Conditions: Solid Tumors
Keywords: Solid Tumors HPV-16 Positive Incurable Solid Tumors ISA101 HPV-16 vaccination Nivolumab BMS-936558 Opdivo
Allocation: NA | Intervention model: SINGLE_GROUP
Enrollment: 33
Healthy volunteers: no

Brief summary:
The goal of this clinical research study is to learn if nivolumab combined with ISA101 can help to control cancer that has spread. The safety of the study drugs will also be studied.

This is an investigational study. ISA101 is not FDA approved or commercially available. It is currently being used for research purposes only. Nivolumab is FDA approved to treat certain types of melanoma in patients who no longer respond to other drugs. Combining ISA101 with nivolumab is investigational. The study doctor can explain how the study drugs are designed to work.

Up to 28 participants will be enrolled in this study. All will take part at MD Anderson.

Detailed description:
Study Drug Administration:

There are 3 weeks in Cycle 1 and 2 weeks in Cycles 2 and beyond.

If you are found to be eligible to take part in this study, you will receive ISA101 by injection on Day 1 of Cycles 1, 2, and 4. You will be closely watched for the first 3 hours after each dose in order to check for any allergic reactions. Each time, you will receive 2 injections. One may be in your arm and one in your leg.

You will receive nivolumab by vein over 60 minutes on Day 8 of Cycle 1 and Day 1 of Cycles 2 and beyond.

Study Visits:

On Days 1 and 8 of Cycle 1 and Day 1 of every cycle after that:

* You will have a physical exam.
* Blood (about 4 teaspoons) will be drawn for routine tests.

On Day 1 of Cycle 1 and then 1 time a month after that, if you can become pregnant, blood (about 1 teaspoon) or urine will be collected for a pregnancy test.

At Week 11 and every 6 weeks after that, you will have a CT scan or MRI to check the status of the disease.

Additional Research Tests:

Blood (up to 20 teaspoons each time) will be drawn before you begin to receive the study treatment, before you receive ISA101 at Weeks 3 and 7, before you receive nivolumab at Weeks 9 and 11, then every 12 weeks after that. If the doctor thinks it is needed because of white blood cell recovery from stored cells, one of the every 12 week blood draws may be done earlier. These blood samples will be used for biomarker tests and tests of the immune system.

Length of Treatment:

You may take ISA101 for up to 3 doses. You may continue taking nivolumab for as long as the doctor thinks it is in your best interest. You will no longer be able to take the study drug if intolerable side effects occur, or if you are unable to follow study directions.

If the disease seems like it has gotten worse, you may decide to continue to receive nivolumab, if you are still eligible. It is possible the study drug may be working even though the tumor(s) got larger. However, there are risks of continuing to receive the study drug because the disease may actually be getting worse. This is described in the side effects section below.

Your participation on the study will be over after the follow-up.

Follow-up Visits:

At about 30 days and 70 days after the last study drug dose, and then as often as the doctor decides as needed, the following tests and procedures will be performed:

* You will have a physical exam.
* Blood (about 4 teaspoons) will be drawn for routine tests.

At about 30 days, 70 days, and every 6 weeks after that (if you stop the study drug\[s\] for reasons other than the disease getting worse), you will have a CT or MRI scan to check the status of the disease. If the disease gets worse, these scans will stop.

Every 3 months for up to 3 years after your last study drug dose, you will be asked how you are doing (either at a visit or by phone). The calls should last about 10 minutes.

Arms:
arm 1: HPV-16 vaccination (ISA 101) administered subcutaneously at 100 mcg for a total of 3 doses at 3 to 4 weeks intervals starting on Day 1.

Nivolumab administered intravenously at 3 mg/kg every 2 weeks beginning on day 8 after the first vaccine dose.

There are 3 weeks in Cycle 1 and 2 weeks in Cycles 2 and beyond.

Interventions: intervention 1: ISA 101 intervention 2: Nivolumab
Intervention descriptions: intervention 1: 100 mcg administered subcutaneously for a total of 3 doses at 3 to 4 weeks intervals starting on Day 1. intervention 2: 3 mg/kg administered by vein every 2 weeks beginning on Day 8 after the first vaccine dose.

Protocol document:
Prot_SAP_000.pdf: 
 
 
Phase II Trial of Nivolumab and HPV-16 Vaccination in 
Patients with HPV-16-Positive Incurable Solid Tumors 
 
 
 Coordinating Center:  
 
University of Texas MD Anderson Cancer Center 
 
 Chair:  
Bonnie Glisson, MD 
 
1515 Holcombe Blvd, Unit 0432 
 
Houston, TX  77030 
 
Telephone:  713-792-6363 
 
Fax: 713-792-1220 
 
bglisson@mdanderson.org 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Bristol-Myers Squibb Protocol # CA209-306 
 
NCT # 02426892 
 
 
 
Version Date:  
 
     January 27, 2017 
 
1 
 


TABLE OF CONTENTS 
1.0 INTRODUCTION AND STUDY RATIONALE 
 
Pages 4-21 
1.1 STUDY RATIONALE 
1.1.1 Rationale for Combination of Nivolumab and ISA 101 
1.1.2 Rationale for ISA 101 Dose and Schedule 
1.1.3 Rationale for Nivolumab Dose and Schedule 
1.1.4 Rationale for Initial Tumor Assessment at 11 Weeks 
1.1.5 Rationale for Collection of Tumor Tissue and Evaluation of Tumor 
Immune Related Biomarkers 
1.2 RESEARCH HYPOTHESIS 
1.3 OBJECTIVES 
1.3.1 Primary Objective 
1.3.2 Secondary Objectives 
1.3.3 Exploratory Objectives 
1.4 MECHANISM OF ACTION 
1.4.1 Mechanism of Action of SLP-HPV-16 Vaccine 
1.4.2 Mechanism of Action of Nivolumab 
1.4.3 HPV Positive Malignancies 
1.4.4 ISA 101 Clinical Results 
1.4.5 Nivolumab Clinical Results 
1.5 OVERALL RISK/BENEFIT ASSESSMENT 
2.0 INVESTIGATIONAL PLAN  
 
 
 
Pages 21-27 
2.1 Study Design and Duration 
2.2 Study Population 
2.2.1 Inclusion Criteria 
2.2.2 Exclusion Criteria 
2.2.3 Women of Childbearing Potential 
2.3 Concomitant Treatments 
2.3.1 Prohibited and/or Restricted Treatments 
2.3.2 Other Restrictions and Precautions 
2.3.3 Permitted Therapy 
2.4 Discontinuation of Subjects from Treatment 
3.0 TREATMENTS  
 
 
 
 
 
Pages 27-35 
3.1 Study Treatments 
3.2 Handling and Dispensing 
3.3 Selection and Timing of Dose for Each Subject 
3.3.1 Dose Delay Criteria 
3.3.2 Dose Reductions 
3.3.3 Criteria to Resume Dosing 
3.3.4 Treatment beyond Disease Progression 
3.3.5    Treatment Discontinuation Criteria 
3.3.6    Treatment of Nivolumab-Related Infusion Reactions 
3.3.7 Treatment of ISA101 Related System Reactions 
3.4 Treatment Compliance 
3.5 Destruction and Return of Study Drug 
4.0 ASSESSMENT FOR SAFETY AND EFFICACY 
 
Pages 35-42 
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4.1 Safety  Assessments 
4.2 Efficacy Assessments 
4.3 Other Assessments 
5.0 SAFETY MONITORING AND REPORTING 
 
Pages 42-47 
5.1 ADVERSE EVENTS: Definitions and Reporting   
5.1.1 Serious Adverse Events Reporting 
5.1.2 Communication between Investigator and BMS and ISA 
5.2 Laboratory Test Abnormalities 
5.3 Pregnancy 
5.4 Overdose 
5.5 Potential Drug Induced Liver Injury (DILI) 
5.6 Other Safety Considerations 
 
6.0 STATISTICAL CONSIDERATIONS  
 
 
Pages 47-50 
6.1 Sample Size Determination 
6.2 Populations for Analyses 
6.3 Endpoint Definitions 
6.3.1 Primary Endpoint 
6.3.2 Secondary Endpoints 
6.3.3 Exploratory Endpoints 
6.3.4 Safety Analyses 
7.0 References 
 
 
 
 
 
 
Pages 50-55 
 
Appendix 1 RECIST 1.1 criteria 
 
 
 
 
Pages 55-62 
Appendix 2 Immune-Related Response Criteria (irRC)  
Pages 62-65 
Appendix 3 Toxicity Monitoring 
 
 
 
 
Pages 65-66 
Appendix 4 Toxicity Management Algorithms 
 
 
Pages 67-70 
 
 
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1.0  INTRODUCTION AND STUDY RATIONALE 
 
Infection with Human Papillomavirus (HPV) causes substantial cancer burden including 
nearly all cervical, majority of oropharyngeal, and a significant percentage of anal, 
penile, vulvar, and vaginal cancers. The HPV vaccines currently available are only 
preventive, must be given before sexual debut/HPV exposure, and have little market 
penetration.  Additionally, the latent period between exposure and diagnosis of cancer is 
decades-long; therefore, even if vaccine use is increased in the near term, high risk HPV-
related cancers will continue to increase and persist for decades to come.  
 
Recent work has identified signaling pathways between tumor and immune cells which 
act to suppress immune rejection. Inhibition of signaling with antibodies to key proteins, 
cytotoxic T lymphocyte antigen-4 (CTLA-4) and programmed death receptor-1 (PD-1), 
has resulted in very promising tumor shrinkage and prolonged survival in patients with a 
variety of cancers, including lung cancer, a tumor long-considered non-immunogenic. 
However, only a subset of patients responds, emphasizing the importance of addressing 
other mechanisms of resistance to immune response. This strategy of checkpoint 
inhibition may have particular relevance for virally-driven cancers, which should be 
vulnerable based on expression of non-self, viral-specific antigens, and theoretically, 
could synergize with the effects of vaccination.  
 
Melief et al. have developed and investigated ISA101 and its prototype, designated HPV-
16-SLP, a series of overlapping, fully synthetic long peptides (SLP) based on the 
sequence of HPV-16 oncoproteins E6 and E7 (1, 2). This vaccine showed strong 
immunogenicity and clinical responses in patients with HPV-related vulvar intraepithelial 
neoplasia, the latter directly correlating with induced immune response (1).  The vaccine 
is being evaluated in patients with advanced cervical cancer in combination with standard 
chemotherapy. Although a pilot trial of standard chemotherapy in combination with 
ISA101 treatment in cervical cancer treatment has shown synergy in the induction of 
potent immune responses (Melief et al, unpublished results), another highly promising 
treatment is combination of vaccination and checkpoint blocking. If successful, as 
proposed in the current protocol, at a later stage all three treatment modalities could be 
combined (i.e. chemo-immunotherapy with both vaccine and nivolumab). For now, it is 
obviously not prudent to do this without first exploring the added value of ISA101 
vaccination in combination with nivolumab without chemotherapy. 
 
ISA 101 is a therapeutic HPV-16 vaccine  consisting of 9 overlapping long E6 peptides 
(25-mer to 32-mer E6 peptides) and 4 overlapping long E7 peptides (35-mer E7 peptides) 
(SLP-HPV-16 vaccine). These peptides overlap by 10 to 18 residues and cover the 
complete sequence of HPV16 E6 and E7 onco-proteins. These long peptides have the 
capacity to effectively deliver antigens to dendritic cells (DC). Proper DC activation by 
adjuvant then induces CD4+ and CD8+ T-cell responses by MHC class I and MHC class 
II presentation of the HPV16 E6/E7 processed epitope peptides. Properly activated CD4 
T cells increase surface CD40Ligand (CD40L) expression, causing DC activation 
through CD40L-CD40 triggering. This in turn leads to CD8 T cell activation associated 
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with expansion of CD8+ cytotoxic T cells capable to reach and kill tumor cells that 
express E6 and E7 epitopes.  
 
In a preclinical model of HPV16-induced cervical cancer, vaccination with a HPV-16- 
SLP vaccine, consisting of a single SLP, designed for the MHC type of the homozygous 
inbred mouse strain C57BL/6, elicited a strong HPV16 specific cytotoxic CD8+ T cell 
response in mice, which in an adjuvant setting resulted in increased survival and 
eradication of existing tumors (3). In a second preclinical disease model in rabbits, 
mimicking persistent HPV infections and related papilloma induced lesions, the long 
peptide vaccination approach resulted in similar effects: a strong induction of a 
papilloma-specific immune response, clearing of viral DNA and regression of established 
cottontail rabbit papilloma virus-induced wart growth (4).  
 
In patients with high-grade premalignant vulvar lesions  (VIN) the prototype HPV-16-
SLP vaccine produced regression of lesions in 15/19 patients at 12 months of follow up 
and 9/19 had complete disappearance of disease that was durable in all 9 at 24 months 
(1). Importantly, complete clinical responses were correlated with stronger interferon-
gamma-associated T cell responses and all complete responders developed HPV-16 
specific immunity.  Subsequently a pilot study in 12 patients with advanced cervical 
cancer indicated that T-cell responses are enhanced when combining appropriately timed 
chemotherapy (carboplatin/paclitaxel) and the HPV-16 vaccine (1, 2). The mechanisms 
of enhanced immune response upon delivery of a single vaccine dose 2 weeks after the 
last dose in the second cycle of carboplatin/taxol chemotherapy appeared to be depletion 
of myeloid derived suppressor cells without depletion of T cell function or numbers. An 
additional Phase 2 trial in patients with advanced cervical cancer, CervISA, is being 
conducted to evaluate the optimal dose of ISA101, with or without interferon alpha,that 
produces a robust immune response. Results from this are expected to soon (first half of 
2015). 
 
Nivolumab (BMS-936558, Bristol Myers Squibb)  is a fully human, IgG4 (kappa) isotype 
mAb that binds PD-1 on activated immune cells and disrupts engagement of the receptor 
with its ligands PD-L1 (B7-H1/CD274) and PD-L2 (B7-DC/CD273), thereby reportedly 
abrogating inhibitory signals and augmenting the host antitumor response. In early 
clinical trials, nivolumab has demonstrated activity in several tumor types, including 
melanoma, renal cell cancer (RCC), and NSCLC (5). In particular, substantial activity has 
been noted in the squamous histology subgroup of NSCLC,  for whom objective response 
rates averaged 33% across dose levels, and progression free survival approached ~6 
months (6). In general, nivolumab  has been well tolerated to date, with a favorable safety 
profile consistent with predicted toxicities based on an immunostimulatory mechanism of 
action (7). 
 
1.1 STUDY RATIONALE 
 
1.1.1 Rationale for the combination of nivolumab and ISA101 
In HPV-related oropharyngeal cancer, recent data suggest a key role of the programmed 
death-1 (PD-1) pathway in creating a favorable microenvironment for HPV infection and 
5 
 


subsequent tumor progression (8).  Melief et al. have shown that the combination of 
checkpoint inhibition with antibody to PD-ligand 1 (PD-L1) enhances the antitumoral 
immune response created by vaccination with the single HPV SLP mentioned above in an 
E7-expressing murine tumor model obtained by co-transformation of primary C57BL/6 
mouse lung epithelial cells with HPV-16 E6 and E7 and activated ras oncogene as 
previously described  (TC-1) (9) (unpublished). In addition, in this particular HPV16 
E6/E7 TC-1 tumor, HPV16-specific T cells did not enter the tumor microenvironment 
without HPV SLP vaccination. These findings suggest that the effect of checkpoint 
inhibition (i.e. PD-L1 blockade) is at least in part dependent on vaccine-induced 
infiltration of HPV-specific tumor infiltrating lymphocytes (TIL). Nasman et al have 
reported that the number of CD8-positive TILs in HPV-related oropharyngeal cancer is 
directly correlated with prognosis (10). Badoual et al. reported that vaccination with a 
non-replicative delivery vector targeting dendritic cells increased PD-1 expression on T 
cells and enhanced tumor regression with PD-1 blockade in a mouse model of HPV-
positive oropharyngeal carcinoma (11). These lines of evidence strongly support the 
concept that the SLP anti-HPV vaccine will enhance the efficacy of checkpoint inhibition 
therapy. The rationale to combine vaccine with checkpoint inhibition is further 
strengthened by preliminary data from an ongoing trial with pembrolizumab (MK3475, 
Merck), another PD-1 antibody reported by Seiwert et al. (12).  They reported an ORR of 
20% (4/20), including one CR in patients with HPV-positive OPSCC.  Although these 
data are proof of principle that checkpoint inhibition is effective for a subset of patients, 
they also underline the importance of studying combination immunotherapy approaches 
to increase response rate.  
 
1.1.2 Rationale for ISA 101 dose and schedule 
In completed and ongoing clinical studies with HPV-16-SLP, the precursor vaccine to 
ISA101,,  over 180  patients with HPV-induced pre-malignancy of the cervix and vulva 
have been administered the vaccine at least once at doses ranging from 20 to 300 μg per 
peptide [ISA101 Investigators Brochure, June 2014 (13)].  Previous clinical trials 
utilizing HPV-16-SLP formulated with Montanide as monotherapy have demonstrated an 
acceptable safety profile for patients with malignancy, induction of robust T cell immune 
responses compared to pre-vaccination values, and clinical efficacy in patients with high 
grade VIN (1, 14).  In patients with cervical dysplasia and advanced cervical cancer, it 
has been possible to show induction of specific T cell responses utilizing the HPV-16-
SLP monotherapy approach (2, 15), but these remained below the level associated with 
clinical responses in the VIN trial, and therefore, as expected without convincing clinical 
impact.  This indicates the need for improvement by co-treatment in patients with late 
stage HPV16-positive cervical cancer.  
A phase I/II clinical trial, exploring the aforementioned chemo-immunotherapy co-
treatment, called CervISA (NCT02128126), sponsored by ISA, is currently ongoing in 
Europe.  This trial is investigating the safety and tolerability of different dose levels of 
ISA101 with or without pegylated interferon-alpha (IFNα) in combination with 
carboplatin and paclitaxel in patients with recurrent/metastatic incurable cervical cancer. 
Dose determination for the current trial has been chosen on bases of prior trials that have 
shown 100 mcg to be safe and to elicit appropriate anti HPV-16 immune response (1, 14). 
6 
 


 
1.1.3 Rationale for nivolumab dose and schedule 
The dose and schedule of nivolumab in this study will be 3 mg/kg every 2 weeks, based 
upon a February 24, 2012 analysis of safety, efficacy, and exposure-response data from a  
Phase 1 study (16). Anti-tumor activity was observed in NSCLC subjects at dose levels 
of 1, 3 and 10 mg/kg every 2 weeks. Anti-tumor activity appeared to approach a plateau 
at dose levels of 3 mg/kg and above. Consistent with these observations, the results of 
exposure-response analyses showed that the probability of a tumor response tended to 
approach a plateau for trough concentrations produced by 3 and 10 mg/kg administered 
every 2 weeks. nivolumab was adequately tolerated up to 10 mg/kg, the highest dose 
level tested, and no maximum tolerated dose (MTD) was identified. While the spectrum, 
frequency, and severity of nivolumab-related AEs were generally similar across the dose 
levels tested, the 10 mg/kg dose level had numerically higher rates of Grade 3/4 drug-
related SAEs and AEs leading to discontinuation. Based on these observations, a dose of 
3 mg/kg every 2 weeks was chosen for further study.  
 
