An Open Label, Multicenter, Single Arm Phase II Study to Evaluate the Activity and Tolerability of the Novel mTOR Inhibitor, MLN0128 (TAK-228), in Patients With Locally Advanced or Metastatic Transitional Cell Carcinoma of the Urothelial Tract Whose Tumors Harbor a TSC1 and/or a TSC2 Mutation
Phase: PHASE2
Conditions: Locally Advanced Bladder Urothelial Carcinoma, Metastatic Transitional Cell Carcinoma, Metastatic Urothelial Carcinoma, Recurrent Bladder Carcinoma, Stage III Bladder Urothelial Carcinoma AJCC v6 and v7, Stage IV Bladder Urothelial Carcinoma AJCC v7
Sponsor: National Cancer Institute (NCI)

i 
SUMMARY OF CHANGES: Protocol 
 
For Amendment #5 to: An Open Label, Multicenter, Single arm Phase II study to evaluate the 
Activity and Tolerability of the novel mTOR Inhibitor, MLN0128 (TAK-228), in patients with 
Locally Advanced or Metastatic Transitional Cell Carcinoma of the urothelial tract whose tumors 
harbor a TSC1 and/or a TSC2 mutation 
 
NCI Protocol #: 9767 
Local Protocol #: 2000021268 
 
Protocol Version Date: 09/08/2020 
Pre-Screen Testing Consent Version Date: 09/08/2020 
Main Study Consent Version Date: 09/08/2020 
 
 
I. CTEP Request for amendment to add CATCHUP organizations: 
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II. Additional Changes by Principal Investigator:  
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Updated  Protocol Type / Version # / Version Date 
 
 

1 
NCI Protocol #: 
9767 
 
Local Protocol #: 
2000021268 
 
TITLE: An Open Label, Multicenter, Single arm Phase II study to evaluate the Activity and 
Tolerability of the novel mTOR Inhibitor, MLN0128 (TAK-228), in patients with Locally 
Advanced or Metastatic Transitional Cell Carcinoma of the urothelial tract whose tumors harbor a 
TSC1 and/or a TSC2 mutation.  
 
Corresponding Organization: Yale University Cancer Center LAO (LAO-CT018) 
 
Principal Investigator: 
Joseph W. Kim, MD 
Assistant Professor of Medicine (Medical Oncology) 
Yale Cancer Center 
333 Cedar Street, FMP 121 
New Haven, CT 06520 
joseph.w.kim@yale.edu 
Direct Office: 203-737-6467 
Cell: 203-494-3287 
Administrative Assistant: Michele Messina: 203-737-6980 
 
Translational PI: 
 
Jeffrey Sklar, MD, PhD 
Professor of Pathology and Laboratory Medicine 
310 Cedar Street, Ste LH416B 
New Haven, CT 06520 
jeffrey.sklar@yale.edu 
Office: 203.785.6836 
 
Participating Organizations:  
LAO-11030 / University Health Network Princess Margaret Cancer Center LAO 
LAO-CA043 / City of Hope Comprehensive Cancer Center LAO 
LAO-MA036 / Dana-Farber - Harvard Cancer Center LAO 
LAO-MD017 / JHU Sidney Kimmel Comprehensive Cancer Center LAO 
LAO-MN026 / Mayo Clinic Cancer Center LAO 
LAO-NC010 / Duke University - Duke Cancer Institute LAO 
LAO-NJ066 / Rutgers University - Cancer Institute of New Jersey LAO 
LAO-OH007 / Ohio State University Comprehensive Cancer Center LAO 
LAO-PA015 / University of Pittsburgh Cancer Institute LAO 
LAO-TX035 / University of Texas MD Anderson Cancer Center LAO 
LAO-NCI / National Cancer Institute LAO 
EDDOP / Early Drug Development Opportunity Program 

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 CATCHUP / Creating Access to Targeted Cancer Therapy for Underserved Populations 
 
Statistician: 
 
 
Yu Shyr 
Harold L. Moses Chair in Cancer Research 
Director, Vanderbilt Center for Quantitative Sciences; Director, Vanderbilt Technologies for 
Advanced Genomics Analysis and Research Design (VANGARD) 
Associate Director for Quantitative Sciences Integration, Vanderbilt-Ingram Cancer Center 
Professor of Biostatistics, Biomedical Informatics, and Cancer Biology Researcher 
 
 
Vanderbilt University Medical Center 
2220 Pierce Ave. 
571 Preston Building 
Nashville, TN 37232-6848 
615-936-2572 
 
Responsible Study Coordinator: 
Matthew Piscatelli, BS, CCRP 
Project Manager 
Clinical Trials Office, Yale Cancer Center 
2 Church Street South, Suite 507 
New Haven, CT 06519 
Office Phone: (203) 737-8367 
Fax: (203) 785-6781 
matthew.piscatelli@yale.edu 
Responsible Research Nurse: 
Shelby DeCarlo BSN, RN 
Clinical Research Nurse 
Yale Cancer Center, Clinical Trials Office 
2 Church Street South Suite 507 
New Haven, CT 06519 
Office Phone: (203) 737-6299 
Fax: (203) 785-6781 
 
  
NCI-Supplied Agent:   [MLN0128 (TAK-228) (MLN0128) - NSC# 768435] 
 
 
Investigational Agent  
IND# 
IND Sponsor  
MLN0128 (TAK-228)  
 
DCTD, NCI 
 
 
Protocol Type / Version # / Version Date: [Original / Version #2 / Date 12/22/2014] 
 
 
 
       Revision / Version #3 / Date 03/16/2015 
 
 
 
       Revision / Version #4 / Date 5/18/2016 
 
 
             Revision / Version #5 / Date 7/12/2016 
 
 
 
       Revision / Version #6 / Date 10/03/2016 
 
 
 
       Revision / Version #7 / Date 11/08/2016 
 
 
 
      Amendment / Version #1 / Date 01/23/2017 
 
 
 
      Amendment / Version #2 / Date 09/29/2017 
 
 
 
      Amendment / Version #3 / Date 06/18/2018 
 
 
 
      Amendment / Version #4/ Date 10/01/2019 
 
 
 
      Amendment / Version #5/ Date 09/08/2020 

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SCHEMA 
This is a phase II, open label, multicenter study assessing the activity and tolerability of the novel 
mTOR kinase inhibitor, MLN0128 (TAK-228), in patients with locally advanced or metastatic 
transitional cell carcinoma (TCC) of the urothelial tract harboring a TSC1 and/or a TSC2 mutation. 
The mutation must be identified by a CLIA certified lab. This protocol, as shown in the schema 
below, offers an optional study to perform a pre-screening test of TSC1 and TSC2 gene sequencing 
for patients whose mutation status is unknown. An archival tumor sample along with buccal swab 
needs to be sent to Yale Clinical Molecular Pathology Laboratory (YCMPL), which serves as the 
Study’s central lab.  
 
For those whose TSC gene mutation was previously identified at a CLIA-certified lab other than 
YCMPL, the case must be reviewed by the Study PI and/or Translational PI, and the approval by 
the Study PI must be given for eligibility. In addition, archival FFPE block or 10 unstained 
slides along with a buccal swab, must be sent to YCMPL for confirmation of the mutation.  If 
archival tissue is no longer available, a tumor biopsy would be required for tumor sample 
submission.   
 
 
Figure 1. Flow Schema for Prescreening and Screening.  
  
 

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Figure 2. Diagrammatic illustration of events on clinical trial. 
 

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TABLE OF CONTENTS 
SCHEMA .........................................................................................................................................3 
LIST OF ABBREVIATIONS AND GLOSSARY OF TERMS......................................................7 
1. 
OBJECTIVES ......................................................................................................................8 
1.1 
Primary Objectives ...................................................................................................8 
1.2 
Secondary Objectives ...............................................................................................8 
1.3 
Exploratory Objective ..............................................................................................8 
2. 
BACKGROUND .................................................................................................................8 
2.1 
Study Disease(s).......................................................................................................8 
2.2 
CTEP IND Agent .....................................................................................................8 
2.3 
Rationale ................................................................................................................13 
2.4 
Correlative Studies Background ............................................................................17 
3. 
PATIENT SELECTION ....................................................................................................17 
3.1 
Eligibility Criteria ..................................................................................................17 
3.2 
Exclusion Criteria ..................................................................................................20 
4. 
REGISTRATION PROCEDURES ...................................................................................22 
4.1 
Investigator and Research Associate Registration with CTEP ..............................22 
4.2 
Site Registration Process........................................................................................23 
4.3 
Patient Registration ................................................................................................25 
4.4 
General Guidelines .................................................................................................26 
5. 
TREATMENT PLAN ........................................................................................................26 
5.1 
Agent Administration .............................................................................................26 
5.2 
General Concomitant Medication and Supportive Care Guidelines ......................27 
5.3 
Duration of Therapy ...............................................................................................28 
5.4 
Duration of Follow Up ...........................................................................................28 
5.5 
Criteria for Removal from Study ...........................................................................29 
6. 
DOSING DELAYS/DOSE MODIFICATIONS................................................................29 
6.1 
Special Warnings and Special Precautions for Use ...............................................29 
6.2 
Dose Modification Guidelines: ..............................................................................31 
7. 
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................38 
7.1 
Comprehensive Adverse Events and Potential Risks List(s) (CAEPRs) ...............38 
7.2 
Adverse Event Characteristics ...............................................................................41 
7.3 
Expedited Adverse Event Reporting ......................................................................42 
7.4 
Routine Adverse Event Reporting .........................................................................43 
7.5 
Secondary Malignancy ...........................................................................................44 
7.6 
Second Malignancy ................................................................................................45 
7.7 
Pregnancy ...............................................................................................................45 
7.8 
Pregnancy loss .......................................................................................................45 
7.9 
Neonatal death .......................................................................................................45 

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8. 
PHARMACEUTICAL INFORMATION ..........................................................................45 
8.1 
CTEP IND Agent(s) ...............................................................................................46 
9. 
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES ........................................48 
9.1 
Biomarker Studies ..................................................................................................48 
10. 
STUDY CALENDAR .......................................................................................................50 
11. 
MEASUREMENT OF EFFECT........................................................................................52 
11.1 
Definitions..............................................................................................................52 
11.2 
Disease Parameters ................................................................................................52 
11.3 
Methods for Evaluation of Measurable Disease ....................................................53 
11.4 
Response Criteria ...................................................................................................56 
12. 
STUDY OVERSIGHT AND DATA REPORTING / REGULATORY 
REQUIREMENTS .............................................................................................................58 
12.3 
CTEP Multicenter Guidelines ................................................................................61 
12.4 
Collaborative Agreements Language .....................................................................61 
13. 
STATISTICAL CONSIDERATIONS...............................................................................62 
13.1 
Study Design/Endpoints.........................................................................................62 
13.2 
Sample Size/Accrual Rate ......................................................................................63 
13.3 
Stratification Factors ..............................................................................................65 
13.4 
Analysis of Secondary Endpoints ..........................................................................65 
13.5 
Analysis of Exploratory Endpoints ........................................................................65 
13.6 
Reporting and Exclusions ......................................................................................66 
REFERENCES ..............................................................................................................................67 
APPENDIX A 
PERFORMANCE STATUS CRITERIA ..................................................73 
APPENDIX B 
CTEP MULTICENTER GUIDELINES ....................................................74 
APPENDIX C 
INFORMATION ON POSSIBLE DRUG INTERACTIONS ...................75 
APPENDIX D:                  Diary for MLN0128 (TAK-228) .........................................................77 
Appendix E: New York Heart Association (NYHA) Classification of Cardiac Disease ..............79 
Appendix F: List of Relevant Cytochrome P450 Inhibitors and Inducers.....................................80 
 
 
 

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LIST OF ABBREVIATIONS AND GLOSSARY OF TERMS 
Common abbreviations used in oncology protocols are provided below.  Program-specific or 
protocol-specific abbreviations must be added to this list, and unnecessary abbreviations 
removed, as applicable.  Abbreviations that are retained should not be changed.  
Abbreviation 
Term 
AE 
adverse event 
ALP 
alkaline phosphatase 
ALT 
alanine aminotransferase 
AST 
aspartate aminotransferase 
BID 
bis in die; twice a day 
BUN 
blood urea nitrogen 
CBC 
complete blood count 
CLIA 
Clinical Laboratory Improvement Amendments 
CMS 
Centers for Medicare & Medicaid Services 
CYP 
cytochrome P450 
 
 
ECOG 
Eastern Cooperative Oncology Group 
LDH 
lactate dehydrogenase 
LFT 
liver function test(s) 
MTD 
maximum tolerated dose 
NCCN 
National Comprehensive Cancer Network 
NCI 
National Cancer Institute 
NCI CTCAE 
National Cancer Institute Common Terminology Criteria for Adverse Events 
NYHA 
New York Heart Association 
PK 
pharmacokinetic(s) 
PO 
per os; by mouth (orally) 
QTc 
rate-corrected QT interval (millisec) of electrocardiograph 
SAE 
serious adverse event 
 
 
 
 
 
 
 
 
 
 

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1. OBJECTIVES 
 
1.1 
Primary Objectives 
 
x To determine the Overall Response Rate (ORR) defined as complete response (CR) and partial 
response (PR) in patients with locally advanced or metastatic TCC harboring a TSC1 mutation. 
 
