Clinical trial NCT04555837
Conditions: Head and Neck Squamous Cell Carcinoma Malignant Solid Neoplasm
Keywords: head and neck cancer HPV Immunotherapy squamous cancer
Sponsor: M.D. Anderson Cancer Center
Start date: 2020-09-15; Completion date: 2025-04-08
Enrollment: 24 participants; Allocation: NA; Intervention model: SINGLE_GROUP

Brief summary:
This phase I/II trial investigates the best dose and effect of alisertib in combination with pembrolizumab in treating patients with Rb-deficient head and neck squamous cell cancer. Alisertib may help block the growth of cancer.. Immunotherapy with monoclonal antibodies, such as pembrolizumab, may help the body's immune system attack the tumor, and may interfere with the ability of tumor cells to grow and spread. Giving alisertib in combination with pembrolizumab may help control Rb-deficient head and neck squamous cell cancer. HPV positive head and neck cancers are Rb-deficient.

Detailed description:
PRIMARY OBJECTIVES:

I. To determine the recommend phase II dose of the combination of alisertib and pembrolizumab. (Phase I) II. To determine the overall response rate (ORR) and progression free survival (PFS) of patients with recurrent or metastatic Rb-deficient head and neck squamous cell carcinoma (HNSCC) treated with the combination of pembrolizumab and alisertib. (Phase II)

SECONDARY OBJECTIVES:

I. To evaluate the safety of the combination of pembrolizumab and alisertib in patients with solid tumors.

II. To determine the overall survival in HNSCC patients treated with the combination of pembrolizumab and alisertib.

III. To determine the relationship between pharmacokinetics, pharmacodynamics, baseline immune and tumor biomarkers and clinical responses in patients treated with alisertib and pembrolizumab.

IV. To determine correlations between clinical responses and the effect of the treatment on human papilloma virus (HPV)-reactive T cells in HPV+ cancers.

V. To determine correlations between clinical responses and tumor infiltrating lymphocyte function and T cell repertoire.

OUTLINE: This is a phase I, dose-escalation study of alisertib in combination with fixed dose pembrolizumab followed by a phase II study.

Patients receive alisertib orally (PO) twice daily (BID) on days 1-7 and pembrolizumab intravenously (IV) over 30 minutes on day 1. Cycles repeat every 21 days in the absence of disease progression or unacceptable toxicity.

After completion of study treatment, patients are followed up every 2-3 months.

Arms: arm 1: Patients receive alisertib PO BID on days 1-7 and pembrolizumab IV over 30 minutes on day 1. Cycles repeat every 21 days in the absence of disease progression or unacceptable toxicity.
Interventions: intervention 1: Alisertib intervention 2: Pembrolizumab
Intervention descriptions: intervention 1: Given PO intervention 2: Given IV

Protocol documents:
ICF_002.pdf: 
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NCT04555837


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NCT04555837


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NCT04555837


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NCT04555837


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 !"# $%&' ( !%$#)*)' ( "+!$+#,%)*")' (  $+!$"#,%)- $	$).","$)/012345678192;6<0=>>0?@AC4114DE4??8336DF6D1430@G9DHIJ4>K9@60D@AL' ' ,' +$#$' #$!" +  "$"$#%'$$!"%'$$,!"$#+%'""''"'$'"' ! $"%',!",%'"'+!"+%'$'$M??9A64D95E4??8336DF6DNOHIJ4>K9@60D@ALP30Q80D?RSDTD4UD
'  !##%' $$$!"$"%' $' $$' ' "$+' ,$!" $$
#"%
',,$!" $$ "$$# %' ' $'$'$',' ,
!" 
$+#%
' +',!""#%'$!"%'	+"'!" ""#
$%
NCT04555837


	
   	 !""# $   """%"%  "&"""  $ '"  !""  '" ""# " ()*+,-./+*01-/2133-**045046+7+*.8)49:16;).0+4./< %""!""== ""'  #  $$  	 ""  &"" $$ !"" " " $ ""'% ""&%"" '"    % $$ "# "= $$ ""$$ &"""$!" $"% "" $ "" '""# "  $$ !"" % """" $&$  '""#   $$ !"""" '$# " "  ' $$ " !"""""# " "" &"&" 
" ""!""
 " 
%$ &"!""% ""  " '$ #$  ">
" "" """  $$ !"""# $$  !""  ""  #"?  " "&"  ""  $ "!""% "" '%""#%  =$&!"" "$ "$" '%""# $$  "!""
$  #
  $$ 
"$!""
 $$  "!""&" $"#  $$ !"" $'#  $$   &!""&" """"&"  % $& " '""&"   "#	  "$$ " """"!"" $#$	 """ " "$"   "!"""#$$ " "!" $"% ""#$$ ""$ !""&@ &'"  $  '"="#"&	    !""%
"" 
 '
#
NCT04555837


	
 !!!! ! "#"!$! !"%""&"#"'$""!!&(!$!'!!!$!!&(!!!!!	!!!&(!!!!!!&)*+,-./+02+3-455-6/,78998:;866<..+:=+:98.-/>?:@AB85C?/+-:/,DE  !E E E F GE"HF "''!GEE!H!E  E'"!FH H'G!H'$!!G !!!!!H  GE!!!!F "'!!!'!!$!!"!GE!!"EF GE!!H!"F"!G' !'!$!H!H!EIJ!K!		 !F " !H'!!!!!!!H' !$!GE'!""FL!G!"F!G&M'$""&ML !' L '$!$!&NCT04555837


	
 "#$$%&'()*+,-.-/0 121345660 73456685662342992:66;2:2:<0 672:8=;<0 3:=130 1260 1410 42992:660 :62:0 7>:660 :?245662:0 422652:0 6>2:610 212:0 1:4	6:4=85=61:46;661@2:52:672
::43262:<0 46>2:0 1213468566234236<03:=66=2:6:4;2462:1348566237>:66672:2734566:2153=61:62:=:66:4;629<0:6252:04142:072166034=2:672
:0566=10601=124604=104226772:03:=60@253=685662316:66:442265>2:<02:6426>342:03:=2@668566232@4=<0=6656=6052:03@262:024:41:34=:010422312:02:2:0=51:4672
:A$.B#-.$#"#$$%+.C.$-D&*+,-.-/0 6@153=60 1>0 ==660 :@4=856623:=3:662:2::452:<0 61>0
06@32660672:0663:8566232:<0464347513785662362:41266<034862:16<0462:434602@4=434603:=>24::2:03>47:=6266856623>24:2<02=25:6034	7242:==2:012:6602:2:2:16E2623=64@5:15:8616>=2534:<FG61462:71242@2:52:4:6=12:5=2:
:16>H22::66:4;42:2:FI?52:652:66
:62:==66@245=2:166>6:2F
NCT04555837


	
 !
" !  #$!%&'"   ""#("! !")
" ""#$!!*" " !+ !" ", " + +"+ ""+ !-" #."-""! !!"/"!! " "  !  %'#0+" " !" #
1234257829:;<2="""" !"!!"" "#$!"""!" "!"!" ">?   " ""  "@  #A!""" "" -+ #B+ !+"!!""""! !" """ 
"!!" +!"#C92DE<F:9<45G5;4E9<HE:<F:; !""!"!""#$!  +"""!@"" I!  +#J<F:;K29L9M8HH55;7N9"+ "" I+"#0"" I """! "" "!"!!+  "#>@"+ ""% + "'!!" + ""#OPQ9 !""!*+" !"!RST -""#?"!UKV +"!!+ #$!!"  -"-""#$!"#0+"#W!!" "+" X "Y" +"*!"!""#$!""!""!!-! "! #."* """"!BZ." !"""+ !#$!BZ.@!+" """" "[!BZ.""#$!-""+ "" I""#0!""!""#$!"  "BZ."""!!"
"+ %!+" "-""
'#.+! !-#.!"
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NCT04555837


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
 !"#$	"%%%&'#(##")*(&$+""'"((#,((#"+-(('#'(#"%(".#*#'(#/'++'0"(#1*%((#(#%"##2*-%"##("+#&%#"##(#'*".*(%"#"3(#$("(#"##(#"#4(%#((#"*((-'%"##(#*(&"++/(#'"&(-#&-(#'.%$	+("'5%("'"##'&(#*'%#"#4"-((#"5%"(#(#6(#'""+(#&(#&("(#%(-"#4(%(#,%%-*(&'.+""%("%#%+"#%%(#'(#&""#*%(%'"(#78898!9:;<!=: 7:=>5%(""'(#--#+(&("."%+((+#"?@<A! !>B<7 =<;B:C5.(#+(#%(""#"(#("."##&#&"(#&&""%#&'+##&"&&%%(*%(#%("")'""&(%#(#%"#
"""""("$(-3#&'+##%%('""
%(%(-'%&(%#D"%"&(%#+("('+#"#(#6(#"E#
&('%D#'(+%'-(+EF"GH##"+'*%(#"#"
"%""""5%(%*(+#&'"+##""+"+##3+#4"+"&'"+##*%(
#%(""%"+#"*(.(#'(#&%+##5%""+#"I
"#(#'(#*(&'-(&"%(#+#*(
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"%""""3+##*(#&##%(""3&'+##""+%+##'"(%*5%"+#"*(".(#'(#&%+##K(#+##*("(#'-'%(""L?MLNOP?BLQRSBQTULBVQTSRW
LX=:8! 7?@8<;Y@<Z[3(#%"$+#"(#+%"#
*(%-'&(+"&('."(#"#(##%#&\
NCT04555837


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 ! " ##$
!#!## # # % #$!#$#&$ # #$!## # # '()*+,-.01+2345136*7879"#:*+(7*37 $$ #!#!##! ##;##! <###$<$$! ='>?@>AB0@6CD??D'>BEFAG'6DHEAD'>I'6'0AD'>EJ06'=@KF6@?=*12.3L+512M+*23+NOL37P+1O,+PN+13-2M+N)M3N+..+Q*,R+()*+,-.(1+2345137S'()*+,-.01+234513TSU"! ####!VWX@?
>'YZ='?A?E>K='C0@>?EAD'>[#\# #]U<## " "$9"$!!
## "##$##&#!$!^ #$ ###!]U<##$_##\&$#`]U<##a[b_c
d	c	Vcce#!	#\_####$#"# #`# #;$" $!!  #9"## "#;$!## #!#$##$ ##$ #;f#$"#!!## "#;##$##_# #$! 	$! "## "$ #$! #!&$###!$"!!f$ $#$!" $#$#"# #! $#$$
 
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NCT04555837


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 !"#$%&&'(')*+,.*/)01+(')* #$2345
6	5	767689":$ ;<3=$>
?@"!A$2?@A	"!$85
6	5	755!9"$!$$B #$!:!!$ !$!$!:?$$!#$$$#$?:$$$$$$$$!!$!?!$!$:$<3=$C$#$$7C$:$$!:$ADE4$$3=$243=8FG@2FG@8?@A<3=$5 !:$!$!#$$:#$$$H$!$
<$$$"?!$:"$"!#!!"$I<3=$:$J!$$C$$$J$:KA
?$:$:!!$28J?"9:?@A5
6	5	755LM(M0NONPN+0QRS+(+
 :$$C$:
$:<3=$$A$J$!
NCT04555837


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NCT04555837


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NCT04555837


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NCT04555837

Prot_SAP_000.pdf: 
 
 
MD Anderson IND Sponsor Cover Sheet 
 
Protocol ID 
2020-0210 
Protocol Title 
A phase I-II, open label study evaluating the safety and 
efficacy of alisertib and pembrolizumab in patients with 
Rb-deficient head and neck squamous cell carcinomas 
Protocol Phase 
I-II 
Protocol 
Version 
06 
Version Date 
05/17/2023 
 
Protocol PI 
Faye M. Johnson, MD, PhD 
Department 
Thoracic, Head and Neck Medical Oncology 
 
IND Sponsor 
MD Anderson Cancer Center 
IND # 
151006 
 


2020-0210 V06 
                                                                                                                            
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2 
 
 
PROTOCOL SUMMARY 
 
 
Study Title:  A phase I-II, open label study evaluating the safety and efficacy of alisertib and 
pembrolizumab in patients with Rb-deficient head and neck squamous cell carcinomas 
Phase:  I-II 
 
Objectives 
The primary objective of this study is to: 
• Phase I: To determine the recommend phase II dose of the combination of alisertib and 
pembrolizumab. 
• Phase II: To determine the overall response rate (ORR) of patients with immunotherapy-
refractory recurrent or metastatic Rb-deficient head and neck squamous cell carcinoma 
(HNSCC) treated with the combination of pembrolizumab and alisertib. 
The secondary objectives of this study are to: 
• To evaluate the safety of the combination of pembrolizumab and alisertib in patients with 
solid tumors. 
• To determine the overall survival and progression free survival (PFS) in HNSCC patients 
treated with the combination of pembrolizumab and alisertib. 
• To determine the relationship between pharmacokinetics, pharmacodynamics, baseline 
immune and tumor biomarkers and clinical responses in patients treated with alisertib and 
pembrolizumab. 
• To determine correlations between clinical responses and the effect of the treatment on 
human papilloma virus (HPV)-reactive T cells in HPV+ cancers.  
• To determine correlations between clinical responses and tumor infiltrating lymphocyte 
function and T cell repertoire. 
 
Patient Population 
Specific inclusion and exclusion criteria are detailed in Section 3.2. 
Number of Patients 
24-40 
Study Design and Methodology 
This is a phase I-II, open label study evaluating the safety and efficacy of alisertib and 
pembrolizumab in adult cancer patients.  The phase I cohort will test the safety of the combination of 
these drugs with non-overlapping toxicities in solid tumor patients who have exhausted standard of 
care therapy options. Patients will receive full dose αPD-1 antibody pembrolizumab (200mg IV 
every 3 weeks) in combination with the Aurora A kinase inhibitor alisertib.  Alisertib will be started 
at 40mg po BID x 7 days every 3 weeks) and then escalated in subsequent cohorts as follows: 
 
Dose Level 
Alisertib Dose 
-1 
30 mg po BID x 7 days every 21 days 
1 
40 mg po BID x 7 days every 21 days 
2 
50 mg po BID x 7 days every 21 days 


2020-0210 V06 
                                                                                                                            
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3 
Patients who cannot swallow tablets may use an oral solution of alisertib with greater bioavailability.  
An equivalent dose of the oral solution can be administered with dosing details in section 1.7. 
In the phase II study, patients with Rb-deficient HNSCC with recurrent/metastatic disease who are 
immunotherapy-refractory will be treated with the combination.  Tumors will be measured every 6 
weeks and evaluated using the Response Evaluation Criteria In Solid Tumors (RECIST) 1.1 
guidelines.1   
We will obtain tumor biopsies at baseline and at 6 weeks in patients in phase II portion of the study 
after the first interim analysis (i.e., if the efficacy of the combination passes the futility metric after 
14 patients are treated).  We will obtain blood every 6 weeks for correlative studies on all patients in 
the phase II study.  Pharmacokinetic (PK) analysis of alisertib will be conducted in the first 12 
patients treated at the recommended phase II dose on days 1 and 7 of course 1. 
Duration of Study 
Patients will remain on study until progression of cancer, unacceptable toxicity, or withdrawal of 
consent. 
Treatments Administered 
Pembrolizumab and alisertib 
Efficacy Data Collected 
The following evaluations will be conducted to assess the efficacy of alisertib: 
• Tumor size measured by CT or MRI using RECIST 1.1 every 6 weeks. 
• Progression free survival. 
• Overall survival. 
Pharmacokinetic/Pharmacodynamic/Pharmacogenomic/CorrelativeStudies Collected  
The following studies will be conducted to assess the pharmacokinetics/pharmacodynamics/ 
pharmacogenomics of alisertib: 
• To confirm adequate drug exposure and target inhibition and based on findings from 
prior studies2-4 we will draw blood for pharmacokinetic (PK) analysis of alisertib in the 
first 12 patients treated at the recommended phase II dose on days 1 and 7 of course 1 at 
1, 2, 3, 8, and 10 h after the morning dose of alisertib and calculate Cmax, T ½ , and AUC 
values.  
• To measure target inhibition, pharmacodynamics (PD) studies will be done in pre- and 
post- treatment tumor. Specifically, we will use immunohistochemistry (IHC) to quantify 
the number of cancer cells that stain for phosphorylation of Histone H3 (Ser10)5 and 
mitotic protein monoclonal 2 (MPM2).6 
Safety Data Collected 
The following evaluations will be conducted to assess the safety of alisertib: 
• Continuous serious adverse event (SAE) monitoring from date of consent until 60 days 
after the last dose of study drug. Continuous adverse event (AE) monitoring (as per NCI-
CTCAE classification, version 5.0) from first dose of study drug until 60 days after the 
last dose of study drug. Blood chemistry, hematology, vital signs, and physical 
examination. 
Statistical Procedures 
Bayesian optimal interval design will be applied for the phase I dose escalation part of the study.7-9 
The target toxicity rate for the maximum tolerated dose (MTD) is 0.3. The maximum sample size is 
12. We will enroll and treat patients in cohorts of size 2. To guide dose-escalation decisions, if the 


2020-0210 V06 
                                                                                                                            
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4 
observed dose-limiting toxicity (DLT) rate at the current dose is ≤ 0.236, the next cohort of patients 
will be treated at the next higher dose level; if it is ≥ 0.359, the next cohort of patients will be treated 
at the next lower dose level; otherwise the next cohort of patients will be treated at the same dose. 
We have performed simulation studies and the design will have at least 60% probability selecting the 
correct dose under various scenarios ranging from low to high toxicity profiles.  
In the phase II cohort of immunotherapy-refractory patients, any responses will be of interest.  We 
will use the Bayesian Optimal Phase 2 (BOP2) design. Design.10  The assumptions are that the null 
response rate is 5% and the target response rate is 20%. Fourteen patients will be enrolled initially.  
If there are no responses, then the trial will be terminated due to lack of efficacy.  If any responses 
are observed, an additional 14 patients will be enrolled. The treatment is considered efficacious if 
there are at least 4 responders in 28 patients and inefficacious otherwise.  The design will have 82% 
power if the response rate is at least 0.2 with a one-sided 5% type I error.   
 


