A Phase II Study of Nivolumab in Combination With Cabozantinib for Metastatic Triple-negative Breast Cancer
Phase: PHASE2
Conditions: Breast Cancer
Sponsor: Dana-Farber Cancer Institute

Title: A phase II study of nivolumab in combination with cabozantinib for metastatic triple-negative 
breast cancer 
 
NCT Number: NCT03316586 
 
IRB Approval Date: 04/09/2019 

 
 
Page 1 
 
DF/HCC Protocol #: 17-324  
 
BMS Protocol #: CA209-9AR 
 
Exelixis, Inc. Protocol #:  IST48 
 
TITLE:  A phase II study of nivolumab in combination with cabozantinib for metastatic triple-
negative breast cancer 
 
 
 
Coordinating Center: 
 
 
Dana-Farber Cancer Institute 
 
Principal Investigator (PI): 
Sara Tolaney, MD, MPH 
 
Dana-Farber Cancer Institute  
 
450 Brookline Avenue  
 
Boston, MA 02215 
 
 
Sara_Tolaney@dfci.harvard.edu 
 
Other Investigators: 
Romualdo Barroso-Sousa, MD, PhD 
 
Dana-Farber Cancer Institute  
 
450 Brookline Avenue  
 
Boston, MA 02215 
 
romualdo_barroso@dfci.harvard.edu 
 
 
Beth Overmoyer, MD, FACP 
 
Dana-Farber Cancer Institute 
 
450 Brookline Avenue 
 
Boston, MA 02215 
 
Beth_Overmoyer@dfci.harvard.edu 
 
 
Dan Duda, DMD, PhD 
 
Steele Laboratories for Tumor Biology 
 
149 Thirteenth Street, MGH East, CNY 3.402 
  
Charlestown, MA 02129 
 
dan@steele.mgh.harvard.edu 
 
Statisticians: 
 
 
William Barry, PhD 
Dana-Farber Cancer Institute 
Boston, MA 02215 
 
Hao Guo 
Dana-Farber Cancer Institute  
Boston, MA 02215 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
2 
IND #:  116866 
IND Sponsor:  Sara Tolaney, MD, MPH 
 
 
 
Protocol Type / Version # / Version Date: 
Amendment / Version 6 / April 9, 2019 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
3 
SCHEMA 
 
 
 
 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
4 
TABLE OF CONTENTS 
 
SCHEMA .........................................................................................................................................3 
1. 
OBJECTIVES ......................................................................................................................6 
1.1 
Study Design ............................................................................................................6 
1.2 
Primary Objectives...................................................................................................6 
1.3 
Secondary Objectives...............................................................................................6 
1.4 
Correlative Objectives .............................................................................................7 
2. 
BACKGROUND .................................................................................................................8 
2.1 
Study Disease(s).......................................................................................................8 
2.2 
The PD-1/PD-L1 pathway in cancer ........................................................................8 
2.3 
Nivolumab..............................................................................................................10 
2.4 
Cabozantinib ..........................................................................................................11 
2.5 
Rationale ................................................................................................................20 
2.6 
Correlative Studies Background ............................................................................24 
3. 
PARTICIPANT SELECTION ...........................................................................................27 
3.1 
Eligibility Criteria ..................................................................................................27 
3.2 
Exclusion Criteria ..................................................................................................30 
4. 
REGISTRATION PROCEDURES ...................................................................................33 
4.1 
General Guidelines for DF/HCC Institutions ........................................................33 
4.2 
Registration Process for DF/HCC Institutions .......................................................34 
5. 
TREATMENT PLAN ........................................................................................................34 
5.1 
Treatment Regimen ................................................................................................34 
5.2 
Pre-Treatment Criteria ...........................................................................................34 
5.3 
Agent administration ..............................................................................................35 
5.4 
Definition of Dose-Limiting Toxicity (DLT) ........................................................35 
5.5 
General Concomitant Medication and Supportive Care Guidelines ......................36 
5.6 
Criteria for Taking a Participant Off Protocol Therapy .........................................40 
5.7 
Duration of Follow Up ...........................................................................................41 
5.8 
Criteria for Taking a Participant Off Study ...........................................................42 
6. 
Dosing Delays/Dose modifications....................................................................................42 
6.1 
Dosing Delays/Omission/Modficiation .................................................................42 
6.2 
Management of toxicities attributable to Cabozantinib and Nivolumab ...............45 
6.3 
Management of toxicities attributable to Cabozantinib .........................................52 
6.4 
Management of toxicities attributable to Nivolumab ............................................61 
7. 
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................68 
7.1 
Adverse Events Lists..............................................................................................68 
7.2 
Adverse Event Characteristics ...............................................................................69 
7.3 
Expedited Adverse Event Reporting ......................................................................69 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
5 
7.4 
Routine Adverse Event Reporting .........................................................................71 
8. 
PHARMACEUTICAL INFORMATION ..........................................................................71 
8.1 
Nivolumab..............................................................................................................71 
8.2 
Cabozantinib ..........................................................................................................73 
9. 
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES ........................................75 
9.1 
Archival Tissue ......................................................................................................77 
9.2 
Fresh Tissue Biopsy ...............................................................................................77 
9.3 
Blood Collection ....................................................................................................83 
9.4 
Additional analysis.................................................................................................87 
10. 
STUDY CALENDAR .......................................................................................................89 
11. 
MEASUREMENT OF EFFECT........................................................................................92 
11.1 
Antitumor Effect – Solid tumors............................................................................92 
11.2 
Antitumor Effect – Hematologic Tumors ..............................................................99 
11.3 
Other Response Parameters ...................................................................................99 
12. 
DATA REPORTING / REGULATORY REQUIREMENTS .........................................101 
12.1 
Data Reporting .....................................................................................................101 
12.2 
Data Safety Monitoring........................................................................................102 
12.3 
Multicenter Guidelines.........................................................................................102 
12.4 
Collaborative Agreements Language ...................................................................102 
13. 
STATISTICAL CONSIDERATIONS.............................................................................103 
13.1 
Study Design/Endpoints.......................................................................................103 
13.2 
Sample Size, Accrual Rate and Study Duration ..................................................104 
13.3 
Stratification Factors ............................................................................................105 
13.4 
Interim Monitoring Plan ......................................................................................105 
13.5 
Analysis of Primary Endpoint ..............................................................................105 
13.6 
Analysis of Secondary Endpoints ........................................................................106 
13.7 
Reporting and Exclusions ....................................................................................107 
14. 
PUBLICATION PLAN ...................................................................................................108 
15. 
REFERENCES ................................................................................................................109 
APPENDIX A 
PERFORMANCE STATUS CRITERIA ................................................117 
APPENDIX B 
Guidelines for collecting research biopsy tissue ......................................118 
Risks of Research Biopsy and Procedures for Minimizing Risk .....................................118 
Risks of Anesthesia ..........................................................................................................119 
 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
6 
1. OBJECTIVES 
 
1.1 
Study Design 
1.1.1 This is an open-label, single-arm, single center, phase 2 study of 
cabozantinib given orally at 40mg per day in combination with 
nivolumab given intravenously at 480mg every four weeks in 
subjects with metastatic triple-negative breast cancer (TNBC) 
previously treated with 0 to 3 chemotherapy regimens in the 
metastatic setting.  Mandatory research biopsies will be 
performed at baseline (if tissue is safely accessible) and during 
days 15-28 of Cycle 2 (prior to beginning Cycle 3). 
 
1.2 
Primary Objectives 
1.2.1 To evaluate the efficacy of nivolumab in combination with 
cabozantinib, as defined by objective response rate (ORR) 
according to RECIST 1.1 [Eisenhauer et al., 2009] in patients 
with metastatic TNBC previously treated with 0 to 3 lines of 
chemotherapy in the metastatic setting. 
 
1.3 
Secondary Objectives 
Safety objectives 
1.3.1 To evaluate the safety and tolerability of nivolumab in 
combination with cabozantinib in patients with metastatic TNBC 
previously treated with 0 to 3 lines of chemotherapy in the 
metastatic setting. 
 
Efficacy objectives 
1.3.2 To evaluate the ORR of the combination according to immune-
related response criteria (irRC) [Wolchok et al., 2009]. (Section 
11). 
1.3.3 To evaluate the Clinical Benefit Rate (CR + PR + SD ≥ 24 weeks) 
of the combination 
1.3.4 To evaluate the progression-free survival according to the 
RECIST 1.1. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
7 
1.4 
Correlative Objectives 
1.4.1 To characterize a broad array of immune markers in metastatic 
TNBC (characterization will be based on histology, protein 
expression, and mRNA expression). 
1.4.2 To explore how different immunosuppressive and/or immune-
stimulating immune marker profiles at baseline correlate with 
disease response to therapy (PFS, objective response assessed by 
RECIST 1.1 and immune-related response criteria). 
1.4.3 To characterize changes in tumor-infiltrating lymphocytes, PD-L1 
expression and immune gene signatures in the tissue 
microenvironment (TME) from baseline to after 2 cycles of the 
experimental combination. 
1.4.4 To explore whether induction of changes in the 
immunosuppressive and/or immune-stimulating immune marker 
profile in TME correlates with disease response to therapy 
(response assessed by RECIST 1.1 and immune-related response 
criteria). 
1.4.5 To evaluate MET and phospho MET expression in tumor tissue at 
baseline by immunohistochemistry 
1.4.6 To explore the effect of treatment on plasma biomarkers 
(sVEGFR2, sMET, IL-2, IFN-γ, TNF-α) 
1.4.7 To characterize serial changes in immune marker profile in 
peripheral blood mononuclear cells (PBMCs) and in plasma over 
the course of the trial treatment. 
1.4.8 To explore whether induction of changes in the 
immunosuppressive and/or immune-stimulating immune marker 
profile in PBMCs correlates with disease response to therapy 
(response assessed by RECIST 1.1 and immune-related response 
criteria). 
1.4.9 To investigate whether there is an immune marker in circulating 
PBMCs that corresponds to tumor infiltrating lymphocyte (TIL) 
percentage in baseline tumor. 
1.4.10 To collect blood to study cell-free DNA for comparison to tumor 
specimens before and after immunotherapy. 
1.4.11 To characterize the structure and function of the gut microbiome 
in patients with breast cancer prior to starting this clinical trial. 
1.4.12 To determine whether pre-treatment characteristics of the 
structure and function of the gut microbiome in patients with 
breast cancer is associated with disease response to therapy 
(response assessed by RECIST 1.1 and irRC, and PFS). 
1.4.13 To characterize changes in the structure and function of the gut 
microbiome of patients with breast cancer after two cycles of 
nivolumab compared to baseline.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
8 
1.4.14 To determine whether changes in the overall diversity of the gut 
microbiome, estimated by the Shannon Index, of patients with 
breast cancer after two cycles of therapy is associated with disease 
response (response assessed by RECIST 1.1, irRC and PFS). 
1.4.15 To determine if the abundance and functional profile of specific 
gut bacteria are associated with objective response therapy 
(response assessed by RECIST 1.1, irRC and PFS). 
1.4.16 To evaluate the functional pathways that may play a role as a 
predictive biomarker of disease response to therapy (response 
assessed by RECIST 1.1, irRC and PFS). 
1.4.17 To determine whether pre-treatment characteristics of the 
structure and function of the gut microbiome in patients with 
breast cancer is associated with therapy-induced grade ≥2 
diarrhea. 
1.4.18 To explore whether the number and/or type of mutations 
identified using a next generation sequencing (NGS) panel is 
correlated with patient outcomes (PFS, ORR, and CBR). This will 
be done on DFCI patients only.  
 
 
 
 
2. BACKGROUND 
2.1 
Study Disease(s) 
Breast cancer (BC) is the most frequently diagnosed cancer and the second cause of cancer 
death in women in the Unites States[1]. Approximately, 15% of these cancers are classified as 
triple-negative breast cancer (TNBC), comprising those with absent expression of estrogen 
receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 
(HER2)[2].  
Hormonal therapies are only effective for ER or PR positive breast cancer, and the 
monoclonal antibody trastuzumab is effective only for tumors that have amplified HER2 genes.  
The basal-like tumors have a poor prognosis relative to other subtypes, even with the best available 
chemotherapy.  TNBCs have an aggressive nature with higher rates of relapse and shorter overall 
survival in the metastatic setting compared with other subtypes of breast cancer[3]. Little progress 
has been made in identifying specific molecular pathways that exist for this tumor subtype; 
because of this dismal prognosis, new therapies are need in TNBC setting. 
 
2.2 
The PD-1/PD-L1 pathway in cancer 
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades[Schreiber et al., Schreiber, 2012]. Accumulating 
evidence shows a correlation between tumor-infiltrating lymphocytes (TILs) in cancer tissue and 
favorable prognosis in various malignancies[Mlecnik et al., 2014].  In particular, the presence of 
CD8+ T-cells and the ratio of CD8+ effector T-cells / FoxP3+ regulatory T-cells seems to correlate 
with improved prognosis and long-term survival in many solid tumors[Tosolini et al., 2006, 
Adams et al., 2014, Denkert et al., 2015]. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
9 
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to suppress 
immune control.  The normal function of PD-1, expressed on the cell surface of activated T-cells 
under healthy conditions, is to down-modulate unwanted or excessive immune responses, 
including autoimmune reactions.  PD-1 (encoded by the gene Pdcd1) is an Ig superfamily member 
related to CD28 and CTLA-4 which has been shown to negatively regulate antigen receptor 
signaling upon engagement of its ligands (PD-L1 and/or PD-L2).  The structure of murine PD-1 
has been resolved.  PD-1 and family members are type I transmembrane glycoproteins containing 
an Ig Variable-type (V-type) domain responsible for ligand binding and a cytoplasmic tail which 
is responsible for the binding of signaling molecules.  The cytoplasmic tail of PD-1 contains 2 
tyrosine-based signaling motifs, an immunoreceptor tyrosine-based inhibition motif (ITIM) and 
an immunoreceptor tyrosine-based switch motif (ITSM).  Following T-cell stimulation, PD-1 
recruits the tyrosine phosphatases SHP-1 and SHP-2 to the ITSM motif within its cytoplasmic tail, 
leading to the dephosphorylation of effector molecules such as CD3ζ, PKCθ and ZAP70 which 
are involved in the CD3 T-cell signaling cascade.  The mechanism by which PD-1 down modulates 
T-cell responses is similar to, but distinct from that of CTLA-4 as both molecules regulate an 
overlapping set of signaling proteins.  PD-1 was shown to be expressed on activated lymphocytes 
including peripheral CD4+ and CD8+ T-cells, B-cells, T regs and Natural Killer cells.  Expression 
has also been shown during thymic development on CD4-CD8- (double negative) T-cells as well 
as subsets of macrophages and dendritic cells.  The ligands for PD-1 (PD-L1 and PD-L2) are 
constitutively expressed or can be induced in a variety of cell types, including non-hematopoietic 
tissues as well as in various tumors.  Both ligands are type I transmembrane receptors containing 
both IgV- and IgC-like domains in the extracellular region and contain short cytoplasmic regions 
with no known signaling motifs.  Binding of either PD-1 ligand to PD-1 inhibits T-cell activation 
triggered through the T-cell receptor.  PD-L1 is expressed at low levels on various non-
hematopoietic tissues, most notably on vascular endothelium, whereas PD-L2 protein is only 
detectably expressed on antigen-presenting cells found in lymphoid tissue or chronic inflammatory 
environments.  PD-L2 is thought to control immune T-cell activation in lymphoid organs, whereas 
PD-L1 serves to dampen unwarranted T-cell function in peripheral tissues.  Although healthy 
organs express little (if any) PD-L1, a variety of cancers were demonstrated to express abundant 
levels of this T-cell inhibitor.  PD-1 has been suggested to regulate tumor-specific T-cell expansion 
in subjects with melanoma (MEL).  This suggests that the PD-1/PD-L1 pathway plays a critical 
role in tumor immune evasion and should be considered as an attractive target for therapeutic 
intervention[Intlekofer et al., 2013]. 
 
The PD-1/PD-L1 pathway in breast cancer 
Unlike melanoma and NSCLC, BC has not been intensively investigated for its 
susceptibility to immunotherapy in clinical settings. However, there are accumulating preclinical 
and clinical evidence suggesting that immune system is critical during natural history of breast 
cancer and the immune system can be modulated to improve outcomes in this disease[Kroemer et 
al., 2015]. It has been recognized that BC is capable of stimulating the immune system, as many 
breast tumors have substantial lymphocyte infiltration [Denkert et al., 2010, Denkert et al., 2015]. 
Additionally, this pathologic feature has prognostic implications, as lymphocyte predominant 
breast cancers are associated with improved prognosis [Denkert et al., 2010, Loi et al., 2013]. 
However, the degree of immune infiltration differs by BC subtype; while a substantial proportion 
of triple negative BC can be richly infiltrated, hormone-receptor positive BC is poorly T-cell 
infiltrated[Dushyanthen et al., 2015]. Recently, it has been demonstrated that the expression of 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
10 
PD-1 and PD-L1 differs among breast tumors subtype: HR-positive (30% PD-1; 33% PD-L1), 
triple-negative (70% PD-1; 59% PD-L1) and HER2-positive (60% PD-1; 20% PD-L1)[Gatalica et 
al., 2014]. 
 
2.3 
Nivolumab 
Nivolumab is a fully human, IgG4 (kappa) isotype monoclonal antibody that binds to PD-
1 with nanomolar affinity (KD = 3.06 nM) and a high degree of specificity, thus precluding binding 
to its ligands PD-L1 and PD-L2. Nivolumab does not bind other related family members, such as 
BTLA, CTLA-4, ICOS or CD28. Pre-clinical testing of nivolumab demonstrated that blockade of 
PD-1 results in enhanced T cell proliferation and expression of interferon-gamma (IFN-γ). 
2.3.1 Nivolumab nonclinical toxicology  
Toxicology studies in cynomolgus monkeys revealed that nivolumab was well tolerated at 
doses up to 50 mg/kg given twice weekly for 27 doses. Drug related findings were limited to a 
reversible decrease in triiodothyronine (T3) by 28%, without concomitant abnormalities in other 
markers of thyroid function. Preliminary new non-clinical safety findings of adverse pregnancy 
outcomes and infant losses in the absence of overt maternal toxicity have been reported.66 The 
findings of increased late stage pregnancy loss and early infant deaths/euthanasia in nivolumab 
exposed pregnant monkeys suggest a potential risk to human pregnancy if there is continued 
treatment with nivolumab during pregnancy. 
 
2.3.2 Clinical Experience with nivolumab 
 The overall safety experience with nivolumab, as monotherapy or in combination with 
other therapeutics, is based on experience in approximately 1,500 subjects treated to date. For 
monotherapy, the safety profile is similar across tumor types. The one exception is pulmonary 
inflammation AEs which may be numerically greater in subjects with NSCLC because in some 
cases it can be difficult to distinguish between nivolumab related and unrelated causes of 
pulmonary symptoms and radiographic changes. There was no pattern in the incidence, severity, 
or causality of AEs to nivolumab dose level.  
In several ongoing clinical trials, the safety of nivolumab in combination with other 
therapeutics such as ipilimumab, cytotoxic chemotherapy, anti-angiogenics and targeted therapies 
is being explored. Most studies are ongoing and as such, the safety profile of nivolumab 
combinations continues to evolve. The most advanced combination under development is 
nivolumab and ipilimumab in subjects with MEL. Thus far, the combination of both agents results 
in a safety profile with similar types of AEs as either agent alone, but in some cases with greater 
frequency.  
Overall, the safety profile of nivolumab monotherapy as well as combination therapy is 
manageable and generally consistent across completed and ongoing clinical trials with no MTD 
reached at any dose tested, up to 10 mg/kg. There was no pattern in the incidence, severity, or 
causality of AEs to nivolumab dose level. Most AEs were low grade (grade 1 to grade 2) with 
relatively few related high grade (grade 3 to grade 4) AEs. Most high grade events were 
manageable with the use of corticosteroids or hormone replacement therapy for Endocrinopathies. 
Management algorithms including the use of immunosuppressive agents, such as corticosteroids, 
infliximab, etc., are provided in Section of this protocol. Nivolumab should not be used in subjects 
with active autoimmune disease given the mechanism of action of the antibody. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
11 
Nivolumab has demonstrated clinical activity in response evaluable subjects with a variety 
of solid tumor malignancies in the following studies: 
1) completed Phase 1 single-dose (MDX1106-01): n = 37 subjects with prostate cancer, 
MEL, NSCLC, RCC, and CRC 
2) ongoing Phase 1 multi-dose, dose escalation study with nivolumab monotherapy 
(CA209003/MDX1106-03): NSCLC n = 129, MEL n = 107, RCC n = 34 subjects 
3) ongoing Phase 1b study with nivolumab in combination with ipilimumab 
(CA209004/MDX1106-04): MEL n = 82 subjects 
4) ongoing Phase 1 study with nivolumab monotherapy or in combination with platinum-
based chemotherapy or erlotinib (CA209012): NSCLC, monotherapy n = 20, combination therapy 
n = 77 subjects 
In addition, monotherapy or combination trials with nivolumab are on-going for subjects 
with SCCHN,67 HCC,68 CRC69, GBM70, and NHL.71,72 
Updated overall clinical experience for nivolumab is available in the current version of the 
Investigator’s Brochure. 
 
2.4 
Cabozantinib 
 
A summary of XL184 clinical and nonclinical experience is contained in the Investigator’s 
Brochure supplied by Exelixis (ANEXO XXX). The Investigator’s Brochure should be reviewed 
in conjunction with this study protocol. 
Cabozantinib is a new chemical entity that inhibits multiple RTKs with growth-promoting 
and angiogenic properties. The primary targets of cabozantinib are RET, MET, VEGFR2/KDR, 
and KIT (see below)   
 
CABOZANTINIB IC50 Values in Biochemical, Enzymatic Assays 
Kinase 
IC50 (biochemical) [nM] 
RET 
3.8 
MET 
1.8 
VEGFR2/KDR 
0.035 
KIT 
4.6 
IC50, concentration required for 50 % target inhibition. 
Cabozantinib is an oral receptor tyrosine kinase (RTK) inhibitor, with multiple targets related to 
tumor growth and angiogenesis in the tumor microenvironment, including MET, and 
VEGFR2/KDR [Scagliotti et al., 2013]. Both high tumor microvessel density and elevated 
vascular endothelial growth factor-A (VEGF-A) expression are associated with decreased relapse-
free and overall survival in early stage breast cancer, suggesting that angiogenesis is associated 
with a poor prognosis [Relf et al., 1997, Uzzan et al., 2004]. More importantly, it is well known 
that bevacizumab (an anti-VEGF monoclonal antibody) in combination with chemotherapy has 
been associated with an improvement in the rates of complete pathological response in the 
neoadjuvant setting and with a significant improvement in progression-free survival (PFS) in 
several clinical studies, although it has not prolonged OS in patients with breast cancer [Robert et 
al., 2011]. It has been recognized that inhibition of VEGF signaling alone, although initially 
effective in slowing tumor growth, often culminates in the emergence of an evasive resistance 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
12 
phenotype that ultimately promotes tumor invasiveness and metastasis [Sennino, 2012]. One of 
the potential causes of resistance to anti-angiogenic inhibitors is the overexpression of MET  and 
of its ligand - hepatocyte grow factor (HGF); which have been associated with tumor hypoxia, 
increased invasiveness and metastasis, and reduced survival in metastatic breast cancer [Raghav 
et al., 2012]. Specifically, in patients with TNBC, MET expression is elevated and associated with 
poorer prognosis [Ho-Yen et al., 2014, Zagouri et al., 2013]. In this context, cabozantinib an oral 
bioavailable small molecule inhibitor of multiple receptor tyrosine kinases (RTK), including 
VEGFR-2, was thought to be a drug to be evaluated in combination with anti-PD1 drugs in patients 
with TNBC. We completed a phase II trial evaluating the efficacy of cabozantinib monotherapy in 
heavily pre-treated patients with mTNBC [Tolaney et al., 2016]. They reported a clinical benefit 
rate of 34%, including 9% of partial response rate.  
In vivo data from pharmacodynamic experiments show that cabozantinib inhibits key RTKs 
that promote tumor cell proliferation, migration and/or angiogenesis (RET, MET, and VEGFR2). 
In xenografted tumor models, cabozantinib inhibited VEGFR2 phosphorylation in lung tissue, 
with an ED50 of 26 mg/kg. The duration of action for cabozantinib was sustained with > 50 % 
inhibition observed 10-24 hours post-dose at a dose level of 100 mg/kg for all targets studied.  
Treatment with cabozantinib shows rapid effects on the tumor endothelium, resulting in 
breakdown of the vasculature beginning 24 hours after administration of cabozantinib, thus 
suggesting potent anti-angiogenic effects of cabozantinib. These effects translate into significant 
tumor growth inhibition after cabozantinib treatment in multiple tumor models including human 
MTC, human breast cancer, human lung carcinoma, and rat glioblastoma. Overall, the data 
generated in vivo demonstrate that the target profile of cabozantinib translates to potent 
anti-angiogenic activity and potent anti-tumor efficacy.  
 
2.4.1 Cabozantinib Nonclinical Toxicology 
In nonclinical toxicity studies in rodents and non-rodents, histopathological changes 
associated with cabozantinib administration were observed in gastrointestinal (GI) tract, bone 
marrow, lymphoid tissues, kidney, adrenal, and reproductive tract tissues. Histopathological 
changes present in bone and pancreas were considered secondary to cabozantinib administration. 
Cabozantinib was negative in in vitro bacterial, in vitro mammalian cell, and in vivo mammalian 
genotoxicity bioassays. In reproductive toxicity studies, cabozantinib was embryotoxic in rats, 
produced fetal soft tissue changes in rabbits, and decreased fertility in male and female rats. 
Safety pharmacology studies of cabozantinib administration did not demonstrate adverse 
effects on neurobehavioral or respiratory-system function in rats; furthermore, no significant 
changes in electrocardiographic parameters (including corrected QT [QTc] interval) were 
observed by telemetry in dogs. 
Cabozantinib was not an inhibitor of cytochrome P450 (CYP) 3A4 in vitro and is not 
predicted to have significant effects on CYP3A4 induction. Cabozantinib was shown to be an 
inhibitor of CYP2C8, CYP2C9*3, and CYP2C19 isozyme, in vitro and was also a substrate of 
CYP3A4-mediated metabolism. The mean plasma protein binding by cabozantinib in vitro was 
greater than 98%. 
Additional toxicology information may be found in the Investigator’s Brochure. 
 
2.4.2 Clinical Experience 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
13 
2.4.2.1 
Clinical Safety Profile 
The adverse event (AE) and serious adverse event (SAE) data summarized in the following 
section includes those reported and entered in the clinical database and safety database, 
respectively, as of 29 February 2016. The clinical studies with cabozantinib are ongoing, thus the 
AE data from the clinical database does not yet include all SAEs. Data from double-blinded studies 
are not presented. The severity of AEs was assessed using the Common Terminology Criteria for 
Adverse Events (CTCAE) version 3.0 or 4.0.  
 
2.4.2.2 
Adverse Events 
A pooled analysis through 29 February 2016 included 2410 subjects with cancer who had 
been treated with single-agent cabozantinib in company-sponsored clinical trials (Section 5.4). The 
subjects in that dataset were predominately White (83.4%) and male (77.5%) with a median age 
of 64.0 years (see Table 5-3); the gender distribution reflects the inclusion of CRPC studies in the 
pooled analysis.  
Table: Demographics and Other 
Baseline Characteristics for Pooled 
Single-Agent Studies Subject characteristics  
Total  
Total number of subjects exposed  
2410  
Sex  
Female  
542 (22.5%)  
Male  
1868 (77.5%)  
Age  
Mean  
63.0 (11.47)  
Median  
64.0  
Range  
20 - 91  
Race 
American Indian or Alaska Native  
2 (0.1%)  
Asian  
89 (3.7%)  
Black or African American  
78 (3.2%)  
Multiple  
4 (0.2%)  
Native Hawaiian or other Pacific Islander  
1 (0.0%)  
White  
2009 (83.4%)  
Other  
52 (2.2%)  
Not reported  
175 (7.3%)  
This table summarizes pooled data for cabozantinib-treated subjects with cancer in the clinical database for single-
agent cabozantinib studies (XL184-001, XL184-008, XL184-201, XL184-203, XL184-205, XL184-301, XL184-
306, XL184-307, XL184-308, and XL184-401).  
 
The AE data summarized in the following sections include those reported and entered in 
the clinical database as of the dates presented in Table 5-1. For active clinical studies with a “Data 
Through” date of 29 February 2016, the AE data from the clinical database may not yet include all 
SAEs. A summary of pooled SAEs from company-sponsored clinical studies with single-agent 
cabozantinib is provided in Section 5.4.1.4.  
The severity of AEs was assessed using the Common Terminology Criteria for Adverse 
Events (CTCAE) version 3.0 or version 4.0, and AE and SAE PTs were coded with the Medical 
Dictionary for Regulatory Activities (MedDRA) version 17.0 for all studies. For AEs and SAEs, 
multiple occurrences of the same event in any individual subject are counted once at the highest 
grade reported. Events that were assessed as possibly related or probably related to cabozantinib 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
14 
are reported as “related,” and events that were assessed as not related or unlikely related to 
cabozantinib are reported as “not related.”  
Adverse events that occurred in ≥ 10% of the 2410 subjects in the pooled single-agent 
studies are presented in Table below.  
 
Table : Summary of Adverse Events 
Experienced by ≥ 10% of Subjects 
Treated with Single-Agent Cabozantinib, 
N = 2410 All AEs  
Related AEs  
MedDRA 
Preferred Term  
Subjects with AE n 
(%)  
Subjects with ≥ 
Grade 3 AE n (%)  
Subjects with AE n 
(%)  
Subjects with ≥ 
Grade 3 AE n (%)  
Number of 
subjects with at 
least one event  
2404 (99.8)  
1979 (82.1)  
2324 (96.4)  
1512 (62.7)  
Diarrhoea  
1471 (61.0)  
251 (10.4)  
1300 (53.9)  
226 (9.4)  
Fatigue  
1458 (60.5)  
369 (15.3)  
1281 (53.2)  
312 (12.9)  
Nausea  
1290 (53.5)  
118 (4.9)  
1062 (44.1)  
89 (3.7)  
Decreased 
appetite  
1283 (53.2)  
136 (5.6)  
1080 (44.8)  
104 (4.3)  
Vomiting  
861 (35.7)  
95 (3.9)  
612 (25.4)  
59 (2.4)  
Weight decreased  
860 (35.7)  
97 (4.0)  
671 (27.8)  
75 (3.1)  
Palmar-plantar 
erythrodysaesthesi
a syndrome  
835 (34.6)  
186 (7.7)  
819 (34.0)  
185 (7.7)  
Constipation  
779 (32.3)  
31 (1.3)  
345 (14.3)  
11 (0.5)  
Hypertension  
708 (29.4)  
330 (13.7)  
603 (25.0)  
284 (11.8)  
Dysgeusia  
637 (26.4)  
2 (0.1)  
605 (25.1)  
2 (0.1)  
Dysphonia  
610 (25.3)  
5 (0.2)  
520 (21.6)  
4 (0.2)  
Asthenia  
557 (23.1)  
165 (6.8)  
434 (18.0)  
124 (5.1)  
Dyspnoea  
497 (20.6)  
76 (3.2)  
187 (7.8)  
22 (0.9)  
Anaemia  
479 (19.9)  
200 (8.3)  
217 (9.0)  
70 (2.9) 
Stomatitis  
474 (19.7)  
42 (1.7)  
446 (18.5)  
41 (1.7)  
Abdominal pain  
456 (18.9)  
95 (3.9)  
232 (9.6)  
22 (0.9)  
Aspartate 
aminotransferase 
increased  
446 (18.5)  
69 (2.9)  
382 (15.9)  
46 (1.9)  
Back pain  
444 (18.4)  
90 (3.7)  
56 (2.3)  
6 (0.2)  
Mucosal 
inflammation  
444 (18.4)  
46 (1.9)  
423 (17.6)  
44 (1.8)  
Pain in extremity  
422 (17.5)  
53 (2.2)  
180 (7.5)  
15 (0.6)  
Headache  
415 (17.2)  
30 (1.2)  
149 (6.2)  
3 (0.1)  
Alanine 
aminotransferase 
increased  
389 (16.1)  
74 (3.1)  
343 (14.2)  
58 (2.4)  
Rash  
367 (15.2)  
15 (0.6)  
300 (12.4)  
13 (0.5)  
Hypothyroidism  
359 (14.9)  
6 (0.2)  
301 (12.5)  
3 (0.1)  
Cough  
354 (14.7)  
7 (0.3)  
84 (3.5)  
1 (0.0)  
Oedema 
peripheral  
335 (13.9)  
15 (0.6)  
101 (4.2)  
4 (0.2)  
Dizziness  
307 (12.7)  
12 (0.5)  
154 (6.4)  
3 (0.1)  
Arthralgia  
303 (12.6)  
30 (1.2)  
76 (3.2)  
4 (0.2)  
Dyspepsia  
300 (12.4)  
4 (0.2)  
224 (9.3)  
4 (0.2)  
Hypokalaemia  
300 (12.4)  
90 (3.7)  
136 (5.6)  
42 (1.7)  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
15 
Dry mouth  
279 (11.6)  
0  
231 (9.6)  
0  
Urinary tract 
infection  
269 (11.2)  
35 (1.5)  
31 (1.3)  
3 (0.1)  
Dry skin  
264 (11.0)  
0  
219 (9.1)  
0  
Hypomagnesaemi
a  
262 (10.9)  
24 (1.0)  
170 (7.1)  
17 (0.7)  
Dehydration  
255 (10.6)  
79 (3.3)  
139 (5.8)  
42 (1.7)  
Muscle spasms  
255 (10.6)  
1 (0.0)  
147 (6.1)  
1 (0.0)  
Hair colour 
changes  
251 (10.4)  
2 (0.1)  
243 (10.1)  
2 (0.1)  
Pyrexia  
250 (10.4)  
16 (0.7)  
44 (1.8)  
2 (0.1)  
Insomnia  
244 (10.1)  
0  
82 (3.4)  
0  
AE, adverse event; MedDRA, Medical Dictionary for Regulatory Activities.  
At each level of subject summarization, a subject is counted once if the subject reported one or more events. 
Adverse events were coded based on MedDRA version 17.0.  
Note: This table summarizes pooled data in the clinical database for single-agent cabozantinib studies (XL184-
001, XL184-008, XL184-201, XL184-203, XL184-205, XL184-301 cabozantinib arm, XL184-306 cabozantinib 
arm, XL184-307 cabozantinib arm, XL184-308 cabozantinib arm, and XL184-401).  
 
