Phase II Trial of Alisertib (MLN8237) in Salvage Malignant Mesothelioma
Phase: PHASE2
Conditions: Lung Cancer, Mesothelioma
Sponsor: M.D. Anderson Cancer Center

Alisertib (MLN8237) Manufactured by 
  
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10/28/2015 
 
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CLINICAL STUDY PROTOCOL X14024 
ALISERTIB (MLN8237) 
 
Phase 2 trial of alisertib (MLN8237) in salvage malignant mesothelioma 
 
 
 
 
Protocol Number: 
 
 
  X14024 
 
 
 
Indication: 
 
 
 
  Malignant Mesothelioma 
Phase:  
 
 
 
  2 
Sponsor:  
 
 
 
  MD Anderson Cancer Center 
Study Supporter:  
 
 
  Millennium Pharmaceuticals, Inc. 
Therapeutic Area:   
 
  Oncology 
 
 
 
Protocol History 
Original 
Revision 1 
Revision 1.1 
Revision 2 
Revision 3 
 
28 January 2014 
21 July 2014 
17 November 2014 
04 June 2015 
28 October 2015 
 
 
 
 
Investigator and Study Center: 
 
Anne S. Tsao, MD 
Associate Professor 
Director, Mesothelioma Program 
Director, Thoracic Chemo-Radiation Program 
University of Texas M.D. Anderson Cancer Center 
Department of Thoracic/Head & Neck Medical Oncology 
1515 Holcombe Blvd. Unit 432 
Houston, TX 77030 
Phone (713) 792-6363 
Fax (713) 792-1220 

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PROTOCOL SUMMARY 
Study Title:  Phase 2 trial of alisertib in salvage malignant mesothelioma 
Phase:  2 
 
Objectives 
The primary objective of this study is: 
 To assess 4-month disease control rate (DCR) in pre-treated patients with 
unresectable malignant pleural mesothelioma (MPM) treated with alisertib 
 
The secondary objectives of this study are: 
 To assess the response rate (confirmed and unconfirmed complete + partial 
responses)  
 To assess the progression-free survival.  
 To assess overall survival. 
 To evaluate the side effects and toxicities associated with this treatment regimen. 
 To collect archival tissue, blood, pleural effusion fluid and plasma for correlative 
studies. 
 
The Exploratory Objectives of this study are: 
 To collect archival or new tissue, blood and pleural effusion fluid for correlative 
studies. Tissue biomarkers to be evaluated include aurora kinase pathway and c-
myc gene amplification  
 Next generation sequencing (NGC) will be conducted on adequate tumor tissue 
specimens. 
 
Patient Population 
Pre-treated Malignant Mesothelioma patients with any histology and any primary tumor site. 
Patients can have up to 4 prior lines of therapy.  Patients must have received at least 1 
platinum-pemetrexed or platinum-doublet or pemetrexed-based chemotherapy.  
 
Number of Patients 
53 eligible patients, 58 maximum patients (assumes 5 inevaluable patients) 
 
Study Design and Methodology 
This is single-arm phase II trial in pre-treated malignant mesothelioma patients who will 
receive oral alisertib monotherapy.  1 cycle is 21 days.  Alisertib will be given 50 mg po 
BID on days 1-7.  A treatment break will occur on days 8-21.   
 
Patients will be radiographically evaluated every 2 cycles of therapy for efficacy.  
Patients will remain on trial until unacceptable toxicity, withdrawal of consent, or disease 
progression.   
 
Duration of Study 
3.2 years 

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Treatments Administered 
Alisertib will be administered PO at 50 mg BID for 7 days in each treatment cycle, followed 
by a 14-day, treatment-free period, for a 21-day cycle.  
 
Efficacy Data Collected 
The following evaluations will be conducted to assess the efficacy of alisertib: 
 Radiographic imaging (PET-CT, chest CT, or abdominal-pelvic CT scans) 
 Tumor measurements by modified RECIST (preferred) or RECIST (if modified 
RECIST is not possible) 
 
 
The following specimens will be collected at baseline for storage for subsequent studies.  
 Baseline tissue specimen block (archived tissue block is acceptable) 
 Baseline tumor tissue biopsy if a baseline tissue specimen block is not 
available. (at least 10 unstained slides or a tumor block are requested) 
 Baseline blood specimen 
 
Safety Data Collected 
The following evaluations will be conducted to assess the safety of alisertib: 
 Laboratory values (standard of care hematologic, liver and renal function, 
electrolytes) 
 History and physical exam during each clinic visit 
 Toxicity will be evaluated according to the National Cancer Institute Common 
Terminology Criteria for Adverse Events (NCI CTCAE), Version 4.03, 
effective14 June 2010 (16).  These criteria are provided in the Study Manual and 
are available online at 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm 
 
Statistical Procedures 
The primary objective of this study is to assess the efficacy of alisertib in pretreated patients 
with unresectable malignant mesothelioma (pleural or peritoneal).  The primary endpoint is 
the disease control rate at 4 months in patients with unresectable malignant pleural 
mesothelioma (MPM) treated with alisertib. The trial will be conducted by the Simon’s 
minimax two-stage design and the disease control rate at 4 months will be estimated 
accordingly.[2] 
 
It is assumed that the new regimen will have a target disease control rate of 50% at 4 
months. A disease control rate of 30% or lower is considered a failure and the new regimen 
will be rejected under this circumstance.  When the probability of accepting a “bad” regimen 
(i.e. disease control rate<=30%) is 0.05 and the probability of rejecting a “good” regimen 

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(i.e. disease control rate >=50%) is 0.10, Simon’s minimax design requires to enter 24 
patients in the first stage. If 7 or less patients are alive and free of disease progression to the 
treatment at 4 months, the trial will be stopped and the regimen will be declared as 
ineffective. If there are 8 or more patients are alive and progression-free at 4 months, 29 
more patients will be entered in the study to reach a total of 53 patients. By the end of the 
study, the new regimen will be rejected if disease control rate is less than or equal to 21/53 
and will be accepted otherwise.  The operating characteristics of the trial are given as 
follows. When the true disease control rate is 0.30 the probability of stopping the trial early 
is 57%. On the other hand, if the true disease control rate is 0.50, the probability to stop the 
trial early is 3%.  The expected sample sizes are 36.6 and 52.1 when the true response rates 
are 0.3 and 0.5, respectively.   
 
This design has the minimax property of minimizing the maximum sample size under null 
hypothesis. If the number of disease control required for moving the trial to the second stage 
has not been achieved, the patient enrollment will be halted until enough responses 
observed.   
Analysis of efficacy results will be conducted using standard statistical methods.  
Descriptive statistics including mean, standard deviation, median, and range will be 
provided for continuous variables such as age. Frequency tables will be used to summarize 
categorical variables such as gender, and response. The standard error and confidence 
interval on estimating the disease control rate will be provided. The distribution of time-to-
event endpoints, such as time to progression and overall survival, will be estimated using the 
method of Kaplan and Meier.  Comparison of time-to-event endpoints by important patient 
characteristics will be made using the log-rank test.  Cox proportional hazard regression will 
be employed for multi-covariate analysis on time-to-event outcomes when appropriate. 

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TABLE OF CONTENTS 
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Update entire table, and click OK.) 
CLINICAL STUDY PROTOCOL X14024 .............................................................................1 
PROTOCOL SUMMARY ........................................................................................................2 
TABLE OF CONTENTS .........................................................................................................5 
LIST OF IN-TEXT TABLES ...................................................................................................7 
STUDY FLOW DIAGRAM .....................................................................................................8 
SCHEDULE OF EVENTS .......................................................................................................9 
LIST OF ABBREVIATIONS .................................................................................................11 
1. INTRODUCTION AND STUDY RATIONALE ..............................................................13 
1.1 Overview of the Disease ...............................................................................................13 
1.1.1 Aurora A Kinases and the Aurora A Kinase Inhibitor Alisertib (MLN8237) .......13 
1.2 Preclinical Experience with Alisertib ...........................................................................14 
1.2.1 In Vitro Studies ......................................................................................................14 
1.2.2 In Vivo Studies ......................................................................................................14 
1.2.3 Safety Pharmacology, Toxicology, and Drug Metabolism....................................15 
1.3 Clinical Experience .......................................................................................................16 
1.4 Pharmacokinetics ..........................................................................................................17 
1.5 Potential Risks and Benefits .........................................................................................18 
1.6 Study rationale and selection of drug doses .................................................................19 
2. STUDY OBJECTIVES ......................................................................................................21 
2.1 Primary Objective .........................................................................................................21 
2.2 Secondary Objectives ...................................................................................................21 
2.3 Exploratory Objectives .................................................................................................21 
3. INVESTIGATIONAL PLAN .............................................................................................22 
3.1 Overall Design and Plan of the Study ..........................................................................22 
3.2 Selection of Patients .....................................................................................................22 
3.2.1 Inclusion Criteria ...................................................................................................22 
3.2.2 Exclusion Criteria ..................................................................................................24 
3.3 Study Treatments ..........................................................................................................26 
3.3.1 Preparation, Handling, and Storage of Drugs ........................................................26 
3.3.2 Dose Modification and Delay ................................................................................28 
3.3.3 Criteria for Retreatment and Dose Delays .............................................................28 
3.3.4 Dose Modifications for Hematological Toxicity ...................................................29 
3.3.5 Dose Modifications for Non-Hematological Toxicities ........................................29 
3.3.6 Packaging and Labeling .........................................................................................30 
3.4 Excluded Concomitant Medications and Procedures ...................................................30 
3.5 Permitted Concomitant Medications and Procedures ...................................................31 
3.6 Precautions and Restrictions .........................................................................................31 
3.7 Management of Clinical Events ...................................................................................32 
3.7.1 Nausea and Vomiting ............................................................................................32 
3.7.2 Diarrhea .................................................................................................................32 
3.7.3 Central Nervous System Effects ............................................................................32 

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3.7.4 Treatment Compliance ...........................................................................................33 
3.8 Duration of Treatment and Patient Participation ..........................................................33 
3.9 Termination of Treatment and/or Study Participation ..................................................33 
3.10 Efficacy and Safety Measurements ............................................................................34 
3.10.1 Efficacy Measurements........................................................................................34 
3.10.2 Safety Measurements ...........................................................................................34 
3.11 Study Drug Administration ........................................................................................35 
3.12 Description of Investigational Agents ........................................................................35 
3.13 Preparation, Reconstitution, and Dispensation ...........................................................35 
3.14 Packaging and Labeling ..............................................................................................36 
3.15 Storage, Handling, and Accountability .......................................................................36 
4. ADVERSE EVENTS ..........................................................................................................37 
4.1.1 Adverse Event Definition ......................................................................................37 
4.1.2 Serious Adverse Event Definition .........................................................................37 
4.1.3 Serious Adverse Event Reporting (SAE) Reporting ..............................................38 
4.2 Communication between Investigator and Millennium ...............................................40 
4.3 Procedures for Reporting Drug Exposure during Pregnancy and Birth Events ...........41 
4.4 Product Complaints ......................................................................................................42 
5. STATISTICAL PROCEDURES ........................................................................................43 
5.1 Study Design and Overview of Primary and Secondary Endpoints .............................43 
5.2 Sample Size Estimation/Accrual Rate ..........................................................................44 
5.3 Randomization and Stratification Factors ....................................................................44 
5.4 Evaluation of Efficacy ..................................................................................................44 
5.5 Evaluation of Safety .....................................................................................................45 
5.6 Correlative Studies .......................................................................................................45 
5.7 Interim Analysis ...........................................................................................................49 
6. ADMINISTRATIVE REQUIREMENTS ..........................................................................49 
6.1 Good Clinical Practice ..................................................................................................49 
6.2 Ethical Considerations ..................................................................................................49 
6.3 Patient Information and Informed Consent ..................................................................50 
6.4 Patient Confidentiality ..................................................................................................50 
6.5 Protocol Compliance ....................................................................................................50 
6.6 On-site Audits ...............................................................................................................50 
6.7 Drug Accountability .....................................................................................................51 
6.8 Premature Closure of the Study ....................................................................................51 
6.9 Record Retention ..........................................................................................................51 
7. USE OF INFORMATION ..................................................................................................52 
8. REFERENCES ...................................................................................................................53 
9. APPENDICES ....................................................................................................................55 
9.1 Declaration of Helsinki .................................................................................................55 
9.2 Common Terminology Criteria for Adverse Events Version 4.03 ...............................59 
9.3 New York Heart Association Classification of Cardiac Disease .................................59 
9.4 Eastern Cooperative Oncology Group Scale for Performance Status ..........................59 
9.5 Body Surface Area and Creatinine Clearance Calculations .........................................60 
 
 

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LIST OF IN-TEXT TABLES 
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choose Update entire table, and click OK.) 
Table 3-1    
Table of Dose Adjustments ....................................................................... 2829 
 
 

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Study Flow Diagram 
 
 
 
 
 Any histology MM 
 Up to 4 prior lines 
of therapy 
 ECOG PS 0-2 
Alisertib 50 mg po 
BID days 1-7 
Re-stage Q6 weeks until  
off-study 
 
Method of evaluation:  
Modified RECIST (preferred) but use 
RECIST if modified RECIST not 
possible.[1]  
 Baseline blood banked 
 Baseline tumor specimen 
banked 
 If no tumor tissue is 
available, patients must 
receive a tumor biopsy 
for tissue 
Tissue correlative analysis 
 C-myc amplification 
 Aurora kinase pathway  
 NGS 

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Schedule of Events 
 
  
 
 
 
Required studies 
 
 
 
Prestudya 
 
Cyclea 1 
  
 
Cycle 2 
 
 
Cycle 3 
 
Cycle 4 
 
Cycle 5 
Cycle 6+ 
Restage every 2  
cycles 
 
 
Follow 
Upd 
D1 
D 
1-
7 
D1
D 
1-7
W
K 3 
D1 
D 
1-7
D1
D 
1-7 
W
K 3 
D1
D 
1-7
D1
D 
1-7 
WK 
3 
History and 
physical exam 
X 
X 
 
X 
 
 
X 
 
  
 
 
X 
 
  
 
 
 
Weight and PS 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
 
 
Concurrent 
medications 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
 
 
Toxicity 
evaluation 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
X 
Xd
Electrocardiogram 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
LABORATORY 
 
 
CBC/diff/platelets 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
 
 
Urine Analysis 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
PT, PTT 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Bilirubin, AST, 
ALT 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
 
 
Electrolytesb, 
Creatinine 
Clearance 
X 
X 
 
X 
 
 
X 
 
 
 
 
X 
 
 
 
 
 
Serum βHCG 
Pregnancy Test 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
SCANS 
 
 
Imaging/Restaging 
scans 
X 
 
 
 
 
X 
 
 
 
 
X 
 
 
 
 
X 
 

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SPECIMENS 
 
 
Tumor Tissue 
Collectione 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Blood for bankingc 
(optional) 
X 
 
 
 
 
 
 
X 
 
 
 
 
 
 
 
 
 
 
 
Pleural Effusion 
Fluidf (optional) 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
TREATMENT 
 
 
Alisertib 
 
 
X 
 
X 
 
 
X 
 
X 
 
 
X 
 
X 
 
 
FOLLOW UP 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Chart review or 
phone call 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Xd
a. There is a 14-day window for baseline and ±3 days for clinic visits at every study cycle. 
b. Electrolytes panel includes Carbon Dioxide, Chloride, Potassium, and Sodium  
c. 24mL of blood will be collected each time at baseline, cycle 3 day 1 and at progression. 
d: Toxicities and survival follow-up will be done through chart review or phone call 30 days post treatment, at 3 months and every 6 months 
thereafter.  
e: Leftover tissue collected on study will be stored in a research bank, if allowed.  
f: Pleural effusion fluid will be collected whenever available.