1.2 
Secondary Objectives 
 
x To evaluate the safety and tolerability of MLN0128 (TAK-228) in patients with locally 
advanced or metastatic TCC harboring a TSC1 or TSC2 mutation. 
x To evaluate progression free survival (PFS) and overall survival (OS).  
 
1.3 
Exploratory Objective 
 
x To determine the ORR in patients with locally advanced or metastatic TCC harboring a TSC2 
mutation. 
x To evaluate toxicity, PFS, and OS in TSC2 mutation patients. 
 
 
2. BACKGROUND 
 
2.1 
Study Disease(s) 
 
Bladder cancer is a common malignancy. Approximately 73,000 cases of bladder cancer are 
diagnosed annually in the United States with more than 14,000 disease-related deaths (Siegel et 
al., 2012). TCC is the most frequent histological subtype of bladder cancer, accounting for 
approximately 90 percent of bladder and renal pelvis cancers. The 5-year year overall survival 
(OS) rate of locally advanced and metastatic TCC is approximately 35% and 5%, respectively 
(Howlader et al 2012). Cisplatin-based chemotherapy has been the standard therapeutic approach 
for unrespectable locally advanced and metastatic bladder cancer for the past 30 years with no 
standard second line therapy for progressive disease (NCCN Guidelines 2014; Von der Maase et 
al 2005).  The National Comprehensive Cancer Network (NCCN) recommends participation in 
clinical trials of new agents for second-line therapy of metastatic disease. Exploring novel 
therapeutic agents in the context of relevant drugable genomic alterations represents an urgent 
need. Exploring novel genomic driven therapeutic approaches for this disease is an urgent need 
and understanding the involvement of different molecular pathways may help in developing 
clinical trials in a personalized fashion. 
 
 
2.2 
CTEP IND Agent 
 
Second generation mTOR inhibitors are small molecule ATP-dependent TOR kinase inhibitors 
which target the mTOR kinase domain and are currently being investigated in clinical trials 
(Schenone et al., 2011). They are likely to suppress mTORC1 and mTORC2 functions, a feature 

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that could increase the antitumor effect relative to the currently available rapalogs. Those agents 
have been termed the TORKinibs to distinguish their mode of action from the rapalogs. They seem 
to inhibit protein synthesis with greater potency than rapalogs, due in part to their greater inhibition 
of mTORC1 action on 4EBP1 (Wander et al., 2011). The development of the TORKininbs has led 
scientists to conclude that rapalogs are ineffective at blocking cell proliferation due to their partial 
effect on the mTORC1, sparing mTORC2 (Feldman and Shokat, 2010). The profound anti-
proliferative effect of the TORKinibs suggests that these molecules could be more effective in the 
treatment of cancers where rapalogs have failed. 
 
MLN0128 (TAK-228), formerly known as MLN0128, is an orally available, potent, and highly 
selective ATP-competitive inhibitor of mTOR kinase that exhibits dual specificity against both 
TORC1 and TORC2 (TORC1/2) complexes (CTEP solicitation on MLN0128; 2012). Dual 
TORC1/2 inhibition mitigates the feedback activation of AKT, known to cause resistance to 
TORC-1 selective inhibitors such as rapamycin (De et al., 2012).  MLN0128 (TAK-228) displayed 
cellular inhibition of TORC1 and TORC2 pathways with IC50 less than 10 nM. MLN0128 (TAK-
228) is believed to have the potential of achieving greater clinical benefit than the currently 
available rapalogs. In vitro studies have demonstrated that MLN0128 (TAK-228) selectively and 
potently inhabits the mTOR kinases but relative to mTOR inhibition, MLN0128 (TAK-228) has 
>100-IROGOHVVSRWHQF\DVDQLQKLELWRURI&ODVV,3,NLQDVHLVRIRUPVĮȕȖįFODVV,,3,.&Į
DQG 3,.& ȕ DQG FODVV ,,, 936 3,. IDPLO\ PHPEHUV DV ZHOO DV 3,.Į DQG 3,.ȕ
(Investigator's Brochure, CTEP solicitation on MLN0128, 2012). MLN0128 (TAK-228) was also 
found to inhibit (>80%) the biochemical activity of five kinases (mTOR, DNA-3.3'*)5Į
Flt3, and CK1 epsilon kinases) out of a panel of 222 protein kinases. MLN0128 (TAK-228) 
inhibited ligand binding of 10 receptor and intracellular protein kinases including (ACVR1, 
%035%&6)5&61.'&61.(''50(.0(.3'*)5ĮDQG5,3.RXWRID
panel of 402 distinct kinases. In PTEN deficient cells, MLN0128 (TAK-228) had 
pharmacodynamic properties comparable to the dual inhibition of the TORC1 and PI3K utilizing 
rapamycin and PI-103 (Figure2) 

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In Vivo Studies: 
MLN0128 (TAK-228) has inhibited mTOR signaling and has demonstrated anticancer activity 
against a number of human solid tumor cell-line xenograft mouse models, including PTEN mutant 
endometrial (AN3-CA) and breast carcinomas (ZR-75-1), among other PTEN mutant carcinomas 
like glioblastoma and renal cell carcinoma (Investigator's Brochure, CTEP solicitation on 
MLN0128, 2012). MLN0128 (TAK-228), administered orally in multiple human tumor xenograft 
mouse models, inhibited angiogenesis and tumor growth by inhibiting mTOR signaling at plasma 
concentrations associated with in vitro inhibition of mTOR in a dose- and time-dependent manner 
and displayed a clear pharmacokinetic to pharmacodynamic (PK/PD) relationship (Jessen et al., 
2009). MLN0128 (TAK-228) also inhibits both the phosphorylation of S6 and 4EBP1, the 
downstream substrates of TORC1, and selectively inhibits AKT phosphorylation at Ser473 
evidenced by decrease pAKT, the downstream substrate of TORC2, in vitro and in vivo, including 
cell lines that are resistant to rapamycin and pan-PI3K inhibitors (Jessen et al., 2009; Kessler et 
al., 2010; Hassan et al., 2013).  
Safety Pharmacology: MLN0128 (TAK-228) has a low potential to affect the human ether-a-go-
go related gene (hERG) potassium ion channel and did not affect cardiovascular (CV) parameters 
in vivo in telemeterized monkeys. 
 
Drug Metabolism and Pharmacokinetics: MLN0128 (TAK-228) was rapidly absorbed after PO 
administration to mice, rats, dogs, and monkeys,with high oral bioavailability.  MLN0128 (TAK-
228) displayed dose-proportional plasma exposures, a moderate propensity to cross the blood-
brain barrier, and was modestly bound (70.5%) to human plasma proteins.  MLN0128 (TAK-
228) did not inhibit P-glycoprotein, but did inhibit breast cancer-resistance protein (BCRP), 
organic cation transporter (OCT)1 and OCT2. 

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The main isozymes responsible for phase 1 metabolism appear to be cytochrome P450 (CYP) 
2C9, 2C19, and 3A4. MLN0128 (TAK-228) did not induce CYP1A2, 2B6, and 3A4 activity and 
expression at concentrations up to 10 PM. MLN0128 (TAK-228) displayed low potential for 
inhibition and is not a time-dependent inhibitor of CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 
3A4/5. 
 
Oral administration of MLN0128 (TAK-228) in humans has a low potential for metabolic and 
transporter-based drug-drug interactions (DDIs), especially given clinical exposures 
observed to date after administration of the highest anticipated therapeutic dose to be used in the 
clinic in oncology indications (total maximum plasma concentration [Cmax] of 0.48 PM [free 
Cmax of 0.14 PM] at 30 mg once weekly [QW]). 
 
Toxicology: Adverse events of MLN0128 (TAK-228) in rats and monkeys included body weight 
loss, decreased activity, increased glucose and insulin levels, alterations in white blood cells, 
bone marrow and lymphoid depletion, thymic necrosis, oligospermia, testes 
degeneration/atrophy, nonglandular stomach epithelial degeneration/ulceration/hyperplasia, 
pancreatic islet degeneration and fibrosis, lens fiber degeneration with cataract correlate, adrenal 
cortex hypertrophy, pituitary atrophy secondary to body weight loss, liver hepatocellular 
vacuolation, retinal dysplasia with or without optic nerve atrophy, and alveolar histiocytosis.  
MLN0128 (TAK-228) was negative for genotoxicity in an in vitro bacterial mutagenesis (Ames) 
assay, an in vivo rat micronucleus assay, and an in vivo rat comet assay.  MLN0128 (TAK-228) 
was negative for phototoxicity in the 3T3 fibroblast assay. 
 
Summary of Effects in Humans: 
MLN0128 (TAK-228) has been studied in 2 different phase I clinical trials in patients with solid 
malignancies and an additional phase I trial in patients with hematologic malignancies utilizing 
different dosing schedules (QD, QW, QDx3d every week and QDx5d every week) in 28-day cycles 
(Infante et al., 2012; Ghobrial et al., 2012; Tabernero et al., 2012). The original trials with 
MLN0128 (TAK-228) used the original unmilled MLN0128 (TAK-228) active pharmaceutical 
ingredient (API); current manufacturing process produces milled MLN0128 (TAK-228) API. The 
recommended phase 2 dose for unmilled MLN0128 (TAK-228) for the daily dosing schedule of 
the unmilled formulation were determined at 5 mg/day and for a weekly dosing schedule at 30 
mg/week. (Infante et al., 2012; Ghobrial et al., 2012). A dose limiting toxicity of grade 3 rash was 
reported in in these trials (Infante et al., 2012).  
Clinical Pharmacokinetics: MLN0128 (TAK-228) was well tolerated at the doses and schedules 
tested and showed a high oral bioavailability and dose-linear PK across all dosing regimens 
evaluated with exposures in the range of predicted biological activity (Infante et al., 2012 and 
Tabernero et al., 2012). MLN0128 (TAK-228) exhibits fast oral absorption (time to reach Cmax 
[tmax], generally between 1-4 hours after dosing); has dose-linear PK, with a mean plasma half-
life of approximately 8 hours; and does not accumulate meaningfully in plasma when dosed as 
frequently as once daily (QD)  
 
The PK of MLN0128 (TAK228) has been evaluated in over 130 patients in ongoing studies. 
The mean steady-state plasma Cmax ranged from 52-232 nM.  No significant change in the PK 

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parameters of MLN0128 (TAK228) was observed on repeat dosing; the mean accumulation 
index of MLN0128 (TAK228) ranged from 0.7-1.7-fold following multiple doses. PK 
parameters in 25 patients with advanced solid tumors receiving MLN0128 (TAK228) on the 
QD dosing are presented in Table 5.4 from the Investigator’s Brochure v.7. 
 