The most common AEs (≥ 5% incidence) reported at severity of Grade 3 and above were 
fatigue (15.3%), hypertension (13.7%), diarrhea (10.4%), anemia (8.3%), PPES (7.7%), asthenia 
(6.8%), pulmonary embolism (6.1%), and decreased appetite (5.6%).  
The most frequently (≥ 20% incidence) observed AEs reported as related to cabozantinib, 
were diarrhea (53.9%), fatigue (53.2%), decreased appetite (44.8%), nausea (44.1%), PPES 
(34.0%), weight decreased (27.8%), vomiting (25.4%), dysgeusia (25.1%), hypertension (25.0%), and 
dysphonia (21.6%). 
 
2.4.2.3 
Serious Adverse Events 
 
The most commonly reported SAEs (≥ 1% incidence) excluding events of disease progression are 
shown in Table below. 
Table: Summary of Serious Adverse 
Events Experienced by ≥ 1% of Subjects 
Treated with Single-Agent Cabozantinib 
Excluding Events of Disease Progression, 
N = 2410 All SAEs  
Related SAEs  
MedDRA 
Preferred Term  
Subjects with SAE 
n (%)  
Subjects with ≥ 
Grade 3 SAE n 
(%)  
Subjects with SAE 
n (%)  
Subjects with ≥ 
Grade 3 SAE n 
(%)  
Subjects 
reporting at least 
one SAE  
1332 (55.3)  
1221 (50.7)  
602 (25.0)  
516 (21.4)  
Pulmonary 
embolism  
120 (5.0)  
119 (4.9)  
85 (3.5)  
84 (3.5)  
Vomiting  
81 (3.4)  
48 (2.0)  
40 (1.7)  
27 (1.1)  
Nausea  
72 (3.0)  
44 (1.8)  
47 (2.0)  
31 (1.3)  
General physical 
health 
deterioration  
71 (2.9)  
65 (2.7)  
13 (0.5)  
9 (0.4)  
Dehydration  
69 (2.9)  
54 (2.2)  
41 (1.7)  
32 (1.3)  
Pneumonia  
69 (2.9)  
58 (2.4)  
5 (0.2)  
4 (0.2)  
Anaemia  
59 (2.4)  
49 (2.0)  
17 (0.7)  
13 (0.5)  
Abdominal pain  
53 (2.2)  
43 (1.8)  
13 (0.5)  
9 (0.4)  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
16 
Diarrhoea  
52 (2.2)  
36 (1.5)  
42 (1.7)  
31 (1.3)  
Deep vein 
thrombosis  
46 (1.9)  
36 (1.5)  
21 (0.9)  
16 (0.7)  
Fatigue  
43 (1.8)  
36 (1.5)  
27 (1.1)  
25 (1.0)  
Asthenia  
41 (1.7)  
30 (1.2)  
20 (0.8)  
13 (0.5)  
Back pain  
41 (1.7)  
36 (1.5)  
1 (0.0)  
1 (0.0)  
Dyspnoea  
39 (1.6)  
26 (1.1)  
7 (0.3)  
5 (0.2)  
Pyrexia  
36 (1.5)  
9 (0.4)  
5 (0.2)  
2 (0.1)  
Urinary tract 
infection  
35 (1.5)  
25 (1.0)  
4 (0.2)  
3 (0.1)  
Hyponatraemia  
31 (1.3)  
29 (1.2)  
15 (0.6)  
14 (0.6)  
Pleural effusion  
30 (1.2)  
22 (0.9)  
6 (0.2)  
5 (0.2)  
Renal failure 
acute  
30 (1.2)  
24 (1.0)  
7 (0.3)  
5 (0.2)  
Convulsion  
29 (1.2)  
18 (0.7)  
5 (0.2)  
2 (0.1)  
Decreased 
appetite  
28 (1.2)  
20 (0.8)  
19 (0.8)  
14 (0.6)  
Bone pain  
27 (1.1)  
23 (1.0)  
0  
0  
Sepsis  
27 (1.1)  
27 (1.1)  
5 (0.2)  
5 (0.2)  
Metastatic pain  
26 (1.1)  
20 (0.8)  
1 (0.0)  
0  
Confusional state  
25 (1.0)  
17 (0.7)  
7 (0.3)  
5 (0.2) 
Constipation  
25 (1.0)  
9 (0.4)  
9 (0.4)  
4 (0.2)  
Spinal cord 
compression  
23 (1.0)  
22 (0.9)  
1 (0.0)  
1 (0.0)  
MedDRA, Medical Dictionary for Regulatory Activities; SAE, serious adverse event.  
Note: Reported SAEs were coded using MedDRA version 17.0. At each level of subject summarization, a subject 
is counted once if the subject reported one or more events.  
Note: This table summarizes pooled data from the safety database for single-agent cabozantinib studies (XL184-
001, XL184-008, XL184-201, XL184-203, XL184-205, XL184-301 cabozantinib arm, XL184-306 cabozantinib 
arm XL184-307 cabozantinib arm, XL184-308 cabozantinib arm, and XL184-401).  
Note: Disease progression is expected for subjects with advanced cancer on cabozantinib clinical trials, and as 
such, events of progression of underlying cancer are not included.  
a Twenty (20) out of 29 of the observed convulsion events were reported in subjects with glioblastoma (GB) 
enrolled in Studies XL184-201 or XL184-205. For more information on safety observed in subjects with GB, see 
Section 5.4.3.1.  
 
 
As of 29 February 2016, the incidence of Grade 5 AEs from the pooled single-agent studies 
was 10.5% (254 subjects). The Grade 5 events that occurred at the highest frequency (≥ 1% 
incidence) were prostate cancer (2.9%) and general physical health deterioration (1.0%). Per 
convention, prostate cancer was the PT for disease progression of the cancer under study for 
Studies XL184-203 (CRPC cohorts), XL184-306, and XL184-307. Only one event of general 
physical health deterioration (on Study XL184-307) was assessed as related to study treatment; no 
events of prostate cancer were assessed as related to study treatment.  
Thirty-three (33) of the 254 subjects with Grade 5 AEs had events assessed as related to 
the study treatment. The only related Grade 5 AEs that occurred more than once were pulmonary 
embolism (n=4), death (unspecified; n=3), hemorrhage (n=2), respiratory failure (n=2), and sudden 
death (n=2). 
  
Detailed information regarding the safety profile of Cabozantinib from all studies may be 
found in the Investigator’s Brochure.  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
17 
2.4.2.4 
Clinical Pharmacokinetics 
Pharmacokinetic (PK) analysis showed dose proportional increases in maximum plasma 
concentration (Cmax) and area under the plasma concentration-vs-time curve (AUC) both for the 
powder-in-bottle (PIB) formulation (dose range: 0.08 to 11.52 mg/kg) and the capsule formulation 
(dose range: 125 mg to 175 mg). Terminal-phase half-life (t1/2, z) values were 59.1 to 136 hours. 
More detailed information regarding cabozantinib PK from all studies and product metabolism in 
humans may be found in the Investigator’s Brochure. 
 
 
2.4.3 Clinical Activity 
 
Efficacy in Phase 3 Clinical Trials  
2.4.3.1 
Renal Cell Carcinoma: Study XL184-308 (METEOR; N=658)  
The population, enrollment, and study design of XL184-308 are summarized in Table 5-1. 
In order to be eligible for the study, subjects were required to have histologically or cytologically 
confirmed advanced RCC with a clear cell component, to have measurable disease by CT/MRI per 
Response Evaluation Criteria in Solid Tumors (RECIST), and to have received treatment with at 
least one prior VEGFR-TKI. Tumor assessments were evaluated by the blinded IRC to determine 
response and/or progression. Eligible subjects were randomized 1:1 to receive either cabozantinib 
(60 mg, tablet formulation) or everolimus (10 mg) which was the standard of care for the second-
line setting at the time of the initiation of the study. 
It was estimated that 375 randomized subjects would have been adequate to evaluate the 
primary endpoint of PFS alone. However, a much larger sample size of 650 subjects was needed 
to provide reasonable power for the secondary endpoint of OS. To minimize the effects of bias due 
to the influence of subjects with early progression and allow for longer, more robust PFS follow-
up among fewer subjects, the primary analysis of PFS was planned to be conducted for the first 
375 randomized subjects.  
Only the first 375 subjects randomized were included in the population for the primary PFS 
analysis (Primary Endpoint Intent-to-Treat [PITT] population). The results of the analysis 
demonstrated a statistically significant improvement in PFS per IRC for subjects in the 
cabozantinib arm (n=187) compared with the everolimus arm (n=188): the HR adjusted for 
stratification factors was 0.58 (95% CI: 0.45, 0.74; stratified log-rank p-value < 0.0001). The 
Kaplan-Meier estimates for median duration of PFS were 7.4 months in the cabozantinib arm vs 
3.8 months in the everolimus arm. Kaplan-Meier estimates of the percent of subjects event-free at 
6- and 12-month landmarks after treatment randomization were higher for the cabozantinib arm 
than for the everolimus arm (6 months: 55% cabozantinib, 34% everolimus; 12 months: 29%, 
15%). The PFS analysis was repeated in the ITT population (658 subjects), and results were similar 
to those obtained for the PITT population. The HR adjusted for stratification factors was 0.51 (95% 
CI: 0.41, 0.62).  
A pre-specified interim analysis of OS was conducted for the ITT population as of the 22 
May 2015 database cutoff, at the time of the primary analysis of PFS. There were a total of 202 
deaths (89 cabozantinib, 113 everolimus) by this date, representing 49% (202/408) of the total 
required for the pre-specified primary analysis of OS. The minimum time of follow-up (from 
randomization of the last subject through 22 May 2015) was 5.9 months. The interim analysis 
demonstrated a strong trend for improvement in duration of OS for subjects in the cabozantinib 
arm compared with the everolimus arm: the HR, adjusted for stratification factors was 0.68 (95% 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
18 
CI: 0.51, 0.90; stratified log-rank p-value = 0.006). The OS results nearly met the criteria required to 
reject the null hypothesis at the interim analysis; the critical p-value was ≤ 0.0019 (HR ≤ 0.645).  
Following these results, in August 2015 an unplanned second interim OS analysis was 
specified, with a prospectively-defined cutoff date of 31 December 2015 to provide at least 12 
months of follow-up from the last subject randomized. The second interim OS analysis with 13 
months of follow-up demonstrated a highly statistically significant prolongation of OS for subjects 
in the cabozantinib arm compared with the everolimus arm: the HR, adjusted for stratification 
factors was 0.66 (95% CI: 0.53, 0.83; stratified log-rank p-value 0.0003). The critical value for 
rejecting the null hypothesis at the current analysis was p<0.0163. Kaplan-Meier estimates for 
median duration of OS were 21.4 months in the cabozantinib arm and 16.5 months in the 
everolimus arm. The proportion of subjects estimated to be alive by Kaplan-Meier analysis was 
greater among subjects in the cabozantinib arm compared with everolimus at each time point. The 
respective landmark estimates of survival were 73% and 63% at 12 months and 58% and 47% at 
18 months. 
The primary analysis of ORR per IRC was conducted in the ITT population at the time of 
the primary analysis of PFS. The same data cutoff date was used as for the PFS analysis. Tumor 
assessments that occurred after the individual subject PFS-censoring dates were excluded from 
this analysis. The ORR in the ITT population for the cabozantinib and everolimus arms, 
respectively, was 17% (95% CI: 13, 22) and 3% (95% CI: 2, 6) (unstratified p-value < 0.0001). 
All responses were PRs. Of note there was a low incidence in the cabozantinib arm of PD as best 
response (12% vs 27%) which indicates a low incidence of primary refractory disease with 
cabozantinib in this study population. 
In conclusion, cabozantinib demonstrated a robust and statistically significant 
improvement in PFS, OS, and ORR in a Phase 3 trial for subjects with advanced RCC in the 
second-line setting.  
 
2.4.3.2 
Medullary Thyroid Cancer: Study XL184-301 (EXAM; N=330)  
Subjects were required to have radiographically documented disease progression by 
modified RECIST (mRECIST) compared with a radiologic assessment performed within the 
previous 14 months. Tumor assessments were evaluated by the blinded IRC to determine response 
and/or progression. 
The estimated median PFS was 11.2 months for cabozantinib versus 4.0 months for placebo 
(HR 0.28; 95% CI, 0.19 to 0.40; p < .001). Prolonged PFS with cabozantinib was observed across 
all subgroups including by age, prior TKI treatment, and RET mutation status (hereditary or 
sporadic). Kaplan-Meier estimates of subjects alive and progression-free at 1 year are 47.3% for 
cabozantinib and 7.2% for placebo. 
Patient subgroups harboring any RET mutation, the RET M918T mutation, or no RET 
mutation all demonstrated an HR of less than 1, indicating benefit of cabozantinib treatment; 
however, the upper bound for the 95% CI for RET mutation negative subjects exceeded 1.  
The final analysis of the secondary endpoint of OS included 218 events (217 were required) 
and showed a trend for increased survival in the cabozantinib arm. The estimated median OS for 
the cabozantinib arm was 26.6 months versus 21.1 months for the placebo arm (HR = 0.85; 95% 
CI 0.64, 1.12; p = 0.2409). 
Because MTC is a relatively rare disease, this study was not designed to be large enough 
to provide high power to detect the minimum clinically meaningful difference in the secondary 
endpoint of OS. Instead, the study size was chosen to provide reasonable power (80%) for a large 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
19 
(50%) improvement in OS (HR 0.667; improved median from 22 to 33 months). The final analysis 
was consistent with analyses at information fractions of 75%, 85%, and 90% which included 162, 
185, and 196 of the required 217 deaths respectively. The consistency of the OS results at different 
information fractions supports the conclusion that although not statistically significant, the trend 
in increased survival with cabozantinib treatment did not likely arise by chance.  
The subgroup analysis of subjects with a RET M918T mutation revealed a larger 
improvement in OS for the cabozantinib arm: the median OS was 44.3 months for the cabozantinib 
arm versus 18.9 months for the placebo arm (HR = 0.60; 95% CI 0.38, 0.94; p = 0.0255 not 
adjusted for multiple subgroup analyses. In the current study 126 subjects or 38% had RET M918T 
mutation (the majority of which were somatic mutations), representing 54% of 233 subjects whose 
RET M918T status was known. 
The analysis of tumor response among subjects with measurable disease at baseline was 
conducted at the time of the primary analysis of PFS. The ORRs per IRC were 28% (95% CI: 
21.9%, 34.5%) and 0% for subjects in the cabozantinib and placebo arms, respectively. All 
responses were PRs, no subjects in either treatment group had a confirmed CR. The p-value from 
the stratified Cochran-Mantel-Haenszel test was highly significant (p < 0.0001). The median 
duration of objective responses was 14.6 months (95% CI: 11.1, 17.5) for subjects in the 
cabozantinib arm. The median duration of the best overall response (BOR) of SD, as determined 
by the IRC, was 10.8 months (95% CI: 8.3, 11.2) for the cabozantinib arm compared with 5.7 
months (95% CI: 5.6, 8.4) for the placebo arm. 
 
2.4.3.3 
Castration-Resistant Prostate Cancer  
Study XL184-307 (COMET-1; N=1023)  
The study enrolled subjects with advanced CRPC with bone metastases. The prespecified 
primary analysis of the primary endpoint (OS) was based on an ITT analysis of all randomized 
subjects. The analysis included 614 events (578 were required) and did not demonstrate a 
statistically significant improvement in OS for subjects in the cabozantinib arm compared with the 
prednisone arm: the HR, adjusted for prior cabazitaxel use, baseline Brief Pain Inventory (BPI; 
Item 3) score, and baseline ECOG performance status was 0.90 (95% CI: 0.76, 1.06; stratified 
logrank p-value 0.213). The Kaplan-Meier estimates for median duration of OS were 11.0 months 
in the cabozantinib arm and 9.8 months in the prednisone arm, an estimated 1.2 month difference 
in the medians.  The secondary efficacy endpoint was the proportion of subjects with a BSR per 
IRC at Week 12. BSR was defined as a ≥ 30% decrease in total bone-scan lesion area compared 
with baseline without soft-tissue disease progression. The analysis demonstrated a statistically 
significant improvement in the cabozantinib arm compared with the prednisone arm (42% vs 3%; 
stratified Cochran-Mantel-Haenszel [CMH] p-value < 0.001). The median duration of BSR was 
5.8 vs 1.8 months. Median PFS per Investigator was 5.6 months in the cabozantinib arm and 2.8 
months in the prednisone arm. The HR adjusted for randomization stratification factors was 0.48 
(95% CI 0.40, 0.57; stratified logrank p-value < 0.0001). 
  
Study XL184-306 (COMET-2; N=119)  
The study enrolled subjects with advanced CRPC with bone metastases. Enrollment was 
stopped before the planned study population size of 246 was reached; a total of 119 subjects were 
enrolled. The primary analysis for the ITT population (n=119) did not demonstrate an 
improvement in the proportion of subjects with a pain response at Week 6 confirmed at Week 12 
in the cabozantinib arm compared with the mitoxantrone plus prednisone arm; the proportions of 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
20 
subjects experiencing a confirmed pain response were 15% and 17% for the two arms, respectively. 
The secondary endpoints were BSR per IRC and OS. BSR was defined as a ≥ 30% decrease in 
total bone-scan lesion area compared with baseline without soft-tissue disease progression. The 
analysis of BSR per IRF at Week 12 without progression in soft tissue per mRECIST 1.1 
demonstrated a greater improvement in the cabozantinib arm (31%; 95% CI: 20%, 43%) compared 
with the mitoxantrone plus prednisone arm (5%; 95% CI: 0%, 11%). In the analysis of OS that 
included 78 deaths out of the 196 pre-specified deaths, the stratified HR was 0.70 (95% CI: 0.44, 
1.10). The Kaplan-Meier estimates for median duration of OS were 9.0 months in the cabozantinib 
arm versus 7.9 months in the mitoxantrone plus prednisone arm. 
 
2.4.3.4 
Efficacy Results in Other Clinical Trials  
Cabozantinib has been studied in a broad selection of tumor types. A brief summary of the available 
clinical activity results for cabozantinib in these tumor types is provided in Table 5-14.  
Table: Assessment 
of Cabozantinib 
Seen in Multiple 
Tumor Types 
Tumor Type  
Study  
Median PFS  
(months)  
Week 12 DCRa  
(%)  
DTC  
XL184-008  
not reached  
80b  
RCC  
XL184-008  
12.9  
72b  
Ovarian Cancer  
XL184-203 RDT  
5.5  
50  
XL184-203 NRE  
4.0  
NA  
CRPC  
XL184-203 RDT  
6.8  
66  
XL184-203 NRE  
4.6c  
NA  
XL184-203 NRE  
6.5d  
NA  
HCC  
XL184-203 RDT  
5.2  
66  
Breast Cancer  
XL184-203 RDT  
4.3  
47  
Melanoma  
XL184-203 RDT  
2.8  
43  
NSCLC  
XL184-203 RDT  
4.0  
38  
SCLC  
XL184-203 RDT  
3.4  
43  
Pancreatic Cancer  
XL184-203 RDT  
2.7  
35  
Gastric/GEJ Cancer  
XL184-203 RDT  
1.4  
33  
GB  
XL184-201  
3.7e  
NA  
CRPC, castration-resistant prostate cancer; DCR, disease control rate; DTC, differentiated thyroid cancer; GB, 
glioblastoma; GEJ, gastroesophageal junction; HCC, hepatocellular carcinoma; PFS, progression-free survival; NA, 
not available; NRE, non-randomized expansion; NSCLC, non-small cell lung cancer; RCC; renal cell carcinoma; 
RDT, randomized discontinuation trial; SCLC, small-cell lung cancer.  
Note: Data reported in this table is from the final endpoint analyses.  
a DCR = (confirmed response [CR] + partial response [PR] + stable disease [SD])  
b DCR at Week 17  
c For the CRPC cohort that was assigned a dose of 40 mg qd  
d For the CRPC cohort that was assigned a dose of 100 mg qd  
e For Treatment Group C (100 mg qd). See Section 5.5.2.2 for further details.  
 
 
 
2.5 
Rationale 
Recognizing that overexpression of immune checkpoint molecules in the tumor 
microenvironment has a critical role for antitumor immunity evasion and for cancer progression 
has revolutionized cancer treatment[4]. In particular, anti-PD-1/PD-L1 antibodies have 
demonstrated clinical activity in more than 15 cancer types and two PD-1 inhibitors (nivolumab 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
21 
and pembrolizumab) are FDA approved for treatment of advanced melanoma, non-small-cell lung 
carcinoma and renal cell carcinoma[5-7]. More than 1,000 clinical trials of checkpoint blockers 
are currently ongoing. 
Immune checkpoint inhibitors (ICI), have revolutionized cancer therapy for patients with 
advanced solid tumors [Leach et al., 1996, Pardoll, 2012, Freeman et al., 2000]. A large body  of 
preclinical and clinical evidence suggesting that the immune system can recognize and fight 
against breast cancer [Kroemer et al., 2015, Savas et al., 2015]. It is now recognized that a fraction 
of breast tumors, especially TNBC, have substantial lymphocyte infiltration and that this 
pathologic feature has prognostic implications [Savas et al., 2015]. Furthermore, the high rates of 
PD-L1 and PD-1 expression in patients with TNBCs led to clinical trials to address the role of PD-
1 blockers in this population [Gatalica et al.,  2014]. 
The recently presented KEYNOTE 086 trial, the largest study evaluating the efficacy of 
PD-1 inhibitors (Pembrolizumab given in monotherapy; flat dose of 200mg every 3 weeks) in 
patients with mTNBC showed different outcomes based on the number of previous lines of 
therapy: cohort A included 170 patients who had received ≥1 prior chemotherapy for metastatic 
disease, and showed an objective response rate of 4.7% (2% - 9%) [Adams et al., 2015] ; Perhaps, 
more important is the duration of response with the PD-1 inhibitors in patients with mTNBC: 6.3 
months; with more than 5 (63%) responders without progression of disease at study data cut off; 
cohort B included 52 patients no prior systemic anticancer therapy for metastatic disease, and 
showed an objective response rate of 23% (14% - 36%) [Adams et al., 2017]. While checkpoint 
blockade shows activity in a subset of mTNBC, these results suggest that there must be additional 
immunosuppressive factors causing resistance to immunotherapy in this population, and other 
agents must be added to anti-PD-1/PD-L1 treatment in order to enhance the benefit of 
immunotherapy in TNBC.  
Despite BC not being considered an immunogenic neoplasia, an increasing body of 
preclinical and clinical evidence suggests that the interaction with the immune system is critical 
for disease outcome in this disease as well[8]. It is now recognized that a fraction of breast tumors, 
especially TNBC, have substantial lymphocyte infiltration and that this pathologic feature has 
prognostic implications[9]. Furthermore, the high rates of PD-L1 and PD-1 expression in patients 
with TNBCs led to clinical trials to address the role of PD-1 blockers in this population[10]. The 
anti-PD-L1 atezolizumab was evaluated in patients with metastatic TNBC PD-L1 positive and 
showed an objective response rate (ORR) of 19% and a 6-month PFS of 27%[11]. Similar results 
were found in a PD-L1 positive population with the anti-PD-1 inhibitor pembrolizuamb (ORR of 
18% and 6-month PFS of 23%)[12]. Data from a trial with avalumab has demonstrated that in a 
non-selected population, the use of PD-1/PD-L1 inhibitors presented an objective response rate 
(ORR) of 8.6%[13].  
Clearly, these results show that, while checkpoint blockade may show activity in TNBC, 
other agents must be added to anti-PD-1/PD-L1 treatment in order to enhance the benefit. In 
addition, the fact that the majority of patients with advanced cancer, including TNBC, still do not 
derive clinical benefit from these drugs suggests that additional immunosuppressive mechanisms 
within the tumor microenvironment have a role in de novo resistance to these therapies. Some of 
these mechanisms have been identified, and now provide targets for combination therapy[14]. In 
this context, vascular endothelial growth factor-A (VEGF-A), the key molecule in tumor 
angiogenesis, has been recognized as a critical mediator of tumor immune suppression[15]. In 
addition to its role in angiogenesis, VEGF modulates anti-tumor immunity on multiple levels, 
including promotion and expansion of inhibitory immune cell subsets, such as T regulatory cells 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
22 
(Tregs) and myeloid-derived suppressor cells (MDSCs), inhibition of dendritic cell (DC) 
maturation, mitigation of effector T cell responses, and alteration of lymphocyte development and 
trafficking[16]. Consequently, targeting angiogenesis may be an effective strategy to increase the 
efficacy of primarily T cell-directed immunotherapy, such as immune checkpoint blockade [17]. 
Recently, Voron at al. showed in a mouse model that that VEGF-A produced in the tumor 
microenvironment enhances expression of PD-1 and other inhibitory checkpoints mediating CD8+ 
T cell exhaustion, which could be reverted by different anti-angiogenic agents (anti-VEGF-A 
antibody 
or 
tyrosine 
kinase 
inhibitors 
(TKI), 
such 
as 
sunitinib, which target VEGF 
receptor 
family 
member 
(VEGFR). The administration of 
masatinib, a TKI that does not 
target VEGFR, was not able to 
revert the PD-L1 overexpression 
VEGF-induced (Figure 1). Importantly, the authors demonstrated in vitro that the expression of 
PD-1 on CD8+ T cells is induced by VEGF-A in a VEGFR-2-dependent manner, but is not 
VEGFR-1-dependent. Because anti–VEGF-A treatment decreased PD-1 expression on 
intratumoral CD8+ T cells but does not fully restore the steady-state level of PD-1 expression 
(Figure 2a), the authors hypothesized that VEGF-A blockade could help to sensitize T cells to 
anti–PD-1 antibody treatment in some tumors. Interestingly, anti– PD-1 antibody induced a 
significant antitumor effect only in VEGF-deleted tumor-bearing mice and not in wild-type tumor-
bearing mice (Fig. 2b), suggesting that 
VEGF produced by tumor cells limits anti–
PD-1–induced antitumor effects. Next, the 
authors combined anti-VEGF-A antibody 
with anti–PD-1 antibody in a CT26 mouse 
model of colorectal cancer expressing high 
levels 
of 
VEGF-A. 
Anti–VEGF-A 
treatment reduced tumor growth, and anti–
PD-1 antibody alone had no significant 
effect, but the anti–VEGF-A and anti–PD-1 
combination induced a strong antitumor 
effect as compared with anti–VEGF-A 
alone or anti-PD-1 alone (Fig. 2c). This 
result suggests that high VEGF-A levels 
may be involved in resistance to anti–PD-1 
treatments and that antiangiogenic therapies 
targeting 
VEGF-A–VEGFR-2 
could 
synergize 
with 
anti–PD-1 
treatment 
strategies 
and 
enhance 
anti–PD-1–
dependent antitumor effects. 
 In the clinical setting, a phase I 
study using bevacizumab (anti-VEGF 
antibody) plus the immune checkpoint ipilimumab (anti-CTLA4) conducted in patients with 
advanced melanoma showed an objective partial response rate of 17% and  a disease control rate 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
23 
of 67%[18]. Currently, several clinical trials are evaluating the combination of immune checkpoint 
blockade and angiogenesis inhibition in cancer patients. 
Both high tumor microvessel density and elevated VEGF expression are associated with 
decreased relapse-free and OS in early stage BC, suggesting that angiogenesis is associated with a 
poor prognosis[19, 20]. Moreover, it is well known that bevacizumab in combination with 
chemotherapy has been associated with improvement in complete pathological response in 
neoadjuvant setting and with significantly improvement in progression-free survival (PFS) in 
several studies, although it has not prolonged OS in BC [21]. It has been recognized that inhibition 
of VEGF signaling alone, although initially effective in slowing tumor growth, often culminates 
in emergence of an evasive resistance phenotype that ultimately promotes tumor invasiveness and 
metastasis [22]. In this context, cabozantinib an oral bioavailable small molecule inhibitor of 
multiple receptor tyrosine kinases (RTK), including VEGFR-2, seems to be a very interesting drug 
to evaluate in combination with anti-PD1 drugs in patients with TNBC. Another important 
property of cabozantinib is that it inhibits MET, a RTK that promotes cell proliferation, invasion, 
and survival when activated by its ligand, hepatocyte growth factor (HGF, also known as the 
“scatter factor”)[23]. In vivo, besides its antiangiogenic effects, cabozantinib rapidly induces tumor 
cell apoptosis, resulting in tumor regression in various xenograft models. In addition, increased 
expression of MET has been implicated in the development of resistance to antiangiogenic drugs 
in preclinical models of several cancers [24]. More recently, Balan et al reported that the MET-
induced signaling promotes PD-L1 overexpression in renal cancer cells, establishing a link 
between MET pathway and antitumor immunity evasion [25].  
Of note, MET and HGF overexpression have been associated with tumor hypoxia, 
increased invasiveness and metastasis, and reduced survival in metastatic breast cancer [26]. 
Specifically, in patients with TNBC, MET expression is elevated and associated with poorer 
prognosis [27, 28] . Preclinical data showed that cabozantinib synergizes with immunotherapy in 
different tumor mice models [Kwilas et al., 2014, Lu et al., 2017]. Recently, in a phase II trial, 
cabozantinib monotherapy demonstrated a clinical benefit rate of 34%, including 9% of partial 
response rate, in heavily pre-treated patients with mTNBC[29]. Furthermore, correlative studies 
performed in this trial showed: 1) high baseline plasma concentration of sMET was associated 
with longer PFS and tended to correlate with clinical benefit; 2) the concentration of plasma HGF 
was lower in patients with clinical benefit versus those without, though this association did not 
reach statistical significance; 3) cabozantinib treatment was associated with changes in biomarker 
concentrations that are consistent with anti-vascular effects and increases in tissue hypoxia, i.e., 
increases in plasma CAIX, PlGF, VEGF and SDF1α; 4) Flow cytometric analyses showed a 
significant and persistent increase in the fraction of circulating CD3+ T cells after cabozantinib 
therapy, which appeared to be driven by an increase in the CD4–/CD8+ cytotoxic T lymphocyte 
(CTL) population, and a significant decrease in the CD14+ monocytic population, which is 
considered as an immunosuppressive myeloid population. These findings highlight the possibility 
that combinations of cabozantinib with immunotherapy will improve the outcomes in this 
population. In the clinical setting, other groups including investigators at DF/Harvard Cancer 
Center have been explored the immunological effects of the combination of antiangiogenic drugs 
plus ICI. Two early phase trials showed an increase in the tumor-infiltrating lymphocytes rates in 
patients with melanoma and kidney cancer [Hodi et al., 2014, Wallin et al., 2016]. Altogether, 
these data highlight the possibility that combinations of cabozantinib with immunotherapy will 
improve the outcomes in this population.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
24 
Based on the above rationale, we hypothesize that cabozantinib (by increasing the number 
of CTLs) will synergize with nivolumab (which will activate the CTLs), resulting in improvement 
of efficacy of immunotherapy. We propose to test this hypothesis by evaluating the combination 
of cabozantinib plus nivolumab (anti-PD-1 monoclonal antibody) in patients with metastatic 
TNBC in an open-label, single arm phase II study. The primary endpoint will be to evaluate the 
efficacy of cabozantinib in combination with nivolumab, as defined by objective response rate 
(ORR) according to RECIST 1.1 in patients with metastatic TNBC previously treated with 0 to 3 
lines of chemotherapy in the metastatic setting. Additionally, we will perform correlative studies 
in order to explore the effect of treatment on serum markers relevant to VEGF-VEGFR2 and 
HGF/MET pathways, as well on immunologic biomarkers (plasma sVEGFR2, IL-2, IFN-γ, TNF-
α, sMET) in peripheral blood. In addition, research biopsies will be performed at baseline 
(mandatory if the lesion is accessible) and within 7-14 days before starting cycle 3 of treatment. 
  
2.6 
Correlative Studies Background 
 
2.6.1 Blood and Tissue Analysis  
 
The importance of tumor microenvironment and the immunosurveillance in natural history of 
cancer and its outcomes was proved to be true in the last years, with clinical approval of immune 
checkpoint inhibitors[Sharma et al., 2015]. However, less than half of patients with solid tumors 
will derive benefit with these drugs [Hwu et al., 2012, Smith et al., 2012]. Thus, it is crucial to 
elucidate the exact mechanisms of antitumor immunity evasion ongoing in tumor 
microenvironment to successfully develop new cancer immunotherapy and correctly choose the 
best drug for the right patient. This goal can be pursuit through the discovery and validation of 
prognostic and predictive biomarkers. 
 
A growing body of evidence suggests that patients with advanced solid tumors shows differences 
in tumor microenvironment regarding the presence or absence of a gene expression profile 
indicative of a pre-existing T-cell–inflamed tumor microenvironment[Gajewski, 2015]. Tumors 
classified as T-cell inflamed present a significant infiltration of CD8+ T cells and a type I IFN 
signature. In this group, the main mechanisms of immune evasion are the overexpression of 
immunessupressor molecules acting at the level of the tumor micro- environment, such as immune 
checkpoint molecules (CTLA-4, PD-1/PD-L1, TIM-3, LAG-3), indoleamine-2,3-dioxygenase 
(IDO), and FoxP3. Interestingly, such immunosuppressive molecules seem to be upregulated after 
deflagration of a type I Interferon antitumor response, resulting in T-cell exhaustion, and the so 
called adaptive immune resistance[Gajewski, 2015, Ribas, 2015]. The other group of patients 
presents tumors characterized by a low or absence of intratumoral CD8 T cells and a lack evidence 
of a type I IFN transcriptional signature. This tumor phenotype is called non-T-cell-
inflamed[Gajewski, 2015]. 
 
The T-cell inflamed phenotype has positive prognostic value for several types of early stage 
cancer, including breast cancer[Dushyanthen et al., 2015, Perez et al., 2015], suggesting that the 
attempt by the host to generate an anti-tumor immune response reflects a biologic process 
associated with improved patient outcomes[Gajewski, 2015]. In breast oncology, different groups 
have demonstrated that the amount of tumor-infiltrating lymphocytes (TILs) in a tumor specimen, 
commonly assessed simply by histological evaluation of a standard hematoxylin and eosin-stained 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
25 
slide by a trained pathologist, is a significant predictor of both response to therapy and overall 
disease outcomes in the neoadjuvant and adjuvant settings [Denkert et al., 2010, Loi et al., 2013, 
Adams et al., 2014, Ali et al., 2014, Salgado et al., 2014, Denkert et al., 2015, Denkert et al., 
2015]. Recently, more in-depth methods of immunologic profiling are being explored in breast 
cancer, for example mRNA expression of immune-activating and immunosuppressive factors, and 
these additional immune profiles also appear to have prognostic significance[Perez et al., 2015]. 
Furthermore, in metastatic setting, the phenotype T-cell-inflamed appears to be associated with 
clinical response to several immunotherapies, including checkpoint blockade[Herbst et al., 2014]. 
Patients with this tumor phenotype seem to be good candidates for immune checkpoint inhibitor 
therapy, alone or in combination. Thus, the bulk of our correlative science in this trial highlights 
our especial interest in characterize a broad array of immune markers in metastatic HR-positive 
breast cancer, investigating whether those markers predict disease response to therapy. 
 