2020-0210 V06 
                                                                                                                            
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5 
TABLE OF CONTENTS 
PROTOCOL SUMMARY ........................................................................................................2 
TABLE OF CONTENTS .........................................................................................................5 
STUDY FLOW DIAGRAM .....................................................................................................7 
SCHEDULE OF EVENTS .......................................................................................................8 
LIST OF ABBREVIATIONS...................................................................................................9 
1. INTRODUCTION AND STUDY RATIONALE ..............................................................11 
1.1 Overview of the Diseases .............................................................................................11 
1.2 Alisertib ........................................................................................................................11 
1.3 Nonclinical Summary ...................................................................................................12 
1.3.1 Nonclinical Pharmacology .....................................................................................12 
1.3.2 Nonclinical Pharmacokinetics ...............................................................................13 
1.3.3 Safety Pharmacology and Toxicology ...................................................................15 
1.4 Summary of Effects in Humans ....................................................................................15 
1.5 Risks and Benefits ........................................................................................................20 
1.6 Pembrolizumab .............................................................................................................25 
1.6.1 Scientific Background............................................................................................25 
1.6.2 Nonclinical Pharmacology .....................................................................................25 
1.6.3 Nonclinical Toxicity ..............................................................................................25 
1.6.4 Clinical Pharmacokinetics and Pharmacodynamics ..............................................25 
1.6.5 Clinical Experience ................................................................................................26 
1.6.6 Potential Risks of pembrolizumab .........................................................................27 
1.7 Study rationale and selection of drug doses .................................................................27 
2. STUDY OBJECTIVES ......................................................................................................29 
2.1 Primary Objective .........................................................................................................29 
2.2 Secondary Objectives ...................................................................................................29 
3. INVESTIGATIONAL PLAN .............................................................................................30 
3.1 Overall Design and Plan of the Study ..........................................................................30 
3.2 Selection of Patients .....................................................................................................31 
3.2.1 Inclusion Criteria ...................................................................................................31 
3.2.2 Exclusion Criteria ..................................................................................................32 
3.3 Study Treatments ..........................................................................................................35 
3.3.1 Clinical Trial Materials Note: ................................................................................35 
3.3.2 Preparation, Handling, and Storage of Drugs ........................................................35 
3.3.3 Dose Modification and Delay ................................................................................38 
3.3.4 Criteria for Retreatment and Dose Delays .............................................................39 
3.3.5 Dose Modifications for Hematological Toxicity ...................................................41 
3.3.6 Dose Modifications for Non-Hematological Toxicities ........................................41 
3.3.7 Treatment Assignment ...........................................................................................42 
3.3.8 Packaging and Labeling .........................................................................................42 
3.4 Excluded Concomitant Medications and Procedures ...................................................43 
3.5 Permitted Concomitant Medications and Procedures ...................................................44 
3.6 Precautions and Restrictions .........................................................................................45 
3.7 Management of Clinical Events ...................................................................................46 
3.7.1 Nausea and Vomiting.............................................................................................46 


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3.7.2 Diarrhea .................................................................................................................46 
3.7.3 Central Nervous System Effects ............................................................................46 
3.7.4 Management of New or Worsening Pulmonary Symptoms ..................................46 
3.7.5 Treatment Compliance ...........................................................................................47 
3.7.6 Pembrolizumab-related Adverse Events ................................................................47 
3.8 Duration of Treatment and Patient Participation ..........................................................47 
3.9 Termination of Treatment and/or Study Participation ..................................................47 
3.10 Efficacy, Pharmacodynamic/Pharmacogenomic/Correlative studies, and Safety 
Measurements .......................................................................................................48 
3.10.1 Efficacy Measurements........................................................................................48 
3.10.2 Pharmacokinetic and optional Pharmacodynamic/ 
Pharmacogenomic/Correlative Studies ...........................................................51 
3.10.3 Safety Measurements ...........................................................................................52 
3.11 Study Drug Administration ........................................................................................52 
3.12 Description of Investigational Agents ........................................................................52 
3.13 Preparation, Reconstitution, and Dispensation ...........................................................53 
3.14 Packaging and Labeling ..............................................................................................53 
3.15 Storage, Handling, and Accountability .......................................................................54 
4. ADVERSE EVENTS..........................................................................................................56 
4.1.1 Adverse Event Definition ......................................................................................56 
4.2 Moclia database ............................................................................................................56 
4.2.1 Adverse Event Attribution and Severity Definition ..............................................56 
4.3 Investigator Communications with Puma Biotechnology ............................................57 
4.4 Serious Adverse Events Reporting ...............................................................................60 
4.5 Procedures for Reporting To the FDA .........................................................................61 
4.6 Procedures for Reporting Drug Exposure During Pregnancy and Birth Events ..........61 
4.7 Product Complaints and Medication Errors .................................................................62 
5. STATISTICAL PROCEDURES ........................................................................................63 
5.1 Study Design and Overview of Primary and Secondary Endpoints .............................63 
5.2 Randomization and Stratification Factors ....................................................................65 
5.3 Evaluation of Efficacy ..................................................................................................65 
5.4 Evaluation of Safety .....................................................................................................65 
5.5 Correlative Studies .......................................................................................................66 
5.6 Interim Analysis ...........................................................................................................68 
5.7 Consent Process and Documentation ...........................................................................69 
6. REFERENCES ...................................................................................................................70 
7. APPENDICES ....................................................................................................................77 
7.1 Declaration of Helsinki .................................................................................................77 
7.2 Common Terminology Criteria for Adverse Events Version 5.0 .................................81 
7.3 New York Heart Association Classification of Cardiac Disease .................................81 
7.4 Eastern Cooperative Oncology Group Scale for Performance Status ..........................81 
7.5 Body Surface Area and Creatinine Clearance Calculations .........................................82 
7.6 Management of pembrolizumab toxicity ......................................................................83 
 
 
 


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Study Flow Diagram  
 
 


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Schedule of Events 
 
 
Cycle 1 
Cycle 1 
Cycle 2 
Subsequent 
Cycles11 
 
Assessments1  
Screening 
C1D1 
C1D7 
C2D1 
D1 
At PD or 
Termination10 
Day -22 to Day -1 
Physical Exam and PS2 
X 
X 
X 
X 
X 
X 
Vitals 
X 
X 
X 
X 
X 
X 
Hematology3 
X 
X 
X 
X 
X 
X 
Chemistry4, 9 
X 
X 
X 
X 
X 
X 
TSH and free T45 
X 
 
 
 
X 
 
EKG6 
X 
 
 
 
 
X 
Pharmacokinetics on selected patients 
X 
X 
 
 
 
Serum or urine pregnancy test in 
WOCBP 
X 
X 
 
X 
X 
 
Imaging with tumor measurements7 
X 
 
 
X 
 
AE assessment 
X 
X 
X 
X 
X 
Optional biopsies8 
X 
 
 
 
X8 
 
Correlative blood studies8 
X 
 
 
 
X 
 
Blood tests for HIV, hepatitis B, and 
hepatitis C 
X 
 
 
 
 
 
1 Assessments may be done within 24-48 hours of dosing with drug administration 
2 Symptom directed 
3 CBC with differential. 
4 Chemistry: electrolyte panel, LFTs and kidney function tests, direct bilirubin, LDH, ALP, BUN, total protein, calcium, phosphate, magnesium, glucose. 
5 Thyroid function tests every two cycles. 
6 Single, 12-lead EKG will be collected at screening (within 22 days of first dose), end of treatment (i.e., at PD or termination). 
7Every two cycles, up to 3 days prior to day 1 of the subsequent cycles. 
8Tumor biopsies at baseline (up to 22 days prior to C1D1) and at 6 weeks (± 3 days) in patients in phase II portion of the study after the first interim analysis. Any biopsies 
performed will exclude biopsies of lesions in proximity to cardio-pulmonary, visceral, or vital neurovascular structures that can be considered high risk procedures.  Blood every 
6 weeks (± 3 days) for correlative studies as described in section 3.10.2. 
9Add serum osmolarity, lactic acid levels and calculate the anion gap and osmolar gap for those using the Alisertib oral solution. 
10Patients withdrawn from the study will be continuously monitored for survival through chart review and/or phone call every 2-3 months. 
11Patients who remain on study for ≥ 10 cycles without progression  may opt for tumor measurements every 3 cycles  rather than every 2 cycles. 


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LIST OF ABBREVIATIONS 
 
Abbreviation 
Definition 
°C 
degrees Celsius 
µM 
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 
ctDNA 
circulating tumor DNA 
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 
HNSCC 
head and neck squamous cell carcinoma 
HPV 
human papilloma virus 
ht 
Height 
IκB 
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 
IκBα 
I kappa B alpha-associated protein kinase 


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Abbreviation 
Definition 
kg 
Kilogram 
Ki 
inhibitory constant 
lbs 
Pounds 
m2 
square meters 
mg 
Milligram 
min 
Minute 
mL 
Milliliter 
mm3 
cubic millimeters 
mmol 
Millimole 
MTD 
maximum tolerated dose 
NCI 
National Cancer Institute 
NF-κB 
nuclear factor-κB 
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 
SCLC 
small cell lung cancer 
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 Diseases 
The drug combination will be tested in head and neck squamous cell carcinoma (HNSCC) 
which is the seventh leading cause of cancer-related deaths globally; killing more than 
375,000 individuals yearly.11 Most HNSCC is caused by tobacco or the human 
papillomavirus (HPV).  The incidence of HPV-driven HNSCC is increasing in the US and 
worldwide.12-14 HPV+ HNSCC affects predominantly young (aged <55 years) people who 
suffer chronic adverse effects from therapy for decades – making less toxic therapy (i.e., 
therapy de-intensification) a research priority.15   
The majority of HNSCC patients are diagnosed with locally advanced disease and treated 
with a combination of surgery, radiotherapy, and/or chemotherapy. Most of those who recur 
following initial definitive therapy receive palliative systemic therapy. 
Comprehensive genomic characterization of HNSCC has not translated into clinical 
advances, largely because of a lack of druggable, driver oncogenes.16-21  The lack of a 
biomarker-selected, molecular targeted therapies for HNSCC, permanent toxicity resulting 
from current therapy, and poor prognosis for those who progress after definitive therapy 
demonstrate an unmet clinical need for HNSCC.  
Following progression after first-line, cisplatin-based chemotherapy, the standard of care for 
metastatic or recurrent HNSCC is αPD1 immune checkpoint therapy (ICT) with 
pembrolizumab or nivolumab. This standard is based on three pivotal studies that 
demonstrated response rates of 14-18%, six-month progression-free survival rates of 23%, 
and a one-year survival rate of 36%.22-25 Although ICT has a striking effect in some HNSCC 
patients,26 the majority (~85%) still experience progression. Response rates to non-ICT, 
standard of care therapies in platinum-resistant patients is 5.8%.25  First-line pembrolizumab 
in HNSCC has a response rate of 17%.27 Pembrolizumab was approved on June 10, 2019 by 
the federal drug administration (FDA) in combination with platinum and 5-fluorouracil (5-
FU) for all recurrent and metastatic HNSCC patients and as a single agent for those whose 
tumors express PD L1 (Combined Positive Score [CPS] ≥1) as front line therapy.  
1.2    Alisertib 
Alisertib (International Nonproprietary Name, also known as MLN8237, TAK823) is a 
selective small molecule inhibitor of Aurora A kinase that is being developed for the 
treatment of advanced malignancies. Aurora A kinase is expressed in all actively dividing 
cells; it is localized to centrosomes and the proximal mitotic spindle during mitosis, where it 


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functions in a diverse set of mitotic processes. The chemical name for alisertib is sodium 4-
([9-chloro-7-(2-fluoro-6-methoxyphenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino)-2-
methoxybenzoate hydrate. Alisertib has demonstrated activity against a broad range of 
nonclinical tumor models grown in vitro and in vivo, as described in the following. Alisertib 
is also expected to be toxic to proliferating normal tissues, such as the bone marrow and 
gastrointestinal (GI) epithelium, because any cell that is in mitosis, where Aurora A kinase 
is expressed and active, should be susceptible to the effects of an Aurora A kinase inhibitor. 
1.3 Nonclinical Summary 
1.3.1 Nonclinical Pharmacology 
Alisertib is a selective, potent, adenosine triphosphate (ATP)-competitive, and reversible 
inhibitor of Aurora A kinase. Alisertib inhibited proliferation of a wide variety of tumor cell 
lines grown in culture and induced phenotypes consistent with Aurora A kinase inhibition, 
including mitotic spindle defects, mitotic delay, and apoptosis. 
Alisertib demonstrated antitumor activity when orally administered daily for approximately 
21 days in a broad spectrum of nonclinical xenograft tumor models including human solid 
and hematologic tumors. 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). 
Less frequent dosing was also efficacious, demonstrating that continuous dosing is not 
necessary for antitumor activity. A single oral (PO) dose of alisertib resulted in inhibition of 
activated Aurora A kinase and an increase in mitotic cells, demonstrating that mitotic index 
(MI) can be used as a pharmacodynamic marker of alisertib in some in vivo settings. The 
pharmacokinetic (PK)/pharmacodynamic studies in mice bearing HCT-116 tumor 
xenografts suggest that the maximum pharmacodynamic effect (mitotic accumulation) and 
efficacy are achieved at steady state plasma concentrations of 1 µM. The oral dose of 
alisertib at 30 mg/kg QD resulted in plasma concentrations of 1 µM for 8 to 12 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). 
Alisertib can be combined with standard of care agents and results in synergistic or additive 
antitumor effects in multiple tumor models. (see IB for additional information) 
[Combination treatment 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 diffuse large B-cell lymphoma (DLBCL) xenograft 


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models, combination treatment 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. Combination treatment with paclitaxel or carboplatin in small cell 
lung cancer (SCLC) xenograft models, and with paclitaxel in a human breast cancer model, 
generally resulted in additive or synergistic antitumor activity.] 
1.3.2  Nonclinical Pharmacokinetics 
Alisertib was orally bioavailable in all animal species tested with limited distribution to red 
blood cells. Alisertib was highly bound to the plasma protein of all 5 species studied, with 
percent binding of 97.5% in humans. M1 (acyl glucuronide) and M2 (O-demethylated) 
metabolites of alisertib were also highly bound to human plasma protein. 
Alisertib had low to moderate intrinsic hepatic clearance (CLint), as determined in vitro in 
rat, monkey, dog, and human liver S9 fractions. On the basis of the results from the 
radiolabeled human absorption, distribution, metabolism, and excretion (ADME) study and 
the in vitro investigations, alisertib was metabolized by both oxidation and glucuronidation 
pathways. In human liver microsomes (HLMs), alisertib was metabolized by multiple 
cytochrome P450 (CYP) (CYP1A2, 2C8, 2C9, and 3A4) and uridine diphosphate-
glucuronosyltransferase (UGT) (UGT1A1, 1A3, and 1A8) isozymes. CYP3A4 was the 
major (86.2%) CYP isozyme contributing to the oxidative metabolism of alisertib. 
Therefore, moderate and strong inhibitors of CYP3A4 and clinically significant enzyme 
inducers may alter the systemic exposure of alisertib.  
The major metabolic route of [14C]alisertib in rats in vivo was acyl glucuronidation, with 
>77.9% of the dose metabolized by this pathway. In rats, unchanged alisertib was the 
predominant circulating component in plasma over a 24-hour period. With repeated dosing 
of alisertib, the metabolite profiles in rat and dog plasma on Days 1 and 7 were similar, 
suggesting the lack of accumulation of metabolites. After PO administration of [14C]alisertib 
to bile duct-cannulated rats, radioactivity was primarily eliminated in the bile. 
Following a single oral dose of [14C]alisertib to human subjects, alisertib was the major 
circulating drug-related component in plasma, and the average percentage of alisertib was 
48% (n = 3) of the total plasma radioactivity (TRA). Two major circulating oxidative 
metabolites were O-demethyl (M2) and hydroxy (M3) metabolite with average percentages 
of 35% and 6% of TRA, respectively. Acyl glucuronide (M1) and an isomeric glucuronide 
conjugate were also observed, and each represented ≤10% of the total plasma radioactivity. 


