units 
Action 
taken  
Did the adverse event cause Merck product to be discontinued? 

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Relationship 
to Merck 
Product  
Did Merck product cause the adverse event? The determination of the likelihood that Merck  product caused the adverse event 
will be provided by an investigator who is a qualified physician. The investigator’s signed/dated initials on the source document 
or worksheet that supports the causality noted on the AE form, ensures that a medically qualified assessment of causality was 
done. This initialed document must be retained for the required regulatory time frame. The criteria below are intended as 
reference guidelines to assist the investigator in assessing the likelihood of a relationship between the test drug and the adverse 
event based upon the available information. 
The following components are to be used to assess the relationship between Merck product and the AE; the greater the 
correlation with the components and their respective elements (in number and/or intensity), the more likely Merck product 
caused the adverse event (AE): 
 
Exposure 
Is there evidence that the subject was actually exposed to Merck product such as: reliable history, acceptable 
compliance assessment (pill count, diary, etc.), expected pharmacologic effect, or measurement of 
drug/metabolite in bodily specimen? 
 
Time 
Course 
Did the AE follow in a reasonable temporal sequence from administration of Merck product?  
Is the time of onset of the AE compatible with a drug-induced effect (applies to trials with investigational 
medicinal product)? 
 
Likely 
Cause 
Is the AE not reasonably explained by another etiology such as underlying disease, other drug(s)/vaccine(s), or 
other host or environmental factors 
 

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

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7.9.6 Definitions for Reporting Adverse Events – VRP-HER2 Vaccine  
The definitions in this section have been adapted from the Code of Federal Regulations (CFR) 
and the International Conference on Harmonization (ICH) Guidelines for Good Clinical 
Practices (GCPs). Please refer to the complete regulations and guidelines for additional details 
regarding these definitions.  
Adverse Event (AE) [ICH GCP]: An Adverse Event (AE) shall mean any untoward medical 
occurrence whether thought to have been caused by the Study Drug or not. 
Serious Adverse Event (SAE) [21 CFR 312.32]: Serious Adverse Event (SAE) shall mean 
any adverse event which is fatal, life-threatening, disabling or incapacitating, requires in-
patient treatment or prolongs existing hospitalization, is a congenital anomaly in the off-spring 
of the patient or which may require intervention to prevent the previously stated outcomes. 
• A life-threatening adverse experience. 
o The subject was at immediate risk of death from the reaction as it occurred. 
o Does not include a reaction that, had it occurred in a more severe form, could 
have led to death. 
• In-patient hospitalization or prolongation of existing hospitalization. Hospitalizations 
do not include: 
o Preplanned (prior to the study) hospital admissions unless the hospitalization is 
prolonged. 
o Planned admissions (as part of a study – e.g. routine biopsies). 
o 23 hour re-hospitalizations. 
o Hospitalization for elective procedures. 
o Emergency room visits. 
• A persistent or significant disability/incapacity. 
o The event resulted in a substantial disruption of the subject’s ability to conduct 
normal life functions. 
• A congenital anomaly/birth defect. 
• Important medical events that may not result in death, be life-threatening, or require 
hospitalization, but based upon appropriate medical judgment may jeopardize the patient 
or subject, and may require medical or surgical intervention to prevent one of the 
outcomes listed above. 
• Death 
 
Unexpected Adverse Event (UAE) [21 CFR 312.32]:  Any adverse drug experience or 
adverse reaction, the specificity or severity of which is not consistent with the applicable 
product information (e.g., the current Investigator’s Brochure for an unapproved 
investigational product or package insert/summary of product characteristics for an approved 
product); or if the drug label is not required or available, the specificity or severity of which is 

