Randomized Phase II Trial to Evaluate Alisertib Alone or Combined With Fulvestrant for Women With Advanced, Endocrine-Resistant Breast Cancer
Phase: PHASE2
Conditions: Estrogen Receptor Status, HER2/Neu Negative, Invasive Breast Carcinoma, Postmenopausal, Stage III Breast Cancer, Stage IIIA Breast Cancer, Stage IIIB Breast Cancer, Stage IIIC Breast Cancer, Stage IV Breast Cancer
Sponsor: Mayo Clinic

 
 
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Randomized Phase II Trial to Evaluate Alisertib Alone or Combined with Fulvestrant for 
Women with Advanced, Endocrine-resistant Breast Cancer 
Protocol Number 
MC1431/TBCRC-041 
Protocol Chair 
 
 
Co-Investigators 
 
 
 
 
Statistician 
 
Supporters 
Johns Hopkins University on behalf of the Translational Breast 
Cancer Research Consortium (TBCRC) 
Takeda/Millennium (X14032) 
Coordinating Center 
 
 
 
 
 

 
 
 
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Randomized Phase II Trial to Evaluate Alisertib Alone or Combined with Fulvestrant for 
Women with Advanced, Endocrine-resistant Breast Cancer 
- Protocol Revision Record - 
Original Protocol: 
08/19/2016 (Activation to Mayo Clinic) 
Amendment 1: 
01/23/2017 
Amendment 2: 
12/20/2017 
Activation to TBCRC: 
02/09/2018 
Amendment 3: 
06/13/2018 
Amendment 4: 
02/01/2019 
Amendment 5: 
02/25/2019 
Amendment 6: 
08/13/2019 
Amendment 7: 
03/17/2022 
Amendment 8 
07/06/2022 
 
 
 

 
 
 
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Protocol Resources 
 
Questions: 
Contact Name: 
Patient eligibility*, test schedule, 
treatment delays/interruptions/adjustments, 
dose modifications, adverse events, 
forms completion and submission 
 
 
  
Forms completion and submission (Mayo 
Clinic only – TBCRC sites contact Data 
Manager above) 
 
 
 
Protocol document, consent form, 
regulatory issues 
 
 
 
 
  
  
Paraffin-embedded tissue pathology  
 
 
Non-paraffin biospecimens  
 
 
Serious Adverse Event Reporting 
Serious Adverse Events Coordinator 
 
*No waivers of eligibility will be granted  
 
 

 
 
 
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TABLE OF CONTENTS 
RANDOMIZED PHASE II TRIAL TO EVALUATE ALISERTIB ALONE OR COMBINED WITH 
FULVESTRANT FOR WOMEN WITH ADVANCED, ENDOCRINE-RESISTANT BREAST CANCER ...... 1 
TABLE OF CONTENTS ............................................................................................................................................ 4 
SCHEMA ...................................................................................................................................................................... 7 
1. 
STUDY DESIGN/SUMMARY ................................................................................................................. 8 
2. 
OBJECTIVES ............................................................................................................................................ 9 
2.1 
PRIMARY OBJECTIVE .................................................................................................................................... 9 
2.2 
SECONDARY OBJECTIVES .............................................................................................................................. 9 
2.3 
CORRELATIVE RESEARCH ............................................................................................................................. 9 
2.4 
EXPLORATORY OBJECTIVES .......................................................................................................................... 9 
3. 
BACKGROUND ...................................................................................................................................... 10 
3.1 
SCOPE OF THE PROBLEM OF HORMONE REFRACTORY ADVANCED BREAST CANCER .................................. 10 
3.2 
PRECLINICAL SCIENCE ................................................................................................................................ 11 
3.3 
CLINICAL DATA WITH FULVESTRANT .......................................................................................................... 15 
3.4 
RATIONALE FOR COMBINATION OF ALISERTIB AND FULVESTRANT ............................................................ 16 
3.5 
RATIONALE TO ALLOW WOMEN WITH ER-NEGATIVE DISEASE TO PARTICIPATE ........................................ 18 
3.6 
PHASE I TRIAL OF ALISERTIB AND FULVESTRANT ...................................................................................... 19 
3.7 
CIRCULATING TUMOR CELLS ...................................................................................................................... 19 
3.8 
STUDY SAFETY ASSESSMENT ...................................................................................................................... 20 
4. 
PARTICIPANT SELECTION ............................................................................................................... 22 
4.1 
PRE-REGISTRATION ELIGIBILITY CRITERIA ................................................................................................. 22 
4.2 
REGISTRATION ELIGIBILITY CRITERIA ........................................................................................................ 24 
4.3 
REGISTRATION EXCLUSION CRITERIA ......................................................................................................... 25 
4.4 
INCLUSION OF UNDERREPRESENTED POPULATIONS .................................................................................... 26 
5. 
REGISTRATION/RANDOMIZATION PROCEDURES ................................................................... 27 
5.1 
PRE-REGISTRATION (STEP 0) ...................................................................................................................... 27 
5.2 
REGISTRATION PROCEDURES ...................................................................................................................... 28 
5.3 
RANDOMIZATION PROCEDURES .................................................................................................................. 30 
5.4 
OPTIONAL CROSSOVER PHASE .................................................................................................................... 30 
6. 
TREATMENT PLAN .............................................................................................................................. 31 
6.1 
ARM 1 (ALISERTIB MONOTHERAPY) ........................................................................................................... 31 
6.2 
ARM 2 (ALISERTIB WITH FULVESTRANT) .................................................................................................... 32 
6.3 
CONCOMITANT TREATMENT AND SUPPORTIVE CARE GUIDELINES ............................................................. 33 
6.4 
TREATMENT/FOLLOW-UP DECISION AT EVALUATION OF PATIENT ............................................................. 34 
7. 
EXPECTED TOXICITIES AND DOSING DELAYS/DOSE MODIFICATIONS ........................... 36 
7.1 
DOSE MODIFICATION BASED ON ADVERSE EVENTS ................................................................................... 36 
7.2  
DOSE MODIFICATIONS – PRIOR TO EACH CYCLE OF TREATMENT ................................................................ 36 
7.3  
DOSE MODIFICATIONS – CYCLE 1 DAY 15 .................................................................................................. 41 
8. 
DRUG FORMULATION/STORAGE/SUPPLY ................................................................................... 41 
8.1 
ALISERTIB (MLN8237, ML00653668) ....................................................................................................... 41 
8.2 
FULVESTRANT (FASLODEX®) ..................................................................................................................... 45 
9. 
CORRELATIVE/SPECIAL STUDIES ................................................................................................. 48 

 
 
 
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9.1 
BODY FLUID BIOSPECIMENS ....................................................................................................................... 48 
9.2 
PATHOLOGY CONSIDERATIONS/TISSUE BIOSPECIMENS .............................................................................. 51 
10. 
SPECIMEN BANKING .......................................................................................................................... 54 
11. 
STUDY CALENDAR .............................................................................................................................. 55 
12. 
MEASUREMENT OF EFFECT ............................................................................................................ 60 
12.1 
DEFINITIONS ............................................................................................................................................... 60 
12.2 
DISEASE PARAMETERS ................................................................................................................................ 60 
12.3 
RESPONSE CRITERIA ................................................................................................................................... 62 
13. 
ADVERSE EVENT REPORTING REQUIREMENTS ....................................................................... 66 
13.1 
GENERAL .................................................................................................................................................... 67 
13.2 
DEFINITIONS ............................................................................................................................................... 67 
13.3 
REPORTING PROCEDURES ........................................................................................................................... 69 
13.4 
OTHER REQUIRED REPORTING .................................................................................................................... 73 
13.5 
REQUIRED ROUTINE REPORTING................................................................................................................. 76 
14. 
DATA AND SAFETY MONITORING ................................................................................................. 78 
14.1 
DATA MANAGEMENT AND REPORTING ....................................................................................................... 78 
14.2 
ALL PAPER FORMS SHOULD BE SENT TO: ..................................................................................................... 80 
14.3 
LABELING ................................................................................................................................................... 80 
14.4 
INCOMPLETE MATERIALS ............................................................................................................................ 80 
14.5 
OVERDUE LISTS .......................................................................................................................................... 80 
14.6 
CORRECTIONS FORMS ................................................................................................................................. 80 
14.7 
EXTERNAL MONITORING ............................................................................................................................ 80 
15. 
REGULATORY CONSIDERATIONS ................................................................................................. 81 
15.1 
PROTOCOL REVIEW AND AMENDMENTS ..................................................................................................... 81 
15.2 
INFORMED CONSENT ................................................................................................................................... 81 
15.3 
ETHICS AND GCP ........................................................................................................................................ 81 
16. 
MULTI-CENTER GUIDELINES .......................................................................................................... 82 
16.1 
STUDY DOCUMENTATION ........................................................................................................................... 82 
16.2 
RECORDS RETENTION ................................................................................................................................. 82 
16.3 
PUBLICATION .............................................................................................................................................. 82 
17. 
STATISTICAL CONSIDERATIONS AND METHODOLOGY ........................................................ 82 
17.1 
ASSESSING THE IMPACT OF ADDING FULVESTRANT TO ALISERTIB ............................................................... 82 
17.2 
SAMPLE SIZE/ ACCRUAL RATE ................................................................................................................... 83 
17.3 
STRATIFICATION FACTORS .......................................................................................................................... 84 
17.4 
ANALYSIS OF SECONDARY ENDPOINTS ....................................................................................................... 85 
17.5 
MONITORING .............................................................................................................................................. 86 
17.6 
INCLUSION OF WOMEN AND MINORITIES .................................................................................................... 87 
18. 
BUDGET .................................................................................................................................................. 87 
REFERENCES .......................................................................................................................................................... 88 
APPENDICES ............................................................................................................................................................ 91 
APPENDIX I – ECOG PERFORMANCE STATUS AND KARNOFSKY PERFORMANCE STATUS ......... 91 
APPENDIX II – NYHA HEART FAILURE CLASSIFICATION ........................................................................ 92 
APPENDIX III – MEDICATION DIARY .............................................................................................................. 93 

 
 
 
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APPENDIX IV – PROTON PUMP INHIBITOR (PPI) AND H2 ANTAGONIST ............................................. 95 

 
 
 
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SCHEMA 
 
 
 
Pre-Registration 
 
 
 
 
 
 
 
 
 
Pre-registration biopsy 
for determination of ER* 
by central pathologist 
 
 
 
 
 
 
 
 
 
 
Randomization 
 
 
 
 
 
 
 
 
 
 
 
 
 
Arm 1: Alisertib orally twice daily 
Days: 1-3, 8-10, 15-17 of a 28-day 
cycle 
until disease progression 
 
 
Arm 2: Alisertib orally twice daily  
Days: 1-3, 8-10, 15-17 of a 28-day cycle 
+ 
Fulvestrant intramuscular injection 
Cycle 1: Days 1 and 15 
Cycle 2 & subsequent cycles: Day 1 
of 28-day cycles 
until disease progression 
 
 
 
 
 
Crossover: Patient who has 
documented  
1)ER+ disease at registration, or 
2) ER- disease at registration and 
ER+ disease at progression 
(Otherwise, patient will go to 
event monitoring) 
 
 
 
Event 
Monitoring 
 
 
Crossover patients only 
Alisertib orally twice daily  
Days: 1-3, 8-10, 15-17 of a 28-day cycle 
+ 
Fulvestrant intramuscular injection 
Cycle 1: Days 1 and 15 
Cycle 2 & subsequent cycles: Day 1 
of 28-day cycles 
until disease progression 
 
 
 
 
 
 
 
 
 
 
Event Monitoring 
 
 
 
 
*Standard ER testing for ERα 
NOTE: If insufficient or no tissue was obtained by the pre-registration biopsy, an archival tissue 
specimen must be submitted for Central Laboratory ER determination prior to registration. 
Archived metastatic specimen preferred. 

 
 
 
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1. STUDY DESIGN/SUMMARY 
Patients with ER+ metastatic breast cancer are typically treated with multiple lines of endocrine 
therapy, and tumor response rates to serial agents after first-line therapy tend to decrease. This 
coincides with ERα down-regulation, aggressive tumor behavior, and poor clinical outcomes. 
Novel therapies to overcome endocrine resistance are needed. Currently, there are no drugs 
either FDA-approved or in development to reverse endocrine resistance that results from down-
regulation of the ERα. 
Our preclinical data suggests that in ER+ breast cancer, Aurora A Kinase (AAK) is associated 
with the development of epithelial to mesenchymal transition (EMT) reprogramming and the 
expansion of breast tumor initiating cells that are ERαlow/- and resistant to endocrine therapy. We 
postulate that this is a mechanism by which ER down-regulation occurs. Thus targeted treatment 
with alisertib, an AAK inhibitor, is projected to reverse EMT and restore tumor ERα expression 
and sensitivity to endocrine therapy. 
A randomized phase II trial to evaluate alisertib alone and in combination with fulvestrant is 
proposed. Based on our preclinical data, we project that the patients most likely to derive benefit 
from treatment with alisertib will be those that are resistant to endocrine therapy, so this will be 
our target population. Given the striking clinical activity of single agent alisertib observed in the 
cohort of heavily pretreated, ER+ metastatic breast cancer patients (n=26, CBR 88% and PFS 7.9 
months), additional exploration of single agent activity in this patient population is warranted 
and justified. Based on our preclinical data, we project that the combination of alisertib and 
fulvestrant will result in superior clinical outcomes compared to alisertib alone. For this reason a 
head-to-head comparison of these two treatment strategies was selected. 
Patients with a history of primary ER+ breast cancer or de novo metastatic ER+ breast cancer 
will be eligible. They will undergo a registration biopsy for determination of ER and HER2 
status. Patients with HER2 positive disease will be ineligible. Based on historical literature, we 
predict that 10% of patients enrolling with a history of primary ER+ disease will have ER 
negative metastatic disease. These patients have a worse prognosis compared with those who 
retain ER+ expression. Given the preclinical data in vitro and in vivo data that supports that 
alisertib can restore ER+ expression and endocrine sensitivity, the investigators will offer 
enrollment to these patients to test this working hypothesis. 
Patients will be randomized 1:1 to alisertib alone or in combination with fulvestrant. They will 
be stratified by (1) primary (de novo) or secondary (acquired) endocrine resistance and (2) level 
of ER expression (<10% or ≥10%). 
Patients will remain on therapy until progression or intolerable toxicity or physician discretion. 
At the time of progression those on alisertib monotherapy may have the option to cross-over to 
the combination therapy. Those with baseline ER expression ≥10% can cross-over. Those with 
ER negative or <10% expression on the registration biopsy will only be allowed to cross-over if 
the ER status is clinically re-evaluated on the post-progression research biopsy. In that scenario 
only those that have disease ER ≥10% will be allowed to cross-over. 
A rich panel of correlative studies will be included in the study design. Tumor biopsy and blood 
draw for circulating tumor cell assessment will be obtained at baseline, after completion of 
Cycle 1 treatment, and at the time of progression. In addition to this, in the Mayo Clinic cohort 

 
 
 
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of patients, research core biopsies will be utilized to generate patient-derived xenografts as a 
means to assess mechanisms of alisertib resistance. 
2. OBJECTIVES 
2.1 Primary Objective 
To assess the impact on objective tumor response rate (using RECIST criteria) with the 
addition of fulvestrant to alisertib in women with endocrine resistant, advanced, estrogen 
receptor positive breast cancer.  
2.2 Secondary Objectives 
2.2.1 To evaluate the safety profile of each treatment regimen 
2.2.2 To assess the impact on median progression-free survival with the addition of 
fulvestrant to alisertib 
2.2.3 To obtain estimated tumor response rate and the median progression-free survival 
time during alisertib and fulvestrant treatment in the cohort of patients who 
progress during alisertib monotherapy, and crossover to receive the combination 
of alisertib and fulvestrant. 
2.3 Correlative Research 
2.3.1 To assess the changes in Aurora A kinase, SMAD5 and SOX2 expression and 
phosphorylation in tumor tissue after first cycle of assigned treatment 
2.3.2 To assess the changes in ER expression and function in tumor tissue after the first 
cycle of assigned treatment 
2.4 Exploratory Objectives 
2.4.1 To generate patient derived xenografts (PDX) from tumors collected at baseline 
and progression of disease (PD) in order to identify mechanisms associated with 
both de novo and acquired alisertib resistance. 
NOTE: Xenografting will only be done for patients who enroll at Mayo Clinic 
in Rochester, Minnesota. 
2.4.2 After the first cycle of treatment, to assess changes in Aurora A kinase, p~SOX2 
and ER expression on circulating tumor cells (CTCs), and to assess concordance 
between change in expression with tumor tissue and CTCs. 
 

 
 
 
 
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3. BACKGROUND 
3.1 Scope of the Problem of Hormone Refractory Advanced Breast Cancer 
Despite the clinical benefit of hormonal treatment in Estrogen Receptor positive 
(ER+) breast cancer, de novo and acquired resistance to therapies remains a 
significant clinical problem1, 2. Patients with metastatic ER+ breast cancer are 
typically treated with multiple lines of endocrine therapy, and tumor response 
rates to serial agents after first-line therapy tend to decrease3. This coincides with 
ERα down-regulation and aggressive tumor behavior and poor clinical 
outcomes4,5. Novel therapies to overcome endocrine resistance are needed. 
The development of endocrine resistance is usually associated with aggressive 
tumor behavior and the development of distant metastases. One of the major 
barriers to eradicating metastatic cancer cells is overcoming their ability to self-
renew and become resistant to conventional therapies.  
The discovery that breast carcinomas contain a sub-population of cells harboring 
stem-like properties has generated excitement because these breast tumor 
initiating cells (BTICs) may represent a source of therapeutic failure.6 Cancer 
cells that undergo the epithelial to mesenchymal transition (EMT) programming 
acquire a basal CD44+/CD24low/- cancer stem-like phenotype with increased 
capacity for self-renewal, drug resistance, tumor initiation and metastases7, 8. 
Importantly, luminal breast cancer cells that undergo EMT display clonal 
expansion of BTICs that are ERαlow/- thus resulting in the generation of a 
“luminobasal” phenotype that is ultimately associated with the development of 
endocrine resistance and high risk of tumor recurrence9, 10. Aberrant activation of 
HER-2/MAPK and TGFβ/SMAD oncogenic signaling induces EMT and plays an 
important role in the maintenance and clonal expansion of BTICs11-14. This 
phenomenon is well established, however, the molecular mechanisms underlying 
ERα down-regulation and endocrine resistance by means of activation of EMT in 
ER+ breast cancer remain elusive and the subject of intense ongoing 
investigation. 
Translational studies have demonstrated that breast cancer tumors with a higher 
population of BTICs are associated with shorter metastases-free survival in lymph 
node-negative, ER+/HER2- breast cancer, but not in ER- or HER2+ subtypes15. 
Additional studies demonstrate that ER+ tumor specimens collected from women 
following treatment with the aromatase inhibitor, letrozole, demonstrate a 
significant increase in mesenchymal-associated genes, as well as the 
CD44+/CD24low/- cancer cell population, in the residual tumor16. These results 
suggest that the population of CD44+/CD24low/- BTICs, particularly those 
surviving standard treatment with anti-estrogens, are relevant targets for novel 
anti-neoplastic therapeutics. 
 
 

 
 
 
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3.2 Preclinical Science 
3.2.1 In Vitro and In Vivo Studies 
Preclinical studies conducted by 
 
 constitutive expression of MAPK in MCF-7 cells (vMCF-7Raf1) 
is associated with over-expression of the mitotic kinase Aurora A and the 
development of EMT and an invasive CD44+/CD24low/- stem cell-like phenotype. 
Cancer cells undergoing EMT have increased motility and invasive behavior. 
They also are characterized by over-expression of proteins promoting EMT and 
stemness (SMAD5 and SOX2), as well as down-regulation of tumor suppressors 
involved in epithelial cell adhesion (PCDH8), inhibition of Aurora-A kinase 
activity (CHFR), and suppression of metastasis (TIMP2) and angiogenesis 
(THBS1) (Figure 1A).  
In vivo studies demonstrate that vMCF-7Raf1 tumor xenografts display a loss of 
progesterone receptor (PR) and increased HER2 expression, higher tumor grade 
and development of spontaneous lung metastases (Figure 1C). These findings 
collectively reveal a novel, non-mitotic mechanism for the development of distant 
metastases and tumor survival by Aurora A kinase in ER+ breast cancer cells. 

 
 
 
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The raf-1 overexpressing xenografts contain heterogeneity for the CD24 epithelial 
marker (Figure 2A-B). The CD24 low/- cell sub-population displays overexpression 
and phosphorylation of Aurora A and is functionally linked to the mesenchymal 
phenotype; but importantly, these cells demonstrate a loss of ER expression, the 
primary target for endocrine therapy (Figure 2C). 
Targeted treatment of CD44+/CD24low/- breast cancer cells with alisertib, an 
aurora-A kinase inhibitor, suppressed EMT and restored the CD24+ epithelial 

 
 
 
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phenotype (Figure 2D-E). These tumors were furthermore characterized by loss of 
HER-2 expression and nuclear SMAD5 phosphorylation, as well as restoration of 
ER expression. To validate in vivo the therapeutic effect of molecular inhibition 
of Aurora-A activity in the suppression of metastases, vectors were engineered to 
express shRNAs to knockdown Aurora-A in the vMCF-7Raf1 xenograft model 
(Figure 2F)18. Inhibition of Aurora-A kinase induced tumor regression and 
reduced the number of lung metastases.  
 
 
 
These in vitro and in vivo pre-clinical results demonstrate that pharmacologic 
inhibition of Aurora-A kinase activity by alisertib offers a novel therapeutic 
strategy to selectively target CD44+/CD24low/- invasive cancer cells, suppress the 

Randomized PhII Alisertib ER + Breast Cancer 
Tufia C. Haddad, MD  
TBCRC041 / MC1431 
 
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early stages of EMT, and consequent metastatic dissemination to distant organs. 
These results have recently been suggested by others19. 
3.2.2 Evaluation of Aurora A in human breast cancer biospecimens 
In translational studies by 
 (unpublished data), Aurora A 
kinase, p~SMAD5, p~SOX2 expression was evaluated in a cohort of 100 tissue 
biospecimens obtained from women with early stage breast cancer treated with 
optimal locoregional therapy and 5 years of adjuvant endocrine therapy. The “bad 
outcome” group is defined as patients enduring early breast cancer relapse or 
death within 5 years of diagnosis, and the “good outcome” group is defined as 
those with disease-free survival of at least 7 years. Aurora A kinase is measured 
by immunohistochemistry on a tissue microarray, and the extent and intensity of 
staining is scored. Tumor samples exhibiting higher levels of Aurora A expression 
were associated with increased p~SMAD5 and p~SOX2 expression as well as 
poor clinical outcomes (Figure 3). 
 
