Phase II Trial of Exemestane With Immunomodulatory Cyclophosphamide in ER and/or PR-positive and HER2/Neu Negative Metastatic Breast Cancer
Phase: PHASE2
Conditions: Metastatic Beast Cancer
Sponsor: NYU Langone Health

Phase II trial of exemestane with immunomodulatory 
cyclophosphamide in ER and/or PR-positive and HER2/neu 
negative metastatic breast cancer 
Regulatory Sponsor/ 
Principal Investigator:
Sylvia Adams, MD
New York University Cancer Institute
Clinical Cancer Center
160 East 34th Street
Bellevue Hospital
462 First Avenue, New York, NY 10016
Tel:( 212) 263-6485
Sylvia.adams@nyumc.org
Co-PI:
Funding Sponsor:
Derya Unutmaz, MD
New York University Cancer Institute
NYU Cancer Institute
Study Product:
Exemestane – Aromasin
Cyclophosphamide - Cytoxan
Protocol Number:
S13-00761
IND:
Exempt
Clinical Co-Investigators 
Yelena Novik, MD
James Speyer, MD
Komal Jhaveri, MD
Marleen Meyers, MD 
Ruth Oratz, MD
Medical Monitor
Anna Pavlick, MD
160 East 34th Street, CCC 913
New York, NY 10016
Tel: (212) 731-5431
Anna.pavlick@nyumc.org
Laboratory Co-Investigators
Achim Jungbluth, MD MSKCC
Sacha Gnjatic, PhD MSSM
Co-Investigator- Biostatistician: 
Judith D. Goldberg, Sc.D. 
650 First Avenue 5 534 
New York, NY 10016 
Telephone: (212) 263-0314 
Fax: (212) 263-8570 
Regulatory/Nursing/Data mgt Support:
NYU Cancer Institute Clinical Trials Office
Tel: 212-263-6485
Initial version:
06/13/2013
Amended:
09/12/2013
Clinical Research Protocol

2
Table of Contents
STUDY SUMMARY......................................................................................................................................4
1
INTRODUCTION....................................................................................................................................5
1.1
BACKGROUND...................................................................................................................................5
 1.1.1 METASTATIC BREAST CANCER…………………………………………..………………………….…5 
                 1.1.2 ER/PR POSITIVE, HER2 NEGATIVE MBC AND TREATMENT OPTIONS FOR 2ND LINE ENDOCRINE 
THERAPY…………………………………………………...………………………………………......5
1.2
INVESTIGATIONAL AGENT...................................................................................................................7
 1.2.1 EXEMESTANE……………………..…………………………………………………………………….7
  1.2.2 CYCLOPHOSPHAMIDE…………….…………………………………...……………………………….7
1.3
PRECLINICAL DATA............................................................................................................................7
1.4
CLINICAL DATA TO DATE....................................................................................................................8
1.5
DOSE AND SCHEDULE RATIONALE....................................................................................................10
1.6
RESEARCH RISKS & BENEFITS .........................................................................................................12
     1.6.1 Risk of Study Drug ...............................................................................................................12
     1.6.2 Other Risks of Study Participation .......................................................................................12
     1.6.3 Potential benefits..................................................................................................................12
    1.7   CORRELATIVE STUDIES BACKGROUND…………………………………………………………………...….12
2
STUDY OBJECTIVES .........................................................................................................................13
     2.1  Risk of Study Drug..........................................................................................................................13
     2.2  Other Risks of Study Participation…………………………………………………………………….…..14
     2.3  Translational Objectives (if additional funding available)……………………………………………….14
3
STUDY DESIGN ..................................................................................................................................14
3.1
GENERAL DESIGN ...........................................................................................................................14
3.2
PRIMARY STUDY ENDPOINTS ...........................................................................................................14
3.3
SECONDARY STUDY ENDPOINTS ......................................................................................................14
3.4
SAFETY ENDPOINTS ........................................................................................................................15
4
SUBJECT SELECTION AND WITHDRAWAL ....................................................................................15
4.1
INCLUSION CRITERIA .......................................................................................................................15
4.2
EXCLUSION CRITERIA ......................................................................................................................15
4.3
SUBJECT RECRUITMENT AND SCREENING.........................................................................................16
4.4
EARLY WITHDRAWAL OF SUBJECTS..................................................................................................16
5
STUDY DRUG......................................................................................................................................16
5.1
DESCRIPTION..................................................................................................................................16
5.2
TREATMENT REGIMEN .....................................................................................................................17
5.3
DOSE MODIFICATIONS .....................................................................................................................17
5.4
PREPARATION, STORAGE AND ADMINISTRATION OF STUDY DRUG ......................................................17
5.5
SUBJECT COMPLIANCE MONITORING ................................................................................................17
5.6
CONCOMITANT THERAPY .................................................................................................................18
6
STUDY PROCEDURES.......................................................................................................................15
6.1
STUDY CALENDAR...........................................................................................................................16
6.2
MEASUREMENT OF ANTITUMOR EFFECT (RESPONSE ASSESSMENT BY RECIST 1.1). ...........................16
6.3
CORRELATIVE STUDIES....................................................................................................................16
6.4
FOLLOW UP. ...................................................................................................................................16
7
STATISTICAL PLAN ...........................................................................................................................16

3
7.1
SAMPLE SIZE DETERMINATION .........................................................................................................16
7.2
STATISTICAL METHODS....................................................................................................................16
7.3
SUBJECT POPULATION(S) FOR ANALYSIS ..........................................................................................16
8
SAFETY AND ADVERSE EVENTS.....................................................................................................17
8.1
EXPECTED ADVERSE EVENTS ..........................................................................................................17
8.2
DEFINITIONS ...................................................................................................................................17
8.3
RECORDING OF ADVERSE EVENTS .................................................................................................127
8.4
REPORTING OF SERIOUS ADVERSE EVENTS AND UNANTICIPATED PROBLEMS...................................127
8.4.1
Investigator reporting: notifying the IRB.................................................................................27
8.5
UNBLINDING PROCEDURES ..............................................................................................................28
8.6
STOPPING RULES............................................................................................................................28
8.7
MEDICAL MONITORING.....................................................................................................................28
8.7.1
Data Monitoring Committee...................................................................................................28
9
DATA HANDLING AND RECORD KEEPING.....................................................................................29
9.1
CONFIDENTIALITY ............................................................................................................................29
9.2
CONFIDENTIALITY AND HIPAA..........................................................................................................29
9.3
SOURCE DOCUMENTS .....................................................................................................................29
9.4
CASE REPORT FORMS.....................................................................................................................29
9.5
RECORDS RETENTION .....................................................................................................................29
10
STUDY MONITORING, AUDITING, AND INSPECTING...................................................................29
10.1
STUDY MONITORING PLAN.............................................................................................................29
10.2
AUDITING AND INSPECTING ............................................................................................................29
11
ETHICAL CONSIDERATIONS ..........................................................................................................30
12
STUDY FINANCES............................................................................................................................31
12.1
FUNDING SOURCE.........................................................................................................................31
12.2
CONFLICT OF INTEREST .................................................................................................................31
12.3
SUBJECT STIPENDS OR PAYMENTS.................................................................................................31
13
PUBLICATION PLAN ........................................................................................................................31
14
REFERENCES...................................................................................................................................31

4
Study Summary
Title
Phase II trial of exemestane with immunomodulatory cyclophosphamide in ER 
and/or PR-positive and HER2/neu-negative metastatic breast cancer. 
Short Title
Combination of endocrine and immune therapy in advanced breast cancer.
Phase
Phase 2
Methodology
Single-arm open label
Hypothesis
The treatment regimen of low dose immunomodulatory cyclophosphamide in 
combination with exemestane will result in a target 3-month PFS of > 75% 
(extrapolated from median PFS of 6.9 months seen in the combination arm of 
Bolero 2, current standard of care exemestane + everolimus but with 
significant toxicity).
Study Duration
Three years
Study Center(s)
NYU Cancer Center, Bellevue Hospital
Objectives
To estimate progression-free survival (PFS) and PFS rate at 3 months, 
response rate (RR), clinical benefit rate (CBR) and evaluate the safety of 
immunomodulatory doses of cyclophosphamide with exemestane after 
progression on at least one line of endocrine therapy. 
Number of Subjects
23
Diagnosis and Main 
Inclusion Criteria
Metastatic ER or PR positive, Her2 negative breast cancer
Progression on aromatase inhibitor (AI), tamoxifen and/or fulvestrant
Postmenopausal
Study Product, Dose, 
Route, Regimen
Cyclophosphamide at 50 mg tablet po daily and exemestane at 25 mg tablet 
po daily. 
Duration of 
administration
Treatment until progression or removal from study
Statistical 
Methodology
This is an open label single arm Phase II study to estimate the median PFS 
and the PFS on this regimen at 3 months. The primary outcome, PFS rate at 3 
months, will be estimated with an exact 95% confidence interval at the 
conclusion of the study. 