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LIST OF ABBREVIATIONS 
(Update with additional abbreviations/remove un-used abbreviations as necessary.) 
Abbreviation 
Definition 
C 
degrees Celsius 
M 
micromolar 
20S 
20S proteasome subunit 
AE 
adverse event 
ANC 
absolute neutrophil count 
Bc1-2 
B-cell lymphoma-2; a gene that inhibits apoptosis 
BSA 
body surface area 
CAM 
cell adhesion molecules  
cm 
centimeter 
CR 
complete response 
CTCAE 
(NCI) Common Terminology Criteria for Adverse Events 
CTEP 
Cancer Therapy Evaluation Program 
dL 
deciliter 
DLT 
dose-limiting toxicity 
DNA 
deoxyribonucleic acid 
ECT 
enteric-coated tablet 
FDA 
Food and Drug Administration 
GCP 
Good Clinical Practice 
GLP 
Good Laboratory Practice 
ht 
height 
IB 
I kappa B kinase; cytokine response kinase that activates transcription 
factor NF-kappa b at serine 32 and 36 
ICAM-1 
intercellular adhesion molecule 1 
ICH 
International Conference on Harmonisation 
IEC 
independent ethics committee 
IND 
Investigational New Drug 
IRB 
institutional review board 
IV 
intravenous 
IB 
I kappa B alpha-associated protein kinase 
kg 
kilogram 
Ki 
inhibitory constant 
lbs 
pounds 

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Abbreviation 
Definition 
m2 
square meters 
mg 
milligram 
min 
minute 
mL 
milliliter 
mm3 
cubic millimeters 
mmol 
millimole 
MTD 
maximum tolerated dose 
NCI 
National Cancer Institute 
NF-B 
nuclear factor-B 
ng 
nanogram 
nM 
Nanomole 
OS 
oral solution 
p21 
p21(ras) farnesyl-protein transferase 
p27 
cyclin-dependent kinase inhibitor 
p53 
tumor suppressor protein with molecular weight of 53 kDa 
PIC 
powder-in-capsule 
SAE 
serious adverse event 
US 
United States 
USP 
United States Pharmacopeia 
VCAM-1 
vascular cell adhesion molecule 1 
w/w 
weight-to-weight ratio 
wt 
Weight 

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1.    INTRODUCTION AND STUDY RATIONALE 
1.1    Overview of the Disease 
 
Unresectable malignant mesothelioma is a challenging disease that has typically had 
poor responses to chemotherapy.  Response rates to systemic chemotherapy have ranged 
from 3% to 30%.[3]  In the front-line setting, the Evaluation of Mesothelioma in a Phase III 
study of Pemetrexed with Cisplatin randomized 456 patients to single agent cisplatin or the 
combination of cisplatin and pemetrexed.  This study reported improvement in median 
overall survival (12.1 months vs. 9.3 months; p=0.02).[4]  There are currently no Food and 
Drug Administration (FDA) approved agents in the salvage setting for mesothelioma.  Novel 
agents for refractory patients are desperately needed to improve the therapeutic landscape.    
1.1.1    Aurora A Kinases and the Aurora A Kinase Inhibitor Alisertib 
(MLN8237) 
Alisertib (International Proprietary Name, also known as MLN8237) is a selective small 
molecule inhibitor of Aurora A kinase that is being developed for the treatment of advanced 
malignancies.  Aurora A kinase belongs to a highly conserved family of serine/threonine 
protein kinases that also includes Aurora B and Aurora C.  Aurora A and Aurora B are 
expressed in all actively dividing cells, while Aurora C expression is largely restricted to 
dividing germ cells.[5]  Aurora A localizes to centrosomes and the proximal mitotic spindle 
during mitosis where it functions in a diverse set of mitotic processes.  
The evidence supporting Aurora A kinase as a therapeutic target for the treatment of 
malignancies comes from several sources.  First, 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.[3, 6-9]  Aurora A 
overexpression in human cancers has been correlated with increased aneuploidy and 
centrosome amplification.[10]  Second, forced overexpression of Aurora A kinase in 
experimental models results in the transformation of normal cells, suggesting that Aurora A 
overexpression may be oncogenic.[6]  Lastly, in a number of different experimental systems, 
Aurora A inhibition leads to mitotic delays and severe chromosome alignment and 
segregation defects, followed by cell death.[11-14]  Overall, the essential role of Aurora A 
in mitotic progression and its dysregulation in certain cancers makes it an attractive 
therapeutic target.   
Given the obligatory role of mitosis in tumor proliferation, an Aurora A inhibitor would be 
expected to have potential applications across a broad range of human tumors.  Indeed, 
alisertib has demonstrated activity against a variety of nonclinical solid tumor and 

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hematological malignancy models grown in vitro and in vivo, as described below.  Alisertib 
is also expected to be toxic to proliferating normal tissues, such as the bone marrow, 
gastrointestinal (GI) epithelium, and hair follicles because 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. 
1.2    Preclinical Experience with Alisertib 
1.2.1       In Vitro Studies 
Alisertib is an ATP-competitive and reversible inhibitor of Aurora A kinase in vitro with an 
inhibition constant (Ki) of 0.43 nM. The data from both enzymatic and cell-based assays 
demonstrated that alisertib is a selective and potent inhibitor of Aurora A kinase. Alisertib 
inhibited proliferation of a wide variety of tumor cell lines grown in culture. Moreover, 
treatment of tumor cell lines with alisertib induced phenotypes consistent with Aurora A 
kinase inhibition, including mitotic spindle defects, mitotic delay, and apoptosis.[3, 6-9] For 
further details, refer to the Investigators’ Brochure (IB).  
1.2.2       In Vivo Studies 
Alisertib demonstrated antitumor activity when administered orally on a daily basis for 
approximately 21 days (maximal tumor growth inhibition [TGI] > 90%) in several 
experimental human solid and hematologic tumor models grown as xenografts in 
immunocompromised mice. The maximally efficacious dose (ED) for each model varied: 
between 10 and 30 mg/kg if given once daily (QD) and 20 mg/kg if given twice daily (BID). 
Studies in the HCT-116 colon tumor model showed that less frequent dosing (eg, 5 days on 
followed by 5 days off) was also efficacious, demonstrating that continuous dosing is not 
necessary for antitumor activity. A single oral dose of alisertib given to nude mice bearing 
subcutaneous HCT-116 human colon tumors resulted in inhibition of activated Aurora A 
kinase and an increase in mitotic cells. Therefore, mitotic index (MI) can be used as a 
pharmacodynamic marker of alisertib in some in vivo settings. The relationship between 
pharmacokinetics (PK), pharmacodynamics, and efficacy was further studied in HCT-116 
xenografts using oral dosing and subcutaneous osmotic mini-pumps. Both a 
pharmacodynamic response and efficacy (antitumor activity) were achieved using either 
route of administration. The data from these studies suggest that the maximum 
pharmacodynamic effect (mitotic accumulation) and efficacy are achieved at steady state 
plasma concentrations of 1-µM. Moreover, the maximally efficacious oral doses of alisertib 
in the HCT-116 model (30 mg/kg QD) resulted in plasma concentrations of 1 µM for 8 to 12 

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hours postdose. Plasma concentrations of alisertib associated with saturating levels of 
pharmacodynamic and antitumor activity (1 μM) were exceeded at the recommended phase 
2 dose (RP2D) of alisertib in patients (50 mg BID).To determine whether alisertib would 
enhance the antitumor effects of standard of care agents in solid and hematologic 
malignancies, nonclinical combination studies were performed. Combination therapy with 
alisertib and docetaxel resulted in additive or synergistic effects during the dosing period, 
with prolonged tumor growth delay in multiple solid tumor xenograft models after 
terminating treatment. These effects were also observed in alternative intermittent dosing 
schedules. In DLBCL xenograft models, combination therapy with alisertib and rituximab 
resulted in synergistic, additive, or subadditive effects depending on the dose and model; 
however, prolonged tumor growth delays were observed in every case after terminating 
treatment, and in some cases complete cures were maintained. 
1.2.3    Safety Pharmacology, Toxicology, and Drug Metabolism 
Safety pharmacology studies with alisertib did not identify significant adverse effects in 
nonclinical studies, including in the central nervous system (CNS) and cardiovascular 
systems. No alisertib-related effects on clinical signs or physical examination findings 
indicative of impaired respiratory function (ie, labored or shallow breathing), or microscopic 
changes in the lungs of animals that survived until scheduled termination, were noted at 
tolerated doses in Good Laboratory Practice (GLP)-compliant, repeat-dose, toxicology 
studies. Alisertib exhibited minimal activity against the rapidly activating component of IKr, 
which is encoded by hERG (IC50 and Ki > 100 µM). Alisertib had in vitro activity against 
the GABAAα1 benzodiazepine binding site (Ki = 290 nM). 
The dose-limiting toxicities (DLTs) for alisertib in both rats and dogs after repeat daily oral 
dosing for 2 cycles (each cycle consisted of 7 consecutive days separated by a 14-day dose 
holiday) or for 6 cycles (each cycle consisted of 21 consecutive days of dosing separated by 
a 7-day dose holiday) were consistent with inhibition of Aurora A kinase by alisertib. 
Principal findings in toxicology studies in rats and dogs included gastrointestinal (GI) signs, 
panleukopenia, decreased reticulocyte counts, and increased mitotic figures and apoptosis 
(single-cell necrosis) in tissues with a high basal cellular replication rate. These findings are 
indicative of toxicity to rapidly replicating cell populations and are consistent with the 
outcomes associated with Aurora A kinase inhibition. No off-target effects were seen in the 
GLP-compliant toxicology studies.Alisertib was negative in the bacterial reverse mutation 
assay (Ames assay) both in the absence and presence of Aroclor™ 1254-induced rat liver S9 

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fractions. In a rat bone marrow micronucleus assay, alisertib was considered to be equivocal 
for clastogenicity. 
Alisertib is metabolized by multiple phase I (cytochrome P450 [CYP]3A4, CYP2C9, 
CYP2C19, and CYP1A2) and phase II (uridine diphosphate glucuronosyltransferase [UGT] 
1A1, 1A3, and 1A8) enzymes.  Using human liver microsomes with the appropriate 
cofactors, the percent contribution of CYP and UGT was calculated to be 13.1% and 86.9%, 
respectively, showing that CYP isozymes play a minor role in the metabolism of MLN8237.  
MLN8237 is unlikely to inhibit the 5 major CYP enzymes, 1A2, 2C9, 2C19, 2D6, and 
3A4/5 (IC50 > 100 M) when administered at the projected human efficacious dose.  
MLN8237 is not a mechanism-based inhibitor of CYP3A4/5.  Alisertib inhibited the 
P-glycoprotein (Pgp)-mediated efflux of paclitaxel (Taxol) in Caco 2 cells with an IC50 of 
4.0 M. 
Detailed information regarding the nonclinical pharmacology and toxicology of alisertib 
may be found in the IB. 
1.3    Clinical Experience 
As of 29 March 2012, the following company-sponsored alisertib studies were in progress or 
completed: 6 single-agent phase 1 studies, 3 single-agent phase 2 studies, 1 single-agent 
phase 1/2 study, and 3 combination studies. 
Alisertib for clinical studies is being developed in 2 dosage formulations:  Enteric-coated-
tablet (ECT) and oral solution (OS).  
The dose-escalation, phase 1 study, C14007, evaluated multiple dose levels from 10 to 60 
mg BID for 7 days in repeat, 21-day cycles and 50 mg BID has been determined to be the 
MTD. 
Alisertib is structurally related to the benzodiazepines (BZD) (eg, diazepam, lorazepam) and 
also has activity against the GABAA1 BZD receptor.  BZD-like effects (eg, somnolence, 
confusion, memory loss) have been observed to be associated with the onset of maximal 
plasma concentration (eg, Tmax [time to maximum plasma concentration]).  CNS effects 
associated with peak plasma levels have been generally managed by administration of 
divided doses (eg, BID administration), although dose reductions have sometimes been 
required.  While CNS effects attributed to alisertib were also generally reversible and 
manageable by dose delay or reduction, the causal relationship, and thus optimal approach to 