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not consistent with the risk information described in the general investigational plan or 
elsewhere in the current application, as amended.   
Related/Associated [ICH GCP]: There is a reasonable possibility (more likely than not) that 
the event may have been caused by the drug, device or research. Determining the possible 
cause of an event includes assessing temporal relationships, dechallenge/rechallenge 
information, association (or lack of association) with underlying diseases, and the presence (or 
absence) of a more likely cause. 
7.9.7 Procedures for Reporting – VRP-HER2 Vaccine  
All adverse events that are identified from the time of written informed consent through 30 
days post study drug stop should be recorded on the CRFs. 
Serious Adverse Events (SAEs) must ALSO be recorded on the Duke Cancer Institute Safety 
SAE Report Form and reported within 24 hours of learning of an event. The form should be 
completed as much as possible but should not be held until all information is available. 
Additional information and/or corrections may be submitted as they are obtained. All SAEs 
must be followed through resolution or stabilization.  
SAEs should be reported by fax to the following: 
a. Duke Site PI: Micheal Morse, MD 
      Address:  DUMC Box 3233, Durham, NC 27710 
Telephone: (919) 681-3480 
Fax: (919) 681-7970 
E-mail: michael.morse@duke.edu 
 
      b.   Duke Breast Oncology Research Office 
Address: DUMC Box 2965, Duke South White Zone, Room 2592, Durham, NC 
27710 
Phone: (919) 660-1278 
Fax: (919) 681-7335 
 
• Each notification shall be made as soon as possible and in no event later than 15 calendar 
days after Duke University’s initial receipt of the information. Each written notification 
may be submitted on the Duke Cancer Institute Safety SAE Report Form or in a narrative 
format. In each written IND safety report, Duke University shall identify all safety reports 
previously filed with the IND concerning a similar adverse experience, and shall analyze 
the significance of the adverse experience in light of the previous, similar reports.  

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• Duke University shall also notify the FDA by telephone or by fax of any unexpected fatal 
or life-threatening experience associated with the use of the drug as soon as possible but 
no later than 7 calendar days after the initial receipt of the information. 
• Follow-up information to a safety report shall be submitted as soon as the relevant 
information is available. 
 
Additionally, adverse events will be reported to the FDA in an annual report according to 
annual report requirements. Events will be reviewed and reported to the Duke IRB according 
to local IRB guidelines. 
 
8.0 STATISTICAL ANALYSIS PLAN 
8.1 
Statistical Analysis Plan Summary 
8.1.1 Primary Endpoint 
The primary endpoint for this study is to determine whether pembrolizumab increases tumor 
infiltrating (T cell) and the peripheral blood (T cell and antibody) immune response to the 
VRP-HER2 vaccine. 
T cell immunologic response (IR) will be measured by ELISPOT and/or cytokine flow 
cytometry assay for HER2 specific T cell responses, and ELISA for anti-HER2 antibody 
responses. In the ELISPOT assay, a T-cell response will be considered positive if the mean 
number of spots in six wells with antigen exceeds the number of spots in six control wells by 
a magnitude of 10 and the difference between single values of the six wells containing antigen 
and the six control wells is statistically significant at a level of p=0.05 by the t-test. We propose 
a 3-arm trial; Her2-vaccine, PD-1 blockade, and Her2+PD-1, with n=12 patients randomized 
to each arm. If 5 or more patients in each arm exhibit a T-cell response the therapy will be 
considered efficacious. Each arm is based on an exact single stage phase II trial with 
randomization to achieve representativeness of patients in each arm under the assumption that 
10% response is too low and 50% or higher response rates is indicative of further study 
(alpha=0.05 and 90% power). There is no planned statistical comparison across the arms for 
the primary outcome, T-cell response. We will report results in aggregate by arm and by 
hormone receptor status. Samples will also be archived for future TCR Sequencing to identify 
changes in clonality of the T cell response. 
Antibody responses to HER2 will be measured by an ELISA assay. HER2 antibody titer will 
be defined as the serum dilution which has an absorbance that is twice the negative control 
value for the same dilution. Positive results may be confirmed by Western blot analysis and 
additional immune assays.  