 
 
Consistent with the QD dosing, MLN0128 (TAK228) displayed dose-dependent PK on all three 
intermittent dosing regimens, with rapid absorption (Tmax ranging from 0.5-4 hours) and mean 
plasma t1/2 8 hours (Tabernero et al., AACR 2012). 
 
Safety: As of the clinical data cutoff (09 December 2014), a total of 335 patients had received 
 1 dose of study drug across studies. A total of 18 deaths that occurred within 30 days of the last 
study drug dose had been reported to the clinical database as of the data cutoff; of these events, 
1 (cardiac arrest; Study INK128-001) was considered related to MLN0128 (TAK-228). 
 
At least 1 treatment-emergent SAE, regardless of causality, had been reported in 125/335 
patients (37%). Across the studies and regardless of causality or dosing regimen, the most 
common TEAEs included nausea, fatigue, hyperglycemia, vomiting, diarrhea, stomatitis, and 
decreased appetite. 
Due to the cardiac death on study INK128-001, study C31002, a phase 1 single-arm study to 
evaluate the effect of a single dose of 40 mg MLN0128 (TAK-228) on the QT/QTc interval was 
initiated in patients with advanced solid tumors.  After completing the per-protocol 
PK/ECG/cardiac contractility monitoring, the patients  continued MLN0128 (TAK-228) 30 mg 
QW with continued cardiac monitoring.  The study results showed that treatment with MLN0128 
(TAK-228) was not associated with clinically meaningful effects on the overall 
elecrocardiographic safety profile, and that ECHO/MUGA at screening was not required.   
 
Development of a Milled Formulation of MLN0128 (TAK-228) 
In order to allow more predictable absorption of MLN0128 (TAK-228) after oral administration 

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and to allow scale-up manufacturing of MLN0128 (TAK-228) capsules, Millenium/Takeda 
developed a new milled formulation of the agent.  The physical milling step during the granulation 
process controls particle size distribution of MLN0128 (TAK-228).  In order to observe whether 
this milling step altered the safety and PK profile of MLN0128 (TAK-228), the company 
performed in vivo studies with PK analysis of milled MLN0128 (TAK-228).  These studies 
indicated that the milled formulation may result in faster absorption with possibly higher maximum 
concentration (Cmax), which could result in a different safety profile, compared to the previous 
unmilled API capsules. 
Takeda developed new MLN0128 (TAK-228) capsules containing milled active pharmaceutical 
ingredient (API) for clinical studies in 1 mg, 3 mg, and 5 mg strengths.  Patients receiving the 
milled formulation were added onto ongoing studies C31001 and C31002, as well as a new study 
MLN0128-1004, with various treatment cohorts including daily and weekly administration of 
milled MLN0128 (TAK-228) 
The recommended dose of milled MLN0128 (TAK-228) was evaluated in 17 patients of 
MLN0128-1004, with PK, safety, and tolerability assessed.  Six patients were given a 4 mg QD 
dose of milled MLN0128 (TAK-228) and 3 patients had observed DLT (rash, appetite loss and 
fatigue).  A dose of 3 mg QD was given to 11 patients with only 1 DLT (decreased platelets) 
observed.  The 3 mg QD dose of MLN0128 (TAK-228) was declared the RP2D, and was generally 
well tolerated and demonstrating objective responses in patients.   
A significant and meaningful difference in tolerability was observed in the comparison of the 
MTDs between unmilled and milled MLN0128 (TAK-228) when administered QD.  This 
difference in tolerability may be possibly explained due to the effect of food on the 
safety/tolerability of unmilled MLN0128 (TAK-228) in study IND128-001.  Consequently, a dose 
of 3 mg QD was chosen as the RP2D of milled MLN0128 (TAK-228) dose in empty stomach 
conditions.   
The RP2D for milled MLN0128 (TAK-228) on a weekly schedule was determined to be 30 mg, 
the same weekly RP2D as seen for the older unmilled formulation.  Six patients treated at 30 mg 
weekly with the milled formulation did not demonstrate any DLT, but the agent was not escalated 
further.  No DLT had been demonstrated for milled MLN0128 (TAK-228) at the prior 20 mg QW 
dose as well.  
 
 
2.3 
Rationale 
 
The molecular characteristics of different tumor subtypes and the involvement of distinct pathways 
in tumor pathogenesis play an important role in how these tumors respond to different targeted 
therapies. Searching for therapeutically actionable genomic alterations and selecting patients 
during early drug development is being rapidly adopted to define patients who may benefit the 
most from these therapies. Somatic mutations and resultant molecular alterations that control the 
regulatory pathways of the mechanistic (formerly known as, mammalian) target of rapamycin 
(mTOR) complex deserve further investigation as we develop more drugs targeting this crucial 
pathway. 
 
The mTOR is a complex multimolecular and multifunctional serine/threonine kinase protein that 
integrates a variety of incoming signals and regulates cell growth, proliferation, survival, motility 

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and angiogenesis  (Bjornsti et al., 2004; Chan S. 2004; Wen et al., 2013; Chiang et al., 2007). The 
mTOR-signaling network involves two functionally and physically distinct and complex proteins, 
TORC1 and TORC2. A regulatory associated protein (Raptor) distinguishes mTORC1 complex, 
whereas mTORC2 contains a distinct set of protein subunits including Rictor (rapamycin-
insensitive companion of mTOR), mSin1 (mammalian stress-activated protein kinase interacting 
protein 1), and Protor-1 subunit in place of Raptor (Figure 3) (Guertin and Sabatini, 2007; 
Sabatini, 2006; Chiang et al., 2007).  
 
The mTORC1, stimulated by growth factors and amino acids, exerts its effects through 
downstream phosphorylation of p70S6 Kinase (S6K1) and 4EBP1 (Weinberg R., 2007; Sabatini 
et al., 2006). The phosphorylation of S6K1 Kinase results in its activation, which in turn 
phosphorylates S6 protein, an important step in 40-S ribosomal subunit formation and protein 
biosynthesis.  Additionally, mTOR phosphorylates 4EBP1, which in turn activates eIF4E 
(eukaryotic Initiation Factor 4E) through forming a complex with several other initiating factors 
that enable the ribosomes to initiate certain mRNA translations. (Weinberg R., 2007; Sabatini et 
al., 2006). 
 
There are several critical upstream regulators of the mTOR pathways (Fingar et al., 2004).  The 
phosphatidylinositol 3’-kinases (PI3K) are lipid kinases that exert their function by the production 
of the second messenger phosphatidylinositol 3,4,5-triphosphate (PIP3), which in turn contributes 
to the recruitment and activation of a wide range of down-stream targets, including Akt (also 
known as protein kinase B", PKB) (Stokoe et al., 1997). PTEN (phosphatase and tensin homolog 
deleted on chromosome ten) is a lipid phosphatase that counteracts the activity of PI3K by 
dephosphorylating PIP3 (Stambolic et al., 1998).  Activation of AKT/PKB results in increased cell 
growth and proliferation, a shift to glycolytic metabolism, and increased cell migration in addition 
to its anti-apoptotic activity. (Bhaskar et al., 2007; Sabassov et al., 2005).  AKT/PKB exerts its 
effect through phosphorylation and inactivation of the mTOR-inhibitory tuberous sclerosis (TSC) 
complex formed by hamartin and tuberin (also called TSC1 and TSC2 respectively) (Bjornsti et 
al., 2004; Weinberg R., 2007; Chiang et al., 2007).  TSC is a GTPase activating protein (GAP) 
that exerts its effect through binding to the Rheb (Ras homolog enriched in brain) forming a 
complex (Rheb-GTPase) that directly binds to the mTORC1 and inhibit downstream effects of the 
mTOR pathway. As a Rheb specific GAP, the TSC complex acts as a signal-modulated suppressor 
of Rheb by driving Rheb into the inactive, GDP-bound state and thus prevents Rheb-GTP mediated 
mTORC1 activation. (Chiang et al., 2007; Tee et al., 2003; Long et al., 2005). AKT also 
phosphorylates and functionally inhibits TSC2, which indirectly activates the mTORC1. (Potter 
et al., 2002; Manning et al., 2002; Inoki et al., 2002).  Evidence suggests that a loss of function 
mutation in PTEN, TSC1 and TSC2 results in constitutive activation of the mTORC1 pathway 
(Mehran et al., 2001; Magri et al., 2011) with persistent phosphorylation of the p70S6K (S6K) 
and its substrate S6 that is sensitive to pharmacologic inhibition` of the mTOR. (Kwiatkowski et 
al., 2002; Inoki et al., 2009; Zhang et al., 2003; Mehran et al., 2001).  
 
 

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Figure 3. The mTOR-signaling network. Adapted from 
 Chiang G, Abraham R. Trends Mol Med 2007 
 
To add to the complexity of this network, it is important to recognize that mTORC1 is a 
downstream recipient of AKT dependent stimulatory signals while mTORC2 is an upstream 
activator of AKT.  In other words, mTORC2 phosphorylates AKT/PKB, which is an oncogenic 
regulator of apoptosis and proliferation (Weinberg R., 2007; Sarbassov et al., 2005; Chiang et al., 
2007). So, inhibiting both TORC complexes is important to gain better control over this pathway. 
Additionally, there are other known proteins that regulate the mTOR pathways include FBXW7. 
The latter is a protein product of the tumor suppressor gene, FBXW7, which binds and targets the 
mTOR for ubiquitination and consequent degradation (Mao et al. 2008). Somatic mutations that 
result in loss of function of FBXW7 occur in approximately 6% of human cancers and are believed 
to result in constitutive activation of the mTOR complex. (Akhoondi et al., 2007; Mao et al., 2008) 
 
 
Targeting the mTOR-signaling pathway has already proven itself in the clinic; however, with 
limited success.  The first generation mTOR inhibitors such as rapamycin and its analogs 
(everolimus, temsirulimus, ridaforolimus) are called the rapalogs. They are allosteric modulators 
of the TORC1 complex that exhibited limited anticancer activity through downstream inhibition 
of phosphorylation of p70S6 Kinase (S6K1) and 4EBP1 (Weinberg R., 2007; Sabatini et al., 2006). 

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One of the limitations of these drugs that may explain their limited success in the clinic is that they 
selectively inhibit TORC1 without affecting TORC2 failing to inhibit all mTOR functions.  Also, 
mTOR may influence PI3K signaling via the S6K-IRS1 feedback loop and via mTORC2-mediated 
phosphorylation of AKT at serine 473 (Chiang et al., 2007; Markman et al., 2010). Finally, 
resistance to TORC1 inhibition by rapalogs may develop from activation of the MAPK pathway 
(Carracedo et al., 2008). Inhibition of TORC2 has been shown to reverse the AKT activation 
induced by TORC1 inhibition (Nardella et al., 2009). 
 