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management, were sometimes confounded by diverse causes including, but not limited to, 
concomitant medications (eg, narcotic analgesics, antianxiety medications), comorbidities 
(eg, infection, anemia, electrolyte abnormalities), or progressive malignancy (eg, brain 
metastases). 
The clinical experience with alisertib includes treatment with multiple doses and schedules 
and is summarized in the IB.   
1.4    Pharmacokinetics 
Upon oral administration to patients with advanced nonhematologic malignancies, 
absorption of alisertib was fast, with peak plasma concentrations generally achieved by 3 
hours postdose. Negligible urinary excretion of alisertib was observed in humans. The renal 
clearance of alisertib in humans was less than 0.1% of apparent oral clearance. Steady-state 
plasma exposures of alisertib increased in an approximately dose-proportional manner over 
the range of 5 to 200 mg/day in patients with advanced solid tumors. Overall mean steady-
state terminal half-life following multiple-dose administration in patients with 
nonhematologic malignancies was approximately 22 hours. The overall mean peak/trough 
ratios were 2.6 and 5.0 for BID and QD dosing, respectively. The overall mean 
accumulation ratios were 2.8 and 1.9 for BID and QD dosing, respectively. Pharmacokinetic 
steady-state conditions were approximately achieved by Day 7 following daily oral 
administration. The PK properties of alisertib in patients with hematologic malignancies 
were generally consistent with those observed in patients with nonhematologic 
malignancies. Based on PK and genotype data in patients with nonhematologic 
malignancies, there was a substantial overlap in exposures (dose-normalized steady-state 
area under the plasma concentration versus time curve [AUC]) of alisertib in patients with 0, 
1, or 2 copies of the UGT1A1 *28 allele, indicating the lack of readily apparent effects of 
UGT1A1 genotype on alisertib systemic exposure. 
Clinical pharmacokinetic data available as of 20 April 2012 are summarized in the IB. Upon 
oral administration to patients with advanced nonhematologic malignancies, absorption of 
alisertib was fast, with peak plasma concentrations generally achieved by 2 hours post dose. 
Negligible urinary excretion of alisertib was observed in humans. The renal clearance of 
alisertib in humans was less than 0.1% of apparent oral clearance. Steady-state plasma 
exposures of alisertib increased in an approximately dose proportional manner over the 
range of 5 to 200 mg/day in patients with advanced solid tumors. Overall mean steady-state 
terminal half-life following multiple-dose administration in patients with nonhematologic 

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malignancies was approximately 22 hours. The overall mean peak/trough ratios were 2.6 
and 5.0 for BID and QD dosing, respectively. The overall mean accumulation ratios were 
2.8 and 1.9 for BID and QD dosing, respectively. Pharmacokinetic steady-state conditions 
were approximately achieved by Day 7 following daily oral administration.  
Based on the results of a population PK analysis in 294 adult cancer patients, the apparent 
oral clearance of alisertib CL/F was unaffected by age, body weight, BSA, or the UGT1A1 
genotype (number of *28 alleles). These results support the use of a common fixed starting 
dose of alisertib independent of UGT1A1 genotype status, age or body size in the adult 
patient population, in the ongoing and planned clinical trials. 
The absolute bioavailability of alisertib in humans has not been determined; however, the 
single-dose pharmacokinetics of a prototype oral solution formulation of alisertib (25-mg 
dose) were characterized in a cross-over relative bioavailability evaluation in Study C14010 
in 15 patients with nonhematologic malignancies.  
The effect of a standardized high-fat meal on the PK of single-dose alisertib administered as 
a 50-mg strength was evaluated in 14 patients with advanced solid tumors.  The lack of an 
effect of food on alisertib AUCinf observed in this study supports the conclusion of the lack 
of a clinically meaningful effect of food on the PK of alisertib.  The results of this study, 
therefore, support a recommendation that alisertib may be dosed without regard to the 
timing of meals in future clinical studies, unless otherwise specified in the clinical study 
protocol. 
1.5    Potential Risks and Benefits 
Seven-hundred fourteen patients (excluding 13 patients from a company-sponsored, non-US 
IND study in Japan) have been treated with alisertib as of 29 March 2012. Clinical safety 
data includes experience from patients who received multiple cycles followed by treatment-
free periods between each cycle, and from patients who reduced or discontinued treatment. 
Based on the available clinical data, drug abuse, dependency, and drug withdrawal effects 
were not observed.  
To date, the observed risks associated with alisertib treatment, as detailed in the Safety 
Management Attachment of the IB, include: (1) reversible myelosuppression including 
leukopenia, neutropenia, febrile neutropenia, lymphopenia, thrombocytopenia, and anemia; 
(2) GI toxicity including stomatitis/mucositis/oral pain, nausea, vomiting, anorexia, 
abdominal pain, dyspepsia, diarrhea, and dehydration; (3) sedation, somnolence, confusional 

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state, disorientation (and associated memory loss), and gait disturbances; (4) alopecia; (5) 
asthenia/fatigue; (6) fever, (7) infection, (8) abnormal liver function tests (including 
aspartate transaminase [AST], alanine transaminase [ALT], bilirubin, alkaline phosphatase 
[ALP], and gamma glutamyl transferase [GGT]), and (9) rash, which may include bullous 
dermatitis, and palmar-plantar erythrodysaesthesia syndrome.While these toxicities are 
potentially associated with risk or discomfort to the patient, they are anticipated to be 
reversible.   
To mitigate the inherent risks in clinical studies of alisertib, patients are evaluated frequently 
while they are receiving treatment.   
Because alisertib inhibits Aurora A kinase, it is possible that alisertib may interfere with 
cancer growth and cause cancer cell death. Preclinical results indicate that alisertib is not a 
major substrate for efflux mechanisms that have been associated with cross-resistance 
between some types of anticancer agents. Thus, alisertib has potential through a potentially 
non-cross resistant pathway as compared to other agents the patients may have received.  
The clinical utility of these effects will be investigated in current and future studies. 
This study will be conducted in compliance with the protocol, applicable regulatory 
requirements, and International Conference on Harmonisation (ICH) Good Clinical Practice 
(GCP), guidelines. 
1.6    Study rationale and selection of drug doses 
Study Rationale 
 
There are 3 subtypes of aurora kinases (A, B, C), but only aurora kinase A and B are 
potential therapeutic targets.  Aurora kinase A inhibition leads to mitotic delay, monopolar 
spindles, and chromosomal segregation errors whereas aurora kinase B inhibition causes 
dysfunctional cytokinesis, polyploidy, and apoptosis.  Preclinical studies have strongly 
suggested aurora kinases to be a relevant therapeutic target in mesothelioma patients.  
Several independent groups have reported that aurora kinase gene expression is upregulated 
in mesothelioma tumor tissue and is a negative prognostic factor.[15, 16](also our group – 
publication pending).  Crispi et al.[17] have also shown that inhibition of mesothelioma cell 
lines with an aurora kinase inhibitor ZM447439 led to cell growth arrest and was target 
specific.  Kim et al. also reported on irradiated mesothelioma cells and how inhibition of 
surviving and aurora kinase B resulted in mitotic cell arrest.   
There are several aurora kinase inhibitors under investigation.  For aurora kinase A 
inhibitors, alisertib, (MLN8237, Millenium) are under investigation in phase I and II trials.  
Preliminary results suggest dose limiting toxicity to be myelosuppression and mucositis.  
Aurora kinase B inhibitors, GSK1070916A (GlaxoSmithKline) and AZD1152 
(AstraZeneca) are also under investigation in phase I and II trials in solid tumors and AML.  

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Several additional phase I and II trials of pan-aurora kinase inhibitor trials are underway in 
solid tumors.  Alisertib (International Proprietary Name, also known as MLN8237) is a 
selective small molecule inhibitor of Aurora A kinase that is being developed for the 
treatment of advanced malignancies.    
To date, there are no aurora kinase inhibitor-specific mesothelioma trials and the 
proposed study would be the first to assess this class of drug in the disease.  Based on the 
preclinical data reported in the literature and our own profiling studies, we believe that 
aurora kinase is a feasible and relevant target in mesothelioma therapeutics.  Alisertib is a 
novel compound that has a reasonable safety profile and may show efficacy in this 
population of patients.   
 
1.6.1. Selection of Drug Dosages 
 
The alisertib dose employed in this study will be 50 mg po BID (enteric coated tablet ECT) 
for 7 days then a 2 week treatment free period for a 21-day cycle.  BID doses should be 
taken at least over 6 hours apart.  This phase II dosing was established from phase I studies 
detailed in Section 1.3. 
 

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2.    STUDY OBJECTIVES 
2.1    Primary Objective 
The primary objective of this study is to: 
 To assess the 4-month disease control rate (DCR) in pre-treated patients with 
unresectable malignant pleural mesothelioma (MPM) treated with alisertib. 
 
2.2    Secondary Objectives 
The secondary objectives of this study are: 
 To assess the response rate (confirmed and unconfirmed complete + partial 
responses) 
 To assess the progression-free survival 
 To assess overall survival. 
 To evaluate the side effects and toxicities associated with this treatment regimen. 
 To collect archival tissue, blood, pleural effusion fluid and plasma for correlative 
studies. 
 
2.3 
Exploratory Objectives 
 To collect archival or new tissue, blood and pleural effusion fluid for correlative 
studies.  Tissue biomarkers to be evaluated include aurora kinase pathway and c-myc 
gene amplification.   
 Next generation sequencing (NGS) will be conducted on adequate tumor tissue 
specimens.  
 

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3.    INVESTIGATIONAL PLAN 
This is an investigator-initiated study.  The principal investigator, Dr. Anne Tsao, is 
conducting the study. 
3.1    Overall Design and Plan of the Study 
This is a standard single-arm, single institution phase II trial that will enroll patients with 
malignant mesothelioma and treat them with alisertib monotherapy.  The patients will be 
monitored for efficacy by either modified RECIST (preferred) or RECIST criteria (if 
modified RECIST cannot be performed) every 6 weeks.  Patients with disease progression 
by either modified RECIST or RECIST criteria will be taken off active treatment from the 
trial and begin long-term follow-up.   
The primary endpoint is 4-month disease-control rate.  Secondary and exploratory endpoints 
include response rates, progression-free survival, overall survival, safety/toxicity profile, and 
collection of archival or fresh tissue and blood for correlative studies (See Section 5.6). 
The alisertib dose employed in this study will be 50 mg po BID (enteric coated tablet ECT) 
for 7 days then a 2 week treatment free period for a 21-day cycle.  BID doses should be 
taken at least over 6 hours apart.    
Enrollment is defined as the first day of alisertib treatment (ie, Day 1 of Cycle 1). 
Evaluable patients are defined as completing at least 1 cycle of alisertib treatment and 
having a documented radiographic response. 
Radiographic assessments will occur every 6 weeks using modified RECIST (preferred) or 
RECIST (if modified RECIST is not feasible).     
3.2 
Selection of Patients 
The total number of patients to be enrolled on this study is 58 subjects for 53 evaluable 
patients. 
3.2.1    Inclusion Criteria 
Each patient must meet all of the following inclusion criteria to be enrolled in the study: 

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 Voluntary written informed consent before performance of any study-related 
procedure not part of normal medical care, with the understanding that consent 
may be withdrawn by the subject at any time without prejudice to future medical 
care. 
 Female subject is either:  
o post-menopausal for at least one year before the screening visit, or 
o  surgically sterilized, or  
o willing to use an acceptable method of birth control (ie, a hormonal 
contraceptive, intra-uterine device, diaphragm with spermicide, 
condom with spermicide, or abstinence) for the duration of the study 
and at least 1 month after the last dose of alisertib. 
 Male subject, even if surgically sterilized (ie, status postvasectomy), agrees to use 
an acceptable barrier method for contraception (condom with a spermicidal 
agent), or completely abstain from heterosexual intercourse during the entire 
study treatment period through 4 months after the last dose of alisertib. 
 Absolute neutrophil count (ANC) > 1500/mm³, platelets > 100,000/mm³, Hgb > 9 
g/dL. Total bilirubin ≤ 1.5 x upper limit of nomal (ULN), SGOT (AST) and 
SGPT (ALT)< 2.5 x ULN. AST and/or ALT may be up to 5X ULN if with known 
liver mets 
 Adequate renal function as defined by:  Calculated creatinine clearance must be ≥ 
30 mL/minute(see Cockcroft-Gault formula in Section 9.5) 
 Eastern Cooperative Oncology Group (ECOG) performance status 0-2 (refer to 
Section 9.4) 
 Pathologic diagnosis of malignant mesothelioma (any primary site is acceptable) 
 Have unresectable malignant mesothelioma (any histology) 
 Received at least one prior pemetrexed-based chemotherapy for unresectable 
disease, unless within 3 months of receiving platinum-pemetrexed therapy for 
neoadjuvant or adjuvant treatment that has been unsuccessful.   