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8.1.2 Secondary Endpoints 
The secondary endpoint for this study is safety of concurrent VRP-HER2 vaccine and 
pembrolizumab. 
Since the experimental arm is a novel combination, we will enroll a preliminary safety study 
of 3 patients receiving the combination of VRP-HER2+pembrolizumab. If there are no 
toxicities related to study drug therapy in these patients, monitored continually according to 
the upper half of the table below, then we will proceed with the randomization across the 3 
arms. In addition, we will incorporate toxicity monitoring within the randomized VRP-
HER2+pembrolizumab arm so that it can be stopped in the event of too much toxicity. The 
toxicity monitoring is based on 20% or lower toxicity as acceptable and 33% or higher toxicity 
as unacceptable. The stopping rule indicates that for each patient number achieved in 
enrollment the arm should stop if the number of toxicities exceeds the corresponding number 
in the table.  
Patient # 
1 
2 
3 
4 
5 
6 
Max # of 
toxicities 
- 
1 
2 
2 
2 
2 
Patient # 
7 
8 
9 
10 
11 
12 
Max # of 
toxicities 
3 
3 
3 
4 
4 
4 
 
9.0 LABELING, PACKAGING, STORAGE AND RETURN OF CLINICAL 
SUPPLIES 
9.1 
Investigational Product - Pembrolizumab 
The investigator shall take responsibility for and shall take all steps to maintain appropriate 
records and ensure appropriate supply, storage, handling, distribution and usage of 
investigational product in accordance with the protocol and any applicable laws and 
regulations. 
Clinical Supplies will be provided by Merck as summarized in Table 8. 
Table 8  Product Descriptions 

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Product Name & Potency 
Dosage Form 
Pembrolizumab 50 mg 
Lyophilized Powder for Injection 
Pembrolizumab 100 mg/ 4mL 
Solution for Injection 
 
9.2 
Packaging and Labeling Information - Pembrolizumab 
Clinical supplies will be affixed with a clinical label in accordance with regulatory 
requirements. 
9.3 
Clinical Supplies Disclosure - Pembrolizumab 
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. 
9.4 
Storage and Handling Requirements - Pembrolizumab 
Clinical supplies must be stored in a secure, limited-access location under the storage 
conditions specified on the label.   
Receipt and dispensing of trial medication must be recorded by an authorized person at the 
trial site. 
Clinical supplies may not be used for any purpose other than that stated in the protocol. 
9.5 
Returns and Reconciliation - Pembrolizumab 
The investigator is responsible for keeping accurate records of the clinical supplies received 
from Merck or designee, the amount dispensed to and returned by the subjects and the amount 
remaining at the conclusion of the trial.  
Upon completion or termination of the study, all unused and/or partially used investigational 
product will be destroyed at the site per institutional policy. It is the Investigator’s 
responsibility to arrange for disposal of all empty containers, provided that procedures for 
proper disposal have been established according to applicable federal, state, local and 
institutional guidelines and procedures, and provided that appropriate records of disposal are 
kept. 

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9.6 
Investigational Product – VRP-HER2 Vaccine 
The investigator must maintain appropriate records and ensure appropriate supply, storage, 
handling, distribution and usage of investigational product in accordance with the protocol and 
any applicable laws and regulations. 
VRP-HER2 is supplied as a sterile, clear solution in a 2 mL single-dose vial. The vaccine is 
provided at 5.2 x 108 IU/mL (2.6 x 108 IU per 0.5 mL, and contains phosphate buffered saline, 
pH 7.3, human serum albumin, sodium gluconate and sucrose as a cryopreservative). Each vial 
contains an extractable vaccine volume of 0.5 mL. The product should be stored at –80 ± 10°C. 
9.7 
Packaging and Labeling Information – VRP-HER 
Clinical supplies will be affixed with a clinical label in accordance with regulatory 
requirements. 
9.8 
Clinical Supplies Disclosure – VRP-HER2 
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. 
 
9.9 
Returns and Reconciliation – VRP-HER2 
Unless other arrangements are agreed in writing, all unused vaccine should be returned to H. 
Kim Lyerly, MD at the completion of the clinical study. 
 