Thus, considering the mechanism of action of drugs like anti-PD-1/anti-PD-L1, is the lack of a 
significant T-cell infiltrate and low expression of immune checkpoint molecules may explain the 
reason that certain non inflamed tumor phenotype are associated with de novo resistance to those 
class of drugs. For this group of patients, therapeutic strategies that promote an increase in 
cytotoxic T-cell infiltration, such as anti-angiogenic therapies, will be crucial to successfully 
overcoming T-cell exclusion and improve the likelihood of benefit of PD-1 blockers.  
 
In BC, particularly the HR-positive subset, the vast majority of patient’s tumors do not harbor 
significant TILs or demonstrate PD-L1 expression and will therefore most likely be classified as 
non-T-cell-inflamed tumors. This may explains why ORR recently reported in this population 
ranges from 2.8%-12%[Dirix et al., 2015, Hugo et al., 2015]. Clearly, new approaches to boost 
antitumor immunity are needed in this population.  RT can potentially improve the activity of 
immune checkpoint inhibitors. Because of the preclinical data supporting RT induced immune 
modulation of the tumor microenvironment, we intend to explore how immune biomarkers change 
after the beginning of treatment, including the expression of immune checkpoint molecules, TILs 
and T-cell receptor diversity. 
 
Additionally, as a correlative study to this trial, we will characterize the immune marker profile of 
peripheral blood mononuclear cells (PBMCs) in enrolled breast cancer patients.  Furthermore, 
given the demonstrated clinical significance of TILs in breast cancer specimens, we will 
investigate whether there is a peripheral marker whose level corresponds to TIL percentage.  
Lastly, we will evaluate whether there is a correlation between changes in PBMC immune profiles 
and disease response.  Evidence of a correlation would be of significant interest as it would suggest 
the potential presence of a predictive biomarker in the peripheral blood. 
 
These correlative projects are made possible by collaboration with Drs. Scott Rodig and Evisa 
Gjini, and Mariano Severgnini, all of whom are laboratory scientists with extensive experience 
with immune profiling in melanoma.  Further details can be found in Section 9. 
 
2.6.2 Microbiome Analysis 
 
Breast Cancer (BC) is the most frequently diagnosed cancer and the second cause of cancer 
death in American women [DeSantis et al., 2015].  In the advanced setting, despite multiple 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
26 
available systemic therapies, virtually all patients will die from their disease.  Thus, the 
exploration of new treatments, such as immune checkpoint inhibitors (ICI), including nivolumab, 
is imperative. 
 
An increasing body of preclinical and clinical evidence suggests that breast cancer is an 
immunogenic malignancy [Kroemer et al., 2015].  It is now recognized that a fraction of breast 
tumors, mainly triple-negative breast cancer (TNBC), have substantial lymphocyte infiltration, 
and that this pathologic feature has prognostic implications [Stanton, 2016].  Early clinical trials 
assessing the efficacy of PD-1/PD-L1 inhibitors given as monotherapy showed that only a small 
fraction of patients derive benefit from immunotherapy with an approximate 20% objective 
response rate (ORR) among patients with PDL1+ TNBC [Dirix et al., 2016, Nanda et al., 2016], 
and a 12% ORR among those with PDL1+ hormone receptor (HR)-positive BC [Rugo et al., 
2016].  Therefore, new research approaches combining therapeutic agents aiming to boost 
antitumor immunity, as well as developing predictive biomarkers of response, are needed to 
increase the rates of clinical success of immunotherapy in BC. 
 
In this context, the gut microbiota has been recognized as a modulator of immune system 
development [Tinchieri, 2015]. Healthy individuals have microbial populations in their intestinal 
tract that vary markedly in composition [Human Microbiome Project, 2012, Qin et al., 2010].  
The diversity of intestinal microbiota represents a significant challenge to the host’s immune 
defenses, which must balance immune tolerance of beneficial microbes with inflammatory 
responses against pathogens.  Alterations in the gut microbiota and their resulting interactions 
with intestinal epithelieum and the host immune system are associated with many disease, 
including cancer [Roy et al. 2017].  Recently, two preclinical studies provided to ICI, raising the 
possibility that stool microbiota could be used as biomarker predictors of efficacy to 
immunotherapy [Sivan et al., 2015, Vetizou et al., 2015].  Interestingly, postmenopausal women 
with breast cancer have altered composition and low diversity of their gut microbiota compared 
to healthy controls [Goedert et al., 2015]. 
 
Identification of biomarkers that predict response to ICI-based therapies can spare de novo 
resistant patients from the unnecessary risks of immune-related adverse events.  In addition, the 
identification of bacterial species associated with response could open new strategies to 
maximize the clinical benefit of cancer immunotherapy through the modulation of gut 
microbiota. 
 
This correlative project is made possible by collaboration with the BWH/Harvard Cohorts 
Biorepository and Dr. Andrew Chan. Further details can be found in Section 9.   
 
2.6.3 Tumor Genomic Profile 
 
In addition to the immune microenvironment, intrinsic tumor factors may be associated 
with response to immune checkpoint inhibitors. Although some of the mechanisms related to de 
novo or acquired resistance to ICI have been recently described, including loss of function in beta-
2- microglobulin or defects in the interferon signaling pathway[Gao et al., 2016, Zaretsky et al., 
2016], the knowledge of immune resistance remains largely unknown. Several gene/pathways 
have been described as possible candidates of having an immunosuppressive role in different 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
27 
advanced solid tumor, including MYC amplification[Casey et al., 2016], activation in WNT-β-
catenin pathway[Spranger et al., 2015], activation in MAPK pathway, loss of PTEN[Li et al., 
2016, Peng et al., 2016, George et al., 2017]. On the other hand, few possible biomarkers of 
response to ICI have emerged, including mutational load[Snyder et al., 2014, Rizvi et al., 2015], 
tumor aneuploidy[Davoli et al., 2017], mismatch repair defects[Le et al., 2015], and BRCA2 
mutation[Hugo et al., 2016]. Notably, there is no data on genomic mechanisms of de novo 
resistance to anti-PD-1 therapy in patients with breast cancer. 
 
Therefore, as a correlative study to this trial, we will to explore whether the number and/or 
type of mutations identified using a next generation sequencing (NGS) panel – OncoPanel - is 
correlated with patient outcomes (PFS, ORR, and CBR). This tool is a cancer genomic assay to 
detect somatic mutations, copy number variations and structural variants in tumor DNA extracted 
from fresh, frozen or formalin-fixed paraffin-embedded samples. The OncoPanel assay surveys 
exonic DNA sequences of 447 cancer genes and 191 regions across 60 genes for rearrangement 
detection. DNA is isolated from tissue containing at least 20% tumor nuclei and analyzed by 
massively parallel sequencing using a solution-phase Agilent SureSelect hybrid capture kit and an 
Illumina HiSeq 2500 sequencer. The targeted NGS assay (OncoPanel) will be performed at the 
Center for Advanced Molecular Diagnostics (Department of Pathology, Brigham and Women's 
Hospital). This assay has been extensively validated and is used as a CLIA-approved clinical 
molecular test in our institution without any additional sequencing assays to validate the findings 
[Wagle et al., 2012].  
 
 
3. PARTICIPANT SELECTION 
 
Eligibility will be assessed as part of the screening procedures for all patients. 
 
3.1 
Eligibility Criteria 
3.1.1 Participants must have histologically or cytologically confirmed 
invasive breast cancer, with metastatic disease.  Participants 
without pathologic or cytologic confirmation of metastatic disease 
should have unequivocal evidence of metastasis from physical 
examination or radiologic evaluation. 
 
3.1.2 Estrogen-receptor and progesterone-receptor expression both 
<10% by immunohistochemistry (IHC) and HER2 negative by 
IHC or non-amplified as determined by the current ASCO-CAP 
criteria. If patient has more than one histological result, the most 
recent one has to be considered for inclusion. 
 
3.1.3 Participants must have measurable disease by RECIST version 
1.1 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
28 
3.1.4 Participants must agree to undergo a research biopsy, if tumor is 
safely accessible, at baseline and within14 days prior to C3D1. 
Participants for whom newly-obtained samples cannot be 
provided (e.g. inaccessible or participant safety concern) may 
submit an archived specimen.   
Note:  After the first 6 participants undergo biopsy on cabozantinib, we will review their 
adverse event profiles to ensure no more than a 20% rate of grade 3 or higher bleeding or 
wound healing complications occur.  If more than 2 patients (>20%) have safety 
concerns, we will reassess the safety of collecting the research biopsies. Full review of all 
grade (including grade 1 and 2) may also prompt changes and will be reviewed by the 
study team.  Exelixis may be consulted if necessary. 
 
3.1.5 Prior chemotherapy: Participants may have received 0-3 prior 
chemotherapeutic regimens for metastatic breast cancer and must 
have been off treatment with chemotherapy for at least 14 days 
prior to registration.  Participants should also be adequately 
recovered from acute toxicities of prior treatment. 
 
3.1.6 Prior biologic therapy: Patients must have discontinued all 
biologic therapy at least 14 days prior to registration.  
 
3.1.7 Prior radiation therapy: Patients may have received prior radiation 
therapy in either the metastatic or early-stage setting.  Radiation 
therapy must be completed per the following timelines: 
 
i) Radiotherapy to the thoracic cavity or abdomen within 4 weeks prior to 
registration. 
 
ii) Radiotherapy to bone lesions within 2 weeks prior to registration. 
 
iii) Radiotherapy to any other site within 4 weeks prior to registration. 
 
NOTE: In all cases, there must be complete recovery and no ongoing complications from 
prior radiotherapy. 
 
3.1.8 The subject is ≥18 years old. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
29 
3.1.9 ECOG performance status ≤1(Karnofsky ≥60%, see Appendix A)  
 
3.1.10 Participants must have normal organ and marrow function as 
defined below: 
• absolute neutrophil count 
≥1,000/mcL 
• platelets 
 
 
≥100,000/mcL 
• hemoglobin  
 
≥ 9 g/dl 
• total bilirubin 
 
≤1.5 × institutional upper limit of normal (ULN) 
 (or ≤ 2.0 x ULN in patients with documented 
Gilbert’s Syndrome) 
• AST(SGOT)/ALT(SGPT) 
≤2.5 × institutional ULN or  
≤ 3 × institutional ULN for participants with 
documented liver metastases 
• creatinine  
 
>1.5 ×within normal institutional ULN  OR 
creatinine clearance ≥40 mL/min (using Cockcroft-
Gault formula) for participants with creatinine 
levels above institutional ULN. 
• Urine protein/creatinine ratio (UPCR) ≤1 
 
 
3.1.11 Female subjects of childbearing potential must have a negative 
pregnancy test at screening 
 
Childbearing potential is defined as: participants who have not reached a postmenopausal 
state (≥ 12 continuous months of amenorrhea with no identified cause other than 
menopause) and has not undergone surgical sterilization (removal of ovaries and/or uterus). 
 
 
 
3.1.12 Female and male participants of childbearing potential must agree 
to use an adequate method of contraception.  Contraception is 
required starting with the first dose of study medication through 
150 days (5 months) after the last dose of study medication .  
Examples of contraceptive methods with a failure rate of < 1% per 
year include bilateral tubal ligation, male sterilization, established 
and proper use of hormonal contraceptives that inhibit ovulation, 
hormone-releasing intrauterine devices, and copper intrauterine 
devices.  The reliability of sexual abstinence should be evaluated 
in relation to the duration of the clinical trial and the preferred and 
usual lifestyle of the patient. Periodic abstinence (e.g., calendar, 
ovulation, symptothermal, or postovulation methods) and 
withdrawal are not acceptable methods of contraception. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
30 
3.1.13 Participants on bisphosphonates may continue receiving 
bisphosphonate therapy during study treatment.   
 
3.1.14 The participant is capable of understanding and complying with 
the protocol and has signed the informed consent document 
 
3.2 
Exclusion Criteria 
3.2.1 Major surgery within 12 weeks before the first dose of study 
treatment. Complete wound healing from major surgery must 
have occurred 1 month before the first dose of study treatment. 
Minor surgery (including uncomplicated tooth extractions) within 
28 days before the first dose of study treatment with complete 
wound healing at least 10 days before the first dose of study 
treatment. Allclinically relevant ongoing complications from prior 
surgery should be resolved before the first dose of study 
treatment. 
 
3.2.2 The participant has tumor in contact with, invading, or encasing 
major blood vessels or radiographic evidence of significant 
cavitary pulmonary lesions. 
 
3.2.3 The subject has pathologic evidence of tumor invading the GI 
tract (esophagus, stomach, small or large bowel, rectum or anus), 
or any evidence of endotracheal or endobronchial tumor within 28 
days before the first dose of cabozantinib; 
 
3.2.4 Concurrent administration of other anti-cancer therapy within 14 
days of starting protocol therapy and during the course of this 
study. 
 
3.2.5 The participant has received another investigational agent within 
14 days of the first dose of study drug. 
 
3.2.6 The participant has received a prior c-Met inhibitor 
 
3.2.7 Has received prior therapy with an anti-PD-1, anti-PD-L1, anti-
PD-L2, anti-CD137, or anti-Cytotoxic T-lymphocyte-associated 
antigen-4 (CTLA-4) antibody (including pembrolizumab, 
ipilimumab, and any other antibody or drug specifically targeting 
T-cell co-stimulation or checkpoint pathways) 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
31 
3.2.8 Known brain metastases that are untreated, symptomatic, or 
require therapy to control symptoms.  Participants with a history 
of treated central nervous system (CNS) metastases are eligible.  
Treated brain metastases are defined as those having no evidence 
of progression for ≥ 1 month after treatment, and no ongoing 
requirement for corticosteroids, as ascertained by clinical 
examination and brain imaging (magnetic resonance imaging or 
CT scan) completed during screening.  Any corticosteroid use for 
brain metastases must have been discontinued without the 
subsequent appearance of symptoms for ≥2 weeks prior to 
registration.  Treatment for brain metastases may include whole 
brain radiotherapy, radiosurgery, or a combination as deemed 
appropriate by the treating physician. Participants with CNS 
metastases treated by neurosurgical resection or brain biopsy 
performed within 2 months before day 1 will be excluded. 
 
3.2.9 The subject has uncontrolled, significant intercurrent or recent 
illness including, but not limited to, the following conditions: 
a. Cardiovascular disorders including: 
i. 
Congestive heart failure (CHF): New York Heart Association (NYHA) 
Class III (moderate) or Class IV (severe) at the time of screening; 
ii. 
Concurrent uncontrolled hypertension defined as sustained blood pressure 
(BP) > 150 mm Hg systolic or > 100 mm Hg diastolic despite optimal 
antihypertensive treatment within 7 days of the first dose of study 
treatment; 
iii. 
Any history of congenital long QT syndrome; 
iv. 
Any of the following within 6 months before the first dose of study 
treatment: 
• unstable angina pectoris; 
• clinically-significant cardiac arrhythmias; 
• stroke (including transient ischemic attack (TIA), or other ischemic 
event); 
• myocardial infarction; 
b. GI disorders particularly those associated with a high risk of perforation or fistula 
formation including: 
i. 
Tumors invading the GI tract, active peptic ulcer disease, active 
inflammatory bowel disease (eg, Crohn’s disease), active diverticulitis, 
cholecystitis, symptomatic cholangitis or appendicitis, acute pancreatitis 
or acute obstruction of the pancreatic duct or common bile duct, or gastric 
outlet obstruction 
ii. 
Abdominal fistula, GI perforation, bowel obstruction, intra-abdominal 
abscess within 6 months before  randomization,  
Note: Complete healing of an intra-abdominal abscess must be confirmed 
prior to randomization 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
32 
c. Other clinically significant disorders that would preclude safe study participation; 
 
3.2.10 QTcF interval >500 msec  
Note:  Three ECGs must be performed for eligibility determination. If the average of 
these three consecutive results for QTcF is ≤ 500 msec, the subject meets eligibility 
in this regard. 
 
3.2.11 Thromboembolic events requiring therapeutic anticoagulation.  
Concomitant anticoagulation with oral anticoagulants (eg, 
warfarin, direct thrombin and Factor Xa inhibitors), platelet 
inhibitors (eg, clopidogrel) are prohibited.   
Note: Low-dose aspirin for cardioprotection (per local applicable guidelines) and 
low-dose LMWH are permitted (in subjects who are on a stable dose of LMWH for at 
least 6 weeks before the first dose of study treatment, and who have had no clinically 
significant hemorrhagic complications from the anticoagulation regimen or the 
tumor).   
Note:  Subjects with a venous filter (eg vena cava filter) are not eligible for this 
study). 
 
3.2.12 Individuals with a history of different malignancy are ineligible 
except for the following circumstances. Individuals with a history 
of other malignancies are eligible if they have been disease-free 
for at least 3 years or are deemed by the investigator to be at low 
risk for recurrence of that malignancy.  
 
3.2.13 Participant has an active infection requiring IV antibiotics  
 
 
3.2.14 Patient has a medical condition that requires chronic systemic 
steroid therapy or on any other form of immunosuppressive 
medication. For example, participants with autoimmine disease 
that requires systemic steroids or immunosuppression agents 
should be excluded. Replacement therapy (eg., thyroxine, insulin, 
or physiologic corticiosteroid replacement therapy for adrenal or 
pituitary insufficiency, etc.) is not considered a form of systemic 
treatment. 
 
3.2.15 The participant is known to be positive for the human 
immunodeficiency virus (HIV), HepBsAg, or HCV RNA. HIV-
positive participants on combination antiretroviral therapy are 
ineligible. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
33 
3.2.16 Known hypersensitivity to any of the components of cabozantinib 
or nivolumab. 
 
3.2.17 The participant has received a live vaccine within 28 days prior to 
the first dose of trial treatment and while participating in the 
trial.  Examples of live vaccines include, but are not limited to, 
the following: measles, mumps, rubella, varicella/zoster, yellow 
fever, rabies, BCG, and typhoid vaccine. The use of the 
inactivated seasonal influenza vaccine (Fluzone®) is allowed. 
 
3.2.18 The subject has experienced any of the following: 
− Clinically significant gastrointestinal bleeding within 6 months before the first dose of 
study treatment 
− Clinically significant hemoptysis within 3 months of the first dose of study treatment 
− Any other signs indicative of pulmonary hemorrhage within 3 months before the start 
of study treatment 
 
3.2.19 The participant is unable to swallow oral dosage forms. 
 
3.2.20 The participant is pregnant or breastfeeding. 
 
Inclusion of Women and Minorities 
 
Both men and women of all races and ethnic groups are eligible for this trial. 
 
 
 
4. REGISTRATION PROCEDURES 
 
4.1 
General Guidelines for DF/HCC Institutions 
 
Institutions will register eligible participants in the Clinical Trials Management System 
(CTMS) OnCore. Registrations must occur prior to the initiation of protocol therapy. Any 
participant not registered to the protocol before protocol therapy begins will be considered 
ineligible and registration will be denied. 
An investigator will confirm eligibility criteria and a member of the study team will 
complete the protocol-specific eligibility checklist. 
Following registration, participants may begin protocol therapy. Issues that would cause 
treatment delays should be discussed with the Overall Principal Investigator (PI). If a participant 
does not receive protocol therapy following registration, the participant’s registration on the study 
must be canceled. Registration cancellations must be made in OnCore as soon as possible.  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
34 
4.2 
Registration Process for DF/HCC Institutions 
 
DF/HCC Standard Operating Procedure for Human Subject Research Titled Subject Protocol 
Registration (SOP #: REGIST-101) must be followed.   
 
5. TREATMENT PLAN 
 
5.1 
Treatment Regimen 
 
This is an open-label, single-arm, phase 2 study of nivolumab given every 28 days 
intravenously in combination with cabozantinib given orally once daily for 28 days.  Thirty-five 
participants will be enrolled to the study to assess the efficacy of the combination as defined by 
objective response rate (ORR) according to RECIST 1.1, in patients with metastatic TNBC.  
 
No investigational or commercial agents of therapies other than those described below may 
be administered with the intent to treat the participant’s malignancy. 
 
Table 1: Regimen Description 
Agent 
Premedication
; Precautions 
Dose 
Route 
Schedule 
Cycle 
Length 
Nivolumab 
(BMS-936558-01) 
Not routinely 
necessary 
unless prior 
infusion 
reaction. 
480 mg 
IV 
Every 28 
days (4 
weeks) 
28 days 
(4 weeks) 
Cabozantinib 
Not necessary 
40mg  
Oral 
Continuous, 
once daily 
28 days 
(4 weeks) 
 
 
5.2 
Pre-Treatment Criteria 
5.2.1 Cycle 1, Day 1 
Participants do not need to re-meet eligibility criteria on Cycle 1, Day1if screening 
laboratory evaluations are completed within 3 days of Cycle 1 Day 1.  
 
− 
absolute neutrophil count 
≥1,000/mcL 
− 
platelets 
≥100,000/mcL 
− 
hemoglobin  
≥ 9 g/dl 
− 
total bilirubin 
≤1.5 × institutional upper limit of normal (ULN)  
 
 
 
 
(or 2.0 x ULN in patients with documented Gilbert’s 
Syndrome) 
− 
AST(SGOT)/ALT(SGPT) 
≤2.5 × institutional ULN or ≤ 3 × institutional ULN for 
 participants with documented liver metastases 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
35 
• creatinine  
>1.5 ×within normal institutional ULN  OR 
creatinine clearance ≥40 mL/min (using Cockcroft-Gault 
formula) for participants with creatinine levels above 
institutional ULN. 
− 
urine protein/creatinine ratio (UPCR) ≤ 1. 
 
 
5.2.2 Subsequent Cycles, Day 1  
− 
absolute neutrophil count 
≥1,000/mcL 
− 
platelets 
≥75,000/mcL 
− 
AST(SGOT)/ALT(SGPT) 
≤ 2.5 × institutional ULN or ≤ 3 × institutional ULN for 
participants with documented liver metastases 
− 
total bilirubin 
≤1.5 × institutional ULN (or 2.0 x ULN in patients with 
documented Gilbert’s Syndrome) 
 
5.3 
Agent administration 
On days when Nivolumab and Cabozantinib are administered on the same day (i.e. Day 1 
of each cycle) the order of agent administration does not matter..   
 
5.3.1 Nivolumab Administration 
 
Nivolumab is available as 100 mg vials (10 mg/mL), which include an overfill. It is 
supplied in 10 mL type I flint glass vials with butyl stoppers and aluminum seals. Nivolumab 
injection can be infused undiluted (10 mg/mL) or diluted with 0.9% Sodium Chloride Injection, 
USP (USP to concentrations no less than 0.35 mg/mL) or 5% Dextrose.   
 
Nivolumab will be administered every 28 days at a dose of 480mg given intravenously 
over 30 minutes (+/- 10 minutes) using a volumetric pump with 0.2 to 1.2 micron pore size, low-
protein binding polyethersulfone membrane in-line filter. 
 
5.3.2 Cabozantinib administration 
 
Cabozantinib will be administered orally, once daily for 28 days at a dose of  40 mg.  
Cabozantinib should be taken 2 hours after a meal (water is permitted) with a full glass of water 
(8oz/240mL).  Participants should continue to fast for 1 hour after taking cabozantinib. Participants 
will be provided with dosing instructions, a drug diary and a sufficient supply of cabozantinib for 
continuous daily dosing.  Cabozantinib should be dosed on an outpatient basis even on days where 
Nivolumab and Cabozantinib are dose together (i.e. Day 1 of each cycle). While taking 
Cabozantinib, participants should avoid consumption of grapefruit and Seville oranges.  
 
 
5.4 
Definition of Dose-Limiting Toxicity (DLT)  
 
We will perform a safety run-in analysis on the first 6 participants enrolled to the trial. If 
there are 2 or more dose-limiting toxicity (DLTs) in the first 6 participants, the trial will be 
closed for further enrollment.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
36 
After the first safety run-in of 6 patients, which ended on 4/3/2018, 2 DLTs had been 
identified. Given that new safety data provided by Exelixis using the same dosages of 
Nivolumab and Cabozantinib proved to be tolerable, this study will enroll an additional 6 
participants in a second safety run-in. If there are 2 or more DLTs in the second safety run-in, the 
trial will be closed to further enrollment. If less than or equal to 1, the trial will continue to enroll 
to the efficacy run-in.   
 
Dose-limiting toxicity is defined as any of the following occurring during the first cycle 
(28 days) of therapy, if judged by the investigator to be possibly, probably, or definitely related to 
study drug administration: 
 
• Any grade 5 toxicity 
• Grade 3 Thrombocytopenia if associated with bleeding 
• Grade 4 Thrombocytopenia of any duration 
• Grade 3 or higher Febrile neutropenia  
• Any other grade 4 hematologic toxicity lasting >14 days, unless deemed by the 
investigator to be clinically insignificant 
• ≥ Grade 3 elevation in AST or ALT  
• Grade 2 bilirubin  elevation  
• Cases of Hy’s Law defined as: 
o  AST or ALT 3X ULN and bilirubin 2X ULN, not cholestatic and probably 
caused by study drug. 
• Any ≥ Grade 3 non-hematologic laboratory value if: 
o Medical intervention is required to treat the patient, or 
o The abnormality leads to hospitalization, or 
o The abnormality persists >7 days 
Excluding: 
 Alkaline phosphatase <10.0x ULN in a patient with grade 2 alkaline 
phosphatase elevation at baseline as a result of bone metastasis  
 Any laboratory values deemed by the investigator to be clinically 
insignificant 
• ≥ Grade 3 Pneumonitis of any duration 
• ≥ Grade 3 Fatigue lasting >5 days 
• > Grade 3 other non-laboratory toxicity lasting >3 days despite optimal supportive care, 
excluding Alopecia of any grade 
 
Management and dose modifications associated with the above adverse events are outlined in 
Section 6. 
 
 
5.5 
General Concomitant Medication and Supportive Care Guidelines 
 
5.5.1 Concomitant Medication Guidelines 
 
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed during 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
37 
the ongoing trial.  If there is a clinical indication for one of these or other medications or 
vaccinations specifically prohibited during the trial, discontinuation from trial therapy or 
vaccination may be required.  The investigator should discuss any questions regarding this with 
the overall PI.   
 
Acceptable Concomitant Medications 
All treatments that the investigator considers necessary for a subject’s welfare may be administered 
at the discretion of the investigator in keeping with the community standards of medical care and 
documented in the medical record. Selected medications of interest received within 28 days before 
the first dose of trial treatment and 30 days after the last dose of trial treatment, including dosage, 
frequency, route, and dates of administration will be recorded.  
Concomitant medications that are known to prolong the QTc interval and should be used with 
caution in subjects who receive cabozantinib until they have permanently discontinued 
cabozantinib treatment (refer to http://www.qtdrugs.org for a list of drugs which have the 
potential to prolong the QTc interval). 
 
Every effort to avoid radiation therapy while participating on this protocol should be made; 
however, if it is of clinical necessity for the patient, the circumstances should be discussed with 
the PI and it may be permitted.  
 
Prohibited Concomitant Medications 
Subjects are prohibited from receiving the following therapies during the Screening and Treatment 
Phase of this trial: 
• Antineoplastic systemic chemotherapy or biological therapy  
• Immunotherapy not specified in this protocol 
• Investigational agents other than nivolumab and cabozantinib  
• Any systemically active oral, injected, or implanted hormonal method of contraception 
except for progesterone coated intrauterine devices (IUDs) that had been previously 
implanted. 
• Estrogen replacement therapy. 
• Live vaccines within 28 days prior to the first dose of trial treatment and while participating 
in the trial.  Examples of live vaccines include, but are not limited to, the following: 
measles, mumps, rubella, varicella/zoster, yellow fever, rabies, BCG, and typhoid vaccine. 
The use of the inactivated seasonal influenza vaccine (Fluzones, BCG, and ty 
• Systemic glucocorticoids should be avoided for any purpose other than to modulate 
symptoms from radiation or an event of clinical interest of suspected immunologic 
etiology.  If corticosteroids are required for this purpose, the minimum effective dose 
should be used.  The use of physiologic doses of corticosteroids (10 mg prednisone daily 
or equivalent) can be used without principal investigator (PI) authorization. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
38 
 
• Concomitant anticoagulation with oral anticoagulants (eg, warfarin, direct 
thrombin and Factor Xa inhibitors), platelet inhibitors (eg, clopidogrel) are prohibited. 
Note: Low-dose aspirin for cardioprotection (per local applicable guidelines) and low-
dose LMWH are permitted. Anticoagulation with therapeutic doses of LMWH is 
allowed. 
 
• Subjects may receive other medications that the investigator deems to be medically 
necessary. 
There are no prohibited therapies during the Post-Treatment Follow-up Phase. 
5.5.2 Supportive Care Guidelines – general medications 
 
The following treatments are permitted throughout the duration of the study treatment phase and 
during follow-up: 
 
• Standard therapies for pre-existing medical conditions unless listed as prohibited therapy. 
Any medication intended solely for supportive care (e.g., analgesics, anti-diarrheal, anti-
depressants) may be used at the investigator’s discretion.  Antiemetics and anti-diarrheal 
medications should not be administered prophylactically before initial treatment with study 
drugs.  At the discretion of the investigator, prophylactic antiemetic and anti-diarrheal 
medication(s) may be used as per standard clinical practice before subsequent doses of 
study drugs or before, during or after radiation treatment. 
• Bisphosphonate or denosumab therapy to be used in accordance with the approved labeled 
indication and/or nationally recognized treatment guidelines.  Participants already 
receiving bisphosphonate/denosumab at the time of study entry can continue the treatment.  
Participants may initiate treatment with bisphosphonate/denosumab after study entry with 
physician discretion.  
• Concomitant anticoagulation with oral anticoagulants (eg, warfarin, direct 
thrombin and Factor Xa inhibitors), platelet inhibitors (eg, clopidogrel) are prohibited. 
Note: Low-dose aspirin for cardioprotection (per local applicable guidelines) and low-
dose LMWH are permitted. Anticoagulation with therapeutic doses of LMWH is 
allowed. 
• Pain medications administered per standard clinical practice are acceptable while the 
patient is enrolled in the study. 
 
Patients who experience toxicities should be treated symptomatically as clinically indicated.  
Medications that are considered necessary for the subject’s welfare and that are not expected to 
interfere with the evaluation of study treatment or be restricted may be given at the discretion of 
the investigator.  Ancillary treatments will be given as medically indicated. 
 
Potential Drug Interactions: 
Cytochrome P450:  Preliminary data from a clinical drug interaction study (Study XL184-
008) show that clinically relevant steady-state concentrations of cabozantinib appear to have no 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
39 
marked effect on the AUC of co-administered rosiglitazone, a CYP2C8 substrate.  Therefore, 
cabozantinib is not anticipated to markedly inhibit CYP2C8 in the clinic, and by inference, is not 
anticipated to markedly inhibit other CYP450 isozymes that have lower [I]/Ki values compared to 
CYP2C8 (i.e., CYP2C9, CYP2C19, CYP2D6, CYP1A2, and CYP3A4).  In vitro data indicate that 
cabozantinib is unlikely to induce cytochrome P450 enzymes, except for possible induction of 
CYP1A1 at high cabozantinib concentrations (30 μM).  
 
Cabozantinib is a CYP3A4 substrate (but not a CYP2C9 or CYP2D6 substrate), based on 
data from in vitro studies using CYP-isozyme specific neutralizing antibodies.  
 
Preliminary results from a clinical pharmacology study, XL184-006, showed that 
concurrent administration of cabozantinib with the strong CYP3A4 inducer, rifampin, resulted in 
an approximately 80% reduction in cabozantinib exposure (AUC values) after a single dose of 
cabozantinib in healthy volunteers.  Co-administration of cabozantinib with strong inducers of the 
CYP3A4 family (e.g., dexamethasone, phenytoin, carbamazepine, rifampin, rifabutin, rifapentin, 
phenobarbital, and St. John’s Wort) may significantly decrease cabozantinib concentrations.  The 
chronic use of strong CYP3A4 inducers should be avoided.  Other drugs that induce CYP3A4 
should be used with caution because these drugs have the potential to decrease exposure (AUC) to 
cabozantinib (e.g., chronic use of modafinil) should be avoided because of its potential to reduce 
cabozantinib exposure.  Selection of alternate concomitant medications with no or minimal 
CYP3A4 enzyme induction potential is recommended.  In addition, caution must be used when 
discontinuing treatment with a strong CYP3A4 inducer in a subject who has been concurrently 
receiving a stable dose of cabozantinib, as this could significantly increase the exposure to 
cabozantinib.  
 
Preliminary results from a clinical pharmacology study, XL184-007, showed that 
concurrent administration of cabozantinib with the strong CYP3A4 inhibitor, ketoconazole, 
resulted in a 33-39% increase in the cabozantinib exposure (AUC values) after a single dose of 
cabozantinib in healthy volunteers.  Co-administration of cabozantinib with strong inhibitors of 
the CYP3A4 family (e.g., ketoconazole, itraconazole, clarithromycin, indinavir, nefazodone, 
nelfinavir, and ritonavir) may increase cabozantinib concentrations.  Grapefruit / grapefruit juice 
and Seville oranges may also increase plasma concentrations of cabozantinib.  Strong CYP3A4 
inhibitors and other drugs that inhibit CYP3A4 should be used with caution because these drugs 
have the potential to increase exposure (AUC) to cabozantinib. Selection of alternate concomitant 
medications with no or minimal CYP3A4 enzyme inhibition potential is recommended.  
 
Because in vitro studies only assessed the metabolizing capacity of the CYP3A4, CYP2C9, 
and CYP2D6 pathways, the potential for drugs that inhibit/induce other CYP450 pathways (e.g., 
CYP2C8, CYP2C19, CYP2B6, CYP1A2) to alter cabozantinib exposure is not known.  Therefore, 
these drugs should be used with caution when given with cabozantinib.  
 
Please refer to the Flockhart drug interaction tables for lists of substrates, inducers, and 
inhibitors 
of 
selected 
CYP450 
isozyme 
pathways 
(Flockhart 
2007; 
http://medicine.iupui.edu/clinpharm/ddis/table.aspx).  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
40 
Protein Binding: Cabozantinib is highly bound (≥ 99.7%) to human plasma proteins. Therefore, 
highly protein bound drugs should be used with caution with cabozantinib because there is a 
potential displacement interaction that could increase free concentrations of cabozantinib and/or 
a co-administered highly protein-bound drug (and a corresponding increase in pharmacologic 
effect). 
 
In vitro data suggest that cabozantinib is unlikely to be a substrate for P glycoprotein (P-
gp), but it does appear to have the potential to inhibit the P-gp transport activity.  
 
Additional details related to these overall conclusions are provided in the Investigators 
Brochure. 
 