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The total percentages of the 2 combined isomeric forms of the M1 metabolite averaged 12% 
of plasma radioactivity. 
Urinary excretion was a minor route of clearance of total radioactivity with an average of 
<3% of the total administered dose recovered in urine over 14-days post-dose. Fecal 
excretion was the major route of clearance of total radioactivity in humans with an average 
of 88% of the total dose recovered in feces over 14 days post dose. Unchanged alisertib was 
one of the major drug-related components. Among the metabolites, M3 was one of the major 
drug-related components in feces. Overall, metabolites resulting from phase 1 oxidative 
pathways contributed to approximately 60% of the administered dose in human subjects. 
Therefore, cytochrome P450-mediated oxidation (particularly CYP3A4, as inferred from 
follow-up reaction phenotyping studies in vitro) is the most important clearance mechanism 
for alisertib. These findings suggest that there is a potential for increased systemic exposure 
of alisertib when co-administered with inhibitors of CYP3A4.  
Alisertib was not an inducer of CYP1A2, 2B6, and 3A4/5 isozyme activities at 
concentrations up to 20 µM. Alisertib was a weak inhibitor of CYP2B6 and CYP2C8 in 
HLMs. However, alisertib is unlikely to inhibit the 5 major CYP isozymes, 1A2, 2C9, 2C19, 
2D6, and 3A4/5 and was not a time-dependent inhibitor of CYP1A2, 2B6, 2C8, 2C9, 2C19, 
2D6, or 3A4/5. Additionally, alisertib metabolites M1 and M2 were not potent reversible 
inhibitors of CYP enzymes and therefore, it is unlikely that alisertib, M1, or M2 will cause 
drug-drug interactions (DDIs) by inhibiting major CYP isozymes. 
If studies in combination with irinotecan, erlotinib or paclitaxel [Potential interaction of 
alisertib with other anticancer agents (irinotecan, erlotinib and paclitaxel) was investigated 
in liver microsomes. Alisertib inhibited the formation of 7 ethyl-10-hydroxycamptothecin 
(SN38), the active metabolite of irinotecan, and 7 ethyl 10-hydroxycamptothecine-
glucuronide (SN38 Glu), a metabolite of SN38, in HLMs. In mouse liver microsomes 
(MLMs) and HLMs, erlotinib hydrochloride inhibited the UGT isozyme-mediated 
metabolism of alisertib.28 However, erlotinib hydrochloride did not inhibit the CYP isozyme 
mediated metabolism of alisertib. In addition, alisertib inhibited both CYP2C8- and 
CYP3A4/5-mediated metabolism of paclitaxel in HLMs with half-maximal inhibitory 
concentration (IC50) values of 16.3 and 72.9 µM, respectively.] 
Alisertib demonstrated no efflux transporter activity. Alisertib was not a human 
P-glycoprotein (P-gp) substrate, but inhibited the P-gp-mediated efflux of paclitaxel in 
Caco-2 cells with an IC50 of 4.0 µM. The potential for inhibition of intestinal P-gp efflux by 
higher intestinal luminal concentrations of alisertib cannot be ruled out. Therefore, orally co-


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administered narrow therapeutic range substrates of P-gp (eg, digoxin) should be 
administered with caution. On the basis of in vitro results described in the IB and 
considering the high permeability of alisertib, alisertib is not likely to be involved in other 
transporter-based DDIs. 
1.3.3  Safety Pharmacology and Toxicology 
Safety pharmacology studies with alisertib did not identify significant adverse effects in the 
central nervous system (CNS) and cardiovascular systems at tolerated doses. Alisertib 
exhibited minimal activity against human ether-à-go-go related gene (hERG) current (IC50 
and Ki >100 µM), but did exhibit in vitro activity against the gamma-aminobutyric acid A 
alpha 1 (GABAAα1) benzodiazepine binding site (Ki = 290 nM), and related effects were 
observed at non-tolerated doses/exposures in safety pharmacology studies. 
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 GI signs, panleukopenia, 
decreased reticulocyte counts, and increased mitotic figures and apoptosis (single cell 
necrosis) in tissues with a high basal cellular replication rate. No off-target effects were seen 
in the Good Laboratory Practices (GLP) compliant toxicology studies and in general the 
on-target findings were reversible following cessation of dosing. 
Alisertib was negative for mutagenicity in the Ames assay and equivocal for clastogenicity 
in a rat bone marrow micronucleus assay. 
1.4 Summary of Effects in Humans 
As of 29 March 2016, the following company-sponsored alisertib studies were in progress or 
completed: 10 single-agent phase 1 studies (C14001, C14002, C14003, C14010, C14013, 
C14014, C14017, C14019,  TB-MA010030, and TB-MA010033); 2 single-agent, phase 1, 
DDI studies (C14015 and C14020); 3 single-agent, phase 2 studies (C14004, C14005, and 
C14006); 1 single-agent, phase 1/2 study (C14007); 1 single–agent, phase 3 study (C14012); 
and 5 combination studies (C14008 [phase 1/2] with paclitaxel, C14009 [phase 1] with 
docetaxel, C14011 [phase1] with either rituximab, or rituximab + vincristine, C14018 with 
paclitaxel [phase 2], and C14022 with paclitaxel in Asian patients [phase 1]). 
Three dosage forms of alisertib have been developed for clinical studies: powder in capsule 
(PIC), enteric-coated tablet (ECT), and oral solution. The initial phase 1 (C14001 through 


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C14003) and phase 2 (C14004 through C14006) studies employed the PIC formulation. 
Studies C14001 and C14003 were amended to evaluate the ECT formulation; C14001 
evaluated the relative bioavailability (BA) of the PIC and ECT formulations in solid tumor 
patients, and C14003 evaluated the clinical safety and PK of the ECT formulation in patients 
with hematologic malignancies. Relative BA of the PIC, ECT, and oral solution has also 
been investigated in Study C14010.29 The ECT formulation is being used in more recent 
studies (C14007 through C14009, C14011 through C14015, C14017, TB-MA010030 and 
TB-MA010033) and will be used in future studies. 
 
Study Summary of Company Sponsored Studies 
Study 
Number 
Study Description 
Enrollment 
Status 
C14001/2 
Phase 1 dose escalation study in solid tumor.  
Complete 
C14003 
Phase 1 dose escalation study in advanced hematologic malignancies with a 
peripheral T cell lymphoma and diverse subtype expansion cohort. 
Complete 
C14004 
Phase 2 study in aggressive non-Hodgkin lymphoma.  
Complete 
C14005 
Phase 2 study in acute myelogenous leukemia or high-grade myelodysplastic 
syndrome. 
Complete 
C14006 
Phase 2 study in epithelial ovarian, fallopian tube, or primary peritoneal 
carcinoma. 
Complete 
C14007 
Phase 1/2 study to confirm the MTD in nonhematologic malignancies; phase 
2 evaluation in lung, breast, head and neck, or gastroesophageal malignancies. 
Complete 
C14008 
Phase 1/2 study to determine the MTD of alisertib combined with weekly 
paclitaxel; phase 2 evaluation of efficacy of combination in patients with 
relapsed ovarian cancer (open label, randomized). 
Complete 
C14009 
Phase 1 study to determine the MTD of alisertib combined with docetaxel in 
patients with solid tumors, including prostate cancer, appropriate for 
docetaxel treatment 
Complete 
C14010 
Phase 1 study evaluating the bioavailability of alisertib oral solution versus 
PIC formulation and the effect of food on alisertib PK (ECT formulation). 
Complete 
C14011 
Phase 1 study evaluating patients with relapsed/refractory aggressive B-cell 
lymphoma treated with alisertib combined with rituximab and vincristine. 
Complete 
C14012 
Phase 3 study in patients with relapsed or refractory peripheral T-cell 
lymphoma (international, multicenter). 
Complete 
C14013 
Phase 1 dose escalation and PK study of alisertib in East Asian patients with 
advanced solid tumor or lymphomas. 
Complete 
C14014 
Phase 1 study investigating the mass balance, PK, and metabolism of radio-
labelled alisertib in patients with either advanced solid tumors or lymphomas. 
Complete 
C14015 
Phase 1 study evaluating the effect of either esomeprazole or rifampin on the 
PK of alisertib and evaluation of the effects of alisertib on the QTc interval in 
patients with either advanced solid tumors or lymphomas. 
Complete 
C14017 
Phase 1 study to investigate the effect of food on the PK of alisertib in 
patients with either advanced solid tumors or lymphomas. 
Complete 
C14018 
A randomized, double-blind, placebo-controlled, phase 2 study of alisertib in 
combination with paclitaxel versus placebo in combination with paclitaxel as 
second-line therapy for small cell lung cancer (SCLC) 
Complete 


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Study Summary of Company Sponsored Studies 
Study 
Number 
Study Description 
Enrollment 
Status 
C14019 
A phase 1 study evaluating the PK of alisertib (MLN8237) in adult patients 
with advanced solid tumors or relapsed/refractory lymphoma with varying 
degrees of hepatic function 
Ongoing 
C14020 
A phase 1 study evaluating the effect of itraconazole on the PK of alisertib in 
adult patients with advanced solid tumors or relapsed/refractory lymphoma 
Complete 
C14022 
Phase 1 dose escalation and dose expansion study of alisertib in combination 
with a modified weekly paclitaxel in previously treated Asian patients with 
advanced solid tumors.  
Ongoing 
TB-
MA010030 
Phase 1, open-label, multicenter, dose-escalation study in patients with 
advanced solid tumors conducted in Japan.  
Complete 
TB-
MA010033 
Phase 1, open-label, multicenter, dose-escalation study in patients with 
relapsed or refractory non-Hodgkin lymphoma conducted in Japan.  
Complete 
ECT: enteric coated tablet; MTD: maximum tolerated dose; PIC: powder in capsule; PK: 
pharmacokinetics. 
TB-MA010030 and TB-MA010033 were conducted in Japan and Studies C14013 and 
C14022 were conducted in East Asia. They are company-sponsored studies, but were not 
conducted under the US FDA IND (75,473). Patients in these studies were treated with the 
ECT formulation of alisertib BID for 7 consecutive days (Days 1-7) in a 21-day cycle. 
Clinical PK data available as of 29 March 2016 are summarized below.  Following oral 
administration of alisertib as the ECT formulation, peak concentrations of alisertib were 
generally achieved by 3 hours postdose. The overall peak-to-trough ratio was 2.2, and the 
accumulation ratio (Rac) was 2.4. The terminal half-life was approximately 21 hours 
following 7 days of multiple dosing. 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. Pharmacokinetic steady-state conditions were approximately 
achieved by Day 7 following daily oral administration. The predominant route of 
elimination for alisertib is fecal, consistent with hepatic metabolism and biliary excretion of 
alisertib. Renal clearance of unchanged alisertib was negligible. Based on the results from 
the radio-labeled human ADME study (C14014) and the follow-up in vitro investigations, 
alisertib is metabolized by both oxidation and glucuronidation pathways, and multiple 
cytochrome P450 (CYP) isozymes (CYP3A4, 2C8, 2C9, 2C19, and 1A2) and UGT 
isozymes (UGT1A1, 1A3, and 1A8) are involved. Phase 1 oxidative metabolism was 
identified to be of quantitative importance, with an estimated contribution of CYP3A4 of 
approximately 60% to overall apparent oral clearance (CL/F) in humans. Therefore, strong 
inhibitors of CYP3A4 and clinically significant inducers may alter systemic exposures 
of alisertib and should be avoided. The PK properties of alisertib in patients with 


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hematologic malignancies were generally consistent with those observed in patients with 
nonhematologic malignancies. Based on the results of a population PK analysis in 671 adult 
cancer patients, the CL/F of alisertib was unaffected by age, sex, creatinine clearance, 
bilirubin, formulation (ECT vs PIC), body weight, body surface area (BSA), or UGT1A1 
genotype (number of *28 alleles). Region (West/East) was identified as a significant 
covariate on alisertib relative bioavailability, which was 51.7% (95% CI = 36.5%-70.1%) 
higher for patients from the East region (East Asia/Japan). These results support the use of a 
common fixed starting dose of alisertib in the adult patient with the need to adjust dosing for 
the covariate of region (Japan or East Asia vs. West). The analysis results support 
achievement of comparable systemic exposures of alisertib following administration of 
doses of 50 mg BID to patients in the Western region and alisertib doses of 30 mg BID to 
patients in East Asia/Japan. 
The results of metabolite profiling from the mass balance study (C14014) indicated the 
presence of 2 metabolites M1 (alisertib acyl glucuronide) and M2 (O-desmethyl) in 
circulation, as products of parallel primary pathways of alisertib biotransformation via 
glucuronidation and oxidative metabolism, respectively. Accordingly, plasma samples from 
Study C14015 were used to measure concentrations of M1 and M2 in addition to the parent 
drug to characterize the PK of these metabolites. Systemic exposures of the alisertib 
metabolites M1 and M2 following 50 mg BID multiple dose administration of alisertib were 
44% and 42% of parent drug exposure, respectively. 
The effect of a high-fat meal on the single-dose PK of alisertib administered as 5 × 10-mg 
ECT was evaluated in Study C14017. The geometric mean AUC0-inf following alisertib 
single dose administration under fed conditions was 115% of that under fasted conditions 
(90% CI: 96%, 139%), with a substantial overlap in the range of individual values of 
AUC0-inf when dosed in the fed versus fasted states. Based on the relatively minor (15%) 
increase in alisertib geometric mean AUC0-inf upon administration with a high-fat meal in 
relation to overall PK variability (45% coefficient of variation [CV] in AUC0-inf), it is 
concluded that food does not produce a clinically relevant effect on alisertib PK. These 
results support the conclusion that alisertib can be administered without regard for the 
timing of meals. 
The relative BA of the oral solution in reference to PIC in 14 patients was estimated to be 
1.26 in reference to the PIC (90% CI: 1.09, 1.47). The rate of absorption of alisertib from the 
oral solution was higher than that from the PIC formulation, based on a shorter median time 
to first maximum plasma concentration ([Tmax] 1 hour for the oral solution compared with 2 