5
1
Introduction
This document is a protocol for a human research study. This study is to be conducted in accordance with 
US government research regulations, and applicable international standards of Good Clinical Practice, and 
institutional research policies and procedures.
1.1
Background
1.1.1
Metastatic Breast Cancer
Breast cancer is the most common cancer among women and is after lung cancer a leading cause of 
mortality in women. The majority of breast cancer related deaths are a result of complications from recurrent 
or metastatic disease. As an initial presentation, metastatic breast cancer (MBC) is uncommon, occurring in 
less than 10% of newly diagnosed cases [1]. However, up to 30% of the women who are initially diagnosed 
with early stage breast cancer eventually develop recurrent or metastatic disease. In the metastatic setting, 
treatment goals are generally to prolong life, control symptoms, and maintain quality of life.  Many of these 
patients are likely to have experienced recurrences after receiving prior adjuvant chemotherapy and/or 
endocrine therapy. A major limitation of treatments in the recurrent and metastatic settings is the high 
incidence of tumor resistance to endocrine agents. Over the last decade therapeutic innovation has only 
resulted in modest improvements in survival rates [2]. It is therefore clear that novel therapeutic approaches 
and/or combinations are needed.
1.1.2. ER/PR positive, HER2 negative metastatic breast cancer and treatment options for 2nd line 
endocrine therapy
The majority of breast cancers are hormone receptor (HR) positive breast cancers. The prognostic and 
predictive value of hormone receptor status has been well established. Sensitivity to endocrine therapies is 
typically suggested by a long disease-free interval, a high level of estrogen/progesterone receptor (ER/PR) 
expression in tumors, metastatic disease confined to non-visceral sites and the absence of HER2 
overexpression/amplification. Although there are limited data from RCTs (randomized controlled trials), 
results from non-randomized trials regarding the effects of endocrine sequence suggest that response to 
first-line therapy predicts response to subsequent endocrine therapy. 
While there is no optimized treatment sequence for hormonal therapies, therapeutic options for second-line 
treatment of HR positive metastatic disease have been evaluated in separate RCTs and include anti-
estrogens and aromatase inhibitors (Table 1). Third generation AIs are distinguished into non-steroidal 
(anastrazole and letrozole) and steroidal (exemestane) AIs. With non-steroidal AIs now being widely used in 
the adjuvant setting for postmenopausal women with HR positive breast cancer, the endocrine options for 
first-line treatment after relapse during or shortly after completion of adjuvant therapy are fulvestrant 500 mg, 
steroidal AI, steroidal AI with everolimus or tamoxifen (with or without everolimus).
Fulvestrant is an ER antagonist without known agonistic properties that downregulates cellular levels of ER 
in a dose-dependent manner. In a phase III RCT, the Comparison of Faslodex in Recurrent or Metastatic 
Breast Cancer trial (CONFIRM) [3] two different doses of fulvestrant (given by intramuscular injection) were 
evaluated—the initially approved dose (250 mg every 28 days) and a higher dose regimen including a day 
14 loading dose (500 mg on days 0, 14, and 28, and every 28 days thereafter).  Approximately 50% of 
enrolled patients had experienced relapse on adjuvant endocrine therapy or were within 1 year from 
completion of adjuvant endocrine therapy. For patients who experienced relapse after more than 1 year from 
completion of adjuvant endocrine therapy or for patients presenting with de novo advanced disease, 
eligibility required a previous treatment with either an antiestrogen (57.5% of patients) or an aromatase 
inhibitor (42.5%) as a first-line therapy. High-dose fulvestrant (500 mg monthly), as compared with standard 
dose fulvestrant, provided only a modest improvement in median progression-free survival, from 5.5 to 6.5 
months (hazard ratio, 0.80; P = 0.006). This improvement was less pronounced in patients whose most 

6
recent therapy was an aromatase inhibitor (hazard ratio, 0.85; P = 0.20) and in those who were considered 
to have had a response to the most recent endocrine therapy (hazard ratio, 0.85; P = 0.12).
Exemestane is an oral, steroidal irreversible inhibitor of aromatase. It did not show a difference in PFS in the 
international EFECT trial of fulvestrant 250 mg versus exemestane [4]. Enrolled patients were refractory to 
letrozole or anastrozole, defined as recurrence during or within 12 months after the end of adjuvant 
treatment or progression during or within 1 month after the end of treatment for advanced disease. Prior 
additional endocrine or chemotherapy was allowed and letrozole or anastrozole did not have to be the most 
recent treatment before randomization, approximately 15% of patients had received an anti-estrogen (TAM 
or fulvestrant) and approximately 10% of patients had received chemotherapy (max 1 line) in the metastatic 
setting. 
In the fulvestrant versus anastrozole Phase III trial North American trial [5] the primary analysis of time to 
progression (TTP) showed fulvestrant 250 mg to be at least as effective as anastrozole after failing one line 
of endocrine therapy (96% of patients received tamoxifen). 
It is therefore evident that standard approaches (switch to steroidal AI or fulvestrant) perform poorly once 
acquired resistance is observed and novel therapies for metastatic disease are needed. The 
phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway has been 
implicated in HR positive cancers and endocrine resistance [6]. This has led to studies combining various 
signaling inhibitors with aromatase inhibitors to enhance endocrine responsiveness and delay, or even 
reverse resistance.
BOLERO 2 [7]: This trial evaluated the addition of everolimus, which targets mTOR, to a steroidal AI after 
failure of at least one prior endocrine therapy (letrozole or anastrozole (100%), tamoxifen (48%), fulvestrant 
(16%) although 26% of patients had also received prior chemotherapy in the metastatic setting. The study 
showed longer PFS when everolimus is added to exemestane (published as 6.9 months for the 
combination versus 2.8 months for single agent exemestane). Final PFS data updated for San Antonio’s 
breast conference 2012 showed 7.8 vs 3.2 months PFS. 
This observed benefit of the combination exemestane and everolimus compares favorably with that of all 
alternative options, including fulvestrant at a dose of 250 mg with a median PFS of 3.7 months and 
fulvestrant at 500 mg with a PFS of 6.5 months (see table below).  The BOLERO 2 results also compare 
favorably to those achieved by (first-line) chemotherapy with capecitabine and taxanes or anthracyclines, 
with a median PFS of 6.2 months and 8.2 months, respectively, in patients with HR-positive disease 
(RIBBON-1, arms without bevacizumab [8]. Everolimus (Afinitor) therefore received FDA approval for 
metastatic breast cancer in July 2012 based on the prolongation of PFS in combination with exemestane. 
However, the combination of exemestane and everolimus was associated with a higher incidence of adverse 
events than exemestane alone, serious adverse events were reported in 23% of participants. The adverse 
events observed with everolimus plus exemestane include stomatitis, fatigue and asthenia, anemia, 
diarrhea, cough, dyspnea, pneumonitis, fever, and hyperglycemia. Despite permitted dose interruptions 
and/or reductions, a high percentage of patients discontinued everolimus because of intolerability (19% of 
patients) or withdrawal of consent (5%). 1% of patients in the everolimus arm died due to an adverse event. 
Table 1: Outcomes of Phase III RCT of endocrine therapy in patients with metastatic hormone-
receptor positive breast cancer who failed a non-steroidal aromatase inhibitor or an anti-estrogen
Trial
Agents
RR^
CBR^
PFS^
OS
percent
months
BOLERO 2
2nd line after AI, n=724
Exemestane
Exemestane + Everolimus
0.4
7* 
n.a.
2.8 
  6.9*
n.a.
EFECT
2nd line after AI, n=693
Fulvestrant 250 
Exemestane
7.4
6.7
32.2
31.5
3.7
3.7
n.a.
CONFIRM
2nd line after TAM or AI, n=736
Fulvestrant 500 
Fulvestrant 250
9.1
10.2
36.5
29.4
6.5*
5.5
25.1*
22.8

7
North American trial
2nd line after TAM, n=400
Fulvestrant 250
Anastrozole
17.5
17.5
42.2
36.1
5.4
3.4
27
27
*Statistically significant difference, n.a. not available, RR response rate CBR clinical benefit rate PFS 
progression-free survival OS overall survival
^Frequency of RECIST tumor assessment: Bolero 2 q 6 weeks, North American trial q 12 weeks, CONFIRM 
q 12 weeks, EFECT q 8 weeks (after 6 months q 12 weeks) 
1.2
Investigational Agents
1.2.1
Exemestane 
Exemestane (trade name aromasin) is an oral steroidal aromatase inhibitor indicated for the treatment of 
breast cancer in post-menopausal women. It is a synthetic androgen analogue (6-methylenandrosta-1,4-
diene-3,17-dione), which binds irreversibly to and inhibits the enzyme aromatase, thereby blocking the 
conversion of cholesterol to pregnenolone and the peripheral aromatization of androgenic precursors into 
estrogens, the main pathway providing estrogen after menopause. Exemestane significantly lowers 
circulating estrogen concentrations in postmenopausal women, but has no detectable effect on adrenal 
biosynthesis of corticosteroids or aldosterone.
Aromasin was originally approved in the US in 1999 for the treatment of advanced breast cancer in 
postmenopausal women whose tumors have stopped responding to tamoxifen. On October 5, 2005, the U.S. 
Food and Drug Administration approved exemestane for adjuvant treatment of postmenopausal women with 
estrogen receptor -positive early breast cancer following two-to-three years of tamoxifen based on the results 
of the Intergroup Exemestane Study [9], showing superior DFS in a double-blind, multicenter, international 
clinical trial in 4724 patients randomly assigned to either continue tamoxifen (20-30 mg/day) or switch to 
exemestane (25 mg/day) to complete a total of five years of adjuvant hormonal therapy. The most common 
adverse events on the IES that occurred more frequently on the exemestane arm included hot flashes, 
fatigue, arthralgia, headache, insomnia, increased sweating, hypertension, and dizziness. Cardiac ischemic 
events occurred in 1.6 percent of patients in the exemestane arm of the IES compared to 0.6 percent of 
patients in the tamoxifen arm. Changes in bone mineral density (BMD) were evaluated in a sub-study of the 
IES and in a supporting safety study (027), which compared the effects of two years of exemestane to 
placebo. Mean decreases in BMD of the lumbar spine and femoral neck were more pronounced with 
exemestane than with either tamoxifen or placebo. On the IES, osteoporosis was reported in 4.6 percent of 
patients treated with exemestane compared to 2.8 percent of patients receiving tamoxifen.
1.2.2
Cyclophosphamide
Cyclophosphamide (former trade name cytoxan, CTX) is a synthetic alkylating agent chemically related to 
the nitrogen mustards with antineoplastic and immunosuppressive activities. In the liver, CTX is converted to 
the active metabolites aldophosphamide and phosphoramide mustard, which bind to DNA, thereby inhibiting 
DNA replication and initiating cell death. While conventional (high) dose CTX is cytotoxic and a mainstay of 
treatment in breast cancer, it causes cytopenias and is generally considered as an immunosuppressive 
agent. 
Metronomic cyclophosphamide ("frequent and homogeneously spaced low-dose" 
administrations)
1.3
Preclinical Data
In contrast, low dose metronomic CTX can enhance immune responses. Initially, preclinical models provided 
evidence of the ability of CTX to selectively deplete regulatory T cells (Tregs), thereby improving anti-tumor 
immune responses (summarized in Table 2). 