Several components of the PI3K/Akt/mTOR pathway can be altered during the pathogenesis of 
TCC, which results in uncontrolled cell proliferation. (Garcia et al., 2008; Chen et al., 2010). 
Genomic alterations in three of the key genes in the mTOR pathway (PIK3CA, TSC1/2, and PTEN) 
are not mutually exclusive in TCC but they play a major role in upstream regulation of this pathway 
(Platt et al., 2009). As previously mentioned, loss of function mutation in the TSC1 and TSC2 have 
been shown to activate the mTORC1 pathway constitutively (Magri et al., 2011).  TSC1 is a tumor 
suppressor gene that is involved in the pathogenesis of TCC and loss of heterozygosity (LOH) 
involving the TSC1 locus at 9q34 occurs in more than 50% of these tumors. Several genetic 
alterations of TSC1 have been identified in 8-16% of TCCs (Hornigold et al., 1999; Habuchi et 
al., 1995; Platt et al., 2009, TCGA bladder cancer 2014). The most common alterations described 
in TSC1 and TSC2 bladder cancers are inactivating Copy Number Alterations (CAN) and 
truncating mutations (Iyer et al., 2012; TCGA bladder cancer 2014).  The inactivating somatic 
mutations of TSC1 gene in TCC seem to be, in part, different from the mutation spectrum seen in 
tuberous sclerosis syndrome (Knowles et al., 2003; Pymar et al., 2008). LOH involving the TSC2 
locus at 16q13.3 has been described in about 15% of TCCs with array based CGH analysis showing 
under-representation of TSC2 region in 9.7% (Platt et al., 2009). TSC1, as well as TSC2, were 
reported to be mutated with combined frequency of 15% in bladder cancer in one study (Sjödahl 
et al 2011).  
As many components of the mTOR upstream regulatory pathways are dysregulated in urothelial 
TCC, an agent or multiple agents that can potentially target these pathways may be the best strategy 
to control this disease. The successful use of rapalogs in the treatment of subependymal giant-cell 
astrocytoma in patients with tuberous sclerosis suggested that mTOR inhibitors could be a 
therapeutic option for tumors that harbor a TSC mutation. (Franz et al., 2006; Krueger et al., 
2010). Everolimus has demonstrated a clinical benefit in TCC patients treated on a phase II clinical 
trial. PFS of 3.3 months and an OS of 10.5 months were reported (Seront et al., 2012). Further 
analysis of tumor samples of patients on this trial utilizing Whole Genome Sequencing (WGS) 
identified inactivating mutations in TSC1 as a biomarker of clinical benefit. Examples of these 
mutations included R629*; R509*; Q694*; V220F; E636fs (Iyer et al., 2012).   The majority of 
patients with TSC1 wild type tumors who were treated with everolimus progressed within 2 months 
of therapy, while patients whose tumors were TSC1 mutant remained on therapy for 7.7 months 
(p=0.004) (Iyer et al., 2012). This trial looked only at the relevance of TORC1 inhibition in relation 
to everolimus response in a retrospective manner. The relevance of TSC2 mutations in relation to 
everolimus sensitivity has not been studied.    These results suggest that utilizing mTOR inhibitors 
for TSC1 mutated TCC patients is a rational approach that should be further explored in the context 
of a genomic driven clinical trial. MLN0128 (TAK-228) has demonstrated a broader range of 
activity and this may translate into additional benefit when using MLN0128 (TAK-228) in TSC1/2 
mutated TCC. Dual TORC inhibition in addition to the wide range of activity of MLN0128 (TAK-
228) may help to mitigate possible resistance mechanisms that may develop during the course of 

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treatment. 
It is unknown if the biologic and clinical effects of TSC1 and TSC2 mutations in TCC are identical 
but both TSC1 and TSC2 are upstream regulators of the mTOR pathway.  Utilizing NGS will help 
identify patients with TSC1 and/or TSC 2 mutated tumors who may benefit the most from 
MLN0128 (TAK-228) and shed more light on the complex genomic machinery of mTOR 
regulation. 
Studying the antitumor efficacy and safety of MLN0128 (TAK-228) in the context of a genomic 
driven clinical trial in TCC is warranted with the potential that MLN0128 (TAK-228) could be 
more effective in the treatment of cancers where rapalogs have demonstrated limited activity.  
 
2.4 
Correlative Studies Background 
This study will be using an integral biomarker by identifying bladder cancer patients whose tumors 
harbor a TSC1 and/or TSC2 mutation identified by a CLIA-certified laboratory. If TSC1 and/or 
TSC2 mutation unknown, this protocol will pre-screen patients with locally advanced or metastatic 
TCC for TSC1 and/or TSC2 mutation. It will require submission of tumor tissue in a form of 10 
unstained slides, or fresh frozen, paraffin embedded (FFPE) block to the CLIA-certified Molecular 
Profiling Laboratory at Yale University under the direction of Dr. Jeffrey Sklar. The TSC1/TSC2 
test panel is described in Section 9.1.  
 
Only those patients who harbor mutations in the TSC1 and/or TSC2 and meet other eligibility 
criteria will be treated with MLN0128 (TAK-228). It is unknown if the biologic and clinical effects 
of TSC1 and TSC2 mutations in TCC are identical.  The available literature supports a positive 
correlation between TSC1 mutation and clinical benefit with rapalog treatment; however, it is 
unknown if the same benefit is possible with TSC2 mutated TCC.  The primary objective will be 
to study the activity of MLN0128 (TAK-228) in TSC1 mutated TCC. We will also evaluate the 
activity and tolerability of MLN0128 (TAK-228) in TSC2 mutated TCC in an exploratory fashion 
to gain experience as we accrue in the TSC1 cohort to meet its accrual objectives of evaluable 
patients. 
 
3. PATIENT SELECTION 
 
3.1 
Eligibility Criteria  
 
3.1.1 Patients must have measurable disease as defined by RECIST version 1.1.  See Section 11 
for the evaluation of measurable disease. 
 

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3.1.2 Must have a histologically confirmed transitional cell carcinoma (TCC, also known as 
urothelial carcinoma), locally advanced or metastatic.  
 
3.1.3 Patient must have TCCs tumors harboring a TSC1 or TSC2 mutation identified by a CLIA 
certified laboratory. 
 
3.1.4 Unless the prescreening was performed at Yale Clinical Molecular Pathology Lab 
(YCMPL), patients must have TCC tumor tissue available for submission in a form of at 
least 10 unstained slides or FFPE block (FFPE block highly recommended and preferred) 
along with a buccal swab (See 9.1 for tissue submission procedure). If the number of 
slides is less than 10, a biopsy should be considered. If a biopsy is deemed unsafe, the 
case may be discussed with the Study PI and approval must be given for eligibility.   
 
3.1.5 Patient must have developed disease progression during or following treatment with at 
least one platinum-containing regimen (e.g., GC, MVAC, CarboGem) for inoperable 
locally advanced or metastatic urothelial carcinoma or disease recurrence, or must be 
unfit or ineligible for cisplatin-based chemotherapy as defined below.  There is no 
restriction on the number of prior lines of chemotherapeutics agents received.  
 
x Patients who progressed within 12 months of treatment with a platinum-containing 
neoadjuvant or adjuvant regimen are considered second-line patients. Therefore, these 
patients may be also eligible. 
 
x Patients who are unfit or ineligible for cisplatin-based chemotherapy as defined by 
any one of the following criteria are eligible for this trial:  
a. ECOG performance score of 2 
b. Creatinine clearance < 60 mL/min  
c. A hearing loss (measured by audiometry) of 25 dB at two contiguous frequencies  
d. *UDGHSHULSKHUDOQHXURSDWK\ 
 
3.1.6 Age 18 years.   
Because no dosing or adverse event data are currently available on the use of MLN0128 
(TAK-228) in patients <18 years of age, children are excluded from this study. 
 
3.1.7 ECOG performance status  2 (Karnofsky 60%, see Appendix A). 
 
3.1.8 Life expectancy of greater than 12 weeks. 
 
3.1.9 Patients must have normal organ and marrow function as defined below: 
 
 
+HPRJORELQJG/ 
 
Fasting serum glucose             130 mg/dL  
 
HbA1c                                    <7.0% 
 
Fasting triglycerides                300 mg/dL 
 
Leukocytes 
3,000/mcL 
 
Absolute neutrophil count 
1,500/mcL 

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 
Platelets 
100,000/mcL 
 
Total bilirubin 
within normal institutional limits 
 
AST (SGOT)/ALT (SGPT)  2.5 × institutional upper limit of normal (ULN) and   
                                                5 ULN if liver metastases are present.  
 
Creatinine 
[XSSHU normal institutional limits (UNL) 
OR 
 
Creatinine clearance 
 40 mL/min based either on Cockroft-Gault estimate 
or based on urine collection (12 or 24 hour) 
 
3.1.10 Patients with controlled Diabetes are allowed on study. Controlled diabetes is defined as 
FBS 130 mg/dL or less, and patients whose FBS can be brought in this range with 
medical therapy are eligible for trial inclusion. 
 
3.1.11 The effects of MLN0128 (TAK-228) on the developing human fetus are unknown. 
Fertility and developmental studies with MLN0128 (TAK-228) have not been conducted. 
On the basis of potential hazard of other mTOR inhibitors (i.e., rapamycin and other 
rapalogs) on the developing fetus, women of childbearing age should avoid becoming 
pregnant while taking any mTOR inhibitor including MLN0128 (TAK-228).    
 
Female patients must: 
x be postmenopausal for at least 1 year before the screening visit, OR 
x be surgically sterile, OR 
x 
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 90 days (or longer, as mandated by local labeling 
[e.g., USPI, SmPC, etc.;]) after the last dose of study drug, OR 
x 
agree to practice true abstinence, when this is in line with the preferred and usual lifestyle of 
the patient.  NOTE: 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. 
 
Male patients, even if surgically sterilized (i.e., status postvasectomy), must  
x agree to practice highly effective barrier contraception during the entire study 
treatment period and through 120 days after the last dose of study drug, OR  
x 
agree to practice true abstinence, when this is in line with the preferred and usual lifestyle of 
the patient (NOTE: Periodic abstinence [e.g., calendar, ovulation, symptothermal, 
postovulation methods for the female partner], withdrawal, spermicides only, and lactational 
amenorrhea are not acceptable methods of contraception.  Female and male condoms should 
not be used together). 
x AND agree not to donate sperm during the course of this study or within 120 days 
after receiving their last dose of study drug.  
 
3.1.12 Ability to swallow oral medications. 
 
3.1.13 Ability to understand and the willingness to sign a written informed consent document. 
 

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3.2 
Exclusion Criteria 
 
3.2.1 Patients who have had chemotherapy, immunotherapy, or investigational therapy, within 4 
weeks (6 weeks for nitrosoureas or mitomycin C), or palliative radiotherapy within 2 weeks 
prior to the first dose of the study drug.. 
 
3.2.2 Patients who have not recovered from adverse events due to prior anti-cancer therapy to 
grade 1 or baseline. Patients with stable, controlled grade 2 AEs such as peripheral 
neuropathy, hypothyroidism, hypertension, adrenal insufficiency or alopecia are allowed 
after discussing with the PI. 
 
3.2.3 Patients with known symptomatic, untreated central nervous system (including brain, 
spinal cord).  Patients who have a history of brain/CNS metastasis are eligible for the study 
provided that all the following criteria are met: 
a) 
Brain/CNS metastases which have been treated 
b) 
1RHYLGHQFHRIGLVHDVHSURJUHVVLRQIRUPRQWKVEHIRUHWKHILUVWGRVHRI
study drug. 
c) 
No hemorrhage after treatment 
d) 
Off-treatment with dexamethasone for 4 weeks before administration of the 
first dose of TAK-228 
e) 
No ongoing requirement for dexamethasone or anti-epileptic drugs 
 
3.2.4 History of allergic reactions attributed to compounds of similar chemical or biologic 
composition to MLN0128 (TAK-228). 
 
3.2.5 Subjects who are on systemic corticosteroids (IV or oral steroids, excluding inhaled, topical 
or ophthalmic corticosteroids), or anti-epileptic drugs for treated brain metastasis.  
 
3.2.6 Subjects taking strong inhibitors and/or inducers of cytochrome P450 (CYP) 3A4, 
CYP2C19 or CYP2C9 within 1 week preceding the first dose of MLN0128 (TAK-228).  
 