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hours for the PIC). The geometric mean ratio of dose-normalized Cmax of oral solution 
versus PIC was 1.90 (90% CI: 1.52, 2.37).] 
Co-administration of alisertib with esomeprazole, a proton pump inhibitor (PPI) resulted in a 
28% increase in total systemic exposure (AUC0-inf) of alisertib, supporting the conclusion 
that gastric acid-reducing agents be avoided in patients receiving alisertib. 
Co-administration of alisertib with rifampin, a strong metabolic enzyme inducer resulted in a 
47% decrease in total systemic exposure (AUC0-inf) of alisertib, supporting the conclusion 
that chronic use of concomitant strong inducers of pregnane x-receptor (PXR)-
inducible enzymes be avoided in patients receiving alisertib. 
Alisertib (50 mg) in single doses and after multiple doses BID for 7 days was not associated 
with any clinically relevant changes or findings in the electrocardiogram (ECG), did not 
prolong the QT interval, and can be concluded not to affect cardiac repolarization dynamics. 
No alisertib concentration-effect relationship was identified, consistent with findings from 
the statistical analyses in supporting a lack of effect on the QT interval. 
Pharmacodynamic evaluations have been performed in patient skin and tumor biopsies using 
assays that reflect Aurora A kinase inhibition. The data collected to date from these biopsies 
provide evidence that a dominant mechanism of alisertib is inhibition of Aurora A kinase in 
both skin and tumor, and these effects are generally dose- and/or exposure-dependent. 
Adverse events (AEs) observed to date (as of 29 March 2016) are generally reversible, 
dose-dependent, and are consistent with the pharmacologic profile of alisertib as an 
anti-mitotic agent with predominant effects in proliferative tissues. The more commonly 
observed (≥ 30% incidence) treatment-emergent AEs (TEAEs) all grades from pooled data 
across the alisertib single-agent studies include: neutropenia (48%), anemia (47%), fatigue 
(47%), diarrhea (44%), alopecia (36%), stomatitis (32%), nausea (31%), and 
thrombocytopenia (30%). 
Central nervous system (CNS) effects, including transient dose-dependent somnolence 
and/or confusion, have also been observed. These CNS effects may not be associated with 
Aurora A kinase inhibition but instead likely represent benzodiazepine-like effects of 
alisertib due to its structural similarity to benzodiazepine. At higher dose levels evaluated in 
early phase 1 studies, severe CNS effects were sometimes considered DLTs, although these 
effects abated during the planned treatment-free period. In the phase 1 studies, CNS effects 
appeared to be related to high peak plasma levels resulting from single daily doses of 
alisertib. The frequency and/or severity of benzodiazepine-associated CNS toxicities may be 
reduced in adult patients enrolled to recent studies that administered alisertib with divided 


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doses (eg, BID), a schedule designed to reduce peak plasma levels while maintaining overall 
AUC. CNS effects have been reversible with cessation of alisertib treatment, dose reduction, 
and dose modification of other sedative medications. 
Studies C14001 and C14002, conducted in patients with solid tumors determined the RP2D 
of the PIC formulation of alisertib administered in a 21-day cycle as 50 mg BID. Similarly, 
Study C14003 in hematologic malignancies identified alisertib ECT 50 mg BID for 7 days 
in a 21-day cycle as the recommended dosing regimen to take forward into future studies. 
While most clinical experience supports a 7-day schedule followed by a 2-week 
treatment-free period, clinical experience also supports treatment schedules with up to 
14 days of drug administration in a 28-day cycle, and up to 21 days of drug administration in 
a 35-day cycle. The clinical experience includes treatments with multiple doses and 
schedules as described in the IB. 
Alisertib is also available in an oral solution (OS). The relative bioavailability of alisertib 
oral solution is ~130% in reference to PIC formulation in adult cancer patients.29 That is, the 
OS is expected to achieve 30% higher alisertib exposures than that of PIC. In addition, the 
alisertib exposures from 50 mg ECT were comparable to that of 50 mg PIC (investigated in 
study C14001). Taken together, the alisertib oral solution is expected to achieve 30% higher 
exposures than that of ECT as well. This was the rational for the alisertib mass balance study 
(C14014) using 35 mg oral solution to achieve comparable exposures at 50 mg ECT in adult 
patients, which was the unit dose of alisertib MTD. 
An investigator-initiated study (IIS) (NCT02219789) showed that in patients with endocrine 
resistant ER+ metastatic breast cancer a favorable safety profile and preliminary efficacy 
was observed with a pulse dose of alisertib in combination with standard dose of Fulvestrant 
consisting of 50 mg twice daily alisertib on days 1–3, 8–10, and 15–17 of a 28-day cycle. 
This regimen of alisertib resulted in significantly lower grade ≥3 event rates relative to those 
observed with the traditional dose and schedule.30  
1.5 Risks and Benefits 
As of 29 March 2016, 1292 patients have been treated with alisertib, in company-sponsored 
studies. Clinical safety data include 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. 
The identified risks associated with alisertib treatment include: reversible myelosuppression 
including anemia; febrile neutropenia (including fatal febrile neutropenia); leukopenia; 


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lymphopenia; neutropenia (including fatal neutropenia); pancytopenia (including fatal 
pancytopenia); thrombocytopenia; GI toxicity including abdominal pain, diarrhea, 
dyspepsia, mucosal inflammation, nausea, oral pain, stomatitis, and vomiting; asthenia; 
fatigue; pyrexia; infection (including fatal infection); sepsis (including fatal sepsis); liver 
function test abnormal including aspartate aminotransferase (AST), alanine aminotransferase 
(ALT), bilirubin, alkaline phosphatase (ALP), and gamma-glutamyltransferase (GGT); 
decreased appetite; dehydration; gait disturbance; sedation; somnolence; confusional state; 
disorientation (and associated memory loss); alopecia; rash (including bullous dermatitis); 
and palmar-plantar erythrodysesthesia syndrome. 
While all of these toxicities are potentially associated with risk or discomfort to the patient, 
they are anticipated to be reversible. However, it is possible that alisertib will have other 
toxicities that have not been observed in or predicted from its evaluation in rats and dogs 
and from ongoing studies in humans.  
Results from the alisertib human ADME Study C14014 indicate that oxidative metabolism 
is the predominant route of elimination for alisertib. Results of subsequent in vitro drug 
metabolism studies suggest that the oxidative metabolism of alisertib is mainly mediated via 
CYP3A4. These findings suggest that alisertib systemic exposures may be potentially 
increased when co-administered with clinically significant CYP3A inhibitors. The DDI 
study (C14020) with itraconazole (a strong CYP3A inhibitor) revealed that itraconazole 
produced an approximately 40% increase in alisertib systemic exposures. These results 
validate recommendations that the concomitant use of strong CYP3A inhibitors be avoided. 
Selection of an alternate concomitant medication with no or minimal CYP3A inhibition 
potential is recommended. If co-administration of strong CYP3A inhibitors is medically 
necessary, investigators should monitor for toxicities and follow the dose modifications for 
toxicity per study protocol. 
To mitigate the inherent risks in clinical studies of alisertib, patients are evaluated frequently 
while they are receiving treatment.  
The oral solution formulation of alisertib contains propylene glycol and polyethylene glycol 
400 (PEG400). The concentrations of these excipients in the formulation are within the 
range of levels used in Food and Drug Administration (FDA)-approved drug products and 
are generally considered safe for use as an excipient in liquid medications. Information may 
be found at https://www.atsdr.cdc.gov/csem/csem.asp?csem=12&po=0. Ingestion of large 
amounts of propylene glycol increases the risk of metabolic lactic acidosis.  Approximately 
55% to 75% of propylene glycol is metabolized to pyruvate, acetate, and lactate, while 25% 


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to 45% remains unchanged; accumulation of lactic acid is the reason that propylene glycol 
toxicity commonly presents with an anion gap metabolic acidosis.31   Therefore, in clinical 
trials evaluating the oral solution, patients will be closely monitored for signs and 
symptoms of metabolic acidosis. The schedule will include a treatment-free period within 
every treatment cycle. The risks related to propylene glycol administration (as a component 
of the oral solution) have not been established however it is very likely that the low dose, 
intermittent exposure to oral propylene glycol in patients with normal renal function poses a 
low risk for toxicity. 
Because alisertib inhibits Aurora A kinase, it is possible that alisertib may interfere with 
cancer growth and cause cancer cell death. Nonclinical 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 to provide antitumor 
activity through a non-cross-resistant pathway. Based on laboratory studies with agents that 
target Aurora A kinase, it is also possible that alisertib will induce cancer cell senescence,32 
leading to a terminal outcome for cancer cells that may be initially represented by stable 
disease (SD) instead of immediate tumor reduction (response).  
Alisertib has shown antitumor activity in the form of objective tumor responses and/or 
prolonged disease stabilization in a number of different tumor types, including solid tumors 
(SCLC, ovarian, head/neck, NSCLC, liposarcoma, colorectal, and breast) and hematological 
tumors (peripheral T-cell lymphoma [PTCL], multiple myeloma, follicular lymphoma, 
DLBCL, Burkitt’s lymphoma, MCL, and acute myeloid leukaemia [AML]). 
Reference Safety Information for Assessment of Expectedness of Serious Adverse 
Reactions 
The table below contains the expected SARs for regulatory reporting purposes only along 
with their reported frequency. Refer to the IB  for a comprehensive overview of the safety 
profile of alisertib, including expected nonserious adverse drug reactions ( ADRs). Fatal 
SARs are considered unexpected and will be reported as SUSARs. 
 


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SARs Considered Expected for Safety Reporting Purposes 
SARs 
 
Number of Patients From Sponsored 
Clinical Trials 
(N=927) 
MedDRA 
 
All SARs 
Life-threatening 
SARs 
System Organ Class 
 
   Preferred Term 
n (%) 
n (%) 
Blood And Lymphatic 
System Disorders 
  Febrile Neutropenia 
69 (7.4) 
28 (3.0) 
  Neutropenia 
35 (3.8) 
33 (3.6) 
  Anemia 
22 (2.4) 
9 (1.0) 
  Thrombocytopenia 
16 (1.7) 
13 (1.4) 
  Leukopenia 
10 (1.1) 
9 (1.0) 
  Pancytopenia 
7 (0.8) 
6 (0.6) 
  Febrile Bone Marrow Aplasia 
1 (0.1) 
1 (0.1) 
Gastrointestinal 
Disorders 
  Stomatitis 
29 (3.1) 
3 (0.3) 
  Diarrhea 
20 (2.2) 
N/A 
  Vomiting 
8 (0.9) 
N/A 
  Nausea 
5 (0.5) 
N/A 
  Aphthous Ulcer 
3 (0.3) 
N/A 
  Dysphagia 
3 (0.3) 
N/A 
  Abdominal Pain 
2 (0.2) 
N/A 
Infections And 
Infestations 
  Pneumonia 
14 (1.5) 
2 (0.2) 
  Sepsis 
5 (0.5) 
3 (0.3) 
  Lung Infection 
2 (0.2) 
N/A 
  Septic Shock 
2 (0.2) 
1 (0.1) 
  Urinary Tract Infection 
2 (0.2) 
N/A 
General Disorders And 
Administration Site 
Conditions 
  Pyrexia 
7 (0.8) 
N/A 
  Fatigue 
6 (0.6) 
N/A 
  Asthenia 
4 (0.4) 
N/A 
Metabolism And 
Nutrition Disorders 
  Dehydration 
10 (1.1) 
N/A 
  Hypokalemia 
4 (0.4) 
2 (0.2) 
Investigations 
  White Blood Cell Count 
Decreased 
4 (0.4) 
2 (0.2) 
  Neutrophil Count Decreased 
3 (0.3) 
2 (0.2) 


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SARs 
 
Number of Patients From Sponsored 
Clinical Trials 
(N=927) 
MedDRA 
 
All SARs 
Life-threatening 
SARs 
System Organ Class 
 
   Preferred Term 
n (%) 
n (%) 
  Platelet Count Decreased 
2 (0.2) 
N/A 
Nervous System 
Disorders 
  Somnolence 
3 (0.3) 
N/A 
  Balance Disorder 
1 (0.1) 
N/A 
  Depressed Level Of 
Consciousness 
1 (0.1) 
N/A 
  Dizziness 
1 (0.1) 
N/A 
  Sedation 
1 (0.1) 
N/A 
Respiratory, Thoracic 
And Mediastinal 
Disorders 
  Dyspnea 
3 (0.3) 
N/A 
Skin And Subcutaneous 
Tissue Disorders 
  Acute Generalized 
Exanthematous Pustulosis 
2 (0.2) 
N/A 
  Palmar-Plantar 
Erythrodysaesthesia Syndrome 
2 (0.2) 
N/A 
  Dermatitis Bullous 
1 (0.1) 
1 (0.1) 
  Rash 
1 (0.1) 
N/A 
Hepatobiliary Disorders   Hyperbilirubinemia 
2 (0.2) 
N/A 
Psychiatric Disorders 
  Confusional State 
3 (0.3) 
N/A 
Renal And Urinary 
Disorders 
  Acute Kidney Injury 
4 (0.4) 
N/A 
Source: Clinical Database (cutoff date: 29 March 2016: with correction 29 March 2019). 
MedDRA: Medical Dictionary of Regulatory Activities; n: number of subjects in the group; N: total 
number of subjects; SAR: serious adverse reactions. 
Note: System Organ Class and Preferred Term are coded by MedDRA V21.0. Studies included in the 
analyses: C14001 - C14007, C14010, C14012 - C14014, C14017, C14019, TB-MA010030, TB-
MA010033.   
 


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1.6    Pembrolizumab 
1.6.1    Scientific Background  
Pembrolizumab has been evaluated for the treatment of HNSCC as outlined in section 1.1. 
In KEYNOTE 01222 patients with recurrent or metastatic HNSCC with no prior 
immunotherapy were treated with pembrolizumab at 200mg IV weekly with an overall 
response rate of 18%.22  Long term follow up demonstrated that 85% of responses lasted ≥6 
months and the overall survival at 12 months was 38%.26  Pembrolizumab was approved on 
June 10, 2019 by the FDA in combination with chemotherapy for all recurrent and 
metastatic HNSCC patients and as a single agent for those whose tumors express PD L1 
(CPS ≥1) as front line therapy based on data from KEYNOTE 048.33  Pembrolizumab alone 
was non-inferior to chemotherapy plus cetuximab in the total population and resulted in an 
improved survival in those with CPS ≥1.  The response rates to pembrolizumab alone were 
17%, 19%, and 23% in the overall population, CPS ≥1, and CPS ≥20 populations 
respectively.33 
1.6.2    Nonclinical Pharmacology 
Pembrolizumab is a potent humanized immunoglobulin G4 monoclonal antibody with high 
specificity of binding to the PD-1 receptor, thus inhibiting its interaction with PD-L1 and 
programmed cell death ligand 2 (PD-L2). Based on preclinical in vitro data, pembrolizumab 
has high affinity and potent receptor blocking activity for PD-1.  
1.6.3    Nonclinical Toxicity 
Pembrolizumab has an acceptable preclinical safety profile. For summary of preclinical 
study data for pembrolizumab, refer to Keytruda ® IB. 
1.6.4    Clinical Pharmacokinetics and Pharmacodynamics 
Pharmacokinetics and pharmacodynamics of pembrolizumab will not be evaluated in this 
study. 
The planned dose of pembrolizumab for this study is 200 mg Q3 weeks. Based on the 
totality of data generated in the Keytruda development program, 200 mg Q3 weeks is the 
appropriate dose of pembrolizumab for adults across all indications and regardless of tumor 
type. As outlined below, this dose is justified by:  
• Clinical data from 8 randomized studies demonstrating flat dose- and exposure 
efficacy relationships from 2 mg/kg Q3 weeks to 10 mg/kg every 2 weeks (Q2 
weeks), 


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• Clinical data showing meaningful improvement in benefit-risk including overall 
survival at 200 mg Q3 weeks across multiple indications, and 
• Pharmacology data showing full target saturation in both systemic circulation 
(inferred from pharmacokinetic [PK] data) and tumor (inferred from 
physiologically based PK [PBPK] analysis) at 200 mg Q3 weeks. 
Among the 8 randomized dose-comparison studies, 2262 participants were enrolled with 
melanoma and non-small cell lung cancer (NSCLC), covering different disease settings 
(treatment naïve, previously treated, PD-L1 enriched, and all-comers) and different 
treatment settings (monotherapy and in combination with chemotherapy). Five studies 
compared 2 mg/kg Q3 weeks versus 10 mg/kg Q3 weeks (KN001 Cohort B2, KN001 
Cohort D, KN002, KN010, and KN021), and 3 studies compared 10 mg/kg Q3 weeks versus 
10 mg/kg Q2 weeks (KN001 Cohort B3, KN001 Cohort F2 and KN006). All of these studies 
demonstrated flat dose- and exposure-response relationships across the doses studied 
representing an approximate 5- to 7.5-fold difference in exposure. The 2 mg/kg (or 200 mg 
fixed-dose) Q3 weeks provided similar responses to the highest doses studied. Subsequently, 
flat dose-exposure response relationships were also observed in other tumor types including 
head and neck cancer, bladder cancer, gastric cancer and classical Hodgkin Lymphoma, 
confirming 200 mg Q3 weeks as the appropriate dose independent of the tumor type. These 
findings are consistent with the mechanism of action of pembrolizumab, which acts by 
interaction with immune cells, and not via direct binding to cancer cells. 
Additionally, pharmacology data clearly show target saturation at 200 mg Q3 weeks. First, 
PK data in KN001 evaluating target-mediated drug disposition conclusively demonstrated 
saturation of PD-1 in systemic circulation at doses much lower than 200 mg Q3 weeks. 
Second, a PBPK analysis was conducted to predict tumor PD-1 saturation over a wide range 
of tumor penetration and PD-1 expression. This evaluation concluded that pembrolizumab at 
200 mg Q3 weeks achieves full PD-1 saturation in both blood and tumor. 
Finally, population PK analysis of pembrolizumab, which characterized the influence of 
body weight and other participant covariates on exposure, has shown that the fixed-dosing 
provides similar control of PK variability as weight-based dosing, with considerable overlap 
in the distribution of exposures from the 200 mg Q3 weeks fixed dose and 2 mg/kg Q3 
weeks dose. 
1.6.5    Clinical Experience 
Pembrolizumab is in clinical development as an intravenous (IV) immunotherapy for 
advanced malignancies. Keytruda® (pembrolizumab) is indicated for the treatment of 