10.0 ADMINISTRATIVE AND REGULATORY DETAILS 
10.1 Confidentiality 
All subject data will be identified by a subject identification number and the subject’s initials 
only, to protect the subject's privacy. The data will be blinded accordingly in all data analysis. 
However, in compliance with federal guidelines regarding the monitoring of clinical studies, 
it is required that the investigator permit a representative of the FDA that portion of the 
subject's medical record that is directly related to the study. This will include all relevant study 
documentation including medical histories, to verify eligibility, laboratory test results to verify 
transcription accuracy, X-ray reports, admission, discharge summaries for hospital/outpatient 
admissions while the subject is on-study, and autopsy reports for deaths occurring during the 
study. As part of the required content of informed consent, the subject must be informed that 

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his, medical chart may be reviewed by a representative of the FDA. Should access to the 
medical record require a separate waiver or authorization, it is the investigator's responsibility 
to obtain such permission from the subject in writing before the subject is entered into the 
study. 
10.2 Compliance with Financial Disclosure Requirements 
All study personnel will be required to comply with Financial Disclosure Requirements while 
participating in the administration and oversight of this phase II clinical trial. 
10.3 Compliance with Law, Audit and Debarment 
Research Monitor 
The Research Monitor may discuss the research protocol with the investigators, interview 
human subjects, and consult with others outside the study about the research. The Research 
Monitor shall have the authority to stop a research protocol in progress, remove individual 
human subjects from a research protocol, and take whatever steps are necessary to protect the 
safety and well-being of human subjects until the IRB can assess the Monitor's report. Research 
Monitors shall have the responsibility to promptly report their observations and findings to the 
IRB or other designated official. 
This clinical research study will be monitored both internally by the PI and institutionally by 
the Duke Cancer Institute (DCI). In terms of internal review the PI will continuously monitor 
and tabulate adverse events. Appropriate reporting to the Duke University Medical Center IRB 
will be made. If an unexpected frequency of Grade III or IV events occur, depending on their 
nature, action appropriate to the nature and frequency of these adverse events will be taken. 
This may require a protocol amendment, dose de-escalation, or potentially closure of the study. 
The PI of this study will also continuously monitor the conduct, data, and safety of this study 
to ensure that: 
 
• Interim analyses occur as scheduled; 
• Stopping rules for toxicity and/or response are met; 
• Risk/benefit ratio is not altered to the detriment of the subjects; 
• Appropriate internal monitoring of AEs and outcomes is done; 
• Over-accrual does not occur; 
• Under-accrual is addressed with appropriate amendments or actions; 
• Data are being appropriately collected in a reasonably timely manner. 
• DCI review and monitoring of this protocol occurs in accordance with the NCI-
approved Data and Safety Monitoring Plan. Briefly, protocol review begins with an 
initial review by the Cancer Protocol Committee (CPC), which assesses the ethics and 
safety of the protocol. Documentation of these assessments will be maintained.  Formal, 
independent monitoring will be conducted by the DCI Monitoring Team after the first 