8
Table 2:  Pre-clinical studies of cyclophosphamide alone or in combination with immunotherapies 
Reference
Murine 
Model
CTX dose and schedule
Combination 
agent
Immune responses
Outcome
Hermans 
Ca Res 2003 [10]
Melanoma
175 mg/kg every 6 days 
or 150 mg/kg every other 
day over 6 days followed 
by 15 days of rest 
Vaccine d1, 
boosted 14-60 
days later
Higher in combination with 
175 mg/kg
Improved survival 
with 175 mg/kg
Lutsiak Blood 
2005 [11]
Healthy 
100 mg/kg day 0
none
Decrease in CD4+25+ Treg 
number (halved on d4), 
function and enhanced 
apoptosis
Motoyoshi Oncol 
Rep 2006 [12]
Hepato-
cellular 
cancer
200 mg/kg or 20 mg/kg 
after tumor inoculation
none
high dose decreased all T 
cell subsets while low dose 
decreased Tregs selectively
Anti-tumor effect 
with low dose, only 
in immuno-
competent mice and 
if given after tumor 
inoculation
Malvicini 
Oncoimmunol 
2012 [13] and 
Mol Oncol 2011 
[14]
Colorectal 
and 
pancreas 
cancer
50mg/kg once day 8 
versus 25mg/kg 3x/week 
Adenovirus 
expressing IL-12 
Both initially decreased Treg 
and MDSC but 25 mg/kg did 
not sustain, better IR with 50 
mg/kg
Seen with 50 mg/kg 
(RR and OS)
Mkrtichyan Eur J 
Immunol 2011 
[15]
TC-1 tumor 
cells
50mg/kg the day before 
vaccine 
Anti-PD-1
HPV16 E7 
peptide /GM-
CSF/anti-CD40
Tumor 
regression 
and 
increased 
survival
Sevko JID 2012 
[16]
Melanoma
50 and 125 mg/kg once
none
Treg decrease but MDSC 
expansion
No benefit
Son J 
Immunother 
2012 [17]
Colon 
cancer
30 mg/kg 3 days before 
every iDC injection 
3x/week
RT and 
intratumoral iDC
Treg decrease, increased 
anti-tumor 
immune 
response 
Improved survival
Dewan CCR 2012 
[18]
Breast 
cancer
100 mg/kg once 
RT and 
imiquimod
reduces Tregs and IL-10 
production, 
enhances 
tumor-specific IFN-g
production by TDLNs
Prevented 
tumor 
recurrence 
and 
rejected
tumor challenge
1.4
Clinical Data to Date
More recently low dose CTX has been studied in patients based on the preclinical evidence discussed 
above. Extensive reviews of low-dose CTX in combination with immunotherapies demonstrate an excellent 
safety profile [19-21]. CTX (50 or 100 mg/d) is well tolerated even in elderly and/or heavily pretreated 
patients. Toxicities are usually grade I/II and manageable, only when combined with bevacizumab, have 
severe adverse events (hemorrhagic complications) been reported. 
Several of the clinical trials confirmed immune modulating properties of low dose CTX; relevant studies are 
summarized in Table 3. Numerous single agent and combination studies have demonstrated some signs of 
activity, although most clinical studies reported are non-randomized. In small but randomized studies CTX 
was confirmed to be effective and safe as both, single agent in refractory solid tumors [22] and in 
combination with letrozole in the neoadjuvant treatment of ER positive breast cancers [23]. 
Table 3: Clinical trials of low dose cyclophosphamide alone or in combination therapy 
Reference
Setting
CTX regimen
Immune changes
Safety and efficacy
Single agent cyclophosphamide

9
Ghiringhelli, 
CII 2007 [24]
End-stage 
cancer (n=9)
1.4 mg/kg CTX per day (i.e. 50 mg 
BID) for weeks 1 and 3 of 4 week 
cycle
Selective depletion of Tregs, 
restored NK and T effector 
function, (non-selective depletion 
of all leukocytes and decreased 
NK and T function at 100 mg 
BID)
 
Greten, J 
Immunother 
2010 [25]
HCC (n=13)
150, 250, or 350 mg/m2 (3.4, 5.7, 
and 6.8 mg/kg) on d 1 and d29
Selectively depletes Tregs in low 
groups only (reduction of 34.1% 
by d 8, 80% by d 29, and 65% by 
d 71, endogenous Ag-spec T cell 
responses unmasked in 6/13
 No DLT
Ge, CII 2012 
[26]
Breast cancer 
(n=12)
50 mg CTX daily x 3 mos (0.7 
mg/kg)
Transiently
reduced Tregs, rebounded after d 
42
Anti-tumor response and 
SD, 
no 
grade 
III/IV 
toxicity, 
grade 
I 
leucopenia in all patients
Penel, Br J 
Cancer 2010 
[22]
End-stage 
cancer (n=88; 
no 
breast 
cancer)
50 mg BID CTX (1.4 mg/kg/d) 
continuously 
versus 
megestrol 
acetate
 Not evaluated
Safe, PFS 20%, 11% and 
4% at 2, 4 and 6 months, 
TTP 2 months both arms
Viaud, Ca Res 
2011 [27]
Advanced 
cancers (n=21)
50 mg/d CTX daily (0.7 mg/kg) x 3 
weeks
Expansion 
of 
Th17 
cells 
in 
periphery and tumor
Cyclophosphamide in combination with immune-, biological or chemotherapy
Hoon, Cancer 
Res 1990 [28]
Melanoma
75, 150 and 300 mg/m2 (1.7, 3.4 
and 6.8 mg/kg) CTX or no CTX prior 
to vaccine
Selective 
depletion 
of 
CD8+ 
suppressor T cells, greater with 
first 2 cycles
Possibly benefit
Laheru, CCR 
2008 [29]
Pancreatic 
cancer
250 mg/m2 (5.7 mg/kg) CTX versus 
none on day -1 prior to each 
vaccination
Greater CD8-T cell response with 
CTX
Safe, improved OS with 
CTX
Emens, JCO 
2009 [30]
Breast 
cancer
200, 250, and 350 mg/m2
(4.5, 5.7 or 6.8 mg/kg) CTX prior to 
each vaccine versus no CTX
HER2-specific immunity only in 
lowest dose (and no) CTX groups
Safe
Greten, BMC 
Cancer 2010 [25]
 Liver 
cancer 
300 mg/m2 CTX (6.8 mg/kg) d-3 
prior to peptide vaccine and GM-
CSF
Decreased Tregs, but no vaccine 
response
Safe
Slingluff, JCO 
2011 [31]
 Melanoma
300 mg/m2 (6.8 mg/kg) CTX given 
with each vaccination versus no 
CTX
No 
impact 
on 
Ag-specific 
immunity
Safe (g 4 hypoglycemia?)
Chu, CII 2011 [32]
Ovarian 
cancer
300 
mg/m2 
CTX 
(6.8 
mg/kg) 
intravenous CTX two days before 
vaccine
No change in Tregs
Safe
Cerullo, Mol Ther 
2011 [33]
Advanced 
cancers
50 mg/day oral (x 7 days before 
vaccine) (=0.7 mg/kg/d), 1000 mg 
(15 mg/kg) IV x1, or a combination 
of oral and IV CTX prior to vaccine
Decreased 
Tregs 
without 
compromised anti-tumor / anti-
viral IR in both po arms
Safe, best OS in third 
group
Berd, Cancer Res 
1987/88 [34, 35]
Melanoma
300 mg/m2 (6.8 mg/kg)  CTX 3 d 
prior to vaccine
Increased Ag-specific immunity in 
CTX arm
Safe, tumor regression 
and 2 CRs
Colleoni, Ann 
Oncol 2002 [36]
Breast 
cancer
50 
mg/d 
CTX 
(0.7 
mg/kg) 
continuously, with low dose MTX 
Not evaluated
 Safe, 19% RR, TTP 2.8 
months
Orlando, Antica 
Drugs 2006 [37]
Breast 
cancer
50 
mg/d 
CTX 
(0.7 
mg/kg) 
continuously, with low dose MTX 
Not evaluated
Safe, 
15% 
RR, 
one 
durable CR>4 years
Dellapasqua, 
JCO 2008 [38]
Breast 
cancer
50 
mg/d 
CTX 
(0.7 
mg/kg) 
continuously, with capecitabine and 
bevacizumab 
Not evaluated
Safe, 48% RR
Wong, JCO 2010 
[39]
Breast 
cancer
50mg/d 
CTX 
(0.7 
mg/kg) 
continuously with dalteparin, MTX 
and prednisone
Not evaluated
Safe, 17% RR
Bottini, JCO 2006 
[23]
Breast 
cancer
Preoperative letrozole +/- CTX 50 
mg/d (0.7 mg/kg) continuously for 6 
months
Not evaluated
Increased RR with CTX, 
greater decrease in Ki67
Colleoni, Ann 
Oncol 2006 [40]
Breast 
cancer
50 
mg/d 
CTX 
(0.7 
mg/kg) 
continuously with low dose MTX +/- 
thalidomide
Not evaluated
Without thalidomide: safe, 
21% RR, TTP 3.8 months
Ongoing trials utilizing immunomodulatory cyclophosphamide
Emens 
(NCT00971737):
Breast 
cancer
CTX 200 mg/m2 IV (4.5 mg/kg) over 30 minutes on day before each vaccine (q 4-6 weeks) 
Knutson 
(NCT01606241)
Breast 
cancer
CTX 100 mg CTX orally daily (1.4 mg/kg) for 1 week followed by 1 week rest, then another 1 week of 
CTX, followed by vaccine 7-10 days after 

10
Bhardwaj 
(NCT01740401)
Melanoma
CTX 300 mg/m2 orally (6.8 mg/kg), 2 days prior to each ipilimumab dose
Conversions based on assumptions of a patient with BSA 1.6 m2 and 70kg: for example CTX 300 mg/m2 = 
480 mg = 6.8 mg/kg or CTX 50 mg total = 0.7 mg/kg 
1.5
Dose and Schedule Rationale
The beneficial anti-tumor effects of low dose CTX are mediated by selectively depleting circulating Tregs, 
thereby restoring levels to those seen in healthy volunteers [24, 26]. Circulating Tregs are increased in 
patients with cancer (approximately 5% of circulating CD4 T cells) and have a higher proliferative capacity 
compared with healthy individuals [26]. Tregs can exert functional inhibition on tumor-specific T cells and 
blunt the innate arm of immunity by inhibiting NK cell proliferation and effector functions. Therefore, Tregs 
can limit the induction of anti-tumor immune responses, immune rejection via innate and adaptive 
mechanisms and promote disease progression, all of which likely contribute to the positive correlation of 
Treg –especially T cells infiltrating the tumor- with worse outcomes in a variety of solid tumors, including 
breast cancer [41]. 
Treatment of cancer patients with low dose CTX has been shown to:
1.
Selectively deplete Tregs, thereby restoring levels to those seen in healthy volunteers , 
2.
limit the suppressive function of remaining Tregs 
3.
restore NK cell-dependent cytotoxicity (innate killing)
4.
restore peripheral T cell proliferation
5.
unmask pre-existing (endogenous) tumor antigen-specific T cell responses
6.
induce T cell responses to endogenous tumor antigens
7.
normalize proliferative ability of effector T cells, especially CD8 T cells
8.
increase Th17 cells
9.
enhance vaccine responses
These effects of CTX were only seen at certain doses (for instance with CTX 100 mg/d but not with 200 mg/d 
as higher doses depleted lymphocytes in a non-selective manner and decreased NK cell-dependent 
cytotoxicity and T cell proliferation). 
Treg depletion is usually transient. With the CTX 50 mg daily for 3 months regimen used by Ge et al [26], 
Treg numbers were reduced for 4-6 weeks, then rebounded to pre-treatment levels at week 8, remaining at 
that level until the end of treatment; the proliferative capacity of Treg recovered as well. Interestingly, 
induced and unmasked anti-tumor T cell responses continued to increase throughout the 3 months treatment 
period (despite an only transient decrease of Tregs) and correlated with clinical benefit. In a study by 
Ghiringhelli et al utilizing CTX 50 mg BID 1 week on and 1 week off [24], Treg were significantly reduced at 4 
weeks, residual Treg had lost their suppressive function and T and NK effector function were restored. As 
with continued treatment in the study by Ge, Treg numbers also returned to baseline when measured 2 
months after stopping treatment in the study by Ghiringhelli.
While there is no documented superiority of a specific immune modulating dose/regimen in patients, in the 
proposed clinical trial we will use CTX at 50 mg by mouth daily on a continuous basis, per schedule studied 
by Ge et al, as this regimen has shown a decrease in Tregs for the first 2 months, the induction of breast 
cancer antigen-specific immunity and was exclusively tested in breast cancer patients. Furthermore this dose 
and schedule has been safely and effectively combined with an aromatase inhibitor in the neoadjuvant 
setting for breast cancer [23].
Rationale for the current trial and the combination of exemestane with 
immunomodulatory cyclophosphamide 