5.6 
Criteria for Taking a Participant Off Protocol Therapy 
 
Duration of therapy will depend on individual response, evidence of disease progression and 
tolerance. In the absence of treatment delays due to adverse event(s), treatment may continue for 
an indefinite number of cycles, or until one of the following criteria applies: 
 
1. Disease progression by RECIST 1.1 criteria.  
2. Please note that although the primary endpoint is ORR as defined by RECIST 1.1, 
patients may remain on protocol therapy until the time of disease progression by 
irRC criteria.  The immune criteria allows treatment beyond initial radiographic 
worsening of disease in order to distinguish between pseudoprogression and true 
disease progression.   
 
3. Participants who have attained a confirmed complete response (CR) that have been 
treated for at least 24 weeks on protocol therapy and had at least two treatments with 
nivolumab beyond the date when the initial CR was declared.  Participants who stop 
nivolumab with CR may be eligible for additional nivolumab therapy if they progress 
after stopping study treatment.  This retreatment is termed the Second Course Phase 
Therapy.  See additional details below. 
 
• 
Intercurrent illness that prevents further administration of treatment 
 
• 
Unacceptable adverse event(s) 
 
• 
Participant demonstrates an inability or unwillingness to comply with the medication 
regimen and/or documentation requirements 
 
• 
Participant decides to withdraw from the protocol therapy 
 
• 
General or specific changes in the participant's condition render the participant 
unacceptable for further treatment in the judgment of the treating investigator 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
41 
Participants will be removed from the protocol therapy when any of these criteria apply.  The 
reason for removal from protocol therapy, and the date the participant was removed, must be 
documented in the case report form (CRF) and in the CTMS system (OnCore). Alternative care 
options will be discussed with the participant. 
 
In the event of unusual or life-threatening complications, treating investigators must immediately 
notify the Overall PI, Sara Tolaney, phone: 617-632-2335, or email: stolaney@partners.org. 
 
Second Course Phase (Retreatment Period) 
 
Participants may elect to stop nivolumab and cabozantinib with confirmed CR after at least 24 
weeks of treatment. 
 
Subjects who stop nivolumab with CR may be eligible for additional nivolumab therapy if they 
progress after stopping study treatment.  This retreatment is termed the Second Course Phase of 
this study and is only available if the study remains open and the subject meets the following 
conditions: 
 
o Stopped initial treatment with nivolumab and cabozantinib after attaining an 
investigator-determined  confirmed CR according to RECIST 1.1, was treated for at 
least 24 weeks with nivolumab before discontinuing therapy, and received at least two 
treatments with nivolumab beyond the date when the initial CR was declared 
 
AND 
 
o experienced an investigator-determined confirmed radiographic disease progression 
after stopping their initial treatment with nivolumab 
o did not receive any anti-cancer treatment other than cabozantinib since the last dose of 
nivolumab 
o meets all other study inclusion/exclusion criteria, as per Section 3. 
 
Subjects who restart treatment will be retreated at the same dose and dose interval as when they 
last received nivolumab.  Visit requirements are as outlined for subjects on the initial treatment 
phase of the trial.   
 
5.7 
Duration of Follow Up 
 
Participants removed from protocol therapy for unacceptable adverse event(s) will be followed 
until resolution or stabilization of the adverse event. 
  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
42 
Participants who are alive and free of disease progression at the time of removal from protocol 
therapy will be followed for first disease progression event after removal from protocol therapy. 
 
Tumor assessments should continue to be performed every 6-12 weeks on these participants. 
 
 
5.8 
Criteria for Taking a Participant Off Study 
 
Participants will be removed from study when any of the following criteria apply: 
 
• Disease Progression 
• Lost to follow-up 
• Withdrawal of consent for data submission 
• Death 
 
The reason for taking a participant off study, and the date the participant was removed, must be 
documented in the case report form (CRF) and CTMS (OnCore). 
 
6. DOSING DELAYS/DOSE MODIFICATIONS 
 
Dose delays and modifications will be made as indicated in the following table(s). The 
descriptions and grading scales found in the revised NCI Common Terminology Criteria for 
Adverse Events (CTCAE) version 4.0 will be utilized for dose delays and dose modifications. A 
copy of the CTCAE version 4.0 can be downloaded from the CTEP website 
 http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm.  
 
 
6.1 
Dosing Delays/Omission/Modficiation 
 
Dosing interruptions are permitted in the case of medical / surgical events or logistical 
reasons not related to study therapy (e.g., elective surgery, unrelated medical events, patient 
vacation, and/or holidays). Participants held for these reasons require prior approval from the PI 
and should resume therapy within 6 weeks of the scheduled interruption. The reason for 
interruption should be documented in the participant's study record. 
 
In the absence of an unacceptable therapy-related toxicity and/or clinical signs of disease 
progression, subjects may continue treatment at the discretion of the investigator. Subjects must 
be instructed to notify their physician immediately for any and all toxicities. 
 
Subjects may hold each drug independently of one another and if one must permanently be 
discontinued, they may continue on the other.  
 
Guidelines for the management of AEs (ie, dose interruptions and dose reductions) are 
presented in the next sections. Cabozantinib and nivolumab have class-specific safety profiles 
based on their mechanism of action but may also cause AEs that overlap. For management of AEs 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
43 
which can be clearly attributed to Cabozantinib or Nivolumab, independent dose modification for 
either agent is allowed. For AEs without clear attribution to either study treatment, management 
of toxicity should include dose modifications of both agents. 
 
 Cabozantinib may only  be reduced by one dose level  (see Table 1 below).  If study 
treatment of cabozantinib is restarted after being withheld or interrupted, the subject should be 
instructed not to make up the missed doses of cabozantinib.  
 
Starting Dose 
First Level dose Reduction 
40 mg cabozantinib 
Reduce to 20 mg cabozantinib 
 
 
For toxicities that were considered unrelated to cabozantinib:  If the subject recovers from his 
or her toxicities to CTCAE v.4.0 Grade ≤ 1 or to the baseline value (or lower), then treatment 
with cabozantinib may be restarted with no change in dose. 
Subjects unable to tolerate a daily dose of 20 mg should discontinue study treatment.  
For dose reductions not triggered by myelosuppression or by Grade 4 AEs affecting major 
organs (eg, central nervous system, cardiac, hepatic, renal) dose re-escalation to the 
participants previous dose of cabozantinib (not higher than 40 mg/day) may be allowed after 
discussion with the PI. 
 
There are no dose reductions for nivolumab.  
 
Nivolumab should be held (delayed) or omitted for toxicities that are considered possibly, 
probably or definitely related to nivolumab.  Nivolumab doses may be delayed up to 3 days from 
scheduled dose.  
 
Recommendations for treating the expected toxicities of Nivolumab are provided below. 
Consultation with a medical or surgical specialist, especially prior to an invasive diagnostic or 
therapeutic procedure, is recommended. 
 
 
Doses of nivolumab should be omitted (not delayed) for the following toxicities:  
• Any Grade 3 skin, drug-related adverse event 
• Grade 2 diarrhea or colitis 
• Grade 2 pneumonitis 
• Grade 2 hypophysitis 
• Grade 2 adrenal insufficiency 
• Serum creatinine more than 1.5 and up to 6 times the upper limit of 
normal 
• Grade 1 or 2 new-onset moderate or severe neurologic signs or 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
44 
symptoms 
• Any grade 3 adverse event 
• First occurrence: omit dose 
• Recurrence of same grade 3 AE: discontinue nivolumab 
permanently  
• AST or ALT > 3xULN and up to >5xULN 
• Total bilirubin >3xULN 
After omitting a dose, the following criteria must be met to resume treatment with Nivolumab: 
• AE has resolved to Grade ≤ 1 or baseline value, with the following 
exceptions:  
- Subjects may resume treatment in the presence of Grade 2 fatigue  
- Drug-related endocrinopathies adequately controlled with only physiologic hormone 
replacement may resume treatment. 
Participants should restart treatment at the next scheduled time point per protocol.  
If treatment is withheld > 9 weeks from the last dose of either cabozantinib or nivolumab, the 
patient should discontinue study therapy.   
 
Additionally, 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  
• Grade 3 drug-related thrombocytopenia > 7 days or 
associated with bleeding 
• Creatinine greater than 6 times ULN 
• Grade 4 diarrhea or colitis 
• Grade 3 or 4 pneumonitis 
• Grade 4 hypophysitis 
• Grade 3 or 4 adrenal insufficiency 
• Grade 4 hyperglycemia (related to study drug) 
• Grade 4 skin related AE 
• Immune-mediated encephalitis 
• Recurrent Grade 3 event  (unless otherwise specified in 
tables below) 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
45 
• Any AE that requires 10mg or more of prednisone or 
equivalent for >9 weeks 
• Any severe or Grade 3 immune-mediated adverse reaction that recurs on 
reintroduction of nivolumab, or an inability to reduce corticosteroid dose 
to 10 mg or less of prednisone or equivalent per day within 12 weeks  
• Any Grade 4 drug-related adverse event or laboratory 
abnormality, except for the following events which do not 
require discontinuation: 
• Grade 4 amylase or lipase abnormalities (refer to below table) 
• 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 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 dosing. 
 
 
6.2 
Management of toxicities attributable to Cabozantinib and Nivolumab 
 
6.2.1 Gastrointestinal Disorders 
 
Diarrhea/Colitis 
Subjects should be instructed to notify their physician immediately at the first signs of 
poorly formed or loose stool or an increased frequency of bowel movements as both cabozantinib 
and nivolumab can be associated with severe diarrhea/colitis. General supportive measures should 
be implemented including continuous oral hydration, correction of fluid and electrolyte 
abnormalities, small frequent meals, and stopping lactose-containing products, high fat meals, and 
alcohol. 
  
Immune-mediated colitis has been associated with the administration of nivolumab. 
 
Participants experiencing interolable Grade 2 diarrhea or Grade 3 diarrhea unable to be managed 
with standard antidiarrheal treatments should consult a gastrointestinal (GI) doctor  for 
potential endoscopy and biopsy to help distinguish between cabozantinib vs. nivolumab 
mediated toxicity.   If a biopsy is performed and:  
• there is T cell infiltration indicative of nivolumab-induced 
colitis, nivolumab should be permanently discontinued.  
Once diarrhea returns to Grade 1, restart cabozantinib at a 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
46 
reduced dose.  
• there is no T cell infiltration indicative of nivolumab-
induced colitis, when diarrhea returns to Grade 1 
nivolumab should be resumed at the same dose at the 
discretion of the investigator.  Cabozantinib should also be 
resumed at a reduced dose. 
 
Treatment may be restarted following the resolution of colitis. In addition, if the patient is 
being managed with corticosteroids, treatment should not be restarted until the steroids have been 
tapered down to a prednisone dose ≤ 10 mg/day. Patients who resume treatment should be 
monitored closely for signs of renewed diarrhea.   
 
Table 2: Managment of Diarrhea/Colitis 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
47 
Grade 
Management 
Grade 1 
• Continue nivolumab and cabozantinib. 
• Start Anti-diarrheal agent (e.g., Imodium) – up to 3 agents are 
permitted 
• Close monitoring. 
Grade 2  
• Hold nivolumab and cabozantinib  
• Administer anti-diarrheal agent (e.g., Imodium). 
• If symptoms persist > 5 days or recur, initiate therapy with Prednisone 
60 mg/day or equivalent 
 
• If improved to Grade ≤1 within 9 weeks:  
o Taper steriods over ≥ 1 month 
o Restart Nivolumab when corticosteroids have been 
reduced to the equivalent of prednisone ≤ 10 mg/day. 
o Restart Cabozantinib at a reduced dose when 
corticosteroids have been reduced to the equivalent of 
prednisone ≤ 10 mg/day. 
 
Grade 3  
• Hold nivolumab and cabozantinib. 
• Treat with IV steroids (1-2 mg/kg/day methylprednisolone or 
equivalent) and convert to oral steroids (prednisone 60 mg/day or 
equivalent) after improvement 
• If improved to Grade ≤1 within 9 weeks:  
o Taper steriods over ≥ 1 month 
o Restart Nivolumab when corticosteroids have been 
reduced to the equivalent of prednisone ≤ 10 mg/day. 
o Restart Cabozantinib at a reduced dose when 
corticosteroids have been reduced to the equivalent of 
prednisone ≤ 10 mg/day. 
 
Grade 4 
• Permanently discontinue nivolumab and hold cabozantinib. 
• Treat with IV steroids (1−2 mg/kg/day methylprednisolone or 
equivalent) and convert to oral steroids (prednisone 60 mg/day or 
equivalent) after improvement 
• When symptoms improve to Grade ≤ 1, taper steroids over ≥ 1 month 
• If symptoms are not improving after 48 hours of initiating steroids or 
are worsening, addition of an alternative immunosuppressive agent 
(e.g., mycophenolate or TNF-α antagonist) may be considered. 
• If the subject was unequivocally deriving clinical benefit, the subject 
may be able to resume cabozantinib at 20mg daily as determined by 
the investigator. 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
48 
 
6.2.2 Hepatobilary Disorders 
Elevations of ALT, AST, and bilirubin have been observed during treatment with 
cabozantinib. It is recommended that participants with elevation of ALT, AST, and/or bilirubin 
have more frequent laboratory monitoring of these parameters. If possible, hepatotoxic 
concomitant medications should be discontinued in participants who develop increased values of 
ALT, AST, or bilirubin. Participants on this study may enter with increased ALT/AST serum levels 
up to 3 × ULN to the guidelines in Table 3 should be used for dose modifications. 
 
Table 3. Management of Elevation of transaminases 
Transaminase elevation 
CTCAE v4.0 
 
Intervention 
Grade 1  
AST or ALT > ULN to 3.0 x 
ULN and/or Total bilirubin 
> ULN – 1.5 x  ULN 
Continue study treatment  
Monitor liver function tests (LFTs) weekly for at least 4 weeks. 
Grade 2 
AST or ALT > 3.0 to ≤ 5.0 x 
ULN and/or Total bilirubin 
> ULN – 1.5 x ULN to ≤3 x 
ULN 
Hold cabozantinib and nivolumab. 
 
Monitor LFTs at least twice weekly until return to baseline or 
Grade ≤1 
Consider referral to a hepatologist. 
 
If persistent > 5 days, start prednisone 60 mg/day or equivalent.  
 
When LFTs resolve to baseline or Grade ≤1 and steroid dose is 
prenisone ≤ 10 mg/day or equivalent, restart Nivolumab and 
Cabozantinib at a reduced dose. 
 
Grade 3 
AST or ALT > 5.0 to ≤ 20.0 x 
ULN and/or Total bilirubin 
> ULN – 3.0 x ULN to ≤10.0 
x ULN 
Hold cabozantinib and nivolumab. 
 
Monitor LFTs every 48−72 hours until LFTs return to baseline or 
Grade ≤1 
 
Consider referral to hepatologist and liver biopsy to establish 
etiology of hepatic injury 
 
Start prednisone 60 mg/day or equivalent  
 
 With first occurrence:  
• If LFTs do not resolved to Grade < 3 within 7 days, 
permanently discontinue nivolumab and continue holding 
cabozantinib. 
• When LFTs resolve to baseline or Grade ≤ 1, taper steroids 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
49 
 
 
over ≥1 month.   When steroid dose is prenisone ≤ 10 
mg/day or equivalent, restart Nivolumab and Cabozantinib 
at a reduced dose.  
Subjects receiving cabozantinib at a daily dose of 20 mg 
may be restarted at the same dose if deemed safe at the 
discretion of the principal investigator. 
 
If recurs: permanently discontinue nivolumab .  If the subject was 
unequivocally deriving clinical benefit, the subject may be able to 
resume cabozantinib at 20mg daily as determined by the 
investigator. 
Grade 4  
AST or ALT > 200 x ULN 
and/or Total bilirubin > 
ULN 10.0 x ULN 
Permanently discontinue nivolumab and hold cabozantinib and 
inform the principle investigator.  
 
Obtain hepatology consult and liver biopsy to establish etiology of 
hepatic injury. 
 
Start prednisone 60 mg/day or equivalent. 
 
If LFT results do not decrease within 48 hours after initiation of 
systemic steroids, consider addition of an alternative 
immunosuppressive agent (e.g., mycophenolate) to the 
corticosteroid regimen.  
 
If LFTs resolve to baseline or Grade ≤ 1, taper steroids over ≥1 
month.   If the subject was unequivocally deriving clinical benefit, 
the subject may be able to resume cabozantinib at 20mg daily as 
determined by the investigator. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
50 
 
 
6.2.3 Dermatologic Disorders 
 
Palmar-plantar erythrodysesthesia syndrome (also known as hand-foot syndrome), skin 
rash (including blisters, erythematous rash, macular rash, skin exfoliation, dermatitis acneiform, 
and papular rash), pruritus, dry skin, and erythema have been reported in cabozantinib-treated 
participants.  
 
 
All participants on study should be advised on prophylactic skin care. This includes the use 
of hypoallergenic moisturizing creams, ointment for dry skin, and sunscreen with sun protection 
factor ≥ 30, avoidance of exposure of hands and feet to hot water, protection of pressure sensitive 
areas of hands and feet, and use of thick cotton gloves and socks to prevent injury and to keep the 
palms and soles dry. Participants with pre-existing skin disorders should be carefully monitored 
for signs of infection (e.g., abscess, cellulitis, or impetigo). 
Early signs of hand-foot syndrome could be tingling, numbness, and slight redness or mild 
hyperkeratosis. Early manifestations include painful, symmetrical red and swollen areas on the 
palms and soles. The lateral sides of the fingers or periungual zones may also be affected. 
Adequate interventions are required to prevent worsening of skin symptoms such as 
blisters, desquamations, ulcerations, or necrosis of affected areas.  
Aggressive management of symptoms is recommended, including early dermatology 
referral. In the case of study treatment-related skin changes (eg, rash, hand-foot syndrome), the 
investigator may request that additional assessments be conducted with the subject’s consent. 
These assessments may include digital photographs of the skin changes and/or a biopsy of the 
affected skin and may be repeated until the skin changes resolve. 
 
Table 4: Management of Treatment-emergent PPE Syndrome 
CTCAE 
v.4.0 Grade 
Intervention 
1 
Continue Cabozantinib and Nivolumab treatment may be continued at the 
current dose if PPE is clinically insignificant and tolerable.  
 
Start urea 20% cream twice daily and clobetasol 0.05% cream once daily.  
 
Reassess at least weekly; if PPE worsens at any time or does not improve after 
2 weeks, proceed to the intervention guidelines for Grade 2. 
2 
Cabozantinib and Nivolumab treatment may be continued if PPE is tolerated.  
Cabozantinib may be dose reduced in intolerable. 
 
Start urea 20% cream twice daily and clobetasol 0.05% cream once daily and 
add analgesics (eg, NSAIDs/GABA agonists) for pain control if needed.  
 
Reassess at least weekly; if PPE does not improve within 2 weeks or worsens or 
affects self-care, proceed to the intervention guidelines for Grade 3. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
51 
 
3 
Hold Cabozantinib and Nivolumab treatment 
 
Continue treatment of skin reaction with clobetasol 0.05% cream twice daily 
and analgesics.  
 
If PPE resolves to Grade ≤2, resume Nivolumab (at same dose) and 
Cabozantinib (at reduced dose). 
 
If recurs and is intolerable or does not improve within 6 weeks, permanently 
discontinue cabozantinib and hold Nivolumab until resolves to Grade ≤2. 
 
CTCAE, Common Terminology Criteria for Adverse Events; GABA, gamma-amino butyric acid; 
NSAID, non-steroidal anti-inflammatory drug; PPE, palmar-plantar erythrodysethesia. 
 
Treatment-emergent rash has also been associated with nivolumab.  The majority of cases 
of rash were mild in severity and self-limited, with or without pruritus. 
 
A dermatologist should evaluate persistent and/or severe rash or pruritus.  A biopsy should 
be performed unless contraindicated.  Low-grade rash and pruritus irAEs have been treated with 
symptomatic therapy (e.g., antihistamines).  Topical or parenteral corticosteroids may be required 
for more severe symptoms. 
 
Table 5: Management of Skin Rash and Oral Lesions 
Grade 
Management  
≤ 1 
Continue protocol therapy 
 2 
Continue protocol therapy and monitor. 
 3 
Omit dose of nivolumab and cabozantinib until ≤ Grade 1 
 4 
Discontinue nivolumab and hold cabozantinib.  
If the subject is unequivocally deriving clinical benefit, the subject may be able to 
resume cabozantinib at 20mg daily once resolved to ≤ Grade .1 
• 
Patients with bullous lesions must be evaluated for vasculitis, Steven-Johnson 
syndrome, TEN, and autoimmune bullous disease including oral lesions of bullous 
pemphigus/pemphigoid.  
• 
Pruritus may occur with or without skin rash and should be treated symptomatically. 
• 
Note skin rash typically occurs early and may be followed by additional events 
particularly during steroid taper.  
 
6.2.4  Thyroid Function Disorders  
 
Changes in thyroid function tests (TFTs) and hypothyroidism have been reported with 
nivolumab, cabozantinib and other tyrosine kinase inhibitor treatment as a result of altered 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
52 
thyroid hormone regulation by mechanisms that seem to be specific for each agent (Torino et al. 
2009). Preliminary data from ongoing studies indicate that treatment-emergent elevation of 
thyroid stimulating hormone (TSH) by cabozantinib may be dose-dependent in fashion.  
 
• Cabozantinib and nivolumab do not need to be held for asymptomatic 
participants.  
Management of thyroid dysfunction (eg, symptomatic hypothyroidism) should follow accepted 
clinical practice guidelines. 
 
 
6.3 
Management of toxicities attributable to Cabozantinib 
 
Table 6: General Dose Modifications of Cabozantinib for Treatment Related AEs 
CTCAE v.4.0 Grade 
Recommended Guidelines for Management1 
Grade 1 AEs 
Continue cabozantinib treatment at the current dose level if 
AE is manageable and tolerable. Add supportive care as 
indicated. 
Grade 2 AEs which are 
tolerable and are easily 
managed 
 
Continue cabozantinib treatment at the current dose level with 
supportive care or appropriate intervention. 
 
At the discretion of the investigator, cabozantinib should be 
dose reduced or interrupted. 
 
Note: It is recommended that dose holds be as brief as 
possible. 
Grade 2 AEs which are 
intolerable and cannot be 
adequately managed 
Cabozantinib should be held unless the toxicity can be easily 
managed with a dose reduction and optimal medical care. 
 
If held, cabozantinib can either restarted at same dose or dose 
reduced per investigator discretion. If same toxicity recurs at 
grade ≥2, the dose should be held and reduced when resolves 
to baseline. 
 
Note: It is recommended that dose holds be as brief as 
possible. 
Grade 3 AEs  
(excludging clinically 
insignificant laboratory 
abnormalities) 
Hold Cabozantinib unless the toxicity can be easily managed 
with a dose reduction and optimal medical care. 
 
Note: It is recommended that dose holds be as brief as 
possible. 
Grade 4 AEs  
(excludging clinically 
Hold cabozantinib. 
 
Discontinue cabozantinib unless the following criteria are 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
53 
insignificant laboratory 
abnormalities) 
met: 
• Subject is deriving clear clinical benefit as 
determined by treating investigator and PI. 
• Toxicity can be managed with a dose reduction following 
recovery to Grade 1 (or baseline) and optimal medical care 
*AE: adverse event 
 
1 Study treatment dose adjustment is only needed if the toxicity was deemed related to cabozantinib treatment or had 
an unclear relationship to cabozantinib treatment. 
 
 
6.3.1 Gastrointestinal Disorders  
 
The most common GI AEs reported in clinical studies with cabozantinib are diarrhea, oral 
pain, dyspepsia, stomatitis, and dysphagia. 
 
Nausea and Vomiting 
Antiemetic agents are recommended as clinically appropriate at the first sign of nausea and 
vomiting or as prophylaxis to prevent emesis, along with supportive care according to clinical 
practice guidelines.  
 
• The 5-HT3 receptor antagonists are the preferred antiemetic 
• The following antiemtics should be avoided as they impact CYP3A4 which could 
impact cabozantinib exposure:  
o NK-1 receptor antagonists and dexamethasone  
o Glucocorticoids  
o Nabilone (weak inhibitor) 
 
When therapy with antiemetic agents does not control the nausea or vomiting to tolerable levels, 
study treatment should be temporarily interrupted or dose reduced. 
 
Stomatitis and Mucositis 
Preventive measures may include a comprehensive dental examination to identify any 
potential complications before study treatment is initiated. Removal of local factors should be 
instituted as indicated, such as modification of ill-fitting dentures and appropriate care of 
gingivitis. During treatment with cabozantinib good oral hygiene and standard local treatments 
such as nontraumatic cleansing and oral rinses (e.g., with a weak solution of salt and baking soda) 
should be maintained. The oral cavity should be rinsed and wiped after meals, and dentures should 
be cleaned and brushed often to remove plaque. Local treatment should be instituted at the earliest 
onset of symptoms. Obtain bacterial/viral culture if oral infection is suspected and treat infection 
as indicated by local guidelines. When stomatitis interferes with adequate nutrition and local 
therapy is not adequately effective, dose reduction or temporary withholding of cabozantinib 
should be considered. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
54 
6.3.2 Hematological Disorders 
 
Hematological toxicities (ie, neutropenia and thrombocytopenia) and associated 
complications have been observed after administration of cabozantinib and may be managed with 
dose interruptions and/or dose reductions. Use of granulocyte colony-stimulating factor support 
for neutrophil recovery is allowed per investigator discretion and in accordance with accepted 
guidelines after the first incidence of clinically relevant cytopenia. 
Complete blood counts with differentials and platelets should be performed regularly. 
Participantss with hematologic toxicities may require additional or more frequent laboratory tests 
according to institutional guidelines. Febrile neutropenia or evidence of infection associated with 
neutropenia must be assessed immediately and treated appropriately and in a timely manner 
according to institutional guidelines.  
Dose reductions or dose interruptions for anemia are not mandated but can be applied as 
clinically indicated. Supportive care such as red blood cell transfusions may be managed according 
to institutional guidelines. 
 
6.3.3 Fatigue, Anorexia and Weightloss Disorders 
 
Fatigue has been reported during treatment with cabozantinib and nivolumab, the dose 
modifications are recommended for both drugs. Common causes of fatigue such as anemia, 
deconditioning, emotional distress (depression and/or anxiety), nutrition, sleep disturbance, and 
hypothyroidism should be ruled out and/or these causes treated according to standard of care. 
Individual non-pharmacological and/or pharmacologic interventions directed to the contributing 
and treatable factors should be given. Pharmacological management with psychostimulants such 
as methylphenidate should be considered after disease specific morbidities have been excluded.  
Dose reduction of study treatment should be considered when general or pharmacological 
measures have not been successful in reducing symptoms. Dose interruption may be considered 
for Grade ≥ 3 fatigue despite optimal management, at the investigator’s discretion.  
Anorexia and weight loss should be managed according to local standard of care including 
nutritional support. Pharmacologic therapy such as megestrol acetate should be considered for 
appetite enhancement. Should these interventions prove ineffective, dose holds and reductions may 
be considered for Grade ≥ 3 anorexia or weight loss. If anorexia and/or weight loss do not recur 
after a dose reduction, dose of cabozantinib may be re-escalated to the previous dose. 
 
 
6.3.4 Wound Healing 
 
VEGF inhibitors can cause wound healing complications and wound dehiscence which 
may occur even long after a wound has been considered healed. Therefore, surgical and traumatic 
wounds must have completely healed prior to starting cabozantinib treatment and be monitored 
for wound dehiscence or wound infection while the subject is being treated with cabozantinib. 
 
6.3.5 GI perforation/fistula and non-GI fistula formation 
 
GI perforation/fistula and non-GI fistula formation have been reported with cabozantinib 
and other approved drugs that inhibit VEGF pathways.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
55 
After starting cabozantinib, subjects should be monitored for early signs of GI perforation such 
as abdominal pain, nausea, emesis, constipation, and fever especially if known risk factors for 
developing GI perforation or fistula are present.  
 
• Discontinue cabozantinib treatment in participants diagnosed with GI or 
non-GI perforation/fistula. 
 
6.3.6 Hypertension 
 
Hypertension is a common class effect of drugs that inhibit VEGF pathways and has been 
reported in subjects treated with cabozantinib. Blood pressure should be monitored in a constant 
position at each visit (either sitting or supine). In general, subjects with known hypertension should 
be optimally managed prior to study entry.  
Decisions to decrease or hold the dose of study treatment must be based on blood pressure 
readings taken by a medical professional and must be confirmed with a second measurement at 
least 5 minutes following the first measurement. Other than for hypertension requiring immediate 
therapy, the presence of new or worsened hypertension should be confirmed at a second visit 
before taking therapeutic action. It is recommended that this second visit occurs within 1 week. 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
56 
 
Table 7: Management of Treatment-emergent Hypertension 
Criteria for Dose 
Modification 
Intervention 
> 140 mm Hg (systolic) and < 160 
mm Hg 
OR 
> 90 mm Hg (diastolic) and < 110 
mm Hg 
 
• Maintain dose of cabozantinib and nivolumab 
• Optimize antihypertensive treatment (i.e., increase dose 
of existing medications and/or add new 
antihypertensive medications). Reevaluate in one week  
• If after optimal antihypertensive therapy (usually to 
include 3 agents) BP returns (< 150 mm Hg systolic or 
<100 mm Hg diastolic maintain dose of cabozantinib and 
nivolumab. 
• If after optimal antihypertensive therapy BP is not  < 
150 mm Hg systolic or < 100 mm Hg diastolic, reduce 
cabozantinib treatment by one dose level and continue 
nivolumab. Reevaluate in one week. 
• If optimized antihypertensive therapy (usually to 
include 3 agents) and cabozantinib dose reduction does 
not result in BP < 150 mm Hg systolic or < 100 mmHg 
diastolic, cabozantinib treatment should be interrupted; 
Continue patient on nivolumab. 
≥ 160 mm Hg (systolic) 
OR 
≥ 110 mm Hg (diastolic) 
• Reduce cabozantinib treatment by one dose level and 
continue nivolumab. Optimize antihypertensive 
treatment (i.e., increase dose of existing medications 
and/or add new antihypertensive medications). Monitor 
participant closely for hypotension.  
• Reevaluate in one week. 
• If after optimal antihypertensive therapy (usually to 
include 3 agents) upper limits of BP (< 150 mm Hg 
systolic or <100 mm Hg diastolic) keep cabozantinib on 
the reduced dose and keep nivolumab. 
• Interrupt cabozantinib treatment if upper limits of BP 
(≥ 150 mm Hg systolic or ≥ 100 mm Hg diastolic) are 
sustained manageable or if subject is symptomatic.  
• Restart cabozantinib treatment at the most tolerable 
dose and reescalate cabozantinib dose only if BP falls 
to and is sustained at < 140 mm Hg systolic and < 90 
mm Hg diastolic. 
>180 mm Hg systolic or > 
120 mm Hg diastolic or if 
subject is symptomatic. 
• Hold cabozantinib treatment and continue nivolumab 
• Optimize antihypertensive treatment (i.e., increase dose 
of existing medications and/or add new 
antihypertensive medications). Reevaluate in one week  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
57 
• Restart cabozantinib at reduced dose and re-escalate 
cabozantinib dose only if BP falls to and is sustained at 
< 140 mm Hg systolic and < 90 mm Hg diastolic. 
• Permanently interrupt cabozantinib treatment if upper 
limits of BP (≥ 150 mm Hg systolic or ≥ 100 mm Hg 
diastolic) are sustained and not adequately manageable 
or if subject is symptomatic.  
Hypertensive crisis or 
hypertensive encephalopathy 
• Discontinue cabozantinib treatment. 
• Hold nivolumab until resolution. 
BP, blood pressure. 
 
6.3.7 Thromboembolic Events 
 
Thromboembolic complications are frequent in cancer patients due to procoagulant 
changes induced by the malignancy or anti-cancer therapy including inhibitors of VEGF pathways. 
Deep vein thrombosis and PE have been observed in clinical studies with cabozantinib; including 
fatal events.  
• Subjects who develop a PE or DVT should have cabozantinib treatment 
held until therapeutic anticoagulation with heparins (e.g., LMWH) is 
established.  
• Cabozantinib treatment may be resumed at the same dose in subjects who 
are stable and have uncomplicated PE or DVT and are deriving clinical 
benefit from cabozantinib treatment. 
• During anticoagulation treatment, subjects need to be monitored on an 
ongoing basis for bleeding risk and signs of bleeding which may require 
additional or more frequent laboratory tests according to institutional 
guidelines.  
• If there are any signs of clinically relevant bleeding, cabozantinib 
treatment should be stopped immediately and the PI contacted to discuss 
further study participation. 
• Subjects with life-threatening PE or DVT should have study treatment 
discontinued unless toxicity can be managed and subject is deriving clear 
clinical benefit as determined by the investigator and agreed by the PI.  
 
Arterial thrombotic events (e.g., transient ischemic attack, myocardial infarction) have 
been observed rarely in studies with cabozantinib. Subjects should be evaluated for preexisting 
risk factors for arterial thrombotic events such as diabetes mellitus, hyperlipidemia, hypertension, 
coronary artery disease, history of tobacco use, and cardiac or thromboembolic events that 
occurred prior to initiation of study treatment.  
• Cabozantinib treatment should be discontinued in patients who develop an 
acute myocardial infarction or any other clinically relevant arterial 
thromboembolic complication. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
58 
 
6.3.8 Hemorrhagic Events 
 
Hemorrhagic events have been reported with cabozantinib and other approved drugs that 
inhibit VEGF pathways.  
• Discontinue cabozantinib treatment in participants who have been 
diagnosed with a severe bleeding complication (Grade 3 or 4) suspected to 
be related to drug. 
 
6.3.9 Proteinuria 
Proteinuria is an expected AE with the inhibition of VEGF pathways and has been observed 
in cabozantinib clinical studies.  Nephrotic syndrome has been reported with cabozantinib and 
other inhibitors of VEGF pathways. 
 
Table 8 Management of Treatment-emergent Proteinuria 
Severity of 
Proteinuria (UPCR) 
Intervention 
≤ 1  
(≤ 113.1 mg/mmol) 
• Continue therapy with cabozantinib and nivolumab 
> 1 and < 3.5  
(> 113.1 and < 395.9 
mg/mmol) 
• Continue therapy with cabozantinib and nivolumab 
• Consider confirming with a 24-hour protein assessment within 7 
days 
o If UPCR ≤ 2 or urine protein ≤ 2 g/24 hours on 24-hour 
urine collection, cabozantinib continue at the same dose.  
o If UPCR > 2 on repeat UPCR testing or urine protein > 
2 g/24 hours on 24-hour urine collection,  hold 
cabozantinib and repeat testing in 7 days.  
 If UPCR decreases to < 2, restart cabozantinib at 
a reduced dose.  
 If UPCR remains > 2 mg/mg continue holding 
cabozantinib and repeat testing every 7 days until 
decreases  to <2 or max hold is reached.  When 
<2 restart cabozantinib at a reduced dose. 
•  
≥ 3.5  
(≥ 395.9 mg/mmol) 
• Hold cabozantinib and  nivolumab  
• Repeat UPCR and perform 24-hour protein assessment 
within 7 days 
• If ≥ 3.5 on repeat UPCR, continue to hold cabozantinib 
treatment and check UPCR once per week.  
o If UPCR decreases to < 2, restart cabozantinib 
treatment at a reduced dose and monitoring of urine 
protein/creatinine should continue weekly until the 
UPCR decreases to < 1. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
59 
• Restart nivolumab once UPCR is ≤ 1  
Nephrotic syndrome 
• Discontinue cabozantinib and nivolumab. 
UPCR, urine protein to creatinine ratio. 
 