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 Up to 4 prior lines of systemic therapy (biologic or chemotherapy) are allowed.  
Maintenance therapy after 4-6 cycles of front-line chemotherapy is still 
considered 1 line of therapy and is not considered 2 separate therapies.   
  Patients must have measurable disease by modified RECIST or RECIST.  
Examinations for assessment of measurable disease must have been completed 
within 28 days prior to registration.   
 Patient must be >/= 18 years of age 
3.2.2    Exclusion Criteria 
Patients meeting any of the following exclusion criteria are not to be enrolled in the study. 
 Radiation therapy to more than 25% of the bone marrow. Whole pelvic radiation 
is considered to be over 25%. 
 Prior allogeneic bone marrow or organ transplantation 
 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 with significant removel of the 
small intestine, and celiac disease 
 Known history of uncontrolled sleep apnea syndrome and other conditions that 
could result in excessive daytime sleepiness, such as severe chronic obstructive 
pulmonary disease.  Patients who use CPAP or BIPAP at night and have 
controlled sleep apnea syndrome are allowed.  
 Requirement for constant administration of proton pump inhibitor, H2 antagonist, 
or pancreatic enzymes.  Intermittent uses of antacids or H2 antagonists are 
allowed as described in Section 3.4. 
 Systemic infection requiring IV antibiotic therapy within 14 days preceding the 
first dose of study drug, or other severe infection. 
 Myocardial infarction within 6 months prior to enrollment or has New York Heart 
Association (NYHA) Class III or IV heart failure (see Section 9.3), uncontrolled 
angina, severe uncontrolled ventricular arrhythmias, or electrocardiographic 

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evidence of acute ischemia or active conduction system abnormalities. Prior to 
study entry, any ECG abnormality at Screening has to be documented by the 
investigator as not medically relevant. 
 Female subject who is pregnant or breast-feeding.  Confirmation that the subject 
is not pregnant must be established by a negative serum Beta-human chorionic 
gonadotropin (Beta-hCG) pregnancy test result obtained during screening.  
Pregnancy testing is not required for post-menopausal or surgically sterilized 
women. 
 Patient has received other investigational drugs with 14 days before enrollment 
 Serious medical or psychiatric illness likely to interfere with participation in this 
clinical study. 
 Other severe acute or chronic medical or psychiatric condition, including 
uncontrolled diabetes, malabsorption, resection of the pancreas or upper small 
bowel, requirement for pancreatic enzymes, any condition that would modify 
small bowel absorption of oral medications, or laboratory abnormality that may 
increase the risk associated with study participation or investigational product 
administration or may interfere with the interpretation of study results and, in the 
judgment of the investigator, would make the patient inappropriate for enrollment 
in this study. 
 Diagnosed or treated for another malignancy within 3 years of enrollment, with 
the exception of complete resection of basal cell carcinoma or squamous cell 
carcinoma of the skin, an in situ malignancy, or low-risk prostate cancer after 
curative therapy.   
 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 within 14 days prior to the first 
dose of alisertib and during the study. 
 Known history of human immunodeficiency virus (HIV) infection, hepatitis B, or 
hepatitis C.  Testing is not required in the absence of clinical findings or 
suspicion. For guidance in defining active infection for hepatitis B, please refer to 
the WHO guidelines. (World Health Organization, Global Alert and Response 

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(GAR), Hepatitis B.  
who.int/csr/disease/hepatitis/whocdscsrlyo20022/en/index4.html) 
 Prior administration of an Aurora A kinase-targeted agent, including alisertib 
 Receipt of corticosteroids within 7 days prior to the first dose of study treatment, 
unless patient has been taking a continuous dose of no more than 15 mg/day of 
prednisone for at least 1 month prior to first dose of study treatment.  Low dose 
steroid use for the control of nausea and vomiting will be allowed.  Topical 
steroid use is permitted.  Inhaled steroids are permitted. 
 Inability to swallow oral medication or inability or unwillingness to comply with 
the administration requirements related to alisertib. 
 Administration of myeloid growth factors or platelet transfusion within 14 days 
prior to the first dose of study treatment. 
 Persons who are incarcerated at time of enrollment (e.g., prisoners) or likely to 
become incarcerated during the study. 
3.3    Study Treatments 
Alisertib drug product is supplied as the ECT dosage form in 10 mg strength, with dose 
strength expressed as the milligrams of active drug (free acid).  The key formulation 
excipients of the alisertib tablet formulation that aid in the in vivo absorption of the drug are 
the buffer (sodium bicarbonate), the surfactant (sodium lauryl sulfate), and the enteric 
coating.  
3.3.1    Preparation, Handling, and Storage of Drugs 
Alisertib ECT are packaged in a 60-cc high-density polyethylene (HDPE) bottle with a 
rayon coil, induction seal, desiccant packs, and a polypropylene child-resistant cap. 
Alisertib is an anticancer drug, and as with other potentially toxic compounds, caution 
should be exercised when handling MLN8237. 
Drug Administration and Dosage Schedule 
The alisertib dose employed in this study will be 50 mg po BID (enteric coated tablet ECT) 
for 7 days then a 2 week treatment free period for a 21-day cycle.  This phase II dosing was 
established from phase I studies detailed in Section 1.3. 

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Patients will be instructed to take each oral dose of alisertib with 8 ounces (1 cup, 240 mL) 
of water.  For BID dosing, the doses must be taken at least 6 hours apart. 
Patients will be treated until disease progression by modified RECIST or RECIST criteria, 
withdrawal of consent, or unacceptable side effects.  
Alisertib Administration 
Alisertib will be given PO in a dosage of 50 mg BID for 7 Days (Days 1-7) of each 21-day 
treatment cycle.   
Alisertib will be supplied as 10 mg ECT, with the dose strength expressed as milligrams of 
active drug (free acid).  All tablets are to be ingested whole; patients who have difficulty 
swallowing tablets will be excluded from the study.  Antiemetogenic agents may be 
administered at the discretion of the investigator.   
Neutralizing antacids and calcium-containing supplements cannot be taken from 2 hours 
prior to alisertib dosing until up to 2 hours after dosing 
Although not prohibited, the use of benzodiazepines for the prophylaxis or treatment of 
nausea or vomiting is discouraged because of the potential benzodiazepine-like effects of 
alisertib. 
Study drug will be administered only to eligible patients under the supervision of the 
investigator or identified subinvestigator(s). 
Accountability and Mechanism of Drug Destruction 
The principal investigator and/or the designated study personnel is responsible for 
maintaining accurate dispensing records of the study drug.  All study drugs must be 
accounted for, including study drug accidentally or deliberately destroyed.  All discrepancies 
between amounts of study drug dispensed and amounts returned must be documented. 
Accountability records will include dates, quantities, lot numbers, expiration dates and 
patient numbers. Under no circumstances will the site principal investigator allow the 
investigational drug to be used other than as directed by the protocol without prior 
Millennium approval.  If appropriate, drug storage, drug dispensing, and drug accountability 
may be delegated to the pharmacy section of the investigative site.   

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Documentation indicating study drug was destroyed will be sent to Millennium. 
3.3.2    Dose Modification and Delay 
Toxicity will be evaluated according to the National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI CTCAE), Version 4.03, effective 14 June 2010 (16).  These 
criteria are provided in the Study Manual and are available online at 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm 
To manage excessive toxicity, reduction of the total alisertib dose can be done by reducing 
the daily dose administered and/or by interruption of the schedule treatment within a cycle.  
3.3.3    Criteria for Retreatment and Dose Delays 
Treatment with alisertib will be repeated every 21 days.  In order for a new cycle of therapy 
to begin, the patient must meet the following criteria: 
 ANC must be ≥ 1,500/mm3 
 Platelet count must be ≥ 75,000/mm3.   
If the patient fails to meet the above-cited criteria for retreatment, then initiation of the next 
cycle of therapy should be delayed for up to 1 week.  At the end of that week, the patient 
should be re-evaluated to determine whether the criteria for retreatment have been met.  
Should treatment need to be delayed for more than 1 week (ie, a rest period of more than 21 
days) because of incomplete recovery from treatment-related toxicity, the dose of alisertib 
will be reduced (Table 3-1Table 3-1) to 40 mg BID (Dose Level -1) when therapy resumes.  
A second dose reduction to 30 mg BID (Dose Level -2) may occur should treatment need to 
be delayed for more than 1 week because of incomplete recovery from treatment-related 
toxicity on the reduced dosage of 40 mg BID.  Patients who require further dose reductions 
(Dose Level -3) will be taken off active treatment from the study and begin long-term 
follow-up.  Should treatment need to be delayed for more than 2 weeks at any dose, therapy 
with alisertib will be discontinued. 
Table 3-1    
Table of Dose Adjustments 
Dose Level 
Dose 
Schedule 
Cycle Length 
1 
50 mg 
PO BID day 1-7 
21 days 
-1 
 40 mg 
PO BID day 1-7 
21 days 

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-2 
30 mg 
PO BID day 1-7 
21 days 
-3 
Discontinue 
Level 1 is the starting dose. 
 
3.3.4    Dose Modifications for Hematological Toxicity 
If a patient experiences any of the following hematological toxicities during the dosing 
period, dosing will be discontinued for the remainder of that cycle and the dose will be 
decreased 1 level for all subsequent cycles of treatment. 
 Grade 4 neutropenia (ANC  500 cells/mm3) lasting more than 7 consecutive days 
 Grade 4 thrombocytopenia (platelet count < 25,000/µL) lasting more than 
7 consecutive days 
 Platelet count less than 10,000/µL at any time 
 Grade 3 neutropenia with fever or infection, or both, where fever is defined as an 
oral temperature greater than 38.3C 
 Grade 3 thrombocytopenia with clinically significant bleeding 
3.3.5    Dose Modifications for Non-Hematological Toxicities 
If a patient experiences any of the following toxicities during the dosing period, dosing will 
be discontinued for the remainder of that cycle and the dose will be decreased 1 level for all 
subsequent cycles of treatment, and treatment may resume after drug-related toxicities have 
resolved to ≤ Grade 1 or to baseline. 
 Any Grade 3 nonhematological toxicity that is considered by the investigator to be 
related to study drug other than: 
o Grade 3 or greater nausea or emesis, or both, that occurs in the absence 
of optimal antiemetic therapy (5-hydroxytryptamine 3 [5-HT3] 
serotonin receptor antagonist); 
o Grade 3 or greater diarrhea that occurs in the absence of optimal 
supportive therapy with loperamide or a comparable anti-diarrheal; 
o Grade 3 fatigue that lasts less than 1 week 

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 Grade 2 non-hematological toxicities that are considered by the investigator to be 
related to study drug and in the opinion of the investigator require dose reduction. 
In general, study drug treatment should be discontinued if a patient experiences a Grade 4 
toxicity.  If, in the opinion of the investigator and Millennium it is in the patient’s interest to 
continue therapy with alisertib, then after recovery from the toxicity or toxicities in question 
to ≤ Grade 1 or to baseline values, the dose of alisertib should be reduced by at least 1 dose 
level with subsequent cycles of therapy. 
When a dose reduction of alisertib is required, no re-escalation of dose will be permitted.  If 
a patient requires more than 2 dose reductions, therapy with alisertib will be discontinued. 
3.3.6    Packaging and Labeling 
The study drug, provided by Millennium, will be labeled and handled at the investigative 
site as open-label material; packaging labels will fulfill all requirements specified by 
governing regulations.  Alisertib will be supplied as ECT in 10 mg strength.  The 60-cc 
HDPE bottles will have a child-resistant cap and be labeled for take-home use.  Patients will 
receive instructions for home use of alisertib, including the requirement that Alisertib be 
administered as intact tablets. 
3.4    Excluded Concomitant Medications and Procedures 
The following medications and procedures are prohibited during the study: 
 Any antineoplastic therapy other than alisertib  
 Alternative therapy, including palliative radiotherapy, for definitive treatment of 
the patient’s malignancy  
 Any investigational anti-cancer therapy other than alisertib. 
 Requirement for administration of any proton pump inhibitor.  Use of any PPI in 
either continued or intermittent use will be prohibited during the conduct of the 
study and patients must discontinue any use of PPI within five days prior to the first 
dose of alisertib.  Patients may be administered alternative agents to manage gastric 
acidity or reflux (eg, H2 receptor antagonists, antacids) with exceptions described 
below. 

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 Histamine-2 (H2) receptor antagonists are not permitted from the day prior (Day -
1) through to the end of alisertib dosing (e.g., Day 7), except as required for 
premedication for a protocol-specific agent (eg, taxane). 
 Enzyme inducers, such as the enzyme-inducing antiepileptic drugs phenytoin, 
carbamazepine or phenobarbital, or rifampin, rifabutin, rifapentine or St. John's 
wort within 14 days prior to the first dose of alisertib. 
3.5    Permitted Concomitant Medications and Procedures 
Myeloid growth factors to treat patients with neutropenia according to the American Society 
of Clinical Oncology (ASCO) Guidelines.1  When applicable (eg, Phase 1 studies) use of 
myeloid growth factors should be avoided (if medically appropriate) in Cycle 1 until patients 
have developed a DLT or dose-limiting Grade 4 neutropenia.  Antiemetic agents may be 
administered at the discretion of the investigator but are not commonly required as a 
prophylactic agent.  All other manifestations of the patient’s malignancy should be treated at 
the discretion of the investigator. 
Antacids are permitted; however, they should be administered more than 2 hours before or 
2 hours after administration of alisertib.   
Medications with potential CNS effects are not prohibited in this study, but it is 
recommended that their use be minimized to avoid confusion in the interpretation of CNS 
effects should they occur during the course of treatment with alisertib.  Because of alisertib’s 
structural and pharmacological similarity to the benzodiazepines, concomitant therapy with 
benzodiazepines is discouraged but not prohibited. 
In appropriate settings, such as combinations with agents known to produce frequent 
thrombocytopenia, restricted uses of anticoagulants should be considered. 
All other medical conditions should be treated at the discretion of the investigator in 
accordance with local community standards of medical care. 
3.6    Precautions and Restrictions  
Patients are to be instructed to limit the use of alcohol while enrolled in this study.  Patients 
should consume no more than 1 standard unit of alcohol per day during the study and for 
30 days from the last dose of alisertib.  A standard unit of alcohol is defined as a 12 oz beer 
(350 mL), 1.5 oz (45 mL) of 80-proof alcohol, or one 6-oz (175 mL) glass of wine. 