11
There is an unmet need for therapeutics in hormone-receptor positive metastatic breast cancer after failure 
to respond to non-steroidal aromatase inhibitors or an antiestrogen. The phase III RCTs in this setting (Table 
1) demonstrated that single agent exemestane as second line treatment has low response rates in the 0.4-
6.7% range and a short PFS of 2.8-3.7 months. It is therefore evident that standard approaches perform 
poorly once acquired resistance is observed and novel therapies for metastatic disease are needed. Notably, 
the addition of the targeted agent and mTor inhibitor everolimus to exemestane in the Bolero 2 trial led to a 
significantly better outcome for patients with a four month improvement of PFS over single agent 
exemestane alone (RR remained low at 7%). The benefit of the combination led to its regulatory approval in 
the US in 2012 and offers a new benchmark for clinical benefit in sequential hormonal manipulation for 
metastatic breast cancer. However, the significant toxicity of the combination regimen limits its generalized 
adaptation and patient compliance, with a dropout rate of 24% of patients receiving everolimus [42].
In the current trial we will investigate if exemestane combined with low dose CTX, a known 
immunomodulator, which is also the most commonly used metronomic chemotherapeutic and is 
exceptionally well tolerated [21], can provide a significant clinical benefit similar to that seen with 
exemestane + everolimus in the Bolero 2 trial. Both regimens are available orally, but if successful, 
the exemestane + CTX combination would be a favorable alternative due to its cost-effectiveness and 
tolerability, and a larger randomized trial would be pursued.  
We hypothesize that low dose CTX in combination with exemestane will result in a target 3-month 
PFS rate of > 75% (extrapolated from median PFS of 6.9 months seen in the combination arm of 
Bolero 2). This expected improvement of PFS over exemestane alone is based on the following 
reasons: 
1.
Both modalities have a distinct major mechanism of action (with non-overlapping toxicities)
Exemestane, as discussed above, is a steroidal aromatase inhibitor, which reduces levels of circulating 
estradiol via inhibition of its biosynthesis from androgen precursors. CTX at low immunomodulating doses 
selectively depletes Tregs as discussed above, thereby restoring innate and adaptive anti-tumor immunity. 
2.
Both drugs have the potential to diminish the pool and suppressor function of Tregs 
The Treg modulating potential of low dose CTX has been discussed extensively in Section 2.4; and may lead 
to the induction and/or unmasking of anti-tumor immune responses which could provide a beneficial and 
long-lasting effects on tumor control. 
Anti-estrogen therapies may also modulate Tregs. Endogenous estrogens at physiological (late follicular 
phase of menstrual cycle and pregnancy) and pharmacological ranges have been shown to drive expansion 
of CD4+CD25+ Tregs after their activation, increase the expression of Foxp3 and IL-10 genes as well as 
stimulate the conversion of CD4+CD25− T cells (which express ER) into CD4+CD25+ T cells with similar 
regulatory function as naturally occurring Tregs [43-46]. As the conversion of CD4+CD25− T cells into 
CD4+CD25+ T cells stimulated by E2 could be inhibited by a specific inhibitor of ER [47] and numbers of 
Tregs generally decrease with lower estradiol levels, it is possible that lowering circulating estradiol levels via 
exemestane may contribute to a diminished Treg pool in patients. In a rat model of human arthritis, 
administration of anastrozole for instance suppressed the differentiation of naive T cells to Tregs as well as 
induced IFN-γ and IL-12 (Th1) and decreased levels of IL-4 and IL-10 (Th2 cytokines) [48]. In elderly breast 
cancer patients, neoadjuvant treatment with the non-steroidal AI letrozole decreased intratumoral Tregs, 
especially in responding tumors, which was potentiated by the addition of daily low dose CTX at 50 mg/d, 
albeit not statistically significant [49]. 
3.
Potential other mechanisms of action to overcome endocrine resistance 
It is not known if immunomodulatory CTX in combination with exemestane may overcome endocrine 
resistance, however some older studies suggest that non-specific immune stimulation, for instance with IFN-
γ can restore antiestrogen sensitivity and that the combination of IFN-α and tamoxifen had a greater anti-
proliferative effect on ZR-75-1 breast cancer cells than either drug alone [50]. Pilot studies suggest that IFN-
β can improve clinical benefit in metastatic breast cancer, and a planned study will test IL-2 and an 
antiestrogen [51]. 

12
Importantly, based on two randomized trials performed in the neoadjuvant setting, the efficacy of the 
combination of letrozole with low dose CTX is similar to the one observed with letrozole and 
everolimus, albeit with fewer side effects necessitating treatment interruption or dose reduction 
(Table 4). 
Table 4: Randomized neoadjuvant Phase II trial comparing a single agent aromatase inhibitor with 
the combination of aromatase inhibitor and everolimus (or CTX)
 
Baselga et al, JCO 2009, n= 270
Bottini et al, JCO 2006, n=114
Letrozole
Letrozole + 
everolimus
Letrozole +
low dose CTX
Letrozole
Clinical response
59%
68%
88%
72%
Ki67 reduction
75%
90%
88%
73%
Pathologic response
0.8%
1.4%
3.5%
3.5%
Dose delay or reduction for AE due to 
combination agent (everolimus or CTX)
53%
2%
1.6
Research Risks & Benefits
1.6.1
Risk of Study Drug
Expected adverse events (AEs) for low dose CTX and exemestane are listed in section 8. While this is a 
greater than minimal risk study, exemestane (alone or in combination with everolimus) is a standard of care 
regimen in the proposed setting, and the addition of low dose CTX to an AI has not demonstrated a 
significantly increased rate of AEs in a randomized trial of preoperative letrozole and CTX in breast cancer 
[23]. 
1.6.2
Other Risks of Study Participation
Additional risks to study participation are listed in the consent form and include breach of confidentiality, not 
deriving benefit from the study treatments, procedures performed for research only (immune blood draws 
and tumor FNAs). Privacy protection procedures are in place and good clinical practice guidelines are 
followed for the study to minimized risks associated with research procedures and participation.
1.6.3
Potential benefits
It is not known if participation in the study will be beneficial for the patient, although it is anticipated that 
patients will derive clinical benefit from the combination with prolongation of PFS based on the data 
discussed above. The major theoretical benefits lie in a potentially as effective but less toxic alternative for 
exemestane + CTX (instead of everolimus) and the induction of a long-lasting protective anti-tumor immune 
response. 
1.7
Correlative Studies Background
If funding is available, we plan to do the following correlative studies in all or a subset of trial participants to 
assess a baseline status and changes with treatment. 
Phenotypic and functional profile of peripheral lymphocytes and myeloid lineages 
Low dose CTX treatment has beneficial anti-tumor effects which have been attributed to relatively selective 
depletion of circulating Tregs, thereby restoring levels to those seen in healthy volunteers [24, 26]. Tregs can 
potentially exert functional inhibition of tumor-specific T cell activation and may also blunt the NK and innate 

13
arm of immunity through suppression of their effector functions. Therefore, Tregs can limit the induction of 
anti-tumor immune responses, immune rejection via innate and adaptive mechanisms and promote disease 
progression. It is therefore reasonable to hypothesize that low dose CTX treatment enhances anti-tumor 
immunity through selective depletion of Tregs, as has been previously suggested. However, these studies 
were limited in their analysis of Treg subsets and corollary effector T cell subsets. Further, the perturbations 
in other regulatory compartments, such as myeloid suppressor cells or impact of CTX on the innate immunity 
could contribute to its beneficial effects. As such, we propose to assess the immune compartments in high 
resolution before and after CTX treatment to identify a profile that can provide both biomarker signatures and 
mechanistic insights. These immune profiling studies of Tregs and other lymphoid/myeloid subsets at 
baseline and selected time points during treatment to confirm an effect of CTX by established flow cytometry 
based methodology  is described in section 6.3.
Examination of tumor antigen-specific CD4 and CD8 T cell responses 
Induction of tumor antigen-specific immunity would imply that the treatment facilitates cross-priming and/or is 
unmasked by the inhibition/depletion of Tregs. Antigen-specific immune monitoring is more feasible than 
autologous whole tumor cell monitoring and has been demonstrated to correlate with clinical benefit in 
metastatic breast cancer, when Her2-specific CD4 T cell response was examined during therapy with 
trastuzumab and chemotherapy [52]. Paraffin-embedded tumor tissue (archived or study entry) will be tested 
for the expression of five antigens:  1. PRAME (PReferentially expressed Antigen of Melanoma), 2. WT-1 
(Wilms’ Tumor gene), 3. Her2, 4. NY-ESO-1 and 5. MAGE A3. These tumor antigens (TAA) are selected due 
to their expression in breast cancers (frequencies listed in table below, based on which >90% of patients will 
express at least 2 of the 5 antigens), inclusion of CTL epitopes and the availability of overlapping peptide 
pools. In addition, pre-existing immune responses have been observed for some antigens in breast cancer 
patients [53] and anti-tumor activity has been observed for some antigens when used for vaccination [54-57]. 
Antigen 
Expression in breast cancer 
IHC mAb (Source) 
References
PRAME
27-53%
AB32185 (Abcam)
[58, 59]
WT-1
33-87%
6F-H2 (Dako)
[60, 61]
Her2
24%
Commercial, FISH for 2+
[62]
NY-ESO-1
5-42%
E978 (LICR)
[63, 64] and unpublished data
MAGE A3
10-19%
M3H67 (LICR)
[65] and unpublished data
With the exception of Her2 antigen, for which results will be used from routine 
clinical testing, IHC procedures follow standard techniques as previously published 
by our group with collaborator Dr Jungbluth [66], an example IHC stain is shown for 
NY-ESO-1+ breast cancer), antigens expressed in at least 10% of tumor cells will be 
selected for T cell monitoring for a given patient. 
2
Study Objectives
2.1 Primary Objective  
To estimate the median PFS and PFS rate at 3 months with the addition of immunomodulatory doses of 
cyclophosphamide to exemestane in patients with ER and/or PR-positive, Her2-negative metastatic breast 
cancer who progressed on endocrine therapy with an aromatase inhibitor, fulvestrant and/or tamoxifen.  
Patients treated with exemestane alone in a second line setting have a median PFS of 2.8 months; whereas 
patients treated with a combination of exemestane and everolimus have a median PFS of 6.9 months with 
added toxicity based on the randomized Bolero 2 trial data. For the current trial a target 3-month PFS of > 
75% (based on the assumption of an exponential survival distribution and median PFS of 6.9 months) is 
considered promising. Based on the data from Bolero 2 summarized above, the estimated PFS at 3 months 
on the combination regimen is 75% assuming that the distribution of progression free survival is exponential. 
[Calculations from PASS, NCSS, 2008, J. Hintze, Kaysville, Ut.]. 
2.2.Secondary Objectives