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patients across several indications. For more details on specific indications refer to the 
Keytruda ® IB. For summary of ongoing clinical study data, refer to Keytruda ® IB. 
1.6.6    Potential Risks of pembrolizumab 
For comprehensive list of risks associated with pembrolizumab, please refer to Keytruda ® 
IB. Also see Adverse Events management in Section 7.5.  
1.7    Study rationale and selection of drug doses 
Aurora kinases are serine/threonine mitotic kinases that control centrosome maturation, 
spindle assembly, and chromosome segregation. Cancers with RB1 loss are hyper dependent 
upon Aurora kinases for survival.34, 35  Inhibitors of Aurora A or B selectively killed RB1 
null cancer cells.35-37  Inactivation of the Rb/E2F pathway can lead to a hyperactivated 
spindle assembly checkpoint, replication stress, fork stalling, and double stranded DNA 
breaks.38-40  These defects may underlie the dependence of Rb-deficient cancer cells on 
Aurora kinase for mitotic progression and escape from mitotic catastrophe. 
The Rb pathway is altered in a significant number of HNSCCs.  HPV+ cancer cells express 
the viral oncoprotein E7 that leads to Rb protein degradation. In the Cancer Genome Atlas 
(TCGA), RB1 loss of function (LOF) occurs an about 4% of HPV negative and 6% of HPV 
positive HNSCC by homozygous deletion or mutation.  This LOF was associated with 
decreased RB1 gene expression.17  Analysis of an independent set of 484 oral and 
oropharynx squamous cell carcinomas demonstrated that approximately 6% of them 
harbored deleterious single nucleotide variants (SNVs) in RB1.  Additionally, deletions of 
the genetic locus were discovered in 34% of the HPV+ tumors.21  Deletion or LOF 
mutations of CDKN2A (p16) occurs in about 57% of HPV negative HNSCC17 and may lead 
to the loss of Rb function via activation of CDK4/6.41 
We hypothesize that Rb-deficient cancers rely on mitotic kinases such as Aurora to maintain 
mitotic fidelity such that their inhibition leads to irreversible mitotic arrest, DNA damage, 
and apoptosis. Furthermore, we hypothesize that the resulting DNA damage will stimulate 
the cGAS/STING pathway, producing type I interferons, and that the resulting immunogenic 
cell death (ICD) will lead to host T cell engagement and increased sensitivity to ICT.  This 
second hypothesis is crucial because cancers nearly always develop resistance to even 
highly effective targeted therapies, limiting their long-term benefits. In contrast, ICT results 
in durable responses in some patients, making it imperative to seek strategies that enhance 
the efficacy of ICT. 


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If Aurora kinase inhibition leads to ICD in Rb deficient cancers, then we expect to find that 
the combination of pembrolizumab and alisertib has a higher response rate and longer PFS 
than pembrolizumab alone. The addition of Aurora kinase inhibitors to ICT may reverse 
resistance in refractory patients. We will test baseline PD-L1 and tumor infiltrating 
lymphocytes (TIL) function because they correlate with responses to ICT.22, 24-27, 42-44 
Likewise, we will test the basal protein expression of Rb34, 35 and Myc45, 46 as both are linked 
to sensitivity to Aurora kinase inhibitors. Immunity developed against HPV viral proteins (in 
HPV+ HNSCC) may enhance recurrence-free survival of HPV+ cancers47 so comprehensive 
immune profiling of blood and tumor samples will be used to characterize TIL function, 
HPV reactivity, and the composition of the T cell repertoire. 
In the safety (phase I) cohort, all patients will receive full dose pembrolizumab (200mg IV 
every 3 weeks) because this is a standard of care drug with known efficacy. Please see also 
above section 1.6.4. Alisertib will be started at 40 mg po BID x 7 days every 3 weeks and 
then escalated in subsequent cohorts as follows: 
Dose Level Alisertib Dose Enteric Coated Tablets (ECT) 
-1 
30 mg po BID x 7 days every 21 days 
1 
40 mg po BID x 7 days every 21 days 
2 
50 mg po BID x 7 days every 21 days 
 
The relative bioavailability of ECT vs. oral solution has not been directly evaluated in a 
crossover fashion; however, the relative bioavailability of the oral solution formulation in 
reference to PIC has been determined to be 1.26, with an associated 90% CI of 1.09 – 1.47. 
That is, the oral solution is expected to achieve approximately 30% higher alisertib 
exposures than that of PIC and ECT formulation. Therefore, the dose levels for patients 
requiring alisertib administered as oral solution are as follows: 
 
 
Dose Level Alisertib Dose Oral Solution Formulation (5 mg/mL) 
-1 
21 mg po BID x 7 days every 21 days   (4.2  mL) 
1 
28 mg po BID x 7 days every 21 days (5.6 mL) 
2 
35 mg po BID x 7 days every 21 days (7.0 mL) 


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2. STUDY OBJECTIVES 
2.1    Primary Objective 
The primary objective of this study is to: 
• Phase I: To determine the recommend phase II dose of the combination of 
alisertib and pembrolizumab. 
•  Phase II: To determine the overall response rate (ORR) of patients with 
immunotherapy-refractory recurrent or metastatic Rb-deficient head and neck 
squamous cell carcinoma (HNSCC) treated with the combination of 
pembrolizumab and alisertib. 
2.2    Secondary Objectives 
The secondary objectives of this study are to: 
• To evaluate the safety of the combination of pembrolizumab and alisertib in 
patients with solid tumors. 
• To determine the overall survival and progression free survival (PFS) in HNSCC 
patients treated with the combination of pembrolizumab and alisertib. 
• To determine the relationship between pharmacokinetics, pharmacodynamics, 
baseline immune and tumor biomarkers and clinical responses in patients treated 
with alisertib and pembrolizumab. 
• To determine correlations between clinical responses and the effect of the 
treatment on human papilloma virus (HPV)-reactive T cells in HPV+ cancers.  
• To determine correlations between clinical responses and tumor infiltrating 
lymphocyte function and T cell repertoire. 
 


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3.    INVESTIGATIONAL PLAN 
This is an investigator-initiated study.  The principal investigator is Faye Johnson.  MD 
Anderson is the IND Sponsor. 
3.1    Overall Design and Plan of the Study 
This is an open label, phase I-II study of αPD-1 (pembrolizumab) and Aurora kinase 
(alisertib) inhibition in patients with recurrent or metastatic cancer. 
 
In the phase I portion, we will enroll and treat patients in cohorts of size 2 with a target 
toxicity rate for the MTD of 0.3 (see statistical design). Patients will receive full dose αPD-1 
antibody pembrolizumab (200mg IV every 3 weeks) in combination with the Aurora A 
kinase inhibitor alisertib.  Alisertib will be started at 40 mg po BID x 7 days every 3 weeks 
and then escalated in subsequent cohorts as follows: 
 
Dose Level Alisertib Dose 
-1 
30 mg po BID x 7 days every 21 days 
1 
40 mg po BID x 7 days every 21 days 
2 
50 mg po BID x 7 days every 21 days 
 
The dose levels for patients requiring alisertib administered as oral solution are as follows 
(see section 1.7 for dose conversion details): 
 
In the phase II study, patients with Rb-deficient HNSCC with recurrent/metastatic disease 
who are immunotherapy-refractory will be treated with the combination.  For HPV negative 
HNSCC, those tumors with RB1 loss of function mutation, RB1 homozygous deletion, or 
CDKN2A deletion or CDKN2A LOF mutations will be tested for Rb loss with Rb IHC.41, 48  
Tumors will be measured every 6 weeks and evaluated using the Response Evaluation 
Criteria In Solid Tumors (RECIST) 1.1 guidelines.1   
 
In both the phase I and phase II portions of the study, patients will receive study drugs until 
progression, unacceptable toxicity, or withdrawal of consent.  Tumors will be measured 
every 6 weeks and evaluated using the Response Evaluation Criteria In Solid Tumors 
(RECIST) 1.1 guidelines.1  Patients who remain on study for ≥ 10 cycles without 
progression  may opt for tumor measurements every 3 cycles  rather than every 2 cycles.  To 
confirm adequate drug exposure and target inhibition and based on findings from prior 
studies2, 3 we will draw blood for pharmacokinetic (PK) analysis of alisertib in the first 12 
patients treated at the recommended phase II dose on days 1 and 7 of course 1 at 1, 2, 3, 8, 
and 10 h after the morning dose of alisertib and calculate Cmax, T ½ , and AUC values. 
 
Dose Level Alisertib Dose Oral Solution Formulation (5 mg/mL) 
-1 
21 mg po BID x 7 days every 21 days   (4.2  mL) 
1 
28 mg po BID x 7 days every 21 days (5.6 mL) 
2 
35 mg po BID x 7 days every 21 days (7.0 mL) 


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We will obtain optional tumor biopsies at baseline and at 6 weeks in patients in phase II 
portion of the study after the first interim analysis (i.e., if the efficacy of the combination 
passes the futility metric after 14 patients are treated).   We will obtain blood every 6 weeks 
in all patients on the phase II study for correlative studies described in section 5.5. 
 
3.2    Selection of Patients 
The total number of patients to be enrolled on this study is 24-40. 
Enrollment is defined as the first day of alisertib treatment (i.e., Day 1 of Cycle 1). 
3.2.1    Inclusion Criteria 
Inclusion Criteria – phase II only 
1. 
Histologically or cytological confirmed diagnosis of Rb-deficient HNSCC for which 
no standard curative therapy is available. 
2. 
Rb deficient HNSCC includes CLIA-certified testing confirming one of the following: 
A. HPV positive as determined by any one of the following: p16 immunohistochemistry 
(IHC), HPV RNA in situ hybridization (ISH), RNAscope (mRNA ISH), DNA ISH, 
DNA PCR, or qRT PCR. 
B. No Rb protein expression in the tumor as determined by IHC.41, 48 
3. 
Progression on prior treatment with an anti-PD-1 antibody or an anti-PD-L1 antibody. 
A. Has received at least 2 doses of a PD-1/PD-L1 checkpoint blockade therapy. 
B. Clinical or radiographical progression has been documented within 12 weeks from 
the last dose of PD-1/PD-L1 checkpoint blockade therapy. 
 
Inclusion Criteria – phase I only 
1. 
Histologically or cytological confirmed diagnosis of an invasive solid tumor 
malignancy, for which no standard curative or life prolonging therapy is available. 
 
Inclusion Criteria – both phase I and phase II 
1. 
Male or female patients ≥ 18 years of age. 
2. 
ECOG performance status of ≤ 2 (see section 7.4). 
3. 
Clinical laboratory values as specified below within 22 days before the first dose of 
study drug   
• Absolute neutrophil count (ANC) > 1500/mm³ 
• Platelets > 100,000/mm³ 
• Hgb > 9 g/dL. Values must be obtained without need for myeloid growth factor or 
platelet transfusion support within 14 days, however, erythrocyte growth factor is 
allowed as per published ASCO guidelines. 
• Total bilirubin ≤ 1.5 x upper limit of normal (ULN) 


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• SGOT (AST) and SGPT (ALT)< 2.5 x ULN. AST and/or ALT may be up to 5X 
ULN if with known liver mets or total 3 x ULN with direct bilirubin ≤ ULN in 
patients with well-documented Gilbert syndrome.  
• Adequate renal function as defined by calculated creatinine clearance ≥30 ml/min 
(Cockroft-Gault Formula, see Section 7.5). 
4. Measurable disease according to RECIST version 1.1.  
5. Voluntary written consent must be given before performance of any study related 
procedure not part of standard of care, with the understanding that consent may be 
withdrawn by the patient at any time without prejudice to future medical care. 
6. Patients must be able to either swallow alisertib enteric coated tablets, swallow alisertib 
oral solution formulation, or administer alisertib oral solution formulation via a feeding 
tube that terminates in the stomach. 
7. 
Willing to provide blood and tissue for correlative research purposes. 
8. 
Female patients who:  
• Are postmenopausal for at least 1 year before the screening visit, OR 
• Are surgically sterile, OR 
• If they are of childbearing potential, agree to practice 1 highly effective method of 
contraception and 1 additional effective (barrier) method at the same time, from 
the time of signing the informed consent through 120 days after the last dose of 
study drug, OR 
• Agree to practice true abstinence, when this is in line with the preferred and usual 
lifestyle of the subject. (Periodic abstinence [eg, calendar, ovulation, 
symptothermal, postovulation methods], withdrawal, spermicides only, and 
lactational amenorrhea are not acceptable methods of contraception. Female and 
male condoms should not be used together.) 
 
9. 
Male patients, even if surgically sterilized (i.e., status postvasectomy), who: 
• Agree to practice effective barrier contraception during the entire study treatment 
period and through 120 after the last dose of study drug, OR 
• Agree to practice true abstinence, when this is in line with the preferred and usual 
lifestyle of the subject. (Periodic abstinence [e.g., calendar, ovulation, 
symptothermal, postovulation methods], withdrawal, spermicides only, and 
lactational amenorrhea are not acceptable methods of contraception. Female and 
male condoms should not be used together.) 
 
3.2.2    Exclusion Criteria 
1. 
Radiation therapy to more than 25% of the bone marrow. Whole pelvic radiation is 
considered to be over 25%.  
2. 
Prior allogeneic bone marrow or organ transplantation.  


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3. 
Known gastrointestinal (GI) disease or GI procedures that could interfere with the oral 
absorption or tolerance of alisertib. Examples include, but are not limited to partial 
gastrectomy, history of small intestine surgery, and celiac disease.  
4. 
Inability to swallow (or use a feeding tube to administer) oral medication or inability 
or unwillingness to comply with the administration requirements related to alisertib.  
5. 
Known history of uncontrolled sleep apnea syndrome and other conditions that could 
result in excessive daytime sleepiness, such as severe chronic obstructive pulmonary 
disease; requirement for supplemental oxygen. 
6. 
Requirement for constant administration of proton pump inhibitor, H2 antagonist, or 
pancreatic enzymes throughout the study.  The intermittent use of H2-antagonists and 
antacids (including carafate) is only allowed within these guidelines: 
a. H2 antagonists until D-1 and after the dosing of alisertib is done 
b. Antacid formulations until 2 hours before doing and after 2 hours following 
dosing. 
c. PPI is allowed until D-5 of first alisertib dose. PPIs are prohibited throughout 
the study 
7. 
Myocardial infarction within 6 months prior to enrollment or has New York Heart 
Association (NYHA) Class III or IV heart failure (see Section 7.3), uncontrolled 
angina, severe uncontrolled ventricular arrhythmias, or electrocardiographic 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. 
8. 
Female subject who is pregnant or breast-feeding.  Confirmation that the subject is not 
pregnant must be established by a negative urine or serum β-human chorionic 
gonadotropin (β-hCG) pregnancy test result obtained during screening.  Pregnancy 
testing is not required for post-menopausal or surgically sterilized women. 
9. 
Female patient who intend to donate eggs (ova) during the course of this study or 120 
days after receiving their last dose of study drug(s). 
10. Male patients who intend to donate sperm during the course of this study or 120 days 
after receiving their last dose of study drug(s). 
11. 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. 
12. Diagnosed or treated for another invasive malignancy within 2 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.   
13. Has received any anti-cancer treatment including investigational agents within 21 days 
prior to first dose of alisertib. 