1.1.4 Rationale for initial tumor assessment at 11 weeks 
Accumulating clinical evidence indicates that patients treated with immune system 
stimulating agents may develop progression of disease (by conventional response criteria) 
before demonstrating clinical objective responses and/or stable disease. This phenomenon 
was observed in the Phase 1 study of nivolumab. Two hypotheses have been put forth to 
explain this phenomenon. First, enhanced inflammation within tumors could lead to an 
increase in tumor size appearing as enlarged index lesions and as newly visible small 
non-index lesions. Over time, both the malignant and inflammatory portions of the mass 
may then decrease leading to overt signs of clinical improvement. Another hypothesis is 
that the kinetics of tumor growth may initially outpace anti-tumor immune activity in 
some individuals. With sufficient time, the anti-tumor activity will dominate and become 
clinically apparent. For these reasons, the initial tumor assessment in the phase I trial was 
conducted at 8 weeks, and it is unknown if an earlier assessment would demonstrate 
similar activity due to premature termination of study treatment. 
 
To mitigate the risk of detecting false-progression early in the course of treatment with 
nivolumab in combination with ISA101, the initial tumor assessment in this study will 
take place at Week 11 (±5 days). Thereafter, all subsequent tumor assessments will take 
place regularly every 6 weeks (±5 days) until documented disease progression or 
treatment discontinuation, whichever occurs later.  
 
1.1.5 Rationale for collection of tumor tissue and evaluation of tumor immune 
related biomarkers 
This study will prospectively examine tumor tissues and blood samples from patients in 
the clinical trial to identify potential pharmacodynamic markers reflecting therapy effect 
and biomarkers of response or resistance to therapy. 
 
Tumor tissue will be obtained at baseline, at Week 11 (response evaluation), and at 
progression (as possible).  
7 
 


 
 Among the tumor markers to be studied are the B7 family ligands, PD-L1 (B7-H1), PD-
L2 (B7-DC), B7-H3 and B7-x, which have been reported to be up-regulated in tumors by 
mRNA profiling. While PD-L1 is the major ligand expressed by tumor cells in solid 
malignancies, immunohistochemistry analysis by the Pardoll/Topalian/Taube group has 
demonstrated PD-L2 expression on tumor infiltrating dendritic cells and macrophages 
(17). Allison and Sharma have published data demonstrating expression of B7-H3 and 
B7-x as predictors of poor clinical outcome in patients with prostate cancer (18), which 
we will now extend to study in patients with HPV-related cancers to be treated with anti-
PD-1 and ISA101. Among the lymphocyte receptors to be analyzed, PD-1, LAG-3, 2B4, 
BTLA and Tim3 have all been associated with inhibition of lymphocyte activity and in 
some cases induction of lymphocyte anergy that can be reversed upon antibody blockade 
in animal models (19). Thus, they appear to play non-redundant roles in feedback 
inhibition of T cell responses when their cognate ligands are present. In addition to 
providing inhibitory signals to activated effector T cells, some of these receptors, 
particularly PD-1, LAG-3 and Tim3 (as well as CTLA-4), are highly expressed on 
regulatory T cells (Treg), where they amplify Treg inhibitory activity (17). Ligands for 
LAG-3, 2B4, BTLA and Tim3 are MHC II, CD48, HVEM and galectin 9 respectively, 
some of which have been previously reported as expressed in various human tumors on 
gene expression arrays. These studies will provide us with a comprehensive view of 
cellular subsets and checkpoint molecule expression in tumors from untreated patients 
and how cellular subsets and key immune regulatory molecules are impacted 
intratumorally after treatment with anti-PD-1 and ISA101. Determining which inhibitory 
molecules/pathways are present despite treatment with anti-PD-1 and the ISA101 vaccine 
should inform selection of rational combination therapy in the future.  Importantly, all of 
these parameters of the immune microenvironment will be correlated with clinical 
outcome.  
 
 
1.2 RESEARCH HYPOTHESIS 
 
In patients with recurrent/metastatic incurable HPV-16 positive cancer the combination 
of ISA101 vaccination and checkpoint inhibition will have an acceptable safety profile 
and will produce HPV-specific immune responses and clinical efficacy. 
 
1.3 OBJECTIVES 
 
1.3.1 Primary Objective 
To evaluate the objective response rate (ORR) by RECIST 1.1 criteria of the combination 
of ISA 101 vaccination and nivolumab in patients with recurrent/metastatic incurable 
HPV-16 positive solid malignancies. 
 
1.3.2 Secondary Objectives  
• To evaluate the toxicity of the ISA 101 vaccination and nivolumab individually 
and of the combination; 
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• To evaluate the HPV-specific immune responses of the combination of ISA 101 
vaccination and nivolumab; 
• To evaluate response rate by immune-related criteria of the combination of ISA 
101 vaccination and nivolumab; 
•  To evaluate the progression free survival (PFS) of the combination of ISA 101 
vaccination and nivolumab; 
• To evaluate the immune-related PFS of the combination of ISA 101 vaccination 
and nivolumab; 
• To evaluate the overall survival (OS) of the combination of ISA 101 vaccination 
and nivolumab; 
 
1.3.3 Exploratory Objectives  
•  To explore potential predictive biomarkers of response to the combination of ISA 
101 vaccination and nivolumab in tumor specimens and peripheral blood. 
 
1.4 MECHANISM OF ACTION 
 
1.4.1 Mechanism of action of ISA101 vaccine 
The proposed mode of action in relation to therapy of HPV-associated malignancies, is 
based on the fact that SLP of 25-35 amino acids in length require an obligatory 
processing step by DC in order for the resulting short peptides to bind to MHC class I and 
II molecules and become transported to the cell surface. DC can very efficiently process 
and present long peptides following direct cytoplasmic uptake and only DC can do this 
efficiently. Short exact MHC class I-binding peptides, in contrast, bind exogenously to 
MHC class I molecules of all nucleated cells that express surface MHC class I. Since 
most of these cells are not professional antigen-presenting cells such as DC, this leads to 
suboptimal antigen processing and presentation in the absence of co-stimulatory 
molecules. In addition the use of exact MHC class I-binding peptides does not stimulate 
CD4+ T cell immunity, which is a prerequisite for optimal expansion of CD8+ killer cells 
and for CD8+ T cell memory. 
 
Pharmacokinetic parameters for ISA101 were not determined in the pre-clinical studies. 
Studies with other SLP vaccines, however, indicate that the distribution of the peptides is 
mainly restricted to the draining lymph nodes (20). Furthermore, the investigational 
product is not metabolized in the conventional sense: the peptides are taken up by antigen 
presenting cells, which process the peptides into smaller entities, called T-cell epitopes, 
which are presented on the surface of the antigen presenting cell (APC). In the meantime, 
the APC traffics to a draining lymph node, where naive T cells recognize the T-cell 
epitopes and are activated by these epitopes. The peptides are degraded within APCs 
through normal degradation pathways. 
 
1.4.2 Mechanism of action of nivolumab 
Cancer immunotherapy rests on the premise that tumors can be recognized as foreign 
rather than as self and can be effectively attacked by an activated immune system. An 
effective immune response in this setting is thought to rely on immune surveillance of 
tumor antigens expressed on cancer cells that ultimately results in an adaptive immune 
9 
 


response and cancer cell death. Meanwhile, tumor progression may depend upon 
acquisition of traits that allow cancer cells to evade immunosurveillance and escape 
effective innate and adaptive immune responses (21-23). Support for the role of 
immunosurveillance in many tumor types, including NSCLC,  is suggested in 
retrospective analyses demonstrating a correlation between tumor infiltrating 
lymphocytes in surgically resected specimens and recurrence free survival (24-26). 
Current immunotherapy efforts attempt to break the apparent tolerance of the immune 
system to tumor cells and antigens by either introducing cancer antigens by therapeutic 
vaccination or by modulating regulatory checkpoints of the immune system. 
 
T-cell stimulation is a complex process involving the integration of numerous positive as 
well as negative co-stimulatory signals in addition to antigen recognition by the T-cell 
receptor (TCR). Collectively, these signals govern the balance between T-cell activation 
and tolerance. PD-1 is a member of the CD28 family of T-cell co-stimulatory receptors 
that also includes CD28, CTLA-4, ICOS, and BTLA (27). PD-1 signaling has been 
shown to inhibit CD-28-mediated upregulation of IL-2, IL-10, IL-13, interferon –γ (IFN-
γ) and Bcl-xL. PD-1 expression also been noted to inhibit T cell activation, and 
expansion of previously activated cells. Evidence for a negative regulatory role of PD-1 
comes from studies of PD-1 deficient mice, which develop a variety of autoimmune 
phenotypes (28). These results suggest that PD-1 blockade has the potential to activate 
anti-self T-cell responses, but these responses are variable and dependent upon various 
host genetic factors. Thus, PD-1 deficiency or inhibition is not accompanied by a 
universal loss of tolerance to self-antigens. 
 
In vitro, nivolumab binds to PD-1 with high affinity (EC50 0.39-2.62 nM), and inhibits 
the binding of PD-1 to its ligands PD-L1 and PD-L2 (IC50 ~ 1 nM). Nivolumab binds 
specifically to PD-1 and not to related members of the CD28 family such as CD28, 
ICOS, CTLA-4 and BTLA. Blockade of the PD-1 pathway by nivolumab results in a 
reproducible enhancement of both proliferation and IFN-γ release in the mixed 
lymphocyte reaction (MLR). Using a CMV-re-stimulation assay with human PBMC, the 
effect of nivolumab on antigen specific recall response indicates that BMS-936558 
augmented IFN-γ secretion from CMV specific memory T cells in a dose-dependent 
manner versus isotype-matched control. In vivo blockade of PD-1 by a murine analog of 
nivolumab enhances the anti-tumor immune response and result in tumor rejection in 
several immunocompetent mouse tumor models (MC38, SA1/N, and PAN02) (29). 
 
1.4.3 HPV positive malignancies 
The causal role of HPV infections in the development of preneoplastic lesions and 
subsequent carcinoma has been unambiguously established (30, 31). Genital infections 
with high-risk HPV are mainly acquired through sexual activity (32-34) and are highly 
prevalent in young sexually active individuals. In the majority of infected subjects the 
infection is cleared within one year (35, 36). However, infection with the high-risk HPV 
type 16 (HPV16) is associated with a greater risk for progression and is most common in 
patients with HPV-related cancer (30, 37). HPV-16 encodes the two tumor-specific 
oncoproteins E6 and E7 that can elicit a favorable immune response in which specific T-
cells play a critical role in the control and elimination of the HPV infection. The virus-
specific interferon-γ (IFNγ)-producing CD4+ cells (Th1 cells) and CD8+ cytotoxic T-
10 
 


lymphocytes (CTL) are able to recognize peptides processed from the oncoproteins E6 
and E7 and contribute to the virus elimination (38, 39). 
However, in case of an uncontrolled persistent infection with a high-risk HPV type, the 
expression of the viral oncoproteins E6 and E7 contributes to the development of 
(pre)malignancies. Apparently, the spontaneous HPV-specific T-cell response fails in 
these patients and there is no or a negligible activation and expansion of the proper 
HPV16-specific CD4+ and CD8+ T cells (38, 39). 
Persistent HPV infection causes a variety of solid cancers including cervical, vulvar, 
vaginal, oropharyngeal, anal and penile cancers.  Usually HPV-related cancers are cured 
in the majority of cases when discovered at early stages with multimodality therapy 
including surgery, radiation therapy and chemotherapy. However, distant metastases may 
arise after longer intervals and in unusual sites (40, 41).  
 
Appropriate treatment of incurable advanced disease, consisting mainly of platinum-
based doublet systemic chemotherapy, has only limited efficacy with a response rate and 
median OS of approximately 30% and one year, respectively. Bevacizumab added to 
chemotherapy increases OS to a median of approximately 18 months in patients with 
cervical cancer.  Therefore, novel treatments are needed to improve the survival of 
locoregionally recurrent and metastatic HPV-positive solid tumors. 
 
1.4.4 HPV-16-SLP and ISA 101 clinical results 
 
1.4.4.1 Clinical pharmacology summary 
Early studies were performed with a similar prototype vaccine manufactured at the 
Leiden University Medical Center (LUMC), identified as HPV-16-SLP. ISA101 is 
manufactured by a contract manufacturing organization for current trials sponsored or 
supported by ISA Therapeutics. Data developed with HPV-16-SLP may provide 
important information to help guide the development of ISA101 with respect to 
mechanism of action, the safety profile and biologic activity.  Data from studies 
performed with the prototype vaccine, HPV-16-SLP, as distinct from ISA101, are 
specifically identified within this document. 
 
Clinical experience with HPV-16-SLP, the prototype of ISA101, has been obtained from 
several investigator-sponsored studies and available data have been provided to ISA. 
Initial clinical trials of HPV-16-SLP were mainly designed to assess the safety, 
tolerability and immunogenicity. ISA’s access to the safety data in these trials data is 
limited, and the data may not be complete as these studies have not been conducted, 
monitored or audited by ISA. ISA engaged an independent reviewer, Dr M. van 
Poelgeest, in late 2011 to assess clinical safety data from studies conducted through 
November 18, 2011.  This safety analysis focused on the two most common and 
important allergic reactions to ISA101: local injection site and systemic allergic 
reactions.  This analysis provides the primary basis for understanding of the safety profile 
of HPV-16-SLP and hence, ISA101.  More recent data on HPV-16-SLP have also been 
incorporated, as well as all available non-clinical and clinical data on ISA 101 through 
May 31, 2014. 
11 
 


 
Preclinical efficacy studies showed significant activity of the papilloma virus long 
peptide approach. In a preclinical model of HPV16-induced cervical cancer, vaccination 
with a single synthetic long peptide of HPV-16 E7 induced a strong HPV-16 specific 
immune response in inbred B6 mice, increased survival and mediated eradication of 
existing tumours. A second preclinical disease model in outbred rabbits used a set of long 
overlapping peptides of the entire sequence of cottontail rabbit papilloma virus E6 and 
E7, mimicking persistent HPV infections and related papilloma induced lesions.  In this 
model, the long peptide vaccination approach resulted in similar effects: a strong 
induction of a papilloma-specific immune response, clearing of viral DNA and control of 
papilloma induced wart growth. 
 
Pharmacokinetic parameters of ISA101 were not assessed in the preclinical studies. 
Studies with other synthetic long peptides, however, indicate that the distribution of the 
peptides is mainly restricted to DC in the draining lymph nodes (20). 
 
1.4.4.2 Safety summary 
Toxicology studies in rats (HPV-16-SLP) and rabbits (ISA101) showed that the vaccine 
induced high antibody levels against the immunogen and was well tolerated systemically 
after subcutaneous (s.c.) administration at high doses. In these studies, the vaccine was 
given together with an adjuvant, Montanide ISA 51 VG, hereafter referred to simply as 
Montanide, to mimic clinical studies. Doses in the rat were up to 120 μg per peptide per 
injection, while in the rabbit study the animal dose (300 μg per peptide per injection) was 
the same absolute dose as used in clinical trials, i.e. not adjusted for body weight or 
surface area.   
 
Local inflammation at the injection site was volume dependent which suggests that the 
formulation was at least partially responsible for this effect. The irritation persisted 
throughout the studies; recovery started when treatment stopped but was not completely 
resolved within the 14-day recovery period. Systemic effects included transient, minor 
decreases in albumin content and albumin to globulin (A/G) ratios in the blood, increased 
spleen weight, and microscopic minor inflammatory changes in lungs, spleen and lymph 
nodes. These effects are considered indicative of an immune and/or inflammatory 
response. The immune responses are primarily local in nature and occur in 
microenvironments of the draining lymph nodes. 
 
Clinical experience with ISA101, per se, is limited as clinical studies were initiated in 
June 2013. Two trials with ISA101 are enrolling patients as of the date of writing this 
protocol,   
• CervISA: An open label phase I/II study in patients with advanced or 
metastatic (stage IVb) or recurrent HPV-16 positive cervical cancer for 
whom no curative treatment options exist. 
• VACCAIN1: A study of ISA101 administered by intradermal injection 
without Montanide in patients with Anal Intraepithelial Neoplasia (AIN). 
12 
 


In supporting clinical studies with HPV-16-SLP-Montanide approximately 180 patients 
with HPV-induced pre-malignant lesions and malignancies of the cervix and vulva have 
been administered the vaccine at least once at doses ranging from 50 to 300 μg per 
peptide. Of these patients, approximately 18 (~10%) have terminated vaccination due to 
local and/or systemic adverse events.  
 
The most important adverse events associated with HPV-16-SLP systemic effects include 
fever, chills, nausea, malaise and fatigue.  Local reactions at the vaccination site include 
pain, redness swelling and itching. Adverse effects of HPV-16-SLP appear to be reported 
at a greater frequency and severity in patients with premalignant disease compared to 
patients with advanced cervix carcinoma. Generally the adverse events after HPV-16-
SLP vaccination do not exceed grade 2 according to the CTC criteria. However, a number 
of more serious adverse events (CTC criteria grade 3), have been reported, including 
systemic allergic reactions and more serious local reactions such as ulcerations or fistulas 
at the vaccination sites that have led to withdrawal from study treatment in approximately 
7% and 5.5% of subjects, respectively. Visible, grade 2 ulceration, abscess formation and 
fistulas with granulomatous inflammation have been observed for approximately 24 
months after vaccination, particularly in patients with pre-malignant disease. In addition, 
a significant number (~10-20%) of patients with pre-malignant disease have reported 
fatigue, fever and chills of up to CTC grade 3. For details see the ISA101 Investigator 
Brochure. 
 
Local swelling and discoloration of different size and intensity has persisted for a 
prolonged period (one year or more) in the majority of patients who have received HPV-
16-SLP in Montanide. In some cases these complaints require specific treatment of the 
vaccination site by a dermatologist. In some patients, local excision led to alleviation of 
the symptoms. Long term follow up for up 12 months of the first VIN study (P88/89) 
revealed visible or palpable lesions in about 75% of the patients; about half of the 
biopsies showed a granulomatous inflammatory reaction, sometimes resulting in the 
formation of scar tissue.  
 
In addition to local reactions, systemic allergic reactions leading to study withdrawal 
have been reported in approximately 7% of patients who have received HPV-16-SLP. 
One patient also reported difficulty in breathing. Patients have responded to an anti-
histamine, in those instances when it was given. Vaccinations should therefore only be 
administered in a clinic where immediate treatment of severe allergic reactions is 
possible.  
 
An odorous breath lasting up to approximately > 24 hours, most likely due to the DMSO 
component in the vaccine formulation, was also a frequently reported side effect. 
 
Table 1. HPV-16-SLP safety overview in malignant diseases; local injection site 
reactions 
Malignant diseases (N=69) 
Range (x-y%) - severity grade 
 
Grade 1 (%) 
Grade 2 (%) 
Grade 3 (%) 
Grade1: 29-31% 
Erythema 
25-27 
29-31 
0 
13 
 


Grade 2: 69-70% 
Grade 3: 0% 
Pain 
96-98 
2-4 
0 
Induration or swelling 
48-50 
35-37 
0 
Nodules 
NA 
 
 
Ulceration  
NA 
 
 
Itching 
25-27 
7-8 
0 
Pigmentation 
NA 
 
 
 
Table 2. HPV-16-SLP safety overview in malignant diseases; systemic reactions, 
withdrawals and SAEs 
Malignant diseases (N=69) 
Systemic reactions (%)* 
Max severity 
Withdrawals  
(number, reasons) 
SAE** 
(number, type) 
 
Grade 1 
(%) 
Grade 2 
(%) 
Grade 
3(%) 
 
 
Fever 
Chills 
Malaise 
Nausea 
Vomiting 
Dizziness 
Rash 
Headache 
Fatigue    
Flu like symptoms 
Tingling extremities 
Swelling extremities 
Burning eyes 
Itching other skin 
10-12 
17-19 
9-11 
7-9 
2-3 
1-2 
9-10 
0 
10-12 
9-11 
2-3 
6-8 
1-2 
0 
10-12 
0 
2-3 
0 
0 
0 
1-2 
2-3 
3-4 
3-4 
0 
0 
0 
2-3 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
0 
N=3 
 
• 
1 death duo to local 
recurrence 
• 
1 inconvience 
• 
1 systemic side effects 
N=0 
* 34 patients died in the Phase I End-stage CxCA study in the follow-up phase between 2-17 months, due to PD. 
** In study CHDR0919, the pilot chemo-immunotherapy study (N=18 of which 6 patient did not receive vaccination), 7 SAEs in 7 
patients were reported: 2 deaths due to metastatic disease (one received HPV-16-SLP vaccination); 4 complications as result of 
advanced oncological disease (3 received HPV-16-SLP vaccination); 1 complication with standard treatment of oncological disease 
(no HPV-16-SLP vaccination). Other adverse event data from this study are not yet available. 
 