6.3.10 Hypophosphatemia  
Hypophosphatemia has been reported during treatment with cabozantinib.  
Mild hypophosphatemia is usually asymptomatic or symptoms can be non-specific such as 
weakness, bone pain, rhabdomyolysis, or altered mental status. Other causes of hypophosphatemia 
such as poor nutrition, chronic alcoholism, malabsorption, excessive antacid use, glucocorticoids 
use, kidney dysfunction, respiratory alkalosis, vitamin D deficiency should be ruled out and/or 
these causes treated according to standard of care.  
 
• Mild to moderate hypophosphatemia should be managed by oral 
replacement including food that are high in phosphate (diary items, meats, 
beans) and/or oral phosphate supplements according to standard clinical 
practice guidelines. 
 
6.3.11 Osteonecrosis of the Jaw 
 
Osteonecrosis of the jaw (ONJ) has been reported with cabozantinib, the use of anti-
angiogenic drugs, bisphosphonates and denosumab in cancer patients. Additional risk factors for 
ONJ have been identified such as use of corticosteroids, chemotherapy, local radiotherapy, poor 
oral hygiene, smoking, dental or orofacial surgery procedures, and cancer disease itself.  
 
• As a preventive measure, invasive dental procedures should be avoided if 
possible in subjects who have previously been treated with or 
concomitantly receive bisphosphonates or denosumab. 
• In cases where dental procedures are unavoidable, the risks and benefits of 
a dental procedure,  the extent of the procedure, the  risk of developing 
osteonecrosis of the jaw should be carefully considered when deciding on 
the duration of a temporary treatment interruption of cabozantinib. If 
clinically possible, treatment with cabozantinib should be held for 
approximately 4 weeks prior to a dental procedure and resumed after 
complete healing has occurred. 
• Participants experiencing osteonecrosis should have study treatment with 
cabozantinib held and be managed according to clinical guidelines. . 
Participants may be able to restart cabozantinib if in their best interest 
after discussion with the PI.  
6.3.12  QTc Prolongation 
The effect of orally administered cabozantinib 140 mg qd on QTc interval was evaluated in a 
placebo-controlled study in subjects with MTC. A mean increase in QTcF of 10-15 ms was 
observed after 4 weeks after initiating cabozantinib treatment. A concentration-QTc 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
60 
relationship could not be definitively established. Changes in cardiac wave form morphology 
or new rhythms were not observed. No cabozantinib-treated subjects in this study had a 
QTcF > 500 ms. 
Unless otherwise specified, only subjects with a baseline QTcF ≤ 500 msec are eligible for 
this study. Cabozantinib should be used with caution in subjects with QT prolongation risk, a 
history of QT interval prolongation, or who are taking antiarrhythmics or drugs known to 
prolong the QT interval. Concomitant treatment with strong CYP3A4 inhibitors, which may 
increase cabozantinib plasma concentrations, should be avoided.  
If at any time on study there is an increase in QTcF to an absolute value > 500 ms or an 
increase of > 60 ms above baseline, two additional ECGs must be performed with intervals 
not less than 3 min apart within 30 min after the initial ECG. 
If the average QTcF from the three ECGs is > 500 ms or increased by > 60 ms above 
baseline, the following actions must be taken: 
• Withhold study treatment 
• Immediately notify the Overall PI 
• Hospitalize symptomatic subjects (eg, with palpitations, dizziness, syncope, orthostatic 
hypotension, a significant ventricular arrhythmia on ECG) for a thorough cardiology 
evaluation and management 
• Consider cardiology consultation for asymptomatic subjects for evaluation and 
management 
• Check electrolytes, especially magnesium, potassium and calcium; correct abnormalities 
as clinically indicated 
• Check concomitant medications for any medication that may have contributed to QT 
prolongation, and if possible, discontinue these medications (http://www.qtdrugs.org) 
• Repeat ECG triplicates hourly until the average QTcF is ≤ 500 msec, or otherwise  
• Subjects with QTc prolongation and symptoms must be monitored closely until the QTc 
elevation and symptoms have resolved. Study treatment may be restarted at a reduced 
dose level if all of the following conditions are met: 
• Symptoms are determined to be unrelated to the QT interval prolongation 
• The QTcF value > 500 ms or increase of > 60 ms above baseline is not confirmed 
according to protocol procedures 
• Study treatment has been interrupted through a minimum of 1 week following the return 
of the QTcF to ≤ 500 msec or return to ≤ 60 ms above baseline. 
• QT prolongation can be unequivocally associated with an event other than cabozantinib 
administration and is treatable/has been resolved  
• Overall PI has reviewed all available information and has agreed to the continuation of 
study treatment 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
61 
Following reinitiation of study treatment, ECGs must be repeated weekly for 2 weeks, then 
every 2 weeks for 1 month, then according to the protocol-defined time points. 
All study treatment must be permanently discontinued if either of the following applies: 
• Cardiac evaluation confirms that symptoms are the consequence of QT interval 
prolongation 
• Recurrence of QTcF prolongation (confirmed by central ECG lab) after reinitiation of 
study treatment at a reduced dose 
 
 
 
 
 
 
 
6.4 
Management of toxicities attributable to Nivolumab 
 
6.4.1 Steroid and immunosuppresive agents use on treatment with 
nivolumab: 
• Immunosuppressive agents and the use of systemic corticosteroids are permitted in the 
context of treating adverse events. Subjects receiving corticosteroids for treatment of 
drug-related adverse events must be at < 10 mg/day prednisone or equivalent prior to re-
initiation of study therapy. 
 
6.4.2 Elevated Amylase and/or Lipase  
 
Patients may develop symptomatic and/or radiographic evidence of pancreatitis, DM, or 
pancreatic dysfunction. Amylase and lipase should be checked if there is clinical suspicion for 
pancreatitis. Asymptomatic elevations can be self-limited and treatment continued per guidelines 
above. Corticosteroids do not seem to alter the natural history of lipase/amylase elevations. 
Laboratory values tend to fluctuate on a day-to-day basis and eventually return to baseline or low 
grade over the course of weeks, whether or not subjects receive corticosteroids. Asymptomatic 
elevations should be monitored approximately on a weekly basis 
 
Patients with symptomatic or radiographic pancreatitis should discontinue nivolumab and 
consider consulting a gastroenterologist for management.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
62 
 
Table 9: Elevated Amylase and/or Lipase 
Grade   
Management/Next Dose for Nivolumab 
≤ 3 
Continue protocol therapy if asymptomatic.  
Ensure that participants have associated symptoms consistent with pancreatitis, such 
as abdominal pain, or hyperglycemia or radiographic pancreatic inflammation. 
 4 
Hold nivolumab and cabozantinib.  
 
Ensure that participants have associated symptoms consistent with pancreatitis, such 
as abdominal pain, or hyperglycemia or radiographic pancreatic inflammation. 
 
If patient remains asymptomatic, resume treatment when ≤ Grade 1. 
 
 
6.4.3 Pulmonary Toxicity 
Dyspnea, cough, fatigue, hypoxia, pneumonitis, and pulmonary infiltrates have been 
associated with the administration of nivolumab and have primarily been observed in patients with 
underlying NSCLC. 
Mild-to-moderate events of pneumonitis have been reported with nivolumab.  All 
pulmonary events should be thoroughly evaluated for other commonly reported etiologies such as 
pneumonia/infection, lymphangitic carcinomatosis, pulmonary embolism, heart failure, chronic 
obstructive pulmonary disease (COPD), or pulmonary hypertension and the following should be 
performed: 
• 
Measurement of oxygen saturation (i.e., arterial blood gas) 
• 
High-resolution CT scan of the chest 
• 
Bronchoscopy with bronchoalveolar lavage and biopsy 
• 
Pulmonary function tests (with diffusion capacity of the lung for carbon monoxide 
[DLCO]) 
 
Patients will be assessed for pulmonary signs and symptoms throughout the study.  Patients 
will also have CT scans of the chest at every tumor assessment (see Section 11.1.3). 
 
Table 10: Management of Pneumonitis 
Grade  
Management 
≤ 1 
Continue protocol therapy if radiologic findings only; dose may be held for further 
evaluation per investigator discretion 
 2 
Hold nivolumab pending evaluation.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
63 
Grade  
Management 
Resume protocol therapy after pulmonary and/or ID consultation if lymphocytic 
pneumonitis is excluded.  
 
Patient should discontinue nivolumab if prolonged steroids are required unless an 
alternative etiology of findings is identified. 
Withhold cabozantinib until resolved to ≤ Grade 1. 
 3 
Discontinue nivolumab. 
 
Withhold cabozantinib until resolved to ≤ Grade 1. 
 4 
Discontinue nivolumab. 
Withhold cabozantinib until resolve to ≤ Grade 1. 
Distinguishing inflammatory pneumonitis is often a diagnosis of exclusion for patients who do 
not respond to antibiotics and have no causal organism identified including influenza.  Most 
patients with respiratory failure or hypoxia will be treated with steroids.  Bronchoscopy may be 
required and analysis of lavage fluid for lymphocytic predominance may be helpful.  Patients 
with new lung nodules should be evaluated for sarcoid like granuloma.  Please consider 
recommending seasonal influenza inactivated vaccine for all patients. 
 
6.4.4 Fatigue 
 
Table 11: Management of Fatigue 
Grade 
Management 
≤ 2 
Continue protocol therapy  
 3 
Hold nivolumab and cabozantinib. 
 
When ≤ Grade 2, resume treatment with nivolumab at the same dose and cabozantinib 
at a reduced dose. 
 
If it recurs, discontinue cabozantinib.  
 4 
Hold nivolumab and discontinue cabozantinib. 
 
When ≤ Grade 2, resume treatment with nivolumab at the same dose. 
Fatigue is the most common adverse event associated with immune checkpoint therapy. Grade 
2 or greater fatigue should be evaluated for associated or underlying organ involvement 
including pituitary, thyroid, hepatic, or muscle (CPK) inflammation.  
 
6.4.5 Neurologic Events 
The principal treatments for neurologic toxicity are dose delay, corticosteroids, and 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
64 
IV immunoglobulin as outlined in the safety algorithm. Patients with any CNS events 
including aseptic meningitis, encephalitis, symptomatic hypophysitis, myopathy, 
peripheral demyelinating neuropathy, cranial neuropathy (other than peripheral n. 
VII), Guillain-Barre syndrome, and myasthenia gravis should discontinue nivolumab. 
Table 12: Management of Neurologic Events 
Grade 
Management 
≤ 1 
Continue protocol therapy 
 2 
Hold nivolumab 
 
If treatment with steriods is required, permanently discontinue 
nivolumab. 
 
If no treatment with steroids is required, and it has resolved to ≤ Grade 
1, resume nivolumab at same dose. 
 
 Participants are permitted to resume treatment with nivolumab for 
peripheral isolated CN VII (Bell’s palsy) when stable. 
 3 
Discontinue nivolumab. Hold cabozantinib.  
 
If the subject was unequivocally deriving clinical benefit, the subject 
may be able to resume cabozantinib at a lower dose as determined by 
the investigator. 
 4 
Discontinue nivolumab. Hold cabozantinib. 
 
 If the subject was unequivocally deriving clinical benefit, the subject 
may be able to resume cabozantinib at a lower dose as determined by 
the investigator. 
 
6.4.6 Endocrinopathy including hypophysitis and adrenal insufficiency 
 
Note all patients with symptomatic pituitary enlargement, exclusive of hormone deficiency, but 
including severe headache or enlarged pituitary on MRI or aseptic meningitis or encephalitis 
should be considered grade 3 events.  Isolated thyroid or testosterone deficiency may be treated 
as grade 2 if there are no other associated deficiencies and adrenal function is monitored.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
65 
 
Table 13: Management of Endocrinopathy including hypophysitis and adrenal insufficiency 
Grade   
Management 
≤ 2 
Asymptomatic abnormalities do not require dose delay*. 
 
 If symptomatic, hold until on a stable replacement hormone regimen. If 
treated with steroids patients must be stable off of steroids for two 
weeks with the exception of adrenal replacement therapy. 
3 
Hypophysitis:  
Hold nivolumab and cabozantinib* until ≤ Grade 1, then resume at 
same dose.  
 
Other endocrinopathies:   
Hold nivolumab and cabozantinib* until ≤ Grade 1 and stable on 
replacement hormones, then resume at same dose.  
 
4 
Discontinue nivolumab.  
Discontinue cabozantinib. If the subject was unequivocally deriving 
clinical benefit, the subject may be able to resume cabozantinib at a 
lower dose as determined by the investigator. 
* Patients must be evaluated to rule out pituitary disease prior to initiating thyroid replacement, 
and steroids including baseline serum: cortisol, ACTH, TSH and free T4 
 
6.4.7 Creatinine Levels/Renal Insufficiencies  
 
Table 14: Management of Creatinine Levels/Renal Insufficiencies 
Grade 
Management 
≤ 1 
Continue protocol therapy.  
Monitor weekly until return to baseline. 
2-3 
(>1.5 baseline to ≤ 6 
3.0 x ULN) 
Hold nivolumab and cabozantinib until ≤ Grade 1. 
Monitor creatinine every 2-3 days. 
Start 0.5 to 1.0 mg/Kg/day methylprednisolone IV or oral equivalent. 
Consider consulting nephrology and obtaining a renal biopsy. 
 
4 
( >6.0 x ULN) 
Discontinue nivolumab and hold cabozantinib.  
Monitor creatinine daily. 
Start 1.0 – 2.0 mg/Kg/day methylprednisolone IV or oral equivalent. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
66 
Grade 
Management 
Consult nephrologist and consider obtaining a renal biopsy. 
 
If the subject was unequivocally deriving clinical benefit, the subject 
may be able to resume cabozantinib at a lower dose as determined by 
the investigator. 
 
6.4.8 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, pruritis, arthralgias, 
hypo- or hypertension, bronchospasm, or other symptoms. All Grade 3 or 4 infusion reactions 
should be reported within 24 hours to the study PI and reported as an SAE if criteria are met. 
Infusion reactions should be graded according to National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI CTCAE (version 4.0)) guidelines. Treatment recommendations 
are provided below and may be modified based on local treatment standards and guidelines as 
appropriate:  
 
Table 15: Management of Infusion reaction 
Grade  
Management  
≤ 1 
Continue nivolumab infusion, remain at bedside. Continue 
cabozantinib. 
 
Institute prophylactic medications with subsequent infusions. 
 2 
Hold nivolumab until resolution to ≤ Grade 1. 
 Refer to management and rechallenging instructions below. 
Continue cabozantinib. 
 3 
Discontinue nivolumab. Continue cabozantinib. 
 4 
Discontinue nivolumab. Continue cabozantinib. 
 
 
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 paracetamol 325 to 1000 mg (acetaminophen) at least 30 minutes before additional 
nivolumab administrations.  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
67 
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).  
 
Stop the nivolumab infusion, begin an IV infusion of normal saline, and treat the subject with 
diphenhydramine 50 mg IV (or equivalent) and/or paracetamol 325 to 1000 mg (acetaminophen); 
remain at bedside and monitor subject until resolution of symptoms. Corticosteroid or 
bronchodilator therapy may also be administered as appropriate. Restart the infusion at 50% of the 
original infusion rate when symptoms resolve to Grade ≤ 1; if no further complications ensue after 
30 minutes, the rate may be increased to 100% of the original infusion rate. Monitor participant 
closely. If symptoms recur then no further nivolumab will be administered at that visit. Administer 
diphenhydramine 50 mg IV, and remain at bedside and monitor the participant until resolution of 
symptoms. The amount of study drug infused must be recorded on the electronic case report form 
(eCRF). The following prophylactic premedications are recommended for future infusions: 
diphenhydramine 50 mg (or equivalent) and/or paracetamol 325 to 1000 mg (acetaminophen) 
should be administered at least 30 minutes before additional nivolumab administration. If 
necessary, corticosteroids (recommended dose: up to 25 mg of IV hydrocortisone or equivalent) 
may be used.  
 
For Grade 3 or Grade 4 symptoms:  
 
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, treat with 
bronchodilators, epinephrine 0.2 to 1 mg of a 1:1,000 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. 
Participant should be monitored until the investigator is comfortable that the symptoms will not 
recur.  
 
Investigators should follow their institutional guidelines for the treatment of anaphylaxis. Remain 
at bedside and monitor subject until recovery from symptoms. In the case of late-occurring 
hypersensitivity symptoms (e.g., appearance of a localized or generalized pruritis within 1 week 
after treatment), symptomatic treatment may be given (e.g., oral antihistamine, or corticosteroids) 
 
6.4.9 Fever  
Patients with fever should be evaluated as clinically appropriate.  Patients may experience 
isolated fever during infusion reactions or up to several days after infusion.  Evaluation over the 
course of 1-2 weeks should be done for other autoimmune events that may present as fever. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
68 
Grade 
Management 
≤ 1 
Continue nivolumab and cabozantinib and monitor. 
2 
Hold nivolumab and cabozantinib until ≤ Grade 1   
3 
Hold nivolumab  and cabozantinib until ≤ Grade 1 
4 
Hold nivolumab  and cabozantinib until ≤ Grade 1 
 
6.4.10 All other non-laboratory adverse events 
 
Table 16: General Guidance for All other non-laboratory adverse events  
Grade 
Management/Next Dose for Nivolumab  
≤ 1 
Continue protocol therapy.  
2 
Hold nivolumab until ≤ Grade 1 OR baseline (exceptions as noted below) 
3 
Omit dose of nivolumab if not recurrent (exceptions as noted below)  
4 
Discontinue nivolumab therapy 
Recommended management:  Low-grade events that are considered drug related and any high-
grade events of unclear etiology should be fully evaluated and treated with systemic 
corticosteroids if an alternative etiology is not identified. 
 
7. ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS  
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial.  The following 
list of reported and/or potential AEs (Section 7.1) and the characteristics of an observed AE 
(Section 7.2) will determine whether the event requires expedited reporting in addition to routine 
reporting. 
 
7.1 
Adverse Events Lists 
 
7.1.1 Expected adverse event for nivolumab 
The PD-L1/PD-1 pathway is involved in peripheral tolerance; therefore, such therapy may 
increase the risk of immune-related AEs, specifically the induction or enhancement of autoimmune 
conditions.  AEs with potentially immune-related causes, including rash, hypothyroidism, 
hepatitis/transaminitis, colitis, myositis, and myasthenia gravis, have been observed. 
 
7.1.2 Expected adverse event for cabozantinib 
The general adverse event profile of cabozantinib includes GI symptoms (such as nausea, 
vomiting, and diarrhea), fatigue, anorexia, palmar-plantar erythrodysesthesia (PPE) syndrome, 
skin rash, elevated ALT and AST, increased pancreatic enzymes with rare cases of  pancreatitis, 
as well as side effects associated with inhibition of VEGF signaling such as thrombotic events 
(eg, pulmonary embolism [PE] and deep vein thrombosis [DVT]), hypertension, proteinuria, 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
69 
hemorrhagic events, and rare cases of gastrointestinal [GI] perforation and rectal/perirectal 
abscess. Additionally, events of arterial thromboembolism (transient ischemic attack [TIA], 
myocardial infarction [MI]) have been reported.  For a full listing of safety events please refer to 
the Cabozantinib Investigational Brochure. 
 
 
 
7.2 
Adverse Event Characteristics 
 
• CTCAE term (AE description) and grade:  The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
4.0 will be utilized for AE reporting.  All appropriate treatment areas should have access 
to a copy of the CTCAE version 4.0.  A copy of the CTCAE version 4.0 can be 
downloaded from the CTEP web site 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 
 
• For expedited reporting purposes only:   
- 
AEs for the agent(s) that are listed above should be reported only if the adverse event 
varies in nature, intensity or frequency from the expected toxicity information which 
is provided. 
- 
Other AEs for the protocol that do not require expedited reporting are outlined in the 
next section (Expedited Adverse Event Reporting) under the sub-heading of Protocol-
Specific Expedited Adverse Event Reporting Exclusions. 
 
• Attribution of the AE: 
- 
Definite – The AE is clearly related to the study treatment. 
- 
Probable – The AE is likely related to the study treatment. 
- 
Possible – The AE may be related to the study treatment. 
- 
Unlikely – The AE is doubtfully related to the study treatment. 
- 
Unrelated – The AE is clearly NOT related to the study treatment. 
 
 
7.3 
Expedited Adverse Event Reporting  
 
Investigators must report to the Overall PI any serious adverse event (SAE) that occurs 
after the initial dose of study treatment, during treatment, or within 30 days of the last 
dose of treatment.   
 
Investigators must report to the Overall PI any serious adverse event (SAE) suspected to 
be related to study drug or protocol-specified procedure within 30 days of the last dose of 
treatment.   
 
 
7.3.1 Reporting to the Institutional Review Board (IRB) 
 
Investigative sites within DF/HCC will report all serious adverse events directly to the DFCI 
Office for Human Research Studies (OHRS). 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
70 
 
7.3.2 Expedited Reporting to the Food and Drug Administration 
(FDA) 
 
The Overall PI, as study sponsor, will be responsible for all communications with the FDA.  
Any event that is both serious and unexpected must be reported to the Food and Drug 
Administration (FDA) as soon as possible and no later than 7 days (for a death or life-threatening 
event) or 15 days (for all other SAEs) after the investigator’s or institution’s initial receipt of the 
information.  
SAEs should be reported on MedWatch Form 3500A, which can be accessed at: 
http://www.accessdata.fda.gov/scripts/medwatch/. 
 
MedWatch SAE forms should be sent to the FDA at: 
Phone: 1-800-FDA-1800 (1-800-332-1088) 
Fax: 1-800-FDA-0178 (1-800-332-0178) 
http://www.accessdata.fda.gov/scripts/medwatch/ 
 
7.3.3 Expedited Reporting to Hospital Risk Management 
 
Participating investigators will report to their local Risk Management office any participant safety 
reports or sentinel events that require reporting according to institutional policy.  
 
 
7.3.4 Expedited Reporting to BMS  
 
SAEs, whether related or not related to study drug, and pregnancies must be reported to BMS 
within 24 buiness hours of the awareness of the event. SAEs must be recorded on a Medwatch 
Form 3500A. 
SAE Email Address:  Worldwide.Safety@BMS.com 
SAE Facsimile Number:  609-818-3804 
 
If only limited information is initially available, a follow-up report is required and 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 of awareness to BMS 
(or designee) using the same procedure used for transmitting the initial SAE report.  
All SAEs should be followed to resolution or stabilization. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
71 
7.3.5 Expedited Reporting to Exelexis 
 
As soon as an investigator becomes aware of an AE that meets the definition of ‘serious,’ this 
must be documented on an SAE Report Form or in an electronic database and include the 
following: (i) all SAEs that occur after starting cabozantinib and through 30 days after the 
decision to discontinue study treatment and (ii) any SAEs assessed as related to study treatment 
or study procedures, from the time of informed consent, even if the SAE occurs more than 30 
days after the decision to discontinue study treatment. 
 
All SAEs that are assessed by the PI as related to drug or study procedure and all 
pregnancy/lactation reports regardless of outcome must be sent to Exelixis within one (1) 
business day of the PI’s knowledge of the event. The reports, on a MedWatch 3500A Form, must 
be sent to drugsafety@exelixis.com or fax 650-837-7392. 
 
• The PI will perform adequate due diligence with regard to obtaining follow-up 
information on incomplete reports. All follow-up information must be sent to Exelixis 
within one (1) business day of the PI’s receipt of the new information. Upon Exelixis 
request, the PI will query for follow-up information. 
 
 
7.4 
Routine Adverse Event Reporting 
 
All Grade 2 or higher Adverse Events (excluding non-clinically significant laboratory values) 
must be reported in routine study data submissions to the Overall PI on the toxicity case report 
forms.  AEs reported through expedited processes (e.g., reported to the IRB, FDA, etc.) must 
also be reported in routine study data submissions. 
 
 
8. PHARMACEUTICAL INFORMATION 
 
A list of the adverse events and potential risks associated with the investigational agents 
administered in this study can be found in Section 7.1. 
 
8.1 
Nivolumab 
 
8.1.1 Description 
 
Nivolumab is also referred to as BMS-936558-01 or BMS-936558. Nivolumab is a soluble 
protein consisting of 4 polypeptide chains, which include 2 identical heavy chains and 2 identical 
light chains. The physical and chemical properties of nivolumab are provided in Table 8.1.1 
below. 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. 
 
Table 8.1.1: Nivolumab Physical and Chemical Properties 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
72 
 
 
8.1.2 Storage and Stability 
 
Vials of Nivolumab injection must be stored at 2°-8°C (36°-46°F) and protected from light, 
freezing and shaking. Shelf-life surveillance of the intact vials is ongoing. 
 
The administration of undiluted and diluted solutions of Nivolumab must be completed within 24 
hours of preparation. If not used immediately, the infusion solution may be stored up to 24 hours 
in a refrigerator at 2°-8°C (36°-46°F) and a maximum of 4 hours of the total 24 hours can be at 
room temperature (20°-25°C, 68°-77°F) and room light. The maximum 4-hour period under room 
temperature and room light conditions includes the product administration period. 
 
CAUTION: The single-use dosage form contains no antibacterial preservative or bacteriostatic 
agent. Therefore, it is advised that the product be discarded 8 hours after initial entry. 
 
8.1.3 Compatibility 
 
No incompatibilities between Nivolumab injection and polyvinyl chloride (PVC), non-
PVC/non-DEHP (di(2-ethylhexyl)phthalate) IV components, or glass bottles have been observed.  
 
8.1.4 Handling 
 
Qualified personnel, familiar with procedures that minimize undue exposure to themselves 
and the environment, should undertake the preparation, handling, and safe disposal of the 
chemotherapeutic agent in a self-contained and protective environment.  
 
8.1.5 Availability 
 
Nivolumab is available as 100 mg vials (10 mg/mL) with a 0.7mL overfill. It is supplied 
in 10 mL type I flint glass vials, with butyl rubber stoppers and aluminum seals. 
 
8.1.6 Preparation 
 
Nivolumab is available as 100 mg vials (10 mg/mL), which include an overfill. It is 
supplied in 10 mL type I flint glass vials, with butyl stoppers and aluminum seals. Nivolumab 
injection can be infused undiluted (10 mg/mL) or diluted with 0.9% Sodium Chloride Injection, 
USP or 5% Dextrose, USP to concentrations no less than 0.35 mg/mL. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
73 
8.1.7 Administration 
 
Nivolumab will be delivered in infusion bags with IV infusion lines over 30 minutes (+/- 
10 minutes) using a volumetric pump with 0.2 to 1.2 micron pore size, low-protein binding 
polyethersulfone membrane in-line filter.  
 
8.1.8 Ordering 
 
Nivolumab will be provided by BMS. 
 
8.1.9 Accountability 
 
The investigator, or a responsible party designated by the investigator, should maintain a 
careful record of the inventory and disposition of the agent using the NCI Drug Accountability 
Record Form (DARF) or another comparable drug accountability form.  (See the NCI 
Investigator’s Handbook for Procedures for Drug Accountability and Storage.) 
 
8.1.10 Destruction and Return 
 
At the end of the study, unused supplies of nivolumab should be destroyed according to 
institutional policies. Destruction will be documented in the Drug Accountability Record Form. 
 
8.2 
Cabozantinib 
 
8.2.1 Description 
Cabozantinib is the (S)-malate salt of cabozantinib, a kinase inhibitor. Cabozantinib (S)-malate 
is described chemically as N-(4-(6,7-dimethoxyquinolin-4-yloxy)phenyl)-N’-(4- 
fluorophenyl)cyclopropane-1,1-dicarboxamide, (2S)-hydroxybutanedioate. The molecular 
formula is C28H24FN3O5·C4H6O5 and the molecular weight is 635.6 Daltons as malate salt. The 
chemical structure of cabozantinib (S)-malate salt is: 
 
 
 
In vitro biochemical and/or cellular assays have shown that cabozantinib inhibits the tyrosine 
kinase activity of MET, VEGFR-1, -2 and -3, AXL, RET, ROS1, TYRO3, MER, KIT, TRKB, 
FLT-3, and TIE-2. These receptor tyrosine kinases are involved in both normal cellular function 
and pathologic processes such as oncogenesis, metastasis, tumor angiogenesis, drug resistance, 
and maintenance of the tumor microenvironment. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
74 
 
8.2.2 Form 
 
Cabozantinib/XL184  Tablets  
 
The Sponsor will provide each investigator with adequate supplies of cabozantinib, which will be 
supplied as 20-mg yellow film-coated tablets. The 20-mg tablets are round. The components of 
the tablets are listed in Table 10. 
Table 10: 
Cabozantinib Tablet Components and Composition 
Ingredient  
Function 
% w/w 
Cabozantinib Drug Substance (25% drug load as free base) Active Ingredient 
31.7 
Microcrystalline Cellulose (Avicel PH-102) 
Filler 
38.9 
Lactose Anhydrous (60M) 
Filler 
19.4 
Hydroxypropyl Cellulose (EXF) 
Binder 
3.0 
Croscarmellose Sodium (Ac-Di-Sol) 
Disenegrant 
6.0 
Colloidal Silicon Dioxide, 
Glidant 
0.3 
Magnesium Stearate 
Lubricant 
0.75 
Opadry Yellow Film Coating which includes: 
- 
HPMC 2910 / Hypromellose 6 cp  
- 
Titanium dioxide  
- 
Triacetin  
- 
Iron Oxide Yellow 
Film Coating 
4.00 
 
8.2.3 Storage and Stability 
 
Store cabozantinib at 20°C to 25°C (68°F to 77°F); excursions are permitted from 15°C to 30°C 
(59°F to 86°F) [see USP Controlled Room Temperature]. 
 
8.2.4 Compatibility 
 
Not applicable 
 
8.2.5 Availability 
 
Cabozantinib is an investigational agent and will be supplied free-of-charge from Exelixis. 
 
8.2.6 Preparation 
 
Not applicable 
  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
75 
8.2.7 Administration 
 
Cabozantinib is administered once daily as an oral tablet.  Participants will be provided with a 
sufficient supply of study treatment and instructions for taking the study treatment on days without 
scheduled clinic visits. After fasting (with exception of water) for 2 hours, participants will take 
study treatment daily each morning with a full glass of water (minimum of 8 oz/ 240 mL) and 
continue to fast for 1 hour after each dose of study treatment. If doses are withheld, the original 
schedule of assessments should be maintained when cabozantinib is restarted. The participant 
should be instructed to not make up the missed doses and to maintain the planned dosing schedule. 
Participants must be instructed to not make up missed doses that are vomited. 
 
8.2.8 Ordering 
 
Cabozantinib will be provided by Exelixis. 
 
8.2.9 Accountability 
 
The investigator, or a responsible party designated by the investigator, must maintain a 
careful record of the inventory and disposition of cabozantinib using the NCI Drug Accountability 
Record or another comparable drug accountability form.  
 
8.2.10 Destruction and Return 
 
At the end of the study, unused supplies of cabozantinib should be destroyed according to 
institutional policies. Destruction will be documented in the Drug Accountability Record Form. 
 
9. BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES 
 
 
In all patients in whom a tumor safely accessible, a baseline tumor biopsy is required. We plan to 
use baseline biopsy tissue to perform a number of immune profiling assays, detailed below.  On 
baseline tumor biopsies, we will perform characterization based on histology (TILs), protein 
expression, and mRNA expression.  Additionally, we will bank specimens for possible future DNA 
analysis, and other further testing. 
 
Serial blood draws for correlative science are required on this trial; blood draws will be obtained 
every 4 weeks prior to the infusion of study drugs, at the end-of-treatment visit in patients who go 
off study for progressive disease, and all efforts will be made to obtain an additional blood draw 
at the time of progressive disease, in patients who went off study for anything other than 
progressive disease.  On each blood draw, we will perform flow cytometry to characterize protein 
expression of immune mediators, detailed below, and additional blood will be banked for future 
testing. 
 
All patients will additionally be asked to provide a stool sample at three separate timepoints: 
prior to treatment, during treatment, and at the time of disease progression. A fourth collection 
may be requested from patients who experience grade ≥ 2 diarrhea after discussion with the PI. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
76 
This collection is not required, but is strongly encouraged. These samples will be analyzed for 
microbiota content. Please refer to the separate collection information sheet for additional 
correlative details including collection, processing, and shipping instructions. 
 
Please note that some of the downstream correlative plans for blood and tissue include whole 
exome and single cell sequencing, plus analysis of the data generated, that will be performed by 
the Broad Institute of MIT. The individuals at the Broad Institute will be providing these services 
as fee-for-service and research only purposes. The Broad Institue will provide barcode labels for 
all samples that are generated at random by their laboratory software. All samples will be sent in 
a completely de-identified fashion and staff involved at the Broad Institute will not have any 
access to patient health information (PHI).  
 
 
Summary of Specimens 
 
Research Sampling 
Timepoint 
Contents 
Destination 
Archival Tissue 
Anytime on study 
1 FFPE Block or 10-
20 5 micron 
unstained slides 
Current DFCI CRC 
Fresh Tissue 
Baseline 
5-7 cores 
1 DMEM Core – 
JF406 / Mariano 
Severgnini 
 
Prior to C3D1  
5-7 cores 
RNAlater Cores – 
Breast Bank 
 
Formalin Cores – 
Current DFCI CRC 
1-2 DMEM Cores – 
DA520 / Wu Lab 
Blood 
Baseline, Restaging 
Visits, Time of 
Progression  
1 – 10mL Streck 
Tube (cfDNA) 
 
Breast Bank 
5 – 10mL green tops 
(PBMCs)* 
 
JF406 / Mariano 
Severignini 
1 – 10mL EDTA 
purple tops (Plasma 
Biomarker) 
MGH Steele Lab / 
Dan Duda 
C2D1 
1 – 10mL EDTA 
purple tops (Plasma 
Biomarker) 
MGH Steele Lab / 
Dan Duda 
 
5 – 10mL green tops 
(PBMCs)* 
JF406 / Mariano 
Severignini 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
77 
Every Cycle, Day 1 
1 – 10mL EDTA 
purple tops (Plasma 
Biomarker) 
MGH Steele Lab / 
Dan Duda 
Stool 
Baseline 
Home Collection Kit 
(DNA Genotek) 
BWH/Harvard 
Cohorts 
Biorepository 
Prior to C3D1  
End of treatment 
Optional collection at 
the time of grade ≥ 2 
diarrhea 
* Green tops may be substituted with 10mL purple EDTA tubes or 10mL CPT tubes as availability 
allows  
 
 
9.1 
Archival Tissue 
 
1 block or 10-20 5 micron unstained, charged slides will be collected for future research. 
  