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It is not known what effects alisertib has on human pregnancy or development of the embryo 
or fetus.  Therefore, male patients should avoid impregnating a female partner.   
Male patients, even if surgically sterilized (ie, status post-vasectomy) must agree to one of 
the following:  
Practice effective barrier contraception during the entire study treatment period and through 
four months after the last dose of study drug, or completely abstain from heterosexual 
intercourse. 
3.7    Management of Clinical Events 
3.7.1    Nausea and Vomiting 
Prophylactic antiemetic therapy will not be used in this study unless it becomes clear that 
alisertib causes acute nausea and vomiting.  If prophylactic antiemetic therapy is needed, 
5-HT3 receptor antagonists (without corticosteroids) should be tried first.  Because of the 
potential of benzodiazepines to cause sedation, the use of benzodiazepines for antiemetic 
prophylaxis should be reserved for patients who cannot be satisfactorily managed otherwise. 
Although this study will not initially employ prophylactic antiemetics, there is no 
prohibition against antiemetic use in the management of a patient who develops nausea or 
vomiting, or both. 
3.7.2    Diarrhea 
Antidiarrheal medications will not be used prophylactically; however, patients will be 
instructed to take loperamide, 4 mg, at the occurrence of the first loose stool and then 2 mg 
every 2 hours until they are diarrhea-free for at least 12 hours.  During the night, patients 
may take 4 mg of loperamide every 4 hours.  Fluid intake should be maintained to avoid 
dehydration. 
3.7.3    Central Nervous System Effects 
If a patient experiences excessive sedation believed to be related to alisertib, treatment with 
alisertib should be interrupted.  Patients whose sedation is not considered immediately life-
threatening should be carefully monitored and given appropriate supportive care. 

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3.7.4    Treatment Compliance 
All drug(s) will be administered to eligible patients under the supervision of the investigator 
or identified sub-investigator(s).  The research staff will maintain records of drug receipt (if 
applicable), drug preparation, and dispensing, including the applicable lot numbers, patients’ 
height, body weight, and body surface area (see Section 9.5), and total drug administered in 
milliliters and milligrams.  Any discrepancy between the calculated dose and dose 
administered and the reason for the discrepancy must be recorded in the source documents. 
3.8    Duration of Treatment and Patient Participation 
Once patients register and enroll on this trial, they will be monitored per study guidelines 
while on treatment.   
Patients enrolled and treated on this trial will continue with therapy until:   
1) Unacceptable toxicities requiring removal from study 
2) Disease progression defined by modified RECIST or RECIST 
3) Patient withdraws consent 
4) Treating physician removes patient from the trial for the reasons outlined in Section 
3.9. 
Once patients are taken off active treatment and begin long-term follow-up, they will be 
monitored for both first disease progression and overall survival.   
3.9    Termination of Treatment and/or Study Participation 
Patients will be informed that they have the right to withdraw from the study at any time for 
any reason, without prejudice to their medical care.  The investigator also has the right to 
withdraw patients from the study for any of the following reasons: 
 Intercurrent illness 
 Occurrence of an unacceptable adverse event 
 A treatment cycle delay or alisertib interruption of> 2 weeks because of toxicity 
 Patient request 

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 Protocol violations 
 Non-compliance 
 Administrative reasons 
 Failure to return for follow-up 
 General or specific changes in the patient’s condition unacceptable for further 
treatment in the judgment of the investigator 
 Progressive disease at any time 
At the time of withdrawal, all study procedures outlined for the End of Study visit should be 
completed.  The primary reason for a patient’s withdrawal from the study is to be recorded 
in the source documents. 
3.10    Efficacy and Safety Measurements 
3.10.1    Efficacy Measurements 
Patients will be re-staged every 2 cycles of therapy (6 weeks).  1 cycle = 21 days or 3 weeks. 
Imaging studies will consist of any of the following studies: PET-CT scans, chest CT scans, 
abdominal-pelvic CT scans. Modified RECIST (preferred) or RECIST (if modified 
RECIST cannot be used) measurements will be performed after every 2 cycles of therapy.  
The radiologist or the PI will review and determine response based on the RECIST. 
Examples of these measurements are described in Tsao et al.[1] 
3.10.2    Safety Measurements 
Patients will be evaluated with a history and physical exam during each clinic visit.  
Baseline laboratory values will be obtained during each clinic visit.  All toxicities reported 
will be recorded by the research RN and graded using the National Cancer Institute 
Common Terminology Criteria for Adverse Events (NCI CTCAE), Version 4.03, effective 
14 June 2010 (16).  These criteria are provided in the Study Manual and are available online 
at http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 

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3.11    Study Drug Administration 
Alisertib will be administered PO at 50 mg BID for 7 days in each treatment cycle, followed 
by a 14-day, treatment-free period.   
Patients will be instructed to take each oral dose of alisertib with 8 ounces (1 cup, 240 mL) 
of water.  For BID dosing, the doses must be taken at least 6 hours apart. 
Alisertib will be supplied as 10 mg ECT, with the dose strength expressed as milligrams of 
active drug (free acid); higher strengths may be supplied depending on the observed MTD.  
All tablets are to be ingested whole; patients who have difficulty swallowing tablets will be 
excluded from the study.  Antiemetogenic agents may be administered at the discretion of 
the investigator.  Although not prohibited, the use of benzodiazepines for the prophylaxis or 
treatment of nausea or vomiting is discouraged because of the potential benzodiazepine-like 
effects of alisertib. 
Study drug will be administered only to eligible patients under the supervision of the 
investigator or identified subinvestigator(s). 
3.12    Description of Investigational Agents 
Alisertib drug product is supplied as the ECT dosage form in 10 mg strengths with dose 
strength expressed as the milligrams of active drug (free acid); other strengths may be 
supplied based on the observed MTD.  The key formulation excipients of the alisertib tablet 
formulation that aid in the in vivo absorption of the drug are the buffer (sodium 
bicarbonate), the surfactant (sodium lauryl sulfate), and the enteric coating. 
3.13    Preparation, Reconstitution, and Dispensation 
Alisertib ECT are packaged (10 tablets to a bottle) in a 60-cc high-density polyethylene 
(HDPE) bottle with a child-resistant cap. 
Alisertib is an anticancer drug, and as with other potentially toxic compounds, caution 
should be exercised when handling alisertib.  It is recommended that gloves and protective 
garments be worn during preparation. 

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3.14    Packaging and Labeling 
The packaged and labeled study drug, alisertib ECT, will be provided by Millennium and 
will be handled at the investigative site as open-label material.  The labels on the study drug 
will fulfill all requirements specified by governing regulations.  Ten alisertib ECT are 
packaged into each 60-cc HDPE bottle.  Alisertib will be supplied as ECT in 10 mg or 
50 mg strengths.  The bottles will have a child-resistant cap and be labeled for take-home 
use.  Patients will receive instructions for home use of alisertib, including the requirement 
that alisertib be administered as intact tablets. 
As required by local regulations, any modifications to the plan for drug supply or storage 
will be communicated to the investigator and detailed in the Study Manual. 
3.15    Storage, Handling, and Accountability 
Tablets should remain in the bottle provided until use.  The container should be stored at the 
investigative site at controlled room temperature (20-25°C; 68-77°F; excursions are 
permitted from 15-30C; 59-86F) and used before the retest expiry date provided by 
Millennium.  Containers should be kept closed during storage. 
Because alisertib is an investigational agent, it should be handled with due care. In case of 
contact with broken tablets, raising dust should be avoided during the cleanup operation. 
The product may be harmful by inhalation, ingestion, or skin absorption.  Gloves and 
protective clothing should be worn during preparation and the cleanup operation.  The area 
should be ventilated and the spill site washed after material pick-up is complete.  The spilled 
material should be disposed of as hazardous medical waste in compliance with federal, state, 
and local regulations. 
In case of contact with the powder (eg, from a broken tablet), skin should be washed 
immediately with soap and copious amounts of water for at least 15 minutes. 
In case of contact with the eyes, copious amounts of water should be used to flush the eyes 
for at least 15 minutes.  Medical personnel should be notified. 
Patients are to be instructed on proper storage, accountability, and administration of 
alisertib, including that alisertib is to be taken as intact tablets. 

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4.    ADVERSE EVENTS 
4.1.1    Adverse Event Definition 
Adverse event (AE) means any untoward medical occurrence in a patient or subject 
administered a pharmaceutical 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. 
For this protocol 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. 
Adverse events are documented in the Case Report Forms (CRF) and CORe is the database 
for AE collection. The PI and the designees will be responsible for assigning attribution to 
study drug, and how this will be documented. 
4.1.2    Serious Adverse Event Definition 
Serious adverse event (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). 
 Requires inpatient hospitalization or prolongation of an existing hospitalization 
(see clarification below on planned hospitalizations in Section Error! Reference 
source not found.). 
 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). 

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 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 (eg, prion protein transmitting 
Transmissible Spongiform Encephalopathy), pathogenic or nonpathogenic, is 
considered 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 (eg, prion protein transmitting Transmissible Spongiform Encephalopathy), 
whether pathogenic or non-pathogenic, is considered an infectious agent.   
 Clarification should be made between a serious AE (SAE) and an AE that is 
considered severe in intensity (Grade 3 or 4), because the terms serious and severe 
are NOT synonymous.  The general term severe is often used to describe the 
intensity (severity) of a specific event; the event itself, however, may be of relatively 
minor medical significance (such as a Grade 3 headache).  This is NOT the same as 
serious, which is based on patient/event outcome or action criteria described above, 
and is usually associated with events that pose a threat to a patient’s life or ability to 
function.  A severe AE (Grade 3 or 4) does not necessarily need to be considered 
serious.  For example, a white blood cell count of 1000/mm3 to less than 2000 is 
considered Grade 3 (severe) but may not be considered serious.  Seriousness (not 
intensity) serves as a guide for defining regulatory reporting obligations. 
4.1.3    Serious Adverse Event Reporting (SAE) Reporting 
An adverse event or suspected adverse reaction is considered “serious” if, in the view of 
either the investigator or the sponsor, it results in any of the following outcomes: 
 
Death 

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 
A life-threatening adverse drug experience – any adverse experience that places the 
patient, in the view of the initial reporter, at immediate risk of death from the adverse 
experience as it occurred. It does not include an adverse experience that, had it occurred in a 
more severe form, might have caused death. 
 
Inpatient hospitalization or prolongation of existing hospitalization 
 
A persistent or significant incapacity or substantial disruption of the ability to conduct 
normal life functions. 
 
A congenital anomaly/birth defect. 
 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered a serious adverse drug experience when, based upon 
appropriate medical judgment, they may jeopardize the patient or subject and may require 
medical or surgical intervention to prevent one of the outcomes listed in this definition. 
Examples of such medical events include allergic bronchospasm requiring intensive 
treatment in an emergency room or at home, blood dyscrasias or convulsions that do not 
result in inpatient hospitalization, or the development of drug dependency or drug abuse (21 
CFR 312.32). 
 
 
Important medical events as defined above, may also be considered serious adverse 
events. Any important medical event can and should be reported as an SAE if deemed 
appropriate by the Principal Investigator or the IND Sponsor, IND Office. 
 
All events occurring during the conduct of a protocol and meeting the definition of a 
SAE must be reported to the IRB in accordance with the timeframes and procedures outlined 
in “The University of Texas M. D. Anderson Cancer Center Institutional Review Board 
Policy for Investigators on Reporting Serious Unanticipated Adverse Events for Drugs and 
Devices”.  Unless stated otherwise in the protocol, all SAEs, expected or unexpected, must be 
reported to the IND Office, regardless of attribution (within 5 working days of knowledge of 
the event). 
 
All life-threatening or fatal events, that are unexpected, and related to the study 
drug, must have a written report submitted within 24 hours (next working day) of knowledge 
of the event to the Safety Project Manager in the IND Office.   
 
Unless otherwise noted, the electronic SAE application (eSAE) will be utilized for 
safety reporting to the IND Office and MDACC IRB.  
 
Serious adverse events will be captured from the time of the first protocol-specific 
intervention, until 30 days after the last dose of drug, unless the participant withdraws 
consent. Serious adverse events must be followed until clinical recovery is complete and 
laboratory tests have returned to baseline, progression of the event has stabilized, or there has 
been acceptable resolution of the event. 
 
Additionally, any serious adverse events that occur after the 30 day time period that 
are related to the study treatment must be reported to the IND Office. This may include the 
development of a secondary malignancy. 
 
Reporting to FDA: 
 
Serious adverse events will be forwarded to FDA by the IND Sponsor (Safety Project 
Manager IND Office) according to 21 CFR 312.32. 

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It is the responsibility of the PI and the research team to ensure serious adverse events 
are reported according to the Code of Federal Regulations, Good Clinical Practices, 
the protocol guidelines, the sponsor’s guidelines, and Institutional Review Board 
policy. 
 
4.2    Communication between Investigator and Millennium 
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 dost of alisertib.  Any 
SAE that occurs at any time after completion of alisertib treatment or after the designated 
follow-up period that the 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 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. Anne Tsao, , is 
responsible for reporting serious adverse events (SAEs) to any regulatory agency and to the 
investigator’s EC or IRB.   Regardless of expectedness or causality, all SAEs must also be 
reported to Millennium Pharmacovigilance or designee as soon as possible, but no later than 
4 calendar days of the investigator’s observation or awareness of the event.  See below for 
contact information for the reporting of SAEs to Millennium Pharmacovigilance.   
The -investigator should fax the SAE Form within four calendar days after becoming aware 
of the event.  A sample of an SAE Form will be provided.  Follow-up information on the 
SAE may be requested by Millennium.  The SAE report must include event term(s), serious 
criteria, and the investigator’s or sub-investigator’s determination of both the intensity of the 
event(s) and the relationship of the event(s) to study drug administration.  Intensity for each 
SAE, including any lab abnormalities, will be determined by using the NCI CTCAE version 
used at your institution, as a guideline, whenever possible.  The criteria are available online 
at http://ctep.cancer.gov/reporting/ctc.html. 