If a subject requires treatment with strong inhibitors and/or inducers of CYP3A4, 
CYP2C19 and/or CYP2C9, alternative treatment must be considered. If no alternative is 
available, one such medication may be allowed after discussing with the Study PI. (See 
Appendix F). 
 
3.2.7 Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, 
symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia 
(excluding rate controlled atrial fibrillation/flutter), or psychiatric illness/social situations 
that would limit compliance with study requirements. 
 

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3.2.8 Pregnant and breastfeeding women are excluded from this study because fertility and 
developmental studies with MLN0128 (TAK-228) have not been conducted and there is a 
potential risk for adverse events including teratogenicity and risk of abortion. 
Breastfeeding should be discontinued if the mother is treated with MLN0128 (TAK-228).  
 
3.2.9 HIV-positive patients on combination antiretroviral therapy are ineligible because of the 
potential for pharmacokinetic interactions with MLN0128 (TAK-228); however, HIV 
patients treated with regimens that have low CYP450 inhibition may be allowed as long as 
the patient’s general health and CD4 counts are within acceptable levels.   
 
3.2.10 Patients with baseline prolongation of the rate-corrected QT interval (QTc) (e.g., repeated 
demonstration of QTc interval > 480 milliseconds, or history of congenital long QT 
syndrome, or torsades de pointes).   
 
3.2.11 Patients with untreated or active Hepatitis B or C infection.    
 
3.2.12 Significant active cardiovascular or pulmonary disease at the time of study entry 
including 
A. Uncontrolled high blood pressure (i.e., systolic blood pressure >180 mm Hg, 
diastolic blood pressure > 95 mm Hg)  
B. Pulmonary hypertension   
C. Uncontrolled asthma or O2 saturation < 90% by ABG (Arterial Blood Gas) analysis 
or pulse oximetry on room air    
D. Significant valvular disease; severe regurgitation or stenosis by imaging 
independent of symptom control with medical intervention, or history of valve 
replacement   
E. Medically significant (symptomatic) bradycardia    
 
3.2.13 Manifestations of malabsorption due to prior gastrointestinal (GI) surgery, GI disease, or 
for an unknown reason that may alter the absorption of MLN0128 (TAK-228). 
 
3.2.14 Concomitant administration of any proton pump inhibitor (PPI) is not permitted during 
the study. Patients receiving PPI therapy before enrollment must stop using the PPI for 7 
days before their first dose of study drugs. 
 
3.2.15 History of any of the following within the last 6 months prior to study entry: 
A. Ischemic myocardial event, including angina requiring therapy and artery 
revascularization procedures   
B. Ischemic cerebrovascular event, including TIA and artery revascularization 
procedures 
C. Requirement for inotropic support (excluding digoxin) or serious (uncontrolled) 
cardiac arrhythmia (including atrial flutter/fibrillation, ventricular fibrillation or 
ventricular tachycardia)  
D. Pulmonary embolism  
E. New York Heart Association (NYHA) Class III or IV heart failure  

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F. Placement of a pacemaker for control of rhythm 
 
3.2.16 Subjects who have initiated treatment with bisphosphonates less than 30 days prior to the   
first administration of MLN0128 (TAK-228). Concurrent bisphosphonate use is only 
allowed if the bisphosphonate was initiated at least 30 days prior to the first 
administration of MLN0128 (TAK-228). 
 
3.2.17 Patients who received prior PI3K, AKT or mTOR inhibitors are not allowed.  
 
3.2.18 Patients who received radiation therapy within the last 4 weeks. Radiation exposure may 
not exceed 30% of marrow area. 
 
 
4. REGISTRATION PROCEDURES 
 
4.1 
Investigator and Research Associate Registration with CTEP 
 
Food and Drug Administration (FDA) regulations and National Cancer Institute (NCI) policy 
require all individuals contributing to NCI-sponsored trials to register and to renew their 
registration annually.  To register, all individuals must obtain a Cancer Therapy Evaluation 
Program (CTEP) Identity and Access Management (IAM) account 
(https://ctepcore.nci.nih.gov/iam).  In addition, persons with a registration type of Investigator 
(IVR), Non-Physician Investigator (NPIVR), or Associate Plus (AP) (i.e., clinical site staff 
requiring write access to OPEN or RAVE or acting as a primary site contact) must complete their 
annual registration using CTEP’s web-based Registration and Credential Repository (RCR) 
(https://ctepcore.nci.nih.gov/rcr).  Documentation requirements per registration type are outlined 
in the table below. 
Documentation Required 
IVR 
NPIVR AP 
A 
FDA Form 1572 
D 
D 
 
 
Financial Disclosure Form 
D 
D 
D 
 
NCI Biosketch (education, training, employment, 
license, and certification) 
D 
D 
D 
 
HSP/GCP training 
D 
D 
D 
 
Agent Shipment Form (if applicable) 
D 
 
 
 
CV (optional) 
D 
D 
D 
 
 
An active CTEP-IAM user account and appropriate RCR registration is required to access all 
CTEP and CTSU (Cancer Trials Support Unit) websites and applications.  In addition, IVRs and 

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NPIVRs must list all clinical practice sites and IRBs covering their practice sites on the FDA 
Form 1572 in RCR to allow the following: 
• 
Added to a site roster 
• 
Assigned the treating, credit, consenting, or drug shipment (IVR only) tasks in OPEN 
• 
Act as the site-protocol PI on the IRB approval 
• 
Assigned the Clinical Investigator (CI) role on the Delegation of Tasks Log (DTL).     
 
Additional information can be found on the CTEP website at 
https://ctep.cancer.gov/investigatorResources/default.htm.  For questions, please contact the 
RCR Help Desk by email at < RCRHelpDesk@nih.gov> 
 
4.2 
Site Registration Process 
 
This study is supported by the NCI Cancer Trials Support Unit (CTSU). 
 
Each investigator or group of investigators at a clinical site must obtain IRB approval for this 
protocol and submit IRB approval and supporting documentation to the CTSU Regulatory Office 
before they can be approved to enroll patients.  Assignment of site registration status in the 
CTSU Regulatory Support System (RSS) uses extensive data to make a determination of whether 
a site has fulfilled all regulatory criteria including but not limited to the following: 
• 
An active Federal Wide Assurance (FWA) number 
• 
An active roster affiliation with the Lead Network or a participating organization 
• 
A valid IRB approval 
• 
Compliance with all protocol specific requirements 
In addition, the site-protocol Principal Investigator (PI) must meet the following criteria: 
• 
Active registration status 
• 
The IRB number of the site IRB of record listed on their Form FDA 1572 
• 
An active status on a participating roster at the registering site. 
 
Sites participating on the NCI CIRB initiative that are approved by the CIRB for this study are 
not required to submit IRB approval documentation to the CTSU Regulatory Office. For sites 
using the CIRB, IRB approval information is received from the CIRB and applied to the RSS in 
an automated process.  Signatory Institutions must submit a Study Specific Worksheet for Local 
Context (SSW) to the CIRB via IRBManager to indicate their intent to open the study locally.  
The CIRB’s approval of the SSW is then communicated to the CTSU Regulatory Office.  In 
order for the SSW approval to be processed, the Signatory Institution must inform the CTSU 
which CIRB-approved institutions aligned with the Signatory Institution are participating in the 
study. 
 
4.2.1 
Downloading Regulatory Documents 
 
Site registration forms may be downloaded from the NCI#9767 protocol page located on 
the CTSU Web site.  Permission to view and download this protocol is restricted and is 
based on person and site roster data housed in the CTSU RSS.  To participate, 
Investigators and Associates must be associated with the Corresponding or Participating 
protocol organization in the RSS.  

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x Go to https://www.ctsu.org and log in using your CTEP IAM username and 
password. 
x Click on the Protocols tab in the upper left of your screen.  
x Either enter the protocol # in the search field at the top of the protocol tree, or 
x Click on the By Lead Organization folder to expand, then select LAO-CT018, and 
protocol #9767. 
x Click on LPO Documents, select the Site Registration documents link, and 
download and complete the forms provided.  (Note: For sites under the CIRB 
initiative, IRB data will load to RSS as described above.) 
 
4.2.2 
Submitting Regulatory Documents 
 
Submit required forms and documents to the CTSU Regulatory Office, where they will 
be entered and tracked in the CTSU RSS.   
Regulatory Submission Portal: www.ctsu.org  (members’ area) Æ Regulatory Tab 
ÆRegulatory Submission  
When applicable, original documents should be mailed to: 
CTSU Regulatory Office 
1818 Market Street, Suite 3000 
Philadelphia, PA 19103 
 
Institutions with patients waiting that are unable to use the Portal should alert the CTSU 
Regulatory Office immediately at 1-866-651-2878 in order to receive further instruction 
and support. 
 
4.2.3 
Requirements For Protocol #9767 Site Registration: 
 
x IRB approval (For sites not participating via the NCI CIRB; local IRB 
documentation, an IRB-signed CTSU IRB Certification Form, Protocol of Human 
Subjects Assurance Identification/IRB Certification/Declaration of Exemption 
Form, or combination is accepted) 
 
 
4.2.4 Checking Site Registration Status 
 
You can verify your site registration status on the members’ section of the CTSU 
website.   
x Go to https://www.ctsu.org and log in to the members’ area using your CTEP-IAM 

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username and password 
x Click on the Regulatory tab at the top of your screen 
x Click on the Site Registration tab 
x Enter your 5-character CTEP Institution Code and click on Go 
Note: The status given only reflects compliance with IRB documentation and institutional 
compliance with protocol-specific requirements as outlined by the Lead Network. It does 
not reflect compliance with protocol requirements for individuals participating on the 
protocol or the enrolling investigator’s status with the NCI or their affiliated networks. 
 
4.3 
Patient Registration 
4.3.1 OPEN / IWRS 
 
Patient enrollment will be facilitated using the Oncology Patient Enrollment Network 
(OPEN).  OPEN is a web-based registration system available to users on a 24/7 basis.  It 
is integrated with the CTSU Enterprise System for regulatory and roster data interchange 
and with the Theradex Interactive Web Response System (IWRS) for retrieval of patient 
registration/randomization assignment.  Patient enrollment data entered by Registrars in 
OPEN / IWRS will automatically transfer to the NCI’s clinical data management system, 
Medidata Rave. 
 
The OPEN system will provide the site with a printable confirmation of registration and 
treatment information.  Please print this confirmation for your records.  
 
This trial uses slot reservation.  For this study, OPEN will connect to IWRS at enrollment 
initiation to check slot availability.  Registration staff should ensure that a slot is 
available and secured for the patient before completing an enrollment. 
 
IMPORANT NOTE: Patient’s slot reservation must be done first before sending the 
samples for TSC pre-screening test.  The Study PI or his delegate will be in charge of 
approving the slot reservation request. 
 
 
4.3.2 
OPEN/IWRS User Requirements 
 
OPEN/IWRS users must meet the following requirements: 
x Have a valid CTEP-IAM account (i.e., CTEP username and password). 
x To enroll patients:  Be on an ETCTN Corresponding or Participating Organization 
roster with the role of Registrar. Registrars must hold a minimum of an AP 
registration type. If a DTL is required for this study, the registrar(s) must also be 
assigned the OPEN Registrar task on the DTL. 
x Have regulatory approval for the conduct of the study at their site. 
 
Prior to accessing OPEN/IWRS, site staff should verify the following: 

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x All eligibility criteria have been met within the protocol stated timeframes.  
x If applicable, all patients have signed an appropriate consent form and HIPAA 
authorization form. 
 
4.3.3 
OPEN/IWRS Questions? 
 
Further instructional information on OPEN is provided on the OPEN tab of the CTSU 
website at https://www.ctsu.org or at https://open.ctsu.org.  For any additional questions 
contact the CTSU Help Desk at 1-888-823-5923 or ctsucontact@westat.com.  
 