14
a.
To estimate the response rate of the combination of exemestane and cyclophosphamide. 
Published data suggest that patients treated with exemestane alone or in combination with everolimus in 
a second line setting have a RR of less than 10 %. 
b.
To estimate the clinical benefit rate (defined as objective response plus stable disease for at least 24 
weeks) of the combination of exemestane and cyclophosphamide. 
c.
To determine the adverse event profile in patients treated with exemestane and cyclophosphamide 
(CTCAE v 4.0).
2.3. Translational Objectives (if additional funding available)
i.
To assess changes in circulating T regulatory effector T cells and innate subsets during combination 
treatment with exemestane and immunomodulatory cyclophosphamide.
ii.
 To measure changes in tumor antigen-specific T cells from baseline and during combination 
treatment with exemestane and immunomodulatory cyclophosphamide.
iii.
To assess if tumor-infiltrating T regulatory lymphocytes in archival paraffin embedded tumor 
specimens from either the primary tumor or metastatic disease is predictive of PFS. 
3
Study Design
3.1
General Design
This is a Phase II open label non-randomized single arm trial of exemestane and cyclophosphamide to 
estimate the median PFS and the PFS rate at 3 months in patients with metastatic ER/PR positive, HER2 
negative breast cancer who progress on at least one line of endocrine therapy. The median progression-free 
survival estimated from the Bolero 2 trial for a single agent exemestane is 2.8 months, whereas the 
combination exemestane + everolimus achieved a median PFS of 6.9 months but added significant toxicity. 
For the current trial a target 3-month PFS of > 75% (based on the assumption of an exponential survival 
distribution and median PFS of 6.9 months) is considered promising. With a single stage design, we can 
reject the null hypothesis that the progression-free survival rate at 3 months is 50% or less versus that 
alternative that the progression free survival rate at 3 months is 75 % or greater with a alpha of 0.05 and 
power of 80% with 23 patients enrolled over 2-2.5 years. If the number of patients surviving progression-free 
at 3 months is 15 or fewer, then the regimen will be rejected.  
3.2
Primary Study Endpoints
The primary endpoint is Progression-free survival (PFS).  PFS is defined as the time from first treatment day 
until objective disease progression or death from any cause. Assessment of disease progression (eg, tumor 
measurements as per RECIST 1.1) will be performed every 12 weeks on study.  
3.3
Secondary Study Endpoints
Response rates and clinical benefit rates will be estimated using exact 95% confidence intervals. Changes 
from baseline in circulating T regulatory cells during combination treatment and in tumor antigen-specific T 
cells during treatment will be summarized using descriptive statistics at each time point and mixed effects 
regression models to incorporate repeated observations within a patient and missing data.
3.4
Safety Endpoints
Adverse events will be recorded along with grade (CTCAE v 4.0), attribution, onset, duration, outcome and 
treatment if indicated. The proportions of patients with various type/grade of adverse events will be 
summarized and reported. 

15
4
Subject Selection and Withdrawal
4.1
Inclusion Criteria
4.1.1
 Patients must have histologically confirmed breast cancer that is ER positive and/or PR positive, 
and HER2/neu negative and have disease that is metastatic (stage IV [TanyNanyM1]) 
 

HER2/neu negative disease determined using commercially available/approved assay in local 
institutional or reference laboratory, according to ASCO/CAP guidelines (IHC 0-1+ or 2+ with 
HER2/17 ratio on FISH < 1.8). 

ER/PR expression performed by standard immunohistochemical assay and classified as ER 
and/or PR-positive according to ASCO/CAP guidelines (1-100% expression)

Histologic and/or cytologic confirmation of metastatic disease is encouraged whenever feasible, 
furthermore, if feasible, the biopsy should confirm that the metastatic tumor is ER and/or PR 
positive and HER2/neu negative. For patients in whom histologic biopsy confirmation and/or 
assessment of ER/PR/HER2 of metastatic disease is not feasible, it is required that the primary 
tumor be ER and/or PR-positive and HER2/neu negative. 
4.1.2
Measurable disease (RECIST 1.1) or non-measurable (assessable) disease
4.1.3
Patients must have had progressive disease during at least one line of endocrine therapy for 
metastatic disease or have recurrent disease while or within 12 months of receiving adjuvant 
endocrine therapy. Prior treatments accepted include a non-steroidal aromatase inhibitor, tamoxifen, 
fulvestrant or combinations. 
4.1.4
Patients taking bisphosphonates for bone disease are permitted to enter the trial, but their bone 
lesions are not considered to be assessable for response, although they are assessable for 
progression.
4.1.5
Female or male subjects age > 18 years. 
4.1.6
ECOG performance status 0, 1, or 2.
4.1.7
Patients must have normal organ and marrow function as defined below:
                                

absolute neutrophil count
>1,200/mcL

platelets
>100,000/mcL

hemoglobin                                 > 9g/dl 

total bilirubin
<2 X ULN [unless  due to Gilbert’s disease]

AST(SGOT)
<2.5 X ULN

ALT(SGPT)
<2.5 X ULN

creatinine
< 1.5 X ULN
4.1.8
Patients must be able to swallow and tolerate oral medications.
4.1.9
Postmenopausal status, defined as 60 years and older, being 45 years and older and having 
amenorrhea x 12 months or follicle stimulating hormone levels within postmenopausal range, OR 
having undergone a bilateral oophorectomy.   
4.1.10
Ability to understand and the willingness to sign a written informed consent document.
4.2
Exclusion Criteria
4.2.1
Patients may not be receiving any other investigational agents.
4.2.2
Prior treatment for breast cancer with a steroidal aromatase inhibitor; with the exception of patients 
who were started on the combination of exemestane with everolimus less than 4 weeks prior to 
study entry and discontinued everolimus due to poor tolerability. 
4.2.3
Presence of life threatening metastatic visceral disease (defined as extensive hepatic involvement or 
symptomatic pulmonary lymphangitic spread) or uncontrolled brain metastases. 

16
4.2.4 
Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, symptomatic 
congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or psychiatric illness/social 
situations that would limit compliance with study requirements.
4.3
Subject Recruitment and Screening
Patients will be recruited from physicians at the NYU Medical Center and Bellevue as well as through outside 
referrals. Consenting, screening and treatment takes place at the NYU Clinical Cancer Center and Bellevue 
Cancer Center under the supervision of the PI. Prospective subjects receive detailed information about this 
study and its investigational nature, required study procedures, alternative treatments, risks and potential 
benefits of the study. They also receive the informed consent document to read. All questions are answered 
by the PI and qualified research personnel. 
Recruitment and consenting will take place in a private area such as an exam room to protect the patient’s 
privacy. The informed consent process and documentation follows the established procedures of the NYUCI 
Clinical Trials Office. 
4.4
Early Withdrawal of Subjects
Subjects may be withdrawn from the study prior the expected completion of that subject for the following 
reasons: 

Significant noncompliance on the part of the patient

Refusal of the patient to continue treatment or observations

Intercurrent illness that prevents further administration of treatment

Disease progression

Unacceptable adverse events regardless of grade

Termination of study

Subject consent withdrawal

Decision by the Investigator that termination is in the patient’s best medical interest, for 
instance for significant disease progression

Unrelated medical illness or complication
5
Study Drug 
5.1
Description
Cyclophosphamide (former trade name cytoxan, CTX) is a synthetic alkylating agent chemically related to 
the nitrogen mustards, which at the low dose utilized in this study is an immunomodulatory agent.
Cyclophosphamide:
Bioavailability >75% (oral)
Protein binding >60%,
Metabolism: Hepatic, CTX is metabolized by cytochrome P450 (CYP2B6, 2C9 and 
3A4 (with 2A6, 2C8 and 2C19 making more minor contributions)), glutathione S-
transferase (GST) and aldehyde dehydrogenase (ALDH) enzymes
Half-life: 3-12 hours
Excretion: Renal
Exemestane (trade name aromasin) is an oral steroidal aromatase inhibitor indicated for the treatment of 
breast cancer in post-menopausal women. It is a synthetic androgen analogue (6-methylenandrosta-1,4-
diene-3,17-dione), which binds irreversibly to and inhibits the enzyme aromatase

17
Exemestane:
Bioavailability 42% (oral)
Protein binding 90%,
Metabolism: Hepatic, exemestane is metabolized by cytochrome P 450 3A4 (CYP 
3A4) and aldoketoreductases. 
Half-life: 24 hours
Excretion: Renal and GI
5.2
Treatment Regimen
Treatment will be administered on an outpatient basis. A treatment cycle is defined as 4 weeks (28 days). 
Exemestane: Exemestane will be given as one tablet (25mg) daily by mouth (PO). The first dose of 
exemestane should be given the same day as CTX. Dosing for patients on concurrent CYP3A4 inducers is 
detailed in section 5.6
Cyclophosphamide: Cyclophosphamide will be given as one tablet (50mg) daily by mouth (PO). The first 
dose of cyclophosphamide should be given the same day as exemestane.
Patients who enroll into the study who have received exemestane with everolimus and have stopped 
everolimus due to intolerance, may resume exemestane throughout and start CTX once toxicities have 
resolved to Grade 1 or less. The day CTX is started is considered day 1 of the study. 
5.3
Dose modifications