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In the event that this is a multisite study, the -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 so that the principal 
investigator can meet his/her foregoing reporting obligations to the required regulatory 
agencies and to Millennium Pharmacovigilance, unless otherwise agreed between the 
principal 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)? 
The principal investigator must also provide Millennium Pharmacovigilance with a copy of 
all communications with applicable regulatory authorities related to the study or study 
drug(s), including, but not limited to, telephone conversation logs, as soon as possible but no 
later than 4 calendar days of such communication. 
SAE and Pregnancy Reporting Contact Information 
Millennium Pharmacovigilance 
SAE and Pregnancy Reporting Contact Information: 
 
Millennium Pharmacovigilance or Designee 
SAE and Pregnancy Reporting Contact Information 
FAX Number 1-800-963-6290 
Email: TakedaOncoCases@cognizant.com 
 
 
4.3    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 must permanently discontinue 
study drug(s).  The investigator must fax a completed Pregnancy Form to the Millennium 
Department of Pharmacovigilance or designee (or designee; see Section 4.2 for contact 
information) immediately.  The pregnancy must be followed for the final pregnancy 
outcome (ie, delivery, still birth, miscarriage) and Millennium Pharmacovigilance will 
request this information from the investigator. 
If a female partner of a male patient becomes pregnant during the male patient’s 
participation in this study, this must be reported to Millennium Pharmacovigilance (or 

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designee) immediately (see Section 4.2 for contact information).  Every effort should be 
made to follow the pregnancy for the final pregnancy outcome. 
4.4 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 event.  Whenever possible, the associated product 
should be maintained in accordance with the label instructions pending further guidance 
from a Millennium Quality representative. 
For Product Complaints, 
call MedComm Solutions at 
877-674-3784 (877 MPI DRUG)  
(US and International) 
 
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. 
 

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5.    STATISTICAL PROCEDURES 
5.1    Study Design and Overview of Primary and Secondary Endpoints 
The primary objective of this study is to: 
 Assess 4-month disease control rate (DCR) in pre-treated patients with 
unresectable MPM treated with alisertib 
The secondary objectives of this study are to: 
 To assess the response rate (confirmed and unconfirmed complete + partial 
responses)  
 To assess the progression-free survival.  
 To assess overall survival. 
 To evaluate the side effects and toxicities associated with this treatment regimen. 
 To collect archival tissue, blood, pleural effusion and plasma for correlative 
studies. 
The primary endpoint is the disease control rate at 4 months in patients with unresectable 
malignant pleural mesothelioma (MPM) treated with alisertib. The trial will be conducted by 
the Simon’s minimax two-stage design and the disease control rate at 4 months will be 
estimated accordingly (Simon, 1989) 
It is assumed that the new regimen will have a target disease control rate of 50% at 4 
months. A disease control rate of 30% or lower is considered a failure and the new regimen 
will be rejected under this circumstance.  When the probability of accepting a “bad” regimen 
(i.e. disease control rate<=30%) is 0.05 and the probability of rejecting a “good” regimen 
(i.e. disease control rate >=50%) is 0.10, Simon’s minimax design requires to enter 24 
patients in the first stage. If 7 or less patients are free of disease progression to the treatment 
at 4 months, the trial will be stopped and the regimen will be declared as ineffective. If there 
are 8 or more patients are alive and progression-free at 4 months, 29 more patients will be 
entered in the study to reach a total of 53 patients. By the end of the study, the new regimen 
will be rejected if disease control rate is less than or equal to 21/53 and will be accepted 
otherwise.  The operating characteristics of the trial are given as follows. When the true 
disease control rate is 0.30 the probability of stopping the trial early is 57%. On the other 

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hand, if the true disease control rate is 0.50, the probability to stop the trial early is 3%.  The 
expected sample sizes are 36.6 and 52.1 when the true response rates are 0.3 and 0.5, 
respectively.  This design has the minimax property of minimizing the maximum sample 
size under null hypothesis. If the number of disease control required for moving the trial to 
the second stage has not been achieved, the patient enrollment will be halted until enough 
responses observed. 
Descriptive statistics including mean, standard deviation, median, and range will be 
provided for continuous variables such as age. Frequency tables will be used to summarize 
categorical variables such as gender, and response. The standard error and confidence 
interval on estimating the disease control rate will be provided. The distribution of time-to-
event endpoints, such as time to progression and overall survival, will be estimated using the 
method of Kaplan and Meier.  Comparison of time-to-event endpoints by important patient 
characteristics will be made using the log-rank test.  Cox proportional hazard regression will 
be employed for multi-covariate analysis on time-to-event outcomes when appropriate. 
5.2    Sample Size Estimation/Accrual Rate 
It is anticipated to accrue 1-2 patients per month.   
Sample size = 53 evaluable patients, 58 maximum patients (estimating 5 inevaluable 
patients) 
5.3    Randomization and Stratification Factors 
None. 
5.4    Evaluation of Efficacy 
Patients will be re-staged every 2 cycles of therapy.  1 cycle = 21 days or 3 weeks. Imaging 
studies will consist of any of the following studies: PET-CT scans, chest CT scans, 
abdominal-pelvic CT scans. Modified RECIST (preferred) or RECIST (if modified 
RECIST cannot be used) measurements will be performed after every 2 cycles of therapy. 
The radiologist or the PI will review and determine response based on the RECIST and the 
data will be documented in the Case Report Form (CRF).  Examples of these measurements 
are described in Tsao et al.[1] 

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The primary objective of this study is to assess the efficacy of alisertib in pretreated patients 
with unresectable malignant mesothelioma (pleural or peritoneal).  The primary endpoint is 
the disease control rate at 4 months in patients with unresectable malignant pleural 
mesothelioma (MPM) treated with alisertib. The trial will be conducted by the Simon’s 
minimax two-stage design and the disease control rate at 4 months will be estimated 
accordingly (Simon, 1989).  
Standard RECIST measurement definitions will be used.   
Complete Response (CR): Complete disappearance of all measurable and non-measurable 
disease.  No new lesions.   
Partial Response (PR): Greater than or equal to 30% decrease under baseline of the sum of 
longest diameters of all target measurable lesions.  No unequivocal progression or non-
measurable disease.  No new lesions.   
Stable disease (SD): Does not qualify for CR or PR or Progression.   
Progression (PD): One or more of the following must occur: 20% increase in the sum of 
longest diameters of target measurable lesions over smallest sum observed (over baseline if 
no decrease during therapy).  Unequivocal progression of non-measurable disease in the 
opinion of the treating physician (an explanation must be provided).  Appearance of any new 
lesion/site. Death due to disease without prior documentation of progression and without 
symptomatic deterioration.  
5.5    Evaluation of Safety 
Patients will be evaluated with a history and physical exam during each clinic visit.  
Baseline laboratory values will be obtained during each clinic visit.  All toxicities reported 
will be recorded by the research RN and graded using the National Cancer Institute 
Common Terminology Criteria for Adverse Events (NCI CTCAE), Version 4.03, effective 
14 June 2010 (16).  These criteria are provided in the Study Manual and are available online 
at http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 
5.6    Correlative Studies   
Blood Specimens will be collected at baseline (pretreatment), cycle 3 – day 1 and at 
progression and banked at MD Anderson Cancer for subsequent analysis.  At each time 

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point, blood will be collected into three (3) x 8 mL EDTA Vaccutainer top tubes separated; 
plasma and buffy coat will be collected and stored at -70 until analysis. 
Pleural Effusion Fluid: in cases when pleural effusion fluid is available, a 10 mL aliquot of 
the pleural effusion fluid will be collected in a sterile container, aliqouted and stored at -70C 
until analysis. 
Patients must have either archived baseline tumor specimens available and adequate for 
biomarker analysis or must undergo a tumor tissue biopsy.  Tumor specimens will be 
batched until the end of the clinical trial and subsequently evaluated for aurora kinase 
pathway molecules by immunohistochemistry, fluorescent in situ hybridization (FISH) for c-
myc gene amplification, and next-generation sequencing. Correlation of biomarkers to 
patient demographics and clinical outcome will be analyzed by the below statistical analysis.  
Descriptive statistics including mean, standard deviation, median, and range will be 
provided for continuous variables such as age. Frequency tables will be used to summarize 
categorical variables such as gender, and response. The standard error and confidence 
interval on estimating the disease control rate will be provided. The distribution of time-to-
event endpoints, such as time to progression and overall survival, will be estimated using the 
method of Kaplan and Meier.  Comparison of time-to-event endpoints by important patient 
characteristics will be made using the log-rank test.  Cox proportional hazard regression will 
be employed for multi-covariate analysis on time-to-event outcomes when appropriate.  
5.6.1. Tissue Biomarker Analysis 
A total of 10 unstained slides or a tumor block will be requested from each patient.  
Archived baseline tissue blocks or unstained slides will be accepted. If no baseline tissue is 
available, then patients will be asked to undergo a tumor tissue biopsy.  The tumor tissue 
will be subjected to immunohistochemistry analysis of aurora kinase pathway biomarkers 
and fluorescent in situ hybridization analysis of the copy numbers of the c-myc gene.  
5.6.1.1. Immunohistochemistry  
Standard immunohistochemistry (IHC) will be conducted on tumor tissue slides for aurora 
kinase pathway biomarkers.  The precise antibodies are to be determined.  A general 
methodology for standard IHC is described below.   

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We will perform standard IHC studies of aurora kinase pathway biomarkers and evaluate 
them in subcellular locations (cytoplasmic, stromal, membrane, and nuclear.   The histology 
sections will be incubated with primary antibodies TBD for a predescribed amount of time 
at room temperature. Tissue sections will then be incubated with the secondary antibody 
(TBD) for 30 min, after which diaminobenzidine chromogen was applied for 5 min.  Tumor 
malignant cells and stroma will be evaluated using the same methodology for protein 
expressions. Briefly, for each marker, two experienced thoracic pathologists (I.I.W. and J.F.) 
will examine both the intensity and extent of immunostaining by light microscopy using a 
×20 magnification objective. Immunoreactivity of all antibodies will be detected in the 
cytoplasm of malignant cell and stroma fibroblast, and in the cytoplasm and nucleus.  
Cytoplasmic or nuclear expressions will be quantified using a four-value intensity score (0, 
none; 1+, weak; 2+, moderate; and 3+, strong) and the percentage (0-100%) of the extent of 
reactivity. A final expression score was obtained by multiplying the intensity and reactivity 
extension values (range, 0-300).  
5.6.1.2. c-myc copy number analysis rationale for study 
We[18] have previously evaluated potential therapeutic targets for malignant pleural 
mesothelioma (MPM) and one of the most common chromosomal amplification sites in 
cancer tissues is the 8q24 region which contains the genes C-MYC and PVT1 [19-21]. C-
MYC encodes a transcription factor that regulates the expression of multiple genes involved 
in cellular responses such as growth, proliferation, apoptosis, and differentiation [22, 23]. 
Deregulated amplification and expression of the MYC locus occurs in ~30% of human 
cancers, including colon, prostate and breast carcinomas, and has been associated with poor 
prognosis [19, 24, 25]. PVT1 is a candidate oncogene located adjacent to the MYC locus on 
chromosomal region 8q24 [25-27]. PVT1 has been shown to act as a non-coding RNA with 
many alternatively spliced isoforms  [20]. The PVT1 locus has recently been found to 
contain a cluster of at least six microRNAs (miRNAs) (miR-1204, -1205, -1206, -1207-3p, -
1207-5p, and -1208) that span the PVT1 region, adding further complexity to the locus [20]. 
PVT1 copy number gains (CNGs) and PVT1 overexpression both have been implicated in 
the pathophysiology of many tumors, including breast and ovarian cancers and acute 
myeloid leukemia [26, 28]. Additionally, PVT1 alteration has been shown to contribute to 
tumor survival and chemoresistance [28, 29].  
We sought to elucidate these roles and the specific mechanisms of action of C-MYC and 
PVT1 involved in the pathogenesis of malignant pleural mesothelioma (MPM) by 
characterizing the molecular abnormalities found in the 8q24 locus in malignant pleural 
mesothelioma (MPM) cell lines and in specimens from surgically resected malignant pleural 
mesotheliomas. The miRNA (miR-1204, -1205, 1206, -1207 3p, 1207-5p, and -1208) 
expression in malignant pleural mesothelioma (MPM) cell lines was evaluated. We also 
determined the biological impact of siRNA-mediated C-MYC and PVT1 abrogation on 
malignant pleural mesothelioma (MPM) cellular processes such as apoptosis, cell 
proliferation, and response to cisplatin and then determined the effect of C-MYC, PVT1, and 
miR-1204 knockdown on the expression levels of apoptosis related genes.  Finally, we 
studied C-MYC and PVT1 copy number and gene expression in malignant pleural 
mesothelioma (MPM) tumor specimens.[18] 