For a more detailed description of the local and systemic side effects in the various 
studies with HPV-16-SLP, see ISA101 Investigator’s Brochure (42). 
The vegetable sourced adjuvant Montanide is based on mineral oil and is a more pure 
form of mineral oil than Freund’s incomplete adjuvant (IFA). It is an adjuvant that non-
specifically induces an immune response and functions as a depot for the peptides, to 
assure a slow and consistent release. In preclinical mouse experiments the adjuvants IFA 
or Montanide were shown to be safe and to support robust anti-T cell immunity induced 
by long peptides.  
In this study Montanide will be used for emulsification of the peptides before injection, 
resulting in a formulation of DMSO/WFI/Montanide of 20/30/50%. The dose level of 
ISA101 peptides and therefore the amount of Montanide will be based on available data 
from the CervISA trial.   In clinical trials conducted previously, HPV-16-SLP was also 
14 
 


formulated in DMSO/WFI (or PBS)/Montanide 20/30/50%, and administered at the same 
highest dose and same volume of Montanide.  
The subcutaneous route of administration has been used in the preclinical experiments in 
rats and rabbits conducted by ISA Pharmaceuticals B.V. (ISA). These repeated dose 
toxicology studies involved dosing the vaccine reconstituted and emulsified in DMSO 
and Montanide in the same manner as proposed for the clinic. In both species the vaccine 
was well tolerated systemically after repeated s.c. administration although local 
inflammation at the site of injection could be attributed to the adjuvant Montanide 
[Investigator’s Brochure, Montanide ISA 51 VG, August 2013].  
Although the use of the adjuvant Montanide has been associated with a number of side 
effects, most notably of a local nature, the evidence that this adjuvant is needed for robust 
T cell response induction by ISA101 is strong and the side effects are considered 
acceptable for a therapeutic vaccine modality that is capable of the induction of vigorous 
T cell immune responses against HPV-16 E6/E7 in patients with HPV induced 
malignancies. 
 
1.4.4.3 Antitumor activity summary 
Clinical experience with ISA101, per se, is limited as clinical studies were initiated in 
June 2013.  
 
CervISA: An open label phase I/II study in patients with advanced or metastatic 
(stage IVb) or recurrent HPV-16 positive cervical cancer for whom no curative 
treatment options exist. This is a sequential group study of patients who have advanced 
(stage IIIb-IVa with involvement of lymph nodes beyond the renal vein) or metastatic 
(stage IVb) or recurrent HPV-16 positive cervical cancer for whom no curative treatment 
options exist.  All subjects will receive ISA101 in Montanide by subcutaneous injection 
at the dose levels described in Table 1.  The study was designed to enroll cohorts of six 
patients each to evaluate the safety and HPV-specific immune responses following 
different vaccination regimens. Patients will receive chemotherapy considered standard 
of care for this disease: starting with carboplatin at an AUC of 6 plus paclitaxel at a dose 
of 175 mg/m2; dose reductions in chemotherapy are allowed, consistent with the standard 
of care, with continuation of vaccination (with or without pegylated IFNα, depending on 
the assigned cohort).  The maximum total treatment duration for a patient is six cycles (1 
cycle is 21 days) of carboplatin and paclitaxel for a total of 18 weeks, if there are no dose 
interruptions or delays. On Day 15 (±3 days) of cycles 2, 3 and 4, the vaccination scheme 
of ISA101 with or without pegylated IFNα (depending on cohort assignment in Table 1) 
will start. The patients will be vaccinated with a fixed dose of ISA101 every three weeks 
for a total of three ISA101 vaccinations. Four dose levels of ISA101 may be assessed. 
The primary endpoints of the study are safety and HPV-specific immune responses. The 
secondary endpoints are antitumor efficacy according to RECIST 1.1 (overall response 
rate, disease control rate, progression free survival). Exploratory endpoints include 
general responsiveness of the immune system. As of May, 2014, only the first cohort was 
evaluated, and patient recruitment is ongoing. The AEs and SAEs observed to date 
appear to be expected complications of advanced cervical cancer and/or 
standard chemotherapy. Virtually all of the AEs and SAEs that are reported as “related" 
to the protocol-specified therapy (e.g. thrombocytopenia, neutropenia, anemia), are 
15 
 


expected complications of chemotherapy. No new or unexpected safety concerns 
potentially related to ISA101 have been identified in this ongoing study to date. 
VACCAIN1: A study of ISA101 administered by intradermal injection without 
Montanide in patients with Anal Intraepithelial Neoplasia (AIN). Study ISA101-
AIN is an investigator initiated study, which is designed to assess therapeutic vaccination 
against HPV-16 with ISA101 for the treatment of anal intraepithelial neoplasia in HIV-
positive (HIV+) men. It should be noted that this study is being conducted using ISA101 
without Montanide administered by intradermal (i.d.) injection. The Academic Medical 
Center in Amsterdam has started a sequential group dose-response study with ISA101 in 
HIV-positive MSM, with 3 different dosage schedules, based on intra-patient dose 
escalation: schedule I: 1,5,10 µg, schedule II: 5,10,20 μg and schedule III: 10,20,40 μg of 
ISA101 administered i.d. with a three-week interval.  Each dosage schedule will be 
evaluated with or without the co-administration of pegylated interferon-α (Pegintron 1 
μg/kg s.c.) on the day of vaccine administration. Each vaccination schedule is to be tested 
in 5 patients. The vaccination regimen that induces the best HPV-16-specific response 
with an acceptable safety profile will be considered the optimal schedule in this clinical 
setting. The size of this dose group will be increased to a total of 20 patients by 
vaccinating an additional 15 patients.   
Data developed with HPV-16-SLP may inform the development of ISA101 with respect 
to mechanism of action, the safety profile and biologic activity. However, due to changes 
in manufacturing and analytical methods, HPV-16-SLP and ISA101 are considered 
different products from a regulatory point of view. The clinical trials described below are 
all investigator-sponsored studies of the prototype vaccine HPV-16-SLP. As summarized 
in the following tables, multiple studies evaluating HPV-16-SLP vaccination have been 
conducted in the past.  These studies using HPV-16-SPL have included patients with 
different types of high-risk pre-malignant and malignant HPV-induced diseases (Table 
3). 
 
Table 3. HPV-16-SLP vaccination clinical trials. 
Study ID 
Indication 
Study design 
Key (immunological) results 
Pre-malignant diseases 
P88/89 
Phase II 
High-grade VIN 
22 patients: 4 
vaccinations at 3 
week interval 
Clinical responses in women with HPV-16 
positive, grade VIN3, correlated with 
induction of HPV-16 specific immunity (1). 
P06.227 
Phase II 
High-grade CIN 
9 patients (planned 
50): Two arms, 
placebo controlled, at 
3 week interval 
 
Vaccination of HSIL patients results in 
increased 
HPV-16- 
specific 
T-cell 
immunity. (43). 
Study was terminated after 9 of planned 50 
patients were recruited, due to lack of 
recruitment. 
P06.226 
Low-grade CIN or 
persistent PAPII 
50 patients: 4 
vaccinations at 3 
week interval, three 
arms, placebo 
controlled 
Robust HPV-16-specific T-cell responses 
detected after vaccination (44). 
16 
 


Study ID 
Indication 
Study design 
Key (immunological) results 
P08.062 
Phase II 
High-grade VIN or 
VaIN 
39 patients: Two 
arms, 4 vaccinations 
at 3 week interval 
Patients with high-grade VIN (or VaIN) 
Analysis is pending. 
Malignant diseases 
P88/89 
Phase I 
End-stage cervical 
cancer 
43 patients: 4 
vaccinations at 3 
week interval 
The vaccinations resulted in a strong and 
broad T-cell response (2). 
P88/89 
Phase II 
FIGO stage 1B1 
cervical cancer 
6 patients: 4 
vaccinations at 3 
week interval 
The HPV-16 E6 and E7 SLP increases the 
number and activity of HPV-16-specific 
CD4(+) and CD8(+) T-cells to a broad array 
of epitopes in all patients (45). 
P05.086 
Phase II 
End-stage 
gynecological cancer 
20 patients: 4 
vaccinations at 3 
week interval 
The HPV-16-SLP vaccine induced a broad 
IFNγ-associated T-cell response in patients 
with advanced or recurrent HPV-16-induced 
gynecological 
carcinoma 
but 
neither  
induced tumor regression nor prevented 
progressive disease (15). 
CHDR0912 
Pilot 
chemo-
immuno 
therapy 
Advanced or 
recurrent cervical 
cancer where 
carboplatin/paclitaxel 
is appropriate 
18 patients:  
6 patients 
carboplatin/paclitaxel 
only 
12 patients 
vaccinated on D15 of 
cycle 2 of 
carboplatin/paclitaxel 
Interim analysis 
a single vaccine dose of HPV-16-SLP 
+Montanide could  induce strong T cell 
responses if the timing in relation to 
chemotherapy delivery was optimized (46) 
and unpublished observations).  
 
1.4.5 Nivolumab clinical results 
Nivolumab has demonstrated clinical activity in subjects with a variety of malignancies 
in the following indications and studies with available data: 
 
Non-small cell lung cancer (NSCLC)  
MDX1106-03: completed Phase 1 multidose escalation study with nivolumab 
monotherapy (total number of subjects [N] = 129). The ORR was 17%; the most active 
doses were 3 mg/kg and 10 mg/kg. Only a single response was reported at 1 mg/kg. 
Responses were observed in subjects with NSCLC (both squamous and nonsquamous 
subtypes) with a median duration of response of 17 months.  
 
CA209012: ongoing Phase 1 study with nivolumab monotherapy or in combination with 
platinum-based chemotherapy or erlotinib (N = 52 with monotherapy, N = 137 with 
combination therapy). Preliminary analysis  at 24 weeks for subjects treated with 
nivolumab monotherapy (N = 20, median follow-up 66.1 weeks), nivolumab + 
ipilimumab (N = 49, median follow-up 38.1 weeks), nivolumab + chemotherapy (N = 56, 
median follow-up 75.2 weeks), and nivolumab + erlotinib (N = 21, median follow-up 
71.9 weeks) in CA209012 showed that among responders, the median durations of 
responses ranged from 25.4 weeks to 45 weeks for nivolumab + chemotherapy, while the 
17 
 


median durations of responses for nivolumab monotherapy, nivolumab + ipilimumab, 
and nivolumab + erlotinib were not reached at the time of analysis. 
 
Melanoma  
MDX1106-03: completed Phase 1 multidose escalation study with nivolumab 
monotherapy (N = 107). The ORR was 31% for melanoma subjects (N = 107) in 
MDX1106-03 who were administered nivolumab monotherapy Q2W at doses ranging 
from 0.1 mg/kg to 10 mg/kg. The majority of responses were durable and exceeded 6 
months.        
 
CA209038: ongoing exploratory, open-label, pharmacodynamic study of nivolumab 
monotherapy and nivolumab in combination with ipilimumab (N = 85). A total of 85 
subjects with advanced melanoma were treated with nivolumab 3 mg/kg monotherapy in 
CA209038 (preliminary data). The ORR was 32% for ipilimumab-naive subjects and 
18% in ipilimumab-progressed subjects. 
 
CA209004: ongoing Phase 1b study with nivolumab in combination with ipilimumab (N 
= 126). Of the 125 response-evaluable subjects in CA209004, 53 subjects received 
concurrent therapy with nivolumab + ipilimumab, and 40 subjects (in an expansion 
treatment group) received concurrent therapy at the selected registrational dose and 
schedule The ORR (modified World Health Organization criteria) for all subjects in the 
concurrent-regimen group and concurrent expansion group was 42% and 43%, 
respectively. The 12-month OS rate was 85% (95% CI: 75 - 95) for subjects in the 
concurrent treatment group. 
 
Renal cell carcinoma (RCC)  
MDX1106-03: completed Phase 1 multidose escalation study with nivolumab 
monotherapy (N = 34). The ORR was 21% for RCC subjects (N = 34) in MDX1106-03, 
who were administered nivolumab monotherapy Q2W at doses of 1 mg/kg or 10 mg/kg. 
The majority of responses were durable and exceeded 6 months. 
 
CA209010: completed Phase 2 dose-ranging monotherapy study in subjects with 
advanced/metastatic clear-cell RCC who received prior anti-angiogenic therapy (N = 
167). Of the 168 randomized subjects with advanced/metastatic clear-cell RCC in 
CA209010, the ORR in the 0.3-, 2-, and 10-mg/kg treatment groups were similar (20%, 
22%, and 20%, respectively). Median PFS (mPFS) was reached for each treatment group 
(2.7 months, 4.0 months, and 4.2 months in the 0.3-, 2-, and 10-mg/kg treatment groups, 
respectively). No dose-response relationship was noted for ORR or mPFS. The median 
OS was reached for the 0.3-mg/kg treatment group (18.2 months), but was not reached 
for the 2-mg/kg or 10-mg/kg treatment groups. 
 
CA209016: ongoing Phase 1 dose-escalation study of nivolumab in combination with 
VEGFR-TKIs or ipilimumab in subjects with metastatic RCC (N = 53 in combination 
with TKIs, N = 44 in combination with ipilimumab). A total of 44 subjects with 
metastatic RCC were treated with nivolumab (1 or 3 mg/kg) and ipilimumab (1 or 3 
mg/kg). In addition, a total of 53 subjects with metastatic RCC were treated with 
18 
 


nivolumab (2 or 5 mg/kg) and sunitinib (n = 33) or nivolumab (2 mg/kg) and pazopanib 
(n = 20) in CA209016. The confirmed ORR was 43% and 48% in subjects treated in 3-
mg/kg nivolumab/1-mg/kg ipilimumab and 1-mg/kg nivolumab/3-mg/kg ipilimumab 
cohorts, respectively, and 52% and 45% in subjects treated in sunitinib and pazopanib 
cohorts, respectively. 
 
1.4.5.1 Clinical pharmacology summary 
Single-dose PK of nivolumab was studied in 39 subjects with cancer. The single-dose PK 
of nivolumab was linear and dose-proportional in the range of 0.3 mg/kg to 10 mg/kg. 
The mean terminal T-HALF of nivolumab ranged between 17 and 25 days across the 
dose range of 0.3 mg/kg to 10 mg/kg. Geometric mean total clearance varied from 0.13 
mL/h/kg to 0.19 mL/h/kg, while mean volume of distribution varied between 83 mL/kg 
and 113 mL/kg across doses. The clearance and half-life of nivolumab are consistent with 
that of IgG4. 
 
The multiple-dose PK of nivolumab given Q2W was determined from MDX1106-03 
study as well as by population PK using data from 669 subjects across nivolumab studies. 
Multiple-dose PK of nivolumab following Q2W dosing was linear with dose-proportional  
increase in Cmax and AUC(TAU) in the studied range of 0.1 mg/kg to 10 mg/kg. 
nivolumab accumulation with Q2W dosing frequency was in the range of 2.9 to 3.3 based 
on AUC(TAU), 2.0 to 2.4 based on Cmax, and 3.1 to 4.8 based on Cmin. 
A PPK model was developed by nonlinear mixed effect modeling using data from 669 
subjects. nivolumab concentration-time data were well described by a linear, 2-
compartment, 0-order IV infusion model with first-order elimination. nivolumab PK was 
found to be linear, dose independent, and time invariant. The geometric mean of terminal 
T-HALF was 25.6 days and the typical clearance was 8.8 mL/h, which are consistent 
with those of full human immunoglobulin antibodies. Clearance of nivolumab is 
independent of dose in the dose range (0.1 mg/kg to 10 mg/kg) and tumor types studied. 
Body weight normalized dosing showed approximately constant trough concentrations 
over a wide range of body weights. Additional details are provided in IB (47). 
 
1.4.5.2 Safety summary 
A total of 39 and 306 subjects with selected recurrent or treatment-refractory 
malignancies have been treated in a completed Phase 1 single-dose study (MDX1106-01) 
and a completed Phase 1 multidose study (MDX1106-03), respectively. As the safety 
profile from MDX1106-03 to date is consistent with that observed for MDX1106-01, 
only data from the larger and more recent study (MDX1106-03) is presented in this IB. 
The baseline disease diagnosis by treatment for MDX1106-03 is provided in the final 
CSR (47). A review of the safety data by tumor type (RCC, NSCLC, mCRPC, CRC, and 
melanoma) did not show any clinically meaningful differences in the proportion of 
subjects with AEs noted across tumor types. 
 
Overall, the safety profile of nivolumab monotherapy was generally manageable and was 
consistent with the mechanism of action of nivolumab. No MTD was reached at doses 
tested up to 10 mg/kg Q2W. The nature, frequency, and severity of any causality and 
treatment-related safety events were similar across tumor types. 
19 
 


The following were the key safety findings for the subjects in MDX1106-03 (47): 
• Drug-related AEs (any grade) were reported in 75.2%, and drug-related Grade 3-4 
AEs were reported in 17.0% of subjects. The most frequently reported drug-
related AE was fatigue (28.1%). Other drug-related AEs Grade 3-4 reported in 
more than 2 subjects were pneumonitis (1.3%), lymphopenia (1.3%), diarrhea 
(1.0%), abdominal pain (1.0%), CD4 lymphocytes decreased (1.0%), and 
hypophosphatemia (1.0%). 
• The most frequently reported drug-related SAE was pneumonitis (7 subjects, 
2.3%). Drug-related Grade 3-4 pneumonitis was reported in 4 (1.3%). 
• The most frequently reported drug-related select AE categories (any grade) were 
skin (24.5%), GI (14.1%), and endocrine (9.5%). AEs belonging to the pulmonary 
and renal select AE categories were unexpected, drug-related toxicities associated 
with the use of nivolumab. AEs belonging to select AE categories were generally 
manageable and reversible with the use of immunosuppressants. 
 
The majority of the deaths were due to disease progression. Three subjects (1.0%) died 
due to study drug toxicity at the time of database lock; 2 out of 3 subjects died within 100 
days of last dose of nivolumab, and 1 died > 100 days after the last dose of nivolumab. 
The reported causes of death for these 3 subjects were: 
• Non-drug-related cardiopulmonary arrest due to complications from Grade 5 
sepsis (drug-related) 
• Drug-related sepsis 
• Drug-related respiratory failure secondary to pneumonitis and progressive disease  
 
After database lock for the final CSR, 2 subjects were reported to have died; both were 
subjects with NSCLC treated with 3-mg/kg nivolumab. The reported causes of death for 
these 2 subjects were: 
• Drug-related pneumonitis 
• Non-drug-related infection after experiencing drug-related Grade 3 pneumonitis 
 
Although not considered to be the primary cause of death in all 5 subjects described 
above, pneumonitis was considered a contributory factor in each case (47). 
 