 
 

 
 
 
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These findings are further supported by others15. In this study the tumor tissue 
expression of Aurora A was evaluated in three (3) separate cohorts of women with 
early stage breast cancer treated without adjuvant therapy (n=766). Their work 
demonstrated an association of Aurora A with shorter metastases-free survival. The 
correlation was statistically significant in ER+/HER2- breast cancer, but not in the 
biologically more aggressive ER-/HER2- or HER2+ molecular subtypes. Further 
support and validation of our preclinical and translational work is provided by 
Thrane et al19. Thus, patients with ER+ breast cancer and high levels of tumor 
expression of Aurora A kinase may benefit from targeted treatment with alisertib; 
in fact, it is feasible that patients with initial ER+ primary disease that is ERlow/- at 
metastatic relapse or progression may also benefit. These women are known to have 
particularly inferior clinical outcomes compared with women who retain ER+ 
expression at relapse.20 
3.2.2.1 Early Phase Clinical Trials of Alisertib 
To date, alisertib has been extensively evaluated in up to 1100 patients with 
hematological malignancies and to a lesser extent in those with solid 
tumors, including breast cancer21, 22. The maximum tolerated dose has been 
found to be 50 mg twice daily on Days 1-7 of a 21-day cycle, and it has 
been used without untoward toxicities in ongoing phase II clinical trials22. 
An alternative 28-day regimen with alisertib given Days 1-3, 8-10 and 15-
17 was studied in combination with paclitaxel in xenograft breast and 
ovarian cancer models, and it is associated with equivalent drug levels, 
decreased incidence of dose limiting neutropenia with negligible 
compromise to efficacy.23 Results of a phase II study of single agent 
alisertib (21-day schedule) in relapsed/refractory metastatic breast cancer 
(from a cohort of all solid tumors) were presented at the San Antonio Breast 
Cancer Symposium, December 2013 (Abstract PD5-5) and subsequently 
published in 201524. Of 26 patients in the heavily-pretreated, hormone 
receptor positive cohort, 23% had an objective response (complete or partial 
response), and 31% achieved disease stabilization (at least 6 months without 
disease progression) for a clinical benefit rate of 54%. The median PFS was 
7.9 months. Therapy was generally well tolerated with the most commonly 
Grade 2 or less adverse events being neutropenia, fatigue, and diarrhea. 
Given the safety and efficacy profile of alisertib in ER+/HER2- metastatic 
breast cancer, further evaluation to validate these findings is warranted and 
justifies the inclusion of an alisertib monotherapy arm in this trial. 
3.3 Clinical data with fulvestrant 
Fulvestrant is an FDA-approved agent for the treatment of post-menopausal ER+ 
metastatic breast cancer. It is a pure ER antagonist given by intramuscular 
injection in a 28-day cycle. It is exceptionally well-tolerated with the most 
frequent side effects being mild hot flashes and arthralgias. The CONFIRM trial25 
is a published phase III randomized trial of fulvestrant (500 mg Day 1 and 15 of 
cycle 1 and 500 mg Day 1 of subsequent cycles) and fulvestrant (250 mg Day 1 

 
 
 
 
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each cycle) as first line treatment for advanced ER+ breast cancer. The trial 
population included patients who relapsed on adjuvant endocrine treatment or 
within one year of completing adjuvant endocrine therapy; for those with relapse 
>1year after completion of adjuvant therapy or de novo stage IV disease, 
progression on first line anti-estrogen therapy was required. Among 240 patients 
with measurable disease receiving the 500mg dose, the ORR was 13.8%. 
Fulvestrant can induce anti-tumor response in disease with prior hormonal 
treatment exposure; however, the ORR is less than desirable and in part reflects 
the scope of the problem of resistance to hormonal therapy. 
3.4 Rationale for Combination of Alisertib and Fulvestrant 
The rationale to support this phase II clinical trial evaluating alisertib in 
combination with fulvestrant is based on the in vitro studies from 
 
lab. These experiments demonstrate decreased cell proliferation by single agent 
alisertib in MCF-7 ER+ breast cancer cells (Figure 3). The effect on cell 
proliferation is further enhanced when alisertib is combined with fulvestrant when 
compared to either agent alone. These preliminary results have been confirmed in 
tamoxifen-resistant vMCF-7raf-1 1GX cells whereby combination of fulvestrant 
with alisertib induced a stronger inhibition of cell proliferation18 (Figure 4).  
 

 
 
 
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Finally, studies in 
 lab have demonstrated that alisertib restored 
sensitivity to fulvestrant in variant MCF-7/LCC9 ex-vivo cancer cells that display 
intrinsic resistance to tamoxifen and fulvestrant in tumor xenografts (Figure 5). 
Because treatment with fulvestrant induces activation of apoptosis in endocrine 
sensitive breast cancer cells, a real-time apoptosis assay was performed to 
establish the extent to which restoration of fulvestrant sensitivity was linked to 
activation of apoptosis in alisertib-treated MCF-7/LLC9 cells. Notably, while 
MCF-7/LCC9 cells treated with fulvestrant showed nominal levels of apoptosis, 
combination of fulvestrant with alisertib significantly increased the percentage of 
apoptotic cells (Figure 6). Importantly, fulvestrant resistance in MCF-7/LCC9 
cells was linked to increased expression of AAK and ERα down-regulation when 
compared to endocrine sensitive MCF-7 parental cells (Figure 7), indicating that 
intrinsic endocrine resistance is associated to aberrant AAK activity leading to 
loss of dependence on ERα signaling.  
Collectively, these preliminary findings support the rationale for the proposed 
combination therapy and the underlying hypothesis that in women with ER+ 
metastatic breast cancer that is resistant to fulvestrant, alisertib will target the 
subpopulation of CD44+/CD24low/- BTICs that over-express Aurora-A kinase and 
restore ERα expression, functional activity, and thereby sensitivity to fulvestrant. 
 
 
 
 
 
 
 
 
 

 
 
 
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3.5 Rationale to Allow Women with ER-negative Disease to Participate 
It is feasible that women with a history of primary, operable breast cancer that is ER+ 
who endure metastatic relapse that is ER <10% or ER negative, may derive benefit from 
alisertib. This is known to occur in up to 20% of patients. The hazard of death in women 
with ER+ primary breast cancer whose recurrence is ER <10% or ER negative is 1.48 
times (95% CI, 1.08 to 2.05) that of woman who retain ER+ at metastatic relapse.20 These 
tumors may be heavily comprised of the Aurora-A kinase over-expressing 
CD44+/CD24low/- ERαlow/- BTICs that alisertib targets. In fact, alisertib may allow for 
reversion of the luminobasal phenotype and restoration of ERα expression, functional 
activity, and thus sensitivity to hormonal treatment. 
 
 

 
 
 
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3.6 Phase I Trial of Alisertib and Fulvestrant 
A phase I trial to evaluate the safety of the combination of alisertib and fulvestrant is 
active, but has completed enrollment at the Mayo Clinic Rochester (MC1231; 
NCT02219789). Post-menopausal women with advanced hormone receptor-positive 
breast cancer were eligible, including those who have previously experienced disease 
progression on fulvestrant. This trial examined the pulse dose 28-day schedule and 
dosing of alisertib in conjunction with standard dose and 28-day schedule fulvestrant 
(500 mg IM on Days 1 and 15 of Cycle 1, then day 1 of all subsequent cycles). A 
standard 3+3 study design approach was utilized to evaluate 2 dose levels of alisertib (40 
and 50mg) given oral twice daily on days 1-3, 8-10, 15-17 of a 28-day cycle. The primary 
endpoint was safety and tolerability assessment of the combination therapy. The RP2D 
was determined for the purpose of this phase II trial. 
Ten patients enrolled during the period September 2014 - April 2015. One was found to 
be ineligible and was not included in the analysis. The median patient age was 59 (range 
48, 73). Prior endocrine therapies included an aromatase inhibitor (9, 100%), fulvestrant 
(6, 67%), and everolimus+exemestane (5, 56%) amongst others. Eight (89%) had prior 
chemotherapy. There were no severe (Grade 3+) toxicities reported during cycle 1 at 
either dose level, thus the MTD was not reached. The recommended phase II dose of 
alisertib in combination with fulvestrant is 50mg. The cycle 1 grade 1/2 adverse events 
regardless of attribution were fatigue (6, 67%), neutropenia (5, 56%), anemia (5, 56%), 
diarrhea (3, 33%), nausea (3, 33%), and mucositis (1, 11%). As of December 30, 2015, a 
median of 10 cycles of therapy have been administered (range 2, 16+), and the 6-month 
clinical benefit rate was 77.8% (95% CI: 40.0-87.2%). Five patients remain on treatment 
with stable disease. 
3.7 Circulating Tumor Cells 
Because the onset of metastases results from the successful 
dissemination of cancer cells from the primary tumor to 
distant organs, the relative abundance of CTCs in the 
peripheral blood has strong correlation with tumor 
recurrence and distant metastases in both early stage and 
advanced breast tumors27-29. The development of CTCs as 
a “liquid biopsy” by which to perform ongoing tumor 
assessments in relation to treatment exposure is possible 
with recent technologic advances that allow for the capture 
of CTCs with epithelial, EMT-like, and/or stem cell like 
phenotypes, and for molecular characterization by 
immunocytochemistry, fluorescence in situ hybridization, 
RT-PCR, and next generation sequencing. Mayo Clinic 
Rochester has access to several platforms for CTC capture 
and analysis with the goal of studying the most clinically 
relevant population of CTCs for a given translational research question. Preliminary 
studies at Mayo demonstrate that p~SOX2 nuclear expression in CTCs from a patient 
with MBC can be observed (Figure 8). 

 
 
 
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3.8 Study Safety Assessment 
The safety stopping boundary was crossed after 12 patients had received at least one 
cycle of treatment, with 5 of these 12 patients developing a Grade 4 toxicity or dying on 
treatment. The study was temporarily closed to accrual on 02Apr2018 for the protocol 
chair and the study biostatistician to review all the AE data. 
The findings are summarized below: 
Alisertib monotherapy arm: 
Three of the 5 patients randomized to this treatment arm had adverse events associated 
with the safety stopping rule: two deaths on study and one patient with Grade 4 toxicities. 
The two patients who died on study were symptomatic of their disease at time of 
enrollment. 
• The first death was due to Grade 5 hemolysis (thrombotic microangiopathy) felt 
to be likely due to disease progression; however, it was attributed by the treating 
physician as ‘possibly’ related to alisertib. 
• The second death was a Grade 5 acute respiratory failure as initial manifestation 
of an acute coronary syndrome, attributed as ‘possibly’ related to alisertib. 
• The third event was a patient who developed Grade 4 toxicities during Cycle 1, 
including neutropenia on Day 15, but also a Grade 4 cerebral edema due to newly 
diagnosed brain metastases. The latter event was not attributed to the drug, and 
the patient came off treatment due to disease progression. 
• Of note: Two additional patients have been treated in Arm 1, having received 4-
5 cycles of therapy without any severe (grade ≥4) toxicities. 
In review of the investigator’s brochure, in over 1300 patients treated with alisertib, 
hemolysis had not been previously reported prior to this event, and there was only a 
single report of acute respiratory failure and acute coronary syndrome each. It remains 
unknown if alisertib contributed to any of these toxicities. 
Alisertib in combination with fulvestrant arm:  
Two of the 7 patients randomized to this treatment arm had adverse events associated 
with the safety stopping rule: one death on treatment and one patient with Grade 4 
toxicities. 
• The patient who died did so on Day 8 of Cycle 1. She was not symptomatic of her 
disease at enrollment; however, she went on to have declining performance and 
respiratory status during her 21-day wash out from chemotherapy prior to 
registration. She was subsequently hospitalized days after initiating treatment due 
to increasing lethargy and declining respiratory condition attributed to an 
aspiration pneumonia event. She died due to disease progression. 
• The second event was a patient who was symptomatic of her hepatic metastasis 
and had evidence of pseudocirrhosis at enrollment. She received 4 cycles of 
therapy on study during which time she experienced several Grade 4 toxicities, 
including cytopenias, hyperbilirubinemia, as well as hyponatremia. The 

 
 
 
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hematologic toxicities were attributed to alisertib, but exacerbated by her 
underlying liver disease. She came off study due to disease progression. 
• Of note: Five additional patients have been treated in Arm 2, having received 2-4 
cycles of therapy without any severe (grade ≥4) toxicities. 
Decision: 
After some discussions, the study team has revised the protocol (Amendment #3) to 
tighten the eligibility criteria such that patients who are moderately to severely 
symptomatic of their disease (clinically or by laboratory analysis) or experiencing a 
decline in performance status would not be eligible to participate. An adverse event 
assessment will be performed and the laboratory evaluation will be repeated at the time of 
registration insuring washout from the most recent therapy to reduce the risk of having a 
patient with rapidly progressive disease participating. 
 
 

 
 
 
 
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4. PARTICIPANT SELECTION 
4.1 Pre-registration Eligibility Criteria 
4.1.1 Females age ≥18 years  
4.1.2 Post-menopausal defined as 
• Age ≥60 and amenorrhea >12 consecutive months 
OR  
• Previous bilateral oophorectomy  
OR 
• Age <60 and amenorrhea >12 consecutive months and 
documented follicle stimulating hormone (FSH) level within 
post-menopausal range according to institutional standard 
NOTE: If FSH level not within post-menopausal range according 
to institutional standard, but there is other evidence of post-
menopausal status, exceptions may be granted by the PI. 
4.1.3 Histologic proof of metastatic or locally advanced, unresectable breast cancer  
4.1.4 History of ER positive (+) (≥10% of cells positive on H&E), HER2 
negative (−) breast cancer disease, either as a 
(1) History of primary, operable ER+/HER2− invasive breast cancer  
OR 
(2) History of de novo metastatic breast cancer that is ER+/HER2−  
Note: HER2− (negative) disease defined as one of the following: 
− HER2 IHC expression of 0, 1+ and ISH non-amplified 
− HER2 IHC expression of 0, 1+ and ISH not done 
− HER2 IHC expression of 2+ and ISH non-amplified 
− IHC not done and ISH non-amplified 
Note: supporting documentation such as a pathology report from 
their primary diagnosis that indicates ER+/Her2- invasive 
breast cancer or a biopsy report of de novo metastatic breast 
cancer that is ER+/HER2− should be submitted through the 
RAVE database 
4.1.5 Prior treatment 
− No more than two prior chemotherapy regimens in the metastatic 
setting. 
− Prior treatment with fulvestrant in the metastatic setting is required, 
except for patients with a history of ER-negative metastatic breast 
cancer 
− Unlimited prior endocrine therapy regimens in the metastatic setting 
are allowed 

 
 
 
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− No prior treatment with an Aurora Kinase inhibitor (either an Aurora 
A or pan-Aurora kinase inhibitor) 
4.1.6 Disease that is measurable where:  
-A non-nodal lesion is considered measurable if its longest diameter can 
be accurately measured as ≥2.0 cm with chest x-ray, or as ≥1.0 cm with 
CT scan, CT component of a PET/CT, or MRI. 
-A malignant lymph node is considered measurable if its short axis is 
>1.5 cm when assessed by CT scan (CT scan slice thickness 
recommended to be no greater than 5 mm). 
Note: Tumor lesions in a previously irradiated area are not considered 
measurable disease. 
Note: Disease that is measurable by physical examination only is not 
eligible. 
4.1.7 No history of tumors involving spinal cord or heart. 
4.1.8 Fully recovered from acute, reversible effects of prior therapy regardless 
of interval since last treatment  
EXCEPTION: Neuropathies – if Grade 2 neuropathies have been stable 
for at least 3 months since completion of prior treatment, patient is 
eligible. 
4.1.9a ECOG Performance Status: 0 or 1(See Appendix I) 
4.1.9b No requirement for constant administration of proton pump inhibitor, H2 
antagonist, or pancreatic enzymes (see Appendix IV) 
4.1.9c Willing to limit daily alcohol intake to the following: one 12-oz glass of 
beer, one 6-oz glass of wine, or one 1.5-oz portion of 80-proof alcohol. 
4.1.9d No uncontrolled intercurrent illness including, but not limited to: 
− ongoing or active infection 
− symptomatic congestive heart failure 
− unstable angina pectoris 
− uncontrolled symptomatic cardiac arrhythmia 
− uncontrolled hypertension (defined as blood pressure >160/90) 
4.1.9e  No history of uncontrolled sleep apnea syndrome and other conditions that 
could result in excessive daytime sleepiness, such as severe chronic 
obstructive pulmonary disease, or requirement for supplemental oxygen. 
4.1.9f No other active second malignancy other than non-melanoma skin cancers 
and in situ cervical cancers within 5 years of registration.  
NOTE: A second malignancy is not considered active if all treatment for 
that malignancy is completed and the patient has been disease-free for at 
least 5 years prior to registration 
4.1.9g Ability to provide written informed consent. 

 
 
 
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4.1.9h Willing to return to enrolling institution for follow-up during the active 
treatment. Event monitoring following completion of therapy may occur 
outside the enrolling institution. 
4.1.9i No history of myocardial infarction ≤6 months prior to pre-registration or 
New York Heart Association (NYHA) Class III or IV heart failure (see 
Appendix II), uncontrolled angina, severe uncontrolled ventricular 
arrhythmias, or electrocardiographic evidence of acute ischemia or active 
conduction system abnormalities 
4.1.9j No prior allogeneic bone marrow or organ transplantation 
4.1.9k No known clinical finding or suspicion of human immunodeficiency virus 
(HIV) infection, hepatitis B, or hepatitis C. 
4.1.9l No co-morbid systemic illnesses or other severe concurrent disease which, 
in the judgment of the investigator, would make the patient inappropriate 
for entry into this study or interfere significantly with the proper 
assessment of safety and toxicity of the prescribed regimens. 
4.1.9m Able to swallow oral medication  
4.1.9n No known GI disease or GI procedures that could interfere with the oral 
absorption or tolerance of alisertib. Examples include, but are not limited 
to partial gastrectomy, history of small intestine surgery, and celiac 
disease. 
4.1.9o No visceral crisis: Visceral crisis is moderate-to-severe organ dysfunction 
as assessed by symptoms and signs, laboratory studies, and rapid 
progression of disease. 
4.1.9p Willing to undergo a biopsy of a metastatic site of breast disease for 
central laboratory determination of ER and correlative research purposes. 
NOTE: If insufficient or no tissue is obtained by the pre-registration 
biopsy, an archival tissue specimen (preferably from a metastatic site) 
must be available to submit for Central Laboratory ER determination prior 
to registration. 
4.2 Registration Eligibility Criteria 
4.2.1 ≤28 days post pre-registration 
4.2.2 Central Laboratory ER determination completed. 
4.2.3 The following laboratory values obtained ≤14 days prior to randomization: 
• Absolute neutrophil count (ANC) ≥1500/mm3 
• Platelet count ≥100,000/mm3 
• Hemoglobin ≥9.0 g/dL 
• Total bilirubin ≤ULN  
NOTE: If total bilirubin is out of range then direct bilirubin must be 
≤ULN 

 
 
 
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• Alanine transaminase (ALT) ≤2.5 x ULN (≤5 x ULN for patients with 
liver involvement) 
• Calculated creatinine clearance must be ≥45 ml/min using the 
Cockcroft-Gault formula below: 
Cockcroft-Gault Equation: 
Creatinine clearance for females = 
(140 - age)(weight in kg)(0.85) 
(72)(serum creatinine in mg/dL) 
4.2.4 ECOG Performance Status: 0 or 1 (See Appendix I) 
4.2.5 Life expectancy of ≥6 months. 
4.2.6 Willing to provide blood and tissue for correlative research purposes. 
4.3 Registration Exclusion Criteria 
4.3.1 Any of the following therapies prior to registration: 
• Chemotherapy ≤21 days  
• Immunotherapy ≤21 days 
• Biologic therapy (includes monoclonal antibodies) ≤21 days 
• Hormonal therapy ≤14 days except fulvestrant ≤21 days 
• Targeted therapies including CDK 4/6 inhibitors (e.g. palbociclib, 
abemaciclib, ribociclib, etc.) and mTOR inhibitors (e.g. everolimus) 
≤21 days 
• Other investigational agents ≤21 days 
• Radiation therapy ≤14 days 
• Minor surgical or interventional procedure ≤7 days 
• Major surgical procedure ≤21 days 
4.3.2  Administration of myeloid growth factors or platelet transfusion ≤14 days 
prior to registration. 
4.3.3 Systemic infection requiring IV antibiotic therapy ≤14 days prior to 
registration. 
4.3.4 Treatment with clinically significant enzyme inducers, such as the 
enzyme-inducing antiepileptic drugs phenytoin, carbamazepine or 
phenobarbital, or rifampin, rifabutin, rifapentine or St. John's wort 
≤14 days prior to registration. 
4.3.5 Require constant administration of proton pump inhibitor, H2 antagonist, 
or pancreatic enzymes (see Appendix IV). 
4.3.6 Development of visceral crisis since pre-registration. 
NOTE: Visceral crisis is moderate-to-severe organ dysfunction as assessed 
by symptoms and signs, laboratory studies, and rapid progression of 
disease. 
4.3.7 History of brain metastases. 

 
 
 
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4.4 Inclusion of Underrepresented Populations 
Individuals of all races and ethnic groups are eligible for this trial. There is no 
bias towards age or race in the clinical trial outlined. This trial is open to the 
accrual of women only. 
 