9.2 
Fresh Tissue Biopsy  
 
9.2.1 Objectives:  
 
• Characterizing immune markers in metastatic TNBC. 
• To evaluate MET and phospho MET expression in tumor tissue at baseline by 
immunohistochemistry 
 
9.2.2 Collection 
 
Biopsies are required at screening and C3D1 (Any time from C2D14-C2D28 is allowed). 
 
Biopsies should not be performed on Friday afternoons, as there may not be time for processing 
of the fresh tissue.  If a biopsy must be performed on Friday morning, the lab of Mariano 
Severgnini must be notified ahead of time to ensure that there will be adequate time for processing 
fresh tissue, since fresh tissue cannot be stored over the weekend.  The specimens in RNALater 
and formalin may be stored over the weekend and shipped on Monday. Specimens in RNA Later 
and formalin should be stored at room temperature until shipment.  
 
Ideally five core biopsies will be obtained: 
• One core should be placed in 10% neutral buffered formalin tube supplied by the study. 
• One core should be placed in RNAlater 
• Two core should be placed in sterile DMEM 
 
The order of specimen collection should be: 
• First core: 10% neutral buffered formalin 
• Second core: Sterile DMEM 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
78 
• Third core: RNAlater 
• Fourth core: Sterile DMEM 
• Fifth core: Sterile DMEM  
 
If additional cores are obtained, they should be processed as follows: 
• Sixth core: RNAlater 
• Seventh core: 10% neutral buffered formalin 
 
Guidelines for biopsy from various metastatic sites can be found in Appendix B. 
 
9.2.3 Handling and Shipping  
 
After being obtained, processing of the cores is as follows: 
• All samples should be de-identified and labeled with the Participant initials, Participant 
Study ID number and date of procedure. 
• Core #5 in sterile DMEM should be brought as fresh tissue immediately to the lab of 
Mariano Severgnini at:  
Center for Immuno-Oncology 
Dana-Farber Cancer Institute 
1 Jimmy Fund Way, JF0406 
Boston, MA 02215 
Phone: (617) 632-2421 
Pager: 42093 
 
Cores must arrive to the lab to be processed for TILs (as described below) within 1.5 hours 
of its collection, though an additional 2 hour window is allowed  In addition, a small piece 
of onecore will be immediately frozen in liquid nitrogen upon arrival to Mariano 
Severgnini, for later use for RNA sequencing. Please notify the lab of expected specimen 
collection approximately one week in advance of specimen drop-off (contacts: Tara Patel, 
tara_patel@dfci.harvard.edu; or Amy Cunningham, amy_cunningham@dfci.harvard.edu; 
or Martha Holland, marthak_holland@dfci.harvard.edu). 
 
• Cores in formalin should be brought to the Brigham and Women’s SHL lab (with 
appropriate work order submitted and printed) on the 6th floor of the Thorn building, where 
a block will be made.  An email will be sent to the CRC within 2-3 days to confirm that 
the block has been made.  The block should then be picked up from the SHL lab and 
brought to Dr. Scott Rodig on the 6th floor of the Thorn building. 
 
• Cores in RNAlater should be brought to the DF/HCC Clinical Trial Core Laboratory 
(Deborah Dillon, MD) on Smith 9.  Please email the DF/HCC  Clinical Trials Core 
Laboratory (dfcibreastbank@partners.org) with patient name, study ID, date of collection, 
approximate time of collection, and study time point the day prior to collection.  
 
• Core #2 and Core #4 in Sterile DMEM should be brought immediately to the 
Translational Immunogenomis Laboratory (TIGL) located on Dana 520. As soon as the 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
79 
biopsy procedure is scheduled, please notify Derin Keskin 
derin_keskin@dfci.harvard.edu of the date and time. Sterile DMEM in conical tubes will 
be provided by the TIGL can can be picked up from Dana 520. 
 
 
Tissue remaining after specific protocol testing described below will be banked in the Clinical 
Trial Core Laboratory (Deborah Dillon, MD) and may be used for additional or future analyses as 
needed. 
 
 
9.2.4 Potential Testing 
Assay 1: Tumor infiltrating lymphocyte (TIL) percentage and determination of lymphocyte 
predominant breast cancer (LPBC) 
 
Paraffinized, hematoxylin and eosin-stained slides taken from two tissue planes 
will be derived from each biopsy and will be reviewed by certified pathologists.  In 
the research setting, all cases are reviewed by two pathologists and any discordant 
results resolved by consensus review.  The extent of lymphocytic infiltrate in tumor 
tissue will be assessed, and stromal TIL percentage will be determined.  More 
detailed guidelines for the quantification of stromal TILs in breast cancer can be 
found in the recommendations from the International TILs Working Group 
2014.[Salgado et al., 2015] 
 
After assessment of the TIL percentage, the pathologists will categorize the 
specimen as lymphocyte predominant breast cancer (LPBC), defined as a tumor 
that contains >60% stromal lymphocytes, or non-LPBC. 
 
Assay 2: Immunohistochemistry 
 
Tissue will be collected and fixed by 10% neutral buffered formalin overnight, 
dehydrated, and paraffin embedded.  Four micrometer-thick sections will be cut.  
The paraffin blocks and unstained slides will be stored at room temperature.  All 
immunohistochemical staining will be performed in the Center for Immuno-
Oncology Pathology Core at Dana-Farber/Harvard Cancer Center (DF/HCC) 
Specialized Histopathology Core. 
 
Formalin fixed-paraffin embedded (FFPE) tumor slides will be prepared and H&E 
stained for assessment of TIL in pre- and post-treatment tumor samples.  To identify 
subsets of different immune populations (effector/memory CD8 cells, T regulatory 
cells, dendritic cells, tumor associated macrophages, and Tie-2 expressing 
monocytes (TEM)), immunohistochemical (IHC) staining will be performed on 
FFPE tumor slices using some or all of the following antibodies: 
Core set: CD8, PD-1, PD-L1, PD-L2 
Others: CD3, CD4, CD25, FoxP3, Indoleamine 2,3 deoxygenase-1 (IDO1), CD11c, 
CD83, CD86, CD56, CD14, CD16, Tie2 (See also Appendix B) 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
80 
Investigators at our institution have developed IHC staining on paraffin embedded 
tissues for PD-L1, PD-L2, TIM-3, and LAG-3 through our center for Immuno-
Oncology Pathology Core (Scott Rodig MD, PhD Core Director, is a co-
investigator on this protocol).  PD-L1 IHC has recently been established in a CLIA 
approved laboratory and the remaining assays for CLIA laboratory conduct are 
being finalized. 
 
These investigators have published the methods, protocols, and data establishing 
the sensitivity and specificity of IHC staining assays using the monoclonal 
antibodies recognizing PD-L1 (CD274, B7-H1, antibody clone 7G11, generated in 
the lab of Gordon Freeman, DFCI) and PD-L2 (CD273, B7-DC, clone 9E5, 
generated in the laboratory of Gordon Freeman, DFCI in two recent 
manuscripts.[Chen et al., 2013, Shi et al., 2014] 
 
 
Below is a schematic of the workflow for the tissue-based biomarker analysis. 
 
 
 
Tumor will be considered positive if >5% (PD-L1)[Topalian et al., 2012] or >10% 
(PD-L2) of the tumor cell population demonstrates unequivocal staining.  PD-1 
positivity will be defined as >3% positive cells/high power field.[Bachireddy et al., 
2014]  All IHC stained slides will be evaluated and scored by a pathologist.  A 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
81 
subset of slides will be reviewed by a second pathologist to ensure concordance of 
interpretation. 
 
The semi-quantitative scoring for this study is in accordance with those published 
previously and, as described above, will include scores for both the neoplastic and 
non-neoplastic cells within the tumor microenvironment.  Data derived from 
pathologist visual scoring (semi-quantitative, but with increased specificity for 
delineating neoplastic and non-neoplastic cells) and pathologist-assisted, 
automated scoring (quantitative, but without accurately delineating neoplastic and 
non-neoplastic cells) for each marker of interest will be assessed for its clinical 
value.  As necessary, the data from combinations of markers will also be considered 
(i.e. combined scores from PD-L1 and PD-L2 expression).  All data will be 
analyzed in conjunction with the biostatistics group. 
 
 
 
 
Assay 3: Flow cytometry 
 
TILs will be isolated from the biopsy specimen as described in the lab manual 
 
Surface staining followed by flow cytometry on the resultant TILs will then be 
performed as described in the lab manual.  The following antibodies may be used 
on all specimens: (core set) 
CD8 
PD-1 
PD-L1 
PD-L2 
 
A selection of the following antibodies may also be used, and additional antibodies 
may be used as well, as deemed appropriate and informative based on the state of 
the immune profiling literature at the time of correlative science performance: 
CD4 
FOXP3 
CD127 
(Other antibodies as listed in Appendix B) 
 
Assay 4: RNA analysis 
 
RNA analysis may be performed, and tissue for RNA analysis will be stored, in the 
Clinical Trials Core Laboratory (Deborah Dillon, MD). 
 
Messenger RNA (mRNA) expression within tumor biopsy specimens may be 
assessed using the most current and informative methodologies at the time that 
correlative science is performed on all specimens.  NanoString signatures and 
comprehensive RNA sequencing may be used.  Potential genes of interest, based 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
82 
on prior immune profiling of breast tumors,[Denkert et al., 2015] include CXCL9, 
CCL5, CD8ACD80, CXCL13, IGKC, CD21, IDO1, PD-1, PD-L1, PD-L2, 
CTLA4, and FOXP3. 
 
Assay 5: Evaluate c-Met and phospho-c-Met expression in tumor tissue  
 
Tumor tissue sections will be deparaffinized prior to antigen retrieval, blocking, 
and incubation with primary antibodies.  Patients will be dichotomized as to 
whether or not their tumor expresses c-Met and the association between 
expression and response to therapy will be evaluated 
 
Assay 6: Single cell sequencing 
 
 
1. TNBC tumor biopsies in DMEM media will be delivered to Dr. Derin Keskin 
(Immunology Lead, TIGL*), Wandi Zhang (Research Technician), or Phuong Le 
(Research Technician) at the Tissue Immunogenomics Lab, TIGL (Dana 520). 
2. The tumor will be processed using collagenase, hyalurinidase and DNase to generate 
single cell suspension. 
3. These cells will be stained with CD45 antibody. CD45 positive vs negative single cells 
will be sorted into 96 wells plates at the Hematology/Oncology flow cytometry core 
facility (Mayer 584).  
4. Single cell sorted plates will be transferred to Dr. Kenneth Livak (Technology Lead, 
TIGL) and Dr. Shuqiang Li (Senior Scientist) at the Genomics Lab, TIGL (Smith 1048, 
Dana Farber), who will generate single cell RNA-seq libraries. For single-cell TCR 
analysis, the RNA-seq libraries will be sequenced in the TIGL Genomics Lab using next-
generation sequencing (NGS). For single-cell transcriptome analysis, Dr. Li will drop off 
the RNA-seq libraries at the Broad Institute walk-up sequencing station (6th floor, 415 
Main St, Cambridge) for sequencing using NGS. 
 
*Dr. Catherine Wu is the faculty mentor of TIGL (Translational Immunogenomics Laboratory), 
which was established in 2017.  
 
 
9.2.5 Sites Performing Correlatives 
 
BWH 
DFCI CIO  
DFCI Clinical Trials Core Lab 
Translation Immunogenomics Laboratory (TIGL) 
The Broad Institute of MIT 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
83 
9.3 
Blood Collection 
 
Research blood collection is mandatory for all patients for flow cytometry and potential DNA 
isolation.  The samples will be banked in the DFCI breast tissue repository for these and future 
research purposes. These specimens will become the property of the DF/HCC.  
 
Please note that if green top tubes are unavailable, they may be substituted with either purple top 
tubes or CPT tubes. 
 
The following research blood samples are required:  
Baseline / Cycle 1 Day 1:  
• 1-10 mL Streck Tube for cfDNA 
• 5-10mL green top tubes for PBMCs 
• 1-10mL purple top EDTA tube for plasma biomarkers 
 
Cycle 2 Day 1: 
• 5-10mL green top tubes for PBMCs 
• 1-10mL purple top EDTA tube for plasma biomarkers 
 
All other cycles, Day 1:  
• 1 - 10mL purple top EDTA tube for plasma biomarkers 
 
Every Restaging Visit:  
• 1- 10mL Streck Tube for whole blood 
• 5-10mL green top tubes for PBMCs 
• 1-10mL purple top EDTA tube for plasma biomarkers 
 
Off Treatment (if for progressive disease): 
• 1-10 mL Streck Tube for whole blood 
• 5- 10mL green top tubes for whole blood 
• 1-10mL purple top EDTA tube for plasma biomarkers 
 
The following Time of Progression research blood samples are optional for patients who came off 
treatment for a reason other than progressive disease: 
• 1-10 mL Streck Tube for whole blood 
• 5-10mL green top tubes for whole blood 
• 1-10mL purple top EDTA tube for plasma biomarkers 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
84 
9.3.1.1 
Handling and Shipping  
 
All samples should be de-identified and labeled with the Participant initials, Participant Study ID 
number and date of collection and time point (e.g., “Baseline” or “Cycle 1” or “Progressive 
Disease”).  
 
• PBMCs (Green/Purple/CPT): 
 
Blood draws should not be performed on Friday afternoons, as there may not be time for 
processing of the blood.  If a blood draw must be performed on Friday morning, the lab 
of Mariano Severgnini must be notified ahead of time to ensure that there will be 
adequate time for processing the blood, since it cannot be stored over the weekend. 
 
Must be processed within 3-4 hours of  being drawn.  Will be hand carried at ambient 
temperature to Mariano Severgnini.  Please contact the lab approximately one week in 
advance to notify of upcoming specimen drop off (contacts: Tara Patel, 
tara_patel@dfci.harvard.edu; or Amy Cunningham, 
Amy_Cunningham@dfci.harvard.edu; or Martha Holland, 
marthak_holland@dfci.harvard.edu).  Please deliver to: 
 
Center for Immuno-Oncology 
Dana-Farber Cancer Institute 
1 Jimmy Fund Way, JF0406 
Boston, MA 02215 
Phone: (617) 632-2421 
Pager: 42093 
 
• cfDNA (Streck tube): 
 
Fill the Streck tube completely and immediately mix by gentle inversion 8 to 10 times. 
Inadequate or delayed mixing may result in accurate results. 
 
Tube precautions: 
- 
DO NOT FREEZE OR REFRIGERATE TUBES as this could result in cfDNA 
breakage. Blood collected in the Streck tube can be stored for 14 days between 
6-37 degrees Celsius. 
- 
Do not use tubes after expiration date. 
- 
Fill the tube completely; overfilling or underfilling of tubes will result in an 
incorrect blood-to-additive ratio and may lead to incorrect analytical results. 
 
Blood in Streck tubes should be brought to the Clinical Trial Core Laboratory (Deborah 
Dillon, MD) on Smith 9 for processing. 
 
In small batches or at the end of the trial, samples will be shipped to the Broad Institute 
under the care of Nikhil Wagle, MD for genomic sequencing.  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
85 
• Plasma biomarkers (10mL purple tube): 
 
This tube should be shipped the same day, on wet ice, ideally within 2 hours of 
collection to:  
 
Dr. Dan G. Duda 
Steele Laboratories for Tumor Biology 
Attn: Mrs. Anna Khachatryan / Mrs. Julia Kahn 
MGH, Cox-734 
100 Blossom St. 
Boston, MA 02114, USA 
Phone: (617) 726-4088 or (617) 726-8143 or (617) 724-1353 
Fax: (617) 724-5841 
Pager: 14082 
Email: annak@steele.mgh.harvard.edu, julia@steele.mgh.harvard.edu 
  
Please email Anna Khachatryan and Julia Kahn ahead of the shipment so the lab can 
expect it. Samples may be couriered via Skycom.  
 
 
9.3.1.2 
Potential Testing 
 
Assay 1: Flow cytometry 
 
PBMCs will be generated as described in the lab manual, and used to assess immune cell 
populations. 
 
Surface staining with a panel of antibodies and flow cytometry on PBMCs will then be 
performed as described in Appendices.  The following antibodies will be used on all 
specimens: (core set) CD8, PD-1, PD-L1, PD-L2,  
A selection of the following antibodies may also be used, and additional antibodies may be 
used as well, as deemed appropriate and informative based on the state of the immune 
profiling literature at the time of correlative science performance: CD4, FOXP3, CD127. 
 
Assay 2: Evaluate potential plasma biomarkers of cabozantinib  
 
Exploratory analyses of potential biomarkers of cabozantinib activity will be performed 
by measuring proteins in the plasma and circulating cells at baseline, and on days 1 of 
each cycle of therapy, and, if available, at the time of progression. 8cc of blood will be 
collected in purple top (plasma EDTA) vacutainers, with a minimum of 5cc required. 
Each sample will be shipped on wet ice to the CLIA certified clinical correlative studies 
core of the Steele Laboratories. Blood will be separated by centrifugation into plasma and 
a cellular phase by standard methods. The plasma will be prepared in standard fashion 
and stored at –78 degrees Celsius until analysis. Plasma analysis will be carried out for a 
panel of circulating angiogenic and inflammatory molecules previously identified as 
potential biomarkers of response to anti-VEGF therapy in TNBC patients. They include 
VEGF, placental-derived growth factor (PlGF), VEGF-C, VEGF-D, sVEGFR1, basic 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
86 
fibroblast growth factor (bFGF), and sTie-2 (using a 7-plex Growth Factor array) and 
granulocyte-macrophage colony stimulating factor (GM-CSF), interferon gamma (IFN-
γ), tumor necrosis factor alpha (TNF-α), and interleukin (IL)-1β, IL-2, IL-6, IL-8, IL-10, 
and IL-12 heterodimer p70 (using a 9-plex Inflammatory Factor array; both Meso-Scale 
Discovery, Gaithersburg, MD), and stromal-derived factor 1alpha (SDF1α) using ELISA 
from R&D Systems (Minneapolis, MN). In addition, we will measure the plasma 
concentration of biomarkers that are related to cabozantinib activity: HGF, s-MET, s-c-
KIT and sVEGFR2 using ELISA from R&D Systems (Minneapolis, MN). Finally, we 
will evaluate biomarkers of tumor hypoxia, by measuring plasma carbonic anhydrase IX 
(CAIX) levels as well as biomarkers of osteoclast and osteoblast activity (plasma C-
telopeptide and total alkaline phosphatase) using ELISA from R&D Systems 
(Minneapolis, MN). The number of circulating cells will be evaluated by using cell 
counters at routine visits and by flow cytometry in fresh blood samples collected at the 
same time-points as for plasma measurements. The fraction of stem/progenitor cell, 
lymphocyte, and myeloid populations of total circulating mononuclear cells were counted 
by flow cytometry using a LSR-II cytometer and FACSDiva software in fresh blood 
samples using the following markers: CD3, CD4, CD8, CD14, CD25, CD34, CD45, 
CD56, CD127, and CD133 (Becton Dickinson), as described{Tolaney, 2016 #1433}. 
 
All biomarker analyses will be done in the CLIA-certified Core of the Steele Laboratories 
at MGH, under the supervision of Dr. Dan G. Duda.  
 
 
9.3.2 Cell-free DNA (cfDNA) analysis 
 
Blood will be collected at baseline, restaging visits and at time of progression for evaluation of 
cell-free DNA (cfDNA).  The banked samples will be used to analyze DNA, RNA and protein in 
future studies. 
 
9.3.2.1 
Collection of cfDNA specimen(s) 
 
One 10 ml of whole blood will be collected in Streck Tubes.  The blood sample will be collected 
and processed at baseline, restaging visits and time of progression for evaluation of cfDNA.  Fill 
the Streck tube completely and immediately mix by gentle inversion 8 to 10 times.  Inadequate 
or delayed mixing may result in accurate results.  The banked samples will be used to analyze 
DNA, RNA and protein in future studies. 
9.3.2.2 
Handling and shipping of cfDNA specimens 
 
One 10 ml Streck tube will be collected and processed at baseline, restaging visits and at time of 
progression for evaluation of cfDNA.  Fill the Streck tube completely and immediately mix by 
gentle inversion 8 to 10 times.  Inadequate or delayed mixing may result in accurate results.  Ship 
within 24 hours of collection at ambient temperature overnight to: 
 
Dana-Farber Cancer Institute 
Attn: Lynda Chichester 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
87 
Smith 9th Floor, Rm 948 
450 Brookline Avenue 
Boston, MA 02215 
dfcibreastbank@partners.org 
 
Email the blood bank (dfcibreastbank@partners.org) and the current Dana-Farber CRC with the 
sample information and tracking information the day before shipping specimens. 
 
Tube precautions: 
• If samples cannot be shipped within 24 hours of collection, contact DFCI.  DO NOT 
FREEZE OR REFRIDGERATE TUBES as this could result in cfDNA breakage.  Blood 
collected in the Streck tube can be stored for 14 days between 6-37 degrees Celsius.  
• Do not use tubes after expiration date. 
• Fill the tube completely; overfilling or underfilling of tubes will result in an incorrect 
blood-to-additive ratio and may lead to incorrect analytical results. 
 
Shipping Note:  Streck tube samples are sent ambient.  Frozen and ambient specimens 
obtained and shipped on the same day to the DFCI blood bank (e.g., Progression or Off 
Study Biopsy Specimens, Streck Tubes, and Circulating Tumor Cells) may be placed 
in a combination shipping box which contains separate compartments for frozen and 
ambient samples.  If a combination shipping box is not available, two shipping boxes 
should be used. 
 
At a future date, these banked cfDNA samples will be shipped in batches to The Broad Institute 
under to care of Nikhil Wagle, MD, where they will be sequenced on their Genomics Platform. 
 
 
9.3.2.3 
Sites Performing Correlatives 
 
DFCI Clinical Trials Core Lab 
The Broad Institute 
Steele Laoratories of MGH 
DFCI CIO Laboratories 
 
9.4 
Stool Collection 
 
9.4.1.1 
Handling and shipping 
 
All stool samples will be collected by each patient at home using a home-based kit with a pre-
paid mailer that provides nearly equivalent metagenomic and metatranscriptomic data to state-of-
the-art fresh-frozen sample-collection protocol.  Patients will be asked to provide samples at the 
following timepoints: 
 
• Baseline 
• After two cycles of therapy 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
88 
• At the end of treatment 
• Optional collection at the time of grade ≥ 2 diarrhea 
 
Most kits will be provided to the patients at their clinic visits. If the study team is unable to 
provide the kits to the patients in clinic, they may be mailed to patients by members of the study 
team. All kits will contain a questionnaire for patients to complete and return with their samples 
regarding timing and conditions surrounding their stool sample.  
 
Please refer to the separate stool information sheet for collection and processing instructions. 
 
Samples will be stored at the BWH/Harvard Cohorts Repository and will be shipped in batches 
by the biorepository to an external lab vendor, Microbiome Dx, who will perform the analysis of 
the samples. 
 
 
9.4.2 Analysis of DNA extraction from stool samples 
 
Microbial DNA is extracted using the Mag-Bind Universal Pathogen DNA Kit (Omega Bio-
Tek). Briefly, 250 mg of the specimen is transferred to a deep-well plate for bead beating 
followed by DNA precipitation and purification following the manufacturer’s instructions. 
Finally, DNA is eluted in 100 uls of Elution Buffer and stored at -80°C until further use. 16S 
sequencing libraries are generated by amplifying the v3-v4 hypervariable regions of the 16S 
gene in a polymerase chain reaction using primers F341and R785. Resulting amplicons are 
tagged with unique molecular barcodes that are later used to demultiplex sequencing reads into 
individual sample buckets. Libraries are loaded on a MiSeq flowcell and sequenced following 
Illumina’s loading instructions. Sequence data are retrieved from the instrument by converting 
base call format files into fastq files for data processing purposes.  
 
MicrobiomeDX uses BacPro™, a proprietary algorithm, to inspect and validate sequencing files 
by employing demultiplexing, trimming, merging, and quality filtering steps. Paired sequencing 
reads are merged using an overlap of 25 bp allowing for 10 base mismatches. Merged sequences 
are dereplicated and clustered in a de-novo fashion using VSEARCH, while filtering out 
sequence chimeras and singletons. Representative sequences from each cluster are mapped 
against the SILVA database at 99% sequence identity to obtain accurate taxonomic 
classifications and relative abundances. In parallel, feature tables are constructed to derive alpha 
diversity indices, and distance matrices are built to derive beta diversity indices. The BacProTM 
pipeline generates a comprehensive report that includes alpha diversity scores describing 
community richness and evenness, taxonomic composition with relative abundances, and beta 
diversity metrics to determine the in-between sample differences based on the bacterial 
communities identified.  
 
 
 
9.4.3 Shotgun sequencing and metabolic pathway reconstruction of 
stool samples 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
89 
Stool samples from patients included in the trial 2 will be subjected to whole genome shotgun 
sequencing. Libraries will be constructed with Illumina barcodes from the TruSeq DNA Sample 
Prep kit (Illumina) and reagents from KAPA Library Preparation kit (Kapa Biosystems), and 
then sequenced on an Illumina MiSeq platform using 2_250 nucleotide paired-end sequencing, 
according to the manufacturer’s instructions. Sequencing reads will be converted into relative 
abundances of microbial metabolic modules using HUMAnN35, the Human Microbiome Project 
metabolic reconstruction pipeline and mapped to the KEGG36. Relative species abundances will 
be calculated by the MetaPhlAn pipeline37. 
 
 
9.4.4 Sites performing correlative analysis 
 
BWH/Harvard Cohorts Biorepository  
Microbiome Dx 
 
9.5 
Additional analysis 
 
The above-mentioned analyses may be altered based on novel developments in the field of cancer 
immune profiling at the time of correlative science.  Additional markers or alternative technologies 
(based on scientific developments and/or novel technologies) may also be used, to explore 
potential prognostic or predictive candidate markers/panels or markers related to treatment benefit 
and/or safety, to improve diagnostic tests, or to understand breast cancer biology. 
 
10. STUDY CALENDAR 
 
Screening evaluations are to be conducted within 28 days prior to start of protocol therapy unless 
otherwise specified.  Screening assessments occurring within 3 days prior to initiating study 
treatment do not need to be repeated on Cycle 1 Day 1.   
 
As detailed in the Study Calendar, laboratory assessments including a negative pregnancy test in 
women of child-bearing potential must be documented within 7 days before the first dose of study 
medication. 
 
In the event that the participant’s condition is deteriorating, laboratory evaluations should be 
repeated within 48 hours prior to initiation of the next cycle of therapy. 
 
Assessments must be performed prior to administration of any study agent. Study assessments and 
agents should be administered within + 3 days of the protocol-specified date, unless otherwise 
noted. 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
90 
 
Screeninga 
Cycle 1 
C2  
Cycle 3 
Cycle 4 + 
End of 
Treatmentp 
Follow-Up 
Day  
 
Day 1 Day 15 
Day 1 
Day 15 
Day 22  
Day 1 
 
Day 1 
Day 22 
 
 
Informed consent 
X 
 
 
 
 
 
 
 
 
 
 
Medical Historyb 
X 
 
 
 
 
 
 
 
 
 
 
Physical examc 
X 
X 
X 
X 
X 
 
X 
 
X 
 
X 
 
Concurrent medicationsd 
X 
 
 
 
 
 
 
 
 
 
 
ECOG  
X 
X 
 
X 
 
 
X 
X 
 
X 
 
Adverse event evaluation 
 
X 
X 
X 
X 
 
X 
 
X 
 
X 
 
Vital signse 
X 
X 
X 
X 
X 
 
X 
 
X 
 
X 
 
Hematology panelf 
X 
X 
X 
X 
 
 
X 
X 
 
X 
 
Chemistry panelg 
X 
X 
X 
X 
 
 
X 
X 
 
X 
 
Urine Protein Creatinine Ratio 
X 
 
 
X 
 
 
X 
X 
 
X 
 
TSH/fT4 
X 
X 
 
X 
 
 
X 
Xh 
 
X 
 
LDHs 
X 
 
 
 
 
 
X 
 
 
 
 
Coagulation panel (PT/PTT) 
X 
 
 
 
 
 
 
 
 
 
 
Pregnancy testi 
X 
 
 
 
 
 
 
 
 
 
 
Triplicate 12- lead EKG 
X 
 
 
 
 
 
 
 
 
 
 
Tumor Assessmentj 
X 
 
 
 
 
X 
 
 
X 
Xk 
Xk 
Brain MRIl 
X 
 
 
 
 
 
 
 
 
 
 
Research Bloodm 
 
X 
 
X 
 
 
X 
X 
 
X 
X 
Research Biopsyn 
X 
 
 
 
 
 
X 
 
 
 
 
Archival Tumor Retrievalo 
X 
 
 
 
 
 
 
 
 
 
 
Research Stool Collectionq 
X 
 
 
 
 
 
X 
 
 
X 
 
Stool Questionnairer 
X 
 
 
 
 
 
X 
 
 
X 
 
Cabozantinib: 40mg PO days 1-28 of a 28 day cycle 
Nivolumab: 480mg IV on day 1 of a 28 day cycle. 
 
a. Screening assessments are to be conducted within 28 days prior to start of protocol therapy unless otherwise specified.  If these screening assessments occur within 
3 days before start of study treatment, then they may serve as the baseline Cycle 1 Day 1 values. 
b. Medical history includes clinically significant diseases, surgeries, and cancer history (including prior cancer therapies and procedures). 
c.  A complete physical examination will be performed at baseline.  A limited physical exam will be completed prior to therapy on Days 1 and 15 for Cycles 1 and 2 
and on Day 1 of every cycle beginning with Cycle 3. 
d. Selected medications of interest  taken from the time informed consent is signed through 30 days after the last dose of study therapy will be recorded.  This 
includes: name, indication, dosage, frequency, route, and dates of administration.  
e. Vital sign assessments include measurements of heart rate, systolic and diastolic blood pressures, respiratory rate, temperature and weight.  
f. Hematology includes: hemoglobin, hematocrit, platelet count, RBC count, WBC count, and percent and absolute differential count.  Results must be available 
prior to the administration of study drug. 
g. Chemistry testing includes: sodium, potassium, chloride, bicarbonate, glucose, BUN, creatinine, calcium, total bilirubin, total protein, albumin, ALT, AST, 
alkaline phosphatase, and LDH. Results must be available prior to the administration of study drug. 
h. TSH and free T4 will be performed during screening, on Day 1 of Cycles 1-4 and then every other cycle on Day 1. 
i. In female subjects of child-bearing potential as defined in the eligibility criteria, pregnancy test must be performed within 7 days before the first dose of study 
medication.   
j. Tumor assessments should consist of 1) CT and/or MRI of the chest/abdomen/pelvis, 3) any other imaging studies (CT neck, plain films, etc.) as clinically 
indicated by the treating physician. The same radiographic procedures and technique must be used throughout the study for each patient (e.g., if the patient had CT 
chest/abdomen/pelvis performed during screening, then she should subsequently undergo CT performed using the same radiologic protocol throughout the 
remainder of the study). Tumor assessments will be performed at baseline, between days 22-28 of Cycles 2, 4, and 6 and then between days 22-28 of every 3 
cycles (C9, C12, C15, etc.).  Additional scans are permitted as clinically indicated. All known sites of disease documented at screening should be re-assessed at 
each subsequent tumor evaluation.  
k. For those taken off the study for reasons other than progressive disease, tumor measurements should continue to be repeated every 6-12 weeks.  
l. Brain MRI should be done with and without contrast. If a participant is unable to have an MRI, a CT of the brain with contrast is acceptable.  If  CT with contrast 
is contraindicated, a CT without contrast is acceptable.   
m. Collected at screening, every D1, end of treatment (if removed for progressive disease) and optionally at time of progression. See section 9.0 for description of 
collections at each visit. 
n. Baseline tumor biopsy should be obtained within 28 days of initiating protocol therapy.  The C3D1 tumor biopsy should be performed as close to C3D1 as possible 
but may be collected up to 14 days prior.   
o. Archival tumor sample should be collected (block or if not possible, 10-20 5mincron, unstained positively charged slides). 
p. End of treatment visit is to occur within 30 days of final administration of study treatment.  End of treatment assessments do not have to be repeated if the same 
assessments were performed within 7 days (28 days for tumor assessments) prior to the visit. 
q. Baseline stool collection should be obtained within 28 days before starting protocol therapy. The C3D1 stool collection should be performed as close to C3D1 as 
possible, but may be collected up to 14 days prior. A sample will additionally be collection at the time of disease progression. An optional stool sample may be 
collected at the time of grade ≥ 2 diarrhea after discussion with the PI. As these collections are for exploratory correlative purposes, failure to provide a sample at 
these timepoints will not constitute a protocol violation. See section 9 and/or lab manual for stool collection and processing instructions. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
91 
r. Each stool collection kit will contain a questionnaire for the patients to complete regarding the conditions surrounding their collection. These will be a part of the 
kit and are not to be administered in clinic. Failure to complete these questionnaires at the required or optional timepoints will not constitute a protocol violation 
s. LDH to be collected with screening labs and at C3D1. 
 
 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
92 
 
11. MEASUREMENT OF EFFECT 
In this study, response and progression in the CNS and in non-CNS sites will be evaluated 
and recorded separately in this trial. For the purposes of this study, participants should be re-
evaluated for response every 6 weeks for the first 24 weeks and then every 9 weeks thereafter. 
 
11.1 
Antitumor Effect – Solid tumors  
 
Response and progression in sites of metastases will be evaluated in this study using the 
international criteria proposed by the RECIST 1.1 criteria [Eisenhauer et al., 2009].  Changes in 
the largest diameter (unidimensional measurement) of the tumor lesions and the shortest diameter 
in the case of malignant lymph nodes are used in the RECIST criteria.  
 
11.1.1 RECIST 1.1 Definitions 
 
Evaluable for Target Disease response.  Only those participants who have measurable 
disease outside the field of radiation present at baseline, have received at least one cycle of 
therapy, and have had their disease re-evaluated will be considered evaluable for target 
disease response.  These participants will have their response classified according to the 
definitions stated below.  (Note:  Participants who exhibit objective disease progression 
prior to the end of cycle 1 will also be considered evaluable.) 
 
Evaluable Non-Target Disease Response.  Participants who have lesions present at baseline 
that are evaluable but do not meet the definitions of measurable disease, have received at 
least one cycle of therapy, and have had their disease re-evaluated will be considered 
evaluable for non-target disease.  The response assessment is based on the presence, 
absence, or unequivocal progression of the lesions.  
 
11.1.2 Disease Parameters 
 
Measurable disease.  Measurable lesions are defined as those that can be accurately 
measured in at least one dimension (longest diametB er  to be recorded) as ≥ 20 mm by 
chest x-ray or ≥10 mm with CT scan, MRI, or calipers by clinical exam.  All tumor 
measurements must be recorded in millimeters (or decimal fractions of centimeters). 
 