1.4.5.3 Antitumor activity summary 
Efficacy data from CA209003 was evaluated as of July 1, 2011, which provided a 
minimum follow-up of 8 months. Clinical antitumor activity was observed in melanoma, 
RCC, and NSCLC at all nivolumab doses tested. NSCLC subjects were treated at doses 
of 1, 3, and 10 mg/kg. Antitumor activity was mainly observed in the 3 and 
10 mg/kg dose groups, and exposure-response appeared to be relatively flat at doses ≥ 3 
mg/kg. At the 3 and 10 mg/kg dose levels, the RECIST-defined objective response rates 
for all histologies were 32% and 18%, respectively. The corresponding disease control 
rates (which included any subject who achieved a best overall response of CR, PR or SD) 
were 53% and 46%, respectively. PFS rates at 24 weeks were 41%, and 24%, 
respectively, indicating durable disease control. Differential activity was observed 
between squamous versus non-squamous histologies. Substantial activity was noted in 
the squamous histology subgroup (n=18), where the ORR and DCR in the 3 mg/kg dose 
20 
 


group were 50% and 67%, respectively (the ORR for squamous histology subjects across 
all dose groups was 33%). Responses were durable; as of the cutoff date, the median PFS 
in the 3mg/kg squamous group had not been reached, and 3 of 6 subjects had experienced 
PFS > 6 months. One subject who achieved PR (67% tumor reduction) experienced a 
response duration of 134 weeks. Activity in NSCLC is especially notable in that the 
majority of subjects had received 2 or more prior therapies. These preliminary data 
suggest that nivolumab induces substantial durable disease control in heavily pretreated 
subjects with NSCLC, and in particular in subjects with squamous histology. 
 
 
1.5 OVERALL RISK/BENEFIT ASSESSMENT 
 
Subjects with recurrent/metastatic incurable HPV-positive oropharyngeal and anogenital 
tract cancers represent a population for whom immunotherapy holds potential that has yet 
to be realized. HPV-16-SLP, the precursor vaccine to ISA 101, induced HPV-16 
proliferative T cell responses in approximately 50% of patients with end-stage 
gynecological cancers, but did not cause any objective tumor regression. These data 
provide rationale to pursue combination strategies to amplify immune response. 
Similarly, the 20% ORR with anti-PD-1 therapy in HPV-positive OPSCC demonstrates 
the promise of this approach, and at the same time, the need to pursue relevant 
combinations.    Combining ISA-101 with nivolumab is clearly rational and should be 
studied; however, it is only the first of several immunotherapy combinations of interest 
for these virally driven cancers.  
 
ISA 101 has been very well-tolerated with injection site reactions the most common AE.  
Systemic reactions, typically readily manageable with anti-histamines or steroids, have 
also been observed.  nivolumab has the potential for clinically relevant AEs including 
liver toxicities, thyroiditis, pneumonitis, and diarrhea. However, the activity and 
manageable AEs profile observed with nivolumab supports the combination with ISA 
101. 
 
To assure safety for subjects enrolled onto this clinical trial, we will continuously assess 
toxicity in cohorts of 4 subjects (section 6.3.4) throughout the conduct of the trial.   
 
 
2.0 INVESTIGATIONAL PLAN 
 
2.1 Study Design and Duration 
This is a single arm Phase 2 study in adult (≥ 18 years old) male and female subjects with 
recurrent/ metastatic HPV-16 positive oropharyngeal, cervical, vulvar, vaginal, penile 
and anal cancers treatment naïve or after progression during or after one prior 
chemotherapy regimen. Subjects will undergo screening evaluations to determine 
eligibility within 28 days prior to inclusion into the trial. A cycle is 2 weeks in duration 
with the exception that the first cycle is 3 weeks. 
 
STUDY SCHEMA 
21 
 


 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Treatment will be initiated with the administration of the ISA101 vaccine on day 1, 1 
week before starting nivolumab IV infusion to facilitate migration of HPV-specific TILs 
to the microenvironment. Cycle 1 therefore will last 3 weeks instead of 2 weeks. 
 
This study will consist of 3 phases: screening (Table 5), treatment (Table 6), and follow-
up (Table 7). 
 
This study will end when analysis of survival is complete. The duration of study will be 
approximately 3 years (36 months). 
 
2.2 Study Population 
For entry into the study, the following criteria MUST be met. 
 
2.2.1 Inclusion Criteria 
 
1) Signed Written Informed Consent 
a) Subjects must have signed and dated an IRB/IEC approved written informed consent 
form in accordance with regulatory and institutional guidelines. This must be obtained 
before the performance of any protocol related procedures that are not part of normal 
subject care. 
b) Subjects must be willing and able to comply with scheduled visits, treatment schedule, 
laboratory tests and other requirements of the study. 
 
2) Target Population 
a. Men and women ≥ 18 years of age 
b. Eastern Cooperative Oncology Group (ECOG) performance status of ≤ 1 
c. Subjects with histologically- or cytologically-documented incurable Human 
Papillomavirus (HPV)-16 positive solid tumors including oropharyngeal squamous cell 
carcinoma (OPSCC), cervical, vulvar, vaginal, anal, penile cancer. Incurable HPV-16 
ISA101 vaccine 
Dose #1                      Dose #2                                                 Dose #3 
Day1 
Day 8 
Day 36 
Dose #1       Dose #2            Dose #3             Dose #4 and then q. 2 w until PD* 
Nivolumab 
Day 50 
W=week; PD=disease progression 
*Subjects may be allowed to continue taking nivolumab beyond PD 
Day 22 
22 
 


solid tumors are defined as tumors which are not curable by salvage approaches including 
resection and/or re-irradiation. HPV-16 serotype will be assessed by Cervista assay 
(Table 5) 
 Subjects can be treatment naïve for metastatic or incurable locally advanced HPV-16 
positive solid tumors or can have one prior line of treatment. Patients  are eligible upon 
progression after definitive local treatment (usually concurrent chemoradiation) if they 
are not candidates for salvage surgery or re-irradiation.  Patients are also eligible after 
progression on first line chemotherapy for recurrent disease.   d. Subjects must have 
measurable disease by CT or MRI per RECIST 1.1 criteria; Radiographic Tumor 
Assessment performed within 28 days of study inclusion. e. Target lesions may be 
located in a previously irradiated field if there is documented (radiographic) disease 
progression in that site. f. Subject entering the study will need to consent for mandatory 
biopsy at study entrance and as an optional procedure at Week 11 and at progression for 
biomarker evaluation, as described in Table 5. Biopsy should be excisional, incisional or 
core needle. Fine needle aspiration is insufficient. 
g. Prior radiotherapy or radiosurgery must have been completed at least 2 weeks prior to 
start 
h. All baseline laboratory requirements will be assessed and should be obtained within -
14 days of study registration. Screening laboratory values must meet the following 
criteria 
i) WBCs ≥ 2000/μL 
ii) Neutrophils ≥ 1500/μL 
iii) Platelets ≥ 100 x 10³/μL 
iv) Hemoglobin ≥ 9.0 g/dL 
v) Serum creatinine of ≤ 1.5 X ULN or creatinine clearance > 40 mL/minute (using 
Cockcroft/Gault formula) 
Female CrCl= (140- age in years) x weight in kg x 0.85 
72 x serum creatinine in mg/ dL 
Male CrCl= (140- age in years) x weight in kg x 1.00 
72 x serum creatinine in mg/ dL 
vi) AST ≤ 1.5X ULN 
vii) ALT ≤ 1.5X ULN 
viii) Total bilirubin ≤ ULN (except subjects with Gilbert Syndrome who must have total 
bilirubin <3.0 mg/dl)  
 
3) Age and Reproductive Status 
a) Women of childbearing potential (WOCBP) must use method(s) of contraception for 
30 days + 5 half-lives (60 days) of the study drugs. For a teratogenic study drug and/or 
when there is insufficient information to assess teratogenicity (preclinical studies have 
not been done), a highly effective method(s) of contraception (failure rate of less than 1% 
per year) is required. Highly effective birth control in this study is defined as a double 
barrier method.  Examples include a condom (with spermicide) in combination with a 
diaphragm, cervical cap, or intrauterine device (IUD).  The individual methods of 
contraception should be determined in consultation with the investigator. 
23 
 


b) WOCBP must have a negative serum or urine pregnancy test (minimum sensitivity 25 
IU/L or equivalent units of HCG) within 24 hours prior to the start of investigational 
product. 
c) Women must not be breastfeeding 
d) Men who are sexually active with WOCBP must use any contraceptive method with a 
failure rate of less than 1% per year. The investigator shall review contraception methods 
and the time period that contraception must be followed. 
Men that are sexually active with WOCBP must follow instructions for birth control for a 
period of 90 days plus the time required for the investigational drug to undergo 5 half-
lives (60 days). 
 
2.2.2 Exclusion Criteria 
 
1) Target Disease Exceptions 
a. Subjects with active CNS metastases are excluded. Subjects are eligible if CNS 
metastases are adequately treated and subjects are neurologically returned to baseline 
(except for residual signs or symptoms related to the CNS treatment) for at least 2 weeks 
prior to enrollment. In addition, subjects must be either off corticosteroids, or on a stable 
or decreasing dose of ≤ 10 mg daily prednisone (or equivalent) for 2 weeks. 
b. Subjects with carcinomatous meningitis. 
 
2) Medical History and Concurrent Diseases 
a. Subjects with active, known or suspected systemic autoimmune disease. Subjects with 
vitiligo, type I diabetes mellitus, residual hypothyroidism due to autoimmune thyroiditis 
only requiring hormone replacement, or conditions not expected to recur in the absence 
of an external trigger are permitted to enroll. 
b. Subjects with a condition requiring systemic treatment with either corticosteroids (>10 
mg daily prednisone equivalent) or other immunosuppressive medications within 14 days 
of start. Inhaled or topical steroids, and adrenal replacement steroid doses > 10 mg daily 
prednisone equivalent, are permitted in the absence of active autoimmune disease. 
c. Prior therapy with anti-PD-1, anti-PD-L1, anti-PD-L2, anti-CD137, or anti-CTLA-4 
antibody (including ipilimumab or any other antibody or drug specifically targeting T-
cell co-stimulation or checkpoint pathways). 
d. Subjects with a history of interstitial lung disease. 
e. Other active malignancy requiring concurrent intervention. 
f. Subjects with previous malignancies (except non-melanoma skin cancers, and the 
following in situ cancers: bladder, gastric, colon, endometrial, cervical/dysplasia, 
melanoma, or breast) are excluded unless a complete remission was achieved at least 2 
years prior to study entry AND no additional therapy is required during the study period 
g. Subjects with toxicities attributed to prior anti-cancer therapy other than alopecia and 
fatigue that have not resolved to grade 1 (NCI CTCAE version 4) or baseline before 
administration of study drug. 
h. Subjects who have not recovered from the effects of major surgery or significant 
traumatic injury at least 14 days before the first dose of study treatment. 
i. Treatment with any investigational agent within 28 days of first administration of study 
treatment 
24 
 


 
3) Physical and Laboratory Test Findings 
a) Known history of testing positive for human immunodeficiency virus (HIV) or known 
acquired immunodeficiency syndrome (AIDS). 
b) Positive test for hepatitis B virus surface antigen (HBV sAg) or hepatitis C virus 
ribonucleic acid (HCV RNA) indicating acute or chronic infection. 
 
4) Allergies and Adverse Drug Reaction 
a) History of severe hypersensitivity reactions to other monoclonal antibodies. 
b) History of allergy or intolerance (unacceptable adverse event) to study drugs 
components.. 
 
5) Sex and Reproductive Status 
a) WOCBP who are pregnant or breastfeeding 
b) Women with a positive pregnancy test at enrollment or prior to administration of study 
medication 
 
6) Prohibited Treatments and/or Restricted Therapies 
a) Ongoing or planned administration of anti-cancer therapies other than those specified 
in this study 
b) Use of corticosteroids or other immunosuppressive medications as per Exclusion 
Criteria 2b 
 
7) Other Exclusion Criteria 
a) Any other serious or uncontrolled medical disorder, active infection, physical exam 
finding, laboratory finding, altered mental status, or psychiatric condition that, in the 
opinion of the investigator, would limit a subject’s ability to comply with the study 
requirements, substantially increase risk to the subject, or impact the interpretability of 
study results. 
b) Prisoners or subjects who are involuntarily incarcerated. 
c) Subjects who are compulsorily detained for treatment of either a psychiatric or 
physical (eg, infectious disease) illness. 
Eligibility criteria for this study have been carefully considered to ensure the safety of the 
study subjects and to ensure that the results of the study can be used. It is imperative that 
subjects fully meet all eligibility criteria. 
 
2.2.3 Women of Childbearing Potential 
A Woman of Childbearing Potential (WOCBP) is defined as any female who has 
experienced menarche and who has not undergone surgical sterilization (hysterectomy or 
bilateral oophorectomy) or is not postmenopausal. Menopause is defined clinically as 12 
months of amenorrhea in a woman over age 45 in the absence of other biological or 
physiological causes.  
 
2.3 Concomitant Treatments 
2.3.1 Prohibited and/or Restricted Treatments 
25 
 


The following medications are prohibited during the study (unless utilized to treat a drug-
related adverse event): 
• Immunosuppressive agents 
• Immunosuppressive doses of systemic corticosteroids (except as stated in this Section 
2.3.3). 
• Any concurrent antineoplastic therapy (ie, chemotherapy, hormonal therapy, 
immunotherapy, extensive, non-palliative radiation therapy, or standard or investigational 
agents  
 
Palliative and supportive care for disease related symptoms (including local radiotherapy, 
bisphosphonates and RANK-L inhibitors) may be offered to all subjects prior to first dose 
of study therapy (prior radiotherapy must have been completed at least 2 weeks prior to 
start). 
 
2.3.2 Other Restrictions and Precautions 
Subjects with active, known or suspected systemic autoimmune disease. Subjects with 
vitiligo, type I diabetes mellitus, residual hypothyroidism due to autoimmune thyroiditis 
only requiring hormone replacement, or conditions not expected to recur in the absence 
of an external trigger are permitted to enroll. 
 
Subjects are excluded if they have a condition requiring systemic treatment with either 
corticosteroids (>10mg daily prednisone equivalent) or other immunosuppressive 
medications within 14 days of start. Inhaled or topical steroids, and adrenal replacement 
steroid doses > 10 mg daily prednisone equivalent, are permitted in the absence of active 
autoimmune disease. 
 
2.3.3 Permitted Therapy 
Subjects are permitted the use of topical, ocular, intra-articular, intranasal, and 
inhalational corticosteroids (with minimal systemic absorption). Physiologic replacement 
doses of systemic corticosteroids (eg, prednisone ≤ 10 mg/day) are permitted. A brief 
(less than 3 weeks) course of corticosteroids for prophylaxis (eg, contrast dye allergy) or 
for treatment of non-autoimmune conditions (eg, delayed-type hypersensitivity reaction 
caused by a contact allergen) is permitted. 
 
The potential for overlapping toxicities with radiotherapy and nivolumab or ISA 101 
currently is not known. Therefore, palliative radiotherapy is not recommended while 
receiving the study drugs. If palliative radiotherapy is required, then the study drugs 
should be withheld for at least 1 week before, during, and 1 week after radiation. Subjects 
should be closely monitored for any potential toxicity during and after receiving 
radiotherapy, and AEs should resolve to Grade ≤ 1 prior to resuming the study drugs. 
Only non-target bone lesions that do not include lung tissue in the planned radiation field 
may receive palliative radiotherapy. Details of palliative radiotherapy should be 
documented in the source records. Details in the source records should include: dates of 
treatment, anatomical site, dose administered and fractionation schedule, and adverse 
events. If warranted, symptoms requiring palliative radiotherapy should be evaluated for 
objective evidence of disease progression. 
26 
 


 
2.4 Discontinuation of Subjects from Treatment 
Subjects MUST discontinue investigational products at the discretion of the investigator 
for any of the following reasons: 
• Withdrawal of informed consent (subject’s decision to withdraw for any reason) 
• Any clinical adverse event (AE), laboratory abnormality or intercurrent illness which, in 
the opinion of the investigator, indicates that continued participation in the study is not in 
the best interest of the subject 
• Pregnancy 
• Termination of the study  
• Loss of ability to freely provide consent through imprisonment or involuntary 
incarceration for treatment of either a psychiatric or physical (eg, infectious disease) 
illness 
• Additional protocol-specific reasons for discontinuation (See Section 3.3.5) 
 
All subjects who discontinue should comply with protocol specified follow-up and 
survival procedures as outlined in section 4.2.2. The ONLY exception to this requirement 
is when a subject withdraws consent for all study procedures or loses the ability to 
consent freely (ie, is imprisoned or involuntarily incarcerated for the treatment of either a 
psychiatric or physical illness). 
 
If a subject was withdrawn before completing the study, the reason for withdrawal must 
be entered on the appropriate case report form (CRF) page. 
 
3.0 TREATMENTS 
 
3.1 Study Treatments 
Nivolumab 100 mg (10 mg/mL) will be packaged in an open-label fashion. 
Five or ten 10 mL vials will be packaged within a carton. Vial assignments by subject 
will be tracked on specific forms. See the product information table for more information. 
  
Table 4. Product Information Table 
Product Description:(Other names = MDX-1106, ONO-4538, anti-PD-1 
Product 
Description 
and Dosage 
Form 
Potency 
Primary 
Packagi
ng 
(Volume
)/ Label 
Type 
Secondary 
Packaging 
(Qty) /Label 
Type 
Appearance 
Storage 
Conditions 
(per label) 
nivolumab 
(BMS-
936558-01)* 
Injection 
drug product 
100 
mg/Vial 
(10 
mg/mL). 
Carton of 
5 or 10 
vials 
10-cc Type 1 
flint glass vials 
stoppered with 
butyl stoppers 
and sealed 
Clear to 
opalescent, 
colorless to 
pale yellow 
liquid.  May 
BMS-936558-01 
Injection must 
be stored at 2 to 
8 degrees C (36 
to 46 degrees F) 
27 
 


*nivolumab may be labeled as BMS-936558-01 Solution for Injection 
 
ISA101 vaccine will be packaged in an open-label fashion. The ISA101 vaccine contains  
six HPV-16 E6 and seven HPV-16 E7 SLP. For technical details reference is made to the 
IB (42). The peptides are dissolved in dimethylsulfoxide and subsequently diluted in WFI 
and emulsified with Montanideas detailed in the pharmacy manual. The final ratio of 
dimethylsulfoxide / WFI / Montanide is 20/30/50. The vaccine will be injected in two s.c. 
injections, one containing HPV-16 E6 and one containing HPV-16 E7. 
 
Treatment should be initiated after registration. Each subject will be dosed at a frequency 
according to the treatment schedule until disease progression (or until discontinuation of 
study therapy in patients receiving nivolumab beyond progression), discontinuation due 
to toxicity, withdrawal of consent, or the study ends. 
 
No premedications are recommended for initiation of dosing for nivolumab or ISA101. 
 
Nivolumab and ISA 101 should be stored in a secure area according to local regulations. 
It is the responsibility of the investigator to ensure that investigational product is only 
dispensed to study subjects. The investigational product must be dispensed only from 
official study sites by authorized personnel according to local regulations. 
 
In this protocol, investigational products are: 
• nivolumab 
• ISA 101 
 
Nivolumab will be provided by BMS. ISA101 and Montanide will be provided by ISA. 
The sites will also procure IV bags, diluents, and micron in-line filters (ie 0.2/ 0.22 
micron; see current nivolumab Investigator Brochure for required filter details). 
Additional information can be found in the ISA101 Investigator Brochure and pharmacy 
manual.  
 