Exemestane: no dose modifications planned

Cyclophosphamide: discontinue cyclophosphamide for grade 3 or greater cystitis, neutropenia, anemia 
or thrombocytopenia. Patients are allowed to continue exemestane alone if they had to stop CTX due to 
toxicity
5.4
Preparation, Storage and Administration of Study Drug
Both, cyclophosphamide and exemestane are commercially available and will be prescribed by the treating 
physician and can be filled at a pharmacy. Patients will follow the study doctor’s instruction, take exemestane 
25 mg po and CTX 50 mg po daily. Both, CTX and exemestane tablets should be stored out of reach of 
children, at room temperature (25°C (77°F)); the temperature is not to exceed 30°C (90 F°). 
5.5
Subject Compliance Monitoring
The patient will be requested to maintain a medication diary of each dose of medication.  The medication 
diary will be reviewed by study personnel at all study visits and returned to research staff at the end of study.
5.6
Concomitant Therapy
Cyclophosphamide is minimally emetogenic when administered as a low daily oral dose. No prophylactic 
antiemetics are needed, however, patients may be pre-medicated with prochloperazine or an alternative 
antiemetic if clinically indicated.  
Agent
Dose
Route
Schedule
Cycle Length
 Exemestane
One 25mg tablet
PO
Daily continuously
28 days
 Cyclophosphamide
One 50mg tablet
PO
Daily continuously
28 days

18
No investigational or commercial agents or therapies other than CTX, exemestane and bisphosphonates 
may be administered with the intent to treat the patient's malignancy.
As both, CTX and exemestane are metabolized by cytochrome P450, physicians should be aware of 
possible interactions with other medicines with metabolism by CYP450 and patients should report all 
medications (prescription and nonprescription), herbal remedies, and vitamins to the study team. 

6
Per the January 2013 exemestane package insert the recommended dose of exemestane for 
patients receiving a potent CYP3A4 inducer such as rifampicin or phenytoin is 50mg po daily. 
No significant effect on pharmacokinetics of exemestane is expected for inhibitors of CYP3A4 
such as ketoconazole. Study Procedures
6.1  STUDY CALENDAR
The following guidelines will be followed:

Screening/baseline evaluations are to be conducted within 6 weeks prior to start of therapy. 

Tumor evaluation (eg, tumor measurements as per RECIST 1.1 by CT scan) will be performed every 12 
weeks on treatment, or earlier if medically indicated. It is preferred but not mandated to use the identical 
imaging technique throughout the study period.

Each treatment cycle is 4 weeks (28 days). The study calendar shows only 3 cycles, study procedures of 
subsequent cycles are identical (except research bloods are optional). Patients should continue 
treatment until disease progression, prohibitive toxicity, or other reasons listed in section 4.4. 
Pre-Study 
Wk 1
Wk 5
Wk 9
Wk 12
Cycle 1
Cycle 2
Cycle 3
Informed consent
X
Concurrent meds
X
X
X
X
History/physical exam, ECOG PS
X
X
X
X
CBC/Diff, Liver/renal functiona
X
Xc
X
X
Exemestane
Continuous daily
Cyclophosphamide 
Continuous daily
Review of treatment diary
X
X
X
Adverse event evaluation
Throughout
Tumor measurementd, 
X
X
CA 27-29
X
X
Baseline formalin preserved paraffin 
embedded biopsies (archived)
X
Research bloods (if funding available), max 
40cc per time point b
X
X
X
a  Mandatory: total bilirubin, AST, ALT, creatinine, BUN 
b Immune correlates: see section 6.3, for patients on trial > 3months, only required at the 6, 9, 12, 15 mos 
time points  
c  Not required if screening labs done within 2 weeks 

19
d Imaging modality depending upon metastatic sites (see section 6.2.; CT scan, bone scan, PET/CT, MRI, 
clinical measurement) 
6.2 .
MEASUREMENT OF ANTITUMOR EFFECT (by RECIST 1.1)
For the purposes of this study, patients should be re-evaluated for response every 12 weeks.  Confirmatory 
scans should be obtained not less than 4 weeks following initial documentation of objective response.
Response and progression will be evaluated in this study using the international criteria proposed by the 
revised Response Evaluation Criteria in Solid Tumors (RECIST) guideline (version 1.1) [Eur J Ca 45:228-
247, 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.
6.2.1
Definitions
Evaluable for objective response.  Only those patients who have measurable disease present at baseline, 
have received at least one cycle of therapy, and have had their disease re-evaluated will be considered 
evaluable for response.  These patients will have their response classified according to the definitions stated 
below.  (Note:  Patients who exhibit objective disease progression prior to the end of cycle 1 will also be 
considered evaluable.)
Evaluable Non-Target Disease Response.  Patients 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. 
6.2.2
Disease Parameters
Measurable disease.  Measurable lesions are defined as those that can be accurately measured in at least 
one dimension (longest diameter to be recorded) as >20 mm by chest x-ray, as >10 mm with CT scan, or 
>10 mm with 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, pleural/pericardial effusions, lymphangitis 
cutis/pulmonitis, inflammatory breast disease, and abdominal masses (not followed by CT or MRI), are 
considered as non-measurable.
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 

20
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. 
6.2.3
Methods for Evaluation of Measurable Disease
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 diameter as 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 slice thickness is 5 mm or less.  If CT scans have slice thickness greater than 5 mm, the 
minimum size for a measurable lesion should be twice the slice thickness.  MRI is also acceptable in certain 
situations (e.g. for body scans).  
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, for this study 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.  
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 patient to be considered in complete clinical response.  
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.
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.

21
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 greater than twice 
that of the surrounding tissue on the attenuation corrected image.
6.2.4
Response Criteria
6.2.4.1 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
6.2.4.2 Evaluation of Non-Target Lesions
Complete Response (CR):
Disappearance of all non-target lesions and normalization of tumor marker 
level.  All lymph nodes must be non-pathological in size (<10 mm short axis). 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).
6.2.4.3 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 Patients with Measurable Disease (i.e., Target Disease)
Target 
Lesions
Non-Target 
Lesions
New 
Lesions
Overall 
Response
Best Overall Response 
when Confirmation is 

22
Required*
CR
CR
No
CR
>4 wks. Confirmation**
CR
Non-CR/Non-PD
No
PR
CR
Not evaluated
No
PR
PR
Non-CR/Non-
PD/not evaluated
No
PR
>4 wks. Confirmation**
SD
Non-CR/Non-
PD/not evaluated
No
SD
documented at least once 
>4 wks. from baseline**
PD
Any
Yes or No
PD
Any
PD***
Yes or No
PD
Any
Any
Yes
PD
no prior SD, PR or CR
*      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:
Patients with a global deterioration of health status requiring discontinuation of treatment 
without objective evidence of disease progression at that time should be reported as 
“symptomatic deterioration.”  Every effort should be made to document the objective 
progression even after discontinuation of treatment.
        For Patients 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
6.2.5
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).
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.
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. 
6.2.6
Progression-Free Survival
PFS is defined as the duration of time from start of treatment to time of progression or death, whichever 
occurs first.

23
6.3. Correlative studies 
Subjects and sample processing: Blood samples (20-40 ml) will be processed at the Unutmaz laboratory to 
isolate PBMC using Ficoll separation as previously described. The PBMC will be counted and viable cells will 
be frozen in 2-3 vials using freezing media and will be stored at -140 degrees along with serum for the 
following analysis. Samples will be stored for the intended immune analyses only, which may include 
improving methods for analyzing the patient’s immune response, for instance by culturing immune cells.   
Samples will not be used nor stored for other research purposes.
Immune profiling panels:
One vial of cells will be thawed and stained with fluorescently conjugated antibodies for flow cytometry 
(FACS) analysis for immune profiling, using LSR-II FACS machine at Unutmaz laboratory. The data will be 
analyzed using Flowjo software. 
1.
T cell differentiation and activation panel: To identify following T cell subsets:
a) Naïve, central memory, effector and terminally differentiated and follicular helper subsets of CD4 or CD8+ 
T cell subsets
b) The proportion of T cells that express activation and differentiation markers CD38, PD1 and HLA-DR and 
CD57.
2. Chemokine receptor panel: To determine the proportion of T cells, including Tregs, with essential 
chemokine receptors, involved in tissue homing. Each chemokine receptor identifies tissue homing as well 
as T cells with different effector functions. For example, Th1 cells express higher CCR5 and CXCR3, 
whereas Th2 cells are higher in CCR4 expression. Cells expressing CLA home to skin, whereas CCR6+ 
cells home to mucosal tissues and contain most of the Th17/Th22 functional effector T cells.
3. Treg/Th17 cell subset panel: PBMC will be stained with T cell marker CD3, CD4 and memory marker 
CD45RO and following Treg markers. In addition cells will be stained with newly identified markers that 
define novel subsets of Tregs and Th17 cells.  In this panel we perform stainings for intracellular transcription 
factors Foxp3 and Helios to identify Treg cells together with a viability dye to discriminate dead cells.
4. Treg differentiation and activation panel: In this panel we determine recently activated and cycling Treg 
and other T cell subsets, by using a cell cycle protein called Ki67 in conjunction with FoxP3, Helios and T cell 
activation markers. 
5. Myeloid and dendritic cell panel: This panel identifies several myeloid lineages:
a) Monocytes
b) Two different dendritic cells subsets (CD1c+ and CD1c-)
c) Plasmacytoid DCs, which secrete IFN alpha
d) Myeloid suppressor cells (monocytic and granulocytic)
6. NK cells, gd-T cells and mucosa homing T cells panel: The goal of this panel is to determine the 
proportion of non-classical T cells and NK cells:
a) NK cells (both CD16+/- CD56+/- subsets)
b) Gammadelta T cells
c) Mucosal associated invariant T (MAIT) T cells
d) invariant Natural Killer T cells (iNKT), which recognize CD1d molecules
Potential pitfalls and Quality control:  All of these panels are well-established in the Unutmaz laboratory and 
are routinely performed on hundreds of human samples. Every antibody in each of the panels is extensively 
tested to ensure optimal staining and reproducibility. We do not anticipate any problems. For quality control, 
in each staining we utilize one known donor for frozen in aliquots for each batch of staining to ensure quality 
of antibodies and FACS machines. 