 

 
 
 
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5. REGISTRATION/RANDOMIZATION PROCEDURES 
5.1 Pre-Registration (Step 0)  
5.1.1 TBCRC Institutions other than Mayo Clinic 
To pre-register a patient, 
 a completed eligibility 
checklist to the 
 
between 8 a.m. and 4:30 p.m. Central Time Monday through Friday. 
5.1.2 Mayo Clinic Institutions 
To register a patient, access the 
 web 
page and enter the registration/randomization application. The registration/ 
randomization application is available 24 hours a day, 7 days a week. 
Back up and/or system support contact information is available on the 
website. If unable to access the website, call the 
 
 between the hours of 8 a.m. and 5:00 p.m. 
Central Time (Monday through Friday). 
The instructions for the registration/randomization application are 
available on the 
 
and detail the process for completing and confirming patient registration. 
Prior to initiation of protocol treatment, this process must be completed in 
its entirety and an MCCC subject ID number must be available as noted in 
the instructions. It is the responsibility of the individual and institution 
registering the patient to confirm the process has been successfully 
completed prior to release of the study agent. Patient registration via the 
registration/randomization application can be confirmed in any of the 
following ways: 
• Contact the 
 If the 
patient was fully registered, 
 
staff can access the information from the centralized database 
and confirm the registration. 
• Refer to “Instructions for Remote Registration” in section 
“Finding/Displaying Information about A Registered Subject.” 
5.1.3 Prior to accepting the pre-registration, the registration/randomization 
application will verify the following: 
• IRB approval at the registering institution 
• Patient pre-registration eligibility 
• Existence of a signed consent form 
• Existence of a signed authorization for use and disclosure of protected 
health information 
5.1.4 Pre-registration tests/procedures (see Section 11.0) must be completed 
within the guidelines specified on the test schedule. 
 
 

 
 
 
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5.2 Registration Procedures 
5.2.1 TBCRC Institutions other than Mayo Clinic 
5.2.1.1 Registration 
To register a patient, 
 a completed eligibility checklist 
to the 
 between 8 
a.m. and 4:30 p.m. Central Time Monday through Friday. 
5.2.1.2 Correlative Research 
A mandatory correlative research component requiring blood and tissue 
(see Section 9) is part of this study. The patient will be registered onto this 
component by the 
 
5.2.2 Mayo Clinic Institutions 
5.2.2.1 Registration 
To register a patient, access the 
web 
page and enter the registration/randomization application. The registration/ 
randomization application is available 24 hours a day, 7 days a week. Back-
up and/or system support contact information is available on the Web site. If 
unable to access the Web site, call the 
 
 between the hours of 8 a.m. and 5:00 p.m. Central Time (Monday 
through Friday). 
The instructions for the registration/randomization application are 
available on the 
and 
detail the process for completing and confirming patient registration. Prior 
to initiation of protocol treatment, this process must be completed in its 
entirety and a MCCC subject ID number must be available as noted in the 
instructions. It is the responsibility of the individual and institution 
registering the patient to confirm the process has been successfully 
completed prior to release of the study agent. Patient registration via the 
registration/randomization application can be confirmed in any of the 
following ways: 
• Contact the 
. If the 
patient was fully registered, the MCCC Registration Office 
staff can access the information from the centralized database 
and confirm the registration. 
• Refer to “Instructions for Remote Registration” in section 
“Finding/Displaying Information about A Registered Subject.” 
5.2.2.2 Correlative Research  
A mandatory tissue and blood correlative research component is part of 
this study. The patient will be automatically registered onto this 
component (see Section 9). 
 
 

 
 
 
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5.2.3 All Institutions 
5.2.3.1 Documentation of IRB approval must be on file in the 
 
before an investigator may register any patients. 
In addition to submitting initial IRB approval documents, ongoing IRB 
approval documentation must be on file (no less than annually) at the 
 If the necessary documentation is 
not submitted in advance of attempting patient registration, the registration 
will not be accepted and the patient may not be enrolled in the protocol 
until the situation is resolved. 
When the study has been permanently closed to patient enrollment, 
submission of annual IRB approvals to the Registration Office is no longer 
necessary. 
5.2.3.2 Prior to accepting the registration, registration/randomization application 
will verify the following: 
• IRB approval at the registering institution 
• Patient eligibility 
• Existence of a signed consent form 
• Existence of a signed authorization for use and disclosure of 
protected health information  
 
5.2.3.3 At the time of registration, the following will be recorded: 
• Patient has/has not given permission to store and use his/her 
sample(s) for future research of cancer. 
• Patient has/has not given permission to store and use his/her 
sample(s) for future research to learn, prevent, or treat other health 
problems. 
• Patient has/has not given permission for someone to contact them 
about future participation in more research 
• Patient has/has/not given permission to have coded genetic 
information and coded medical information placed in password 
protected, secured database for research analyses. 
5.2.3.4 Treatment on this protocol must commence at a TBCRC institution under 
the supervision of a medical oncologist. 
5.2.3.5 Treatment cannot begin prior to randomization and must begin ≤7 days 
after randomization. 
5.2.3.6 Pretreatment tests/procedures (see Section 11) must be completed within 
the guidelines specified on the test schedule. Prior to registration/ 
randomization a research biopsy of metastatic breast tissue must be taken 
for central pathologic review. 
5.2.3.7 All required baseline symptoms must be documented and graded. 
5.2.3.8 Study drug is available on site. 

 
 
 
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5.2.3.9 Blood draw kit is available on site.  
5.3 Randomization Procedures 
All institutions 
5.3.1 
The factors defined in Section 17.3, together with the registering 
membership, will be used as stratification factors. 
5.3.2 
After the patient has been registered into the study, the values of the 
stratification factors will be recorded, and the patient will be assigned to 
one of the following treatment groups using the Pocock and Simon 
dynamic allocation procedure26 which balances the marginal distributions 
of the stratification factors between the treatment groups. 
- 
Alisertib alone 
- 
Alisertib in combination with Fulvestrant 
5.4 Optional Crossover Phase 
5.4.1 Patients in Arm 1 who meet the criteria in Section 6.1.2 are eligible to 
crossover. 
5.4.2 If the patient and physician want to cross over to Arm 2, 
a completed continuation phase eligibility checklist to the 
Registration Office between 8 a.m. and 4:30 p.m. central time Monday 
through Friday.  
5.4.3 Treatment cannot begin prior to registering to the crossover phase and 
will ideally begin ≤7 days after registration for the crossover phase. 

 
 
 
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6. 
TREATMENT PLAN 
For both treatment arms: 
− Study treatment by a local medical doctor (LMD) is not allowed. Routine and acute 
clinical care may be provided by LMD and reported to treating institution. 
− If there is any interruption of treatment of ≥21 days contact Study Chair to determine 
whether the patient may restart treatment or will enter the event monitoring phase of 
the study. 
− If hepatic panel on C1D1 indicates progressive liver involvement (increase in total 
bilirubin to >1.5 x ULN or increase in ALT to >5 x ULN), then patient is not allowed 
to start study treatment.  
Note to study staff: A comment should be added to the CRF stating that the patient 
had unacceptable liver enzyme levels on Cycle 1 Day 1 and did not start treatment. 
− If CBC on C1D1 indicates new or worsening cytopenia(s), then starting dose of 
alisertib may be reduced based on discussion with overall study chair
 
− Patients who have achieved complete response, partial response, or stable disease for 
≥2 years may reduce imaging to every fourth cycle. 
6.1 Arm 1 (Alisertib Monotherapy) 
One treatment cycle=28 (±3) days 
Alisertib Monotherapy Alone 
Agent 
Dose 
Schedule 
Route 
Retreatment 
Alisertib 
50 mg 
BID* 
Days 1-3, 8-10, 15-17 
orally 
every 28 (±3) days 
until disease 
progression 
*Doses should be taken 12 hours apart with a minimum of 6 hours in between 
Note: Cycle 1 Day15: The morning dose of alisertib should be taken prior to Cycle 1 Day15 
blood draws 
6.1.1 Patients randomized to Arm 1 will initially receive alisertib until 
progression (PD) or intolerability. 
6.1.2 At the time of progression on alisertib treatment, patients will be allowed to 
add fulvestrant to alisertib if all 3 of the following conditions (a thru c) are 
met: 
a) Pre-registration biopsy finding of ER+ disease 
OR 
Pre-registration biopsy finding of ER <10% positive or ER negative 
disease and a biopsy performed at the time of progression on alisertib 
demonstrates ER+ ≥10% disease  
b) Recovered from any non-hematologic toxicities to ≤Grade 1 and blood 
chemistries are such that  

 
 
 
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• Absolute neutrophil count (ANC) ≥1500/mm3 
• Platelet count ≥100,000/mm3 
• Hemoglobin >9.0 g/dL 
• Total bilirubin ≤ULN 
NOTE: If total bilirubin is out of range then direct bilirubin must 
be ≤ULN 
• Alanine transaminase (ALT) ≤2.5 x ULN(≤5 x ULN for patients 
with liver involvement) 
• Calculated creatinine clearance ≥45 ml/min 
c) Treatment with alisertib and fulvestrant must start at most 35 days after 
documentation of disease progression on alisertib alone  
6.1.2.1 Patients who are not eligible or choose not to continue on with the 
combination of fulvestrant and alisertib will go to Event 
Monitoring (see Section 14.0).  
6.1.3 Crossover Combination Therapy 
One treatment cycle=28 (±3) days 
6.1.3.1 On the days both fulvestrant and alisertib are given, alisertib 
should be taken before fulvestrant is administered. 
Agent 
Dose 
Schedule 
Route 
Retreatment 
Fulvestrant 
500 mg 
Day 1 and Day 15 of 1st crossover 
cycle; Day 1 of all subsequent cycles 
intramuscular 
injection 
every 28 (±3) days 
until disease 
progression 
Alisertib 
at dose level 
last used when 
given as a 
single agent* 
Days 1-3, 8-10, 15-17 
orally 
* Doses should be taken 12 hours apart with a minimum of 6 hours in between 
Note: Cycle 1 Day15: The morning dose of alisertib should be taken prior to Cycle 1 Day15 
blood draws. 
6.2 Arm 2 (Alisertib with Fulvestrant) 
One treatment cycle=28 (±3) days 
6.2.1 Patients randomized to Arm 2 will receive the combination of fulvestrant 
and alisertib until progression (PD) or intolerability and then enter the 
event monitoring phase of the protocol. 
6.2.2 Patients will receive a loading dose of fulvestrant unless fulvestrant was 
the most recent therapy prior to registration and most recent dose was 
≤30 days and >21 days prior to C1D1. 
6.2.3 On the days both fulvestrant and alisertib are given, alisertib should be 
taken before fulvestrant is administered. 

 
 
 
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Agent 
Dose 
Schedule 
Route 
Retreatment 
Fulvestrant 
500 mg 
Day 1 and Day 15 of Cycle 1 
Day 1 of Cycle 2 and all cycles 
thereafter 
intramuscular 
injection 
every 28 (±3) days 
until disease 
progression 
Alisertib 
50 mg BID* 
Days 1-3, 8-10, 15-17 
orally 
every 28 (±3) days 
until disease 
progression 
* Doses should be taken 12 hours apart with a minimum of 6 hours in between 
Note: Cycle 1 Day15: The morning dose of alisertib should be taken prior to Cycle 1 Day15 
blood draws. 
6.3 Concomitant Treatment and Supportive Care Guidelines 
6.3.1 Pre-treatment anti-emetics are not recommended prior to Cycle 1. 
Supportive care pre-treatment medications may be added with subsequent 
cycles per discretion of the treating oncologist. 
6.3.2  Blood products and growth factors should be utilized as clinically 
warranted and following institutional policies and recommendations. The 
use of growth factors should follow published guidelines of the American 
Society of Clinical Oncology (42) 2006 Update of Recommendation for 
the Use of White Blood Cell Growth Factors: An Evidence-Based Clinical 
Practice Guideline Journal of Clinical Oncology 2006; 24(19):3187-3205. 
6.3.3 Patients should receive full supportive care while on this study. This 
includes blood product support, antibiotic treatment, and treatment of 
other newly diagnosed or concurrent medical conditions. All blood 
products and concomitant medications such as antidiarrheals, analgesics, 
and/or antiemetics received from the first day of study treatment 
administration until 30 days after the final dose will be recorded in the 
medical records. 
6.3.4 Diarrhea: This event could be managed conservatively with loperamide. 
The recommended dose of loperamide is 4 mg at first onset, followed by 
2 mg every 2-4 hours until diarrhea free (maximum 16 mg/day). 
In the event of Grade 3 or 4 diarrhea, the following supportive measures 
are allowed: hydration, octreotide, and antidiarrheals. 
If diarrhea is severe (requiring intravenous rehydration) and/or associated 
with fever or severe neutropenia (Grade 3 or 4), broad-spectrum 
antibiotics must be prescribed. Patients with severe diarrhea or any 
diarrhea associated with severe nausea or vomiting should be 
hospitalized for intravenous hydration and correction of electrolyte 
imbalances. 
6.3.5 Zoledronic acid, pamidronate, or denosumab may be administered per 
institutional guidelines as appropriate for patients with bone metastases. 
6.3.6 PPI and histamine-2 (H2) receptor antagonists are not permitted. 
6.3.7 Neutralizing antacids and calcium-containing supplements cannot be taken 
from 2 hours prior to alisertib dosing until up to 2 hours after dosing. 
6.3.8 Concomitant use of moderate or strong CYP3A4 inhibitors (including but 
not limited to: clarithromycin, itraconazole, voriconazole, ketoconazole, 

 
 
 
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posaconazole, nefazodone, telithromycin, aprepitant, erythromycin, 
fluconazole, verapapmil, diltiazem) or grapefruit juice/grapefruit-
containing products should be avoided. Selection of an alternate 
concomitant medication with no or minimal CYP3A4 inhibition potential 
is recommended. If co-administration of moderate or strong CYP3A4 
inhibitors is medically necessary, investigators should monitor for 
toxicities and follow the dose modifications per study protocol. 
6.4 Treatment/Follow-up Decision at Evaluation of Patient 
6.4.1 Patients who have not had systemic disease progression and have 
experienced acceptable toxicity will be eligible for re-treatment at their 
current dose level until disease progression, unacceptable toxicity, or 
refusal. 
6.4.2 Those patients who have not progressed and who have experienced 
unacceptable toxicity may be eligible for re-treatment at a lower dose. See 
Section 7. 
6.4.3 Patients randomized to the alisertib alone arm that progress may begin 
treatment with fulvestrant and alisertib if the conditions listed in 
Section 6.1 are met. 
Patients who are not eligible to continue on to fulvestrant plus alisertib or 
who choose not to continue on to fulvestrant plus alisertib will proceed to 
the Event Monitoring phase where patients will be followed every 
6 months until death or a maximum of 5 years post-randomization for 
disease progression and death information. 
Patients who proceed with fulvestrant plus alisertib treatment will 
continue until: disease progression, patient request, intolerability, or 
refusal. 
6.4.4 Criteria for discontinuation of all protocol therapy include: 
• Tumor progression during combination treatment with fulvestrant and 
alisertib 
• Arm 1 only: tumor progression during alisertib and patient will not be 
switching to combination treatment with fulvestrant and alisertib 
• Request by the patient to withdraw from all protocol treatment 
• Unacceptable adverse events 
• Treatment delay of >21 days (exception: recovery from Cycle 1 
Day 15 severe neutropenia where treatment delay of >30 days triggers 
treatment discontinuation [see Section 7.3]) 
• Intercurrent illness which would, in the judgment of the investigator, 
affect assessments of clinical status to a significant degree that require 
discontinuation of drug 
• Administration of radiotherapy, non-protocol chemotherapy, or an 
experimental drug during the trial 

 
 
 
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Patients who discontinue treatment for any of the above reasons will go to 
event monitoring. Once a patient has entered the event monitoring phase 
of the trial, his/her therapy is at the discretion of the treating physician. 
6.4.5 If an eligible patient refuses treatment following registration (and is 
classified as a “cancel” by the Research Base), all on-study materials must 
be submitted to the Research Base. 
6.4.6 A patient is deemed ineligible if at the time of registration, the patient did 
not satisfy each and every eligibility criteria for study entry.  
 If the patient never received any study treatment, on-study 
materials (with the exception of biospecimens) must be submitted. 
No further follow-up is required. 
 If the patient is receiving study treatment at the time the 
ineligibility is discovered, the patient may continue on study at the 
discretion of the treating physician as long as there are no safety 
concerns, and the patient was properly registered. All protocol 
procedures must be followed. Otherwise, the patient enters the 
event monitoring phase of the study. 
6.4.7 If protocol requirements regarding treatment in Cycle 1 of the initial 
therapy are severely violated to the point the Study Team finds that the 
patient is not evaluable for primary end point, the patient will be flagged 
in to study database as a protocol violation. The patient may continue on 
study at the discretion of the treating physician as long as there are no 
safety concerns, and the patient was properly registered. All protocol 
procedures must be followed. Otherwise, no further follow-up is required. 
6.4.8 If a patient withdraws consent prior to receiving any study treatment or is 
found to have unacceptable liver enzyme levels [either (1) total bilirubin 
>1.5 x ULN or (2) alanine transaminase >5 x ULN] on Cycle 1 Day 1 and 
does not receive protocol treatment, the patient will be deemed a cancel. 
On-study material (with the exception of biospecimens) and the End of 
Active Treatment/Cancel Notification Form must be submitted. For 
patients who are cancelled due to unacceptable liver enzyme levels on 
Cycle 1 Day 1. A comment should be added to the CRF stating that the 
patient had unacceptable liver enzyme levels on Cycle 1 Day 1 and did not 
start treatment. No further data submission is necessary. 
 
 

 
 
 
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7. 
EXPECTED TOXICITIES AND DOSING DELAYS/DOSE MODIFICATIONS 
7.1 Dose Modification Based on Adverse Events  
7.1.1 Dose modifications based on Adverse Event documented prior to each 
cycle of treatment. Strictly follow the modification in the table provided 
below until individual treatment tolerance can be ascertained. If multiple 
adverse events occur, administer the dose based on the greatest dose 
reduction required for any single adverse event observed. Dose 
modifications apply to the treatment given in the preceding cycle and are 
based on adverse events observed in the prior dose. 
7.1.2 Note that fulvestrant administration is not modified for any adverse event. 
- If alisertib is held due to toxicity then fulvestrant should also be held. 
Both agents should be restarted together.  
- If alisertib is discontinued due to intolerability then fulvestrant is also 
discontinued.  
7.1.3 If treatment is held greater than 21 days without resolution of any adverse 
events other than severe neutropenia or a 3rd dose reduction is required 
then study treatment is to be discontinued* and the patient will enter the 
Event Monitoring phase of the study.(see Section 14.0). 
*Note: If patient is deriving benefit from study treatment and the event can 
be managed safely, consult Study Chair (Dr. Haddad) regarding 
continuation. 
7.1.4 Dose reduction levels 
Dose 
Level 
Alisertib (twice daily)  
Days 1-3, 8-10, 15-17 
-1 
40 mg 
-2 
30 mg 
 
  Use the NCI Common Terminology Criteria for Adverse Events (CTCAE) version 4.0* unless 
otherwise specified   
* 
Located at 
 
7.2  
Dose Modifications – Prior to each cycle of treatment 
Strictly follow the modification in the table provided below until individual 
treatment tolerance can be ascertained. If multiple adverse events occur, 
administer the dose based on the greatest dose reduction required for any single 
adverse event observed. Dose modifications apply to the treatment given in the 
preceding cycle and are based on adverse events observed in the prior dose. 
 