3.2 Handling and Dispensing 
The product storage manager should ensure that the study drugs are stored in accordance 
with the environmental conditions (temperature, light, and humidity) as determined by 
BMS (for nivolumab) and ISA (for ISA101). If concerns regarding the quality or 
appearance of the study drug arise, do not dispense the study drugs and contact BMS (for 
is a sterile, 
non-
pyrogenic, 
single-use, 
isotonic 
aqueous 
solution 
formulated at 
10 mg/mL   
with aluminum 
seals. 
contain 
particles 
and protected 
from light and  
freezing  
28 
 


nivolumab) or ISA (for ISA101) immediately. Nivolumab vials must be stored in the 
refrigerator at 2-8°C, protected from light freezing and shaking. If stored in a glass front 
refrigerator, vials should be stored in the carton.   
 
ISA101 is a lyophilized powder of the two peptides/drug products which must be 
stored in glass vials in the dark at -20°C  as specified in the pharmacy manual. 
 
Investigational product documentation must be maintained that includes all processes  
required to ensure study drug is accurately administered. This includes documentation of 
study drug storage, administration and, as applicable, storage temperatures, re-
constitution, and use of required processes (e.g. required diluents, administration sets). 
 
Recommended safety measures for preparation and handling of nivolumab and ISA101 
include laboratory coats and gloves. 
 
After nivolumab has been prepared for administration, the total storage time 
(combination of refrigeration and room temperature) is not to exceed 24 hours. For 
details on prepared drug storage and use time under room temperature/light and 
refrigeration, please refer to the current nivolumab Investigator Brochure (29).  
 
The maximum recommended hold time between ISA101 vaccine preparation and 
administration is 2 hours. The final formulation for s.c. administration consists of 
20/30/50 v/v/v-% DMSO/WFI/Montanide.  
 
Care must be taken to assure sterility of the prepared solution as the product does not 
contain any anti-microbial preservative or bacteriostatic agent.  
 
Nivolumab is to be administered as a 60 minute IV infusion.  It is not to be administered 
as an IV push or bolus injection. At the end of the infusion, flush the line with a sufficient 
quantity of normal saline or 5% dextrose.  For details regarding preparation and 
administration of nivolumab, please refer to the current Investigator Brochure (29). 
 
The ISA101 preparation is administered as two separate injections in two anatomically 
distinct locations (e.g. one injection in an upper extremity and the other in a lower 
extremity).   
 
3.3 Selection and Timing of Dose for Each Subject 
Nivolumab will be given at 3mg/kg as a 60 minute IV infusion, on Day 1 of a treatment 
cycle every 2 weeks. The first dose of nivolumab will be one week following first 
vaccination with ISA 101, that is, day 8 of treatment on the trial. Dosing calculations 
should be based on the body weight assessed at the start of each cycle as per Table 6. All 
doses should be rounded to the nearest milligram. There will be no dose escalations or 
reductions allowed. Subjects may be dosed no less than 12 days from the previous dose. 
There are no premedications recommended for nivolumab on the first cycle. If an acute 
infusion reaction is noted, subjects should be managed according to Section 3.3.6. 
 
29 
 


ISA101 will be administered at 3 specific time points, on days 1, 22 and 50. On each 
occasion it will be administered as two s.c. injections, one injection for HPV-DP-6P 
(containing 6 peptides) and one injection for HPV-DP-7P (containing 7 peptides) in two 
anatomically distinct locations (e.g. one injection in an upper extremity and the other in a 
lower extremity or one in each upper extremity with different sites used for each at each 
specified ISA101 vaccination time point). Dose of ISA 101 will be 100 mcg per peptide 
per injection.  
 
Subjects will be monitored continuously for AEs while on study. Treatment 
modifications (eg, dose delay, or discontinuation) will be based on specific laboratory 
and adverse event criteria. 
 
In some cases, the natural history of immunotherapy-related AEs of special interest can 
differ and be more severe than AEs caused by other therapeutic classes. Early recognition 
and management may mitigate severe toxicity. Evaluation and Management Guidelines 
were developed to assist investigators and can be found in Appendix 4: 
• Suspected Pulmonary Toxicity 
• Diarrhea and Colitis 
• Suspected Hepatotoxicity (including asymptomatic LFT elevations) 
• Suspected Endocrinopathy 
 
3.3.1 Dose Delay Criteria 
Tumor assessments for all subjects should continue as per protocol even if dosing is 
interrupted. 
 
3.3.1.1 Investigational drugs Dose Delay Criteria 
nivolumab and/or ISA101 administration should be delayed for the following: 
• Any Grade ≥ 2 non-skin, drug-related adverse event, with the following exceptions: 
− Grade 2 drug-related fatigue that does not require a treatment delay 
• Any Grade 3 skin, drug-related adverse event 
• Any Grade 3 drug-related laboratory abnormality, with the following exceptions for 
lymphopenia, leukopenia, AST, ALT, or total bilirubin: 
− Grade 3 lymphopenia or leukopenia does not require dose delay 
− Asymptomatic Grade 3/4 increase in amylase/lipase does not require dose delay 
− If a subject has a baseline AST, ALT or total bilirubin that is within normal limits, 
delay dosing for drug-related Grade ≥ 2 toxicity 
− If a subject has baseline AST, ALT, or total bilirubin within the Grade 1 toxicity range, 
delay dosing for drug-related Grade ≥ 3 toxicity 
• Any AE, laboratory abnormality, or intercurrent illness which, in the judgment of the 
investigator, warrants delaying the dose of study medication. 
 
3.3.2 Dose Reductions 
 
3.3.2.1 Nivolumab Dose Reductions 
There will be no dose modifications of nivolumab. 
 
30 
 


3.3.2.2 ISA101 Dose Reductions 
There will be no dose modifications of ISA101. 
 
3.3.3 Criteria to Resume Dosing 
3.3.3.1 Criteria to Resume Treatment with nivolumab 
Subjects may resume treatment with nivolumab when the drug-related AE(s) resolve(s) to 
Grade ≤ 1 or baseline, with the following exceptions: 
• Subjects may resume treatment in the presence of Grade 2 fatigue 
• Subjects who have not experienced a Grade 3 drug-related skin AE may resume 
treatment in the presence of Grade 2 skin toxicity 
• Subjects with baseline AST/ALT or total bilirubin in the Grade 1 toxicity range who 
require dose delays for reasons other than a 2-grade shift in AST/ALT or total bilirubin 
may resume treatment in the presence of Grade 2 AST/ALT OR total bilirubin 
• Subjects with combined Grade 2 AST/ALT AND total bilirubin values meeting 
discontinuation parameters (Section 3.3.5.1) should have treatment permanently 
discontinued 
• Drug-related pulmonary toxicity, diarrhea, or colitis must have resolved to baseline 
before treatment is resumed. Drug-related endocrinopathies adequately controlled with 
only physiologic hormone replacement may resume treatment 
• If treatment is delayed > 6 weeks, the subject must be permanently discontinued from 
study therapy, except as specified in Section 3.3.5. 
 
3.3.3.2 Criteria to Resume Treatment with ISA101 
 Subjects may resume treatment with ISA101 when the drug-related AE(s) resolve(s) to 
Grade ≤ 1. 
 
3.3.4 Treatment beyond Disease Progression 
Accumulating evidence indicates a minority of subjects treated with immunotherapy may 
derive clinical benefit despite initial evidence of PD. 
Therefore, subjects enrolled in the clinical trial will be permitted to continue treatment 
beyond initial irRC and RECIST 1.1 defined PD as long as they meet the following 
criteria: 
1. Investigator-assessed clinical benefit, and do not have rapid disease progression 
2. Continue to meet all other study protocol eligibility criteria 
3. Tolerance of study drug 
4. Stable performance status 
5. Treatment beyond progression will not delay an imminent intervention to prevent 
serious complications of disease progression (eg, CNS metastases) 
 
A radiographic assessment/ scan should be performed within six (6) weeks of original PD 
to determine whether there has been a decrease in the tumor size, or continued PD. The 
assessment of clinical benefit should be balanced by clinical judgment as to whether the 
subject is clinically deteriorating and unlikely to receive any benefit from continued 
treatment with nivolumab and ISA101 (if <3 doses have been administered). 
 
31 
 


If the investigator feels that the subject continues to achieve clinical benefit by continuing 
treatment, the subject should remain on the trial and continue to receive monitoring 
according to the Time and Events Schedule on Table 6.  
 
For the subjects who continue nivolumab study therapy and ISA101 (if <3 doses have 
been administered) beyond progression, further progression is defined as an additional 
10% increase in tumor burden volume from time of initial PD. This includes an increase 
in the sum of all target lesions and/ or the development of new measurable lesions. 
 
New lesions are considered measureable at the time of initial progression if the longest 
diameter is at least 10 mm (except for pathological lymph nodes which must have a short 
axis of at least 15 mm). Any new lesion considered non-measureable at the time of initial 
progression may become measureable and therefore included in the tumor burden volume 
if the longest diameter increases to at least 10 mm (except for pathological lymph nodes 
which must have a short axis of at least 15 mm). 
 
Global deterioration of health status requiring discontinuation of treatment without 
objective evidence of disease progression at that time should be reported as ‘symptomatic 
deterioration’. Every effort should be made to document objective progression (ie 
radiographic confirmation) even after discontinuation of treatment. 
 
3.3.5 Treatment Discontinuation Criteria 
Tumor assessments for all subjects should continue as per protocol even if dosing is 
discontinued. 
 
3.3.5.1 Nivolumab Dose Discontinuation 
Nivolumab treatment should be permanently discontinued for the following: 
• Any Grade ≥ 2 drug-related uveitis, eye pain or blurred vision that does not respond to 
topical therapy and does not improve to Grade 1 severity within the re-treatment period 
OR requires systemic treatment 
• Any Grade 3 non-skin, drug-related adverse event lasting > 7 days, with the following 
exceptions for laboratory abnormalities, drug-related bronchospasm, hypersensitivity 
reactions, and infusion reactions: 
− Grade 3 drug-related bronchospasm, hypersensitivity reaction, or infusion reaction of 
any duration requires discontinuation 
− Grade 3 drug-related laboratory abnormalities do not require treatment discontinuation 
except: 
♦ Grade 3 drug-related thrombocytopenia > 7 days or associated with bleeding requires 
discontinuation 
♦ Any drug-related liver function test (LFT) abnormality that meets the following criteria 
require discontinuation: 
• AST or ALT > 8xULN 
• Total bilirubin > 5x ULN 
• Concurrent AST or ALT > 3x ULN and total bilirubin > 2x ULN 
• Any Grade 4 drug-related adverse event or laboratory abnormality, except for the 
following events which do not require discontinuation: 
32 
 


− Grade 4 neutropenia ≤ 7 days 
− Grade 4 lymphopenia or leukopenia 
− Isolated Grade 4 electrolyte imbalances/abnormalities that are not associated with 
clinical sequelae and are corrected with supplementation/appropriate management within 
72 hours of their onset 
• Any dosing interruption lasting > 6 weeks with the following exceptions: 
− Dosing interruptions to allow for prolonged steroid tapers to manage drug-related 
adverse events are allowed. Tumor assessments should continue as per protocol even if 
dosing of study drug(s) is interrupted. 
− Dosing interruptions > 6 weeks that occur for non-drug-related reasons may be 
allowed.  Tumor assessments should continue as per protocol even if dosing is 
interrupted. 
• Any adverse event, laboratory abnormality, or intercurrent illness which, in the 
judgment of the investigator, presents a substantial clinical risk to the subject with 
continued nivolumab. 
 
Subjects may remain on study and take the other study drug when the drug-related AE(s) 
resolve(s) to Grade ≤ 1. 
 
3.3.5.2 ISA101 Dose Discontinuation 
ISA101 will be discontinued in case of severe systemic allergic reaction, characterized by 
dyspnea, urticarial, severe generalized skin rash or other signs of systemic allergy, 
particularly if not controllable by epinephrine and/or anti-histamines. 
 
3.3.6 Treatment of nivolumab-Related Infusion Reactions 
Since nivolumab contains only human immunoglobulin protein sequences, it is unlikely 
to be immunogenic and induce infusion or hypersensitivity reactions. However, if such a 
reaction were to occur, it might manifest with fever, chills, rigors, headache, rash, 
pruritus, arthalgias, hypotension, hypertension, bronchospasm, or other allergic-like 
reactions. All Grade 3 or 4 infusion reactions should be reported within 24 hours to BMS 
and reported as an SAE if it meets the criteria. Infusion reactions should be graded 
according to NCI CTCAE (Version 4.0) guidelines. 
 
Treatment recommendations are provided below and may be modified based on local 
treatment standards and guidelines, as appropriate: 
 
For Grade 1 symptoms: (Mild reaction; infusion interruption not indicated; 
intervention not indicated). 
• Remain at bedside and monitor subject until recovery from symptoms. The following 
prophylactic premedications are recommended for future infusions: diphenhydramine 
50 mg (or equivalent) and/or acetaminophen 325 to 1000 mg orally at least 
30 minutes before additional nivolumab administrations. 
For Grade 2 symptoms: (Moderate reaction requires therapy or infusion 
interruption but responds promptly to symptomatic treatment [eg, antihistamines, 
non-steroidal anti-inflammatory drugs, narcotics, corticosteroids, bronchodilators, 
IV fluids]; prophylactic medications indicated for ≤ 24 hours). 
33 
 


• Stop the infusion, begin an IV infusion of normal saline, and treat the subject with 
diphenhydramine 50 mg IV (or equivalent) and/or acetaminophen 325 to 1000 mg PO; 
remain at bedside and monitor subject until resolution of symptoms. Corticosteroid 
and/or bronchodilator therapy may also be administered as appropriate. If the infusion is 
interrupted, then restart the infusion at 50% of the original infusion rate when symptoms 
resolve; if no further complications ensue after 30 minutes, the rate may be increased to 
100% of the original infusion rate. Monitor subject closely. If symptoms recur, then no 
further nivolumab will be administered at that visit. 
• For future infusions, the following prophylactic premedications are recommended: 
diphenhydramine 50 mg (or equivalent) and/or acetaminophen/paracetamol 325 to 
1000 mg PO should be administered at least 30 minutes before nivolumab infusions. If 
necessary, corticosteroids (up to 25 mg i.v.of SoluCortef or equivalent) may be used. 
For Grade 3 or 4 symptoms: (Severe reaction, Grade 3: prolonged [ie, not rapidly 
responsive to symptomatic medication and/or brief interruption of infusion]; 
recurrence of symptoms following initial improvement; hospitalization indicated for 
other clinical sequelae [eg, renal impairment, pulmonary infiltrates]. Grade 4: 
Life-threatening; pressor or ventilatory support indicated). 
• Immediately discontinue infusion of nivolumab. Begin an IV infusion of normal saline 
and treat the subject as follows: Recommend bronchodilators, epinephrine 0.2 to 1 mg of 
a 1:1000 solution for subcutaneous administration or 0.1 to 0.25 mg of a 
1:10,000 solution injected slowly for IV administration, and/or diphenhydramine 
50 mg IV with methylprednisolone 100 mg IV (or equivalent), as needed. Subject should 
be monitored until the Investigator is comfortable that the symptoms will not recur.  
 
Nivolumab will be permanently discontinued. Investigators should follow their 
institutional guidelines for the treatment of anaphylaxis. Remain at bedside and monitor 
subject until recovery of the symptoms. 
 
In case of late-occurring hypersensitivity symptoms (eg, appearance of a localized or 
generalized pruritus within 1 week after treatment), symptomatic treatment may be given 
(eg, oral antihistamine or corticosteroids). 
 
3.3.7 Treatment of ISA101 Related Systemic Reactions 
Systemic allergic reactions up to Grade 2 have been reported in approximately 
7% of patients and have been controlled with antihistamines and/or epinephrine. 
Patients receiving HPV-16-SLP or ISA101 in Montanide should be closely 
monitored for the first 3 hours after vaccination. Immediate treatment of severe 
allergic reactions should be available, including staff well-trained in 
resuscitation, intravenous access for administration of fluids, antihistamines and 
corticosteroids, and epinephrine for intramuscular injection. 
 
3.4 Treatment Compliance 
Treatment compliance will be monitored by drug accountability as well as the subject’s 
medical record. 
 
3.5 Destruction and Return of Study Drug 
34 
 


 
3.5.1 Destruction of Study Drug 
For this study, study drugs (those supplied by BMS or ISA) such as partially used study 
drug containers, vials and syringes may be destroyed on site. 
 
Any unused study drugs can only be destroyed after being inspected and reconciled by 
the responsible pharmaceutical company unless study drug containers must be 
immediately destroyed as required for safety, or to meet local regulations  
On-site destruction is allowed provided the following minimal standards are met: 
• On-site disposal practices must not expose humans to risks from the drug. 
• On-site disposal practices and procedures are in agreement with applicable laws and 
regulations, including any special requirements for controlled or hazardous substances. 
• Written procedures for on-site disposal are available and followed. The procedures must 
be filed with the site’s SOPs and a copy provided to BMS or ISA (as appropriate) upon 
request or termination of the study, all unused and/or partially used study drug that was 
supplied by BMS or ISA must be returned to BMS or ISA, respectively. 
 
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. 
 