Note: Tumor lesions that are situated in a previously irradiated area are not considered 
measurable. 
 
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. 
 
Non-measurable disease.  All other lesions (or sites of disease), including small lesions 
(longest diameter <10 mm or pathological lymph nodes with ≥10 to <15 mm short axis), 
are considered non-measurable disease.  Bone lesions, leptomeningeal disease, ascites, 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
93 
pleural/pericardial effusions, lymphangitis cutis/pulmonitis, inflammatory breast disease, 
abdominal masses (not followed by CT or MRI), and cystic lesions are all considered non-
measurable. 
 
Note: Cystic 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 participant, these are preferred for selection as target 
lesions. 
 
Target lesions.  All measurable lesions up to a maximum of 2 lesions per organ and 5 
lesions in total, representative of all involved organs, should be identified as target lesions 
and 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, but 
in addition should be those that lend themselves to reproducible repeated measurements. It 
may be the case that, on occasion, the largest lesion does not lend itself to reproducible 
measurement in which circumstance the next largest lesion which can be measured 
reproducibly should be selected. A sum of the diameters (longest for non-nodal lesions, 
short axis for nodal lesions) for all target lesions will be calculated and reported as the 
baseline sum diameters. If lymph nodes are to be included in the sum, then only the short 
axis is added into the sum. 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 any measurable lesions 
over and above the 5 target lesions should be identified as non-target lesions and should 
also be recorded at baseline. Measurements of these lesions are not required, but the 
presence, absence, or in rare cases unequivocal progression of each should be noted 
throughout follow up.  
 
11.1.3 Methods for Evaluation of Disease 
 
All measurements should be taken and recorded in metric notation using a ruler, calipers, 
or a digital measurement tool.  All baseline evaluations should be performed as closely as 
possible to the beginning of treatment and never more than 4 weeks before the beginning 
of the treatment. 
 
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 is preferred to evaluation by clinical examination unless the lesion(s) being 
followed cannot be imaged but are assessable by clinical exam.  
 
Clinical lesions. Clinical lesions will only be considered measurable when they are 
superficial (e.g., skin nodules and palpable lymph nodes) and ≥10 mm in diameter as 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
94 
assessed using calipers (e.g., skin nodules).  In the case of skin lesions, documentation by 
color photography, including a ruler to estimate the size of the lesion, is recommended.  
 
Chest x-ray.  Lesions on chest x-ray are acceptable as measurable lesions when they are 
clearly defined and surrounded by aerated lung; however, CT is preferable.  
 
Conventional CT and MRI. This guideline has defined measurability of lesions on CT scan 
based on the assumption that CT thickness is 5mm or less. If CT scans have slice thickness 
greater than 5 mm, the minimum size of a measurable lesion should be twice the slice 
thickness. MRI is also acceptable in certain situations (e.g. for body scans).   
 
Use of MRI remains a complex issue.  MRI has excellent contrast, spatial, and temporal 
resolution; however, there are many image acquisition variables involved in MRI, which 
greatly impact image quality, lesion conspicuity, and measurement.  Furthermore, the 
availability of MRI is variable globally.  As with CT, if an MRI is performed, the technical 
specifications of the scanning sequences used should be optimized for the evaluation of the 
type and site of disease.  Furthermore, as with CT, the modality used at follow-up should 
be the same as was used at baseline and the lesions should be measured/assessed on the 
same pulse sequence.  It is beyond the scope of the RECIST guidelines to prescribe specific 
MRI pulse sequence parameters for all scanners, body parts, and diseases.  Ideally, the 
same type of scanner should be used and the image acquisition protocol should be followed 
as closely as possible to prior scans.  Body scans should be performed with breath-hold 
scanning techniques, if possible. 
 
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. 
(b)  No FDG-PET at baseline and a positive FDG-PET at follow-up:  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 truly 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. 
(c)  FDG-PET may be used to upgrade a response to a CR in a manner similar to a 
biopsy in cases where a residual radiographic abnormality is thought to represent 
fibrosis or scarring.  The use of FDG-PET in this circumstance should be prospectively 
described in the protocol and supported by disease-specific medical literature for the 
indication.  However, it must be acknowledged that both approaches may lead to false 
positive CR due to limitations of FDG-PET and biopsy resolution/sensitivity. 
 
Note:  A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
95 
greater than twice that of the surrounding tissue on the attenuation corrected image. 
 
PET-CT. At present, the low dose or attenuation correction CT portion of a combined PET-
CT is not always of optimal diagnostic CT quality for use with RECIST measurements.  
However, if the site can document that the CT performed as part of a PET-CT is of identical 
diagnostic quality to a diagnostic CT (with IV and oral contrast), then the CT portion of 
the PET-CT can be used for RECIST measurements and can be used interchangeably with 
conventional CT in accurately measuring cancer lesions over time.  Note, however, that 
the PET portion of the CT introduces additional data which may bias an investigator if it 
is not routinely or serially performed.   
MIBG (meta-iodobenzylguanidine).The following is recommended, to assure high 
quality images are obtained.  
Patient preparation: Iodides, usually SSKI (saturated solution of potassium iodide), are 
administered to reduce thyroidal accumulation of free radioiodine, preferably 
beginning the day prior to injection and continuing for 3 additional days (4 days total). 
For infants and children, one drop t.i.d. is sufficient, for adolescents 2 drops t.i.d., and 
for adults 3 drops t.i.d. Participants and/or parents are asked about exposure to potential 
interfering agents. If none is noted, an indwelling intravenous line is established. The 
dose of MIBG is administered by slow intravenous injection over 90 seconds.  
Images from the head to the distal lower extremities should be obtained.  
I-123MIBG scintigraphy is performed to obtain both planar and tomographic images.  
Planar: Anterior and posterior views from the top of the head to the proximal lower 
extremities are obtained for 10 minutes at 24 hours and occasionally at 48 hours 
following injection of 10 mCi/1.7 square meters of body surface area (~150 μCi/kg, 
maximum 10 mCi). Anterior views of the distal lower extremities are adequate. A large 
field of view dual head gamma camera with low energy collimators is preferred.  
 
SPECT: Most participants receiving I-123 MIBG also undergo SPECT at 24 hours, 
using a single or multi-headed camera with a low energy collimator. The camera is 
rotated through 360 degrees, 120 projections at 25 seconds per stop. Data are 
reconstructed using filtered back projections with a Butterworth filter and a cut off 
frequency of 0.2-0.5. SPECT/CT may be performed at institutions with this capacity. 
 
Ultrasound. Ultrasound is not useful in assessment of lesion size and should not be used as 
a method of measurement. Ultrasound examinations cannot be reproduced in their entirety 
for independent review at a later data and, because they are operator dependent, it cannot 
be guaranteed that the same technique and measurements will be taken from one 
assessment to the next. If new lesions are identified by ultrasound in the course of the study, 
confirmation by CT or MRI is advised. If there is concern about radiation exposure from 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
96 
CT, MRI may be used instead of CT in selected instances.  
 
Endoscopy, Laparoscopy. The utilization of these techniques for objective tumor 
evaluation is not advised. However, such techniques may be useful to confirm complete 
pathological response when biopsies are obtained or to determine relapse in trials where 
recurrence following complete response (CR) or surgical resection is an endpoint. 
 
Tumor markers. Tumor markers alone cannot be used to assess response. If markers are 
initially above the upper normal limit, they must normalize for a participant to be 
considered in complete clinical response.  Specific guidelines for both CA-125 response 
(in recurrent ovarian cancer) and PSA response (in recurrent prostate cancer) have been 
published [JNCI 96:487-488, 2004; J Clin Oncol 17, 3461-3467, 1999; J Clin Oncol 
26:1148-1159, 2008].  In addition, the Gynecologic Cancer Intergroup has developed CA-
125 progression criteria which are to be integrated with objective tumor assessment for use 
in first-line trials in ovarian cancer [JNCI 92:1534-1535, 2000]. 
 
Cytology, Histology. These techniques can be used to differentiate between partial 
responses (PR) and complete responses (CR) in rare cases (e.g., residual lesions in tumor 
types, such as germ cell tumors, where known residual benign tumors can remain). 
 
The cytological confirmation of the neoplastic origin of any effusion that appears or 
worsens during treatment when the measurable tumor has met criteria for response or stable 
disease is mandatory to differentiate between response or stable disease (an effusion may 
be a side effect of the treatment) and progressive disease. 
 
11.1.3.1 
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 the diameters of target 
lesions, taking as reference the baseline sum diameters. 
 
Progressive Disease (PD):  At least a 20% increase in the sum of the 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 progressions). 
 
Stable Disease (SD):  Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD, taking as reference the smallest sum diameters while on 
study. 
 
11.1.3.2 
Evaluation of Non-Target Lesions 
 
Complete Response (CR):  Disappearance of all non-target lesions and normalization 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
97 
of tumor marker level.  All lymph nodes must be non-pathological in size (<10 mm 
short axis). 
 
Note:  If tumor markers are initially above the upper normal limit, they must normalize 
for a patient to be considered in complete clinical response. 
 
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):  Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions.  Unequivocal progression should not 
normally trump target lesion status.  It must be representative of overall disease status 
change, not a single lesion increase.     
 
Although a clear progression of “non-target” lesions only is exceptional, the opinion of 
the treating physician should prevail in such circumstances, and the progression status 
should be confirmed at a later time by the review panel (or Principal Investigator). 
 
11.1.3.3 
Evaluation of New Lesions 
 
The finding of a new lesion should be unequivocal (i.e. not due to difference in 
scanning technique, 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). However, a lesion identified on a follow-up scan in an anatomical 
location that was not scanned at baseline is considered new and will indicate PD. If a 
new lesion is equivocal (because of small size etc.), follow-up evaluation will clarify if 
it truly represents new disease and if PD is confirmed, progression should be declared 
using the date of the initial scan on which the lesion was discovered. 
 
11.1.3.4 
Evaluation of Best Overall Response 
 
The best overall response is the best response recorded from the start of the treatment 
until disease progression/recurrence (taking as reference for progressive disease the 
smallest measurements recorded since the treatment started).  The patient's best 
response assignment will depend on the achievement of both measurement and 
confirmation criteria. 
 
For Participants with Measurable Disease (i.e., Target Disease) 
 
Target 
Lesions 
Non-Target 
Lesions 
New 
Lesions 
Overall 
Response 
Best Overall Response when 
Confirmation is Required* 
CR 
CR 
No 
CR 
4 wks Confirmation** 
CR 
Non-CR/Non-
PD 
No 
PR 
4 wks Confirmation** 
CR 
Not evaluated 
No 
PR 
PR 
Non-CR/Non-
No 
PR 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
98 
PD/not 
evaluated 
SD 
Non-CR/Non-
PD/not 
evaluated 
No 
SD 
 
PD 
Any 
Yes or No 
PD 
no prior SD, PR or CR 
Any 
PD*** 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
∗ 
See RECIST 1.1 manuscript for further details on what is evidence of a new lesion. 
**        Only for non-randomized trials with response as primary endpoint. 
***      In exceptional circumstances, unequivocal progression in non-target lesions may be 
            accepted as disease progression. 
 
Note:  Participants 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 the 
objective progression even after discontinuation of treatment. 
 
For Participants with Non-Measurable Disease (i.e., Non-Target Disease) 
 
Non-Target Lesions 
New Lesions 
Overall Response 
CR 
No 
CR 
Non-CR/non-PD 
No 
Non-CR/non-PD* 
Not all evaluated 
No 
not evaluated 
Unequivocal PD 
Yes or No 
PD 
Any 
Yes 
PD 
∗ 
‘Non-CR/non-PD’ is preferred over ‘stable disease’ for non-target disease since SD is 
increasingly used as an endpoint for assessment of efficacy in some trials so to assign 
this category when no lesions can be measured is not advised 
 
11.1.4 Duration of Response 
 
Duration of overall response:  The duration of overall response is measured from the time 
measurement criteria are met for CR or 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 since the treatment started, or 
death due to any cause. Participants without events reported are censored at the last disease 
evaluation). 
 
Duration of overall complete response: The duration of overall CR is measured from the 
time measurement criteria are first met for CR until the first date that progressive disease 
is objectively documented, or death due to any cause. Participants without events reported 
are censored at the last disease evaluation. 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
99 
Duration of stable disease:  Stable disease is measured from the start of the treatment until 
the criteria for progression are met, taking as reference the smallest measurements recorded 
since the treatment started, including the baseline measurements.  
 
 
11.1.5 Clinical Benefit rate  
 
Clinical benefit rate: defined as CR, PR and stable disease (SD) ≥  24 weeks. 
 
 
11.2 
Antitumor Effect – Hematologic Tumors 
 
N/A 
 
11.3 
Other Response Parameters 
 
11.3.1 Definition of Tumor Response Using Immune-Related Response 
Criteria (irRC) 
 
The sum of the longest diameter of lesions (SPD) at tumor assessment using the immune-
related response criteria (irRC) for progressive disease incorporate the contribution of new 
measurable lesions.  Each net Percentage Change in Tumor Burden per assessment using 
irRC criteria accounts for the size and growth kinetics of both old and new lesions as they 
appear. 
 
11.3.1.1 
Impact of New Lesions on irRC 
 
New lesions in and of themselves do not qualify as progressive disease.  However, their 
contribution to total tumor burden is included in the SPD which in turn feeds into the irRC 
criteria for tumor response.  Therefore, new non-measurable lesions will not discontinue 
any subject from the study. 
 
11.3.1.2 
Definition of Target Lesions Response Using irRC 
 
• irComplete Response (irCR): Complete disappearance of all target lesions.  This category 
encompasses exactly the same subjects as “CR” by the mWHO criteria. 
• irPartial Response (irPR): Decrease, relative to baseline, or 50% or greater in the sum of 
the products of the two largest perpendicular diameters of all target and all new measurable 
target lesions (i.e., Percentage Change in Tumor Burden).  Note: the appearance of new 
measurable lesions is factored into the overall tumor burden, but does not automatically 
qualify as progressive disease until the SBD increases by >25% when compared to SPD at 
nadir. 
• irStable Disease (irSD): Does not meet criteria for irRC or irPR, in the absence of 
progressive disease. 
• irProgressive Disease (irPD): At least 25% increase Percentage Change in Tumor Burden 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
100 
(i.e. taking SPD of all target lesions and any new lesions) when compared to SPD at nadir. 
 
11.3.1.3 
Definition of Non-Target Lesions Response Using irRC 
 
• irComplete Response (irCR): Complete disappearance of all non-target lesions.  This 
category encompasses exactly the same subjects as “CR” by the mWHO criteria. 
• irPartial Response (irPR) or irStable Disease (irSD): Non-target lesion(s) are not 
considered in the definition of PR; these terms do not apply. 
• irProgressive Disease (irPD): Increases in number or size of non-target lesion(s) does not 
constitute progressive disease unless/until the Percentage Change in Tumor Burden 
increases by 25% (i.e. the SPD at nadir of the target lesions increases by the required 
amount). 
 
11.3.1.4 
Definition of Overall Response Using irRC 
 
Overall response using irRC will be based on these criteria: 
 
• Immune-Related Complete Response (irCR): Complete disappearance of all tumor 
lesions (target an non-target) together with no new measurable/unmeasurable lesions for at 
least 4 weeks from the date of documentation of complete response. 
• Immune-Related Partial Response (irPR): The sum of the products of the two largest 
perpendicular diameters of all target lesions is measured and captured as the SPD baseline.  
At each subsequent tumor assessment, the SPD of the two largest perpendicular diameters 
of all target lesions and of new measurable lesions are added together to provide the 
Immune Response Sum of Product Diameters (irSPD).  A decrease, relative to baseline, of 
the irSPD compared to the previously SPD baseline  of 50% or greater is considered an 
irPR. 
• Immune-Related Stable Disease (irSD): irSD is defined as the failure to meet criteria for 
immune complete response or immune partial response, in the absence of progressive 
disease 
• Immune-Related Progressive Disease (irPD): It is recommended in difficult cases to 
confirm PD by serial imaging.  Any of the following will constitute PD: 
 At least 25% increase in the SPD of all target lesions over baseline SPD calculated for 
the target lesions. 
 At least 25% increase in the SPD of all target lesions and new measurable lesions 
(irSPD) over the baseline SPD calculated for the target lesions. 
 
Criteria for determining overall response by irRC are summarized as follows: 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
101 
 
 
11.3.1.5 
Immune-Related Best Overall Response Using irRC (irBOR) 
 
irBOR is the best confirmed overall response over the study as a whole, recorded between 
the date of first dose until the last tumor assessment before subsequent therapy (except for 
local palliative radiotherapy for painful bone lesions) for the individual subject in the study.  
For the assessment of irBOR, all available assessments per subject are considered. 
 
irCR or irPR determinations included in the irBOR assessment must be confirmed by a 
second (confirmatory) evaluation meeting the criteria for response and performed no less 
than 4 weeks after the criteria for response are first met. 
 
 
 
12. DATA REPORTING / REGULATORY REQUIREMENTS 
 
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 7.0 
(Adverse Events: List and Reporting Requirements). 
 
12.1 
Data Reporting 
 
12.1.1 Method 
 
The Office of Data Quality (ODQ) will collect, manage, and perform quality checks on the 
data for this study. 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
102 
12.1.2 Responsibility for Data Submission 
 
Investigative sites within DF/HCC or DF/PCC are responsible for submitting data and/or 
data forms to the  Office of Data Quality in accordance with DF/HCC SOPs. 
 
12.2 
Data Safety Monitoring 
 
The DF/HCC Data and Safety Monitoring Committee (DSMC) will review and monitor toxicity 
and accrual data from this study. The committee is composed of clinical specialists with experience 
in oncology and who have no direct relationship with the study. Information that raises any 
questions about participant safety will be addressed with the Overall PI and study team. 
 
The DSMC will review each protocol up to four times a year or more often if required to review 
toxicity and accrual data. Information to be provided to the committee may include: up-to-date 
participant accrual; current dose level information; DLT information; all grade 2 or higher 
unexpected adverse events that have been reported; summary of all deaths occurring with 30 days 
of intervention for Phase I or II protocols; for gene therapy protocols, summary of all deaths while 
being treated and during active follow-up; any response information; audit results, and a summary 
provided by the study team. Other information (e.g. scans, laboratory values) will be provided 
upon request.  
12.3 
Multicenter Guidelines 
 
N/A 
 
12.4 
Collaborative Research and Future Use of Data and Biospecimens 
 
 Tissue, blood, stool, bodily fluids, and other materials derived from these will be collected in this 
study to analyze genes, DNA, RNA, proteins and cells for the study’s correlative endpoints and 
potential future research, utilizing new types of biomarker testing as it becomes available.  
 
These samples and any data generated as a part of these clinical trials may be used for future 
research studies and may be provided to collaborating investigators both within and outside of the 
DF/HCC for either correlative endpoints or secondary use. Samples and data may be shared with 
outside non-profit academic investigators, as well as with for-profit pharmaceutical investigators 
or commercial entitites, with whom we collaborate. When samples or data are sent to collaborators 
and when any research is performed on them, all information will be identified with a code, and 
will not contain any PHI, such as name, birthday, or MRNs.  
 
In order to allow the greatest amount of research to be performed on the specimens and 
information generated as a part of this trial, researchers in this study may share results of genetic 
sequencing with other scientists. De-identified specimen or genetic data may be placed into one 
of more publicly-accessible scientific databases, such as the National Institutes of Health’s 
Database for Genotypes and Phenotypes (dbGaP). The results from the correlative research on 
this study will be shared with these public databases. Through such databases, researchers from 
around the world will have access to de-identified samples or data for future research. More 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
103 
detailed information, beyond the public database, may only be accessed by scientists at other 
research centers who have received special permission to review de-identified data. 
 
 
13. STATISTICAL CONSIDERATIONS 
 
13.1 
Study Design/Endpoints 
 
This is an open-label, single-arm,single-center, phase 2 study of cabozantinib (40mg per oral 
daily) in combination with nivolumab (480mg intravenously on day 1, every 28 days) in subjects 
with metastatic triple-negative breast cancer previously treated with 0 to 3 chemotherapy 
regimens in the metastatic setting.  The target enrollment is 35 patients. 
 
Primary Endpoint 
The primary endpoint is ORR of nivolumab in combination with cabozantinib, according to 
RECIST 1.1 (Section 11), in patients with metastatic TNBC previously treated with 0 to 3 lines of 
chemotherapy in the metastatic setting. 
 
Secondary endpoints include: 
Secondary endpoints include the ORR of the combination according to immune-related response 
criteria (irRC) [Wolchok et al., 2009] (Section 11), the clinical benefit rate, and PFS according to 
RECIST 1.1. 
 
Blood and Tissue correlative science objectives include:  
• To characterize a broad array of immune markers in metastatic TNBC (characterization will be 
based on histology, protein expression, and mRNA expression). 
• To explore how different immunosuppressive and/or immune-stimulating immune marker 
profiles at baseline correlate with disease response to therapy (PFS, objective response assessed 
by RECIST 1.1 and immune-related response criteria). 
• To characterize changes in tumor-infiltrating lymphocytes, PD-L1 expression and immune gene 
signatures in the tissue microenvironment (TME) from baseline to after 2 cycles of the 
experimental combination. 
• To explore whether induction of changes in the immunosuppressive and/or immune-stimulating 
immune marker profile in TME correlates with disease response to therapy (response assessed 
by RECIST 1.1 and immune-related response criteria). 
• To evaluate MET and phospho MET expression in tumor tissue at baseline by 
immunohistochemistry 
• To explore the effect of treatment on plasma biomarkers (sVEGFR2, sMET, IL-2, IFN-γ, TNF-
α) 
• To characterize serial changes in immune marker profile in peripheral blood mononuclear cells 
(PBMCs) and in plasma over the course of the trial treatment. 
• To explore whether induction of changes in the immunosuppressive and/or immune-stimulating 
immune marker profile in PBMCs correlates with disease response to therapy (response 
assessed by RECIST 1.1 and immune-related response criteria). 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
104 
• To investigate whether there is an immune marker in circulating PBMCs that corresponds to 
tumor infiltrating lymphocyte (TIL) percentage in baseline tumor. 
• To collect blood to study cell-free DNA for comparison to tumor specimens before and after 
immunotherapy 
 
Stool and microbiome correlative science endpoints: 
 
Overall, we plan to describe the landscape of gut microbiota in patients with BC who will 
receive the combination of cabozantinib plus nivolumab, and the changes in their gut microbiota 
after two cycles of the combination. Statistical analyses of intestinal microbiota samples will be 
performed using R Statistical Language (v3.1.1) and GraphPad Prism (version 6.0e) software 
packages. Unpaired Mann–Whitney rank sum test (two-tailed) will be used for comparisons of 
continuous variables between two groups. Bar plots will be used to represent the data’s mean at 
the center values, with error bars to indicate standard deviation.  In order to explore the 
association of response (objective response according RECIST 1.1 and PFS) to baseline 
microbiota diversity, and changes from baseline in microbiota, inference will be based on 
Wilcoxon rank sum tests and estimates of predictive value along the continuous scales will be 
visualized using receiver operating characteristic (ROC) curves and reported with c-index and 
confidence intervals derived from variance estimates of Somers rank correlation. Unadjusted P-
values will be considered  significant for the Mann–Whitney rank sum test.  
 
We will quantify microbiome features from amplicon, metagenome, metatranscriptome using 
established pipelines to identify strain-level taxonomic, functional gene, transcriptional, and 
microbially-mediated metabolite profiles associated with BC patients with and without 
immunotherapy70-76. We will use modified multivariate linear modeling to identify statistically 
significant features associated with outcomes. Statistical tests for association with these 
outcomes and covariates will be performed using the sparse generalized linear model MaAsLin, 
which provides random effects models for both log-Gaussian and zero-inflated negative binomial 
link functions. Computational workflows for these steps are implemented as AnADAMA2 
(http://huttenhower.sph.harvard.edu/anadama) workflows, a reproducible data handling 
environment that captures all provenance during the analysis process. 
 
 
13.2 
Sample Size, Accrual Rate and Study Duration 
 
Based on data of recent trials with a similar population treated with anti-PD-1/PD-1 agents 
or cabozantinib in monotherapy{Tolaney, 2016 #1433}{Dirix, 2015 #1075}{Nanda, 2016 
#1389}, and considering that our population will not be previously selected by PD-L1 expression 
status, a true ORR of 10% or less would not be of clinical interest, and is the null hypothesis to the 
Simon optimal two-stage design. A true rate of 30% would be considered a clinically meaningful 
level of response, so the sample size was chosen to have higher power (90%) to declare the 
combination effective at this rate, while controlling the one-sided Type I error at no more than 5% 
under the null. 
Using Simon’s optimal two-stage design, in the first stage, 18 patients will be enrolled. Of 
note, in this first stage we will perform a safety run-in analysis. If there are 2 or more dose-limiting 
toxicity (DLTs) in the first 6 patients included, the trial will be closed for further enrollment. Dose-

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
105 
limiting toxicity (DLT) will be assessed in the first cycle. In the case of enrollment will continued, 
this first 6 patients will be included in the efficacy analysis. Thus, according to Simon’s optimal 
two-stage design, if in this first stage there are at least 3 patients with ORR, accrual will continue 
to the second stage where an additional 17 patients will be enrolled. If there are at least 7 patients 
with ORR among the 35 patients, the regimen will be considered worthy of further study.  If the 
true response rate is 10%, the chance the regimen is declared worthy of further study is less than 
5% (exact alpha = 0.047).  If the true response rate is 30%, the chance that the regimen is declared 
worthy of further study is 90% 
 
Table below shows the probability of continuing enrollment with ≤1 DLTs out of the first 6 
patients. 
 
 
Dose acceptance using 6 patients 
True DLT rate 
0.1 
0.2 
0.3 
0.4 
0.5 
0.6 
0.7 
Probability 
89% 
66% 
42% 
23% 
11% 
4% 
1% 
 
The expected accrual rate is 3-4 patients per month, and the accrual is expected to complete within 
12 months. 
 
13.3 
Stratification Factors 
 
NA   
 
13.4 
Interim Monitoring Plan 
 
In the first stage we will perform a safety run-in analysis. If there are 2 or more dose-limiting 
toxicity (DLTs) in the first 6 patients included, the trial will be closed for further enrollment. 
Section 5.3 describes the DLT definitions used in this current study, which will be assessed in the 
first cycle (28 days of cycle 1). As of April 2018, 2 DLTs were identified during the first safety 
run-in.  
 
The study will perform a safety run-in comprising another 6 patients, given that the toxicities seen 
were not consistent with other safety data available. Similar to the first safety run-in, if there are 2 
or more DLTs in these patients, the trial will be closed to further enrollment.  
 
If enrollment will continue, these first 12 patients will be included in the efficacy analysis. An 
additional interim analysis will happen after 18 patients enroll in the first stage.  If there is at least 
3 responses, accrual will continue to the second stage where up to 17 additional patients will be 
enrolled. 
 
13.5 
Analysis of Primary Endpoint 
 
The primary endpoint is ORR of the experimental combination, which will be assessed among all 
patients who initiated protocol therapy. Radiographic response will be assessed using RECIST 1.1 
criteria as defined in section 11. Objective response will require confirmatory scans as indicated.  
The ORR (CR + PR) will be reported with 90% exact confidence intervals.   (per RECIST 1.1 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
106 
criteria; Section 11).  
 
13.6 
Analysis of Secondary Endpoints 
 
Efficacy Endpoints  
All patients who initiated protocol therapy will also be evaluated for ORR according irRC, and for 
CBR and PFS, according RECIST. Clinical benefit is defined as CR, PR or SD ≥ 24 weeks 
according RECIST 1.1. ORR according to irRC will be reported with 90% exact confidence 
intervals. CBR will be reported respectively with 95% exact confidence intervals. PFS will be 
analyzed using Kaplan–Meier product-limit estimates and will be plotted using Kaplan-Meier 
plots. PFS is defined as the time from study randomization to disease progression according 
RECIST 1.1, medical judgment or death due to any cause, whichever occurred first.  Patients alive 
without disease progression are censored at the date of last disease evaluation.  The hazard ratio 
for each time-to-event endpoint will be estimated with 95% confidence intervals derived from the 
Cox proportional hazard model, but no hypothesis testing will be conducted.   
 
Safety and tolerability  
All patients will be evaluable for toxicity from the time of their first treatment with any study 
agent. Toxicity will be graded according to NCI CTCAE, Version 4.0. Toxicities will be 
summarized by maximum grade and by treatment arm.  Incidence rate of each toxicity will be 
reported with 95% exact CI.  The incidence rates of any grade 3+ toxicity will be compared 
between two arms using Fisher’s exact test. 
 
Correlative endpoints 
Previous studies demonstrated that, in addition to its direct cytoreductive effect, RT-induced cell 
death can be immunogenic, facilitating the recruitment and activation of antigen presenting cells 
(APCs) and priming of tumor antigen-specific T-cells[Shahabi et al., 2015]. Recently, different 
groups demonstrated that RT to the tumor bed led to upregulation of PD-L1 on tumor cells, 
dendritic cells, and on myeloid-derived suppressive cells (MDSCs), which may contribute to 
impairment of T-cell function in the tumor[Liang et al., 2013, Deng et al., 2014, Sharabi et al., 
2014]. Furthermore, these groups also demonstrated that the combination of RT plus blockade of 
the PD-1/PD-L1 axis improved outcomes in different preclinical models compared with RT or 
anti-PD1/PD-L1 alone, including breast cancer models.  
 
Recently, Herbst et al have demonstrated that patients who presented an increase of at least 5% in 
expression of PD-L1 in tumor microenvironment experienced a bigger likelihood to respond to 
treatment with the anti-PD-L1 Atezolizumab[Herbst et al., 2014]. Also, modifications in molecular 
signature of tumor microenvironment also correlated with response rate to this drug. Because of 
this rationale, we plan to perform two research biopsies in tumor lesion: one at baseline and the 
other one just before the begging of cycle 3 of nivolumab.  
 
With a sample size of 35 and assuming that there will be patients without accessible lesions, the 
table below indicates the power available to detect 20%, 30%, 40%, or 50% increases of PD-L1 
positivity rate. The power calculation is based on McNemar’s test with 1-sided alpha of 0.05 and 
assuming 2% of patients unexpectedly show PD-L1 positivity only in the baseline assessment. The 
calculation was done using East v6.3 (Cytel Inc). 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
107 
 
Increase of PD-L1 positivity 
rate post treatment 
# of paired biopsies available 
Power 
20% 
15 
54% 
 
20 
64% 
 
25 
72% 
 
30 
79% 
30% 
15 
75% 
 
20 
85% 
 
25 
91% 
 
30 
95% 
40% 
15 
90% 
 
20 
96% 
 
25 
98% 
 
30 
> 99% 
50% 
15 
97% 
 
20 
> 99% 
 
25 
> 99% 
 
30 
> 99% 
 
PD-L1 positivity seen at baseline and C3D1 samples will be summarized using contingency 
tables. An exploratory analysis is planned to evaluate PD-L1 change in continuous scale. 
 
13.7 
Reporting and Exclusions 
 
13.7.1 Evaluation of Efficacy 
For this Phase II trial, the efficacy evaluable population is a modified intent-to-treat (ITT) 
population.  The modified ITT population consists of all patients who initiate protocol 
therapy, even if there are major protocol therapy deviations.   
Subanalyses may then be performed on the basis of a subset of participants, excluding those 
for whom major protocol deviations have been identified (e.g., early death due to other 
reasons, early discontinuation of treatment, major protocol violations, etc.).  However, 
these subanalyses may not serve as the basis for drawing conclusions concerning treatment 
efficacy, and the reasons for excluding participants from the analysis should be clearly 
reported.  If applicable to the endpoint, the 95% confidence intervals should also be 
provided.  
 
13.7.2 Evaluation of Safety 
The safety population will be used in the safety data summaries.  The safety population 
consists of all patients who took at least one dose of any randomized treatment and who 
have at least one post-baseline safety assessment. Note that a patient who had no adverse 
events constitutes a safety assessment.  Patients who have received at least one dose of 
study drug but have no post-treatment safety data of any kind would be excluded.  

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
108 
 
 
14. PUBLICATION PLAN 
 
The results should be made public within 1 year of reaching the end of the study. The end of the 
study is the time point at which the last data items are to be reported, or after the outcome data are 
sufficiently mature for analysis, as defined in the section on Sample Size, Accrual Rate and Study 
Duration. If a report is planned to be published in a peer-reviewed journal, then that initial release 
may be an abstract that meets the requirements of the International Committee of Medical Journal 
Editors. A full report of the outcomes should be made public no later than three (3) years after the 
end of the study.  
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
109 
15. REFERENCES 
 
 
Adamow, M., Ritter, E., Sedrak, C., Roman, R.-A., Rosner, S., Benson, B. et al. (2012) Effect in 
a Patient with Melanoma.  
 
Adams, S., Diamond, J., Hamilton, E., Pohlmann, P., Tolaney, S., Molinero, L. et al. (2016) 
Abstract P2-11-06: Safety and Clinical Activity of Atezolizumab (Anti-Pdl1) in Combination 
with Nab-Paclitaxel in Patients with Metastatic Triple-Negative Breast Cancer. Cancer Research 
76: P2-11-06. 
 
Adams S, Loi S, Toppmeyer D, et al. Phase 2 study of pembrolizumab as first-line therapy for 
PD-L1–positive metastatic triple-negative breast cancer (mTNBC): Preliminary data from 
KEYNOTE-086 cohort B. Journal of Clinical Oncology. 2017;35(15_suppl):1088-1088. 
 
Adams, S., Gray, R.J., Demaria, S., Goldstein, L., Perez, E.A., Shulman, L.N. et al. (2014) 
Prognostic Value of Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancers from 
Two Phase Iii Randomized Adjuvant Breast Cancer Trials: Ecog 2197 and Ecog 1199. Journal 
of Clinical Oncology 32: JCO.2013.2055.0491--JCO.2013.2055.0491-. 
 
Adams S, Schmid P, Rugo HS, et al. Phase 2 study of pembrolizumab (pembro) monotherapy for 
previously treated metastatic triple-negative breast cancer (mTNBC): KEYNOTE-086 cohort A. 
Journal of Clinical Oncology. 2017;35(15_suppl):1008-1008. 
 
Ahmed, K.A., Stallworth, D.G., Kim, Y., Johnstone, P.A., Harrison, L.B., Caudell, J.J. et al. 
(2016) Clinical Outcomes of Melanoma Brain Metastases Treated with Stereotactic Radiation 
and Anti-Pd-1 Therapy. Ann Oncol 27: 434-441. 
 
Ali, H.R., Provenzano, E., Dawson, S., Blows, F.M., Liu, B., Shah, M. et al. (2014) Association 
between Cd8 + T-Cell in Fi Ltration and Breast Cancer Survival in 12 439 Patients. 1536-1543. 
 