Theradex has developed a Slot Reservations and Cohort Management User Guide, which 
is available on the Theradex website:  
http://www.theradex.com/clinicalTechnologies/?National-Cancer-Institute-NCI-11. This 
link to the Theradex website is also on the CTSU website OPEN tab. For questions about 
the use of IWRS for slot reservations, contact the Theradex Helpdesk at 609-619-7862 or 
Theradex main number 609-799-7580; CTMSSupport@theradex.com 
 
 
4.4 
General Guidelines 
Following registration, patients should begin protocol treatment within 7 days.  Issues that would 
cause treatment delays should be discussed with the Principal Investigator.  If a patient does not 
receive protocol therapy following registration, the patient’s registration on the study may be 
canceled.  The Study Coordinator should be notified of cancellations as soon as possible. 
 
 
5. TREATMENT PLAN 
 
5.1 
Agent Administration 
 
Treatment will be administered on an outpatient basis.  Reported adverse events and potential risks 
are described in Section 7.  Appropriate dose modifications are described in Section 6.  No 
investigational or commercial agents or therapies other than those described below may be 
administered with the intent to treat the patient's malignancy. To ensure compliance, patients will 
be requested to maintain a medication diary of each dose of medication (Appendix D).  The 
medication diary will be returned to clinic staff at the end of each course. 
The starting dose of MLN0128 (TAK-228) is 3mg by mouth once a day. One cycle consists of 28 
calendar days.  
Dose Level 
MLN0128 (TAK-228)  Dose 
-3 
1 mg 5 days per week 
-2 
2 mg daily for 5 days out of 7 
-1 
2 mg, daily 
1 
3 mg, daily 
Level 1 is the starting dose. 
MLN0128 (TAK-228) should be taken on an empty stomach at least 2 hours after food and do not 
eat or drink (except water) for at least one hour after taking MLN0128 (TAK-228).  Do not chew, 
open or manipulate the capsule in any way prior to swallowing.  Each dose should be taken with 

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8 ounces (240 mL) of water). Subjects should be encouraged to drink at least 18-24 ounces of 
liquids a day to stay well hydrated.   
In cases where a subject misses dosing at his/her dosing time, the subject may still take the dose 
within 12 hours of the regular dosing time (subjects should not take 2 consecutive daily doses 
within 12 hours of each other).  Subjects who vomit shortly after receiving MLN0128 (TAK-228) 
will not receive a replacement dose.  If confirmed that the study drug has been vomited, the dose 
should be noted as having been missed.” 
There is a potential for interaction of MLN0128 (TAK-228) with other concomitantly administered 
drugs through the cytochrome P450 system.   MLN0128 (TAK-228) displayed low potential (IC50 
!  ȝ0 IRU LQKLELWLRQ RI WKH PDMRU KXPDQ &<3 LVRIRUPV.  Although potential drug-drug 
interactions with MLN0128 (TAK-228) cannot be ruled out based on the known metabolism 
characteristics of MLN0128 (TAK-228), the potential risk is considered low. Patients receiving 
any medications or substances that are inhibitors or inducers of can be treated with caution.  (See 
Appendix F). 
 
If severe emesis or mucositis prevents the patient from taking scheduled doses, that dose will be 
skipped. If emesis occurs after study medication ingestion, the dose will not be readministered, 
and patients should resume dosing at the next scheduled time with the prescribed dosage. 
Patients should record the occurrence of the emesis in their dosing diaries. Under no 
circumstance should a patient repeat a dose or double-up doses. 
 
5.2 
General Concomitant Medication and Supportive Care Guidelines 
 
As there is a potential for interaction of MLN0128 (TAK-228) with other concomitantly 
administered drugs through the cytochrome P450 system, the case report form must capture the 
concurrent use of all other drugs, over-the-counter medications, or alternative therapies.   
 
The following medications and procedures are prohibited during the study: 
x Other investigational agents or mTOR inhibitors. 
x Other anticancer therapies including chemotherapy, immunotherapy, 
radioimmunotherapy, targeted agents, radiation or surgery (subjects can have palliative 
radiation or surgery in the study for pre-existing lesions) 
x Systemic corticosteroids (either IV or oral steroids, excluding inhalers) unless necessary 
for treatment of MLN0128 (TAK-228) related AE, ie, rash 
x Anti-epileptic drugs for subjects with treated brain metastasis 
x Strong CYP3A4/CYP2C19 inducers/inhibitors (See Appendix F). If a subject requires 
treatment with 1 or more of the strong CYP3A4 and CYP2C19 inhibitors and/or inducers, 
the study doctor should be consulted.  
x Concomitant proton pump inhibitors, due to effects on MLN0128 (TAK-228) absorption.  
 
There are no known strong specific CYP2C9 inhibitors or inducers. Examples of moderate 
inhibitors of CYP2C9 are fluconazole and miconazole; and moderate inducers of CYP2C9 are 
carbamazepine and rifampin. These agents show some degree of overlap with their modulation of 
CYP3A4 and CYP2C19 activity and should hence be considered with similar caution. The 
Principal Investigator should be alerted if the patient is taking any agent known to affect or with 

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28 
the potential to affect selected CYP450 isoenzymes.  Appendix C presents guidelines for 
identifying medications/substances that could potentially interact with the study agent(s). 
 
Subjects should not consume food or beverages containing the fruit or juice from grapefruits or 
Seville oranges within 7 days before first dose of study drug and throughout the study. 
 
Prophylactic use of anti-emetic, anti-nausea, and antidiarrheal medications are encouraged and 
may be used prior to first dose of study drug (MLN0128 (TAK-228)), and as needed throughout 
the study prior to each dosing and as clinically indicated per standard practice. Initiation of 
hematopoietic growth factors, transfusions of blood, and blood products should not be used in 
the first cycle unless absolutely clinically necessary. However, they may be administered after 
&\FOHLIQHHGHG6XEMHFWVZKRKDYHEHHQRQFKURQLFHU\WKURSRLHWLQIRUGD\VPD\FRQWLQXH
to receive the concomitant medication upon study entry. 
 
Concurrent  bisphosphonate use is only allowed if the bisphosphonate was initiated at least 30 
days prior to the first administration of MLN0128 (TAK-228). Bisphosphonates should be given 
after Cycle 1 to minimize confounding factors which may contribute to potential drug related 
toxicities. 
 
 
5.3 
Duration of Therapy 
 
In the absence of treatment delays due to adverse event(s), treatment may continue until one of 
the following criteria applies: 
 
x 
Disease progression, 
 
x 
Intercurrent illness that prevents further administration of treatment, 
 
x 
Unacceptable adverse event(s), 
 
x 
Patient decides to withdraw from the study, or 
 
x 
General or specific changes in the patient's condition render the patient unacceptable 
for further treatment in the judgment of the investigator. 
 
5.4 
Duration of Follow Up 
 
x Patients who discontinued the study treatment due to disease progression will be followed 
for 4 weeks after the last dose of the study drug or until the resolution or stabilization of 
treatment-related adverse events.  
 
x Patients who discontinued the study treatment for reasons other than disease progression 
or death will be followed with the restaging scans as clinically indicated until disease 
progression, or initiation of the subsequent therapy is documented.  
 

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x Patients who discontinue the study treatment due to unacceptable treatment related 
toxicity will be followed until resolution or stabilization of the treatment related adverse 
event.  
 
x All participants’ vital status may be followed after removal from the study treatment via a 
phone call or medical records review every 6 months and using publicly available 
databases. 
 
5.5 
Criteria for Removal from Study 
 
Participants will be removed from study when any of the following criteria apply: 
 
x Lost to follow-up 
x Withdrawal of consent for data submission 
x Death 
 
The reason for taking a participant off study, and the date the participant was removed, must be 
documented in the case report form (CRF). 
 
 
6. DOSING DELAYS/DOSE MODIFICATIONS 
 
6.1 
Special Warnings and Special Precautions for Use 
 
Insulin and Glucose Levels 
Hyperglycemia and hyperinsulinemia are known toxicities associated with inhibition of mTOR 
(mechanistic [formerly mammalian] target of rapamycin) and related pathways based on 
nonclinical studies. 
 
A rise in fasting plasma glucose has been observed as early as 1 to 2 days following oral 
administration of MLN0128 (TAK-228). Early initiation of treatment of the hyperglycemia are 
essential. Subjects with Grade 1 hyperglycemia (fasting serum glucose [FSG] > the upper limit of 
the normal range PJG/DUHWUHDWHGZLWKRUDOK\SRJO\FHPLFDJHQWVHJPHWIRUPLQDQG
subjects with *UDGHK\SHUJO\FHPLD)6*!PJG/DUHWUHDWHGDJJUHVVLYHO\ZLWKRUDO 
hypoglycemic agents and/or insulin as clinically indicated. Early treatment, as noted previously, 
have resulted in good control of glucose levels for the majority of MLN0128 (TAK-228)-treated 
subjects who developed hyperglycemia.  
 
Cardiac Effects 
Cardiac events (including QT interval corrected for heart rate prolongation and arrhythmias) have 
been infrequently observed in clinical studies of MLN0128 (TAK-228). To date, there has been 1 
report of ventricular fibrillation and cardiac arrest postdose that had a fatal outcome and was 
assessed as possibly related to MLN0128 (TAK-228). Routine cardiac monitoring with baseline 
electrocardiogram (ECG) or multigated acquisition scan and on-study ECGs and physical 
examination constitute the core cardiac safety monitoring in all MLN0128 (TAK-228) studies. 
 

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For subjects showing any signs of cardiac instability after MLN0128 (TAK-228) dosing, additional 
monitoring onsite before clinic discharge should be considered. 
 
Renal Function 
Grade 1 and 2 elevations in creatinine (regardless of causality) have been observed in subjects 
receiving MLN0128 (TAK-228), all of which have been reversible with drug interruption and/or 
supportive care with intravenous (IV) hydration. Further evaluation of the renal insufficiency with 
urine electrolytes suggested a pre-renal etiology with a low fractional excretion of sodium < 1%. 
However, the adverse event cases were confounded by multiple factors such as nausea, vomiting, 
hyperglycemia, concomitant medications with GI side effects such as metformin, and 
hydronephrosis, any of which may have also contributed to dehydration and elevated creatinine. 
Subjects should be encouraged to drink at least 20 ounces of fluids a day, especially on days 
requiring fasting (per protocol), with administration of IV fluids in the clinic as indicated to avoid 
dehydration. 
 
Baseline macroscopic urinalysis and routine serum chemistries along with other safety laboratory 
assessments are performed in all MLN0128 (TAK-228) studies. Additionally, microscopic 
urinalysis, a 12-hour urine collection, spot urine electrolytes, protein and creatinine, and serum 
FKHPLVWU\VKRXOGEHFROOHFWHGDWDQ\WLPHZKHQWKHVHUXPFUHDWLQLQHLV*UDGH according to 
National Cancer Institute Common Terminology Criteria for Adverse Events version 5.0, to further 
evaluate possible etiologies for the renal dysfunction. 
 
Rash 
Rash observed in clinical studies of MLN0128 (TAK-228) tends to be maculopapular and pruritic 
and has ranged from Grade 1 to 3. For the most part, rash and pruritus improve with antihistamines, 
topical steroid creams, and/or dose interruption. Some subjects have required pulse systemic 
steroids, dose reduction, and/or study treatment discontinuation. 
 
Pneumonitis 
Early recognition, prompt intervention, and a conservative risk management approach are 
recommended due to pneumonitis that has been observed with rapalog therapy. While no cases of 
pneumonitis assessed as related to MLN0128 (TAK-228) have been reported, this event will be 
closely monitored in all MLN0128 (TAK-228) study subjects. 
 