24
Analysis:  Percent of each lymphoid and myeloid subset will be determined using FlowJo FACS software and 
entered into spreadsheets. The statistics and patient correlative data will be performed by analyzing the 
same donors before and after CTX treatment. We will first determine statistical changes in the proportion of 
Tregs and other subsets analyzed above before and after CTX-treatment. In the second layer analysis we 
will develop signatures that correlate with the effectiveness of the treatment or impact on specific regulatory 
or effector compartments, by stratifying patients at the end of the study.
Examination of tumor antigen-specific CD4 and CD8 T cell responses 
T cell responses to the expressed tumor antigens will be monitored by intracellular cytokine staining (ICS) 
utilizing overlapping peptide (OLP) pools, as previously described by our group and others [67-69]). This 
method is suited for analysis of cryopreserved PBMCs, allows the detection of CD4 and CD8 T cell 
responses (optimized by use of 15-mer peptides with an overlap by 11 amino acid residues) and an 
assessment if multiple cytokines are being secreted by single cells. If antigen-specific T cells are detected, 
confirmatory analysis (ELISA in serum and/or IHC for protein expression in tumor) may be performed. If 
outside laboratories (for instance MSKCC, MSSM) are used, samples will be sent numbered, without 
personal identifiers and no PHI will be shared. 
Antigen 
Expression in breast cancer 
IHC mAb (Source) 
References
PRAME
27-53%
AB32185 (Abcam)
[58, 59]
WT-1
33-87%
6F-H2 (Dako)
[60, 61]
Her2
24%
Commercial, FISH for 2+
[62]
NY-ESO-1
5-42%
E978 (LICR)
[63, 64] and unpublished data
MAGE A3
10-19%
M3H67 (LICR)
[65] and unpublished data
Method: Peripheral blood mononuclear cells (PBMCs) are purified from blood and frozen (by the Unutmaz 
lab) for paired analysis of ex vivo and, if necessary, in vitro stimulated (IVS [67]) T cell responses. For the ex 
vivo assay, thawed pre- and post-treatment PBMCs are washed in complete R-10 medium supplemented 
with 20 IU/ml DNase I (Roche) and cultured overnight at 37C. The following day, the number of viable cells 
are counted, 5 million viable cells/ml in complete R-10 medium are plated at 200 ml/well in 96-well V-bottom 
plates in the presence of 1 mcg/ml anti-CD28 and anti-CD49d antibodies (BD Biosciences), and either 1 
mcg/ml TAA OLP (PRAME, WT-1, Her2, NY-ESO-1, MAGE A3; Proimmune) or control antigen (ProMix CEF 
and ProMix MOG; ProImmune) or no antigen. PMA/Ionomycin will serve as an additional positive control. A 
mixture of Brefeldin A and Monensin (GolgiPlug and GolgiStop, BD Biosciences) is added to each well after 
an 1 hour culture, before culturing for an additional 5 hours. Samples are then washed with PBS, stained for 
20 min at room temperature with anti-CD8 PerCP-Cy5.5 and anti-CD4 FITC antibodies (BD Biosciences) 
and LIVE/DEAD violet (Invitrogen), washed again with PBS, then fixed and permeabilized for 20 min at room 
temperature using Cytofix/Cytoperm solution (BD Biosciences).  Samples are then washed using 
Perm/Wash solution (BD Biosciences) and stained for intracellular antigens using anti-IFNg AlexaFluor 700 
(BioLegend), anti-TNFa PE-Cy7, anti-IL-2 PE and anti-CD3 APC-H7 (BD Biosciences) antibodies for 20 min 
at room temperature. Samples are washed once with Perm/Wash solution, and acquired on a BD LSR II flow 
cytometer. 7-color compensation (parallel controls using cells singly stained for each color) and data analysis 
are done with FlowJo flow cytometry analysis software (TreeStar). Boolean analysis is used determine the 
percentage of single, double and triple cytokine-producing CD4 and CD8 T cells. The induction or boosting 
of TAA-specific T cell immunity for an individual patient  is defined as a post-treatment value at week 9 at 
least 3-fold higher than baseline that is also 3-fold or greater than parallel negative controls (and at least 
0.03) [67]. 
6.4 Follow Up
Following study completion, patients will enter routine follow-up with their primary oncologist, who may be 
contacted to provide follow-up information on the patient’s clinical and disease status. Patients removed from 
study for adverse events will be followed until resolution or stabilization of the adverse event.  

25
7
Statistical Plan
7.1
Sample Size Determination
This is a Phase II open label non randomized single arm trial of exemestane and cyclophosphamide to 
estimate the 3-month PFS in these patients. Based on the data from Bolero 2 summarized above, the 
estimated PFS at 3 months on the combination regimen is 75% assuming that the distribution of progression 
free survival is exponential. [Calculations from PASS, NCSS, 2008, J. Hintze, Kaysville, Ut.]. 
With a single stage design, we can reject the null hypothesis that the progression-free survival rate at 3 
months is 50% or less versus that alternative that the progression free survival rate at 3 months is 75 % or 
greater with an alpha of 0.05 and power of 80% with 23 patients enrolled over 2-2.5 years. If the number of 
patients surviving progression-free at 3 months is 15 or fewer, then the regimen will be rejected.  
7.2
Statistical Methods
Patient characteristics at baseline will be summarized using descriptive statistics (for quantitative variables, 
mean, median, quartiles, standard deviations, etc and graphical displays including boxplots; for qualitative 
variables, proportions and frequency distributions).  The primary endpoint is Progression-free survival (PFS).  
PFS is defined as the time from first treatment day until objective disease progression or death from any 
cause. PFS will be estimated by the Kaplan-Meier method. Analyses will be based on the intent-to-treat 
population. Patients who drop out prior to disease progression (eg due to toxicity, non-compliance, or loss to 
follow-up) will be censored at the time of last study visit. 
With 23 patients, the exact 95% confidence interval for the 3-month PFS will be estimated from the Kaplan 
Meier curve.  
7.3
Subject Population(s) for Analysis
All patients who have received at least one dose of study drug will be included in the analyses of efficacy 
and safety.
8
Safety and Adverse Events
8.1 Expected Adverse Events
Cyclophosphamide 
Side effects vary significantly based on the specific dose and duration of cyclophosphamide. The following 
events have been reported to occur in association with cytotoxic doses of cyclophosphamide:
A. Incidence More Frequent 
1. Anemia, leucopenia, thrombocytopenia 
2. Alopecia
3. Anorexia, nausea and vomiting
4. Gonadal suppression (azoospermia, missed menstrual periods) possibly resulting in infertility. Only 
applicable to men for this study as women are postmenopausal. 
5. Hemorrhagic cystitis, 
6. Infection
B. Incidence Less Frequent 
1. Stomatitis

26
C. Incidence Rare 
1. Anaphylaxis (tachycardia, shortness of breath, wheezing, tightness in throat)
2. Flushing or redness of face
3. Diarrhea
4. Skin rash, pigmentation changes in skin and nails
5. Pneumonitis or interstitial pulmonary fibrosis
6. Syndrome of inappropriate antidiuretic hormone (SIADH)
7. Secondary malignancies
8. Blurred vision
9. Cardiac toxicity (congestive heart failure, mycodarditis, pericarditis)
10. Ovarian fibrosis 
11. Hemorrhagic colitis, oral mucosal irritation, jaundice
12. Malaise and asthenia
Exemestane
A. Incidence More Frequent 
1. Fatigue, hot flashes, pain, malaise
2. Edema (peripheral edema, leg edema)
3. Increased sweating
4. Depression, insomnia, anxiety
5. Dizziness, headache
6. Nausea, vomiting, abdominal pain, anorexia, constipation, diarrhea, increased appetite
7. Dyspnea
8. Cough
9. Hypertension
10. Pain at tumor sites
B. Incidence Less Frequent 
1. Fever
2. Generalized weakness, paresthesia, asthenia, hypoesthesia
3. Pathological fracture
4. Bronchitis, sinusitis, pharyngitis, rhinitis
5. Rash, itching
6. Urinary tract infection, upper respiratory tract infection
7. Lymphedema 
8. Chest pain, 
9. Confusion
10. Dyspepsia
11. Arthralgia, back pain, skeletal pain
12. Alopecia
C. Incidence Rare 
1. Stroke
2. Heart failure
8.2
Definitions
Unanticipated Problems Involving Risk to Subjects or Others
Any incident, experience, or outcome that meets all of the following criteria: 

Unexpected in nature, severity, or frequency  (i.e. not described in study-related documents such as the 
IRB-approved protocol or consent form, the investigators brochure, etc)

27

Related or possibly related to participation in the research (i.e. possibly related means there is a 
reasonable possibility that the incident experience, or outcome may have been caused by the procedures 
involved in the research)

Suggests that the research places subjects or others at greater risk of harm (including physical, 
psychological, economic, or social harm).
Adverse Event
An adverse event (AE) is any symptom, sign, illness or experience that develops or worsens in severity 
during the course of the study.  Intercurrent illnesses or injuries should be regarded as adverse events.  
Abnormal results of diagnostic procedures are considered to be adverse events if the abnormality: results in 
study withdrawal, is associated with a serious adverse event, is associated with clinical signs or symptoms, 
leads to additional treatment or to further diagnostic tests or is considered by the investigator to be of clinical 
significance.
Serious Adverse Event
Adverse events are classified as serious or non-serious.  A serious adverse event is any AE that is: 
Fatal, life-threatening, requires or prolongs hospital stay, results in persistent or significant disability or 
incapacity, a congenital anomaly or birth defect or an important medical event.
Adverse Event Reporting Period
The study period during which adverse events must be reported is defined for this study as the period from 
the first day of study treatment until 30 days following the last administration of study treatment. 
Abnormal Laboratory Values
A clinical laboratory abnormality should be documented as an adverse event if any one of the following 
conditions is met: The laboratory abnormality is not otherwise refuted by a repeat test to confirm the 
abnormality; the abnormality suggests a disease and/or organ toxicity or the abnormality is of a degree that 
requires active management; e.g. change of dose, discontinuation of the drug, more frequent follow-up 
assessments, further diagnostic investigation, etc.
Hospitalization, Prolonged Hospitalization or Surgery
Any adverse event that results in hospitalization or prolonged hospitalization should be documented and 
reported as a serious adverse event unless specifically instructed otherwise in this protocol.  Any condition 
responsible for surgery should be documented as an adverse event if the condition meets the criteria for and 
adverse event. 
Neither the condition, hospitalization, prolonged hospitalization, nor surgery are reported as an adverse 
event in the following circumstances:

Hospitalization or prolonged hospitalization for diagnostic or elective surgical procedures for a preexisting 
condition.  Surgery should not be reported as an outcome of an adverse event if the purpose of the 
surgery was elective or diagnostic and the outcome was uneventful.

Hospitalization or prolonged hospitalization required to allow efficacy measurement for the study.