4.0 ASSESSMENT FOR SAFETY AND EFFICACY 
 
4.1 Safety Assessments 
Safety assessments will be monitored at Screening (Baseline visit), during treatment 
according to the frequency for each treatment starting on Cycle 1 Day 1 and will continue 
at the specified frequency until discontinuation from the study. (See Tables 5, 6, 7) 
 
Table 5. Flow Chart/Time and Events Schedule 
 
Procedure 
Screening 
Visit 
Notes 
Eligibility assessment 
 
 
Informed Consent 
X 
 
Inclusion/Exclusion Criteria 
X 
 
Medical History 
X 
 
Safety Assessment 
 
 
Vital Signs and Oxygen 
Saturation 
X 
Temperature, BP, HR, RR, O2 
saturation by pulse oximetry (also 
monitor amount of supplemental 
oxygen if applicable) 
Obtain vital signs at screening visit 
(within 14 days of registration) and 
within 72 hours of first dose 
Physical Exam 
X 
Review of systems including 
35 
 


measurements of Height and Weight, 
and ECOG Performance status 
Laboratory Tests 
X 
Labs performed: CBC with differential 
including neutrophil and lymphocyte 
count, Serum chemistry (BUN or 
serum urea level, serum creatinine, 
sodium, potassium, calcium, 
magnesium, phosphate, chloride, and 
bicarbonate, glucose), AST, ALT, total 
bilirubin, alkaline phosphatase, 
albumin, LDH, TSH, free T3, free T4, 
HBV sAg, HCV RNA, HIV1/2 
immunoassay 
HPV-16 Confirmation 
X 
 
Pregnancy Test 
X 
Performed within 24 hours of 
registration (serum or urine for 
WOCBP only) 
Procedure 
 
 
Assessment (of signs and 
symptoms) 
X 
 
Concomitant Medication 
collection 
X 
 
Efficacy assessments 
 
 
Radiographic Tumor 
Assessment (chest, abdomen, 
pelvis) 
X 
Should be performed within 28 days of 
start of treatment. CT/MRI of brain 
(with contrast) should only be 
performed in subjects with a known 
history of treated brain metastases. 
Additional sites of known or suspected 
disease (including CNS) should be 
imaged at the screening visit and at 
subsequent on-study assessments 
Biomarker Assessment 
 
 
Mandatory tumor biopsy 
X 
 
 
4.1.1 Cervista HPV Assay 
Tumors are required to be HPV-16 positive in order to be eligible for this clinical trial. 
Cervista HPV-16/18 assay will be conducted according to previously published data (48). 
This assay is not PCR-based but uses proprietary Invader chemistry, a signal-
amplification method for the detection of specific nucleic acid sequences (Hologic, Inc.). 
The Cervista HPV-16/18 assay uses two oligonucleotide mixtures containing probes 
specific for the L1, E6, and E7 genomic regions of either HPV-16 or HPV-18.  In both 
assays, oligonucleotides targeting the human histone 2 gene (H2be, HIST2H2BE) were 
used to serve as an internal control for detection of cellular DNA. A signal-to-noise 
value, referred to as fold over zero (FOZ), was determined for each specimen. The FOZ 
cutoff value for a positive result was 2.13. 
36 
 


 
Table 6. On –study assessment 
Procedure 
C1D1 
(±7 
days) 
C1D8
(±7 
days) 
C2D1
(±7 
days) 
Each cycle 
(every 2 
weeks) on 
Day 1 (±7 
days for 
every clinic 
visit) 
Notes  
 
Tumor Biopsy for 
response evaluation 
 
 
 
 
At Week 11 and at 
progression 
(optional) 
Safety Assessment 
 
 
 
 
 
Vital Signs and 
Oxygen saturation 
X 
X 
X 
X 
Temperature, BP, 
HR, RR, O2 
saturation by pulse 
oximetry (also 
monitor amount of 
supplemental 
oxygen if 
applicable) prior to 
dosing and at any 
time a subject has 
any new or 
worsening 
respiratory 
symptoms 
Adverse Events (AE) 
and Serious Adverse 
Events (SAE) 
Assessment 
……………….Continuously……………………….. 
Physical Exam 
X 
X 
X 
X 
Review of systems 
including 
measurements of 
Height and 
Weight, and 
ECOG 
Performance status 
Complete blood count 
(CBC) 
(Results obtained prior 
to dosing on 
nivolumab infusion 
days) 
X 
X 
X 
X 
Includes WBC 
count with 
differential, ANC, 
lymphocyte count, 
hemoglobin, 
hematocrit, and 
platelet count 
Serum Chemistry 
X 
X 
X 
X 
Serum chemistry 
37 
 


Tests 
(BUN or serum 
urea level, 
serum creatinine, 
sodium, 
potassium, 
calcium, 
magnesium, 
phosphate, 
chloride, and 
bicarbonate, 
glucose), LDH 
Liver Function Testing 
(Results obtained 
within 72 hours prior 
to dosing on 
nivolumab infusion 
days) 
X 
X 
X 
X 
 
Thyroid Function 
Testing 
X 
X 
X 
X 
 
Whole blood for 
research and 
immunology studiesa 
 
 
 
 
 
Review of 
Concomitant 
Medications 
X 
X 
X 
X 
Concomitant 
medications taken 
throughout the 
study duration 
should be recorded 
within the eCRF. 
Pregnancy Test 
C1D1 and then monthly 
Efficacy Assessments 
 
 
 
 
 
Radiographic Tumor 
Assessmentb 
 
 
 
 
 Week 11 (±5 
days) and every 6 
weeks (±5 days) 
thereafter 
Clinical Drug 
Supplies 
 
 
 
 
 
nivolumab 
 
X 
X 
X 
 
ISA101 vaccine 
X 
 
 
 
Only 3 doses: 
C1D1, C2D1 and 
C4D1 (±3 days) 
a. Whole blood will be collected pre-treatment and pre-vaccination at weeks 3 and 
7, pre-nivolumab at weeks 9 and 11, then every 12 weeks for biomarker testing. 
b. Subjects will be evaluated for response according to RECIST 1.1 and immune 
related response criteria.  
 
Table 7. Follow-up and Survival Procedures 
38 
 


 
Procedure 
Initial Follow-up 
phase: 
Follow-up #1 to 
occur 30 days (±5 
days) after last dose. 
follow-up #2 to occur 
approximately 70 
days (±5 days) 
Further 
Follow-up 
Phase 
(beyond 
follow-up #2) 
Notes 
Radiographic 
Tumor 
Assessmenta 
X 
X 
For subjects who 
discontinue study treatment 
for reasons other than PD, 
follow up scans should be 
performed every 6 weeks 
(± 5 days) until PD, 
withdrawal of consent, 
death, lost to follow-up, or 
start of a subsequent 
anticancer therapy 
Tumor Biopsy 
for response 
evaluation 
 
 
At progression (optional) 
Safety 
Assessment 
 
 
 
Vital Signs 
X 
X 
 
Physical Exam 
X 
X 
Review of systems 
including measurements of 
Height and Weight, and 
ECOG Performance status 
Adverse Events 
(AE) and Serious 
Adverse Event 
(SAE) 
Assessmentb 
X 
X 
 
Laboratory Tests 
X 
X 
 
Review of 
Concomitant 
Medications 
X 
 
 
Collection of 
Survival 
Informationc 
X 
X 
Direct contact (office 
visit) or phone call 
a. Radiographic assessments for subjects who have not experienced PD must be 
obtained every 6 weeks (±5 days), and not delayed until follow-up #1 or #2. Patients 
with PD by RECIST 1.1 criteria at any point may be allowed to remain on study 
drugs unless they are demonstrating evidence of clinical progression. If the 
39 
 


investigator feels the patient is benefiting and should continue on study, this should 
be documented in the medical record. 
b. Subjects will have two follow-up visits for safety within the first 100 days from the 
last dose of study therapy. Beyond 100 days from the last dose of study therapy, 
subjects will be followed for ongoing drug-related adverse events until resolved, 
return to baseline or deemed irreversible, or until lost to follow-up, withdrawal of 
study consent, or start of a subsequent anti-cancer therapy. 
c. All subjects will be followed for overall survival every 3 months until death, being 
lost to follow-up, or withdrawal of study consent, for up to 3 years (36 months). 
 
 
4.2 Efficacy Assessments 
 
4.2.1 Screening (Baseline visit) and On-Study Efficacy Assessments 
Study evaluations will take place in accordance with Table 5, and according to irRC and, 
RECIST 1.1 (Appendix 1). High resolution CT with PO/IV contrast or contrast-enhanced 
MRI are the preferred imaging modalities for assessing radiographic tumor response. If a 
subject has a known allergy to contrast material, use local prophylaxis standards to obtain 
the assessment with contrast if at all possible, or use the alternate modality. In cases 
where contrast is strictly contraindicated, a non-contrast scan will suffice. In addition to 
chest, abdomen and pelvis, all known or suspected sites of disease (including CNS) 
should be assessed at screening and at subsequent assessments using the same imaging 
method and technique. If more than one method is used at screening, then the most 
accurate method according to RECIST 1.1 should be used when recording data, and 
should again be used for all subsequent assessments. Bone scan, PET scan, or ultrasound 
are not adequate for assessment of RECIST response. In selected circumstances where 
such modalities are the sole modality used to assess certain non-target organs, those non-
target organs may be evaluated less frequently. For example, bone scans may need to be 
repeated only when complete response is identified in target disease or when progression 
in bone is suspected. Subjects with a history of brain metastasis should have surveillance 
MRI approximately every 12 weeks or as per local standard of care, or sooner if clinically 
indicated. Radiographic tumor assessments will be conducted at Week 11(± 5 days) and 
every 6 weeks from Week 11 (± 5 days) until disease progression (or until 
discontinuation of study therapy in patients receiving nivolumab beyond progression), 
lost to follow-up, withdrawal of study consent, or start of a subsequent anti-cancer 
therapy. Tumor assessments for all subjects should continue as per protocol even if 
dosing is interrupted. Tumor measurements should be made by the same investigator or 
radiologist for each assessment whenever possible. Changes in tumor measurements and 
tumor responses to guide ongoing study treatment decisions will be assessed by the 
investigator using irRC and RECIST 1.1 (see Appendix 1-2).  
 
4.2.2 Follow-up and Survival Procedures 
Subjects who discontinue study treatment prior to progression, and subjects being treated 
beyond disease progression, will be followed with radiographic tumor assessments every 
6 weeks (± 5 days) until documented or further disease progression, withdrawal of study 
consent, lost to follow-up, or beginning of a subsequent anti-cancer treatment. 
40 
 


 
Radiographic assessments should be performed according to Section 4.1. All 
radiographic assessments performed for study purposes during the follow-up phase will 
be submitted to the IRC for adjudication of the primary and secondary efficacy endpoints. 
Survival will be followed for up to 3 years (36 months) after progression, either by direct 
contact (office visits) or via telephone contact, according to Table 6 until death, 
withdrawal of study consent, or lost to follow-up. 
 
4.2.3 Primary Efficacy Assessment 
This study has primary endpoint of ORR See section 6.3 for definitions of ORR. All 
subjects will be monitored by radiographic assessment on an every-6-week schedule 
[beginning from the first on-study assessment on Week 11 (±5 days)] to determine 
changes in tumor size according to Section 4.2.1. irRC and RECIST 1.1 criteria will be 
used for the assessment (see Appendix 1). The PI will determine efficacy assessment and 
it will be documented on the CRF. 
 
4.2.4 Secondary Efficacy Assessments 
For secondary efficacy analyses (response rate by irRC, RECIST, PFS, Immune-related 
PFS, subjects will be monitored by radiographic assessment on an every-6-week schedule 
beginning from the first on-study assessment on Week 11 (±5 days)], as for the primary 
efficacy assessment and according to Section 4.2.1. RECIST 1.1 criteria will be used for 
the assessment (see Appendix 1). The PI will determine efficacy assessment and it will be 
documented on the CRF. Survival information will be collected as for the primary 
efficacy assessment. 
 
4.3 Other Assessments 
 
4.3.1 Exploratory Biomarker Assessments 
Tumor tissue and blood samples will be collected for immune monitoring  as follows:  
 
 
 
4.3.1.1 Peripheral Blood Markers 
The treating physician or designee will have the option to cancel the laboratory protocol 
collection for patient safety without protocol deviation. 
 
 a) 100 mL of peripheral blood will be collected  for evaluation of HPV-specific immune 
response in  immune cell populations, including but not limited to CD4 and CD8 T cells 
in pre and post therapy samples at the following time points: pre-treatment and pre-
vaccination at weeks 3 and 7, pre-nivolumab at weeks 9 and 11, then every 12 weeks.  
In the event of poor recovery of functional lymphocytes from frozen cells, selected 
patients may have phlebotomy performed earlier  than every 12 weeks on one occasion.   
 
 
 
41 
 


HPV-specific immune responses will  include IFN-γ ELISPOT assay, flow cytometry to 
characterize HPV-specific  T cell populations, and T cell receptor  sequencing to track 
the expansion of HPV specific T cells in the blood, (Dr. Chantale Bernatchez’s lab).  
 
 
4.3.1.2 Tumor Markers 
Tumor tissue will be obtained at baseline, and as an optional procedure, at Week 11 
(response evaluation), and at progression (as possible). Where possible tumor biopsy 
samples pre- and post- treatment will be analyzed for expression of costimulatory and co-
inhibitory ligands on tumor cells as well as the corresponding costimulatory / 
coinhibitory receptors, phenotypic differentiation and activation markers on effector cells 
and immune cell subset analysis using a panel of antibodies previously established by Dr. 
Wistuba, who directs the proposed HPV-Related Cancers Pathology Core. This will 
inform the immune response in the context of the tumor microenvironment and may be 
used to predict response to therapy, and evaluate for any correlation with peripheral blood 
analyses and clinical history.  
 
Pathologists  led by Dr. Ignacio Wistuba, will conduct standardized IHC studies to define 
and characterize infiltrating immune cell populations with markers including CD3, CD4, 
FoxP3, CD8, CD68, CD57, CD45RO, granzyme, PD-1, PD-L1, PD-L2, CTLA-4. 
Peritumoral versus intratumoral infiltrates will be scored, as these staining patterns have 
been shown by others to correlate with clinical outcomes (49-53). An intratumoral and 
peritumoral immune cell infiltrate grade of (0) none, (1) rare lymphocytes (2) focal 
lymphohistocytic aggregates or (3) severe diffuse infiltration will be assigned (54). Three 
representative fields will be evaluated by image analysis allowing for the data to be 
reported as a percentage of area with positive staining. Digital images and numerical data 
will be captured and stored in a secure database which will be accessible to team 
members for review.   IHC analysis of exploratory markers may  include: the B7 family 
ligands, PD-L2 (B7-DC), B7-H3 and B7-x/H4, as well as inhibitory receptors on 
lymphocytes, including 2B4, LAG-3, BTLA, and Tim-3; these cell surface molecules are 
candidates for therapeutic antibody blockade.  Expression of the ligands for Tim-3, 
BTLA and 2B4 (galectin 9, HVEM, and CD48, respectively)may also be assessed. These 
studies will provide a comprehensive view of cellular subsets and checkpoint molecule 
expression in tumors from untreated patients and how cellular subsets and key immune 
regulatory molecules are impacted intratumorally after treatment with anti-PD-1 and the 
ISA101 vaccine. Determining which inhibitory molecules/pathways are present despite 
treatment with anti-PD-1 and vaccine should inform selection of rational combination 
therapy in the future. Importantly, all of these parameters of the immune 
microenvironment will be correlated with clinical outcome.  
 
 
5.0 SAFETY MONITORING AND REPORTING  
 
5.1 ADVERSE EVENTS: Definitions and Reporting   
An Adverse Event (AE) is defined as any new untoward medical occurrence or 
worsening of a pre-existing medical condition in a subject or clinical investigation subject 
42 
 


administered an investigational (medicinal) product and that does not necessarily have a 
causal relationship with this treatment. An AE can therefore be any unfavorable and 
unintended sign (including an abnormal laboratory finding, for example), symptom, or 
disease temporally associated with the use of investigational product, whether or not 
considered related to the investigational product. 
 
The causal relationship to either or both study drugs is determined by a physician and 
should be used to assess all adverse events (AE). The casual relationship can be one of 
the following: 
Related: There is a reasonable causal relationship between study drug administration 
(either ISA101, nivolumab or both) and the AE. 
Not related: There is not a reasonable causal relationship between administration of either 
of the two study drugs (or both) and the AE. 
 
The term "reasonable causal relationship" means there is evidence to suggest a causal 
relationship to either or both investigational agents. 
 
Adverse events can be spontaneously reported or elicited during open-ended questioning, 
examination, or evaluation of a subject. (In order to prevent reporting bias, subjects 
should not be questioned regarding the specific occurrence of one or more AEs.) 
 
5.1.1 Serious Adverse Events Reporting 
An adverse event or suspected adverse reaction is considered “serious” if, in the view of 
either the investigator or the sponsor, it results in any of the following outcomes: 
• 
Death 
• 
A life-threatening adverse drug experience – any adverse experience that places the 
patient, in the view of the initial reporter, at immediate risk of death from the adverse 
experience as it occurred. It does not include an adverse experience that, had it occurred in 
a more severe form, might have caused death. 
• 
Inpatient hospitalization or prolongation of existing hospitalization 
• 
A persistent or significant incapacity or substantial disruption of the 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 may be considered a serious adverse drug experience when, based upon 
appropriate medical judgment, they may jeopardize the patient or subject and may require 
medical or surgical intervention to prevent one of the outcomes listed in this definition. 
Examples of such medical events include allergic bronchospasm requiring intensive 
treatment in an emergency room or at home, blood dyscrasias or convulsions that do not 
result in inpatient hospitalization, or the development of drug dependency or drug abuse 
(21 CFR 312.32). 
• 
Important medical events as defined above, may also be considered serious adverse 
events. Any important medical event can and should be reported as an SAE if deemed 
appropriate by the Principal Investigator or the IND Sponsor, IND Office. 
• 
All events occurring during the conduct of a protocol and meeting the definition of 
a SAE must be reported to the IRB in accordance with the timeframes and procedures 
43 
 


outlined in “The University of Texas M. D. Anderson Cancer Center Institutional Review 
Board Policy for Investigators on Reporting Serious Unanticipated Adverse Events for 
Drugs and Devices”.  Unless stated otherwise in the protocol, all SAEs, expected or 
unexpected, must be reported to the IND Office, regardless of attribution (within 5 
working days of knowledge of the event). 
• 
All life-threatening or fatal events, that are unexpected, and related to the study 
drug, must have a written report submitted within 24 hours (next working day) of 
knowledge of the event to the Safety Project Manager in the IND Office.   
• 
Unless otherwise noted, the electronic SAE application (eSAE) will be utilized for 
safety reporting to the IND Office and MDACC IRB.  
• 
Serious adverse events will be captured from the time of the first protocol-specific 
intervention, until 30 days after the last dose of drug, unless the participant withdraws 
consent. Serious adverse events must be followed until clinical recovery is complete and 
laboratory tests have returned to baseline, progression of the event has stabilized, or there 
has been acceptable resolution of the event. 
• 
Additionally, any serious adverse events that occur after the 30 day time period 
that are related to the study treatment must be reported to the IND Office. This may 
include the development of a secondary malignancy. 
 
Potential drug induced liver injury (DILI) is also considered an important medical event. 
(See Section 5.5 for the definition of potential DILI.) 
Suspected transmission of an infectious agent (eg, any organism, virus or infectious 
particle, pathogenic or non-pathogenic) via the study drug is an SAE. 
Although pregnancy, overdose, cancer, and potential drug induced liver injury (DILI) are 
not always serious by regulatory definition, these events must be handled as SAEs. 
(See Section 5.3 for reporting pregnancies). 
 
The following reasons for hospitalization or prolongation of existing hospitalization are 
not considered SAEs: 
• Routine treatment or monitoring of the studied indication, not associated with any 
deterioration in condition (specify what this includes) 
• Elective or pre-planned treatment for a pre-existing condition that is unrelated to 
the indication under study and has not worsened since signing the informed 
consent 
• Treatment on an emergency outpatient basis for an event not fulfilling any of the 
definitions of a SAE given above and not resulting in hospital admission 
• Social reasons and respite care in the absence of any deterioration in the patient’s 
general condition 
 
Note that treatment on an emergency outpatient basis that does not result in hospital 
admission and involves an event not fulfilling any of the definitions of a SAE given 
above is not a serious adverse event. 
 
Reporting to FDA: 
44 
 


• Serious adverse events will be forwarded to FDA by the IND Sponsor (Safety 
Project Manager IND Office) according to 21 CFR 312.32. 
 
It is the responsibility of the PI and the research team to ensure serious adverse 
events are reported according to the Code of Federal Regulations, Good Clinical 
Practices, the protocol guidelines, the sponsor’s guidelines, and Institutional Review 
Board policy. 
 
5.1.2 Communication between Investigator and BMS and ISA 
If applicable, SAEs must be collected that relate to any later protocol-specified procedure 
(eg, a follow-up skin biopsy). An SAE report should be completed for any event where 
doubt exists regarding its status of seriousness. 
 
If the investigator believes that an SAE is not related to either study drug, but is 
potentially related to the conditions of the study (such as withdrawal of previous therapy, 
or a complication of a study procedure), the relationship should be specified in the 
narrative section of the SAE Report Form. 
 
SAEs, whether related or not related to study drug, and pregnancies must be reported to 
BMS and ISA within 24 hours. SAEs must be recorded on the SAE Report Form; 
pregnancies on a MD Anderson SAE Form (electronic or paper forms). When using 
paper forms, the reports are to be transmitted via email or confirmed facsimile (fax) 
transmission to: 
SAE Email Address: BMS:Worldwide.Safety@BMS.com; ISA: Visscher@isa-
pharma.com. 
SAE Facsimile Number: BMS: 609-818-3804; ISA: +31 71 33 22 311. 
SAE Telephone Contact (required for SAE and pregnancy reporting): See Contact 
Information list. 
 
If only limited information is initially available, follow-up reports are required. 
(Note: Follow-up SAE reports should include the same investigator term(s) initially 
reported.) 
 