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3 subjects are enrolled, followed by annual monitoring of 1-3 subjects until the study 
is closed to enrollment and subjects are no longer receiving study interventions that are 
more than minimal risk. DCI Monitoring Team reports and additional 
data/safety/toxicity reports submitted by the PI will be reviewed by the Safety 
Oversight Committee (SOC) on an annual basis. Additional monitoring may be 
prompted by findings from monitoring visits, unexpected frequency of serious and/or 
unexpected toxicities, or other concerns.  Monitoring visits may also be initiated upon 
request by DUHS and DCI Leadership, CPC, SOC, a sponsor, an investigator, or the 
IRB. 
Additional monitoring may be prompted by findings from monitoring visits, unexpected 
frequency of serious and/or unexpected toxicities, or other concerns and may be initiated upon 
request of DUHS and DCI leadership, the CPC, the Safety Oversight Committee (SOC), the 
sponsor, the Principal Investigator, or the IRB. All study documents must be made available 
upon request to the DCI Monitoring Team and other authorized regulatory authorities, which 
may include but is not limited to the National Institute of Health, National Cancer Institute, 
and the FDA. Every reasonable effort will be made to maintain confidentiality during study 
monitoring. 
10.4 Compliance with Trial Registration and Results Posting Requirements 
Under the terms of the Food and Drug Administration Modernization Act (FDAMA) and the 
Food and Drug Administration Amendments Act (FDAAA), the Sponsor of the trial is solely 
responsible for determining whether the trial and its results are subject to the requirements for 
submission to the Clinical Trials Data Bank, http://www.clinicaltrials.gov. Information posted 
will allow subjects to identify potentially appropriate trials for their disease conditions and 
pursue participation by calling a central contact number for further information on appropriate 
trial locations and trial site contact information.     
10.5 Data Management 
10.5.1  Case Report Forms  
Electronic Case Report Forms (CRF) are used to record study data and are an integral part of 
the study and subsequent reports. The database used is Medidata RAVE. Most data will be 
collected from each subject’s electronic record. Each Subject’s CRF will be signed by the 
principal investigator at the end of the study, including those removed from the study for any 
reason. Case Report Forms must be kept current to reflect subject status at each phase during 
the course of the study. Subjects are not to be identified on case report forms by name; 
appropriate coded identification and subject initials must be used. The investigator must keep 
a separate log of subject names, medical record numbers, and subject numbers. This log is 
subject to FDA inspection.   

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10.5.2 
 Maintenance of Study Documentation    
The following will be maintained: 
a. Electronic Case Report Forms - must be kept accurate, and up-to-date. 
b. Electronic Medical Records and/or Shadow Chart - substantiates the data entered on 
the case report forms for all required tests and evaluation procedures and verifies that the 
subject has signed an informed consent to enter the study. 
c. Subject Exclusion Record - which should reflect the reason any subject was screened 
and found ineligible for the study. 
d. Regulatory Documents - including protocol, FDA Form 1572, CVs, IRB 
correspondence, IRB approval/renewals and IRB approved consent form. 
e. Adverse Experience Report Form - which should explain any serious or unexpected 
adverse experiences. 
All study documentation pertaining to the conduct of the study must be kept on file by the 
investigator for a minimum of two years. 
 
 

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11.0 APPENDICES 
11.1 ECOG Performance Status 
Grade 
Description 
0 
Normal activity. Fully active, able to carry on all pre-disease 
performance without restriction. 
1 
Symptoms, but ambulatory. Restricted in physically strenuous 
activity, but ambulatory and able to carry out work of a light or 
sedentary nature (e.g., light housework, office work). 
2 
In bed <50% of the time. Ambulatory and capable of all self-care, but 
unable to carry out any work activities. Up and about more than 50% 
of waking hours. 
3 
In bed >50% of the time. Capable of only limited self-care, confined 
to bed or chair more than 50% of waking hours. 
4 
100% bedridden. Completely disabled. Cannot carry on any self-care. 
Totally confined to bed or chair. 
5 
Dead. 
* As published in Am. J. Clin. Oncol.:  Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., 
McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern Cooperative Oncology 
Group. Am J Clin Oncol 5:649-655, 1982. The Eastern Cooperative Oncology Group, Robert Comis 
M.D., Group Chair. 
 
11.2 Common Terminology Criteria for Adverse Events V5.0 (CTCAE) 
The descriptions and grading scales found in the revised NCI Common Terminology Criteria 
for Adverse Events (CTCAE) version 5.0 will be utilized for adverse event reporting. 
(http://ctep.cancer.gov/reporting/ctc.html) 
11.3 Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 Criteria for 
Evaluating Response in Solid Tumors 
RECIST version 1.1* will be used in this study for assessment of tumor response. While either 
CT or MRI may be utilized, as per RECIST 1.1, CT is the preferred imaging technique in this 
study. 
* As published in the European Journal of Cancer: 
 
E.A. Eisenhauer, P. Therasse, J. Bogaerts, L.H. Schwartz, D. Sargent, R. Ford, J. 
Dancey, S. Arbuck, S. Gwyther, M. Mooney, L. Rubinstein, L. Shankar, L. Dodd, R. Kaplan, 
D. Lacombe, J. Verweij. New response evaluation criteria in solid tumors: Revised RECIST 
guideline (version 1.1). Eur J Cancer. 2009 Jan;45(2):228-47. 