 

 
 
 
 
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CTCAE 
System/ Organ/ 
Class (SOC) 
ADVERSE 
EVENT 
ACTION** 
Blood and 
lymphatic 
system 
disorders 
Anemia  
Grade 3 with 
hemoglobin 
<7.0 g/dL  
or Grade 4 
First or Second Episode: Hold alisertib administration until recovery to 
≤Grade 2 or baseline then decrease by 1 dose level 
If not recovered within 14 days discontinue alisertib and proceed 
to event monitoring phase* 
Third Episode: Discontinue study treatment (see note*). 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
Investigations 
Neutrophil 
Count 
Decreased 
Grade 3 
(neutrophils 
<1000 - 500 
cells/mm3) 
First Episode: Hold alisertib administration and check neutrophil 
counts within 5-7 days of report of Grade 3 ANC (referred to as 
ANC recheck #1). 
(a) results of ANC recheck #1  
− 
If neutrophils ≥1500 cells/mm3, resume alisertib at current dose 
− 
If neutrophils <1500 cells/mm3, continue to hold alisertib and 
re-check neutrophils counts again within the next 7 days but at 
most 14 days after the first report of Grade 3 ANC (ANC 
recheck #2) 
(b) results of ANC recheck #2  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at one 
dose lower 
 
If neutrophils remain <1500 cells/mm3 14 days after first 
report of Grade 3 ANC , discontinue study treatment* 
Second Episode: Hold alisertib administration and check neutrophil 
count within 5-7 days of report of Grade 3 ANC (referred to as 
ANC recheck #1). 
(a) results of ANC recheck #1  
− 
If neutrophils ≥1500 cells/mm3, resume alisertib at first dose 
level below current dose level  
− 
If neutrophils <1500 cells/mm3, continue to hold alisertib and 
re-check neutrophils counts again within the next 7 days but at 
most 14 days after the first report of Grade 3 ANC (ANC 
recheck #2) 
(b) results of ANC recheck #2  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at first 
dose level below current dose 
 
If neutrophils remain <1500 cells/mm3 14 days after first 
report of Grade 3 ANC in this second episode, discontinue 
study treatment* 
Third Episode: discontinue study treatment (see note*) 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
 
 

 
 
 
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Investigations 
Neutrophil 
count decreased 
Grade 4 
(neutrophils 
<500 cells/mm3) 
First Episode: Hold alisertib administration and check neutrophil 
counts within 5-7 days of report of Grade 4 ANC (referred to as 
ANC recheck #1). 
(a ) results of ANC recheck #1  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at first 
dose level below at current dose 
 
If neutrophils <1500 cells/mm3, continue to hold alisertib 
and re-check neutrophils counts again within the next 
7 days but at most 14 days after the first report of Grade 4 
ANC (ANC recheck #2) 
 (b) results of ANC recheck #2  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at first 
dose level below at current dose 
 
If neutrophils remain <1500 cells/mm3 14 days after first 
report of Grade 4 ANC , discontinue study treatment* 
Second Episode: Hold alisertib administration and check neutrophil 
counts within 5-7 days of report of Grade 4 ANC results of ANC 
recheck #1  
(a) results of ANC recheck #1  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at first dose 
level below current dose 
 
If neutrophils <1500 cells/mm3, continue to hold alisertib 
and re-check neutrophils counts again within the next 7 days 
but at most 14 days after the first report of Grade 4 ANC 
(ANC recheck #2) 
(b) results of ANC recheck #2  
 
If neutrophils ≥1500 cells/mm3, resume alisertib at first dose 
level below at current dose 
 
If neutrophils remain <1500 cells/mm3 14 days after first 
report of Grade 4 ANC , discontinue study treatment* 
Third Event: Discontinuestudy treatment (see note*) 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
Investigations 
Platelet count 
decreased  
Grade 1 and 2 
(<100,000 
cells/mm3 but 
>50,000 
cells/mm3) 
Hold alisertib administration and check platelet counts every 3-5 days 
until platelets ≥100,000 cells/mm3 or for a maximum of 21 days after 
Grade 1-2 decrease in PLT reported 
If platelet count recovered to ≥100,000 cells/mm3 within 21 days then 
resume alisertib at current dose 
Otherwise discontinue study treatment * 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation 
 
 

 
 
 
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Investigations 
Platelet count 
decreased  
Grade 3 (25,000 
– 50,000 
cells/mm3) 
First Episode: Hold alisertib administration and check neutrophil 
counts within 5-7 days of report of Grade 3 PLT (referred to as 
PLT recheck #1) 
(a) results of PLT recheck #1  
 
If platelets ≥100,000 cells/mm3, resume alisertib at current 
dose 
 
If platelets <100,000 cells/mm3, continue to hold alisertib 
and re-check platelet count again within the next 5- 7 days 
but at most 14 days after the first report of Grade 3 ANC 
(ANC recheck #2) 
 (b) results of PLT recheck #2  
 If platelets ≥100,000 cells/mm3, resume alisertib at first 
dose level below at current dose 
 If platelets remains <100,000 cells/mm3 14 days after first 
report of Grade 3 PLT decrease, discontinue study treatment 
Second Episode: Hold alisertib administration and check platelet 
counts within 5-7 days of report of Grade 1 ANC results of ANC 
recheck #1  
(a) results of PLT recheck #1  
 If platelets ≥100,000 cells/mm3, resume alisertib at current 
dose 
 If platelets <100,000 cells/mm3, continue to hold alisertib 
and re-check platelet counts again within the next 7 days but 
at most 14 days after the first report of Grade 3 PLT (PLT 
recheck #2) 
(b) results of PLT recheck #2  
 If platelets ≥100,000 cells/mm3, resume alisertib at first 
dose level below at current dose 
 If platelets remains <100,000 cells/mm3 14 days after first 
report of Grade 3 PLT decrease, discontinued 14 days after 
first report of Grade 3 ANC, discontinue study treatment 
Third Event: Discontinue all study treatment (see note*) 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
Platelet count 
decreased  
Grade 4 
(<25,000/mm3) 
or Grade 3 with 
bleeding 
Discontinue all study treatment*  
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 

 
 
 
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Blood and 
lymphatic 
system 
disorders 
Febrile 
neutropenia 
Grade 3 
(neutrophils 
<1000 cells/mm3 
with a single 
temperature of 
>38.3°C (101°F) 
or a sustained 
temperature of 
≥38°C (100.4°F) 
for more than 
one hour) 
Grade 4 
(Life threatening 
consequences) 
Discontinue all study treatment* 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
Gastrointestinal 
disorders 
Mucositis oral  
Grade 3 or 4 
First event:  
Hold alisertib administration until recovered to ≤Grade 1 or pre-
treatment level 
If recovered Grade 1 or baseline within 21 days, continue alisertib 
one dose level below current dose level 
Second event:  
Hold alisertib administration until recovered to ≤Grade 1 or pre-
treatment level 
If recovered to ≤Grade 1 or baseline within 21 days, continue 
alisertib one dose level below current dose level 
If not, discontinue all study treatment* 
Third event: Discontinue all study treatment (see note*) 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation. 
Nervous system 
disorders 
Somnolence  
≥Grade 3 
Hold alisertib administration until recovered to ≤Grade 1 or pre-
treatment level 
If recovered to ≤Grade 1 or baseline within 14 days, continue alisertib 
one dose level below current dose level 
If not, discontinue all study treatment (see note*) 
NOTE: Evaluate whether patient alcohol consumption or utilization of 
benzodiazepines are contributing. If so, counsel patient to restrict 
alcohol and discontinue benzodiazepines with provider guidance. 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation 
Other 
unspecified 
adverse event 
reduction 
instructions 
≥Grade 3 
Hold alisertib administration until recovered to ≤Grade 1 or pre-
treatment level (baseline level) 
If recovered to ≤Grade 1 or baseline within 14 days, continue alisertib 
one dose level below current dose level 
If not, discontinue all study treatment * 
*NOTE: If patient is deriving benefit from study treatment and event 
can be managed safely, consult Study Chair regarding continuation 

 
 
 
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7.3  
Dose Modifications – Cycle 1 Day 15 
The following dose modifications apply to adverse events documented on Cycle 1 
Day 15 and the first crossover Cycle 1 Day 15. 
 
Investigations 
Neutrophil count 
decreased  
Grade 3 or 4 
(neutrophils <1000 
cells/mm3) 
Omit Cycle 1 Days 15-17 administration of alisertib 
Administer fulvestrant loading dose 
Check neutrophil count on Cycle 2 Day 1 
 
8. DRUG FORMULATION/STORAGE/SUPPLY 
8.1 Alisertib (MLN8237, ML00653668) 
Alisertib is an investigational agent and will be supplied free-of-charge from 
Millennium. 
8.1.1 Background: Alisertib is a selective small molecule inhibitor of Aurora A kinase 
inhibitor that is being developed for the treatment of advanced malignancies. 
Aurora A is expressed and active during mitosis. Alisertib is also expected to be 
toxic to proliferating normal tissues, such as the bone marrow, GI epithelium, and 
hair follicles, since any cell that is in mitosis, where Aurora A is expressed and 
active, should be susceptible to the effects of an Aurora A kinase inhibitor. The 
Aurora A kinase gene is amplified, overexpressed, or both, in many tumors 
including: colon, breast, pancreatic, and bladder cancers, as well as certain 
lymphomas, leukemias, and myeloma. 
8.1.2 Formulation: Alisertib is supplied as enteric-coated tablets, formulated with the 
sodium salt of MLN8237 (MLN8237-004). 
The enteric-coated tablet (ECT) dosage form of alisertib is available as 10 and 15 
mg strengths, expressed as MLN8237 free acid. The key formulation excipients 
that aid in the in vivo absorption of the drug are sodium bicarbonate, sodium 
lauryl sulfate, and enteric coating. The other formulation excipients such as 
povidone, microcrystalline cellulose, croscarmellose sodium, and sodium stearyl 
fumarate serve as manufacturing aids. 
Open-label investigational product will be labeled to fulfill all requirements 
specified by applicable governing regulations. 
8.1.3 Preparation and storage: Alisertib is a cytotoxic compound, and should be 
handled with caution. Sites should follow institutional hazardous substance 
procedures for handling, disposal and spill clean-up. 
Enteric-coated tablets are packaged in 60-cc HDPE bottles with rayon coil, 
induction seal, desiccant packs and polypropylene child-resistant caps. 
The oral solution is filled in 2-oz. amber polyethylene terephthalate bottles, sealed 
with 24-mm polypropylene child-resistant caps and polyester liners. 

 
 
 
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Alisertib should be stored at controlled room temperature (20-25ºC) with 
excursions permitted to 15-30 ºC, and used before the retest date provided by the 
manufacturer. 
8.1.4 Administration: Retain alisertib in the bottle provided until use. 
Alisertib should be administered as provided and is not intended to be 
manipulated in any way. Alisertib is a cytotoxic anticancer drug. As with other 
potentially toxic compounds, caution should be exercised when handling. It is 
recommended that gloves and protective garments be worn during preparation 
when dispensed in the clinic. 
Alisertib may be administered regardless of the timing of meals, unless otherwise 
specified in the protocol. The dose should be swallowed with 250 mL (about 1 
cup) of water. Twice daily doses should ideally be taken every 12 hours, and 
doses are required to be separated by a minimum of 6 hours. Vomited doses will 
not be made up. Patients will take their next dose at the regularly scheduled time. 
8.1.5 Pharmacokinetic information: Pharmacokinetics properties of alisertib in 
patients with hematologic malignancies are generally consistent with those 
observed in patients with non-hematologic malignancies. 
a) Absorption –Clinical development has transitioned to the enteric-coated tablet 
formulation which is designed to bypass the stomach and delay dissolution 
until delivery to the upper small intestine, due to reduced solubility of an 
acidic drug in acidic pH. ECT absorption is fast with an overall median Tmax 
of 2.5 hours post-dose. 
b) Distribution – Alisertib is highly bound to plasma proteins with percentage of 
unbound alisertib measured at 2.5% in human plasma. Based on the results of 
in vitro blood-to-plasma partitioning studies in human whole blood, the mean 
blood-to-plasma ratio was 0.57, indicating preferential distribution into human 
plasma. 
c) Metabolism – Alisertib is metabolized by both oxidation and glucuronidation 
pathways, and multiple cytochrome P450 (CYP) isozymes (CYP3A4, 2C8, 
2C9, 2C19, and1A2) and uridine diphosphate-glucuronosyltransferase (UGT) 
isozymes (UGT1A1, 1A3, and 1A8) are involved. Phase 1 oxidative 
metabolism was identified to be of quantitative importance, with an estimated 
contribution of CYP3A4 of approximately 60% to overall apparent oral 
clearance in humans. Therefore, moderate to strong inhibitors of CYP3A4 and 
clinically significant inducers may alter systemic exposures of alisertib. Given 
a partial contribution of UGT1A1 to the metabolism of alisertib based on in 
vitro studies, genotyping for the reduced expression allele UGT1A1 *28 has 
been prospectively performed in the clinical program across phase 1 and 
phase 2 studies. The results of these analyses indicate that pharmacogenetic 
variation in UGT1A1 is not a meaningful contributor to the variability in the 
clinical PK of alisertib. 
d) Excretion – Overall mean steady-state terminal half-life following multiple-
dose administration of enteric coated tablets in patients with non-hematologic 

 
 
 
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malignancies was approximately 21 hours. Preliminary results indicate the 
mean terminal half-life for the oral solution is 22 hours. Negligible urinary 
excretion of alisertib was observed in humans. The predominant route of 
elimination for alisertib was fecal, consistent with hepatic metabolism and 
biliary excretion of alisertib.  
8.1.6 Potential Drug Interactions: Oxidative metabolism is the predominant route of 
elimination for alisertib. Results of subsequent in vitro drug metabolism studies 
have shown that the oxidative metabolism of alisertib is mainly mediated via 
CYP3A4. Study results have shown that co-administration of alisertib with 
rifampin (a strong inducer of CYP3A), and itraconazole (a strong inhibitor of 
CYP3A) have a significant effect on the systemic exposure of alisertib. Therefore, 
it is recommended that the concomitant use of strong CYP3A inhibitors (e.g., 
ketoconazole, itraconazole, clarithromycin, conivaptan, nefazodone, 
telithromycin, voriconazole, posaconazole, boceprevir, telaprevir, and grapefruit 
juice/grapefruit containing products) and strong CYP3A inducers (e.g., rifampin, 
enzyme-inducing antiepileptic agents), be avoided in patients receiving alisertib. 
Selection of an alternate concomitant medication with no or minimal CYP3A 
inhibition potential is recommended. If co-administration of strong CYP3A 
inhibitors is medically necessary, investigators should monitor for toxicities and 
follow the dose modifications for toxicity per study protocol. 
Alisertib exhibits pH-dependent solubility with decreased solubility under acidic 
pH conditions. Results from a completed study evaluating the effect of 
esomeprazole on alisertib PK indicated that co-administration of alisertib with 
esomeprazole resulted in a 28% increase in total systemic exposure of alisertib. 
Co-administration with drugs that alter intragastric pH (e.g. PPIs, H2 antagonists) 
is not permitted in ongoing clinical studies. Studies also prohibit concomitant use 
of pancreatic enzymes or conditions (such as pancreatectomy) that could 
potentially impact drug absorption in the upper bowel. 
8.1.7 Known potential toxicities: 
Very common (>10%): anemia, febrile neutropenia, leukopenia, neutropenia, 
thrombocytopenia, abdominal pain, diarrhea, nausea, oral pain, stomatitis, 
vomiting, asthenia, fatigue, pyrexia, decreased appetite, dehydration, somnolence, 
disorientation (and associated memory loss), alopecia 
Common (≥1% and <10%): lymphopenia, pancytopenia, dyspepsia, mucosal 
inflammation, URTI, UTI, pneumonia, oral candidiasis, sepsis (including fatal 
sepsis), cellulitis, oral herpes, sinusitis, nasopharyngitis, bronchitis, herpes zoster, 
influenza, conjunctivitis, esophagitis, skin infection, fungal skin infection, oral 
fungal infection, septic shock, increased AST, increased ALT, increased blood 
bilirubin, increased alkaline phosphatase, increased GGT, gait disturbance, 
confusional state, rash, pruritic rash, macular rash, maculo-papular rash, 
dermatitis acneiform, palmar-plantar erythrodysesthesia syndrome 
Uncommon (≥0.1% and <1%): sedation, dermatitis bullous 

 
 
 
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Reproductive toxicology studies have not been conducted with alisertib. Given 
the outcomes associated with Aurora A kinase inhibition and the effects of 
alisertib observed in reproductive tissues in repeat-dose toxicology studies, it is 
anticipated that alisertib could be a reproductive and developmental toxicant. 
Because alisertib may cause anemia, neutropenia, leukopenia, lymphopenia, and 
thrombocytopenia, patients on alisertib may experience the anticipated sequelae 
of infection, hemorrhage, or bleeding. 
Because of the effects of alisertib on the gastrointestinal mucosa, there is a 
potential risk of mucosal bleeding, GI bleeding, and the associated infections and 
sepsis. 
Cases of cardiac abnormalities have been infrequently observed in patients 
receiving treatment with alisertib, including decreased left ventricular ejection 
fraction, tachycardia, and 1 case of QT prolongation. The causal relationship 
between cardiac dysfunction and alisertib has been confounded by patients’ prior 
history of other cardiac abnormalities. 
Alisertib is structurally related to the benzodiazepines and may cause somnolence, 
confusion, dizziness or gait disturbance associated with the onset of maximal 
plasma concentration (about 3 hrs post-dose). For this reason, patients should not 
drive, operate dangerous machinery, or perform any other task requiring full 
alertness and/or coordination if these effects are experience while enrolled on 
study. Sedative effects have been managed by administration of divided doses and 
dose administration at bedtime, although dose reductions have sometimes been 
required. 
8.1.8 Drug procurement and ordering: 
Open-label alisertib will be provided free of charge to patients by 
Takeda/Millennium Pharmaceuticals, Inc. 
Each institution will order the drug through drug suppliers. (See Pharmacy 
Manual for order form.) 
NOTE: Local drug destruction may occur if the site provides a copy of their local 
drug destruction policy to the sponsor (Mayo Clinic) and the respective drug 
suppliers (Takeda/Millennium). 
8.1.9 Nursing Guidelines:  
8.1.9.1 Cytopenias have been seen with this agent. Monitor CBC and instruct 
patients to report any signs or symptoms of infection and/or abnormal 
bruising or bleeding to the study team. 
8.1.9.2 GI side effects, including abdominal pain, diarrhea, dyspepsia, nausea, 
and vomiting have been seen. Treat symptomatically and assess for 
effectiveness. 
8.1.9.3 Warn patients that they may experience somnolence, confusion or 
memory loss. Patient should be instructed not to operate a motor vehicle, 

 
 
 
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heavy machinery or participate in other activities that require mental 
sharpness until they know how this agent affects them. 
8.1.9.4 Instruct patients that they may experience alopecia. 
8.1.9.5 Monitor LFTs. Report increases in AST, ALT, bilirubin, GGT and Alk 
Phos to MD. Rarely hepatic veno-occlusive disease is seen. 
8.1.9.6 Patients may experience palmar plantar erythrodysesthesia (hand-foot 
syndrome). Instruct patients to report any redness, pain, or skin issues of 
the hands or feet to the study team.  
8.1.9.7 Alisertib can be administered regardless of the timing of food, unless 
otherwise specified. BID dosing should be taken every 12 hours and must 
be separated by at least 6 hours. Additionally doses should be swallowed 
with 250 mL (about 1 cup) of water and vomited doses should not be 
made up.  
8.1.9.8 Neutralizing antacids should not be taken until 2 hours after alisertib is 
administered.  
8.1.9.9a Gloves and protective garments should be worn during preparation and 
when dispensed in the clinic. 
8.1.9.9b Do not open, crush or manipulate the pills in any way. 
8.1.9.9c Alisertib can be given regardless of meals, unless the protocol dictates 
otherwise. Pills should be taken with at least 250 ml (1 cup) of water. 
Vomited doses should not be made up. Instruct patients that they should 
take their next dose at the regularly scheduled time. 
8.2 Fulvestrant (Faslodex®) 
Fulvestrant is commercially available. 
8.2.1 Background 
Fulvestrant is an estrogen receptor antagonist. Fulvestrant competitively binds to 
estrogen receptors on tumors and other tissue targets, producing a nuclear 
complex that causes a dose-related down-regulation of estrogen receptors and 
inhibits tumor growth. 
8.2.2 Formulation, preparation and storage 
Commercially available for injection as: Injection, solution: 50 mg/mL (5 mL) 
[contains benzyl alcohol, benzyl benzoate, castor oil, ethanol 10% w/v] 
 
 

 
 
 
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8.2.3 Preparation and storage 
Refer to package insert for complete preparation and dispensing instructions. 
Store in original carton under refrigeration at 2°C to 8°C (36°F to 46°F). Protect 
from light. 
8.2.4 Administration 
Refer to the treatment section for specific administration instructions. Administer 
IM only; do not administer IV, SubQ, or intra-arterially. Administer 500 mg dose 
as two 5 mL injections (one in each buttocks) slowly over 1-2 minutes per 
injection. 
8.2.5 Pharmacokinetic information 
Distribution: Vd: ~3-5 L/kg 
Protein binding: 99%; to plasma proteins (FLDL, LDL and HDL lipoprotein 
fractions) 
Metabolism: Hepatic via multiple biotransformation pathways (CYP3A4 
substrate involved in oxidation pathway, although relative contribution to 
metabolism unknown); metabolites formed are either less active or have similar 
activity to parent compound. 
Half-life elimination: 250 mg: ~40 days 
Excretion: Feces (~90%); urine (<1%) 
8.2.6 Potential Drug Interactions 
Cytochrome P450 Effect: Substrate of CYP3A4 (minor). There are no known 
interactions where it is recommended to avoid concomitant use. 
8.2.7 Known potential toxicities 
Consult the package insert for the most current and complete information.  
Common known potential toxicities, >10% 
Endocrine & metabolic: Fertility; Hot flushes 
Hepatic: Alkaline phosphatase increased, transaminases increased 
Local: Injection site pain 
Neuromuscular & skeletal: Joint disorders 
Less common known potential toxicities, 1% - 10% 
Cardiovascular: Ischemic disorder 
Central nervous system: Fatigue, headache 
Gastrointestinal: Nausea, anorexia, vomiting, constipation, weight gain 
Genitourinary: Urinary tract infection 
Neuromuscular & skeletal: Bone pain, arthralgia, back pain, extremity pain, 
musculoskeletal pain, weakness 
Respiratory: Cough, dyspnea 
Rare known potential toxicities, <1% (Limited to important or life-
threatening) 
Angioedema, hypersensitivity reactions, leukopenia, myalgia, osteoporosis, 
thrombosis, urticaria, vaginal bleeding 

 
 
 
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8.2.8 Drug procurement and ordering 
Commercial supplies. Pharmacies or clinics shall obtain supplies from normal 
commercial supply chain or wholesaler. 
8.2.9 Nursing Guidelines 
8.2.9.1 Rarely a blood-tinged vaginal discharge has been reported infrequently 
during therapy. Advise patients that this is a possibility and that studies 
have shown no effects on vagina or endometrium. 
8.2.9.2 Monitor LFTs based on protocol requirements. Report increased LFTs to 
treating physician. 
8.2.9.3 Hot packing the injection site for a short while after injection may 
prevent the possible bruising, tenderness, and/or erythema at the IM 
injection site. 
8.2.9.4 It is recommended that pregnancy be avoided during treatment. Instruct 
patient and partner on adequate methods of birth control, if needed. 
8.2.9.5 Instruct patient to report any signs or symptoms of blood clots. Patients 
with calf tenderness or burning, and/or chest pain (pulmonary embolus) 
should be evaluated by a physician immediately. 
8.2.9.6 Warn patient of possible hot flashes. Assess severity and discuss non-
hormonal treatments with treating physician. Assess treatment for 
efficacy. 
8.2.6.7 May cause mild GI symptoms (nausea, anorexia, vomiting, constipation). 
Treat symptomatically and monitor for effectiveness of intervention. 
 