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14. Patients who receive gamma knife radiosurgery for brain metastases or whole brain 
radiation are eligible if gamma knife radiosurgery was completed > 2 weeks before 
treatment is started or whole brain radiation was performed > 4 weeks before treatment 
is started, and are clinically stable (not requiring steroids or anti-epileptic drugs). 
15. Known hypersensitivity to any of the excipients of alisertib enteric coated tablets or 
severe reaction to any human monoclonal antibody. 
16. Patients with a prior history of clinically significant metabolic acidosis (exclusion only 
for patients receiving alisertib oral solution). 
17. Major surgery within 28 days prior to first dose of alisertib or persisting side effects 
that have not improved to NCI-CTCAE grade 1 or better. 
18. Patients who are on (or will require) prolonged systemic corticosteroid treatment 
during the study except for replacement dosing for adrenal insufficiency. 
19. Concurrent severe and/or uncontrolled medical conditions that would, in the 
investigator’s judgment, contraindicate patient participation in the clinical study or 
require concomitant anti-cancer drugs (e.g. active or uncontrolled severe infection, 
chronic active hepatitis, immuno-compromised, acute or chronic pancreatitis, 
uncontrolled high blood pressure, interstitial lung disease). 
20. Patients with active, known, diagnosed or suspected autoimmune disease.  Patients 
suffering from vitiligo, type I diabetes mellitus, residual hypothyroidism due to 
autoimmune thyroiditis only requiring thyroid hormone replacement therapy, or 
psoriasis not requiring systemic treatment can be enrolled. 
21. Patients diagnosed with active interstitial lung disease (ILD)/pneumonitis or a history 
of ILD/pneumonitis or another condition requiring immunosuppressive doses of 
systemic medication such as systemic corticosteroids or absorbed topical 
corticosteroids (doses ≥ 10 mg/day prednisone or equivalent) or other 
immunosuppressive medications within 14 days of study drug administration. Inhaled 
or topical corticosteroids, adrenal replacement doses, or < 10 mg daily prednisone or 
equivalent are permitted. 
22. Administration of any live vaccine within 30 days before first dose of study drug. 
23. Uncontrolled infection with human immunodeficiency virus (HIV), hepatitis B virus or 
hepatitis C virus, except for:  Patients with HIV who have controlled infection 
(undetectable viral load and CD4 count above 350 cells/mm3 either spontaneously or 
on a stable antiviral regimen) are permitted; Patients with hepatitis B (HepBsAg+) 
virus who have controlled infection (serum hepatitis B virus DNA PCR that is below 
the limit of detection AND receiving antiviral therapy for hepatitis B) are permitted; 
Patients who are hepatitis C virus antibody positive (HCV Ab +) who have controlled 
infection (undetectable HCV RNA by PCR either spontaneously or in response to a 
successful prior course of anti-HCV therapy) are permitted. 
24. Participating in another therapeutic clinical trial. 
25. Prior immune-related adverse events (irAE) as follows: 
A. Any life-threatening irAE will not be eligible. 
B. Any grade irAE of the following types will not be eligible: 
i. Nervous system irAE 
ii. Ocular irAE 
iii. Cardiovascular irAE 
iv. Severe Cutaneous Adverse Reactions (SCAR) 


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v. Hematological irAE  
C. Any grade endocrine irAE will be eligible if replacement therapy can compensate 
for the resulting deficit. 
D. Grade ≥ 2 irAE of the following will not be eligible: 
i. Colitis 
ii. Hepatitis 
iii. Bullous Dermatoses 
iv. Pneumonitis 
v. Musculoskeletal 
vi. Renal 
E. Grade ≥ 3 cutaneous irAE will not be eligible. 
F. All irAEs must have resolved to Grade ≤ 1 at least 14 days before the planned first 
dose. 
 
3.3    Study Treatments 
3.3.1    Clinical Trial Materials Note:  
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. Alisertib ECT must be swallowed whole can be administered with or without food.  
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 
key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
The oral solution formulation of the drug must be given on an empty stomach, at least one 
hour before and two hours after food or drink except water. 
Pembrolizumab is supplied as pembrolizumab 100 mg/4 mL vials (25 mg/ml) solution for 
IV infusion.  
3.3.2    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. 
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 


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permitted from 15-30C; 59-86F) and used before the retest expiry date provided by Puma 
Biotechnology.  Containers should be kept closed during storage 
The packaged and labeled study drug, alisertib oral solution, will be provided by Puma 
Biotechnology 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.  
Fifty-five milliliters of oral solution are packaged into each 2 oz amber HDPE bottle.  
Alisertib will be supplied as an oral solution at 5 mg/mL strength.  The bottles will have a 
child-resistant cap. 
The oral solution 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 15-30C; 59-86F) and used before the retest expiry date provided by 
Puma Biotechnology.  Containers should be kept closed during storage. 
Alisertib is an anticancer drug, and as with other potentially toxic compounds, caution 
should be exercised when handling MLN8237. 
The Pembrolizumab Package Insert contains specific instructions for pembrolizumab 
preparation and administration. The investigator or designee must confirm appropriate 
temperature conditions have been maintained during transit for all study intervention 
received, and any discrepancies are reported and resolved before use of the study 
intervention. 
Only participants enrolled in the study may receive study intervention, and only authorized 
site staff may supply or administer study intervention. All study interventions must be stored 
in a secure, environmentally controlled, and monitored (manual or automated) area in 
accordance with the labeled storage conditions with access limited to the investigator and 
authorized site staff. 
The investigator, institution, or the head of the medical institution (where applicable) is 
responsible for study intervention accountability, reconciliation, and record maintenance 
(i.e., receipt, reconciliation, and final disposition records).  
For all study sites, the local country Sponsor personnel or designee will provide appropriate 
documentation that must be completed for drug accountability and return, or local discard 
and destruction if appropriate. Where local discard and destruction is appropriate, the 
investigator is responsible for ensuring that a local discard/destruction procedure is 
documented. 


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The study site is responsible for recording the lot number, manufacturer, and expiry date for 
any locally purchased product (if applicable) as per local guidelines unless otherwise 
instructed by the Sponsor. 
The investigator shall take responsibility for and shall take all steps to maintain appropriate 
records and ensure appropriate supply, storage, handling, distribution, and usage of study 
interventions in accordance with the protocol and any applicable laws and regulations.  
 
Drug Administration and Dosage Schedule 
Alisertib Administration 
 Alisertib ECT will be given PO in a dosage of 30-50 mg BID for 7 Days (Days 1-7) of each 
21-day treatment cycle (± 3 days).   
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. 
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 
key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
 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). 
Pembrolizumab Administration 
Pembrolizumab administration will consist of a total dose of 200 mg administered 
intravenously every 3 weeks (day 1 of each 21 day cycle ± 3 days).  


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3.3.3    Dose Modification and Delay 
Toxicity will be evaluated according to the National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI CTCAE), Version 5.0.  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.  
Alisertib and pembrolizumab have very distinct toxicity profiles.  If a DLT is clearly due to 
one drug, in the judgement of the principal investigator, then the non-offending agent may 
be continued without dose or schedule adjustment. 
Definition of DLT 
For this protocol, DLT will be defined as an adverse event at least possibly related to the 
study medication and meeting the following criteria.  
Toxicity 
DLT Definition as per NCI CTCAE version 
5 
Blood and lymphatic system disorders 
Febrile neutropenic defined as fever ≥ 38.3 
C (≥ 38 > 1 hour) with grade ≥ 3 
neutropenia 
 
Grade ≥ 4 anemia (Life-threatening 
consequences with urgent intervention) 
Investigations 
Grade 3 neutrophil count decreased (ANC 
< 1.0 – 0.5 x 109/L) for ≥ 5 days, or Grade 
≥ 4 (ANC < 0.5 x 109/L) 
 
Grade 3 platelet count decreased (PLT 
<50,000 – 25,000 /mm3) with any ≥ grade 
3 bleeding, or Grade ≥ 4 platelet count 
decreased (PLT <25,000/mm3) with or 
without bleeding 
Renal and urinary disorders 
Acute kidney injury Grade ≥ 3 
Acidosis Grade ≥ 3 
Nervous system disorders 
Somnolence Grade ≥ 3 (obtundation or 
stupor) 


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Gastrointestinal disorders 
Mucositis oral Grade ≥ 3 
Other non-hematologic** 
Grade ≥ 3 
* Any toxicities that caused a dose delay of >2 weeks of the intended next dose will also be 
considered dose-limiting 
** Grade 3 nausea, vomiting, or diarrhea with maximal supportive treatment(s) resolving 
within 3 days will not be considered dose-limiting. 
Toxicity will be evaluated according to the National Cancer Institute Common Terminology 
Criteria for Adverse Events (NCI CTCAE), Version 5, effective November 27, 2017.  These 
criteria are provided in the Study Manual and are available online at 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm 
The NCI CTCAE is not adequate for monitoring the potential adverse effects of propylene 
glycol for patients receiving the oral solution.  Because propylene glycol is the solvent that 
is used to administer some intravenous benzodiazepines, data exist for how to monitor for 
and manage the potential toxicities of hyperosmolarity and an anion gap metabolic acidosis 
in these patients. An osmolar gap >10 mmoles/L indicates that the serum propylene glycol 
concentration may high enough to cause toxicity.49, 50 If patients receiving the oral solution 
have an osmolar gap >10 mmoles, then the medication will be held and an arterial blood gas 
sample will be obtained to evaluate for propylene glycol toxicity and a metabolic acidosis.  
The oral solution may be resumed if the blood pH is <7.3 and the propylene glycol levels are 
below 2 mg/dL. 
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.  
3.3.4    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.   
• In addition, all toxicities considered by the investigator to be related to therapy with 
alisertib must have resolved to ≤ Grade 1 or to the patient’s baseline values before a 
new cycle of therapy may begin. 


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If the patient fails to meet the above-cited criteria for retreatment, then initiation of the next 
cycle of therapy can be delayed for up to 3 weeks.  At the end of one 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 (i.e., a rest period of more than 7 
days) because of incomplete recovery from treatment-related toxicity, the dose of alisertib 
will be reduced per Table 1.  A second dose reduction to 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.  If a patient requires a third dose reduction or a treatment 
delay of more than 3 weeks at any dose, therapy with alisertib will be discontinued. 
However, pembrolizumab may be continued.  
Table 1A    
Table of Dose Adjustments for alisertib ECT formulation 
Dose Level1 
Dose 
Schedule 
Cycle Length 
-3 
Discontinue or 11 mg of 
the oral solution2,3 
PO BID 
7 days of a 21 day cycle 
-2 
Discontinue or 20 mg2 
PO BID 
7 days of a 21 day cycle 
-1 
30 mg 
PO BID 
7 days of a 21 day cycle 
1 
40 mg 
PO BID 
7 days of a 21 day cycle 
 
 
 
 
2 
50 mg 
PO BID 
7 days of a 21 day cycle 
1Starting dose defined by phase I results. 
2Only two dose reductions are allowed.  If the phase II starts at dose level -1, then dose level -3 may be 
needed. 
3This dose is equivalent to 15 mg ECT but the 15mg ECT is not available. 
 
 
Table 1B    
Table of Dose Adjustments for alisertib oral solution formulation 
Dose Level1 
Dose 
Schedule 
Cycle Length 
-3 
Discontinue or 11 mg 
(2.2 mL)2 
 
 
-2 
Discontinue or 14 mg 
(2.8 mL)2 
PO BID 
7 days of a 21 day cycle 
-1 
21 mg (4.2 mL) 
PO BID 
7 days of a 21 day cycle 
1 
28  mg (5.6 mL) 
PO BID 
7 days of a 21 day cycle 
 
 
 
 
2 
35 mg (7.0  mL) 
PO BID 
7 days of a 21 day cycle 
1Starting dose defined by phase I results. 
2Only two dose reductions are allowed.  If the phase II starts at dose level -1, then dose level -3 may be 
needed. 


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3.3.5    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 38.5°C 
• Grade 3 thrombocytopenia with clinically significant bleeding 
3.3.6    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 study sponsor 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. 
Study-pause criteria 
Any death or ≥ 2 grade 4 events not definitely related to underlying disease, progression of 
disease, or intercurrent illness, and at least possibly related to the investigational product 
will be considered as study-pause criteria. 
3.3.7    Treatment Assignment 
N/A (single-arm study) 
3.3.8    Packaging and Labeling 
The study drug, provided by Puma Biotechnology, 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. 
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 
key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
Please see Pembrolizumab Package Insert for specific instructions on handling and labeling.  


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3.4    Excluded Concomitant Medications and Procedures 
The following medications and procedures are prohibited during the study drug 
administration portion of the study: 
• Alternative therapy, including palliative radiotherapy or surgery, for treatment of 
the patient’s malignancy while on treatment Note: Participants can receive 
palliative radiotherapy for painful bone lesions. Targeted external beam irradiation 
should not be used in the primary tumor field where assessment for tumor is 
indicated. 
• 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. 
• 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. 
• Results from alisertib human absorption, distribution, metabolism, and excretion 
(ADME) study (C14014) indicate that oxidative metabolism is the predominant 
route of elimination for alisertib. Results of subsequent in vitro drug metabolism 
studies suggest that the oxidative metabolism of alisertib is mainly mediated via 
CYP3A4. These findings suggest that alisertib systemic exposures may be 
potentially increased when co-administered with clinically significant CYP3A 
inhibitors. The effect of itraconazole, a strong CYP3A inhibitor on alisertib PK is 
being assessed. Until these results become available, it is recommended that the 
concomitant use of moderate or strong CYP3A inhibitors or grapefruit 
juice/grapefruit-containing products be avoided. Selection of an alternate 
concomitant medication with no or minimal CYP3A inhibition potential is 
recommended. If co-administration of moderate or strong CYP3A inhibitors is 


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medically necessary, investigators should monitor for toxicities and follow the dose 
modifications for toxicity per study protocol 
• Investigational agents other than alisertib and pembrolizumab.  
• Live vaccines during drug administration portion of the study, and within 30 days 
of the last dose of study intervention. Examples of live vaccines include, but are not 
limited to, measles, mumps, rubella, chickenpox, yellow fever, intranasal seasonal 
influenza, rabies, BCG, and typhoid (oral).  
• Anticancer hormonal therapy (e.g. androgen deprivation, androgen receptor 
blockade, anti-estrogens).  
• Systemic glucocorticoids for any purpose other than: (1) to modulate symptoms of 
an AE that is suspected to have an immunologic etiology, (2) as required during 
and after PCI, (3) as needed for the prevention of emesis, (4) topical or ocular use, 
(5) premedication for IV contrast allergies, (6) for inhalation in the management of 
asthma or chronic obstructive pulmonary disease, (7) Replacement for adrenal 
insufficiency. 
• In addition to the medications listed here, site staff should refer to the approval 
product labels for prohibited medications, as well as drug-drug interactions for each 
agent used in this study. Participants who, in the assessment by the investigator, 
require the use of any of the aforementioned treatments for clinical management 
should be removed from treatment but continue in study for assessment of disease 
status and survival.  
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. 


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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 should not drive, operate dangerous tools or machinery, or engage in any other 
potentially hazardous activity that requires full alertness and coordination if they experience 
sedation while enrolled in this study. 
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. 
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 (i.e., status post-vasectomy) must agree to one of 
the following:  
Practice effective barrier contraception during the entire study treatment period and through 
120 days after the last dose of study drug, or completely abstain from heterosexual 
intercourse. 


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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. 
3.7.4       Management of New or Worsening Pulmonary Symptoms 
If new or worsening pulmonary symptoms (eg, dyspnea) or radiological abnormalities occur 
in the absence of a clear diagnosis, an interruption in study intervention dosing is 
recommended and further diagnostic workup (including a highresolution computed 
tomography [CT] scan) should be performed to exclude pneumonitis. Following 
investigation, if no evidence of abnormality is observed on CT imaging and symptoms 
resolve, then study intervention can be restarted, if deemed appropriate by the investigator. 
If significant pulmonary abnormalities are identified, these need to be discussed with the 
Principal Investigator. 