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Our copy number analysis revealed copy number gains (CNGs) in chromosomal region 
8q24 in three of five malignant pleural mesothelioma (MPM) cell lines. MicroRNA analysis 
showed high miR-1204 expression in MSTO-211H cell lines with ≥4 copies of PVT1. 
Knockdown by siRNA showed increased PARP-C levels in MSTO-211H transfected with 
siPVT1 but not in cells transfected with siC-MYC. C-MYC and PVT1 knockdown reduced 
cell proliferation and increased sensitivity to cisplatin. Analysis of the expression of 
apoptosis-related genes in the MSTO-211H cell line suggested that C-MYC maintains a 
balance between pro-apoptotic and anti-apoptotic gene expression, whereas PVT1 and to a 
lesser extent miR-1204, upregulate pro-apoptotic genes and downregulate anti-apoptotic 
genes. FISH analysis of malignant pleural mesothelioma (MPM) tumor specimens showed a 
high frequency of both CNGs (11/75) and trisomy (three copies; 11/75) for the C-MYC 
locus.[18]  
We additionally determined C-MYC and PVT1 mRNA expression levels in a subset of 55 
malignant pleural mesothelioma (MPM) tumor specimens paired with 41 normal tissues 
from our database using Affymetrix U133 plus 2.0 chips. We found significant differences 
in C-MYC and PVT1 gene expression between the normal tissues and the tumor samples 
(Fig. 3F and 3G; p < 0.05).  
Our preclinical results suggest that C-MYC and PVT1 amplification promotes a malignant 
phenotype of malignant pleural mesothelioma (MPM), with C-MYC amplification 
stimulating cell proliferation and PVT1 both stimulating proliferation and inhibiting 
apoptosis. 
This is significantly relevant to this protocol as c-myc expression and pathway upregulation 
has been identified as a potential biomarker in aurora kinase inhibition in other tumor types 
(personal communication Millennium).   
5.6.1.2.1. Methodology c-myc copy number analysis measured by quatitative PCR and 
fluorescence in situ hybridization (FISH) 
Isolation of DNA and Copy Number Profiling 
DNA was extracted from cell lines using DNAzol Reagent (Life Technologies, Grand 
Island, NY) and whole-genome single nucleotide polymorphism (SNP) array profiling can 
be performed using Affymetrix SNP 6.0 chips (Agilent Technologies, Santa Clara, CA). 
Copy number gains (CNGs) were identified using the SNP-Fast Adaptive States 
Segmentation Technique 2  algorithm in Nexus 5.1 software (BioDiscovery, Hawthorne, 
CA)  with the significance threshold for segmentation setting at p < 5 × 10-7. CNGs were 
defined with log2 ratio values of 0.2, and two or more than two CNGs were defined by log2 
ratio values of 0.7.  
 
Copy Number Analysis 
We used fluorescence in situ hybridization (FISH) and real-time quantitative PCR (q-PCR) 
to quantify 8q24 CNGs in malignant pleural mesothelioma (MPM) tumor specimens. We 
used directly labeled fluorescent chromosomal centromeric probes (CEP 8, SpectrumGreen) 
for chromosome 8 and locus-specific probes (LSI) for regions 8q24.12-q13 (C-MYC 
Spectrum Orange) (Vysis, Abbott Laboratories, Chicago, IL). Fluorescence in situ 

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hybridization (FISH) was performed according to the manufacturer’s instructions. Copy 
number analysis was performed in 50 nuclei per tumor in at least four areas. Copy number 
alteration was defined as the presence of more than two gene copies per cell on average of 
the 50 cells.  Trisomy was defined as the presence of three copy number alterations and 
CNG was defined the presence of at least four copies. To enrich for malignant cell content 
for q-PCR analysis, tumor tissues were manually microdissected for subsequent DNA 
extraction from FFPE tissue sections. Tumor DNA was extracted using the Pico Pure DNA 
Extraction Kit (Arcturus, Life Technologies, Grand Island, NY) according to the 
manufacturer's instructions. DNA samples with proportions of microdissected tumor cell 
greater than 70% were qualified for qPCR analysis. MYC and PVT1 gene copy numbers 
were examined by q-PCR using the ABI 7300 real time PCR system (Applied Biosystems, 
Grand Island, NY). A gene copy number ≥4 was considered as CNG [30]. 
 
5.7    Interim Analysis   
Interim analysis will be conducted as per the Simon’s 2-stage design described in Section 
5.1. 
6.    ADMINISTRATIVE REQUIREMENTS 
6.1    Good Clinical Practice 
The study will be conducted in accordance with the International Conference on 
Harmonisation (ICH) for Good Clinical Practice (GCP) and the appropriate regulatory 
requirement(s).  The investigator will be thoroughly familiar with the appropriate use of the 
drug as described in the protocol and Investigator’s Brochure.  Essential clinical documents 
will be maintained to demonstrate the validity of the study and the integrity of the data 
collected.  Master files should be established at the beginning of the study, maintained for 
the duration of the study and retained according to the appropriate regulations.   
6.2    Ethical Considerations 
The study will be conducted in accordance with ethical principles founded in the Declaration 
of Helsinki (see Section 9.1).  The IRB/IEC will review all appropriate study documentation 
in order to safeguard the rights, safety and well-being of the patients.  The study will only be 
conducted at sites where IRB/IEC approval has been obtained.  The protocol, Investigator’s 
Brochure, informed consent, advertisements (if applicable), written information given to the 
patients (including diary cards), safety updates, annual progress reports, and any revisions to 
these documents will be provided to the IRB/IEC by the investigator.  Millennium requests 
that informed consent documents be reviewed by Millennium or designee prior to IRB/IEC 
submission.   

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6.3    Patient Information and Informed Consent 
After the study has been fully explained, written informed consent will be obtained from 
either the patient or his/her guardian or legal representative prior to study participation.  The 
method of obtaining and documenting the informed consent and the contents of the consent 
will comply with ICH-GCP and all applicable regulatory requirement(s). 
6.4    Patient Confidentiality 
For the purpose of this study at MD Anderson Cancer Center, all patients will be registered 
in the Clinical Oncology Research System (CORE). All study related data will be captured 
in the Protocol Data Management System (PDMS).In order to maintain patient privacy, all 
data capture records, drug accountability records, study reports and communications will 
identify the patient by initials and the assigned patient number.  The investigator will grant 
monitor(s) and auditor(s) from Millennium or its designees and regulatory authority(ies) 
access to the patient’s original medical records for verification of data gathered on the data 
capture records and to audit the data collection process.  The patient’s confidentiality will be 
maintained and will not be made publicly available to the extent permitted by the applicable 
laws and regulations. 
6.5    Protocol Compliance 
The investigator will conduct the study in compliance with the protocol given 
approval/favorable opinion by the IRB/IEC and the appropriate regulatory authority(ies).  
Changes to the protocol will require approval from Millennium and written IRB/IEC 
approval/favorable opinion prior to implementation, except when the modification is needed 
to eliminate an immediate hazard(s) to patients.  The IRB/IEC may provide, if applicable 
regulatory authority(ies) permit, expedited review and approval/favorable opinion for minor 
change(s) in ongoing studies that have the approval /favorable opinion of the IRB/IEC.  The 
investigator will submit all protocol modifications to Millennium and the regulatory 
authority(ies) in accordance with the governing regulations.  
Any departures from the protocol must be fully documented in the source documents.   
6.6    On-site Audits 
Regulatory authorities, the IEC/IRB and/or Millennium’s clinical quality assurance group 
may request access to all source documents, data capture records, and other study 

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documentation for on-site audit or inspection.  Direct access to these documents must be 
guaranteed by the investigator, who must provide support at all times for these activities. 
6.7    Drug Accountability 
Accountability for alisertib at all study sites is the responsibility of the Principal 
Investigator.  The investigator will ensure that the drug is used only in accordance with this 
protocol.  Drug accountability records indicating the drug’s delivery date to the site (if 
applicable), inventory at the site (if applicable), use by each patient, and return to 
Millennium or disposal of the drug (if applicable and if approved by Millennium) will be 
maintained by the clinical site.  Accountability records will include dates, quantities, lot 
numbers, expiration dates (if applicable), and patient numbers.   
6.8    Premature Closure of the Study 
This study may be prematurely terminated, if in the opinion of the investigator or 
Millennium, there is sufficient reasonable cause.  Written notification documenting the 
reason for study termination will be provided to the investigator or Millennium by the 
terminating party.   
Circumstances that may warrant termination include, but are not limited to: 
 Determination of unexpected, significant, or unacceptable risk to patients 
 Failure to enter patients at an acceptable rate 
 Insufficient adherence to protocol requirements 
 Insufficient complete and/or evaluable data 
 Plans to modify, suspend or discontinue the development of the drug 
Should the study be closed prematurely, all study materials must be returned to Millennium. 
6.9    Record Retention 
The investigator will maintain all study records according to ICH-GCP and applicable 
regulatory requirement(s).   

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7.    
USE OF INFORMATION 
All information regarding alisertib supplied by Millennium to the investigator is privileged 
and confidential information.  The investigator may use this information to accomplish the 
study, but may not use it for other purposes without consent from Millennium.  In 
accordance with the agreement between Millennium and the principal investigator complete 
study data must be provided to Millennium.  Upon completion of the clinical study and 
evaluation of results by Millennium, the hospital or institution and/or investigator may 
publish or disclose the clinical trial results pursuant to the terms contained in the applicable 
Clinical Trial Agreement. 

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8.    REFERENCES 
 
 
 
1. 
Tsao, A.S., et al., A practical guide of the Southwest Oncology Group to measure malignant 
pleural mesothelioma tumors by RECIST and modified RECIST criteria. J Thorac Oncol, 
2011. 6(3): p. 598-601. 
2. 
Simon, R., Optimal two-stage designs for phase II clinical trials. Control Clin Trials, 1989. 
10(1): p. 1-10. 
3. 
Baas, P., Chemotherapy for malignant mesothelioma: from doxorubicin to vinorelbine. 
Semin Oncol, 2002. 29(1): p. 62-9. 
4. 
Vogelzang, N.J., et al., Phase III study of pemetrexed in combination with cisplatin versus 
cisplatin alone in patients with malignant pleural mesothelioma. J Clin Oncol, 2003. 21(14): 
p. 2636-44. 
5. 
Nigg, E.A., Mitotic kinases as regulators of cell division and its checkpoints. Nature 
Reviews Molecular Cell Biology, 2001. 2(1): p. 21-32. 
6. 
Bischoff, J.R., et al., A homologue of Drosophila aurora kinase is oncogenic and amplified 
in human colorectal cancers. EMBO Journal, 1998. 17(11): p. 3052-65. 
7. 
Camacho, E., et al., Analysis of Aurora-A and hMPS1 mitotic kinases in mantle cell 
lymphoma. International Journal of Cancer, 2006. 118(2): p. 357-63. 
8. 
Ikezoe, T., et al., A novel treatment strategy targeting Aurora kinases in acute myelogenous 
leukemia. Molecular Cancer Therapeutics, 2007. 6(6): p. 1851-7. 
9. 
Chng, W.J., et al., Clinical implication of centrosome amplification in plasma cell neoplasm. 
Blood, 2006. 107(9): p. 3669-75. 
10. 
Katayama, H., W.R. Brinkley, and S. Sen, The Aurora kinases: role in cell transformation 
and tumorigenesis. Cancer & Metastasis Reviews, 2003. 22(4): p. 451-64. 
11. 
Marumoto, T., et al., Aurora-A kinase maintains the fidelity of early and late mitotic events 
in HeLa cells. Journal of Biological Chemistry, 2003. 278(51): p. 51786-95. 
12. 
Glover, D.M., et al., Mutations in aurora prevent centrosome separation leading to the 
formation of monopolar spindles. Cell, 1995. 81(1): p. 95-105. 
13. 
Katayama, H., et al., Interaction and feedback regulation between STK15/BTAK/Aurora-A 
kinase and protein phosphatase 1 through mitotic cell division cycle. Journal of Biological 
Chemistry, 2001. 276(49): p. 46219-24. 
14. 
Hoar, K., et al., MLN8054, a small-molecule inhibitor of Aurora A, causes spindle pole and 
chromosome congression defects leading to aneuploidy. Molecular & Cellular Biology, 
2007. 27(12): p. 4513-25. 
15. 
Lopez-Rios, F., et al., Global gene expression profiling of pleural mesotheliomas: 
overexpression of aurora kinases and P16/CDKN2A deletion as prognostic factors and 
critical evaluation of microarray-based prognostic prediction. Cancer Res, 2006. 66(6): p. 
2970-9. 

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16. 
Romagnoli, S., et al., Identification of potential therapeutic targets in malignant 
mesothelioma using cell-cycle gene expression analysis. Am J Pathol, 2009. 174(3): p. 762-
70. 
17. 
Crispi, S., et al., Antiproliferative effect of Aurora kinase targeting in mesothelioma. Lung 
Cancer, 2010. 70(3): p. 271-9. 
18. 
Riquelme, E., et al., Frequent co-amplification and co-operation between C-MYC and PVT1 
oncogenes promote malignant pleural mesothelioma 2014. 
19. 
Adhikary, S., et al., Miz1 is required for early embryonic development during gastrulation. 
Mol Cell Biol, 2003. 23(21): p. 7648-57. 
20. 
Beck-Engeser, G.B., et al., Pvt1-encoded microRNAs in oncogenesis. Retrovirology, 2008. 
5: p. 4. 
21. 
Beroukhim, R., et al., The landscape of somatic copy-number alteration across human 
cancers. Nature, 2010. 463(7283): p. 899-905. 
22. 
Dang, C.V., et al., The c-Myc target gene network. Semin Cancer Biol, 2006. 16(4): p. 253-
64. 
23. 
Fernandez, P.C., et al., Genomic targets of the human c-Myc protein. Genes Dev, 2003. 
17(9): p. 1115-29. 
24. 
Dang, C.V., et al., The interplay between MYC and HIF in cancer. Nat Rev Cancer, 2008. 
8(1): p. 51-6. 
25. 
Feo, S., et al., The DNA region around the c-myc gene and its amplification in human 
tumour cell lines. Oncogene, 1994. 9(3): p. 955-61. 
26. 
Shtivelman, E., et al., Identification of a human transcription unit affected by the variant 
chromosomal translocations 2;8 and 8;22 of Burkitt lymphoma. Proc Natl Acad Sci U S A, 
1989. 86(9): p. 3257-60. 
27. 
Meyer, K.B., et al., A functional variant at a prostate cancer predisposition locus at 8q24 is 
associated with PVT1 expression. PLoS Genet, 2011. 7(7): p. e1002165. 
28. 
Bertino, P., et al., Preliminary data suggestive of a novel translational approach to 
mesothelioma treatment: imatinib mesylate with gemcitabine or pemetrexed. Thorax, 2007. 
62(8): p. 690-5. 
29. 
You, L., et al., Genome-wide screen identifies PVT1 as a regulator of Gemcitabine 
sensitivity in human pancreatic cancer cells. Biochem Biophys Res Commun, 2011. 407(1): 
p. 1-6. 
30. 
Yang, F., et al., Increased VEGFR-2 gene copy is associated with chemoresistance and 
shorter survival in patients with non-small-cell lung carcinoma who receive adjuvant 
chemotherapy. Cancer Res, 2011. 71(16): p. 5512-21. 
 