 
 
 
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9. CORRELATIVE/SPECIAL STUDIES 
9.1 Body Fluid Biospecimens 
9.1.1 Summary of the blood biospecimen collection schedule 
9.1.1.1 All Patients 
 
Cycle 1, Day 1 prior 
to start of treatment 
(Baseline) 
At the end of Cycle 1 
(prior to start of 
Cycle 2) 
At time of disease 
progression 
Submit to: 
Shipping/storage 
instructions 
CTC  
One 10 mL blood 
sample collected in a 
CellSave® tube and 
one 10 mL blood 
sample collected in 
an AccuCyte tube 
One10 mL blood 
sample collected in 
CellSave® tube and 
one 10 mL blood 
sample collected in an 
AccuCyte tube 
One 10 mL blood 
sample collected in 
CellSave® tube and 
one 10 mL blood 
sample collected in 
an AccuCyte tube 
BAP freezer 
Mayo Clinic 
Samples should be 
kept at ambient 
temperature after 
collection and during 
shipping. Specimens 
must arrive at Mayo 
within 72 hours of 
collection. 
cfDNA 
Two 10 mL blood 
samples collected in 
Streck® tubes 
Two 10 mL blood 
samples collected in 
Streck® tubes 
Two 10 mL blood 
samples collected in 
Streck® tubes 
BAP freezer 
Mayo Clinic 
Samples should be 
kept at ambient 
temperature after 
collection and during 
shipping. Specimens 
must arrive at Mayo 
within 72 hours of 
collection. 
SNP 
One 6 mL blood 
sample collected in a 
K2 EDTA tube. 
Gently invert tube 6-
8 times - Do not 
centrifuge 
- 
- 
BAP Mayo 
Clinic 
Upon processing, 
refrigerate until 
shipment; ship 
refrigerated 
 
 
 

 
 
 
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9.1.1.2 For those patients with crossover from alisertib to the combination of alisertib and fulvestrant 
 
Cycle 1, Day 1 of 
alisertib and 
fulvestrant, 
(if missed at time of 
progression on 
alisertib) 
At the end of Cycle 1 of 
alisertib and 
fulvestrant 
At time of disease 
progression on 
alisertib plus 
fulvestrant 
Submit to: 
Shipping/storage 
instructions 
CTC  
One 10 mL blood 
sample collected in a 
CellSave® tube and 
one 10 mL blood 
sample collected in 
an AccuCyte tube 
One 10 mL blood 
sample collected in a 
CellSave® tube and 
one 10 mL blood 
sample collected in an 
AccuCyte tube 
One 10 mL blood 
sample collected in a 
CellSave® tube and 
one 10 mL blood 
sample collected in an 
AccuCyte tube 
 
 
Samples should be 
kept at ambient 
temperature after 
collection and during 
shipping 
Specimens must 
arrive at Mayo within 
72 hours of collection 
cfDNA 
Two 10 mL blood 
samples collected in 
Streck® tubes 
Two 10 mL blood 
samples collected in 
Streck® tubes 
Two 10 mL blood 
samples collected in 
Streck® tubes 
 
 
Samples should be 
kept at ambient 
temperature after 
collection and during 
shipping 
Specimens must 
arrive at Mayo within 
72 hours of collection 
 
See Lab Manual for detailed instructions 
 
Ship blood samples to: 
 
 
 
 
 
Samples should be collected and shipped Monday – Thursday. However, if the subject can only be 
seen on Fridays, please ensure that Saturday delivery is marked clearly on the shipping boxes.  
9.1.2 Methods 
Circulating Tumor Cell Capture and Phenotyping 
The relative abundance of CTCs in the peripheral blood has strong correlation with tumor 
recurrence and distant metastases in both early stage and advanced breast tumors29. We 
will prospectively isolate CTCs from blood specimens collected from study participants 
at three time points for phenotypic and possibly genotypic analyses.  
One 10 mL blood sample will be collected in the CellSave® Preservation Tube for CTC 
isolation using the Veridex CellSearch™ system (Janssen; Raritan, NJ). CellSave® 
contains an optimized preservative that stabilizes cells for up to 96 hours at room 
temperature. The CellSearch™ system 
allows for the 

 
 
 
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immunomagnetic selection, fluorescence staining, concentration, and enrichment of 
CTCs for enumeration and analysis. The FDA cleared process uses the CellSearch™ 
Epithelial Cell Kit, which contains anti-EpCAM (epithelial cell adhesion molecule) 
Ferrofluid, a fluorescent nucleic acid dye (DAPI), and fluorescently labeled monoclonal 
antibodies specific for leukocytes (CD45) and epithelial cells (cytokeratins 8, 18, and 19) 
to identify CTCs as those that are cytokeratin positive, DAPI positive, and CD45 
negative with the appropriate morphology. At least two-thirds of patients with metastatic 
breast cancer have >1 CTC per 7.5 mL blood assayed with this technology, and the 
enumeration of CTCs relative to a threshold of 5 CTCs per 7.5 mL blood is associated 
with clinical outcomes in this patient population27-29. The standard process has been 
modified to allow for CTC retrieval and subsequent assessment for additional protein 
markers of interest (e.g., Aurora A kinase, ER, p-SMAD5, and p-SOX2). 
CTCs vary in the degree of EpCAM expression, so malignant cells in the circulation may 
be missed by the CellSearch technology. Toward that end, other methodologies that do 
not rely on EpCAM for capture are now available. Therefore, a second 10 mL blood 
sample will be collected in the AccuCyte® Blood Collection Tube for CTC isolation 
using the AccuCyte® Platform (RareCyte; Seattle, WA). The blood collection tube 
contains an optimized preservative that stabilizes cells for up to 96 hours at ambient 
temperature. The AccuCyte® Platform
 is a comprehensive, 
reproducible, and highly sensitive platform for enriching, identifying, and isolating CTCs 
for downstream molecular analyses (ref: Campton DE et al. BMC Cancer 2015. 15:360.). 
The system relies on density gradient centrifugation and allows for virtually complete 
harvesting of the buffy coat into a small volume for application to a microscopic slide 
without cell lysis or washing. Immunofluorescent staining for selected markers (e.g., 
cytokeratins, EpCAM, DAPI, CD45, HER2, ER, Aurora A kinase, p-SMAD5, and p-
SOX2) is used for the efficient positive and negative identification of CTCs via 
automated scanning digital microscopy and image analysis. An integrated device 
provides for mechanically precise CTC retrieval for advanced genomic analyses, 
including next generation sequencing, on single or pooled CTCs. 
 

 
 
 
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9.2 Pathology Considerations/Tissue Biospecimens 
9.2.1 Summary Table of Research Tissue Specimens to be Prospectively Collected for this Protocol 
Note: Only send registration tissue if the patient qualifies for the study 
Correlative 
Study (Section 
for more 
information) 
Mandatory 
or Optional 
Type of 
Tissue to 
Collect 
Slides, 
Core, etc. (# 
of each to 
submit) 
Pre-
registration 
(biopsy)1 
Upon 
completion 
of Cycle 12 
At Disease 
Progression 
At disease 
progression 
after 
combination 
(ARM 1 
ONLY) 
Process 
at site? 
Temperature 
Conditions for 
Storage 
/Shipping 
Aurora A 
Kinase, SMAD5, 
SOX2 and ERα 
Expression 
Mandatory 
Formalin 
Fixed 
Paraffin 
Embedded 
10 
unstained 
slides (2 to 
4 cores) 
X 
X 
X 
X 
Yes 
Ambient via 
Pathol 
coordinator 
Real time PCR 
for ER target 
genes 
Mandatory 
Flash 
Frozen 
1 core (3-4 
mm) 
X 
X 
X 
X 
Yes 
Pathol 
coordinator 
Patient Derived 
Xenograft 
Mandatory 
for Mayo 
Clinic 
Subjects 
Only 
Fresh 
2 cores 
X 
 
X 
 
Yes 
In PBS or 
DMEM 
medium at 
room 
temperature 
within 30 
minutes 
between the 
time when 
samples are 
obtained and 
the time 
samples are 
delivered to the 
xenograft team 

 
 
 
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Correlative 
Study (Section 
for more 
information) 
Mandatory 
or Optional 
Type of 
Tissue to 
Collect 
Slides, 
Core, etc. (# 
of each to 
submit) 
Pre-
registration 
(biopsy)1 
Upon 
completion 
of Cycle 12 
At Disease 
Progression 
At disease 
progression 
after 
combination 
(ARM 1 
ONLY) 
Process 
at site? 
Temperature 
Conditions for 
Storage 
/Shipping 
LMW-E 
expression 
(MDACC) 
Mandatory 
Formalin 
Fixed 
Paraffin 
Embedded 
1-2 
unstained 
slides 
X 
X 
X 
X 
Yes 
MDACC 
Contact 
1. If pre-registration biopsy is attempted and either aborted or insufficient tissue is obtained, the patient may still be eligible. In this case, 
the site may submit slides from archival specimens for central lab determination of ER status for patient stratification. Refer to Lab 
Manual for detailed instructions. 
NOTE: If biopsy does not obtain tissue AND no archived tissue is available for Central Laboratory review, patient is not eligible. A 
repeat biopsy may be attempted at the discretion of the treating physician and patient.  
2. Performed once up to 4 days prior to the start of Cycle 2. Must be performed prior to initiation of treatment for Cycle 2. 
Ship frozen tissue samples to: 
Ship tissue slides/cores to Mayo Clinic Cancer Center Operations Office 
 
 
 
 
 
 
  
 
  
 
 
 

 
 
 
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9.2.2 Correlative Tumor Tissue Collection  
In All Subjects: 
9.2.2.1 Selection of metastatic lesion site for biopsy 
A lung lesion should only be pursued for research biopsy in the event there is no 
other site of disease amenable to biopsy. If a lung lesion is the only site of disease 
amenable to biopsy, then peripheral lesions should be carefully selected due to 
risk of pneumothorax. Biopsy of central lesions is not advised. If a lung lesion is 
the only site of disease amenable to biopsy, then only 2 of the 3 mandatory 
biopsies will be required-- the pre-treatment/baseline and post-Cycle 1 biopsies. 
The biopsy at disease progression will be not be required, nor is it optional. 
9.2.2.2 Two cores will be obtained with each research biopsy 
One core will be formalin-fixed, paraffin-embedded (FFPE) and the tissue block 
will be sent to the Mayo Clinic Pathology Research Core (PRC). Sections (5 
micron) will be cut from the tumor tissue block to obtain 10 unstained slides that 
contain at least 75% tumor tissue. These slides will be used for IHC assessment of 
the following biomarkers: Aurora A Kinase, SMAD5, SOX2 and ERα. One to 
two slides will be submitted to the laboratory of co-investigator, 
 
 for evaluation of both full length (nuclear) and LMW 
cyclin E (cytoplasmic) by IHC in FFPE tissue biospecimens. 
One core will be flash frozen and sent to the Mayo Clinic PRC. RNA will be 
isolated from the biospecimen. Following cDNA synthesis, the expression levels 
of well characterized ERα target genes (TFF1, Progesterone Receptor, and 
amphiregulin) will be assessed by quantitative real-time PCR. Results will be 
expressed relative to an internal control housekeeping gene (TBP). 
9.2.2.3 Aurora A Kinase, SMAD5, SOX2 and ERα Expression 
Antibodies to detect total Aurora-A kinase, ERα, SMAD5 and SOX2, and 
phospho-SMAD5 and phospho-SOX2, are available through the Mayo PRC or 
will be purchased from Cell Signaling Technology, Boston, MA, USA and 
processed according to package insert. The phospho antibodies will be optimized 
through standard procedure with the PRC. Normal human breast tissues from 
reduction mammoplasty will serve as negative control and triple-negative breast 
tumor tissues as positive control. The intensity of biomarkers expression will be 
scored as strong, moderate, or weak-to-none using digital image analysis 
employing an innovative ImageScope viewing software (Leica Biosystems) to 
accurately measure Aurora-A, SMAD5, SOX2 and ERα nuclear expression in 
breast tumor clinical samples.  
 
 

 
 
 
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In Mayo Clinic Subjects Only: 
9.2.2.4 Patient Derived Xenografts (PDX) 
To generate individual patient derived xenografts (PDX), 2 additional research 
core specimens will be obtained during the baseline (pre-treatment) and 
progression of disease (PD) biopsies. The fresh tumor tissue will be immediately 
injected into 3 immunodeficient scid mice for the creation of human tissue 
xenografts (per IACUC A18014). The xenograft tumor samples will be used to 
evaluate mechanisms of de novo and acquired resistance to alisertib. These PDX 
models will be also be used for future research purposes, such as testing novel 
compounds and different regimens. All the tumor tissues from xenografts will be 
stored in the 
 
10. SPECIMEN BANKING 
Any leftover study blood and tissue samples may be stored for future research studies. The 
subjects will consent to the future use of samples in the consent form for the study. Any 
samples will only be released for use in future studies after approval by the TBCRC and 
other regulatory bodies, as appropriate. 
The study PI and collaborators have approval by the TBCRC to use all research bio-
specimens collected during the conduct of this trial to address the research questions 
described in the protocol document. All future use of residual or repository specimens 
collected in this trial for purposes not prospectively defined will require review and approval 
by the TBCRC according to its established policies, whether the specimens are stored in a 
central site or at a local institution in a virtual repository. 
Secondary use of bio-specimens for new endpoints must be submitted to the TBCRC Central 
Office for possible review by the TBCRC Correlative Science Review Committee. 

 
 
 
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11. 
STUDY CALENDAR 
11.1 
Test Schedule for Arm 1: Alisertib 
 
Alisertib Treatment 
Phase 
For patients who meet 
requirements set out in  
Section 6.1.21 
Alisertib + Fulvestrant 
Treatment Phase 
Tests and procedures 
≤28 days 
prior to Pre-
registration 
Pre-registration 
period (spans the 
first 28 days after 
pre-registration)2 
Day 1 of 
each 
treatment 
cycle*3 
At PD or 
discontin-
uation of 
alisertib 
Day 1 of 
each 
treatment 
cycle4 
At PD or 
discontinuation 
of alisertib + 
fulvestrant 
History and exam, wt, PS 
X 
 
X5 
X 
X 
X 
Adverse event assessment 
 
X6 
X6 
X 
X 
X 
Height 
X 
 
 
 
 
 
Follicle-stimulating hormone 
(FSH) level7 
 
X 
 
 
 
 
Hematology group  
− Hemoglobin 
− White blood cell count 
− Absolute neutrophil count 
− Platelets 
 
X 
X8 
X 
X9 
X 
 
1 For crossover registration procedure, see Section 5.4 
2 Hematology and chemistry blood tests and adverse event assessment for registration must be done ≤21 days prior 
to registration 
3Labs, scans, tests and observations may be obtained ≤4 days prior to Day 1 of each cycle. 
4 Labs, H&E, wt, PS and AE assessment completed prior to switch to the combination of fulvestrant and alisertib 
may be used for Day 1 of “new” Cycle 1 tests if obtained ≤14 days prior to start of combination treatment. 
5 For Cycle 1, Day 1, nurse assessment may replace “History and exam, wt and PS” IF most recent 
physician/provider exam is ≤14 days prior to C1D1.  
6 Baseline AE assessment is to be performed anytime in the window of ≤4 days prior to registration. AE assessment 
need not be repeated Cycle 1 Day 1. 
7 For women <60 years of age with amenorrhea for >12 months 
8 Hematologic parameters will be assessed on Cycle 1 Day 15 (±1 day) after the patient has taken their morning dose 
of alisertib 
9 Hematologic parameters will be assessed on Day 15 (±1 day) of first cycle in the crossover phase any time after the 
patient has taken their morning dose of alisertib prior to the administration of the loading dose of fulvestrant. 

 
 
 
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Alisertib Treatment 
Phase 
For patients who meet 
requirements set out in  
Section 6.1.21 
Alisertib + Fulvestrant 
Treatment Phase 
Tests and procedures 
≤28 days 
prior to Pre-
registration 
Pre-registration 
period (spans the 
first 28 days after 
pre-registration)2 
Day 1 of 
each 
treatment 
cycle*3 
At PD or 
discontin-
uation of 
alisertib 
Day 1 of 
each 
treatment 
cycle4 
At PD or 
discontinuation 
of alisertib + 
fulvestrant 
Chemistry group  
− Sodium 
− Potassium 
− BUN 
− Creatinine 
− Calcium 
− Glucose 
− Albumin 
− AST 
− ALT10 
− Alkaline Phosphatase 
− Total Bilirubin10 
 
X 
X 
X 
X 
X 
Tumor measurement11 
X 
 
X 
X 
X12 
X 
Alisertib 
 
 
X 
 
X 
 
Fulvestrant 
 
 
 
 
X13 
 
Patient Medication Diary 
(Appendix III)14  
 
 
X 
X 
X 
X 
 
10 FOR CYCLE 1 DAY 1 ONLY: If  either to the following holds: (1) total bilirubin >1.5 x ULN or (2) Alanine 
transaminase >5 x ULN, then the patient should not begin protocol treatment. The patient should go off study and 
will be considered a cancel (see Section 6.4.8).  
11 The same imaging modality (CT scan, CT component of a PET/CT, or MRI) must be used throughout the study. 
Baseline imaging should be obtained ≤28 days prior to Registration. Tumor measurements are to be done at the 
completion of Cycles 2, 4, 6, etc., for first two years or until disease progression, whichever is first. Patients who 
have achieved complete response, partial response, or stable disease for ≥2 years may reduce imaging to every 
fourth cycle. 
12 Scans are not required Day 1 of Cycle 1 of fulvestrant and alisertib. The scans taken at the time of progression on 
alisertib will serve as the baseline scan for the fulvestrant and alisertib treatment phase of the study. 
13 Fulvestrant will be given on Day 1 of every cycle and on Day 15 (±1 day) of Cycle 1 only. 
14 The diary must begin the day the patient starts taking the medication and must be completed per protocol and 
returned to the treating institution at the completion of each cycle of treatment (approximately every 28 days). 
Compliance must be documented in the medical record by any member of the care team. 

 
 
 
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Alisertib Treatment 
Phase 
For patients who meet 
requirements set out in  
Section 6.1.21 
Alisertib + Fulvestrant 
Treatment Phase 
Tests and procedures 
≤28 days 
prior to Pre-
registration 
Pre-registration 
period (spans the 
first 28 days after 
pre-registration)2 
Day 1 of 
each 
treatment 
cycle*3 
At PD or 
discontin-
uation of 
alisertib 
Day 1 of 
each 
treatment 
cycle4 
At PD or 
discontinuation 
of alisertib + 
fulvestrant 
Mandatory tumor tissue 
specimens for research (see 
Section 9.0) 
 
X15 
X16 
X17 
X 
X18 
Research Correlative blood 
studies (collection for CTCs 
and cf-DNA) 
 
X 
X19 
X 
X20 
X 
* Cycle length is 28 days ±3 days 
 
 
15 The pre-registration biopsy will be utilized for central ER evaluation and correlative studies. 
16 Performed once up to 4 days prior to the start of Cycle 2. Must be performed prior to initiation of treatment for 
Cycle 2. 
17 Performed once up to 14 days after progressive disease is identified. Must be performed prior to initiation of next 
therapy, which may be the combination of fulvestrant and alisertib for those eligible and electing to crossover, or 
may be standard therapy for those who elect to come off study or are not eligible for cross-over. If a lung lesion is 
the only site of disease amenable to a biopsy, then this biopsy will not be mandatory (except for patients with ER 
<10% or ER negative on the pre-registration biopsy who are desiring and eligible for cross-over). 
18 Biopsy at PD after crossover is optional, except for patients with a lung lesion as the only site of disease amenable 
to biopsy in which case the biopsy at PD after crossover is not allowed. 
19 At the end of Cycle 1, prior to treatment initiation on Day 1 of Cycle 2 (only). May be drawn with clinical labs 
≤4 days prior to C2D1. 
20 At the end of the first cycle of combination therapy, prior to treatment initiation on Day 1 of the second cycle of 
combination therapy (only). 

 
 
 
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11.2 
Test Schedule for Arm 2: Alisertib + Fulvestrant 
Tests and procedures 
≤28 days prior to  
Pre-registration 
Pre-registration 
period spans the 
first 28 days after 
pre-registration21 
Day 1 of each 
treatment 
cycle22* 
At PD or 
discontinuation  
of therapy 
History and exam, wt, PS  
X 
 
X23 
X 
Adverse event assessment 
 
X 
X24 
X 
Height 
X 
 
 
 
Follicle-stimulating hormone (FSH) level25 
 
X 
 
 
Hematology group  
− 
Hemoglobin 
− 
White blood cell count 
− 
Absolute Neutrophil count 
− 
Platelets 
 
X 
X26 
X 
Chemistry group 
− 
Sodium 
− 
Potassium 
− 
BUN 
− 
Creatinine 
− 
Calcium 
− 
Glucose 
− 
Albumin 
− 
AST and ALT27 
− 
Alkaline Phosphatase 
 
X 
X 
X 
 
21 Hematology and chemistry blood tests and adverse event assessment for registration must be done ≤21 days prior to registration. 
22 Labs, scans, tests and observations may be obtained ≤4 days prior to Day 1 of each cycle. 
23 For Cycle 1, Day 1, nurse assessment may replace “History and exam, wt and PS” IF most recent physician/provider exam is ≤14 days prior to C1D1. 
24 Baseline AE assessment is to be performed anytime in the window of ≤4 days prior to registration. Adverse event assessment need not be repeated prior to 
Cycle 1, Day 1. 
25 For women <60 years of age with amenorrhea for >12 months. 
26 Hematologic parameters will be assessed on Day 15 of Cycle 1 any time after the patient has taken their morning dose of alisertib but before administration of 
fulvestrant. 
27 FOR CYCLE 1 DAY 1 ONLY: If  either to the following holds: (1) total bilirubin >1.5 x ULN or (2) alanine transaminase >5 x ULN, then the patient should 
not begin protocol treatment. The patient should go off study and will be considered a cancel (see Section 6.4.8). 