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3.7.5  Treatment Compliance 
All drug(s) will be administered to eligible patients under the supervision of the investigator 
or identified sub-investigator(s).  The pharmacist 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 7.5), 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. 
3.7.6 Pembrolizumab-related Adverse Events  
Adverse events associated with pembrolizumab exposure may represent an immunologic 
etiology. These immune-related AEs (irAEs) may occur shortly after the first dose or several 
months after the last dose of pembrolizumab treatment and may affect more than 1 body 
system simultaneously. Therefore, early recognition and initiation of treatment is critical to 
reduce complications. Based on existing clinical study data, most irAEs were reversible and 
could be managed with interruptions of pembrolizumab, administration of corticosteroids 
and/or other supportive care. For suspected irAEs, ensure adequate evaluation to confirm 
etiology or exclude other causes. Additional procedures or tests such as bronchoscopy, 
endoscopy, skin biopsy may be included as part of the evaluation. Based on the severity of 
irAEs, withhold or permanently discontinue pembrolizumab and administer corticosteroids. 
Please see associated Section 7.6 for the management of irAEs.  
 
Pembrolizumab may also cause severe or life-threatening infusion-reactions including 
severe hypersensitivity or anaphylaxis. Signs and symptoms usually develop during or 
shortly after drug infusion and general resolve completely within 24 hours of completion of 
infusion. Dose modification and toxicity management guidelines on pembrolizumab are 
outlined in associated Section 7.6, as well.   
3.8    Duration of Treatment and Patient Participation 
Patients will remain on study until progression of cancer, unacceptable toxicity, or 
withdrawal of consent. 
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: 


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• Intercurrent illness 
• Occurrence of an unacceptable adverse event 
• A treatment cycle delay or alisertib interruption of> 2 weeks because of toxicity 
• Patient request 
• 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. 
Patients withdrawn from the study will be continuously monitored for survival through chart 
review and/or phone call every 2-3 months. 
3.10    Efficacy, Pharmacodynamic/Pharmacogenomic/Correlative studies, and Safety 
Measurements 
3.10.1    Efficacy Measurements 
Tumors will be measured every 6 weeks and evaluated using the Response Evaluation 
Criteria In Solid Tumors (RECIST) 1.1 guidelines.1 Changes in the largest diameter 
(unidimensional measurement) of the tumor lesions and the shortest diameter in the case of 
malignant lymph nodes are used in the RECIST criteria. 
 
Definitions 


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Evaluable for toxicity.  All patients will be evaluable for toxicity from the time of their first 
treatment with any of the protocol agents. 
Evaluable for objective response.  Only those patients who have measurable disease present 
at baseline, have received at least one cycle of therapy, and have had their disease re-
evaluated will be considered evaluable for response.  These patients will have their response 
classified according to the definitions stated below.  (Note:  Patients who exhibit objective 
disease progression prior to the end of cycle 1 will also be considered evaluable.) 
Evaluable Non-Target Disease Response.  Patients who have lesions present at baseline that 
are evaluable but do not meet the definitions of measurable disease, have received at least 
one cycle of therapy, and have had their disease re-evaluated will be considered evaluable 
for non-target disease.  The response assessment is based on the presence, absence, or 
unequivocal progression of the lesions.  
Disease Parameters 
Measurable disease.  Measurable lesions are defined as those that can be accurately 
measured in at least one dimension (longest diameter to be recorded) as ≥20 mm (≥2 cm) 
by chest x-ray or as ≥10 mm (≥1 cm) with CT scan, MRI, or calipers by clinical exam.  
All tumor measurements must be recorded in millimeters (or decimal fractions of 
centimeters). 
Note:  Tumor lesions that are situated in a previously irradiated area may not be considered 
measurable unless there has been demonstrated progression in the lesion. 
Malignant lymph nodes.  To be considered pathologically enlarged and measurable, a lymph 
node must be ≥15 mm (≥1.5 cm) in short axis when assessed by CT scan (CT scan slice 
thickness recommended to be no greater than 5 mm [0.5 cm]).  At baseline and in follow-up, 
only the short axis will be measured and followed. 
Non-measurable disease.  All other lesions (or sites of disease), including small lesions 
(longest diameter <10 mm [<1 cm] or pathological lymph nodes with ≥10 to <15 mm [≥1 
to <1.5 cm] short axis), are considered non-measurable disease.  Bone lesions, 
leptomeningeal disease, ascites, pleural/pericardial effusions, lymphangitis cutis/pulmonitis, 
inflammatory breast disease, and abdominal masses (not followed by CT or MRI), are 
considered as non-measurable. 
Note:  Cystic lesions that meet the criteria for radiographically defined simple cysts should 
not be considered as malignant lesions (neither measurable nor non-measurable) since they 
are, by definition, simple cysts. 


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‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable 
lesions, if they meet the definition of measurability described above. However, if non-cystic 
lesions are present in the same patient, these are preferred for selection as target lesions. 
Target lesions.  All measurable lesions up to a maximum of 2 lesions per organ and 5 lesions 
in total, representative of all involved organs, should be identified as target lesions and 
recorded and measured at baseline.  Target lesions should be selected on the basis of their 
size (lesions with the longest diameter), be representative of all involved organs, but in 
addition should be those that lend themselves to reproducible repeated measurements.  It 
may be the case that, on occasion, the largest lesion does not lend itself to reproducible 
measurement in which circumstance the next largest lesion which can be measured 
reproducibly should be selected.  A sum of the diameters (longest for non-nodal lesions, 
short axis for nodal lesions) for all target lesions will be calculated and reported as the 
baseline sum diameters.  If lymph nodes are to be included in the sum, then only the short 
axis is added into the sum.  The baseline sum diameters will be used as reference to further 
characterize any objective tumor regression in the measurable dimension of the disease. 
Non-target lesions.  All other lesions (or sites of disease) including any measurable lesions 
over and above the 5 target lesions should be identified as non-target lesions and should 
also be recorded at baseline.  Measurements of these lesions are not required, but the 
presence, absence, or in rare cases unequivocal progression of each should be noted 
throughout follow-up.  
 
Response Criteria (Target Lesions) 
Complete Response (CR):  Disappearance of all target lesions.  Any pathological lymph 
nodes (whether target or non-target) must have reduction in short axis to <10 mm (<1 cm). 
Partial Response (PR):  At least a 30% decrease in the sum of the diameters of target lesions, 
taking as reference the baseline sum diameters. 
Progressive Disease (PD):  At least a 20% increase in the sum of the diameters of target 
lesions, taking as reference the smallest sum on study (this includes the baseline sum if that 
is the smallest on study).  In addition to the relative increase of 20%, the sum must also 
demonstrate an absolute increase of at least 5 mm (0.5 cm).  (Note:  the appearance of one or 
more new lesions is also considered progressions). 
Stable Disease (SD):  Neither sufficient shrinkage to qualify for PR nor sufficient increase to 
qualify for PD, taking as reference the smallest sum diameters while on study. 


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Response Criteria (Non-Target Lesions) 
Complete Response (CR):  Disappearance of all non-target lesions and normalization of 
tumor marker level.  All lymph nodes must be non-pathological in size (<10 mm [<1 cm] 
short axis). 
Note:  If tumor markers are initially above the upper normal limit, they must normalize for a 
patient to be considered in complete clinical response. 
Non-CR/Non-PD:  Persistence of one or more non-target lesion(s) and/or maintenance of 
tumor marker level above the normal limits. 
Progressive Disease (PD):  Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions.  Unequivocal progression should not normally 
trump target lesion status.  It must be representative of overall disease status change, not a 
single lesion increase. 
Although a clear progression of “non-target” lesions only is exceptional, the opinion of the 
treating physician should prevail in such circumstances, and the progression status should be 
confirmed at a later time by the review panel (or Principal Investigator). 
 
Evaluation of Best Overall Response 
The best overall response is the best response recorded from the start of the treatment until 
disease progression/recurrence (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started).  The patient's best response assignment 
will depend on the achievement of both measurement and confirmation criteria. 
   
3.10.2    Pharmacokinetic and optional Pharmacodynamic/ 
Pharmacogenomic/Correlative Studies  
To confirm adequate drug exposure and target inhibition and based on findings from prior 
studies2, 3 we will draw blood for pharmacokinetic (PK) analysis of alisertib in the first 12 
patients treated at the recommended phase II dose on days 1 and 7 of course 1 at 1, 2, 3, 8, 
and 10 h after the morning dose of alisertib and calculate Cmax, T ½ , and AUC values. To 
measure target inhibition, pharmacodynamics (PD) studies will be done in pre- and post- 
treatment tumor. Specifically, we will use immunohistochemistry (IHC) to quantify the 
number of cancer cells that stain for phosphorylation of Histone H3 (Ser10)5 and mitotic 
protein monoclonal 2 (MPM2).6 


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3.10.3    Safety Measurements 
Safety parameters commonly used for evaluating investigational systemic anticancer 
treatments are included as safety endpoints, including, but not limited to, the incidence of, 
causality and outcome of AEs/SAEs; and changes in vital signs and laboratory values. 
Adverse events will be assessed as defined by NCI CTCAE, version 5.0. 
3.11    Study Drug Administration 
Alisertib will be administered PO at a dosage of 30-50 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 have the option to take alisertib oral 
solution formulation. 
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 
key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
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.   
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. 
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 


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key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
 
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. 
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 15-30C; 59-86F) and used before the retest expiry date provided by Puma 
Biotechnology.  Containers should be kept closed during storage. 
The packaged and labeled study drug, alisertib oral solution, will be provided by Puma 
Biotechnology 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.  
Fifty-five milliliters of oral solution are packaged into each 2 oz amber HDPE bottle.  
Alisertib will be supplied as an oral solution at 5 mg/mL strength.  The bottles will have a 
child-resistant cap. The oral solution 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 15-30C; 59-86F) and used before the retest expiry 
date provided by Puma Biotechnology.  Containers should be kept closed during storage. 
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. 
3.14    Packaging and Labeling 
The packaged and labeled study drug, alisertib ECT, will be provided by Puma 
Biotechnology 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 
10 mg strength.  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. 
Alisertib drug product can be supplied as the oral solution dosage form at 5 mg/mL, with dose 
strength expressed as the milligrams of active drug (free acid) per milliliter of solution.  The 


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54 
key formulation excipient of the alisertib oral solution formulation that aids in the in vivo 
absorption of the drug is the buffer (sodium bicarbonate). 
The packaged and labeled study drug, alisertib oral solution, will be provided by Puma 
Biotechnology 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.  
Fifty-five milliliters of oral solution are packaged into each 2 oz amber HDPE bottle.  
Alisertib will be supplied as an oral solution at 5 mg/mL strength.  The bottles will have a 
child-resistant cap. 
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 Puma 
Biotechnology.  Containers should be kept closed during storage. 
The oral solution 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 15-30C; 59-86F) and used before the retest expiry date provided by 
Puma Biotechnology.  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. 


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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 medicinal product; the untoward medical occurrence does not necessarily 
have a causal relationship with this treatment.  An AE can therefore be any unfavorable and 
unintended sign (including an abnormal laboratory finding), symptom, or disease temporally 
associated with the use of a medicinal (investigational) product whether or not it is related to 
the medicinal product.  This includes any newly occurring event, or a previous condition 
that has increased in severity or frequency since the administration of study drug. 
An abnormal laboratory value will not be assessed as an AE unless that value leads to 
discontinuation or delay in treatment, dose modification, therapeutic intervention, or is 
considered by the investigator to be a clinically significant change from baseline.   
4.2 Moclia database 
Clinical data capture called Moclia and CORe will be the electronic database used for this 
study’s electronic case report forms. 
 
4.2.1    
Adverse Event Attribution and Severity Definition 
Attribution - the determination of whether an adverse event is related to a medical 
treatment or procedure.  
• 
Definite - the adverse event is clearly related to the investigational agent(s). 
• 
Probable - the adverse event is likely related to the investigational agent(s). 
• 
Possible - the adverse event may be related to the investigational agent(s). 
• 
Unlikely - The adverse event is doubtfully related to the investigational agent(s). 
• 
Unrelated - The adverse event is clearly NOT related to the investigational agent(s). 
 
Severity of the adverse events (AEs) 


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The severity of the adverse events (AEs) will be graded according to the National Cancer 
Institute Common Terminology Criteria for Adverse Events (NCI CTCAE) V.5.0.  Events 
not included in the NCI CTCAE will be scored as follows: 
General grading: 
• 
Grade 1: Mild: discomfort present with no disruption of daily activity, no treatment 
required beyond prophylaxis. 
• 
Grade 2: Moderate: discomfort present with some disruption of daily activity, require 
treatment. 
• 
Grade 3: Severe: discomfort that interrupts normal daily activity, not responding to 
first line treatment.  
• 
Grade 4: Life Threatening: discomfort that represents immediate risk of death 
The investigator (or physician designee) is responsible for verifying and providing source 
documentation for all adverse events and assigning the attribution for all adverse events for 
subjects enrolled. 
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. 
 
4.3    Investigator Communications with Puma Biotechnology 
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 


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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 Puma Biotechnology Pharmacovigilance (or 
designee) from the time of patient consent up to and including 60 days after administration 
of the last dose of study drug.  Any SAE that occurs at any time after completion of study 
treatment or after the designated follow-up period that the sponsor or investigator considers 
to be related to any study drug must be reported to Puma Biotechnology Pharmacovigilance 
(or designee). In addition, new primary malignancies that occur during the follow-up periods 
must be reported, regardless of causality to study regimen, for a minimum of three years 
after the last dose of the investigational product, starting from the first dose of study drug. 
All new cases of primary malignancy must be reported to Puma Biotechnology 
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). 
The principal investigator Dr. Faye Johnson is responsible for reporting serious adverse 
events (SAEs) to the sponsor’s IRB.    
Regardless of expectedness or causality, all SAEs must also be reported to Puma 
Biotechnology Pharmacovigilance or designee: 
Fatal and Life Threatening SAEs within 24 hours of the investigator’s observation 
or awareness of the event 
 
All other serious (non-fatal/non life threatening) events within 4 calendar days of 
the investigator’s observation or awareness of the event 
 
The SAE report must include at minimum: 
• Event term(s) 
• Serious criteria 


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• Intensity of the event(s): Investigator’s or sub-investigator’s determination.  
Intensity for each SAE, including any lab abnormalities, will be determined by using 
the NCI CTCAE version specified in the protocol, as a guideline, whenever 
possible.  The criteria are available online at 
http://ctep.cancer.gov/reporting/ctc.html. 
• Causality of the event(s): Investigator’s or sub-investigator’s determination of the 
relationship of the event(s) to study drug administration.  
Follow-up information on the SAE may be requested by Puma Biotechnology 
Pharmacovigilance (or designee).   
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)? 
Investigator must also provide Puma Biotechnology Pharmacovigilance with a copy of all 
communications with applicable regulatory authorities related to the study product(s) as 
soon as possible but no later than 4 calendar days of such communication. 
 
Recommended Adverse Event Recording Guidelines 
 
Attribution 
Grade 1 
Grade 2 
Grade 3 
Grade 4 
Grade 5 
Unrelated 
Phase I 
Phase I 
Phase I 
Phase II   
 
Phase I 
Phase II   
Phase III 
Phase I  
Phase II   
Phase III 
Unlikely 
Phase I 
Phase I 
Phase I  
Phase II   
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Possible 
Phase I 
Phase II   
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Probable 
Phase I 
Phase II  
 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Definitive 
Phase I 
Phase II  
  
Phase I 
Phase II   
Phase III 
Phase I 
Phase II   
Phase III 
Phase I 
Phase II  
Phase III  
Phase I 
Phase II   
Phase III 
 
Puma Biotechnology Pharmacovigilance or Designee 


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SAE and Pregnancy Reporting Contact Information 
Email: PumaSAE@parexel.com 
Suggested Reporting Form:   
• 
SAE Report Form (a sample will be provided) 
• 
US FDA MedWatch 3500A:  
http://www.fda.gov/Safety/MedWatch/HowToReport/DownloadForms/default.htm 
• 
Any other form deemed appropriate by the investigator 
 
4.4    Serious Adverse Events Reporting 
 
An adverse event or suspected adverse reaction is considered “serious” if, in the view of either 
the investigator or the sponsor, it results in any of the following outcomes: 
 
• Death 
• A life-threatening adverse drug experience – any adverse experience that places the patient, in 
the view of the initial reporter, at immediate risk of death from the adverse experience as it 
occurred. It does not include an adverse experience that, had it occurred in a more severe form, 
might have caused death. 
• Inpatient hospitalization or prolongation of existing hospitalization 
• A persistent or significant incapacity or substantial disruption of the ability to conduct normal 
life functions. 
• A congenital anomaly/birth defect. 
 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered a serious adverse drug experience when, based upon 
appropriate medical judgment, they may jeopardize the patient or subject and may require 
medical or surgical intervention to prevent one of the outcomes listed in this definition. 
Examples of such medical events include allergic bronchospasm requiring intensive treatment 
in an emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse (21 CFR 
312.32). 
 