Abdominal Pain/Pancreatitis 
Abdominal pain and radiologic and biochemical evidence of pancreatitis have recently been seen 
in two patients treated with MLN0128 (TAK-228) and aflibercept.  While this may not be a 
problem on single-agent MLN0128 (TAK-228), amylase and lipase tests should be performed for 
any patient on trial with unexplained abdominal pain.   
 
If the patient develops a toxicity that requires treatment delays or dose modifications, the following 
dose de-escalation schema is suggested:  
 
Dose Level 
MLN0128 (TAK-228)  Dose 
-3 
1 mg 5 days per week 
-2 
2 mg daily for 5 days out of 7 
-1 
2 mg, daily 

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1 (RP2D) 
3 mg, daily 
Level 1 is the starting dose. 
 
 
 
6.2 
Dose Modification Guidelines: 
MLN0128 (TAK-228) dosing should be withheld for any *UDGHMLN0128 (TAK-228)-related 
WR[LFLWLHV,IWKHHYHQWUHVROYHVWR*UDGHRUEDVHOLQHYDOXHVZLWKLQ14 days of interrupting 
therapy, subject may resume study treatment at one dose level lower. 
In general, if MLN0128 (TAK-228) dosing is delayed for > 14 consecutive days for MLN0128 
(TAK-228)-related toxicity despite supportive treatment per standard clinical practice or more than 
3 dose reductions of MLN0128 (TAK-228) is required in a subject, stop MLN0128 (TAK-228) 
therapy, discontinue the subject from the study, and complete the EOT visit within30-40 days of 
the last administration of MLN0128 (TAK-228).   
As a general principle, grade 4 MLN0128 (TAK-228)-related toxicities of any duration require 
permanent discontinuation of the study drug with the following the exception:  
x 
Clinically insignificant lab abnormalities that resolve within two days on optimum treatment. 
 
See the Tables below for specific guidelines, which overrides the aforementioned general 
principle.  
 
The following tables represent some modification guidelines tables for some possible adverse 
events:  
 
6.2.1 
Management of Nausea and/or Vomiting 
 
Nausea and/or Vomiting 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
d 2 
Loss of appetite with or without 
decreased oral intake; 
1-5 episodes of vomiting within 
24 hours 
Maximize anti-emetic 
therapy; 
Consider 
IV 
fluid 
hydration. 
None. 
t 3 
Inadequate oral intake; 
HSLVRGHVRIYRPLWLQJZLWKLQ
24 hours 
Maximize anti-emetic 
therapy; 
Initiate tube feeding, 
IVF, or TPN. 
 ,I H[SHULHQFHG IRU  KRXUV KROG
MLN0128 (TAK-228) XQWLO*UDGHWKHQ
resume MLN0128 (TAK-228) without dose 
modification. If experienced for >72 hours 
despite optimal therapy, hold MLN0128 
(TAK-228) XQWLO  *UDGH  WKHQ UHVXPH
treatment with the dose of MLN0128 (TAK-
228) reduced by 1 level. 
Prevention/Prophylaxis 
Prophylactic use of anti-emetic, anti-nausea, and anti-diarrheal medications are encouraged and may be used before 

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each dose of MLN0128 (TAK-228) as needed throughout the study. 
Abbreviations:  IV = intravenous; IVF = intravenous fluids; TPN = total parenteral nutrition 
 
6.2.2 
  Management of Diarrhea 
 
Diarrhea 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
1 
Increase of <4 stools per day 
over baseline; mild increase in 
ostomy output compared to 
baseline 
Loperamide antidiarrheal 
therapy. 
Dosage schedule:  4 mg 
at first onset, followed by 
2 mg with each loose 
motion until diarrhea-free 
for 12 hours (maximum 
dosage:  16 mg/24 hours) 
No change in dose 
2 
Increase of 4 - 6 stools per day 
over baseline; moderate 
increase in ostomy output 
compared to baseline 
Same Grade 1 
Interrupt MLN0128 (TAK-228) treatment: 
:KHQV\PSWRPV*UDGHUH-initiate 
MLN0128 (TAK-228) treatment at a dose 
reduction  
Discontinue MLN0128 (TAK-228) 
treatment if failure to recover within 4 
weeks. 
3 
Increase of >=7 stools per day 
over baseline; incontinence; 
hospitalization indicated; 
severe increase in ostomy 
output compared to baseline; 
limiting self care ADL 
Same as Grade 1 
Interrupt MLN0128 (TAK-228) treatment 
XQWLOV\PSWRPVUHVROYHWR*UDGH 
Consider re-initiating MLN0128 (TAK-228) 
treatment at a dose reduction  
If toxicity recurs at Grade 3, discontinue 
MLN0128 (TAK-228) treatment. 
4 
Life-threatening 
consequences; urgent 
intervention indicated 
Same as Grade 1 
Discontinue MLN0128 (TAK-228) 
treatment. 
Abbreviations:  ADL = activities of daily living 
Prevention/Prophylaxis 
 Prophylactic use of anti-diarrheal medications are encouraged and may be used before each dose of MLN0128 
(TAK-228) as needed throughout the study. 
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. Patients requiring > three dose 
reductions should go off protocol therapy. 
 
6.2.3 
Management of Hyperglycemia 
 
Hyperglycemia 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose 
Modification 
1 
Fasting blood 
sugar 
> ULN–160 
mg/dL 
Continue close monitoring of blood sugars. 
Initiate oral hypoglycemic agent. 
None. 
2 
Fasting blood 
sugar 
Initiate oral hypoglycemic agent and/or insulin 
if not well controlled on oral agent. 
None. 

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> 160–250 
mg/dL 
Endocrinology consult  
3 
Fasting blood 
sugar 
> 250 -500 
mg/dL 
Initiate oral hypoglycemic agent and/or insulin, 
and hydration. Consider inpatient management. 
Endocrinology consult. 
+ROGGUXJXQWLO*UDGH 
Resume MLN0128 (TAK-228) 
based on timing of recovery: 
ZHHNUHVXPHDWVDPHGRVH
and schedule; 
!EXW4 weeks:  reduce dose  
> 4 weeks:  stop MLN0128 
(TAK-228) and discontinue 
subject from the study. 
4 
>500mg/dL 
Initiate oral hypoglycemic agent and/or insulin; 
hydration and inpatient management.  
Permanent discontinuation of the 
study drug  
Prevention/Prophylaxis 
x 
In-home daily fasting glucose will be monitored. 
x 
Follow fasting serum glucose levels during clinic visits. 
x 
Life-style modifications, as appropriate (balanced diet, limit alcohol consumption, increase physical 
activity). 
x 
Most episodes of Grade 1 and 2 hyperglycemia respond quickly to oral metformin. 
x 
Early initiation of therapy is recommended to prevent higher grade hyperglycemia. 
x 
)DVWLQJEORRGJOXFRVHOHYHOV 150 mg/dL by glucometer should be followed by closer monitoring of 
serum glucose and possible intervention. 
Abbreviations:  dL = deciliters; mg = milligrams; ULN = upper limit of normal. 
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. 
 
In the event that any FSG reading performed at the site indicates hyperglycemia (> upper limit of 
QRUPDO>8/1@RUPJG/WKHVWXG\VWDIIVKRXOGILUVWDVFHUWDLQWKDWWKHVXEMHFWZDVIDVWLQJ
at the time of the blood draw (ie, nothing by mouth for at least 8 hours prior to blood being 
obtained), had continued to take their concomitant antiglycemic medications should the subject 
have underlying diabetes mellitus, and repeat the FSG as needed.  If the repeat FSG continues to 
demonstrate hyperglycemia, investigators should initiate steps to aggressively manage the 
hyperglycemia per standard clinical practice.  The following guidelines are provided to aid the 
investigator in initiating antiglycemic therapies. 
Based on the clinical experience from MLN0128 (TAK-228) trials, most episodes of 
hyperglycemia observed occurred within the first 60 days after initiation of treatment with 
MLN0128 (TAK-228) and have been either Grade 1 or 2 that have responded quickly to oral 
metformin.  Hyperglycemia has not been dose limiting since instituting a standard regimen for 
early treatment of hyperglycemia.  All subjects developing hyperglycemia on the study should 
have their glucose closely monitored by study staff.  The investigator may choose either to continue 
close monitoring of subjects who develop Grade 1 hyperglycemia (FSG > ULN  160 mg/dL) or, 
alternatively, consider initiating treatment with an oral hypoglycemic agent, such as metformin.  
$OOVXEMHFWVZLWK*UDGHK\SHUJO\FHPLD)6* > 160 mg/dL) must be treated aggressively with 
oral hypoglycemic agents and/or insulin as clinically indicated while continuing on MLN0128 
(TAK-228).  The investigator should consult an endocrinologist if needed to aid in optimizing the 
subject’s hyperglycemia treatment plan. 

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It is recommended that subjects be treated initially with a fast acting, insulin sensitizer, such as 
metformin at 500 mg PO QD, and titrate up to a maximum of 1000 mg PO BID as needed.  
Concurrent addition to metformin of DPP-4 inhibitors (eg, sitagliptin or vildagliptin) and/or insulin 
should also be considered.  Oral sulfonylureas (eg, glipizide or glyburide) should be used with 
caution due to the higher risk of inducing hypoglycemia in subjects.  The dose of oral 
hypoglycemic agents should be adjusted in subjects with renal insufficiency. In addition, patients 
should be encouraged to follow a low carbohydrate diet once hyperglycemia is first observed. 
,IDQ\IDVWLQJVHUXPJOXFRVHUHDGLQJSHUIRUPHGDWWKHVLWHLQGLFDWHVK\SHUJO\FHPLD!8/1RU
mg/dL), the study staff should first confirm that the patient was fasting at the time of blood 
specimen collection (ie, nothing by mouth for at least 8 hours before collection). 
 
In-Home Daily Fasting Glucose Monitoring 
In addition to obtaining fasting glucose levels at the clinic visits as outlined in the Schedule of 
Events, all patients randomized to receive MLN0128 (TAK-228) will be given a glucometer to 
monitor their daily FBG levels at home. The level should be collected daily, predose on dosing 
days, and at approximately the same time each day. 
 
On Cycle 1 Day 1, the patient will be provided an in-home glucometer. Patients will be trained on 
proper use of the glucometer and instructed to collect a daily FBG level every morning (predose 
on dosing days), starting on Cycle 1 Day 2. Patients will be instructed to bring the glucometer with 
them to each study visit so that the data collected can be reviewed and recorded in the source 
documents. Investigators will be responsible for reviewing the home glucose monitoring logs for 
hyperglycemia. 
 
7KHSDWLHQWZLOOEHLQVWUXFWHGWRFRQWDFWWKHVLWHLPPHGLDWHO\LIWKHYDOXHLVDEQRUPDOLH
mg/dL) for further instructions on the management of their hyperglycemia. Hyperglycemia 
observed during home glucose monitoring should be confirmed in the clinic. 
 
If no irregularities in the fasting blood glucose level are observed during a minimum of 2 
consecutive months, then the frequency of in-home fasting blood glucose testing can be reduced 
to a minimum frequency of once weekly, depending on the investigator’s judgment and approval. 
Patients will continue to notify the investigator of fasting blood glucose levels that exceed 150 
mg/dL and, if blood glucose levels are not well controlled, or if the patient requires either oral 
hypoglycemic agents or insulin to control blood glucose levels, then the frequency of in-home 
testing of FBG levels will be reinstated to daily. 
 