 
 
 
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Tests and procedures 
≤28 days prior to  
Pre-registration 
Pre-registration 
period spans the 
first 28 days after 
pre-registration21 
Day 1 of each 
treatment 
cycle22* 
At PD or 
discontinuation  
of therapy 
− 
Total Bilirubin27 
Tumor measurement28 
X 
 
X 
X 
Alisertib 
 
 
X 
 
Fulvestrant 
 
 
X29 
 
Patient Medication Diary (Appendix III)30 
 
 
X 
X 
Mandatory tumor tissue specimens for research (see Section 9) 
 
X31 
X32 
X33 
Correlative blood studies (collection for CTCs and cf-DNA) 
 
X 
X34 
X 
* Cycle length is 28 ±3 days 
 
28 The same imaging modality (CT scan, CT component of a PET/CT, or MRI) must be used throughout the study. Baseline imaging should be obtained ≤28 days 
prior to Registration. Tumor measurements are to be done at the completion of Cycles 2, 4, 6 etc., for first two years or until disease progression, whichever is 
first. Patients who have achieved complete response, partial response, or stable disease for ≥2 years may reduce imaging to every fourth cycle. 
29 Fulvestrant will be given on Day 1 of every cycle and on Day 15 of Cycle 1 only. 
30 The diary must begin the day the patient starts taking the medication and must be completed per protocol and returned to the treating institution at the 
completion of each cycle of treatment (approximately every 28 days). Compliance must be documented in the medical record by any member of the care team. 
31 The pre-registration biopsy will be utilized for central ER evaluation and correlative studies. 
32 Biopsy must be performed ≤4 days prior to initiation of Cycle 2 treatment  
33 Performed once up to 14 days after progressive disease is identified. Must be performed prior to initiation of next therapy. If a lung lesion is the only site of 
disease amenable to rebiopsy, then this biopsy will not be mandatory. 
34 At the end of Cycle 1, prior to treatment initiation on Day 1 of Cycle 2 (only). May be drawn with clinical labs ≤4 days prior to C2D1 

 
 
 
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12. 
MEASUREMENT OF EFFECT 
For the purposes of this study, patients should be re-evaluated for response after every 
2 cycles of treatment. 
NOTE: Patients who have achieved complete response, partial response, or stable disease 
for ≥2 years may reduce imaging to every fourth cycle. 
Response and progression will be evaluated in this study using the international criteria 
proposed by the revised Response Evaluation Criteria in Solid Tumors (RECIST) 
Committee (version 1.1).(62) Changes in only the largest diameter (unidimensional 
measurement) of the tumor lesions are used in the RECIST criteria. 
12.1 
Definitions 
Evaluable for toxicity: All patients will be evaluable for toxicity from the time of 
their first treatment with alisertib. 
12.2 
Disease Parameters 
12.2.1 Measurable 
12.2.1.1 A non-nodal lesion is considered measurable if its longest diameter can 
be accurately measured as ≥2.0 cm with chest x-ray, or as ≥1.0 cm with 
CT scan, CT component of a PET/CT, or MRI.  
12.2.1.2 A superficial non-nodal lesion is measurable if its longest diameter is 
≥1.0 cm in diameter as assessed using calipers (e.g. skin nodules) or 
imaging. In the case of skin lesions, documentation by color 
photography, including a ruler to estimate the size of the lesion, is 
recommended. 
12.2.1.3 A malignant lymph node is considered measurable if its short axis is 
>1.5 cm when assessed by CT scan (CT scan slice thickness 
recommended to be no greater than 5 mm). 
NOTE: Tumor lesions in a previously irradiated area are not considered 
measurable disease.  
12.2.2 Non-measurable 
All other lesions (or sites of disease) are considered non-measurable disease, 
including pathological nodes (those with a short axis ≥1.0 to <1.5 cm). Bone 
lesions, leptomeningeal disease, ascites, pleural/pericardial effusions, 
lymphangitis cutis/pulmonis, inflammatory breast disease, and abdominal masses 
(not followed by CT or MRI), are considered as non-measurable as well. 
Note: ‘Cystic lesions’ thought to represent cystic metastases can be considered as 
measurable lesions, if they meet the definition of measurability described 
above. However, if non-cystic lesions are present in the same patient, 
these are preferred for selection as target lesions. In addition, lymph 

 
 
 
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nodes that have a short axis <1.0 cm are considered non-pathological 
(i.e., normal) and should not be recorded or followed. 
12.2.3 Specifications by methods of measurements 
12.2.3.1 Measurement of lesions 
• All measurements should be recorded in metric notation (i.e., decimal 
fractions of centimeters) using a ruler or calipers. 
• The same method of assessment and the same technique must be used to 
characterize each identified and reported lesion at baseline and during follow-
up. For patients having only lesions measuring at least 1 cm to less than 2 cm 
must use CT imaging for both pre- and post-treatment tumor assessments. 
12.2.4 Method of assessment 
• 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. 
• As with CT, if an MRI is performed, the technical specifications of the 
scanning sequences used should be optimized for the evaluation of the type 
and site of disease. The lesions should be measured on the same pulse 
sequence. Ideally, the same type of scanner should be used and the image 
acquisition protocol should be followed as closely as possible to prior scans. 
Body scans should be performed with breath-hold scanning techniques, if 
possible. 
• PET-CT: If the site can document that the CT performed as part of a PET-CT 
is of identical diagnostic quality to a diagnostic CT (with IV and oral 
contrast), then the CT portion of the PET-CT can be used for RECIST 
measurements and can be used interchangeably with conventional CT in 
accurately measuring cancer lesions over time. 
• 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 
scans are preferable. 
• FDG-PET: FDG-PET scanning is allowed to complement CT scanning in 
assessment of progressive disease [PD] and particularly possible 'new' 
disease. A ‘positive’ FDG-PET scanned lesion is defined as one which is 
FDG avid with an update greater than twice that of the surrounding tissue on 
the attenuation corrected image; otherwise, an FDG-PET scanned lesion is 
considered ‘negative.’ 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: 
i. If the positive FDG-PET at follow-up corresponds to a new site 
of disease confirmed by CT, this is PD. 

 
 
 
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ii. If the positive FDG-PET at follow-up is not confirmed as a 
new site of disease on CT at the same evaluation, additional 
follow-up CT scans (i.e., additional follow-up scans at least 4 
weeks later) are needed to determine if there is truly 
progression occurring at that site. In this situation, the date of 
PD will be the date of the initial abnormal PDG-PET scan. 
iii 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, it is not classified as PD. 
12.2.5. Measurement at Follow-up Evaluation: 
• 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. 
• Cytologic and histologic techniques can be used to differentiate between PR 
and CR in rare cases (e.g., residual lesions in tumor types such as germ cell 
tumors, where known residual benign tumors can remain.) 
12.3 
Response Criteria 
12.3.1 Target lesions and target Lymph Nodes 
• Measurable lesions (as defined in Section 12.2.1) up to a maximum of 
5 lesions, representative of all involved organs, should be identified as 
“Target Lesions” and recorded and measured at baseline. These lesions 
can be non-nodal or nodal (as defined in 12.2.1), where no more than 
2 lesions are from the same organ and no more than 2 malignant nodal 
lesions are selected.  
Note: If fewer than 5 target lesions and target lymph nodes are 
identified (as there often will be), there is no reason to perform 
additional studies beyond those specified in the protocol to discover 
new lesions. 
• Target lesions and target lymph nodes should be selected on the basis 
of their size, be representative of all involved sites of disease, but in 
addition should be those that lend themselves to reproducible repeated 
measurements. It may be the case that, on occasion, the largest lesion 
(or malignant lymph node) does not lend itself to reproducible 
measurements in which circumstance the next largest lesion (or 
malignant lymph node) which can be measured reproducibly should be 
selected. 
• Baseline Sum of Dimensions (BSD): A sum of the longest diameter 
for all target lesions plus the sum of the short axis of all the target 
lymph nodes will be calculated and reported as the baseline sum of 

 
 
 
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dimensions (BSD). The BSD will be used as reference to further 
characterize any objective tumor response in the measurable 
dimension of the disease. 
• Post-Baseline Sum of the Dimensions (PBSD): A sum of the longest 
diameter for all target lesions plus the sum of the short axis of all the 
target lymph nodes will be calculated and reported as the post-baseline 
sum of dimensions (PBSD). If the radiologist is able to provide an 
actual measure for the target lesion (or target lymph node), that should 
be recorded, even if it is below 0.5 cm. If the target lesion (or target 
lymph node) is believed to be present and is faintly seen but too small 
to measure, a default value of 0.5 cm should be assigned. If it is the 
opinion of the radiologist that the target lesion or target lymph node 
has likely disappeared, the measurement should be recorded as 0 cm. 
• The minimum sum of the dimensions (MSD) is the minimum of the 
BSD and the PBSD. 
12.3.2. Evaluation of Target Lesions and Target Lymph Nodes 
12.3.2.1 All target lesions and target lymph nodes followed by CT/MRI/PET-
CT/Chest X-ray/ must be measured on re-evaluation. Specifically, a 
change in objective status to either a PR or CR cannot be done without 
re-measuring target lesions and target lymph nodes. 
Note: Non-target lesions and non-target lymph nodes should be 
evaluated at each assessment, especially in the case of first response or 
confirmation of response. In selected circumstances, certain non-target 
organs may be evaluated less frequently. For example, bone scans may 
need to be repeated only when complete response is identified in target 
disease or when progression in bone is suspected. 
12.3.2.2 Definitions 
Complete Response (CR): 
All of the following must be true: 
a. Disappearance of all target lesions. 
b. Each target lymph node must have reduction in 
short axis to <1.0 cm. 
Partial Response (PR): 
At least a 30% decrease in PBSD (sum of the 
longest diameter for all target lesions plus the sum 
of the short axis of all the target lymph nodes at 
current evaluation) taking as reference the BSD (see 
Section 12.3.1). 
Progression (PD): 
At least one of the following must be true: 
a. At least one new malignant lesion, which also 
includes any lymph node that was normal at 
baseline (< 1.0 cm short axis) and increased to ≥ 
1.0 cm short axis during follow-up.  

 
 
 
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b. At least a 20% increase in PBSD (sum of the 
longest diameter for all target lesions plus the 
sum of the short axis of all the target lymph 
nodes at current evaluation) taking as reference 
the MSD (Section 12.31). In addition, the PBSD 
must also demonstrate an absolute increase of at 
least 0.5 cm from the MSD.  
c. See Section 12.2.4 for details in regards to the 
requirements for PD via FDG-PET imaging. 
Stable Disease (SD): 
Neither sufficient shrinkage to qualify for PR, nor 
sufficient increase to qualify for PD taking as 
reference the MSD 
12.3.3 Non-target lesions and Non-Target Lymph Nodes:  
Non-measurable sites of disease (Section 12.2.2) are classified as non-target lesions 
or non-target lymph nodes and should also be recorded at baseline. These lesions 
and lymph nodes should be followed in accordance with 12.3.2.1. 
12.3.3.1 Evaluation of Non-Target Lesions and Non-Target Lymph Nodes 
12.3.3.2 Definitions 
Complete Response (CR): 
All of the following must be true: 
a. Disappearance of all non-target lesions 
b. Each non-target lymph node must have a 
reduction in short axis to <1.0 cm. 
Non-CR/Non-PD: 
Persistence of one or more non-target lesions or 
non-target lymph nodes. 
Progression (PD): 
At least one of the following must be true: 
a. At least one new malignant lesion, which also 
includes any lymph node that was normal at 
baseline (<1.0 cm short axis) and increased to 
≥1.0 cm short axis during follow-up. 
b. Unequivocal progression of existing non-target 
lesions and non-target lymph nodes. (NOTE: 
Unequivocal progression should not normally 
trump target lesion and target lymph node 
status. It must be representative of overall 
disease status change.) 
c. See Section 12.2.4 for details in regards to the 
requirements for PD via FDG-PET imaging. 
 
 

 
 
 
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Table 3: Time point response 
Target Lesions & 
Target Lymph Nodes 
Non-Target Lesions & 
Non-Target Lymph Nodes 
New  
Sites of Disease 
Overall Objective 
Status 
CR 
CR 
No 
CR 
CR 
Non-CR/Non-PD 
No 
PR 
PR 
CR 
Non-CR/Non-PD 
No 
PR 
CR/PR 
Not All Evaluated* 
No 
PR 
SD 
CR 
Non-CR/Non-PD 
Not All Evaluated* 
No 
SD 
Not all Evaluated 
CR 
Non-CR/Non-PD 
Not All Evaluated* 
No 
Not Evaluated 
(NE) 
PD 
Unequivocal PD 
CR 
Non-CR/Non-PD 
Not All Evaluated* 
Yes or No 
PD 
CR/PR/SD/PD/Not all 
Evaluated 
Unequivocal PD 
Yes or No 
PD 
CR/PR/SD/PD/Not all 
Evaluated 
CR 
Non-CR/Non-PD 
Not All Evaluated* 
Yes 
PD 
CR= complete response, PR= partial response, PD= progressive disease,  
SD= stable disease, NE= not evaluable. 
*See Section 12.3.3 
12.3.4 Symptomatic Deterioration 
Patients with global deterioration of health status requiring discontinuation of 
treatment without objective evidence of disease progression at that time, and not 
either related to study treatment or other medical conditions, should be reported as 
PD due to “symptomatic deterioration.” Every effort should be made to document 
the objective progression even after discontinuation of treatment due to 
symptomatic deterioration. A patient is classified as having PD due to 
“symptomatic deterioration” if any of the following occur that are not either 
related to study treatment or other medical conditions: 
• Weight loss >10% of body weight. 
• Worsening of tumor-related symptoms. 
• Decline in performance status of >1 level on ECOG scale. 
 
 

 
 
 
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13. 
ADVERSE EVENT REPORTING REQUIREMENTS 
The site principal investigator is responsible for reporting any/all serious adverse events 
to the sponsor as described within the protocol, regardless of attribution to study agent or 
treatment procedure.  
The sponsor/sponsor-investigator is responsible for notifying FDA and all participating 
investigators in a written safety report of any of the following: 
• Any suspected adverse reaction that is both serious and unexpected. 
• Any findings from laboratory animal or in vitro testing that suggest a significant 
risk for human subjects, including reports of mutagenicity, teratogenicity, or 
carcinogenicity. 
• Any findings from epidemiological studies, pooled analysis of multiple studies, or 
clinical studies, whether or not conducted under an IND and whether or not 
conducted by the sponsor, that suggest a significant risk in humans exposed to the 
drug.  
• Any clinically important increase in the rate of a serious suspected adverse 
reaction over the rate stated in the protocol or Investigator’s Brochure (IB). 
Summary of Adverse Event Reporting for this Study 
WHO: 
WHAT form: 
WHERE to send: 
All 
sites 
Pregnancy Reporting 
 
Takeda: 
 
Mayo Sites – attach to MCCC Electronic 
SAE Reporting Form 
  
 
  
 
Mayo 
 
 
 
 
  
 
 
Takeda: 
 
 
 
Non-
Mayo 
Clinic 
Sites 
MedWatch 3500A:  
 
 
 
 
 

 
 
 
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13.1 
General 
CTCAE term (AE description) and grade: The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
4.0 will be utilized for AE reporting. All appropriate treatment areas should have access 
to a copy of the CTCAE version 4.0. A copy of the CTCAE version 4.0 can be 
downloaded from the CTEP website 
 
a. Identify the grade and severity of the event using the CTCAE version 4.0. 
b. Determine whether the event is expected or unexpected (see Section 13.2.3). 
c. Determine if the adverse event is related to the study intervention (agent, 
treatment or procedure) (see Section 13.2.4). 
d. Determine whether the event must be reported as an expedited report. If yes, 
determine the timeframe/mechanism (see Section 13.3). 
e. Determine if other reporting is required (see Section 13.4). 
f. Note: All AEs reported via expedited mechanisms must also be reported via 
the routine data reporting mechanisms defined by the protocol (see Section 
13.5). 
NOTE: A severe AE, as defined by the grading scale below, is NOT the same as 
serious AE which is defined in the table in Section 13.2. 
13.2 
Definitions 
Adverse Event 
Adverse event (AE) means any untoward medical occurrence in a patient or 
subject administered a medicinal product; the untoward medical occurrence does 
not necessarily have a causal relationship with this treatment. An AE can 
therefore be any unfavorable and unintended sign (including an abnormal 
laboratory finding), symptom, or disease temporally associated with the use of a 
medicinal (investigational) product whether or not it is related to the medicinal 
product. This includes any newly occurring event, or a previous condition that has 
increased in severity or frequency since the administration of study drug. 
An abnormal laboratory value will not be assessed as an AE unless that value 
leads to discontinuation or delay in treatment, dose modification, therapeutic 
intervention, or is considered by the investigator to be a clinically significant 
change from baseline. 
Suspected Adverse Reaction 
Serious AE (SAE) means any untoward medical occurrence that at any dose: 
• Results in death. 
• Is life-threatening (refers to an AE in which the patient was at risk of 
death at the time of the event. It does not refer to an event which 
hypothetically might have caused death if it were more severe). 

 
 
 
 
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• Requires inpatient hospitalization or prolongation of an existing 
hospitalization (see clarification in the paragraph below on planned 
hospitalizations). 
• Results in persistent or significant disability or incapacity. (Disability is 
defined as a substantial disruption of a person’s ability to conduct normal 
life functions). 
• Is a congenital anomaly/birth defect. 
• Is a medically important event. This refers to an AE that may not result 
in death, be immediately life threatening, or require hospitalization, but 
may be considered serious when, based on appropriate medical judgment, 
may jeopardize the patient, require medical or surgical intervention to 
prevent 1 of the outcomes listed above, or involves suspected transmission 
via a medicinal product of an infectious agent. Examples of such medical 
events include allergic bronchospasm requiring intensive treatment in an 
emergency room or at home, blood dyscrasias or convulsions that do not 
result in inpatient hospitalization, or the development of drug dependency 
or drug abuse; any organism, virus, or infectious particle (e.g., prion 
protein transmitting Transmissible Spongiform Encephalopathy), 
pathogenic or nonpathogenic, is considered an infectious agent. 
Expedited Reporting 
Events reported to sponsor within 24 hours, 5 days or 10 days of study team 
becoming aware of the event. 
Routine Reporting 
Events reported to sponsor via case report forms 
Events of Interest 
Events that would not typically be considered to meet the criteria for expedited 
reporting, but that for a specific protocol are being reported via expedited means 
in order to facilitate the review of safety data (may be requested by the FDA or 
the sponsor).  
13.2.1 Expected vs. Unexpected Events 
Expected events - are those described within the Section 8.0 of the protocol, the 
study specific consent form, package insert (if applicable), and/or the investigator 
brochure, (if an investigator brochure is not required, otherwise described in the 
general investigational plan).  
Unexpected adverse events or suspected adverse reactions are those not listed in 
Section 8.0 of the protocol, the study specific consent form, package insert (if 
applicable), or in the investigator brochure (or are not listed at the specificity or 
severity that has been observed); if an investigator brochure is not required or 
available, is not consistent with the risk information described in the general 
investigational plan. 
Unexpected also refers to adverse events or suspected adverse reactions that are 
mentioned in the investigator brochure as occurring with a class of drugs but have 

 
 
 
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not been observed with the drug under investigation. 
An investigational agent/intervention might exacerbate the expected AEs associated 
with a commercial agent. Therefore, if an expected AE (for the commercial agent) 
occurs with a higher degree of severity or specificity, expedited reporting is required. 
13.2.2 Attribution 
Attribution is the relationship between an adverse event or serious adverse event 
and the study treatment. When assessing whether an adverse event (AE) is related 
to a medical agent(s) medical or procedure, the following attribution categories are 
utilized: 
• 
Definite – The AE is clearly related to the study treatment. 
• 
Probable – The AE is likely related to the study treatment. 
• 
Possible – The AE may be related to the study treatment.  
• 
Unlikely - The AE is doubtfully related to the study treatment. 
• 
Unrelated - The AE is clearly NOT related to the study treatment. 
Events determined to be possibly, probably or definitely attributed to a 
medical treatment suggest there is evidence to indicate a causal relationship 
between the drug and the adverse event.  
13.3 
Reporting Procedures 
13.3.1 AEs Experienced Utilizing Investigational Agent(s) and Commercial Agent(s) 
during treatment with Alisertib alone 
• An AE that occurs on an arm using an investigational agent /intervention 
under an IND/IDE must be assessed in accordance with the guidelines for 
investigational agents.  
• An AE that occurs on an arm using a commercial agent on a separate 
treatment arm must be assessed as specified in the protocol.  
Commercial agent expedited reports must be submitted to the FDA via 
MedWatch.3500A 
or 
 
13.3.2 AEs Experienced Utilizing Investigational Agents and Commercial Agent(s) 
during treatment with the combination of fulvestrant and alisertib 
NOTE: When a commercial agent(s) is (are) used on the same treatment 
arm as the investigational agent/intervention (also, investigational drug, 
biologic, cellular product, or other investigational therapy under an IND), 

 
 
 
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the entire combination is then considered an investigational 
intervention for reporting. 
• An AE that occurs on a combination study must be assessed in accordance 
with the guidelines for investigational agents/interventions.  
• An AE that occurs prior to administration of the investigational agent/ 
intervention must be assessed as specified in the protocol. In general, only 
Grade 4 and 5 AEs that are unexpected with at least possible attribution to 
the commercial agent require an expedited report, unless hospitalization is 
required. Refer to Section 10.4 for specific AE reporting requirements or 
exceptions. 
• An investigational agent/intervention might exacerbate the expected AEs 
associated with a commercial agent. Therefore, if an expected AE (for the 
commercial agent) occurs with a higher degree of severity or specificity, 
expedited reporting is required. 
• An increased incidence of an expected adverse event (AE) is based on 
the patients treated for this study at their site. A list of known/expected 
AEs is reported in the package insert or the literature, including AEs 
resulting from a drug overdose. 
• Commercial agent expedited reports must be submitted to the FDA via 
MedWatch 3500A for Health Professionals (complete all three pages of 
the form). 
 