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In addition, volumetric analysis will be explored by central review for response assessment. 
 
12.0 REFERENCES   
1. 
Montemurro F, Donadio M, Clavarezza M, et al. Outcome of patients with HER2-
positive advanced breast cancer progressing during trastuzumab-based therapy. The oncologist 
2006;11:318-24. 
2. 
Geyer CE, Forster J, Lindquist D, et al. Lapatinib plus capecitabine for HER2-positive 
advanced breast cancer. The New England journal of medicine 2006;355:2733-43. 
3. 
Verma S, Miles D, Gianni L, et al. Trastuzumab emtansine for HER2-positive 
advanced breast cancer. The New England journal of medicine 2012;367:1783-91. 
4. 
Gwin WR HA, Osada T, Hartman Z, Cheng Q, Broadwater G, Kimmick GG, Blackwell 
KL, Morse MA, Lyerly HK. Effect of alphavirus vaccine encoding HER2 during concurrent 
anti-HER2 therapies on induction of oligoclonal T cell and antibody responses against HER2.  
Journal of clinical oncology : official journal of the American Society of Clinical 
Oncology2015. 
5. 
Swain SM, Kim SB, Cortes J, et al. Pertuzumab, trastuzumab, and docetaxel for HER2-
positive metastatic breast cancer (CLEOPATRA study): overall survival results from a 
randomised, double-blind, placebo-controlled, phase 3 study. The Lancet Oncology 
2013;14:461-71. 
6. 
Muenst S, Soysal SD, Gao F, Obermann EC, Oertli D, Gillanders WE. The presence 
of programmed death 1 (PD-1)-positive tumor-infiltrating lymphocytes is associated with poor 
prognosis in human breast cancer. Breast cancer research and treatment 2013;139:667-76. 
7. 
Stagg J, Loi S, Divisekera U, et al. Anti-ErbB-2 mAb therapy requires type I and II 
interferons and synergizes with anti-PD-1 or anti-CD137 mAb therapy. Proceedings of the 
National Academy of Sciences of the United States of America 2011;108:7142-7. 
8. 
Karyampudi L, Lamichhane P, Scheid AD, et al. Accumulation of memory precursor 
CD8 T cells in regressing tumors following combination therapy with vaccine and anti-PD-1 
antibody. Cancer research 2014;74:2974-85. 
9. 
Cameron D, Casey M, Press M, et al. A phase III randomized comparison of lapatinib 
plus capecitabine versus capecitabine alone in women with advanced breast cancer that has 
progressed on trastuzumab: updated efficacy and biomarker analyses. Breast cancer research 
and treatment 2008;112:533-43. 