Anders, C., Deal, A.M., Abramson, V., Liu, M.C., Storniolo, A.M., Carpenter, J.T. et al. (2014) 
Tbcrc 018: Phase Ii Study of Iniparib in Combination with Irinotecan to Treat Progressive Triple 
Negative Breast Cancer Brain Metastases. Breast Cancer Res Treat 146: 557-566. 
 
Armstrong, T.S., Mendoza, T., Gning, I., Coco, C., Cohen, M.Z., Eriksen, L. et al. (2006) 
Validation of the M.D. Anderson Symptom Inventory Brain Tumor Module (Mdasi-Bt). J 
Neurooncol 80: 27-35. 
 
Bachireddy, P., Hainz, U., Rooney, M., Pozdnyakova, O., Aldridge, J., Zhang, W. et al. (2014) 
Reversal of in Situ T-Cell Exhaustion During Effective Human Antileukemia Responses to 
Donor Lymphocyte Infusion. Blood 123: 1412-1421. 
 
Brahmer, J.R., Tykodi, S.S., Chow, L.Q., Hwu, W.J., Topalian, S.L., Hwu, P. et al. (2012) Safety 
and Activity of Anti-Pd-L1 Antibody in Patients with Advanced Cancer. N Engl J Med 366: 
2455-2465. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
110 
Casey, S.C., Tong, L., Li, Y., Do, R., Walz, S., Fitzgerald, K.N. et al. (2016) Myc Regulates the 
Antitumor Immune Response through Cd47 and Pd-L1. Science 352: 227-231. 
 
 
Champiat, S., Lambotte, O., Barreau, E., Belkhir, R., Berdelou, A., Carbonnel, F. et al. (2016) 
Management of Immune Checkpoint Blockade Dysimmune Toxicities: A Collaborative Position 
Paper. Ann Oncol 27: 559-574. 
 
Chen, B.J., Chapuy, B., Ouyang, J., Sun, H.H., Roemer, M.G., Xu, M.L. et al. (2013) Pd-L1 
Expression Is Characteristic of a Subset of Aggressive B-Cell Lymphomas and Virus-Associated 
Malignancies. Clin Cancer Res 19: 3462-3473. 
 
Davoli, T., Uno, H., Wooten, E.C., and Elledge, S.J. (2017) Tumor Aneuploidy Correlates with 
Markers of Immune Evasion and with Reduced Response to Immunotherapy. Science 355: 
 
Deng, L., Liang, H., Burnette, B., Beckett, M., Darga, T., Weichselbaum, R.R. et al. (2014) 
Irradiation and Anti – Pd-L1 Treatment Synergistically Promote Antitumor Immunity in Mice. 
The journal of clinical investigation 124: 687-695. 
 
Denkert, C., Loibl, S., Noske, A., Roller, M., Mu, B.M., Komor, M. et al. (2015) J Ournal of C 
Linical O Ncology Tumor-Associated Lymphocytes as an Independent Predictor of Response to 
Neoadjuvant Chemotherapy in Breast Cancer. 28: 105-114. 
 
Denkert, C., Loibl, S., Noske, A., Roller, M., Muller, B.M., Komor, M. et al. (2010) Tumor-
Associated Lymphocytes as an Independent Predictor of Response to Neoadjuvant 
Chemotherapy in Breast Cancer. J Clin Oncol 28: 105-113. 
 
Denkert, C., Von Minckwitz, G., Brase, J.C., Sinn, B.V., Gade, S., Kronenwett, R. et al. (2015) 
Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy with or without 
Carboplatin in Human Epidermal Growth Factor Receptor 2-Positive and Triple-Negative 
Primary Breast Cancers. J Clin Oncol 33: 983-991. 
 
Denkert, C., Von Minckwitz, G., Brase, J.C., Sinn, B.V., Gade, S., Kronenwett, R. et al. (2015) 
Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy with or without 
Carboplatin in Human Epidermal Growth Factor Receptor 2-Positive and Triple-Negative 
Primary Breast Cancers. Journal of Clinical Oncology 33: 983-991. 
 
Dirix, L.Y., Takacs, I., Nikolinakos, P., Jerusalem, G., Arkenau, H.-T., Hamilton, E.P. et al. 
(2015) Avelumab (Msb0010718c), an Anti-Pd-L1 Antibody, in Patients with Locally Advanced 
or Metastatic Breast Cancer: A Phase Ib Javelin Solid Tumor Trial, SABCS. 
 
Dovedi, S.J. and Illidge, T.M. (2015) The Antitumor Immune Response Generated by 
Fractionated Radiation Therapy May Be Limited by Tumor Cell Adaptive Resistance and Can 
Be Circumvented by Pd-L1 Blockade. OncoImmunology 4: e1016709-e1016709. 
 
Dushyanthen, S., Beavis, P.A., Savas, P., Teo, Z.L., Zhou, C., Mansour, M. et al. (2015) 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
111 
Relevance of Tumor-Infiltrating Lymphocytes in Breast Cancer. BMC Medicine 1: 1-13. 
 
Dyer, M.A., Kelly, P.J., Chen, Y.H., Pinnell, N.E., Claus, E.B., Lee, E.Q. et al. (2012) 
Importance of Extracranial Disease Status and Tumor Subtype for Patients Undergoing 
Radiosurgery for Breast Cancer Brain Metastases. Int J Radiat Oncol Biol Phys 83: e479-486. 
 
Eisenhauer, E.A., Therasse, P., Bogaerts, J., Schwartz, L.H., Sargent, D., Ford, R. et al. (2009) 
New Response Evaluation Criteria in Solid Tumours: Revised Recist Guideline (Version 1.1). 
Eur J Cancer 45: 228-247. 
 
Emens, L.A., Braiteh, F.S., Cassier, P., Delord, J.-P., Eder, J.P., Fasso, M. et al. (2015) Abstract 
2859: Inhibition of Pd-L1 by Mpdl3280a Leads to Clinical Activity in Patients with Metastatic 
Triple-Negative Breast Cancer (Tnbc). Cancer Research 75: 2859. 
 
Freeman GJ, Long AJ, Iwai Y, et al. Engagement of the PD-1 immunoinhibitory receptor by a 
novel B7 family member leads to negative regulation of lymphocyte activation. The Journal of 
experimental medicine. Oct 02 2000;192(7):1027-1034. 
Foulkes, W.D., Smith, I.E., and Reis-Filho, J.S. (2010) Triple-Negative Breast Cancer. N Engl J 
Med 363: 1938-1948. 
 
Gajewski, T.F. (2015) The Next Hurdle in Cancer Immunotherapy_ Overcoming the Non–T-
Cell–Inflamed Tumor Microenvironment. Seminars in Oncology 42: 663-671. 
 
Gao, J., Shi, L.Z., Zhao, H., Chen, J., Xiong, L., He, Q. et al. (2016) Loss of Ifn-Gamma 
Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-Ctla-4 Therapy. Cell 167: 
397-404.e399. 
 
Gatalica, Z., Snyder, C., Maney, T., Ghazalpour, A., Holterman, D.A., Xiao, N. et al. (2014) 
Programmed Cell Death 1 (Pd-1) and Its Ligand (Pd-L1) in Common Cancers and Their 
Correlation with Molecular Cancer Type. Cancer Epidemiology Biomarkers & Prevention 23: 
2965-2970. 
 
George, S., Miao, D., Demetri, G.D., Adeegbe, D., Rodig, S.J., Shukla, S. et al. (2017) Loss of 
Pten Is Associated with Resistance to Anti-Pd-1 Checkpoint Blockade Therapy in Metastatic 
Uterine Leiomyosarcoma. Immunity 46: 197-204. 
 
Golden, E.B., Chhabra, A., Chachoua, A., Adams, S., Donach, M., Fenton-Kerimian, M. et al. 
(2015) Local Radiotherapy and Granulocyte-Macrophage Colony-Stimulating Factor to Generate 
Abscopal Responses in Patients with Metastatic Solid Tumours: A Proof-of-Principle Trial. 
Lancet Oncol 16: 795-803. 
 
Herbst, R.S., Soria, J.-C., Kowanetz, M., Fine, G.D., Hamid, O., Gordon, M.S. et al. (2014) 
Antibody Mpdl3280a in Cancer Patients. Nature 515: 563-567. 
 
Ho-Yen CM, Green AR, Rakha EA, et al. C-Met in invasive breast cancer: is there a relationship 
with the basal-like subtype? Cancer. Jan 15 2014;120(2):163-171. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
112 
 
Hodi FS, Lawrence D, Lezcano C, et al. Bevacizumab plus ipilimumab in patients with 
metastatic melanoma. Cancer Immunol Res. Jul 2014;2(7):632-642. 
 
Horky, L.L., Hsiao, E.M., Weiss, S.E., Drappatz, J, Gerbaudo, V.H (2011). Dual phase FDG-
PET imaging of brain metastases provides superior assessment of recurrence versus post-
treatment necrosis. J Neurooncol 103:137-146 
 
Hugo, H.S., Delord, J., Im, S., Ott, P.A., P, S.A., Bedard, P.L. et al. (2015) Preliminary Efficacy 
and Safety of Pembrolizumab in Patients with Pd-L1-Positive, Estrogen Receptor-Positive/Her2-
Negative Advanced Breast Cancer Enrolled in Keynote-028, SABCS. 
 
Hwu, W.-J., Ph, D., Topalian, S.L., Hwu, P., Chen, S., Ph, D. et al. (2012) Safety and Activity of 
Anti–Pd-L1 Antibody in Patients with Advanced Cancer. 2455-2465. 
 
Intlekofer, A.M. and Thompson, C.B. (2013) F Basic-Translational Review at the Bench : 
Preclinical Rationale for Ctla-4 and Pd-1 Blockade as Cancer Immunotherapy. 94: 25-39. 
 
Jemal, A., Bray, F., and Ferlay, J. (2011) Global Cancer Statistics. 61: 69-90. 
 
Kennecke, H., Yerushalmi, R., Woods, R., Cheang, M.C., Voduc, D., Speers, C.H. et al. (2010) 
Metastatic Behavior of Breast Cancer Subtypes. J Clin Oncol 28: 3271-3277. 
 
Kiess, A.P., Wolchok, J.D., Barker, C.A., Postow, M.A., Tabar, V., Huse, J.T. et al. (2015) 
Stereotactic Radiosurgery for Melanoma Brain Metastases in Patients Receiving Ipilimumab: 
Safety Profile and Efficacy of Combined Treatment. Int J Radiat Oncol Biol Phys 92: 368-375. 
Kroemer, G., Senovilla, L., Galluzzi, L., André, F., and Zitvogel, L. (2015) Review Natural and 
Therapy-Induced Immunosurveillance in Breast Cancer. Nature Publishing Group 21: 1128-
1138. 
 
Kwilas AR, Ardiani A, Donahue RN, Aftab DT, Hodge JW. Dual effects of a targeted small-
molecule inhibitor (cabozantinib) on immune-mediated killing of tumor cells and immune tumor 
microenvironment permissiveness when combined with a cancer vaccine. J Transl Med. Nov 13 
2014;12:294. 
 
Leach DR, Krummel MF, Allison JP. Enhancement of antitumor immunity by CTLA-4 
blockade. Science. Mar 22 1996;271(5256):1734-1736. 
 
Li, S., Zhu, M., Pan, R., Fang, T., Cao, Y.Y., Chen, S. et al. (2016) The Tumor Suppressor Pten 
Has a Critical Role in Antiviral Innate Immunity. Nat Immunol 17: 241-249. 
 
Liang, H., Deng, L., Chmura, S., Burnette, B., Liadis, N., Darga, T. et al. (2013) Radiation-
Induced Equilibrium Is a Balance between Tumor Cell Proliferation and T Cell-Mediated 
Killing. The Journal of Immunology 190: 5874-5881. 
 
Lim, E. and Lin, N.U. (2014) Updates on the Management of Breast Cancer Brain Metastases. 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
113 
Oncology (Williston Park) 28: 572-578. 
 
Lin, N.U., Claus, E., Sohl, J., Razzak, A.R., Arnaout, A., and Winer, E.P. (2008) Sites of Distant 
Recurrence and Clinical Outcomes in Patients with Metastatic Triple-Negative Breast Cancer: 
High Incidence of Central Nervous System Metastases. Cancer 113: 2638-2645. 
 
Lin, N.U., Lee, E.Q., Aoyama, H., Barani, I.J., Barboriak, D.P., Baumert, B.G. et al. (2015) 
Response Assessment Criteria for Brain Metastases: Proposal from the Rano Group. Lancet 
Oncol 16: e270-278. 
 
Lin, N.U., Vanderplas, A., Hughes, M.E., Theriault, R.L., Edge, S.B., Wong, Y.N. et al. (2012) 
Clinicopathologic Features, Patterns of Recurrence, and Survival among Women with Triple-
Negative Breast Cancer in the National Comprehensive Cancer Network. Cancer 118: 5463-
5472. 
 
Loi, S., Sirtaine, N., Piette, F., Salgado, R., Viale, G., Van Eenoo, F. et al. (2013) Prognostic and 
Predictive Value of Tumor-Infiltrating Lymphocytes in a Phase Iii Randomized Adjuvant Breast 
Cancer Trial in Node-Positive Breast Cancer Comparing the Addition of Docetaxel to 
Doxorubicin with Doxorubicin-Based Chemotherapy: Big 02-98. Journal of Clinical Oncology 
31: 860-867. 
 
Lu X, Horner JW, Paul E, et al. Effective combinatorial immunotherapy for castration-resistant 
prostate cancer. Nature. Mar 30 2017;543(7647):728-732. 
 
Mathew, M., Tam, M., Ott, P.A., Pavlick, A.C., Rush, S.C., Donahue, B.R. et al. (2013) 
Ipilimumab in Melanoma with Limited Brain Metastases Treated with Stereotactic Radiosurgery. 
Melanoma Res 23: 191-195. 
 
Mlecnik, B., Bindea, G., Angell, H.K., Berger, A., Lagorce, C., Lugli, A. et al. (2014) Towards 
the Introduction of the ‘ Immunoscore ’. 199-209. 
 
Nanda, R., Chow, L.Q., Dees, E.C., Berger, R., Gupta, S., Geva, R. et al. (2016) Pembrolizumab 
in Patients with Advanced Triple-Negative Breast Cancer: Phase Ib Keynote-012 Study. J Clin 
Oncol:  
 
Nayak, L., Deangelis, L., Wen, P., Brandes, A., Soffietti, R., Lin, N. et al. (2014) The 
Neurologic Assessment in Neuro-Oncology (Nano) Scale: A Tool to Assess Neurologic Function 
for Integration in the Radiologic Assessment in Neuro-Oncology (Rano) Criteria (S22.005). 
Neurology 82:  
 
Niwinska, A., Murawska, M., and Pogoda, K. (2010) Breast Cancer Brain Metastases: 
Differences in Survival Depending on Biological Subtype, Rpa Rtog Prognostic Class and 
Systemic Treatment after Whole-Brain Radiotherapy (Wbrt). Ann Oncol 21: 942-948. 
 
Okada, H., Weller, M., Huang, R., Finocchiaro, G., Gilbert, M.R., Wick, W. et al. (2015) 
Immunotherapy Response Assessment in Neuro-Oncology: A Report of the Rano Working 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
114 
Group. Lancet Oncol 16: e534-542. 
 
Pardoll, D.M. (2012) The Blockade of Immune Checkpoints in Cancer Immunotherapy. Nat Rev 
Cancer 12: 252-264. 
 
Peng, W., Chen, J.Q., Liu, C., Malu, S., Creasy, C., Tetzlaff, M.T. et al. (2016) Loss of Pten 
Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov 6: 202-216. 
 
Perez, E.A., Thompson, E.A., Ballman, K.V., Anderson, S.K., and Asmann, Y.W. (2015) 
Genomic Analysis Reveals That Immune Function Genes Are Strongly Linked to Clinical 
Outcome in the North Central Cancer Treatment Group N9831 Adjuvant Trastuzumab Trial. 33:  
 
Powles, T., Eder, J.P., Fine, G.D., Braiteh, F.S., Loriot, Y., Cruz, C. et al. (2014) Mpdl3280a 
(Anti-Pd-L1) Treatment Leads to Clinical Activity in Metastatic Bladder Cancer. Nature 515: 
558-562. 
 
Quine, M.A., Bell, G.D., Mccloy, R.F., Charlton, J.E., Devlin, H.B., and Hopkins, A. (1995) 
Prospective Audit of Upper Gastrointestinal Endoscopy in Two Regions of England: Safety, 
Staffing, and Sedation Methods. Gut 36: 462-467. 
 
Raghav KP, Wang W, Liu S, et al. cMET and phospho-cMET protein levels in breast cancers 
and survival outcomes. Clinical cancer research : an official journal of the American 
Association for Cancer Research. Apr 15 2012;18(8):2269-2277. 
 
Relf M, LeJeune S, Scott PA, et al. Expression of the angiogenic factors vascular endothelial cell 
growth factor, acidic and basic fibroblast growth factor, placenta growth factor, and pleiotrophin 
in human primary breast cancer and its relation to angiogenesis. Cancer Res. Mar 1 1997; 
57(5):963-969 
 
Ribas, A. (2015) Adaptive Immune Resistance : How Cancer Protects from Immune Attack. 915-
920. 
 
Rizvi, N.A., Hellmann, M.D., Snyder, A., Kvistborg, P., Makarov, V., Havel, J.J. et al. (2015) 
Cancer Immunology. Mutational Landscape Determines Sensitivity to Pd-1 Blockade in Non-
Small Cell Lung Cancer. Science 348: 124-128. 
 
Robert NJ, Dieras V, Glaspy J, et al. RIBBON-1: randomized, double-blind, placebo-controlled, 
phase III trial of chemotherapy with or without bevacizumab for first-line treatment of human 
epidermal growth factor receptor 2-negative, locally recurrent or metastatic breast cancer. J Clin 
Oncol. Apr 1 2011;29(10):1252-1260. 
 
Rosenberg, J.E., Hoffman-Censits, J., Powles, T., Van Der Heijden, M.S., Balar, A.V., Necchi, 
A. et al. (2016) Atezolizumab in Patients with Locally Advanced and Metastatic Urothelial 
Carcinoma Who Have Progressed Following Treatment with Platinum-Based Chemotherapy: A 
Single-Arm, Multicentre, Phase 2 Trial. Lancet:  
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
115 
Salgado, R., Denkert, C., Demaria, S., Sirtaine, N., Klauschen, F., Pruneri, G. et al. (2014) The 
Evaluation of Tumor-Infiltrating Lymphocytes (Tils) in Breast Cancer: Recommendations by an 
International Tils Working Group 2014. Annals of Oncology 26: 259-271. 
 
Salgado, R., Denkert, C., Demaria, S., Sirtaine, N., Klauschen, F., Pruneri, G. et al. (2015) The 
Evaluation of Tumor-Infiltrating Lymphocytes (Tils) in Breast Cancer: Recommendations by an 
International Tils Working Group 2014. Ann Oncol 26: 259-271. 
 
Savas, P., Salgado, R., Denkert, C., Sotiriou, C., Darcy, P.K., Smyth, M.J. et al. (2015) Clinical 
Relevance of Host Immunity in Breast Cancer: From Tils to the Clinic. Nat Rev Clin Oncol:  
 
Scagliotti GV, Novello S, von Pawel J. The emerging role of MET/HGF inhibitors in oncology. 
Cancer treatment reviews. Nov 2013;39(7):793-801. 
 
Schoenfeld, J.D., Mahadevan, A., Floyd, S.R., Dyer, M.A., Catalano, P.J., Alexander, B.M. et al. 
(2015) Ipilmumab and Cranial Radiation in Metastatic Melanoma Patients: A Case Series and 
Review. J Immunother Cancer 3: 50. 
 
Schreiber, R.D. (2012) Cancer Immunoediting : Integrating Suppression and Promotion. 1565:  
 
Schreiber, R.D., Old, L.J., and Smyth, M.J. Cancer Immunoediting : Integrating Suppression and 
Promotion.  
 
Sennino B, McDonald DM. Controlling escape from angiogenesis inhibitors. Nature reviews. 
Cancer. Oct 2012;12(10):699-709. 
 
Shahabi, V., Postow, M.A., Tuck, D., and Wolchok, J.D. (2015) Immune-Priming of the Tumor 
Microenvironment by Radiotherapy. American Journal of Clinical Oncology 38: 90-97. 
 
Sharabi, A.B., Nirschl, C.J., Kochel, C.M., Nirschl, T.R., Francica, B.J., Velarde, E. et al. (2014) 
Stereotactic Radiation Therapy Augments Antigen-Specific Pd-1-Mediated Antitumor Immune 
Responses Via Cross-Presentation of Tumor Antigen. Cancer Immunology Research: 345-356. 
 
Sharma, P. and Allison, J.P. (2015) The Future of Immune Checkpoint Therapy. 348:  
 
Shi, M., Roemer, M.G., Chapuy, B., Liao, X., Sun, H., Pinkus, G.S. et al. (2014) Expression of 
Programmed Cell Death 1 Ligand 2 (Pd-L2) Is a Distinguishing Feature of Primary Mediastinal 
(Thymic) Large B-Cell Lymphoma and Associated with Pdcd1lg2 Copy Gain. Am J Surg Pathol 
38: 1715-1723. 
 
Siegel, R., Desantis, C., Virgo, K., Stein, K., Mariotto, A., Smith, T. et al. (2013) Cancer 
Treatment and Survivorship Statistics , 2012.  
 
Smith, D.C., Mcdermott, D.F., Powderly, J.D., Carvajal, R.D., Sosman, J.A., Atkins, M.B. et al. 
(2012) New England Journal. 2443-2454. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
116 
Snyder, A., Makarov, V., Merghoub, T., Yuan, J., Zaretsky, J.M., Desrichard, A. et al. (2014) 
Genetic Basis for Clinical Response to Ctla-4 Blockade in Melanoma. The New England journal 
of medicine: 2189-2199. 
 
Sperduto, P.W., Kased, N., Roberge, D., Chao, S.T., Shanley, R., Luo, X. et al. (2013) The 
Effect of Tumor Subtype on the Time from Primary Diagnosis to Development of Brain 
Metastases and Survival in Patients with Breast Cancer. J Neurooncol 112: 467-472. 
 
Sperduto, P.W., Kased, N., Roberge, D., Xu, Z., Shanley, R., Luo, X. et al. (2012) Summary 
Report on the Graded Prognostic Assessment: An Accurate and Facile Diagnosis-Specific Tool 
to Estimate Survival for Patients with Brain Metastases. J Clin Oncol 30: 419-425. 
 
Spranger, S., Bao, R., and Gajewski, T.F. (2015) Melanoma-Intrinsic Beta-Catenin Signalling 
Prevents Anti-Tumour Immunity. Nature 523: 231-235. 
 
Tolaney SM, Ziehr DR, Guo H, et al. Phase II and Biomarker Study of Cabozantinib in 
Metastatic Triple-Negative Breast Cancer Patients. Oncologist. Oct 27 2016. 
 
Topalian, S.L., Drake, C.G., and Pardoll, D.M. (2015) Immune Checkpoint Blockade: A 
Common Denominator Approach to Cancer Therapy. Cancer Cell 27: 450-461. 
 
Topalian, S.L., Hodi, F.S., Brahmer, J.R., Gettinger, S.N., Smith, D.C., Mcdermott, D.F. et al. 
(2012) Safety, Activity, and Immune Correlates of Anti-Pd-1 Antibody in Cancer. N Engl J Med 
366: 2443-2454. 
 
Tosolini, M., Camus, M., Berger, A., Wind, P., and Lagorce-Page, C. (2006) References and 
Notes 1. 313: 1960-1965. 
 
Uzzan B, Nicolas P, Cucherat M, Perret GY. Microvessel density as a prognostic factor in 
women with breast cancer: a systematic review of the literature and meta-analysis. Cancer Res. 
May 1 2004;64(9):2941-2955. 
 
Wagle, N., Berger, M.F., Davis, M.J., Blumenstiel, B., Defelice, M., Pochanard, P. et al. (2012) 
High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by 
Targeted, Massively Parallel Sequencing. Cancer Discov 2: 82-93. 
 
Wallin JJ, Bendell JC, Funke R, et al. Atezolizumab in combination with bevacizumab enhances 
antigen-specific T-cell migration in metastatic renal cell carcinoma. Nature communications. 
Aug 30 2016;7:12624. 
 
Wolchok, J.D., Hoos, A., O'day, S., Weber, J.S., Hamid, O., Lebbe, C. et al. (2009) Guidelines 
for the Evaluation of Immune Therapy Activity in Solid Tumors: Immune-Related Response 
Criteria. Clin Cancer Res 15: 7412-7420. 
 
Zagouri F, Bago-Horvath Z, Rossler F, et al. High MET expression is an adverse prognostic 
factor in patients with triple-negative breast cancer. Br J Cancer. Mar 19 2013;108(5):1100-

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
117 
1105. 
 
Zaretsky, J.M., Garcia-Diaz, A., Shin, D.S., Escuin-Ordinas, H., Hugo, W., Hu-Lieskovan, S. et 
al. (2016) Mutations Associated with Acquired Resistance to Pd-1 Blockade in Melanoma. N 
Engl J Med:  
 
 
 
APPENDIX A 
PERFORMANCE STATUS CRITERIA 
 
ECOG Performance Status Scale 
Karnofsky Performance Scale 
Grade 
Descriptions 
Percent 
Description 
0 
Normal activity.  Fully active, able 
to carry on all pre-disease 
performance without restriction. 
100 
Normal, no complaints, no evidence 
of disease. 
90 
Able to carry on normal activity; 
minor signs or symptoms of disease. 
1 
Symptoms, but ambulatory.  
Restricted in physically strenuous 
activity, but ambulatory and able 
to carry out work of a light or 
sedentary nature (e.g., light 
housework, office work). 
80 
Normal activity with effort; some 
signs or symptoms of disease. 
70 
Cares for self, unable to carry on 
normal activity or to do active work. 
2 
In bed <50% of the time.  
Ambulatory and capable of all 
self-care, but unable to carry out 
any work activities.  Up and about 
more than 50% of waking hours. 
60 
Requires occasional assistance, but 
is able to care for most of his/her 
needs. 
50 
Requires considerable assistance and 
frequent medical care. 
3 
In bed >50% of the time.  Capable 
of only limited self-care, confined 
to bed or chair more than 50% of 
waking hours. 
40 
Disabled, requires special care and 
assistance. 
30 
Severely disabled, hospitalization 
indicated.  Death not imminent. 
4 
100% bedridden.  Completely 
disabled.  Cannot carry on any 
self-care.  Totally confined to bed 
or chair. 
20 
Very sick, hospitalization indicated. 
Death not imminent. 
10 
Moribund, fatal processes 
progressing rapidly. 
5 
Dead. 
0 
Dead. 
 
 
 
 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
118 
APPENDIX B 
GUIDELINES FOR COLLECTING RESEARCH BIOPSY TISSUE  
 
Tissue specimens will be collected from metastatic lesions using standard institutional 
procedures. The amount of tissue collected may follow the guidelines listed below: 
 
Skin/chest wall: A goal of 2 4-mm punch biopsies will be obtained. 
 
Lymph node: A goal of 3-6 core biopsy specimens will be obtained using an 18-gauge needle. 
 
Liver: A goal of 3-6 core biopsy specimens will be obtained using an 18-gauge needle. 
 
Lung: Because of the risk of pneumothorax associated with core needle biopsies of lung nodules, 
no core biopsies of lung nodules are mandated on this protocol, unless they are clinically 
indicated. 
 
Bone: Because the yield of malignant tissue from bone biopsies tends to be relatively low, if a 
patient has another accessible site of disease (i.e. skin, lymph node, liver), that site should be 
biopsied preferentially. If bone is the only biopsy-accessible site, then a goal of 3-6 core biopsy 
specimens will be obtained using an 11-13 gauge needle. 
 
Please note that the above are guidelines for the amount of tissue to be obtained, and are 
not meant to replace clinical judgment at the time the procedure is performed. Less than the 
goal quantity of tissue is accepted for each type of biopsy, and will be left to the clinical 
judgment of the physician performing the procedure. 
 
Coded laboratory specimens will be stored in the Tumor Bank of the DFCI. These specimens 
will become the property of DFCI. Patients will be informed that their specimens may be used 
for research by investigators at DF/HCC and other approved collaborators. Shared specimens 
will be identified with a sample ID number; all patient identifying material will be removed. 
 
Risks of Research Biopsy and Procedures for Minimizing Risk 
 
Potential risks according to site are: 
Skin/chest wall (punch biopsy): 
• Likely: local discomfort and minor bleeding 
• Less likely: moderate or major bleeding, or infection 
 
Lymph node, liver, or bone (core needle biopsy): 
• Likely: local discomfort and minor bleeding 
• Less likely: moderate or major bleeding, need for blood transfusion, hospitalization 
due 
to bleeding or other complications, infection, damage to adjacent organs. Additional risks may be 
present if intravenous conscious sedation is required 
 
Breast (core biopsy): 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
119 
• Likely: local discomfort and minor bleeding. 
• Less likely: moderate or major bleeding, need for blood transfusion, hospitalization 
due  
to bleeding or other complications, infection, pneumothorax, damage to adjacent organs. 
 
Pleural fluid (thoracentesis): 
• Likely: local discomfort and minor bleeding 
• Less likely: moderate or major bleeding, need for blood transfusion, hospitalization 
due to bleeding or other complications, infection, pneumothorax, damage to adjacent  
organs 
 
Ascites fluid (paracentesis): 
• Likely: local discomfort and minor bleeding 
• Less likely: moderate or major bleeding, need for blood transfusion, hospitalization 
due to bleeding or other complications, infection, bowel perforation or damage to 
adjacent organs. In order to minimize the risk of a biopsy, only qualified personnel 
will perform these procedures.  
 
Prior to the procedure, the physician performing the procedure will discuss the risks with each 
study participant, answer any questions, and obtain separate procedure consent. Patients will be 
evaluated for comorbidities or concomitant medications that may increase the risk of potential 
complications. For biopsies of lesions that are not superficial and clearly palpable, imaging 
studies such as CT or ultrasound will be used to guide the biopsy in order to minimize the risk of 
damage to adjacent structures. After lymph node biopsies, patients will be observed a minimum 
of 2 hours (range 2-4 hours) after the procedure, or according to standard institutional guidelines. 
After liver biopsies, patients will be observed a minimum of 4 hours (range 4-6 hours) after the 
procedure, or according to standard institutional guidelines. Less than the goal quantity of tissue 
is accepted for each type of biopsy, and will be left to the clinical judgment of the physician 
performing the procedure. 
 
Risks of Anesthesia 
 
Local Anesthesia 
All biopsy procedures require local anesthesia using lidocaine, xylocaine, or related 
compounds. There is a small risk of an allergic reaction associated with these drugs. 
In order to minimize the risk of local anesthesia, only qualified personnel will perform 
the biopsy procedure. Patients will be queried if they have had previous allergic 
reactions to local anesthetics. 
 
Intravenous Conscious Sedation 
Certain biopsy procedures, such as lymph node, liver, or bone biopsies, may require 
intravenous conscious sedation (IVCS). IVCS is a minimally depressed level of consciousness 
that retains the patient’s ability to maintain a patent airway independently and continuously and 
respond appropriately to physical stimulation and verbal commands. 
The risks of intravenous conscious sedation include: inhibition of the gag reflex and concomitant 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
120 
risk of aspiration, cardiopulmonary complications (myocardial infarction, cardiac arrhythmias, 
hypoxemia), and allergic reactions to the sedative or analgesic medications. These risks are small 
but real; for example, in a prospective study of 14,149 patients undergoing IVCS during upper 
gastrointestinal endoscopies, the rate of immediate cardiopulmonary events was 2 in 
1000.[Quine et al., 1995] The 30-day mortality was 1 per 2,000 cases. In this study, there was a 
strong association between lack of monitoring and use of high-dose benzodiazepines with 
adverse outcomes. There was also an association between the use of local anesthetic sprays to the 
oropharynx and the development of pneumonia. In order to minimize the risk of intravenous 
conscious sedation, only qualified personnel will be responsible for conscious sedation. A 
minimum of two individuals will be involved in the care of patients undergoing conscious 
sedation—the physician performing the biopsy procedure, and the individual (M.D. or R.N.) who 
monitors the patients and his/her response to both the sedation and the procedure, and who is 
capable of assisting with any supportive or resuscitative measures. The room where the 
procedure utilizing IVCS takes place will have adequate equipment to provide supplemental 
oxygen, monitor vital signs, and maintain an airway should this be necessary. An emergency cart 
will also be immediately accessible to the room where the procedure is to take place, and 
emergency support services will be available on page. Patients will be screened and evaluated for 
their fitness to undergo conscious sedation by a trained physician. Patients with active cardiac 
disease are excluded from this study. No local anesthetic spray to the oropharynx will be 
necessary, given that endoscopy is not a planned procedure. Following the procedure, patients 
will be observed closely in the recovery room for a minimum of 2 hours. 
 
General Anesthesia 
Because of the higher risk of general anesthesia compared with local anesthesia or intravenous 
conscious sedation, biopsies that would require general anesthesia in order to be performed are 
not permitted on this protocol. 
 

 
DF/HCC Protocol #: 17-324 
Protocol Version Date: 4/9/2019 
 
121 
 
For Biopsies of Soft Tissue, Liver, Bone, Breast, Etc: 
1. After biopsy is performed, the tissue mass is placed on a sterile gauze 
2. Using forceps, separate the tumor tissue 
3. Place 2 pieces (cores) of tumor tissue in each cassette (typically end up with 3 cassettes 
per biopsy); the last cassette will contain many small pieces of tumor tissue 
4. Fill cassettes with OCT 
a. Completely cover tissue 
b. Limit the amount of bubbles 
5. Place cassettes on dry ice and prepare for transport by limiting OCT leakage 
6. Return samples to the lab and complete freezing of samples in OCT with dry ice (about 
10 minutes freezing time) 
7. Once samples are frozen, place in plastic bag; label bag with date, protocol number, 
patient number, and number of initials included 
8. Store in –80C freezer 
 
For Effusions and Ascites 
1. Fluid sample should be split into two equal aliquots 
2. One aliquot should be spun down into a pellet and snap frozen in an ETOH/dry ice bath 
or in liquid N2 
3. One aliquot should be fixed and processed as a standard cell block. 
Note: if the sample preparation is done by a clinical cytopathology laboratory, it is important to 
explain that the sample is for research purposes only and that no thin prep should be performed 
as this uses up a significant portion of the sample. 
 
For Fine Needle Aspiration Samples 
A goal of 3 passes: 
1. One pass should be evacuated and rinsed directly into 2mL of room temperature Trizol for 
RNA analysis. 
2. One pass should be evacuated and rinsed directly into 2mL of room temperature Trizol for 
DNA analysis. 
3. One pass should be evacuated and rinsed directly into 10-20mL of RPMI to prepare a cell 
block.