Hospitalization or prolonged hospitalization for therapy of the target disease of the study, unless it is a 
worsening or increase in frequency of hospital admissions as judged by the clinical investigator.
8.3
Recording of Adverse Events
At each contact with the subject, the investigator must seek information on adverse events by specific 
questioning and, as appropriate, by examination.  Information on all adverse events should be recorded 
immediately in the source document, and also in the appropriate adverse event module of the case report 
form (CRF).  
All adverse events occurring during the study period must be recorded.  The clinical course of each event 
should be followed until resolution, stabilization, or until it has been determined that the study treatment or 
participation is not the cause.  Serious adverse events that are still ongoing at the end of the study period 
must be followed up to determine the final outcome.  

28
8.4
Reporting of Serious Adverse Events and Unanticipated Problems
8.4.1
Investigator reporting: notifying the IRB
This section specifies the NYULMC IRB requirements for investigator reporting of unanticipated problems 
posing risk to subjects or other, including adverse events.  The IRB requirements reflect the current guidance 
documents released by the Office of Human Research Protections (OHRP), and the Food and Drug 
Administration (FDA) and are respectively entitled “Guidance on Reviewing and Reporting Unanticipated 
Problems Involving Risks to Subjects or Others and Adverse Events” and “Guidance for Clinical 
Investigators, Sponsors, and IRBs: Adverse Event Reporting – Improving Human Subject Protection.”
Report Promptly, but no later than 5 working days:
Researchers are required to submit reports of the following problems promptly but no later than 5 working 
days from the time the investigator becomes aware of the event:

Unanticipated problems including adverse events that are unexpected and related
– Unexpected: An event is “unexpected” when its specificity and severity are not accurately reflected in 
the protocol-related documents, such as the IRB-approved research protocol, any applicable 
investigator brochure, and the current IRB-approved informed consent document and other relevant 
sources of information, such as product labeling and package inserts. 
– Related to the research procedures: An event is related to the research procedures if in the opinion of 
the principal investigator or sponsor, the event was more likely than not to be caused by the research 
procedures. 
– Harmful: either caused harm to subjects or others, or placed them at increased risk
Other Reportable events:
The following events also require prompt reporting to the IRB, though no later than 5 working days:

Complaint of a research subject when the complaint indicates unexpected risks or the complaint 
cannot be resolved by the research team.

Protocol deviations or violations (includes intentional and accidental/unintentional deviations from the 
IRB approved protocol) for any of the following situations: 
– one or more participants were placed at increased risk of harm 
– the event has the potential to occur again
– the deviation was necessary to protect a subject from immediate harm

Breach of confidentiality

Incarceration of a participant when the research was not previously approved under Subpart C and the 
investigator believes it is in the best interest of the subject to remain on the study.

New Information indicating a change to the risks or potential benefits of the research, in terms of 
severity or frequency. (e.g. analysis indicates lower-than-expected response rate or a more severe or 
frequent side effect; Other research finds arm of study has no therapeutic value; FDA labeling change or 
withdrawal from market)
Reporting Process
The reportable events noted above will be reported to the IRB using the form: “Reportable Event Form” or as 
a written report of the event (including a description of the event with information regarding its fulfillment of 
the above criteria, follow-up/resolution and need for revision to consent form and/or other study 
documentation). Copies of each report and documentation of IRB notification and receipt will be kept in the 
Clinical Investigator’s study file.
8.5
Unblinding Procedures
N/A

29
8.6
Stopping Rules 
N/A
8.7
Medical Monitoring
It is the responsibility of the Principal Investigator to oversee the safety of the study. This safety monitoring 
will include careful assessment and appropriate reporting of adverse events as noted above, as well as the 
construction and implementation of a site data and safety-monitoring plan (see section 10).  Medical 
monitoring will include a regular assessment of the number and type of serious adverse events. The 
independent medical monitor assigned to the trial (Dr. A. Pavlick) is able to review all unexpected events and 
to evaluate/grant any waivers required for enrollment of study conduct in accordance to institutional 
guidelines.
8.7.1
Data Monitoring Committee
This investigator initiated study will be monitored by the Data Safety Monitoring Committee (DSMC) of the 
New York University Cancer Institute (NYUCI). The DSMC operates based on the 2011 National Cancer 
Institute approved Charter. It is a multidisciplinary committee (consisting of clinical investigators/oncologists, 
biostatisticians, nurses and research administration staff knowledgeable of research methodology and 
design and in proper conduct of clinical trials) that is responsible for monitoring safety, conduct and 
compliance in accordance with protocol data monitoring plans for clinical trials conducted in the NYUCI that 
are not monitored by another institution or agency.  The DSMC reports to the Director of the NYUCI (William 
L. Carroll, M D). Per the NYUCI Institutional Data Safety and Monitoring Plan, this phase 2 trial will be 
monitored by DSMC annually (from the date the first patient is enrolled) and at the completion of the study 
prior to study closure. This review includes accrual data, subject demographics and adverse events. 
Principal Investigators are required to attend the review of their studies. Additional reviews can be scheduled 
based on SAE reports, investigator identified issues, external information, etc.
9
Data Handling and Record Keeping
9.1
Confidentiality
The study team will maintain clinical and laboratory data in a designed manner to ensure patient 
confidentiality. All study personnel have passed human subject protection courses. If applicable, tissue 
samples sent to collaborators outside of NYU/Bellevue will only be labeled with an assigned protocol-patient 
identification number without patient identifiers. Systems used for electronic data capture are compliant with 
FDA regulations in 21 CFR Part 11 and applicable local regulatory agency guidelines. All documents are 
kept in strictly confidential files and are only made accessible for review of sponsors, monitors and 
authorized representatives of regulatory agencies as described in the informed consent document. 
9.2
Confidentiality and HIPAA
Information about study subjects will be kept confidential and managed according to the requirements of the 
Health Insurance Portability and Accountability Act of 1996 (HIPAA).  Those regulations require a signed 
subject authorization informing the subject of the following: 

What protected health information (PHI) will be collected from subjects in this study

Who will have access to that information and why

Who will use or disclose that information 

The rights of a research subject to revoke their authorization for use of their PHI. 
In the event that a subject revokes authorization to collect or use PHI, the investigator, by regulation, retains 
the ability to use all information collected prior to the revocation of subject authorization.  For subjects that 
have revoked authorization to collect or use PHI, attempts should be made to obtain permission to collect at 
least vital status (i.e. that the subject is alive) at the end of their scheduled study period.

30
9.3
Source Documents
Source data is all information, original records of clinical findings, observations, or other activities in a clinical 
trial necessary for the reconstruction and evaluation of the trial.  Source data are contained in source 
documents.  Examples of these original documents, and data records include: hospital records, clinical and 
office charts, laboratory notes, memoranda, subjects’ diaries or evaluation checklists, pharmacy dispensing 
records, recorded data from automated instruments, copies or transcriptions certified after verification as 
being accurate and complete, microfiches, photographic negatives, microfilm or magnetic media, x-rays, 
subject files, and records kept at the pharmacy, at the laboratories, and at medico-technical departments 
involved in the clinical trial.
9.4
Case Report Forms
The study case report form (CRF) is the primary data collection instrument for the study.  All data requested 
on the CRF must be recorded.  All missing data must be explained.  
9.5
Records Retention
It is the investigator’s responsibility to retain study essential documents for at least 2 years after the formal 
closure of the study.  
10 Study Monitoring, Auditing, and Inspecting
10.1 Study Monitoring Plan
The proposed trial entails moderate risks to subjects.  
At the NYU Cancer Institute, all investigator-initiated protocols are subject to a standardized data and safety 
monitoring, which includes scientific peer review, IRB review, Phase I/II committee review and DSMC review 
as well as internal auditing. 
The review of AEs and trial conduct for this trial occurs at several levels:
(1) Principal Investigator: Adverse events are evaluated monthly by the principal investigator in conjunction 
with the research nurses, data manager and research team. 
(2) Internal Phase I/II Committee: Study progress, enrollment and AEs are also reviewed monthly by the 
NYU Phase I/II Committee. This review includes nurses and data managers as well. 
(3) DSMC: See 8.7.1. 
(4) Institutional Review Board (IRB): An annual report to the IRB is submitted by the trial PI for continuation 
of the protocol. It includes a summary of all AEs, total enrollment with demographics, protocol violations, and 
current status of subjects as well as available research data.
(5) In addition, the internal audit committee will inspect the source documents, including consent forms for 
randomly selected enrolled participants at regular intervals throughout the trial to verify adherence to the 
protocol; the completeness, accuracy and consistency of the data; and adherence to ICH Good Clinical 
Practice guidelines. 
10.2 Auditing and Inspecting
The investigator will permit study-related monitoring, audits, and inspections by the IRB/EC, the sponsor, 
government regulatory bodies, and University compliance and quality assurance groups of all study related 
documents (e.g. source documents, regulatory documents, data collection instruments, study data etc.).  The 
investigator will ensure the capability for inspections of applicable study-related facilities (e.g. pharmacy, 
diagnostic laboratory, etc.).
Participation as an investigator in this study implies acceptance of potential inspection by government 
regulatory authorities and applicable University compliance and quality assurance offices.

31
11 Ethical Considerations
This study is to be conducted accordance with applicable US government regulations and international 
standards of Good Clinical Practice, and applicable institutional research policies and procedures.
This protocol and any amendments will be submitted to the NYU Institutional Review Board (IRB) in 
agreement with local legal prescriptions, for formal approval of the study conduct.  The decision of the IRB 
concerning the conduct of the study will be made in writing to the investigator and a copy of this decision will 
be provided to the sponsor before commencement of this study.  The investigator should provide a list of IRB 
members and their affiliate to the sponsor.
All subjects for this study will be provided a consent form describing this study and providing sufficient 
information for subjects to make an informed decision about their participation in this study.  This consent 
form will be submitted with the protocol for review and approval by the IRB for the study.  The formal consent 
of a subject, using the IRB-approved consent form, must be obtained before that subject undergoes any 
study procedure.  The consent form must be signed by the subject or legally acceptable surrogate, and the 
investigator-designated research professional obtaining the consent. 
The consenting process and documentation will follow Standard Operating Procedure no 30 (Obtaining 
Informed Consent for Clinical Trials) of the NYUCI CTO. 
12 Study Finances
12.1 Funding Source
This investigator-initiated trial is supported by the NYU Cancer Institute .  
12.2 Conflict of Interest
Any investigator who has a conflict of interest with this study (patent ownership, royalties, or financial gain 
greater than the minimum allowable by their institution, etc.) must have the conflict reviewed by a properly 
constituted Conflict of Interest Committee with a Committee-sanctioned conflict management plan that has 
been reviewed and approved by the study sponsor prior to participation in this study.  All NYULMC 
investigators will follow the applicable University conflict of interest policies.
12.3 Subject Stipends or Payments
N/A
13 Publication Plan
The study PI holds the primary responsibility for publication of the results of the study.    
.
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