 
 
13.3.3 Procedures for Reporting Serious Adverse Events 
AEs may be spontaneously reported by the patient and/or in response to an open 
question from study personnel or revealed by observation, physical examination, 
or other diagnostic procedures. Any clinically relevant deterioration in laboratory 
assessments or other clinical finding is considered an AE. When possible, signs 
and symptoms indicating a common underlying pathology should be noted as one 
comprehensive event. AEs which are serious must be reported to Millennium 
Pharmacovigilance (or designee) from the first dose of <alisertib> up to and 
including <30> days after administration of the last dose of <alisertib>. Any 
SAE that occurs at any time after completion of <alisertib> treatment or after the 
designated follow-up period that the sponsor-investigator and/or sub-investigator 
considers to be related to any study drug must be reported to Millennium 
Pharmacovigilance (or designee). Planned hospital admissions or surgical 

 
 
 
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procedures for an illness or disease that existed before the patient was enrolled in 
the trial are not to be considered AEs unless the condition deteriorated in an 
unexpected manner during the trial (e.g., surgery was performed earlier or later 
than planned). All SAEs should be monitored until they are resolved or are clearly 
determined to be due to a patient’s stable or chronic condition or intercurrent 
illness(es). 
Since this is an investigator-initiated study, the principal investigator, Dr. Tufia 
Haddad, also referred to as the sponsor-investigator, is responsible for reporting 
serious adverse events (SAEs) to any regulatory agency and to the sponsor-
investigator’s EC or IRB. 
Regardless of expectedness or causality, all SAEs must also be reported to 
Millennium Pharmacovigilance or designee: 
Fatal and Life Threatening SAEs within 24 hours but no later than 4 calendar 
days of the sponsor-investigator’s observation or awareness of the event 
All other serious (non-fatal/non life threatening) events within 4 calendar days 
of the sponsor-investigator’s observation or awareness of the event 
The SAE report must include at minimum: 
• Event term(s) 
• Serious criteria 
• Intensity of the event(s): Sponsor-investigator’s or sub-investigator’s 
determination. Intensity for each SAE, including any lab abnormalities, will 
be determined by using the NCI CTCAE version specified in the protocol, as a 
guideline, whenever possible. The criteria are available online at 
 
• Causality of the event(s): Sponsor-investigator’s or sub-investigator’s 
determination of the relationship of the event(s) to study drug administration.  
Follow-up information on the SAE may be requested by Millennium. 
In the event that this is a multisite study, the sponsor-investigator is responsible to 
ensure that the SAE reports are sent to Millennium Pharmacovigilance (or 
designee) from all sites participating in the study. Sub-investigators must report 
all SAEs to the sponsor-investigator so that the sponsor-investigator can meet 
his/her foregoing reporting obligations to the required regulatory agencies and to 
Millennium Pharmacovigilance, unless otherwise agreed between the sponsor-
investigator and sub-investigator(s). 
Relationship to all study drugs for each SAE will be determined by the 
investigator or sub-investigator by responding yes or no to the question: Is there a 
reasonable possibility that the AE is associated with the study drug(s)? 
Sponsor-investigator must also provide Millennium Pharmacovigilance with a 
copy of all communications with applicable regulatory authorities related to the 
study product(s) as soon as possible but no later than 4 calendar days of such 
communication. 

 
 
 
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General Reporting instructions: 
1. For all agents: 
 
 
2. Submit a copy of the completed MedWatch form and all other related forms to 
For questions please see contact listed 
on page 3 of the protocol. 
3. Send completed MedWatch form to Takeda/Millennium (see contact below) 
no later than 4 calendar days. 
Mayo Clinic Cancer Center (MCCC) Institutions: 
Use Mayo Clinic Cancer Center SAE Reporting Form: 
 
 
 
Non-MCCC Institutions: Submit copies to 
 
 
Millennium Pharmacovigilance or Designee 
SAE and Pregnancy Reporting Contact Information 
 
13.3.4 Expedited Reporting Requirements for IND/IDE Agents 
Phase 1 and Early Phase 2 Studies: Expedited Reporting Requirements for Adverse 
Events that Occur on Studies under an IND/IDE within 30 Days of the Last 
Administration of the Investigational Agent/Intervention 1, 2 
FDA REPORTING REQUIREMENTS FOR SERIOUS ADVERSE EVENTS (21 CFR Part 312) 
NOTE: Investigators MUST immediately report to the sponsor ANY Serious Adverse Events, whether or not they 
are considered related to the investigational agent(s)/intervention (21 CFR 312.64) 
An adverse event is considered serious if it results in ANY of the following outcomes: 
1) 
Death 
2) 
A life-threatening adverse event  
3) 
An adverse event that results in inpatient hospitalization or prolongation of existing hospitalization for ≥ 24 
hours  
4) 
A persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions  
5) 
A congenital anomaly/birth defect.  
6) 
Important Medical Events (IME) that may not result in death, be life threatening, or require hospitalization 
may be considered serious when, based upon medical judgment, they may jeopardize the patient or subject 
and may require medical or surgical intervention to prevent one of the outcomes listed in this definition. (FDA, 
21 CFR 312.32; ICH E2A and ICH E6). 
ALL SERIOUS adverse events that meet the above criteria MUST be immediately reported to the sponsor within 
the timeframes detailed in the table below.  
Hospitalization 
Grade 1 and Grade 2 Timeframes 
Grade 3-5 
Timeframes 

 
 
 
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Resulting in 
Hospitalization 
≥24 hrs 
7 Calendar Days 
24-Hour 3 Calendar 
Days 
Not resulting in 
Hospitalization 
≥24 hrs 
Not required 
 
Expedited AE reporting timelines are defined as: 
o “24-Hour; 3 Calendar Days” - The AE must initially be reported within 24 hours of learning of the AE, 
followed by a complete expedited report within 3 calendar days of the initial 24-hour report. 
o “7 Calendar Days” - A complete expedited report on the AE must be submitted within 7 calendar days 
of learning of the AE. 
1Serious adverse events that occur more than 30 days after the last administration of investigational 
agent/intervention and have an attribution of possible, probable, or definite require reporting as follows:  
Expedited 24-hour notification followed by complete report within 3 calendar days for: 
• All Grade 3, 4, and Grade 5 AEs 
Expedited 7 calendar day reports for: 
• Grade 2 AEs resulting in hospitalization or prolongation of hospitalization 
2 For studies using PET or SPECT IND agents, the AE reporting period is limited to 10 radioactive half-lives, 
rounded UP to the nearest whole day, after the agent/intervention was last administered. Footnote “1” above 
applies after this reporting period. 
Effective Date: May 5, 2011 
Additional instructions: 
The 
 will assist the sponsor-investigator in the processing 
of expedited adverse events and forwarding of suspected unexpected serious 
adverse reactions (SUSARs) to the FDA and IRB. 
13.4 
Other Required Reporting 
13.4.1 Unanticipated Problems Involving Risks to Subjects or Others (UPIRTSOs) 
UPIRTSOs in general, include any incident, experience, or outcome that meets all 
of the following criteria: 
1. Unexpected (in terms of nature, severity, or frequency) given (a) the research 
procedures that are described in the protocol-related documents, such as the 
IRB-approved research protocol and informed consent document; and (b) the 
characteristics of the subject population being studied; 
2. Related or possibly related to participation in the research (in this guidance 
document, 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); and 
3. Suggests that the research places subjects or others at a greater risk of harm 
(including physical, psychological, economic, or social harm) than was 
previously known or recognized. 
Some unanticipated problems involve social or economic harm instead of the 
physical or psychological harm associated with adverse events. In other cases, 

 
 
 
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unanticipated problems place subjects or others at increased risk of harm, but no 
harm occurs. 
Note: If there is no language in the protocol indicating that pregnancy is not 
considered an adverse experience for this trial, and if the consent form does not 
indicate that subjects should not get pregnant/impregnate others, then any 
pregnancy in a subject/patient or a male patient’s partner (spontaneously reported) 
which occurs during the study or within 120 days of completing the study should 
be reported as a UPIRTSO. 
 
  
 
 
 
Non-MCCC Institutions: 
Submit to your IRB as required by your institutional policies. 
Submit copies t
13.4.2 Death 
Note: A death on study requires both routine and expedited reporting 
regardless of causality, unless as noted below. Attribution to treatment or 
other cause must be provided. 
Any death occurring within 30 days of the last dose, regardless of attribution to 
an agent/intervention under an IND/IDE requires expedited reporting within  
24-hours. 
Any death occurring greater than 30 days with an attribution of possible, 
probable, or definite to an agent/intervention under an IND/IDE requires 
expedited reporting within 24-hours. 
Reportable categories of Death  
• Death attributable to a CTCAE term. 
• Death Neonatal: A disorder characterized by cessation of life during the 
first 28 days of life.  
• Death NOS: A cessation of life that cannot be attributed to a CTCAE term 
associated with Grade 5. 
• Sudden death NOS: A sudden (defined as instant or within one hour of the 
onset of symptoms) or an unobserved cessation of life that cannot be 
attributed to a CTCAE term associated with Grade 5. 
• Death due to progressive disease should be reported as Grade 5 
“Neoplasms benign, malignant and unspecified (including cysts and 
polyps) – Other (Progressive Disease)” under the system organ class 

 
 
 
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(SOC) of the same name. Evidence that the death was a manifestation of 
underlying disease (e.g., radiological changes suggesting tumor growth or 
progression: clinical deterioration associated with a disease process) should 
be submitted. 
13.4.3 Secondary Malignancy 
• A secondary malignancy is a cancer caused by treatment for a previous 
malignancy (e.g., treatment with investigational agent/intervention, radiation 
or chemotherapy). A secondary malignancy is not considered a metastasis of 
the initial neoplasm. 
• All secondary malignancies that occur following treatment with an agent under 
an IND/IDE will be reported. Three options are available to describe the event: 
o Leukemia secondary to oncology chemotherapy (e.g., Acute Myelocytic 
Leukemia [AML]) 
o Myelodysplastic syndrome (MDS) 
o Treatment-related secondary malignancy 
• Any malignancy possibly related to cancer treatment (including AML/MDS) 
should also be reported via the routine reporting mechanisms outlined in each 
protocol. 
13.4.4 Second Malignancy 
A second malignancy is one unrelated to the treatment of a prior malignancy (and is 
NOT a metastasis from the initial malignancy). Second malignancies require ONLY 
routine reporting unless otherwise specified. 
13.4.5  Pregnancy 
Procedures for Reporting Drug Exposure during Pregnancy and Birth 
Events 
If a woman becomes pregnant or suspects that she is pregnant while participating 
in this study, she must inform the investigator immediately and permanently 
discontinue study drug. The sponsor-investigator must fax a completed Pregnancy 
Form to the Millennium Department of Pharmacovigilance or designee. The 
pregnancy must be followed for the final pregnancy outcome. 
If a female partner of a male patient becomes pregnant during the male patient’s 
participation in this study, the sponsor-investigator must also immediately fax a 
completed Pregnancy Form to the Millennium Department of Pharmacovigilance 
or designee. Every effort should be made to follow the pregnancy for the final 
pregnancy outcome. 
13.4.6 Product Complaints 
A product complaint is a verbal, written, or electronic expression that implies 
dissatisfaction regarding the identity, strength, purity, quality, or stability of a 
drug product. Individuals who identify a potential product complaint situation 
should immediately contact MedComm Solutions (see below) and report the 

 
 
 
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event. Whenever possible, the associated product should be maintained in 
accordance with the label instructions pending further guidance from a 
Millennium Quality representative. 
 
 
 
 
Product complaints in and of themselves are not AEs. If a product complaint 
results in an SAE, an SAE form should be completed and sent to Millennium 
Pharmacovigilance (refer to Section 8.2). 
A product complaint is a verbal, written, or electronic expression that implies 
dissatisfaction regarding the identity, strength, purity, quality, or stability of a 
drug product. Individuals who identify a potential product complaint situation 
should immediately contact MedComm Solutions (see below) and report the 
event. Whenever possible, the associated product should be maintained in 
accordance with the label instructions pending further guidance from a 
Millennium Quality representative. 
A medication error is a preventable event that involves an identifiable patient and 
that leads to inappropriate medication use, which may result in patient harm. 
While overdoses and underdoses constitute medication errors, doses missed 
inadvertently by a patient do not. Individuals who identify a potential medication 
error situation should immediately contact MedComm Solutions (see below) and 
report the event. 
13.5 
Required Routine Reporting 
Pretreatment symptoms/conditions to be graded at baseline and adverse events to be 
graded at each evaluation per CTCAE v4.0 grading unless otherwise stated in the 
table below: 
CTCAE  
System Organ Class (SOC) 
Adverse event/Symptoms 
Baseline 
Each 
evaluation 
Blood and Lymphatic 
System Disorders 
Anemia 
X 
X 
Gastrointestinal Disorders 
# of stools 
X 
 
Diarrhea 
 
X 
Nausea 
X 
X 
Vomiting 
X 
X 
Mucositis Oral 
X 
X 
General disorders and 
administration site conditions Fatigue 
X 
X 
Injection site reaction 
 
X 
Investigations 
Platelet Count Decreased  
X 
X 
 
Neutrophil Count Decreased 
X 
X 
 
White Blood Cell Decreased 
X 
X 

 
 
 
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CTCAE  
System Organ Class (SOC) 
Adverse event/Symptoms 
Baseline 
Each 
evaluation 
Metabolism and nutrition 
disorders 
Anorexia 
X 
X 
Renal and urinary disorders 
Acute Kidney Injury 
X 
X 
Skin and subcutaneous 
tissues 
Rash acneiform 
X 
X 
Rash maculo-papular 
X 
X 
13.5.1 Submit via appropriate MCCC Case Report Forms (i.e., paper or electronic, 
as applicable) the following AEs experienced by a patient and not specified in 
Section 13.5: 
13.5.1.1 Grade 2 AEs deemed possibly, probably, or definitely related to the 
study treatment or procedure. 
13.5.1.2 Grade 3 and 4 AEs regardless of attribution to the study treatment or 
procedure. 
13.5.1.3 Grade 5 AEs (Deaths) 
13.5.1.3.1  Any death within 30 days of the patient’s last study treatment 
or procedure regardless of attribution to the study treatment or 
procedure. 
13.5.1.3.2 Any death more than 30 days after the patient’s last study 
treatment or procedure that is felt to be at least possibly 
treatment related must also be submitted as a Grade 5 AE, with 
a CTCAE type and attribution assigned. 
13.5.2 Late Occurring Adverse Events 
Refer to the instructions in the Forms Packet (or electronic data entry screens, as 
applicable) regarding the submission of late occurring AEs following completion 
of the Active Monitoring Phase (i.e., compliance with Test Schedule in 
Section 11). 
 
 

 
 
 
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14. 
DATA AND SAFETY MONITORING 
14.1 
Data Management and Reporting 
Submission Timetables 
14.1.1 Pre-Registration Material(s) 
Case Report Form (CRF) 
Active-Monitoring Phase 
(Compliance with Test Schedule Section 4.0) 
Pre-Registration Screening 
Failure 
Complete only if patient is NOT registered after she 
is pre-registered 
Pathology materials  
See Section 17.0 (for central review, eligibility, etc. 
confirmation prior to Registration) 
 
14.1.2 Initial Material(s) 
CRF 
Active-Monitoring Phase 
(Compliance with Test Schedule Section 11) 
Pathology Materials (including local 
pathology report) 
See Section 9 (for central review, eligibility, etc. 
confirmation prior to Registration/Randomization) 
On-Study Form 
≤2 weeks after registration 
Adverse Events: Baseline 
Institutional Contact 
On-Study: Prior Disease History (Left 
Breast) as applicable 
On-Study: Prior Disease History (Right 
Breast) as applicable 
On-Study: Prior Neoadjuvant or 
Adjuvant Therapy 
On-Study: Prior Systemic Therapy for 
Metastatic Disease 
Metastatic Disease Status 
RECIST Measurement: Baseline 
Supporting Documentation: Baseline 
Specimen Submission: Tissue (see 
Section 9) 
Specimen Submission: Blood 
Patient Status: Baseline 
Off Treatment 
Submit ≤2 weeks after registration if withdrawal/ 
refusal occurs prior to beginning protocol therapy 
 

 
 
 
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14.1.3 Test Schedule Material(s) 
CRF 
At each evaluation 
during treatment 
At end of 
treatment 
Treatment (Intervention) 
X1 
X 
Treatment (Intervention): Dose Modifications, 
Omission and Delays2 
X 
X 
Adverse Event: Solicited  
X 
X 
RECIST Measurements  
X 
X 
RECIST Measurements: Cross-over Baseline3 – 
Arm 1 patients that cross-over only 
X 
 
RECIST Measurements: Cross-over Arm 1 patients 
that cross-over only 
X 
X 
Specimen Submission: Tissue 
X (see Section 9) 
 
Specimen Submission: Blood 
X (see Section 9) 
 
Supporting Documentation 
X 
X 
Patient Status: Treatment (Intervention) 
X 
X 
End of Initial Treatment2 – Arm 1 patients that 
cross-over only 
 
X 
Off Treatment 
 
X 
Consent Withdrawal (choose appropriate 
withdrawal form): Specimen Only, All Follow-Up2  
If applicable 
 
Lost to Follow-Up2  
If applicable 
 
ADR/AER 
At each occurrence 
(see Section 13) 
 
1. Complete at each evaluation during Active Treatment (see Section 11). 
2. Complete only if applicable  
3. At initial cross-over for Arm 1 patients only 
14.1.4 Follow-up Material(s)  
CRF 
Event Monitoring Phase1 
Every 6 months 
until Death 
Death 
New Primary 
Patient Status: Survival and Disease Status 
Follow-Up/Event Monitoring 
X 
X 
 
Consent Withdrawal (choose appropriate 
withdrawal form): Specimen Only, All 
Follow-Up2  
X 
 
 
Lost to Follow-Up2  
X 
 
 
Notice of New Primary2  
 
 
At each occurrence 
1. If a patient is still alive 5 years after registration, no further follow-up is required. 
2. Complete only if applicable 

 
 
 
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14.2 
All paper forms should be sent to:  
 
 
 
 
 
14.3 
Labeling 
Each co-sponsor/participant will be responsible for insuring that all materials 
contain the patient’s initials, MCCC registration number, and MCCC protocol 
number. Patient’s name must be removed. 
14.4 
Incomplete materials 
Any materials deemed incomplete by the MCCC Operations Office will be 
considered “not received” and will not be edited or otherwise processed until the 
missing information is received. A list of the missing documents will be made 
available to the appropriate co-sponsor/participant. 
14.5 
Overdue lists 
A list of overdue materials and forms for study patients will be generated 
monthly. The listings will be sorted by location and will include the patient study 
registration number. The appropriate co-sponsor/participant will be responsible to 
obtain the overdue material. 
14.6 
Corrections forms 
If a correction is necessary the QAS will query the co-sponsor/participant. The 
query will be sent to the appropriate co-sponsor/participant who will make the 
correction and return the query and documentation of correction back to the QAS.  
14.7 
External Monitoring 
External monitoring of participating sites will occur at pre-determined time 
points. A data monitoring plan will be generated by a contract research 
organization. This document will be independent of the protocol. This document 
will be provided to all study sites for their submission to their local scientific 
review committees and IRBs as their particular requirements dictate. 
 
 

 
 
 
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15. 
REGULATORY CONSIDERATIONS 
15.1 
Protocol Review and Amendments 
Information regarding study conduct and progress will be reported to the Institutional 
Review Board (IRB) per the current institutional standards of each participating center. 
Any changes to the protocol will be made in the form of an amendment and must be 
approved by the IRB of each institution prior to implementation. 
The Protocol Chair (or his designee) is responsible for the coordination and development 
of all protocol amendments, and will disseminate this information to the participating 
centers. 
15.2 
Informed Consent 
The investigator (or his/her designee) will explain to each subject the nature of the study, 
its purpose, the procedures involved, the expected duration, the potential risks and benefits 
involved and any discomfort it may entail. Each subject will be informed that participation 
in the study is voluntary, that s/he may withdraw from the study at any time, and that 
withdrawal of consent will not affect her subsequent medical treatment or relationship with 
the treating physician(s) or institution. The informed consent will be given by means of a 
standard written statement, written in non-technical language, which will be IRB approved. 
The subject should read and consider the statement before signing and dating it, and will 
be given a copy of the document. No subject will enter the study or have study-specific 
procedures done before his/her informed consent has been obtained. 
In accordance with the Health Information Portability and Accountability Act (HIPAA), 
the written informed consent document (or a separate document to be given in conjunction 
with the consent document) will include a subject authorization to release medical 
information to the study sponsor and supporting agencies and/or allow these bodies, a 
regulatory authority, or Institutional Review Board access to subjects’ medical information 
that includes all hospital records relevant to the study, including subjects’ medical history. 
15.3 
Ethics and GCP 
This study will be carried out in compliance with the protocol and Good Clinical Practice, 
as described in: 
1. ICH Harmonized Tripartite Guidelines for Good Clinical Practice 1996. 
2. US 21 Code of Federal Regulations dealing with clinical studies (including parts 50 
and 56 concerning informed consent and IRB regulations). 
3. Declaration of Helsinki, concerning medical research in humans (Recommendations 
Guiding Physicians in Biomedical Research Involving Human Subjects, Helsinki 1964, 
amended Tokyo 1975, Venice 1983, Hong Kong 1989, Somerset West 1996). 
The investigator agrees to adhere to the instructions and procedures described in it and 
thereby to adhere to the principles of Good Clinical Practice that it conforms to. 
 