 

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9.    APPENDICES 
9.1    Declaration of Helsinki 
World Medical Association Declaration of Helsinki: 
 
Ethical Principles for Medical Research Involving Human Subjects 
 
Adopted by the 18th WMA General Assembly Helsinki, Finland, June 1964 and amended 
by the 29th WMA General Assembly, Tokyo, Japan, October 1975 35th WMA General 
Assembly, Venice, Italy, October 1983 41st WMA General Assembly, Hong Kong, 
September 1989 48th WMA General Assembly, Somerset West, Republic of South Africa, 
October 1996 and the 52nd WMA General Assembly, Edinburgh, Scotland, October 2000 
 
A. INTRODUCTION 
1. The World Medical Association has developed the Declaration of Helsinki as a statement 
of ethical principles to provide guidance to physicians and other participants in medical 
research involving human subjects. Medical research involving human subjects includes 
research on identifiable human material or identifiable data. 
2. It is the duty of the physician to promote and safeguard the health of the people. The 
physician's knowledge and conscience are dedicated to the fulfillment of this duty. 
3. The Declaration of Geneva of the World Medical Association binds the physician with the 
words, "The health of my patient will be my first consideration," and the International 
Code of Medical Ethics declares that, "A physician shall act only in the patient's interest 
when providing medical care which might have the effect of weakening the physical and 
mental condition of the patient." 
4. Medical progress is based on research which ultimately must rest in part on 
experimentation involving human subjects. 
5. In medical research on human subjects, considerations related to the well-being of the 
human subject should take precedence over the interests of science and society. 
6. The primary purpose of medical research involving human subjects is to improve 
prophylactic, diagnostic and therapeutic procedures and the understanding of the 
aetiology and pathogenesis of disease. Even the best proven prophylactic, diagnostic, and 
therapeutic methods must continuously be challenged through research for their 
effectiveness, efficiency, accessibility and quality. 
7. In current medical practice and in medical research, most prophylactic, diagnostic and 
therapeutic procedures involve risks and burdens. 
8. Medical research is subject to ethical standards that promote respect for all human beings 
and protect their health and rights. Some research populations are vulnerable and need 
special protection. The particular needs of the economically and medically disadvantaged 
must be recognized. Special attention is also required for those who cannot give or refuse 
consent for themselves, for those who may be subject to giving consent under duress, for 
those who will not benefit personally from the research and for those for whom the 
research is combined with care. 

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9. Research Investigators should be aware of the ethical, legal and regulatory requirements 
for research on human subjects in their own countries as well as applicable international 
requirements. No national ethical, legal or regulatory requirement should be allowed t 
reduce or eliminate any of the protections for human subjects set forth in this Declaration. 
 
B. BASIC PRINCIPLES FOR ALL MEDICAL RESEARCH 
1. It is the duty of the physician in medical research to protect the life, health, privacy, and 
dignity of the human subject. 
2. Medical research involving human subjects must conform to generally accepted 
scientific principles, be based on a thorough knowledge of the scientific literature, other 
relevant sources of information, and on adequate laboratory and, where appropriate, 
animal experimentation. 
3. Appropriate caution must be exercised in the conduct of research which may affect the 
environment, and the welfare of animals used for research must be respected. 
4. The design and performance of each experimental procedure involving human subjects 
should be clearly formulated in an experimental protocol.  This protocol should be 
submitted for consideration, comment, guidance, and where appropriate, approval to a 
specially appointed ethical review committee, which must be independent of the 
investigator, the sponsor or any other kind of undue influence.  This independent 
committee should be in conformity with the laws and regulations of the country in which 
the research experiment is performed.  The committee has the right to monitor ongoing 
trials.  The researcher has the obligation to provide monitoring information to the 
committee, especially any serious adverse events.  The researcher should also submit to 
the committee, for review, information regarding funding, sponsors, institutional 
affiliations, other potential conflicts of interest and incentives for subjects. 
5. The research protocol should always contain a statement of the ethical considerations 
involved and should indicate that there is compliance with the principles enunciated in 
this Declaration. 
6. Medical research involving human subjects should be conducted only by scientifically 
qualified persons and under the supervision of a clinically competent medical person.  
The responsibility for the human subject must always rest with a medically qualified 
person and never rest on the subject of the research, even though the subject has given 
consent. 
7. Every medical research project involving human subjects should be preceded by careful 
assessment of predictable risks and burdens in comparison with foreseeable benefits to 
the subject or to others.  This does not preclude the participation of healthy volunteers in 
medical research.  The design of all studies should be publicly available. 
8. Physicians should abstain from engaging in research projects involving human subjects 
unless they are confident that the risks involved have been adequately assessed and can 
be satisfactorily managed.  Physicians should cease any investigation if the risks are 
found to outweigh the potential benefits or if there is conclusive proof of positive and 
beneficial results. 
9. Medical research involving human subjects should only be conducted if the importance 
of the objective outweighs the inherent risks and burdens to the subject.  This is 
especially important when the human subjects are healthy volunteers. 
10. Medical research is only justified if there is a reasonable likelihood that the populations 

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in which the research is carried out stand to benefit from the results of the research. 
11. The subjects must be volunteers and informed participants in the research project. 
12. The right of research subjects to safeguard their integrity must always be respected. 
Every precaution should be taken to respect the privacy of the subject, the confidentiality 
of the patient's information and to minimize the impact of the study on the subject's 
physical and mental integrity and on the personality of the subject. 
13. In any research on human beings, each potential subject must be adequately informed of 
the aims, methods, sources of funding, any possible conflicts of interest, institutional 
affiliations of the researcher, the anticipated benefits and potential risks of the study and 
the discomfort it may entail.  The subject should be informed of the right to abstain from 
participation in the study or to withdraw consent to participate at any time without 
reprisal.  After ensuring that the subject has understood the information, the physician 
should then obtain the subject's freely-given informed consent, preferably in writing.  If 
the consent cannot be obtained in writing, the non-written consent must be formally 
documented and witnessed. 
14. When obtaining informed consent for the research project the physician should be 
particularly cautious if the subject is in a dependent relationship with the physician or 
may consent under duress.  In that case the informed consent should be obtained by a 
well-informed physician who is not engaged in the investigation and who is completely 
independent of this relationship. 
15. For a research subject who is legally incompetent, physically or mentally incapable of 
giving consent or is a legally incompetent minor, the investigator must obtain informed 
consent from the legally authorized representative in accordance with applicable law.  
These groups should not be included in research unless the research is necessary to 
promote the health of the population represented and this research cannot instead be 
performed on legally competent persons. 
16. When a subject deemed legally incompetent, such as a minor child, is able to give assent 
to decisions about participation in research, the investigator must obtain that assent in 
addition to the consent of the legally authorized representative. 
17. Research on individuals from whom it is not possible to obtain consent, including proxy 
or advance consent, should be done only if the physical/mental condition that prevents 
obtaining informed consent is a necessary characteristic of the research population.  The 
specific reasons for involving research subjects with a condition that renders them 
unable to give informed consent should be stated in the experimental protocol for 
consideration and approval of the review committee.  The protocol should state that 
consent to remain in the research should be obtained as soon as possible from the 
individual or a legally authorized surrogate. 
18. Both authors and publishers have ethical obligations.  In publication of the results of 
research, the investigators are obliged to preserve the accuracy of the results.  Negative 
as well as positive results should be published or otherwise publicly available.  Sources 
of funding, institutional affiliations and any possible conflicts of interest should be 
declared in the publication.  Reports of experimentation not in accordance with the 
principles laid down in this Declaration should not be accepted for publication. 
 
C. ADDITIONAL PRINCIPLES FOR MEDICAL RESEARCH COMBINED 
WITH MEDICAL CARE 

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1. The physician may combine medical research with medical care, only to the extent that 
the research is justified by its potential prophylactic, diagnostic or therapeutic value.  
When medical research is combined with medical care, additional standards apply to 
protect the patients who are research subjects. 
2. The benefits, risks, burdens and effectiveness of a new method should be tested against 
those of the best current prophylactic, diagnostic, and therapeutic methods.  This does 
not exclude the use of placebo, or no treatment, in studies where no proven prophylactic, 
diagnostic or therapeutic method exists. 
3. At the conclusion of the study, every patient entered into the study should be assured of 
access to the best proven prophylactic, diagnostic and therapeutic methods identified by 
the study. 
4. The physician should fully inform the patient which aspects of the care are related to the 
research.  The refusal of a patient to participate in a study must never interfere with the 
patient-physician relationship. 
5. In the treatment of a patient, where proven prophylactic, diagnostic and therapeutic 
methods do not exist or have been ineffective, the physician, with informed consent from 
the patient, must be free to use unproven or new prophylactic, diagnostic and therapeutic 
measures, if in the physician's judgment it offers hope of saving life, re-establishing 
health or alleviating suffering.  Where possible, these measures should be made the 
object of research, designed to evaluate their safety and efficacy.  In all cases, new 
information should be recorded and, where appropriate, published.  The other relevant 
guidelines of this Declaration should be followed. 

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9.2    Common Terminology Criteria for Adverse Events Version 4.03 
http://ctep.cancer.gov/reporting/ctc.html  
9.3    
New York Heart Association Classification of Cardiac Disease 
The following table presents the NYHA classification of cardiac disease. 
Class 
Functional Capacity 
Objective Assessment 
I 
Patients with cardiac disease but without resulting limitations of physical 
activity.  Ordinary physical activity does not cause undue fatigue, 
palpitation, dyspnea, or anginal pain. 
No objective evidence of 
cardiovascular disease. 
II 
Patients with cardiac disease resulting in slight limitation of physical 
activity.  They are comfortable at rest.  Ordinary physical activity results in 
fatigue, palpitation, dyspnea, or anginal pain. 
Objective evidence of 
minimal cardiovascular 
disease. 
III 
Patients with cardiac disease resulting in marked limitation of physical 
activity.  They are comfortable at rest.  Less than ordinary activity causes 
fatigue, palpitation, dyspnea, or anginal pain. 
Objective evidence of 
moderately severe 
cardiovascular disease. 
IV 
Patients with cardiac disease resulting in inability to carry on any physical 
activity without discomfort.  Symptoms of heart failure or the anginal 
syndrome may be present even at rest.  If any physical activity is undertaken, 
discomfort is increased. 
Objective evidence of 
severe cardiovascular 
disease. 
Source:  The Criteria Committee of New York Heart Association.  Nomenclature and Criteria for Diagnosis of 
Diseases of the Heart and Great Vessels.  9th Ed. Boston, MA:  Little, Brown & Co; 1994:253-256. 
 
9.4    
Eastern Cooperative Oncology Group Scale for Performance Status 
Grade 
Description 
 
0 
Normal activity. Fully active, able to carry on all predisease performance without restriction 
1 
Symptoms but ambulatory. Restricted in physically strenuous activity, but ambulatory and 
able to carry out work of a light or sedentary nature (eg, light housework, office work) 
2 
In bed < 50% of the time. Ambulatory and capable of all self-care, but unable to carry out 
any work activities. Up and about more than 50% of waking hours. 
3 
In bed > 50% of the time. Capable of only limited self-care, confined to bed or chair more 
than 50% of waking hours. 
4 
100% bedridden. Completely disabled. Cannot carry on any self-care. Totally confined to 
bed or chair. 
5 
Dead. 
Source: Oken MM, Creech RH, Tormey DC, Horton J, Davis TE, McFadden ET et al. Toxicity and 
response criteria of the Eastern Cooperative Oncology Group. Am J Clin Oncol 1982; 5 (6):649-55. 

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9.5    
Body Surface Area and Creatinine Clearance Calculations 
Body surface area (BSA) should be calculated using a standard nomogram that yields the 
following results in meters squared (m2): 
BSA = 
3131
)
(
)
(
lbs
Wt
inches
Ht

 
or 
BSA = 
3600
)
(
)
(
kg
Wt
cm
Ht

 
 
Creatinine clearance (CrCl) can be calculated using the Cockroft-Gault equation as follows: 
 
CrCl (ml/min) = [(140-age) (body weight in kg) / (72 × serum creatinine in mg/dL)] 
OR 
[(140-age)(body weight in kg) / (0.81 x serum creatinine in μmol/L)] 
For females, use 85% of calculated CrCl value. 
Source: Cockcroft DW, Gault MH. Prediction of creatinine clearance from serum creatinine. Nephron 
1976;16(1):31-41. 
Note:  In markedly obese patients, the Cockroft-Gault formula will tend to overestimate the 
creatinine clearance.  (Adipose tissue tends to contribute little creatinine requiring renal 
clearance.)