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10. 
Curigliano G, Spitaleri G, Dettori M, Locatelli M, Scarano E, Goldhirsch A. Vaccine 
immunotherapy in breast cancer treatment: promising, but still early. Expert review of 
anticancer therapy 2007;7:1225-41. 
11. 
Ladjemi MZ, Jacot W, Chardes T, Pelegrin A, Navarro-Teulon I. Anti-HER2 vaccines: 
new prospects for breast cancer therapy. Cancer immunology, immunotherapy : CII 
2010;59:1295-312. 
12. 
Knutson KL, Schiffman K, Disis ML. Immunization with a HER-2/neu helper peptide 
vaccine generates HER-2/neu CD8 T-cell immunity in cancer patients. The Journal of clinical 
investigation 2001;107:477-84. 
13. 
Disis ML, Gooley TA, Rinn K, et al. Generation of T-cell immunity to the HER-2/neu 
protein after active immunization with HER-2/neu peptide-based vaccines. Journal of clinical 
oncology : official journal of the American Society of Clinical Oncology 2002;20:2624-32. 
14. 
Disis ML, Schiffman K, Guthrie K, et al. Effect of dose on immune response in patients 
vaccinated with an her-2/neu intracellular domain protein--based vaccine. Journal of clinical 
oncology : official journal of the American Society of Clinical Oncology 2004;22:1916-25. 
15. 
Hueman MT, Stojadinovic A, Storrer CE, et al. Analysis of naive and memory CD4 
and CD8 T cell populations in breast cancer patients receiving a HER2/neu peptide (E75) and 
GM-CSF vaccine. Cancer immunology, immunotherapy : CII 2007;56:135-46. 
16. 
Morse MA, Clay TM, Colling K, et al. HER2 dendritic cell vaccines. Clinical breast 
cancer 2003;3 Suppl 4:S164-72. 
17. 
Morse MA, Hobeika A, Osada T, et al. Long term disease-free survival and T cell and 
antibody responses in women with high-risk Her2+ breast cancer following vaccination against 
Her2. Journal of translational medicine 2007;5:42. 
18. 
Xia W, Gerard CM, Liu L, Baudson NM, Ory TL, Spector NL. Combining lapatinib 
(GW572016), a small molecule inhibitor of ErbB1 and ErbB2 tyrosine kinases, with 
therapeutic anti-ErbB2 antibodies enhances apoptosis of ErbB2-overexpressing breast cancer 
cells. Oncogene 2005;24:6213-21. 
19. 
Disis ML, Wallace DR, Gooley TA, et al. Concurrent trastuzumab and HER2/neu-
specific vaccination in patients with metastatic breast cancer. Journal of clinical oncology : 
official journal of the American Society of Clinical Oncology 2009;27:4685-92. 
20. 
Montgomery RB, Makary E, Schiffman K, Goodell V, Disis ML. Endogenous anti-
HER2 antibodies block HER2 phosphorylation and signaling through extracellular signal-
regulated kinase. Cancer research 2005;65:650-6. 

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21. 
Rayner JO, Dryga SA, Kamrud KI. Alphavirus vectors and vaccination. Reviews in 
medical virology 2002;12:279-96. 
22. 
Pushko P, Parker M, Ludwig GV, Davis NL, Johnston RE, Smith JF. Replicon-helper 
systems from attenuated Venezuelan equine encephalitis virus: expression of heterologous 
genes in vitro and immunization against heterologous pathogens in vivo. Virology 
1997;239:389-401. 
23. 
Pushko P, Bray M, Ludwig GV, et al. Recombinant RNA replicons derived from 
attenuated Venezuelan equine encephalitis virus protect guinea pigs and mice from Ebola 
hemorrhagic fever virus. Vaccine 2000;19:142-53. 
24. 
Pushko P, Geisbert J, Parker M, Jahrling P, Smith J. Individual and bivalent vaccines 
based on alphavirus replicons protect guinea pigs against infection with Lassa and Ebola 
viruses. Journal of virology 2001;75:11677-85. 
25. 
Balasuriya UB, Heidner HW, Hedges JF, et al. Expression of the two major envelope 
proteins of equine arteritis virus as a heterodimer is necessary for induction of neutralizing 
antibodies in mice immunized with recombinant Venezuelan equine encephalitis virus replicon 
particles. Journal of virology 2000;74:10623-30. 
26. 
Balasuriya UB, Heidner HW, Davis NL, et al. Alphavirus replicon particles expressing 
the two major envelope proteins of equine arteritis virus induce high level protection against 
challenge with virulent virus in vaccinated horses. Vaccine 2002;20:1609-17. 
27. 
Lee JS, Pushko P, Parker MD, Dertzbaugh MT, Smith LA, Smith JF. Candidate vaccine 
against botulinum neurotoxin serotype A derived from a Venezuelan equine encephalitis virus 
vector system. Infection and immunity 2001;69:5709-15. 
28. 
Lee JS, Dyas BK, Nystrom SS, Lind CM, Smith JF, Ulrich RG. Immune protection 
against staphylococcal enterotoxin-induced toxic shock by vaccination with a Venezuelan 
equine encephalitis virus replicon. The Journal of infectious diseases 2002;185:1192-6. 
29. 
Strauss JH, Strauss EG. The alphaviruses: gene expression, replication, and evolution. 
Microbiological reviews 1994;58:491-562. 
30. 
Davis NL, Powell N, Greenwald GF, et al. Attenuating mutations in the E2 
glycoprotein gene of Venezuelan equine encephalitis virus: construction of single and multiple 
mutants in a full-length cDNA clone. Virology 1991;183:20-31. 
31. 
Davis NL, Willis LV, Smith JF, Johnston RE. In vitro synthesis of infectious 
venezuelan equine encephalitis virus RNA from a cDNA clone: analysis of a viable deletion 
mutant. Virology 1989;171:189-204. 