If an ongoing SAE changes in its intensity or relationship to study drug or if new 
information becomes available, a follow-up SAE report should be sent within 24 hours to 
the BMS (or designee) and ISA using the same procedure used for transmitting the initial 
SAE report. 
 
All SAEs should simultaneously be faxed or e-mailed to BMS at: 
Global Pharmacovigilance & Epidemiology 
Bristol-Myers Squibb Company 
Fax Number: 609-818-3804 
Email: Worldwide.safety@bms.com 
 
And to ISA at: ISA pharmaceuticals  
Attention to Sonja Visscher 
45 
 


Fax Number: +31 71 33 22 311 
Email: Visscher@isa-pharma.com. 
 
5.2 Laboratory Test Abnormalities 
The following laboratory abnormalities should be captured: 
• Any laboratory test result that is clinically significant or meets the definition of an 
SAE 
• Any laboratory abnormality that required the subject to have study drug discontinued or 
interrupted 
• Any laboratory abnormality that required the subject to receive specific corrective 
therapy. 
 
It is expected that wherever possible, the clinical, rather than the laboratory term would 
be used by the reporting investigator (eg, anemia versus low hemoglobin value). 
 
5.3 Pregnancy 
If, following initiation of the investigational product, it is subsequently discovered that a 
study subject is pregnant or may have been pregnant at the time of investigational product 
exposure, including during at least 6 half-lives (72 days) after product administration, the 
investigational product will be permanently discontinued in an appropriate manner 
(eg, dose tapering if necessary for subject safety). Protocol-required procedures for study 
discontinuation and follow-up must be performed on the subject unless contraindicated 
by pregnancy (eg, x-ray studies). Other appropriate pregnancy follow-up procedures 
should be considered if indicated. 
 
The investigator must immediately notify the BMS and ISA of this event and complete 
and forward a MD Anderson SAE form to BMS and ISA within 24 hours and in 
accordance with SAE reporting procedures described in Section 5.1.2. 
 
Follow-up information regarding the course of the pregnancy, including perinatal and 
neonatal outcome and, where applicable, offspring information must be reported on the 
MD Anderson SAE form. 
 
Any pregnancy that occurs in a female partner of a male study participant should be 
reported to BMS and ISA. Information on this pregnancy will be collected on the MD 
Anderson SAE Form. 
 
5.4 Overdose 
An overdose is defined as the accidental or intentional administration of any dose of a 
product that is considered both excessive and medically important. All occurrences of 
overdose must be reported as an SAE (see Section 5.1.1 for reporting details). 
 
5.5 Potential Drug Induced Liver Injury (DILI) 
Wherever possible, timely confirmation of initial liver-related laboratory abnormalities 
should occur prior to the reporting of a potential DILI event. All occurrences of potential 
46 
 


DILIs, meeting the defined criteria, must be reported as SAEs (see Section 5.1.1. for 
reporting details). 
 
Potential drug induced liver injury is defined as 
1) AT (ALT or AST) elevation > 3 times upper limit of normal (ULN) 
AND 
2) Total bilirubin > 2 times ULN, without initial findings of cholestasis (elevated serum 
alkaline phosphatase), 
AND 
3) No other immediately apparent possible causes of AT elevation and 
hyperbilirubinemia, including, but not limited to, viral hepatitis, pre-existing chronic or 
acute liver disease, or the administration of other drug(s) known to be hepatotoxic. 
 
5.6 Other Safety Considerations 
Any significant worsening noted during interim or final physical examinations, 
laboratory evaluations, electrocardiograms, x-rays, and any other potential safety 
assessments, whether or not these procedures are required by the protocol, should also be 
recorded as an AE or SAE, as appropriate, and reported accordingly. 
 
For recommendations regarding suspected pulmonary toxicity, diarrhea and colitis, 
suspected hepatotoxicity (including asymptomatic LFT elevations), or suspected 
endocrinopathy, please see the Evaluation and Management Guidelines found in the 
IB-nivolumab.   
 
ISA101, which includes the adjuvant Montanide, may be associated with ulceration of 
abscess formation up to 2 years after the last vaccination.  In addition, up to Grade 2 
systematic allergic reactions may be expected in approximately 7% of subjects receiving 
ISA101.  Please refer to the Investigator Brochure for ISA101 regarding additional 
information on safety and risk management. 
 
For the purpose of this study at MD Anderson Cancer Center, all patients will be 
registered in the Clinical Oncology Research System (CORE). All study related data will 
be captured in the Protocol Data Management System (PDMS). All adverse events, 
regardless of grade or attribution, will be documented in CORE. 
 
6.0 STATISTICAL CONSIDERATIONS 
 
6.1 Sample Size Determination 
We will use Simon’s two-stage MiniMax design (55) targeting an alternative hypothesis 
response rate of 0.3 versus a null hypothesis response rate of 0.10 with 80% power and a 
one-sided  0.05 significance level. A response is defined as ORR (CR +PR) by the RC at 
11 weeks from the start of treatment.  This design requires a maximum of 25 evaluable 
patients.  Fifteen patients will be treated in the first stage. A response summary will be 
submitted to the IND Medical Monitor after the 15th subject and at the end of the study. If 
< 2 responses are seen, the trial will be stopped for futility.  If there are at least 2 
responses, 10 additional patients will be enrolled into the second stage.  If there are more 
47 
 


than 5 responses out of 25, the combination will be deemed worthy of further study.   
Enrollment will be suspended at the end of the first stage after 15 patients have been 
accrued for response evaluation if less than 2 response were observed.   
 
A total sample size (N) of 28 is planned to obtain 25 evaluable patients.   
 
Dose-limiting toxicity (DLT) is defined for non-hematologic toxicity as a grade 3-4 
adverse event or grade 2 or greater ocular adverse event within 12 weeks of treatment.  
Grade 3 infusion reactions are exempt from the DLT definition. All grade 3 immune-
related adverse events that resolve to grade 1 or less within 28 days are exempt from the 
DLT definition excluding: pancreatitis, colitis, and ocular, hepatic and endocrine 
toxicities. DLT for hematologic toxicity is defined as   grade 4 neutropenia > 7 days 
duration or grade 3-4 neutropenia accompanied by neutropenic fever, grade 3-4 
thrombocytopenia > 7 days duration or grade 3-4 thrombocytopenia accompanied by 
bleeding, and grade 3-4 anemia.  
 
Stopping Rules for Toxicity:  
 
DLT will be monitored continuously in cohorts of 4 patients for 28 all patients to ensure 
safety using the method by Thall et al (56. The trial will be stopped early for toxicity if 
Prob(DLT> 30%) > 0.8 using a prior of beta (0.4, 1.6).  Stopping boundaries 
corresponding to this probability criterion are to terminate the trial if (# of patients with 
DLT) / (# patients evaluated) >= 3/4, 4/8, 6/12, 7/16, 8/20, and 10/24.  If the true DLT 
rates are 0.1, 0.2, 0.3, 0.4 and 0.5, the probabilities of early stopping are 0.01, 0.09, 0.35, 
0.7 and 0.92, receptively, and the average numbers of patients treated under these three 
scenarios are 28, 26, 22, 16 and 11, respectively (Multc Lean version 2.1.0).  
 
Accrual rate is estimated at 2 patients per month.  
 
Analysis plan: Summary statistics will be provided to summarize response, toxicity, and 
other categorical variables. Overall response rate by the RECIST 1.1 criteria will be 
estimated with 95% confidence interval.   Progression free survival and overall survival 
will be summarized using the method of Kaplan and Meier) and Cox proportional 
hazards model. 
 
 
6.2 Populations for Analyses 
• All enrolled subjects: All subjects who signed an informed consent form and were 
registered. 
•  All treated subjects: All subjects who received at least one dose of ISA101 and/or 
one dose of nivolumab. This is the primary dataset for dosing and safety. 
• Evaluable subjects: All subjects who receive at least one dose of ISA 101 and one 
dose of nivolumab and have had repeat imaging.  
• Biomarker subjects: All treated subjects with pre-treatment tumor biopsy and  
blood biomarkers available    
 
6.3 Endpoint Definitions 
48 
 


6.3.1 Primary Endpoint 
The primary objective in the study will be measured by ORR defined as the sum of 
subjects with a CR and PR divided by the number of evaluable subjects at 11 weeks from 
start of treatment. Response can be identified on any date between start of treatment and 
date of progression.  For the purposes of determining response in the first 15 evaluable 
pts (per the mini-max design), only patients who have completed at least one restaging 
assessment will be included.   If there are < 2 responses at that time, accrual of new 
patients will be held while active patients are further followed and declared to be 
responding or progressing.   
 
-CR is defined as disappearance of all target lesions. Any pathological lymph nodes 
(whether target or non-target) must have reduction in short axis to <10 mm. 
-PR: is defined as at least a 30% decrease in the sum of diameters of target lesions, taking 
as reference the baseline sum diameters. 
-PD is defined as at least a 20% increase in the sum of diameters of target lesions, taking 
as reference the smallest sum on study (this includes the baseline sum if that is the 
smallest on study). In addition to the relative increase of 20%, the sum must also 
demonstrate an absolute increase of at least 5 mm. Note: the appearance of one or more 
new lesions is also considered progression. 
-SD is defines as neither sufficient shrinkage from the baseline study to qualify for PR 
nor sufficient increase to qualify for PD, taking as reference the smallest sum diameters 
while on study. 
 
Best overall response (BOR) is defined as the best response designation, recorded 
between the date of start of treatment and the date of objectively documented progression 
per RECIST 1.1 (55) or the date of subsequent anticancer therapy, whichever occurs first. 
For subjects without documented progression or subsequent anti-cancer therapy, all 
available response designations will contribute to the BOR determination. For subjects 
who continue nivolumab beyond progression, the BOR should be determined based on 
response designations recorded up to the time of the initial RECIST 1.1-defined 
progression. 
 
Response can be identified on any date between start of treatment and date of 
progression.  For the purposes of determining response in the first 15 evaluable pts (per 
the mini-max design), only patients who have completed at least one restaging 
assessment will be included.   If there are < 2 responses at that time, accrual of new 
patients will be held while active patients are further followed and declared to be 
responding or progressing.  This has been added to section 6.3.1 
 
6.3.2 Secondary Endpoints 
• The first secondary endpoint is safety and tolerability which will be measured by 
the incidence of adverse events, serious adverse events, deaths, and laboratory 
abnormalities. Adverse event assessments and laboratory tests are performed at 
baseline, and continuously throughout the study at the beginning of each 
subsequent cycle. 
• The second secondary endpoint is HPV-specific immune responses 
49 
 


• The third secondary endpoint is immune-related ORR (ir-ORR) (ir CR + irPR) at 
11 weeks from the start of treatment by the irRC (56).  ORR using the irRC is 
derived from time-point response assessments (based on tumor burden) as 
follows: 
- irCR, complete disappearance of all lesions (whether measurable or not, and no new 
lesions) with confirmation by a repeat, consecutive assessment no less than 4 wk from the 
date first documented 
- irPR, decrease in tumor burden ≥50% relative to baseline confirmed by a consecutive 
assessment at least 4 wks after first documentation 
- irSD, not meeting criteria for irCR or irPR, in absence of irPD 
-irPD, increase in tumor burden ≥25% relative to nadir (minimum recorded tumor 
burden) with confirmation by a repeat, consecutive assessment no less than 
4 wk from the date first documented. 
-Patients are considered to have irPR or irSD even if new lesions are present, as long as 
they meet the respective thresholds of response as described above. Furthermore, patients 
are not considered to have irPD if new lesions were present and the tumor burden of all 
lesions did not increase by ≥25%. In contrast to irCR, irPR, and irPD, a response of irSD 
does not require confirmation. Refer to Appendix 1 for more details about irRC. 
• The fourth secondary endpoint is PFS. It is defined as the time from first day of 
treatment to the date of the first documented tumor progression (per RECIST 1.1), or 
death due to any cause. Subjects who die without a reported prior progression will be 
considered to have progressed on the date of their death. Subjects who did not 
progress or die will be censored on the date of their last evaluable tumor assessment. 
Subjects who did not have any on study tumor assessments and did not die will be 
censored on the date they were randomized. Subjects who started any subsequent 
anti-cancer therapy without a prior reported progression will be censored at the last 
evaluable tumor assessment prior to initiation of the subsequent anti-cancer therapy. 
• The fifth secondary endpoint is irPFS. It is defined as the time from treatment to the 
date of the first documented tumor progression (per irRC), or death due to any cause. 
• The sixth secondary endpoint is OS.  It is defined as the time from treatment to the 
date of death. 
 
6.3.3 Exploratory Endpoints 
• Exploratory endpoints are correlative markers of immune response in the tumor 
and peripheral blood that are discussed in detail in Section 4.3.1. 
 
6.3.4 Safety Analyses 
The safety analysis will be performed in all treated subjects. Descriptive statistics of 
safety will be presented using National Cancer Institute (NCI) Common Terminology 
Criteria for Adverse Events (CTCAE) version 4.0. All treatment emergent AEs, drug-
related AEs, SAEs and drug-related SAEs will be tabulated using worst grade per NCI 
CTCAE v 4.0 criteria by system organ class and preferred term. 
 
On-study lab parameters including hematology, chemistry, liver function, thyroid 
function and renal function will be summarized using worst grade per NCI CTCAE v 4.0 
criteria. Toxicity will be monitored continuously in cohorts of 4 patients.  
50 
 


 
 
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APPENDIX 1 
 
RECIST 1.1 CRITERIA 
This Appendix has been excerpted from the full RECIST 1.1 criteria. For information 
pertaining to RECIST 1.1 criteria not contained in the study protocol or in this Appendix, 
please refer to the full publication.1 
 
1 ASSESSMENT OF OVERALL TUMOR BURDEN AND 
MEASURABLE DISEASE 
To assess objective response or future progression, it is necessary to estimate the overall 
tumor burden at baseline and use this as a comparator for subsequent measurements. 
Measurable disease is defined by the presence of at least one measurable lesion. 
 
1.1 Measurability of tumor 
At baseline, tumor lesions/lymph nodes will be categorized measurable or non-
measurable as follows. All baseline evaluations should be performed as close as possible 
to the treatment start and never more than 4 weeks before the beginning of the treatment. 
Measurable lesions must be accurately measured in at least one dimension (longest 
diameter in the plane of the measurement to be recorded) with a minimum size of: 
• 10 mm by CT scan - (CT scan slice thickness no greater than 5 mm) 
• 10 mm caliper measurement by clinical exam (lesions which cannot be accurately 
measured with calipers should be recorded as non-measurable) 
• 20 mm by chest x-ray 
• Malignant lymph nodes: To be considered pathologically enlarged and measurable, a 
lymph node must be ≥15 mm in short axis when assessed by CT scan (CT scan slice 
thickness recommended to be no greater than 5 mm). At baseline and in follow-up, only 
the short axis will be measured and followed. 
All measurements should be recorded in metric notation, using calipers if clinically 
assessed. 
Special considerations regarding lesion measurability 
Bone lesions: 
• Bone scan, PET scan or plain films are not considered adequate imaging techniques to 
measure bone lesions. However, these techniques can be used to confirm the presence or 
disappearance of bone lesions. 
• Lytic bone lesions or mixed lytic-blastic lesions, with identifiable soft tissue 
components, that can be evaluated by cross sectional imaging techniques such as 
55 
 


CT or MRI can be considered as measurable lesions if the soft tissue component meets 
the definition of measurability described above. 
• Blastic bone lesions are non-measurable. 
Cystic lesions: 
• Lesions that meet the criteria for radiographically defined simple cysts should not be 
considered as malignant lesions (neither measurable nor non-measurable) since they are, 
by definition, simple cysts. 
• ‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable 
lesions, if they meet the definition of measurability described above. 
However, if non-cystic lesions are present in the same patient, these are preferred for 
selection as target lesions. 
Lesions with prior local treatment: 
• Tumor lesions situated in a previously irradiated area, or in an area subjected to other 
loco-regional therapy, are usually not considered measurable unless there has been 
demonstrated progression in the lesion. 
Non-measurable lesions are all other lesions, including small lesions (longest diameter 
< 10 mm or pathological lymph nodes with ≥ 10 to < 15 mm short axis), as well as non-
measurable lesions. Lesions considered non-measurable include: leptomeningeal disease, 
ascites, pleural or pericardial effusion, inflammatory breast disease, lymphangitic 
involvement of skin or lung, abdominal masses/abdominal organomegaly identified by 
physical exam that is not measurable by reproducible imaging techniques. 
 
1.2 Method of assessment 
The same method of assessment and the same technique should be used to 
characterize each identified and reported lesion at baseline and during follow-up. Imaging 
based evaluation should always be performed rather than clinical examination unless the 
lesion(s) being followed cannot be imaged but are assessable by clinical examination. 
CT, MRI: CT is the best currently available and reproducible method to measure lesions 
selected for response assessment. Measurability of lesions on CT scan is based on the 
assumption that CT slice thickness is 5 mm or less. When CT scans have slice thickness 
greater than 5 mm, the minimum size for a measurable lesion should be twice the slice 
thickness. 
Chest x-ray: Chest CT is preferred over chest x-ray, particularly when progression is an 
important endpoint, since CT is more sensitive than x-ray, particularly in identifying new 
lesions. However, lesions on chest x-ray may be considered measurable if they are clearly 
defined and surrounded by aerated lung. 
Clinical lesions: Clinical lesions will only be considered measurable when they are 
superficial and ≥10 mm diameter as assessed using calipers. For the case of skin lesions, 
documentation by color photography including a ruler to estimate the size of the lesion is 
suggested. As noted above, when lesions can be evaluated by both clinical exam and 
imaging, imaging evaluation should be undertaken since it is more objective and may be 
reviewed at the end of the study. 
56 
 


Ultrasound: Ultrasound is not useful in assessment of lesion size and should not be used 
as a method of measurement. If new lesions are identified by ultrasound in the course of 
the study, confirmation by CT or MRI is advised. 
Endoscopy, laparoscopy: The utilization of these techniques for objective tumor 
evaluation is not advised. 
Tumor markers: Tumor markers alone cannot be used to assess objective tumor response. 
 
2 BASELINE DOCUMENTATION OF ‘TARGET’ AND 
‘NONTARGET’ LESIONS 
Target lesions: When more than one measurable lesion is present at baseline all lesions 
up to a maximum of five lesions total (and a maximum of two lesions per organ) 
representative of all involved organs should be identified as target lesions and will be 
recorded and measured at baseline. 
Target lesions should be selected on the basis of their size (lesions with the longest 
diameter), be representative of all involved organs, and should lend themselves to 
reproducible repeated measurements. 
Lymph nodes merit special mention since they are normal anatomical structures which 
may be visible by imaging even if not involved by tumor. Pathological nodes which are 
defined as measurable and may be identified as target lesions must meet the criterion of a 
short axis of ≥15 mm by CT scan. Only the short axis of these nodes will contribute to 
the baseline sum. All other pathological nodes (those with short axis ≥10 mm but < 15 
mm) should not be considered non-target lesions. Nodes that have a short axis <10 mm 
are considered non-pathological and should not be recorded or followed. 
A sum of the diameters (longest for non-nodal lesions, short axis for nodal lesions) for all 
target lesions will be calculated and reported as the baseline sum diameters. The baseline 
sum diameters will be used as reference to further characterize any objective tumor 
regression in the measurable dimension of the disease. 
Non-target lesions: All other lesions (or sites of disease) including pathological lymph 
nodes should be identified as non-target lesions and should also be recorded at baseline. 
Measurements are not required and these lesions should be followed as ‘present’, 
‘absent’, or ‘unequivocal progression’. In addition, it is possible to record multiple non-
target lesions involving the same organ as a single item on the case record form (eg, 
‘multiple enlarged pelvic lymph nodes’ or ‘multiple liver metastases’). 
 