• Important medical events as defined above, may also be considered serious adverse events. 
Any important medical event can and should be reported as an SAE if deemed appropriate by 
the Principal Investigator or the IND Sponsor, IND Office. 
• All events occurring during the conduct of a protocol and meeting the definition of a SAE 
must be reported to the IRB in accordance with the timeframes and procedures 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”.  


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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 60 days after the last dose of drug or protocol specific timeline, 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 60 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. 
 
4.5    
Procedures for Reporting To the FDA 
• Serious adverse events will be forwarded to FDA by the IND Sponsor (Safety Project Manager 
IND Office) according to 21 CFR 312.32. 
 
It is the responsibility of the PI and the research team to ensure serious adverse events 
are reported according to the Code of Federal Regulations, Good Clinical Practices, the 
protocol guidelines, the sponsor’s guidelines, and Institutional Review Board policy. 
 
4.6    
Procedures for Reporting Drug Exposure During Pregnancy and Birth Events 
If a woman becomes pregnant or suspects that she is pregnant while participating in this 
study, she must inform the investigator immediately and permanently discontinue study 
drug.  The investigator must fax a completed Pregnancy Form to the Puma Biotechnology 
Pharmacovigilance or designee immediately (see Section 4.2).  The pregnancy must be 
followed for the final pregnancy outcome (i.e., delivery, still birth, miscarriage) and Puma 
Biotechnology Pharmacovigilance or designee 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, the investigator must also immediately fax a completed 
Pregnancy Form to the Puma Biotechnology Pharmacovigilance or designee (see Section 
4.2).  Every effort should be made to follow the pregnancy for the final pregnancy outcome. 


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4.7     Product Complaints and Medication Errors   
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 Puma 
Biotechnology (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 Puma Biotechnology 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 
Puma Biotechnology (see below) and report the event. 
For Product Complaints or Medication Errors, call 
 1-844-MED-PUMA (1-844-633-7862) 
E-mail: Medinfo@pumabiotechnology.com 
Fax: 1-424-248-6501 
Hours: Mon-Fri, 9 a.m. – 7 p.m. ET  
 
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 Puma Biotechnology 
Pharmacovigilance (refer to Section 4.2). 
 
 


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5.    STATISTICAL PROCEDURES 
5.1    Study Design and Overview of Primary and Secondary Endpoints 
Bayesian optimal interval design will be applied for the phase I dose escalation part of the 
study.7-9 The target toxicity rate for the MTD is 0.3. The maximum sample size is 12. We 
will enroll and treat patients in cohorts of size 2 starting from Dose Level 1. To guide dose-
escalation decisions, if the observed dose-limiting toxicity (DLT) rate at the current dose is 
≤ 0.236, the next cohort of patients will be treated at the next higher dose level; if it is ≥ 
0.359, the next cohort of patients will be treated at the next lower dose level; otherwise the 
next cohort of patients will be treated at the same dose. In addition, For the purpose of 
overdose control, doses 𝑗𝑗 and higher levels will be eliminated from further examination if 
Pr(𝑝𝑝𝑗𝑗> 0.3 | data) > 0.95, where 𝑝𝑝𝑗𝑗 is the true DLT rate of dose level 𝑗𝑗, 𝑗𝑗= 1,⋯, 3. This 
posterior probability is evaluated based on the beta-binomial model 𝑦𝑦𝑗𝑗∣𝑝𝑝𝑗𝑗∼binomial(𝑝𝑝𝑗𝑗) 
with 𝑝𝑝𝑗𝑗∼uniform(0,1), where 𝑦𝑦𝑗𝑗 is the number of patients experienced DLT at dose level 
𝑗𝑗. When the lowest dose is eliminated, stop the trial for safety. The probability cutoff 0.95 is 
chosen to be consistent with the common practice that when the target DLT rate <=1/6, a 
dose with 2/3 patients experienced DLT is eliminated. 
In a cohort of 2, if no subject has a DLT, then we can proceed to the next higher dose. If ≥ 
1 subjects in a cohort of 2 has a DLT then the rate is ≥ 0.359 and we will enroll at the next 
lower dose.  In a cohort of 4, if no subject has a DLT, then we can proceed to the next higher 
dose. One subject with a DLT would lead to the next cohort being treated at the same dose 
and ≥ 2 subjects with a DLT would lead to the next cohort being treated at the lower dose 
level.  The detailed dose escalation / de-escalation rule is given in Table 2. 
Table 2. Dose escalation/deescalation rule for the BOIN design 
 
1 
2 
3 4 5 6 7 8 9 10 11 12 
Number of patients treated at current 
dose 
1 
2 
3 4 5 6 7 8 9 10 11 12 
Escalate if # of DLT <= 
0 
0 
0 0 1 1 1 1 2 2 
2 
2 
Deescalate if # of DLT >= 
1 
1 
2 2 2 3 3 3 4 4 
4 
5 
Eliminate if # of DLT >= 
NA NA 3 3 4 4 5 5 5 6 
6 
7 
Note: # of DLT is the number of patients with at least 1 DLT. When none of the actions (i.e., 
escalate, de-escalate or eliminate) is triggered, stay at the current dose for treating the next 
cohort of patients. 
 


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We have performed simulation studies and the design will have at least 60% probability 
selecting the correct dose under various scenarios ranging from low to high toxicity profiles.  
The operating characteristics in three scenarios are given in Table 3. 
Table 3. Operating characteristics of the BOIN design 
 
Dose Level 
 
 
 
-1 
1 
2 
Number of Patients 
% Early Stopping 
Scenario 1 
 
 
 
 
 
True DLT 
Rate 
0.05 
0.15 
0.3 
 
 
Selection % 
2.4 
35.6 
62 
 
0 
% Pts Treated 
7.3 
42.5 
50.2 
12 
 
Scenario 2 
 
 
 
 
 
True DLT 
Rate 
0.1 
0.3 
0.5 
 
 
Selection % 
22.2 
60.5 
16.9 
 
0.4 
% Pts Treated 
24.5 
52.3 
23.2 
12 
 
Scenario 3 
 
 
 
 
 
True DLT 
Rate 
0.3 
0.5 
0.7 
 
 
Selection % 
64 
23.9 
1 
 
11.1 
% Pts Treated 
52.4 
40.7 
6.9 
11.5 
 
 
For the phase I, any DLT (defined in section 3.3.3) that occurs during the first two cycles 
(first six weeks) of therapy in the phase I portion of this study will be used to make 
decisions about proceeding to the subsequent cohort.” 
In the phase II cohort of immunotherapy-refractory patients, any responses will be of 
interest.  We will use the Bayesian Optimal Phase 2 (BOP2) design.10  The assumptions are 
that the null response rate is 5% and the target response rate is 20%. Fourteen patients will 
be enrolled initially.  If there are no responses, then the trial will be terminated due to lack of 
efficacy.  If any responses are observed, an additional 14 patients will be enrolled. The 
treatment is considered efficacious if there are at least 4 responders in 28 patients and 
inefficacious otherwise.  The design will have 82% power if the response rate is at least 0.2 
with a one-sided 5% type I error.  The operating characteristics are shown below in Table 4 
using the BOP2 web application (BOP2 V1.4.11.0), which is available at http://www.trialdesign.org. 
 
Table 4: Operating characteristics 
Scenario 
Response 
Rate 
Early Stopping 
(%) 
Claim Promising 
(%) 
Average Sample 
Size 
1 
0.05 
48.77 
4.70 
21.2 


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2 
0.20 
4.40 
82.65 
27.4 
 
 
 
If patients withdraw consent or drop out for other reasons unrelated to safety or disease 
progression, they may be replaced.  To account for patients who may not be evaluable for 
the response rate, we will enroll 30 patients in the Phase II part to reach 28 evaluable 
patients. 
To ensure that patients treated at the Phase II part of the study do not experienced excessive 
toxicity, we will implement the Bayesian toxicity monitoring rule. We will suspend the 
accrual if excessive toxicity defined as Probability (DLT > 0.3) > 0.65.  Assuming the prior 
of Prob(DLT) follows a prior distribution of Beta(0.3, 0.7), we will suspend accrual if we 
observe the followings (# of DLT / # of patients): 3/(5-7). 4/(8-10), 5/(11-13), 6/(14-17), 
7/(18-20), 8/(21-23), 9/(24-26), 10/(27-29), 11/(30-32).      
The operating characteristics are given in Table 5. 
Table 5: Operating Characteristics of the Bayesian Toxicity Monitoring Rule. 
Scenario 
Prob.Of.DLT 
Prob.Early.Stop 
Prob.Declare.Tox 
Avg.N.Patients 
1 
0.1 
0.0326 
0.0326 
34.1004 
2 
0.2 
0.2433 
0.2444 
28.8290 
3 
0.3 
0.6337 
0.6402 
19.5662 
4 
0.4 
0.9137 
0.9196 
11.6466 
 
 
5.2    Randomization and Stratification Factors 
None. 
5.3    Evaluation of Efficacy 
See sections 5.1 and 3.10.1 
5.4    Evaluation of Safety 
See Section 3.10.3. 


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5.5    Correlative Studies  
In HNSCC patients treated with single agent αPD1 therapy, PD-L1 protein expression 
measured by IHC and scored using the percentage of tumor cells with membranous PD-L1 
expression or CPS correlated with response to therapy.22, 24-27, 42, 43  In multiple pre-clinical 
cancer models, RB1 loss or Myc overexpression51 correlated with sensitivity to Aurora 
kinase inhibition, although RB1 was clearly a stronger predictor.34, 35, 45, 46   To examine 
potential predictors of therapeutic efficacy, PD-L1, N-Myc C-Myc, L-Myc, and Rb protein 
levels will be determined by IHC using automated immunostaining.  We will calculate the 
number of tumor cells with Rb, Myc and membranous PD-L1 expression as well as the CPS.  
To measure target inhibition, pharmacodynamics studies will be done in pre- and post- 
treatment tumor. Specifically, we will use IHC to quantify the number of cancer cells that 
stain for phosphorylation of Histone H3 (Ser10) 5 and MPM 2.6 
Both peripheral blood mononuclear cells (PBMCs) and TILs will be assessed by flow 
cytometry for different T cell subsets to evaluate the peripheral and anti-tumor immune 
response in these patients.44 Using techniques we described previously,52-54 we will measure 
the immune response through two panels targeted at the immune microenvironment and T-
cell phenotype. The TME panel will assess CD45 (immune cells), CD3 (T cells), CD19 (B 
cells), F4/80 (macrophages), CD11c (dendritic cells), CD49b (natural killer cells), 
Ly6G+Gr-1+ (neutrophils), and live/dead (viability) cells. The T-cell panel will consist of 
CD45 (immune cells), CD3 (T cells), CD4 (Th cells), CD8 (cytotoxic T cells), FoxP3 and 
CD25 (Tregs), CD44 and CD62L (memory, effector, and naive T cells), checkpoint 
molecules PD-1, TIM-3, and LAG-3, proliferation (Ki67), cytokine production (IFNγ, 
TNFα, IL-2), and live/dead cells.  
T-cell recognition is essential to generate a tumor antigen-specific immune response. To 
quantify HPV-reactive T-cells in tissue and in PBMCs, we will analyze the fraction of E6- 
and E7-specific CD8+ T cells in tumor tissue using established tetramer reagents.4 
Tetramers are composed of major histocompatibility complex (MHC) and peptide multimers 
that are highly effective at detecting antigen specific T-cells and can be used in flow 
cytometry to isolate cell populations  as described.52, 55  These tetramers will be used in 
combination with markers of activation and exhaustion to determine the features of HPV-


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reactive T-cells.  To asses HPV-specific T-cell reactivity, we will perform the IFN-γ 
ELISPOT assay in PBMCs with positive and negative controls as we described.56  Spots will 
be developed by 5-bromo-4-chloro-3-indolyl-phosphate in conjunction with nitro blue 
tetrazolium and counted on an ImmunoSpot ELISPOT reader. We will define the strength of 
the HPV-specific immune response as the median-specific spot count. At the completion of 
the IFN-γ ELISPOT assay, the supernatant will be collected to assess production of 
additional cytokines/chemokines using the luminex multiplex protocol.  
The T cell receptor determines the capacity of T cells to react with tumor antigens. 
Diversification in TIL repertoire is associated with response to therapy.57, 58  We will use T-
cell receptor (TCR) sequencing to characterize the T cell repertoire of TILs before and after 
treatment using techniques as previously described.59 Briefly, DNA will be extracted from 
PBMCs and tissues and undergo two rounds of amplification of the CDR3β region of the T 
cell receptor which accounts for the greatest amount of contact with antigens (Adaptive 
Biotechnologies),60 followed by sequencing of the PCR product by MiSeq and 
deconvolution of the data by Adaptive Biotechnologies. Analysis will be performed using 
the Analyzer platform. Metrics such as T cell density, T cell richness (a measure of 
diversity), and T cell clonality (a measure of reactivity of the T cell repertoire) will be 
evaluated. Furthermore, we will study changes in the T cell repertoire over time in the 
periphery and tumor, using the Jaccard and Morisita Overlap Indices which evaluate shared 
TCR rearrangements across samples/timepoints/compartments to study changes or stability 
in the T cell repertoire.59 
Additionally, we will perform TCR sequencing of TILs that react with tetramers (captured 
by flow cytometry) to identify TCRs that are specific to E6 and E7. TCR sequences from 
HPV reactive T-cells will be mapped back to TCR sequences in the blood and tissues to 
track the expansion and contraction of HPV reactive T-cells and we will correlate these 
findings with response.  


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We consider that the sample size is also reasonable to evaluate the correlative science 
endpoints; yet, no explicit sample size justification is made for these exploratory endpoints. 
Summary statistics (e.g., the mean and standard deviation, median, and minimum/maximum 
levels of continuous, and frequencies and percentages of categorical variables) will be 
determined at baseline and post-treatment biomarkers as appropriate. For each pair of 
specimens, the percent change from baseline of these parameters will also be calculated. 
Data from biomarker assays may be analyzed using graphical methods and descriptive 
statistics with additional analyses including linear regression, t-test, and analysis of variance 
(ANOVA) and the corresponding nonparametric tests as appropriate. Correlations of 
biomarkers with measures of anti-tumor efficacy will be analyzed using the Spearman’s 
correlation coefficient and the chi-square or Fisher’s exact test for the discretized variables. 
 
5.6    Interim Analysis  
See section 5.1 for stopping rules in each cohort that require several interim analyses for 
efficacy and toxicity.  In each case, accrual will be suspended temporarily to ensure 
adequate analysis of the stated endpoint.  
The Investigator is responsible for completing Safety and Efficacy Summary Reports and 
submitting them to the IND office Medical Monitor for review.  These should be submitted 
as follows:  
• 
Escalation Phase: 


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After the first 2 evaluable subjects complete the first two cycles (first six weeks) of study 
treatment, and every 2 evaluable subjects thereafter, prior to advancing/changing dose 
levels. 
The study enrollment must be halted until IND Office approval to continue, is obtained. 
 
• 
Expansion Phase: 
After the first 15 evaluable subjects complete 6 months of study treatment, and every 10 
evaluable patients thereafter, until enrollment is complete. 
5.7 Consent Process and Documentation  
This protocol will follow the SOP 04_Informed Consent Process. SOP 04 has been read by 
the research staff and investigators. 
Please indicate what type of consent process will be used (check all that apply): 
☒ Remote consent 
☒ In-person consent 
☐ Waiver of consent 
☐ Waiver of written documentation of consent 
 


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7.    APPENDICES 
7.1    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. 
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 to reduce 
or eliminate any of the protections for human subjects set forth in this Declaration. 


 
 
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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 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 


 
 
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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 
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 judgement 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 


 
 
80 
 
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. 


 
 
81 
 
7.2    Common Terminology Criteria for Adverse Events Version 5.0 
https://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/CTCAE_v5_Qui
ck_Reference_8.5x11.pdf 
7.3    
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. 
 
7.4    
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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7.5    
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.) 
 
 


 
 
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Appendix 
7.6 Management of pembrolizumab toxicity 
 
 


 
 
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