 

 
 
 
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16. MULTI-CENTER GUIDELINES 
16.1 
Study Documentation 
Each participating site is responsible for submitting copies of all relevant regulatory 
documentation to the Coordinating Center. The required documents include, but are not 
limited to the following: local IRB approvals (i.e., protocol, consent form, amendments, 
patient brochures and recruitment material, etc.), IRB membership rosters, summary of 
unanticipated problems or protocol deviations, and documentation of expertise of the 
investigators. The Coordinating Center will provide each participating site with a 
comprehensive list of the necessary documents. It is the responsibility of the participating 
sites to maintain copies of all documentation submitted to the Coordinating Center. 
16.2 
Records Retention 
Following closure of the study, each participating center will maintain a copy of all site 
study records in a safe and secure location.  
16.3 
Publication 
It is understood that any manuscript or releases resulting from the collaborative research 
will be circulated to all participating sites prior to submission for publication or 
presentation. 
17. STATISTICAL CONSIDERATIONS AND METHODOLOGY 
The aims of this clinical trial include assessing the impact of adding fulvestrant to alisertib in 
terms of clinical benefit (response rate and progression-free survival) and safety. 
Among the patients who are assigned to alisertib monotherapy (Arm 1) who progress and 
choose to receive the combination of fulvestrant and alisertib, the primary aims are to 
examine response and the differences in time to progression with alisertib and that with 
fulvestrant and alisertib.  
Initial treatment refers to alisertib alone for those randomized to Arm 1 and alisertib with 
fulvestrant for those randomized to Arm 2. Crossover treatment only applies to patients who 
progress during treatment with alisertib alone on Arm 1.  
17.1 
Assessing the impact of adding fulvestrant to alisertib 
17.1.1 Primary Endpoint 
The primary endpoint is tumor response rate with initial treatment. That is,  
- Arm 1: Tumor response rate is defined as 100% times the number of 
patients who meet the criteria for CR or PR (using RECIST criteria 
version 1.1) on 2 consecutive evaluations approximately 8 weeks apart 
during treatment with alisertib monotherapy divided by the number of 
patients who started alisertib monotherapy. 
-  Arm 2: Tumor response rate is defined as 100% times the number of 
patients who meet the criteria for CR or PR (using RECIST criteria 
version 1.1) on 2 consecutive evaluations approximately 8 weeks apart 

 
 
 
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during treatment with combination of alisertib and fulvestrant divided by 
the number of patients who started treatment with the combination of 
alisertib and fulvestrant. 
The study will test the hypothesis that the addition of fulvestrant to alisertib will 
increase the tumor response rate over that of alisertib alone by at least 20%. 
17.1.2 Secondary Endpoints 
17.1.2.1 Duration of response during initial treatment- time from randomization 
to disease progression among those patients whose disease meets the 
RECIST criteria for CR or PR on 2 consecutive evaluations 
approximately 8 weeks apart during initial treatment.  
17.1.2.2 Clinical Benefit Rate (CBR) during initial treatment - the proportion of 
patients who have completed 6 cycles of treatment without disease 
progression (that is, their objective disease status is a CR, PR, or stable 
for 6 cycles or more) during initial treatment. 
17.1.2.3 Progression-free survival (PFS) - time from randomization to disease 
progression or death due to any cause. If a patient has not had a disease 
evaluation within 3 months of death, the patient will be censored at the 
time of last disease evaluation for estimating the distribution of PFS 
time.  
17.1.2.4 Safety Profile: The CTCAE version 4.0 will be used to grade and assign 
attribution to each adverse event reported during initial treatment and 
crossover treatment separately.  
17.2 
Sample Size/ Accrual Rate 
Melichar et al reported the results of a Phase II clinical trial of alisertib (administered at 
50 mg BID for 7 days of a 21 day cycle) monotherapy in women with chemo-resistant 
metastatic breast cancer24. The response rate among the 14 women with triple negative 
breast cancer was 7.1 % (median PFS: 1.5 months). The response rate among the 
26 women with hormone receptor positive disease was 23.1% (median PFS: 7.9 months). 
Given these results and the expectation that approximately 10% of the patients who will 
be enrolled onto this trial will have triple negative breast cancer, we anticipate the 
response rate with alisertib alone will be 20%. 
A randomized phase II clinical trial design (proposed by Jung et al30) which incorporates 
a prospective control treatment and a futility stopping rule was chosen to assess whether 
the tumor response rate with the addition of fulvestrant to alisertib will be greater than 
that of alisertib alone by at least 20%, when the tumor response rate for alisertib alone is 
assumed to be 20%. The randomized phase II clinical trial design with a prospective 
control group proposed by Jung takes into account the interim analysis for futility so that 
overall design parameters are met. 
With a sample size of 45 patients per arm, a one sided alpha=0.15 sequential binomial 
test of the difference in two independent proportions will have a 85% chance of detecting 
that the response rate with the addition of fulvestrant to alisertib is at least 20% or greater 

 
 
 
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than the response rate with alisertib alone, when the true response rate for alisertib alone 
is 20% or less. The null hypothesis that the difference in tumor responses is less than 
20% would be rejected if at least 4 more tumor responses are seen with the combination 
of fulvestrant and alisertib than with alisertib alone. 
It is anticipated that none of the patients who are pre-registered will fail to obtain an ER 
result from the biopsy of a metastatic lesion. However, some patient may cancel 
participation prior to registration/randomization or after randomization but prior to the 
start of assigned treatment and other patients may be found to be ineligible. These 
patients will be replaced. It is anticipated that an additional 6 patients may be enrolled to 
account for these situations. 
Futility stopping rule: If, after the first 28 patients on each treatment arm have been 
enrolled and completed at least 6 cycles of treatment, the difference in the number of 
tumor responses between the treatment arms is one or fewer, enrollment will be halted 
and the DSMB will be consulted to formulate patient treatment recommendations. 
Other Considerations that might lead to early closure: Toxicity, patterns of treatment 
failure observed in this study and scientific discoveries or changes in standard care will 
be taken into account in any recommendation to the DSMB to terminate this trial earlier 
than anticipated. 
17.2.1 Crossover: Patients who are assigned to alisertib only arm who progress may 
choose to receive the combination of fulvestrant and alisertib. We anticipate that 
at least 14 (if there is no signal that combination therapy may be more 
beneficial) and as many as 22 patients will choose to receive combination 
therapy. As such, a 95% binomial confidence interval will be constructed for 
both the tumor response rate and clinical benefit rate during crossover 
treatment. 
17.3 
Stratification Factors 
This study will use the Pocock and Simon dynamic allocation procedure30 to allocate an 
equal number of patients to each of the treatment strategies. This procedure will balance 
the marginal distributions of the stratification factors, clinical endocrine resistance and 
ER status, between these treatment strategies. 
− Clinical Resistance to Endocrine Therapy:  
1= Primary endocrine resistance- recurrence within the first 2 years of 
adjuvant endocrine therapy, or progression within the first 6 months of 
initiating first-line endocrine therapy for MBC 
2= Secondary endocrine resistance- recurrence during Years 2-5 of adjuvant 
endocrine therapy (or within 12 months of completing adjuvant endocrine 
therapy) or progression occurring 6 or more months after initiating 
endocrine therapy for MBC. 
− ER findings from registration biopsy 
1 = ER positive (≥10% staining) 
2 = ER weakly positive (1 to 9.9% staining) or ER negative (0% staining) 
− Prior therapy with a CDK 4/6 inhibitor (palbociclib, ribociclib or abemaciclib) 
1=yes 

 
 
 
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2=no 
17.4 
Analysis of Secondary Endpoints 
17.4.1 For each treatment arm, the distribution of PFS times, overall survival times, and 
duration of response will be estimated using the Kaplan-Meier method. 
17.4.2 Clinical benefit rate 
For initial treatment in each arm, the clinical benefit rate at 24 weeks will be 
defined as the proportion of patients who completed 6 cycles of treatment without 
documentation of disease progression. A 90% confidence interval for the CBR 
will be constructed using the Duffy-Santner approach to take into account the 
sequential nature of the study design. 
17.4.3 Examination of baseline and 4 week on initial treatment tumor biopsy specimens 
Spearman rank correlation coefficient will be used to examine the association 
between ERα expression and the biomarkers: CD44, CD24, total and 
phosphorylated expression of AURKA, SMAD5, and SOX2 at baseline. 
Assuming that 90% of the 90 patients enrolled onto this trial will have sufficient 
baseline tissue to complete these analyses; there will be 81 patients will data 
available for these analyses. With a sample size of 81, a two-sided alpha=0.05 test 
of Spearman rank correlation coefficient will have a 90% chance of rejecting the 
true correlation is 0 when the true correlation is 35% or more. 
A two sample test of the difference in proportions will be used to examine 
whether weak or no phosphorylated expression of AURKA, SMAD5, and SOX2 
after one cycle of alisertib is associated with clinical benefit (CR +PR + SD on 
treatment for at least 6 months). The clinical response rate in ER+ MBC with 
single agent alisertib was reported to be 54%. As such we will assume that 
approximately 50% of the patients enrolled onto each treatment arm will have a 
documented clinical response. If, in a given treatment arm, 20 patients have a 
clinical response and 20 patients do not, a two sided alpha=0.05 test of the 
difference in two independent proportions will have at least an 85% chance of 
detecting a difference of 45% between the percentage of patients with a no or 
little expression of the biomarker among those who had clinical benefit and the 
percentage of patients with a no or little expression of the biomarker among those 
who did not have clinical benefit when the true percentage of patients with a no or 
little expression of the biomarker among those who did not have clinical benefit is 
10% (or 20% or 25%). 
17.4.4 Examination of changes in tumor biomarkers after one cycle of initial treatment 
For each treatment arm, a Spearman rank correlation coefficient will be used to 
examine the association of maximum percentage of tumor shrinkage during 
treatment with the percent change after 1 cycle of treatment in AAK expressing 
cells, as well as percent changes after 1 cycle of treatment in tissue ERα, 
SMAD5, SOX2 expression and phosphorylation. 
17.4.5 Examination of changes in blood biomarkers after one cycle of initial treatment 

 
 
 
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At the end of Cycle 1, the percent change in CTC expression of Aurora A kinase, 
ER, and phospho- SOX2 expression from pre-treatment levels will be determined 
for each patient. 
Bland-Altman plots and weighted kappa statistics will be used to examine the 
concordance between the percent change in Aurora A kinase, ER, and phospho-
SOX2 expression from pre-treatment levels in CTC and in tumor tissue. 
A plot of the percent change expression of Aurora A kinase, ER, and phospho-
SOX2 expression from pre-treatment levels in CTCs and that in tissue will be 
constructed with using different symbols for each type of clinical response (CR, 
PR, SD or PD) to visually assess for trends. 
17.5 
Monitoring 
17.5.1 Study Monitoring 
The study chair and faculty statistician will review the trial data every 3 months to 
identify accrual, toxicity, and endpoint problems that might be developing. The 
faculty statistician will prepare a report containing accrual, adverse events, and 
efficacy data which will be submitted to the MCCC Data and Safety Monitoring 
Board (DSMB) on a semi-annual basis. 
17.5.2 Safety Stopping Rule 
Pre-Amendment 3: Safety stopping rules will be applied to each treatment arm 
separately. If 3 or more of the first 10 patients randomized to a given treatment 
arm or 30% of more of patients randomized to that treatment arm thereafter 
develops a grade 4 hematologic or non-hematologic toxicity possibly, probably or 
definitely related to treatment, the enrollment to the trial will be temporarily 
suspended so that all AE data can be examined. The study chair and the faculty 
statistician will formulate a trial recommendation to present to the IRB for 
approval. These instances will also be reported to the MCCC DSMB. 
Post-Amendment 3: This safety stopping rule will be applied to each treatment 
arm separately for the patients enrolled after the activation of Amendment 3. If 2 
or more of the first 6 patients randomized to a given treatment arm or 30% of 
more of patients randomized to that treatment arm thereafter develops a Grade 4 
hematologic or non-hematologic toxicity possibly, probably or definitely related 
to treatment, the enrollment to the trial will be temporarily suspended so that all 
AE data can be examined. The study chair and the faculty statistician will 
formulate a trial recommendation to present to the IRB for approval. These 
instances will also be reported to the MCCC DSMB. 
 
 

 
 
 
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17.6 
Inclusion of Women and Minorities 
This study will be available to all eligible patients regardless of race or ethnic 
group. The expected number of patients per racial/ethnicity categories are 
presented in the following table. The sample size for this trial was not increase in 
order to provide additional power for analyses by race or ethnicity. 
Accrual Targets 
Ethnic Category 
Sex/Gender 
Females 
Males 
Total 
Hispanic or Latino 
7 
 
7 
Not Hispanic or Latino 
89 
 
89 
Ethnic Category: Total of all subjects 
96 
 
96 
Racial Category 
American Indian or Alaskan Native 
1 
 
1 
Asian 
6 
 
6 
Black or African American 
7 
 
7 
Native Hawaiian or other Pacific Islander 
0 
 
0 
White 
82 
 
82 
Racial Category: Total of all subjects 
96 
0 
96 
Ethnic 
Categories: 
Hispanic or Latino – a person of Cuban, Mexican, Puerto Rican, South or Central 
American, or other Spanish culture or origin, regardless of race. The term “Spanish 
origin” can also be used in addition to “Hispanic or Latino.” 
Not Hispanic or Latino 
Racial 
Categories: 
American Indian or Alaskan Native – a person having origins in any of the original 
peoples of North, Central, or South America, and who maintains tribal affiliations or 
community attachment. 
Asian – a person having origins in any of the original peoples of the Far East, 
Southeast Asia, or the Indian subcontinent including, for example, Cambodia, China, 
India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and 
Vietnam. (Note: Individuals from the Philippine Islands have been recorded as Pacific 
Islanders in previous data collection strategies.)  
Black or African American – a person having origins in any of the black racial 
groups of Africa. Terms such as “Haitian” or “Negro” can be used in addition to 
“Black or African American.” 
Native Hawaiian or other Pacific Islander – a person having origins in any of the 
original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. 
White – a person having origins in any of the original peoples of Europe, the Middle 
East, or North Africa. 
18. BUDGET 
18.1 
Costs charged to patient: Routine clinical care 
18.2 
Treatment and tests to be research funded: Alisertib, research blood work and tumor 
biopsies at pre-registration, at completion of Cycle 1, and at disease progression. 

 
 
 
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SG, Chadwick WA, Day ML, Kleer CG, Thomas DG, Hayes DF, Korkaya H, Wicha MS: HER2 
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Degnim A, Lange C, Ingle JN, Galanis E, D'Assoro AB: Aurora-A Mitotic Kinase Induces 
Endocrine Resistance through Down-Regulation of ER-alpha Expression in Initially ER+ Breast 
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Clin Oncol 2014, 32:44-50 
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Dansky Ullmann C, Zhang B, Benaim E: Phase 2 study of single agent MLN8237 (alisertib), an 
investigational aurora A kinase (AAK) inhibitor, in patients with relapsed/refractory breast cancer. 
Lancet Oncol. 2015 Apr;16(4):395-405: 
25. 
Di Leo A, Jerusalem G, Petruzelka L, Torres R, Bondarenko IN, Khasanov R, Verhoeven D, 
Pedrini JL, Smirnova I, Lichinitser MR, Pendergrass K, Garnett S, Lindemann JP, Sapunar F, 
Martin M: Results of the CONFIRM phase III trial comparing fulvestrant 250 mg with fulvestrant 
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Allard WJ, Terstappen LW, Hayes DF: Circulating tumor cells, disease progression, and survival 
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Doyle GV, Terstappen LW: Circulating tumor cells at each follow-up time point during therapy 
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Liu MC. By the numbers: does circulating tumor cell enumeration have a role in metastatic breast 
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30. 
Pocock SJ, Simon R: Sequential treatment assignment with balancing for prognostic factors in the 
controlled clinical trial. Biometrics 1975, 31:103-115 
31. 
SH Jung: Randomized phase II trials with a prospective control. Stat Med 2008, 27:568-583 
 

 
 
 
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APPENDICES  
Appendix I – ECOG Performance Status and Karnofsky Performance Status 
PERFORMANCE STATUS CRITERIA 
Please use ECOG Score for this protocol 
ECOG (Zubrod) 
Karnofsky 
Score 
Description 
Score 
Description 
0 
Fully active; able to carry on all 
pre-disease performance without 
restriction 
100 
Normal: no complaints, no evidence of 
disease 
90 
Able to carry on normal activity; minor 
symptoms of disease 
1 
Restricted in physically strenuous 
activity but ambulatory and able 
to carry out work of a light or 
sedentary nature, e.g., light 
housework, office work 
80 
Normal activity with effort; some signs 
or symptoms of disease 
70 
Cares for self; unable to carry on 
normal activities or do active work 
2 
Ambulatory and capable of all 
self care but unable to carry out 
any work activities; up and 
about more than 50% of waking 
hours 
60 
Requires occasional assistance; cares 
for most of his/her needs 
50 
Requires considerable assistance and 
frequent medical care 
3 
Capable of only limited self care; 
confined to bed or chair more than 
50% of waking hours 
40 
Disabled: requires special care and 
assistance 
30 
Severely disabled: hospitalized but 
death not imminent 
4 
Completely disabled; cannot 
carry on any self care; totally 
confined to bed or chair 
20 
Very sick: active supportive care 
needed but death not imminent 
10 
Moribund: fatal processes are 
progressing rapidly 
Karnofsky PS from Karnofsky DA, Abelmann WH, Craver LF, Burchenal JH: The use of the nitrogen mustards in 
the palliative treatment of carcinoma. Cancer 1, 634-656, 1948. 
*ECOG As published in Am. J. Clin. Oncol.: Oken, M.M., Creech, R.H., Tormey, D.C., Horton, J., Davis, T.E., 
McFadden, E.T., Carbone, P.P.: Toxicity And Response Criteria Of The Eastern Cooperative Oncology Group. Am 
J Clin Oncol 5:649-655, 1982. 
The ECOG Performance Status is in the public domain therefore available for public use. To duplicate the scale, 
please cite the reference above and credit the Eastern Cooperative Oncology Group, Robert Comis M.D., Group 
Chair. From 
  

 
 
 
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Appendix II – NYHA Heart Failure Classification 
NYHA 
Class 
Symptoms 
I 
Cardiac disease, but no symptoms and no limitation in ordinary physical activity, e.g. no 
shortness of breath when walking, climbing stairs etc. 
II 
Mild symptoms (mild shortness of breath and/or angina) and slight limitation during 
ordinary activity. 
III 
Marked limitation in activity due to symptoms, even during less-than-ordinary activity, 
e.g. walking short distances (20–100 m). 
Comfortable only at rest. 
IV 
Severe limitations. Experiences symptoms even while at rest. Mostly bedbound 
patients. 
 
Adapted from Dolgin M, Association NYH, Fox AC, Gorlin R, Levin RI, New York Heart Association. 
Criteria Committee. Nomenclature and criteria for diagnosis of diseases of the heart and great vessels. 
9th ed. Boston, MA: Lippincott Williams and Wilkins; March 1, 1994. 
Original source: Criteria Committee, New York Heart Association , Inc.  Diseases of the Heart and Blood 
Vessels. Nomenclature and Criteria for diagnosis, 6th edition  Boston, Little, Brown and Co. 1964, p 114. 
 

 
 
 
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Appendix III – Medication Diary 
Initials (optional)____________________________  
 
Patient Study ID_____________ 
Study Name/Number MC1431/TBCRC041  
 
Cycle_____________ 
Diary Instructions 
• 
Please bring your Medication Diary and any empty or unused medication container(s) with you to every appointment. 
• 
Please use an ink pen when completing the Medication Diary as these will be retained in our research record. 
• 
To correct an error or mistake, please make a single line through that entry and write your initials and date next to the error 
or mistake. 
• 
Please record each dose as soon as you take it and fill in the date as directed. Please also record the number of tablets you 
took for each dose of alisertib. 
• 
Please indicate on the calendar below every day that you take your study medication by placing the time dose was taken on 
the line under the date.  
• 
If you forget to take a dose and the next scheduled dose is to be taken in less than 6 hours, do not take the missed dose. If 
you miss a dose, DO NOT MAKE UP THIS DOSE ON A DIFFERENT DAY. Write the ‘Date’ in the appropriate place, leave the 
‘Time’ blank, and write ‘0’ for number of tablets taken for this missed dose. 
Drug Instructions 
• 
Alisertib should be taken regardless of the timing of meals. You should take your Alisertib with about 250 mL (1 cup) of 
water. 
• 
Your two doses of alisertib should be taken every 12 hours. These doses need to be taken at least 6 hours apart. 
• 
If your cycle starts in PM, you will take the PM dose only on Day 1 and an AM dose on Day 4. 
• 
Do not take proton pump inhibitors (e.g., omeprazole, lansoprazole, pantoprazole), H2 antagonists (e.g., famotidine, 
ranitidine, cimetidine) or pancreatic enzymes. 
• 
Do not take any neutralizing antacids or calcium-containing supplements 2 hours prior to taking alisertib and wait to take 
these until 2 hours after taking your alisertib. 
• 
Store alisertib at room temperature 
• 
If you vomit after taking alisertib, do not take another dose. Wait until your next scheduled dose before taking alisertib. 
Other Instructions 
• 
Please contact your physician or study coordinator any time you go into the hospital. Your physician can advise if you 
should stop taking your medication or continue it. 
Study Medications  
Dose 
Alisertib (oral) 
MG 

 
 
 
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Day 1 
Day 2 
Day 3 
Day 4 
Days 5-7 
Date: 
 
 
 
 
 
Time of Morning Dose 
Number of pills taken 
AM 
# of pills 
AM 
# of pills 
AM 
# of pills 
AM 
# of pills 
NO PILLS AM 
Time of Afternoon Dose 
Number of pills taken 
PM 
# of pills 
PM 
# of pills 
PM 
# of pills 
NO PILLS PM 
NO PILLS PM 
 
 
Day 8 
Day 9 
Day 10 
Days 11-14 
Date: 
 
 
 
 
Time of Morning Dose 
Number of pills taken 
 AM 
# of pills 
AM 
# of pills 
AM 
# of pills  
NO PILLS AM 
Time of Afternoon Dose 
Number of pills taken 
 PM 
# of pills 
PM 
# of pills  
PM 
# of pills  
NO PILLS PM 
 
 
Day 15 
Day 16 
Day 17 
Days 18-28 
Date: 
 
 
 
 
Time of Morning Dose 
Number of pills taken 
 AM 
# of pills 
AM 
# of pills 
AM 
# of pills  
NO PILLS AM 
Time of Afternoon Dose 
Number of pills taken 
 PM 
# of pills 
PM 
# of pills  
PM 
# of pills  
NO PILLS PM 
NOTE: Day 18 through Day 28 you will not take any drug 
Participant Signature________________________________  
Date: ________________ 
Area Below To Be Completed By Study Staff Only 
Number of Pills returned: ____________ 
 
 
Study Coordinator Initials: _________________ 
Date: _________________________ 
Discrepancy: Yes__________ No __________ 
 

 
 
 
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Appendix IV – Proton Pump Inhibitor (PPI) and H2 antagonist 
Alisertib has low and pH-dependent solubility. It is an enteric coated tablet designed to bypass 
the acidic gastric pH. Per a recently completed DDI study with esomeprazole, co-administration 
with PPIs resulted in ~30% increase in alisertib systemic exposure. For this reason chronic use of 
PPI or H2 antagonist medications is not allowed. 
Proton Pump Inhibitors 
• omeprazole (Prilosec) 
• lansoprazole (Prevacid) 
• rabeprazole (Aciphex) 
• pantoprazole (Protonix) 
• esomeprazole (Nexium) 
H2- Blockers 
• ranitidine (Zantac) 
• cimetidine (Tagamet) 
• famotidine (Pepcid) 
• nizatidine (Axid)