3 TUMOR RESPONSE EVALUATION AND RESPONSE 
CRITERIA 
 
3.1 Evaluation of target lesions 
Complete Response (CR): Disappearance of all target lesions. Any pathological lymph 
nodes (whether target or non-target) must have reduction in short axis to <10 mm. 
Partial Response (PR): At least a 30% decrease in the sum of diameters of target lesions, 
taking as reference the baseline sum diameters. 
Progressive Disease (PD): At least a 20% increase in the sum of diameters of target 
lesions, taking as reference the smallest sum on study (this includes the baseline sum if 
57 
 


that is the smallest on study). In addition to the relative increase of 20%, the sum must 
also demonstrate an absolute increase of at least 5 mm. Note: the appearance of one or 
more new lesions is also considered progression. 
Stable Disease (SD): Neither sufficient shrinkage from the baseline study to qualify for 
PR nor sufficient increase to qualify for PD, taking as reference the smallest sum 
diameters while on study. 
Special notes on the assessment of target lesions 
• Lymph nodes: Lymph nodes identified as target lesions should always have the actual 
short axis measurement recorded and should be measured in the same anatomical plane 
as the baseline examination, even if the nodes regress to below 10 mm on study. This 
means that when lymph nodes are included as target lesions, the ‘sum’ of lesions may not 
be zero even if complete response criteria are met, since a normal lymph node is defined 
as having a short axis of <10 mm. 
• Target lesions that become ‘too small to measure’: All lesions (nodal and nonnodal) 
recorded at baseline should have their actual measurements recorded at each subsequent 
evaluation, even when very small (eg, 2 mm). If the radiologist is able to provide an 
actual measure, that should be recorded, even if it is below 5 mm. 
However, when such a lesion becomes difficult to assign an exact measure to then: 
(i) if it is the opinion of the radiologist that the lesion has likely disappeared, the 
measurement should be recorded as 0 mm. 
(ii) if the lesion is believed to be present and is faintly seen but too small to measure, a 
default value of 5 mm should be assigned (note: in case of a lymph node believed to be 
present and faintly seen but too small to measure, a default value of 5 mm should be 
assigned in this circumstance as well). This default value is derived from the 5 mm 
CT slice thickness (but should not be changed with varying CT slice thickness). 
Lesions that split or coalesce on treatment: When non-nodal lesions ‘fragment’, the 
longest diameters of the fragmented portions should be added together to calculate the 
target lesion sum. Similarly, as lesions coalesce, a plane between them may be 
maintained that would aid in obtaining maximal diameter measurements of each 
individual lesion. If the lesions have coalesced such that they are no longer separable, the 
vector of the longest diameter in this instance should be the maximal longest diameter for 
the ‘coalesced lesion’. 
 
3.2 Evaluation of non-target lesions 
While some non-target lesions may actually be measurable, they need not be measured 
and instead should be assessed only qualitatively at the time points specified in the 
protocol. 
Complete Response (CR): Disappearance of all non-target lesions and normalization of 
tumor marker level. All lymph nodes must be non-pathological in size (< 10 mm short 
axis). 
Non-CR/Non-PD: Persistence of one or more non-target lesion(s) and/or maintenance of 
tumor marker level above the normal limits. 
Progressive Disease (PD): Unequivocal progression of existing non-target lesions. (Note: 
the appearance of one or more new lesions is also considered progression). 
58 
 


• The concept of progression of non-target disease requires additional explanation as 
follows: 
• When the patient also has measurable disease: To achieve ‘unequivocal progression’ on 
the basis of the non-target disease, there must be an overall level of substantial worsening 
in non-target disease such that, even in presence of SD or PR in target disease, the overall 
tumor burden has increased sufficiently to merit discontinuation of therapy. A modest 
‘increase’ in the size of one or more non-target lesions is usually not sufficient to qualify 
for unequivocal progression status. 
• When the patient has only non-measurable disease: To achieve ‘unequivocal 
progression’ on the basis of the non-target disease, there must be an overall level of 
substantial worsening such that the overall tumor burden has increased sufficiently to 
merit discontinuation of therapy. A modest ‘increase’ in the size of one or more non-
target lesions is usually not sufficient to qualify for unequivocal progression status. 
Because worsening in non-target disease cannot be easily quantified (by definition: if all 
lesions are non-measurable) a useful test that can be applied when assessing patients for 
unequivocal progression is to consider if the increase in overall disease burden based on 
the change in non-measurable disease is comparable in magnitude to the increase that 
would be required to declare PD for measurable disease: ie, an increase in tumor burden 
representing an additional 73% increase in ‘volume’ (which is equivalent to a 20% 
increase diameter in a measurable lesion). 
Examples include an increase in a pleural effusion from ‘trace’ to ‘large’, an increase in 
lymphangitic disease from localized to widespread, or may be described in protocols as 
‘sufficient to require a change in therapy’. If ‘unequivocal progression’ is seen, the 
patient should be considered to have had overall PD at that point. 
 
3.3 New lesions 
The appearance of new malignant lesions denotes disease progression. The finding of a 
new lesion should be unequivocal: ie, not attributable to differences in scanning 
technique, change in imaging modality or findings thought to represent something other 
than tumor (for example, some ‘new’ bone lesions may be simply healing or flare of pre-
existing lesions). This is particularly important when the patient’s baseline lesions show 
partial or complete response. For example, necrosis of a liver lesion may be reported on a 
CT scan report as a ‘new’ cystic lesion, which it is not. 
A lesion identified on a follow-up study in an anatomical location that was not scanned at 
baseline is considered a new lesion and will indicate disease progression. An example of 
this is the patient who has visceral disease at baseline and while on study has a CT or 
MRI brain ordered which reveals metastases. The patient’s brain metastases are 
considered to constitute PD even if he/she did not have brain imaging at baseline. 
If a new lesion is equivocal, for example because of its small size, continued therapy and 
follow-up evaluation will clarify if it represents new disease. If repeat scans confirm that 
there is a new lesion, then progression should be declared using the date of the initial 
scan. 
 
3.4 Tumor markers 
59 
 


Tumor markers alone cannot be used to assess objective tumor responses. If markers are 
initially above the upper normal limit, however, they must normalize in order for a 
patient to be considered as having attained a complete response. 
 
4 EVALUATION OF BEST OVERALL RESPONSE 
 
4.1 Time point response 
A response assessment should occur at each time point specified in the protocol. 
For patients who have measurable disease at baseline Table 1 provides a summary of the 
overall response status calculation at each time point 
 
Appendix Table 1. Summary of the Overall Response Status Calculation [Time point 
response: patients with target (+/-) non-target disease] 
Target lesions 
Non-target lesions 
New lesions 
Overall response 
CR 
CR 
No 
CR 
CR 
Non-CR/non-PD 
No 
PR 
CR 
Not evaluated 
No 
PR 
PR 
Non-PD or not all 
evaluated 
No 
PR 
SD 
Non-PD or not all 
evaluated 
No 
SD 
Not all evaluated 
Non-PD 
No 
NE 
PD 
Any 
Yes or No 
PD 
Any 
PD 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
 
 
4.2 Missing assessments and inevaluable designation 
When no imaging/measurement is done at all at a particular time point, the patient is not 
evaluable (NE) at that time point. If only a subset of lesion measurements are made at an 
assessment, usually the case is also considered NE at that time point, unless a convincing 
argument can be made that the contribution of the individual missing lesion(s) would not 
change the assigned time point response. This would be most likely to happen in the case 
of PD. 
 
4.3 Special notes on response assessment 
When nodal disease is included in the sum of target lesions and the nodes decrease to 
‘normal’ size (<10 mm), they may still have a measurement reported on scans. This 
measurement should be recorded even though the nodes are normal in order not to 
overstate progression should it be based on increase in size of the nodes. As noted earlier, 
this means that patients with CR may not have a total sum of ‘zero’ on the case report 
form (CRF). 
Patients with a global deterioration of health status requiring discontinuation of treatment 
without objective evidence of disease progression at that time should be reported as 
‘symptomatic deterioration’. Every effort should be made to document objective 
60 
 


progression even after discontinuation of treatment. Symptomatic deterioration is not a 
descriptor of an objective response: it is a reason for stopping study therapy. The 
objective response status of such patients is to be determined by evaluation of target and 
non-target disease as shown in Appendix Table 1. 
For equivocal findings of progression (e.g. very small and uncertain new lesions; cystic 
changes or necrosis in existing lesions), treatment may continue until the next scheduled 
assessment. If at the next scheduled assessment, progression is confirmed, the date of 
progression should be the earlier date when progression was suspected. 
5 ADDITIONAL CONSIDERATIONS 
 
5.1 Duration of response 
Duration of overall response: The duration of overall response is measured from the 
time measurement criteria are first met for CR/PR (whichever is first recorded) until the 
first date that recurrent or progressive disease is objectively documented (taking as 
reference for progressive disease the smallest measurements recorded on study). 
The duration of overall complete response is measured from the time measurement 
criteria are first met for CR until the first date that recurrent disease is objectively 
documented. 
Duration of stable disease: Stable disease is measured from the start of the treatment (in 
randomized trials, from date of start of treatment) until the criteria for progression are 
met, taking as reference the smallest sum on study (if the baseline sum is the smallest, 
this is the reference for calculation of PD). 
 
5.2 Lesions that disappear and reappear 
If a lesion disappears and reappears at a subsequent time point it should continue to be 
measured. However, the patient’s response at the point in time when the lesion reappears 
will depend upon the status of his/her other lesions. For example, if the patient’s tumour 
had reached a CR status and the lesion reappeared, then the patient would be considered 
PD at the time of reappearance. In contrast, if the tumour status was a PR or SD and one 
lesion which had disappeared then reappears, its maximal diameter should be added to 
the sum of the remaining lesions for a calculated response: in other words, the 
reappearance of an apparently ‘disappeared’ single lesion amongst many which remain is 
not in itself en ough to qualify for PD: that requires the sum of all lesions to meet the PD 
criteria. The rationale for such a categorisation is based upon the realisation that most 
lesions do not actually ‘disappear’ but are not visualised because they are beyond the 
resolving power of the imaging modality employed. 
 
5.3 Use of FDG-PET 
While FDG-PET response assessments need additional study, it is sometimes reasonable 
to incorporate the use of FDG-PET scanning to complement CT scanning in assessment 
of progression (particularly possible ‘new’ disease). New lesions on the basis of 
FDG-PET imaging can be identified according to the following algorithm: 
a. Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of 
PD based on a new lesion. Confirmatory CT is recommended. 
b. No FDG-PET at baseline and a positive FDG-PET at follow-up: 
61 
 


• If the positive FDG-PET at follow-up corresponds to a new site of disease confirmed by 
CT, this is PD. 
• If the positive FDG-PET at follow-up is not confirmed as a new site of disease on CT, 
additional follow-up CT scans are needed to determine if there is progression occurring at 
that site (if so, the date of PD will be the date of the initial abnormal FDG-PET scan). 
If the positive FDG-PET at follow-up corresponds to a pre-existing site of disease on CT 
that is not progressing on the basis of the anatomic images, this is not PD. 
 
Reference: 
1 Eisenhauer EA, Therasse P, Bogaerts J, et al. New response evaluation criteria in solid 
tumours: Revised RECIST guideline (version 1.1). Eur J Cancer. (2009); 45:228- 
247. 
 
 
APPENDIX 2 
 
Immune-related Response Criteria (irRC) 
 
Antitumor response based on total measurable tumor burden 
For the irRC, only index and measurable new lesions are taken into account (in contrast 
to conventional WHO criteria, which do not require the measurement of new lesions, nor 
do they include new lesion measurements in the characterization of evolving tumor 
burden). At the baseline tumor assessment, the sum of the products of the two largest 
perpendicular diameters (SPD) of all index lesions (five lesions per organ, up to 10 
visceral lesions and five cutaneous index lesions) is calculated. At each subsequent tumor 
assessment, the SPD of the index lesions and of new, measurable lesions (≥5 × 5 mm; up 
to 5 new lesions per organ: 5 new cutaneous lesions and 10 visceral lesions) are added 
together to provide the total tumor burden: 
 
 
Appendix Table 2. Comparison between WHO criteria and the irRC  
WHO 
irRC 
New, measurable 
lesions (i.e., ≥5 × 5 
mm) 
Always represent PD 
Incorporated into tumor burden 
New, 
nonmeasurable 
lesions (i.e., <5 × 5 
mm) 
Always represent PD 
Do not define progression (but 
preclude irCR) 
Non-index lesions Changes contribute to defining BOR 
of CR, PR, SD, and PD 
Contribute to defining irCR 
(complete disappearance 
required) 
CR 
Disappearance of all lesions in two 
Disappearance of all lesions in 
62 
 


WHO 
irRC 
consecutive observations not less than 
4 wk apart 
two consecutive observations 
not less than 4 wk apart 
PR 
≥50% decrease in SPD of all index 
lesions compared with baseline in two 
observations at least 4 wk apart, in 
absence of new lesions or 
unequivocal progression of non-index 
lesions  
≥50% decrease in tumor 
burden compared with baseline 
in two observations at least 4 
wk apart 
SD 
50% decrease in SPD compared with 
baseline cannot be established nor 
25% increase compared with nadir, in 
absence of new lesions or 
unequivocal progression of non-index 
lesions  
50% decrease in tumor burden 
compared with baseline cannot 
be established nor 25% 
increase compared with nadir 
PD 
At least 25% increase in SPD 
compared with nadir and/or 
unequivocal progression of non-index 
lesions and/or appearance of new 
lesions (at any single time point)  
At least 25% increase in tumor 
burden compared with nadir (at 
any single time point) in two 
consecutive observations at 
least 4 wk apart  
 
Time-point response assessment using irRC 
Percentage changes in tumor burden per assessment time point describe the size and 
growth kinetics of both conventional and new, measurable lesions as they appear. At each 
tumor assessment, the response in index and new, measurable lesions is defined based on 
the change in tumor burden (after ruling out irPD). Decreases in tumor burden must be 
assessed relative to baseline measurements (i.e., the SPD of all index lesions at 
screening). The irRC were derived from WHO criteria and, therefore, the thresholds of 
response remain the same (Table 3). However, the irRC response categories have been 
modified from those of WHO criteria as detailed in Tables 2 and 3. 
Table 3. Derivation of irRC overall responses 
Measurable response 
Nonmeasurable response 
Overall 
response 
Index and new, measurable 
lesions (tumor burden),* %  
Non-index lesions New, nonmeasurable 
lesions 
Using irRC 
↓100 
Absent 
Absent 
irCR† 
↓100 
Stable 
Any 
irPR† 
↓100 
Unequivocal 
progression 
Any 
irPR† 
↓≥50 
Absent/Stable 
Any 
irPR† 
↓≥50 
Unequivocal 
progression 
Any 
irPR† 
↓<50 to <25↑ 
Absent/Stable 
Any 
irSD 
↓<50 to <25↑ 
Unequivocal 
Any 
irSD 
63 
 


Measurable response 
Nonmeasurable response 
Overall 
response 
Index and new, measurable 
lesions (tumor burden),* %  
Non-index lesions New, nonmeasurable 
lesions 
Using irRC 
progression 
≥25? 
Any 
Any 
irPD† 
• *Decreases assessed relative to baseline, including measurable lesions only (>5 × 
5 mm).  
• 
†Assuming response (irCR) and progression (irPD) are confirmed by a second, 
consecutive assessment at least 4 wk apart.  
Overall response using the irRC 
The overall response according to the irRC is derived from time-point response 
assessments (based on tumor burden) as follows: 
 irCR, complete disappearance of all lesions (whether measurable or not, and no 
new lesions) 
o confirmation by a repeat, consecutive assessment no less than 4 wk from the 
date first documented 
 irPR, decrease in tumor burden ≥50% relative to baseline 
o confirmed by a consecutive assessment at least 4 wk after first 
documentation 
 irSD, not meeting criteria for irCR or irPR, in absence of irPD 
 irPD, increase in tumor burden ≥25% relative to nadir (minimum recorded tumor 
burden) 
o confirmation by a repeat, consecutive assessment no less than 4 wk from the 
date first documented 
Patients were considered to have irPR or irSD even if new lesions were present, as long 
as they met the respective thresholds of response as described above. Furthermore, 
patients were not considered to have irPD if new lesions were present and the tumor 
burden of all lesions did not increase by ≥25%. In contrast to irCR, irPR, and irPD, a 
response of irSD does not require confirmation. It is important to note that irCR, irPR, 
and irSD include all patients with CR, PR, or SD by WHO criteria as well as those 
patients that shift to these irRC categories from WHO PD. Patients with irSD, 
particularly those with slow-declining tumor burden ≥25% from baseline at the last tumor 
assessment, are considered clinically meaningful because they show an objectively 
measurable reduction in tumor burden without reaching the 50% threshold that defines 
irPR (it represented an objectively measured reduction not commonly observed in the 
natural history of advanced melanoma patients).  
64 
 


If a patient is classified as having irPD at a post-baseline tumor assessment, then 
confirmation of irPD by a second scan in the absence of rapid clinical deterioration is 
required. The definition of confirmation of progression represents an increase in tumor 
burden ≥25% compared with the nadir at two consecutive time points at least 4 wk apart. 
It is recommended that this be done at the discretion of the investigator because follow-
up with observation alone may not be appropriate for patients with a rapid decline in 
performance status. Confirmation of irPD allows for the capture of all observed responses 
using the irRC (Table 2), as most of these late-responding patients have a trend toward 
response within 4 wk after initial irPD. Whereas WHO criteria consider any new 
measurable lesion to indicate PD, determination of immune-related best overall response 
(irBOR) is based on changes in total tumor burden from the baseline (nadir, for irPD) 
tumor assessment, regardless of any initial increase in baseline lesions or the appearance 
of new lesions.  
 
 
 
APPENDIX 3  
 
Toxicity Monitoring 
 
1.1 
Model Parameters and Stopping Criteria 
Maximum sample size: 28 
Minimum sample size: 4 
Cohort size: 4 
  
Response 
Toxicity 
Standard 
Constant Rate c: 0.1 
Constant Rate c: 0.3 
Experimental Beta a: 0.2 Beta b: 1.8 Beta a: 0.6 Beta b: 1.4 
Stopping 
π* :  1 
π* :  0.8 
Shift 
δR :  0 
δT :  0 
 
 
 
Patients 
(in complete 
 cohorts of 4) 
(inclusive) 
Stop the trial if there are 
this many toxicities total: 
# Toxicities 
(inclusive) 
65 
 


4  
3-4 
8  
4-8 
12  
6-12 
16  
7-16 
20  
8-20 
24  
10-24 
28 
Always stop with this many patients 
 
 
 
APPENDIX 4 
Toxicity Management Algorithms 
These general guidelines constitute guidance to the Investigator and may be 
supplemented by discussions with the Medical Monitor representing the Sponsor. The 
guidance applies to all immuno-oncology agents and regimens. 
 
A general principle is that differential diagnoses should be diligently evaluated according 
to standard medical practice. Non-inflammatory etiologies should be considered and 
appropriately treated. 
 
Corticosteroids are a primary therapy for immuno-oncology drug-related adverse events. 
The oral equivalent of the recommended IV doses may be considered for ambulatory 
patients with low-grade toxicity. The lower bioavailability of oral corticosteroids should 
be taken into account when switching to the equivalent dose of oral corticosteroids. 
 
Consultation with a medical or surgical specialist, especially prior to an invasive 
diagnostic or therapeutic procedure, is recommended. 
 
The frequency and severity of the related adverse events covered by these algorithms will 
depend on the immuno-oncology agent or regimen being used. 
 
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