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32. 
Grieder FB, Davis NL, Aronson JF, et al. Specific restrictions in the progression of 
Venezuelan equine encephalitis virus-induced disease resulting from single amino acid 
changes in the glycoproteins. Virology 1995;206:994-1006. 
33. 
Wecker M, Gilbert P, Russell N, et al. Phase I safety and immunogenicity evaluations 
of an alphavirus replicon HIV-1 subtype C gag vaccine in healthy HIV-1-uninfected adults. 
Clinical and vaccine immunology : CVI 2012;19:1651-60. 
34. 
Davis NL, Caley IJ, Brown KW, et al. Vaccination of macaques against pathogenic 
simian immunodeficiency virus with Venezuelan equine encephalitis virus replicon particles. 
Journal of virology 2000;74:371-8. 
35. 
Schultz-Cherry S, Dybing JK, Davis NL, et al. Influenza virus (A/HK/156/97) 
hemagglutinin expressed by an alphavirus replicon system protects chickens against lethal 
infection with Hong Kong-origin H5N1 viruses. Virology 2000;278:55-9. 
36. 
Wilson JA, Hevey M, Bakken R, et al. Epitopes involved in antibody-mediated 
protection from Ebola virus. Science (New York, NY) 2000;287:1664-6. 
37. 
Wilson JA, Hart MK. Protection from Ebola virus mediated by cytotoxic T 
lymphocytes specific for the viral nucleoprotein. Journal of virology 2001;75:2660-4. 
38. 
Hevey M, Negley D, Pushko P, Smith J, Schmaljohn A. Marburg virus vaccines based 
upon alphavirus replicons protect guinea pigs and nonhuman primates. Virology 1998;251:28-
37. 
39. 
Velders MP, McElhiney S, Cassetti MC, et al. Eradication of established tumors by 
vaccination with Venezuelan equine encephalitis virus replicon particles delivering human 
papillomavirus 16 E7 RNA. Cancer research 2001;61:7861-7. 
40. 
Long MC, Jager S, Mah DC, et al. Construction and characterization of a novel 
recombinant single-chain variable fragment antibody against Western equine encephalitis 
virus. Hybridoma 2000;19:1-13. 
41. 
Long MC, Nagata LP, Ludwig GV, et al. Construction and characterization of 
monoclonal antibodies against western equine encephalitis virus. Hybridoma 2000;19:121-7. 
42. 
Wang X, Wang JP, Maughan MF, Lachman LB. Alphavirus replicon particles 
containing the gene for HER2/neu inhibit breast cancer growth and tumorigenesis. Breast 
cancer research : BCR 2005;7:R145-55. 
43. 
Nelson EL, Prieto D, Alexander TG, et al. Venezuelan equine encephalitis replicon 
immunization overcomes intrinsic tolerance and elicits effective anti-tumor immunity to the 

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'self' tumor-associated antigen, neu in a rat mammary tumor model. Breast cancer research and 
treatment 2003;82:169-83. 
44. 
Morse MA, Hobeika AC, Osada T, et al. An alphavirus vector overcomes the presence 
of neutralizing antibodies and elevated numbers of Tregs to induce immune responses in 
humans with advanced cancer. The Journal of clinical investigation 2010;120:3234-41.