 
 
6.2.4 
Management of Non-infectious Pneumonitis 
 
 Non-infectious Pneumonitis 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
1 
Asymptomatic: 
Radiographic findings only 
Rule out infection and 
closely monitor. 
None. 
2 
Symptomatic: 
Rule out infection and 
consider treatment with 
Interrupt MLN0128 (TAK-228) treatment: 

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35 
 Non-infectious Pneumonitis 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
Not interfering with ADLs 
corticosteroids until 
symptoms improve to 
 Grade 1. 
:KHQV\PSWRPV*UDGHUH-initiate 
MLN0128 (TAK-228) treatment at a dose 
reduction  
Discontinue MLN0128 (TAK-228) 
treatment if failure to recover within 4 
weeks. 
3 
Symptomatic: 
Interfering with ADLs; 
Requires administration of 
O2 
Rule out infection and 
consider treatment with 
corticosteroids until 
symptoms improve to 
 Grade 1. 
Interrupt MLN0128 (TAK-228) treatment 
XQWLOV\PSWRPVUHVROYHWR*UDGH 
Consider re-initiating MLN0128 (TAK-
228) treatment at a dose reduction  
If toxicity recurs at Grade 3, discontinue 
MLN0128 (TAK-228) treatment. 
4 
Life-threatening: 
Ventilatory support 
indicated 
Rule out infection and 
consider treatment with 
corticosteroids. 
Discontinue MLN0128 (TAK-228) 
treatment. 
Abbreviations:  ADL = activities of daily living; O2 = oxygen gas. 
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. 
 
6.2.5 
Management of Hyperlipidemia 
 
Hyperlipidemia 
Management/Next Dose for MLN0128 (TAK-228) 
 
Grade 1 
Cholesterol: 
> ULN - 300 mg/dL 
Triglycerides: 
> 150 - 300 mg/dL 
 
No change in dose  
 
 
 
 
 
 
Grade 2 
 
Cholesterol: 
> 300 – 400 mg/dL 
Triglycerides: 
> 300 - 500 mg/dL 
Treat hyperlipidemia according to standard guidelines. 
7ULJO\FHULGHVPJGOVKRXOGEHWUHDWHGXUJHQWO\GXHWRULVN
of pancreatitis.  
Maintain dose if tolerable. 
If toxicity becomes intolerable, interrupt MLN0128 (TAK-228) 
GRVLQJXQWLOUHFRYHU\WR*UDGH5HLQLWLDWHDWVDPHGRVH 
Grade 3 
 
Cholesterol: 
> 400 - 500 mg/dL 
Triglycerides: 
> 500 - 1000 mg/dL 
Treat hyperlipidemia according to standard 
guidelines. 
7ULJO\FHULGHVPJGOVKRXOGEHWUHDWHGXUJHQWO\
due to risk of pancreatitis.  
+ROGGRVHXQWLOUHFRYHU\WR*UDGHWKHQUHVWDUWat a 
dose reduction. 
Grade 4 
 
Cholesterol: 
> 500 mg/dL 
Triglycerides: 
> 1000 mg/dL 
Treat hyperlipidemia according to standard 
guidelines. 
7ULJO\FHULGHVPJGOVKRXOGEHtreated urgently 
due to risk of pancreatitis.  
Discontinue treatment. 
Prevention/Prophylaxis 

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36 
Hyperlipidemia 
Management/Next Dose for MLN0128 (TAK-228) 
x 
Life-style modifications, as appropriate (balanced diet, limit consumption of alcoholic beverages, increase 
physical activity). 
Abbreviations:  dL = deciliters; mg = milligrams; ULN = upper limit of normal. 
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. 
 
6.2.6 
Management of Oral Mucositis 
 
Oral Mucositis 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
1 
Asymptomatic or mild 
symptoms 
Non-alcoholic mouth wash 
or 0.9% salt water rinse; 
Consider topical 
corticosteroids at earliest 
signs of mucositis. 
None. 
2 
Moderate pain, not 
interfering with oral 
intake 
 
Modified diet indicated 
Topical analgesic mouth 
treatments; 
Topical corticosteroids; 
Initiate antiviral or antifungal 
therapy, if indicated. 
Maintain dose if tolerable. 
If toxicity becomes intolerable, interrupt 
MLN0128 (TAK-228) dosing until recovery 
WR Grade 1.  Reinitiate at same dose. 
3 
Severe pain, interfering 
with oral intake 
Same as for Grade 2; 
Consider intra-lesional 
corticosteroids. 
+ROGGRVHXQWLOUHFRYHU\WR*UDGHWKHQ
restart at a dose reduction 
4 
Life-threatening 
consequences 
Same as for Grade 2. 
Consider intra-lesional 
corticosteroids. 
Discontinue treatment. 
Prevention/Prophylaxis 
x 
Consider initiation of a non- alcoholic mouth wash or 0.9% salt water rinses 4-6 times daily with start of 
therapy before signs of mucositis develop. 
x 
Avoid using agents containing hydrogen peroxide, iodine, and thyme derivatives in management of 
stomatitis as they may worsen mouth ulcers. 
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. 
 
 
6.2.7 
Management of Rash 
 
Rash 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
d 2 
Macules/papules covering 
 30% body surface area 
with or without symptoms 
Consider treatment with 
topical steroid 
cream/ointment and/or 
oral anti-histamines. 
None. 
3 
Macules/papules covering 
! 30% body surface area 
with or without symptoms 
Consider treatment with 
topical steroid 
cream/ointment, oral 
antihistamines, and/or 
pulsed steroids.  
Consult dermatology. 
Hold until d Grade 2; 
Resume MLN0128 (TAK-228) based on 
timing of recovery: 
4 weeks: reduce dose ; 
> 4 weeks: stop MLN0128 (TAK-228) and 
discontinue subject from the study. 

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4 
acneifom/papulopustular  
rash with papules and/or 
pustules covering any % 
body surface area, which 
may or may not be 
associated with symptoms 
of pruritus or tenderness, 
and are associated with 
extensive superinfection 
with intravenous (IV) 
antibiotics indicated; life 
threatening consequences. 
All the above;  
IV antibiotics for 
superinfection.  
Consult dermatology.  
Permanent discontinuation of the study drug.  
a If dose modification is required for subjects receiving d 2 mg QD, then the frequency of dosing should be 
decreased to QDx5 days/week, rather than decreasing the daily dose administered. 
 
Patients who develop Grade 4 rash should permanently discontinue study treatment. Grade 4 rash is defined as rash 
acneifom/papulopustular with papules and/or pustules covering any % body surface area, which may or may not be 
associated with symptoms of pruritus or tenderness, and are associated with extensive superinfection with intravenous 
(IV) antibiotics indicated; life threatening consequences (NCI CTCAE Version 5.0, effective date April 1, 2018). 
 
6.2.8 
Management of QTc Prolongation 
 
QTc Prolongation 
Grade 
Description 
Treatment 
MLN0128 (TAK-228) Dose Modification 
2 
480 ms  QTc  
 501 ms 
Evaluate for other possible causes 
(eg, electrolyte disturbance, 
concomitant medication, etc.) 
None; continue MLN0128 (TAK-228) at the 
same dose and schedule. 
t 3 
QTc t 501 ms 
Evaluate for other possible causes 
(eg, electrolyte disturbance, 
concomitant medication)a; 
Consider a formal consult by a 
cardiologist; 
Notify the study doctor; 
Additional ECGs may be performed 
at intervals that the treating physician 
deems clinically appropriate until 
repeated QTc measurements fall or 
are below the threshold interval that 
triggered the repeat measurement. 
MLN0128 (TAK-228) should be interrupted. 
 
Patients who experience persistent 
symptomatic Grade 3 or Grade 4 QTc 
prolongation without another cause should 
permanently discontinue study treatment. 
 
Abbreviations:  ECG = electrocardiogram; IV = intravenous; ms = milliseconds; QTc = QT interval corrected for 
heart rate 
A  list of medications known to prolong QTc can be found at www.torsades.org and www.QTdrugs.org. 
 
6.2.9 
Management of elevated creatinine 
 
Elevations in creatinine 
Management/Next Dose for MLN0128 (TAK-228) 
*UDGH 
No change in dose 
Grade 2 
+ROGXQWLO*UDGH5HVXPHDWVDPHGRVHOHYHO 
Grade 3 
Hold* until < Grade 2.  Resume at one dose level lower, if indicated.** 
Grade 4 
Off protocol therapy 
*Patients requiring a delay of >4 weeks should go off protocol therapy. 
**Patients requiring > two dose reductions should go off protocol therapy. 
Further evaluation of the renal insufficiency should be performed to rule out other reversible causes like hypovolemia 
or hydronephrosis. Subjects should be encouraged to drink at least 18-24 ounces of fluids a day, especially on days 

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Elevations in creatinine 
Management/Next Dose for MLN0128 (TAK-228) 
requiring fasting (as per protocol), with administration of IV fluids in the clinic as clinically indicated to avoid 
dehydration. Microscopic urinalysis, a 12-hour urine collection, spot urine electrolytes, protein and creatinine, and 
serum chemistry shoulGEHFROOHFWHGDWDQ\WLPHZKHQWKHVHUXPFUHDWLQLQHLV*UDGH 
 
6.2.10 
Management of Transaminitis 
 
Transaminitis 
Management/Next Dose for MLN0128 (TAK-228) 
*UDGH 
No change in dose  
Grade 2 
Hold * XQWLO*UDGH5HVXPHDWVDPHGRVHOHYHO 
Grade 3 
Hold* until < Grade 2.  Resume at one dose level lower, if indicated.** 
Grade 4 
Off protocol therapy 
*Patients requiring a delay of >4 weeks should go off protocol therapy. 
**Patients requiring > two dose reductions should go off protocol therapy. 
 
 
7. ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS  
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial.  The 
following list of AEs (Section 7.1) and the characteristics of an observed AE (Section 7.2) will 
determine whether the event requires expedited reporting (via CTEP-AERS) in addition to 
routine reporting. 
 
7.1 
Comprehensive Adverse Events and Potential Risks List(s) (CAEPRs) 
 
Comprehensive Adverse Events and Potential Risks list (CAEPR) 
for  
MLN0128 (TAK-228, NSC 768435) 
 
 
The Comprehensive Adverse Events and Potential Risks list (CAEPR) provides a single list of reported 
and/or potential adverse events (AE) associated with an agent using a uniform presentation of events by 
body system. In addition to the comprehensive list, a subset, the Specific Protocol Exceptions to 
Expedited Reporting (SPEER), appears in a separate column and is identified with bold and italicized 
text. This subset of AEs (SPEER) is a list of events that are protocol specific exceptions to expedited 
reporting to NCI (except as noted below).  Refer to the 'CTEP, NCI Guidelines: Adverse Event Reporting 
Requirements' http://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/aeguidelines.pdf 
for further clarification. Frequency is provided based on 390 patients. Below is the CAEPR for MLN0128 
(TAK-228). 
NOTE: Report AEs on the SPEER ONLY IF they exceed the grade noted in parentheses next to the 
AE in the SPEER.  If this CAEPR is part of a combination protocol using multiple investigational 
agents and has an AE listed on different SPEERs, use the lower of the grades to determine if 
expedited reporting is required. 
 
7.1.1 
CAEPRs for CTEP IND Agent, MLN0128 (TAK-228) 
 
Version 2.3, July 28, 20191 

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 Adverse Events with Possible  
 Relationship to MLN0128 (TAK-228) 
 (CTCAE 5.0 Term) 
[n= 390] 
 
 
 Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER)  
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
  
 
Anemia 
 
 Anemia (Gr 2) 
CARDIAC DISORDERS 
  
 
 
Cardiac arrest 
  
 
 
Ventricular fibrillation 
  
GASTROINTESTINAL DISORDERS 
  
 
Abdominal pain 
 
 Abdominal pain (Gr 2) 
Constipation 
 
 
 Constipation (Gr 2) 
Diarrhea 
 
 
 Diarrhea (Gr 2) 
 
Dry mouth 
 
 Dry mouth (Gr 2) 
 
Dyspepsia 
 
  
Mucositis oral 
 
 
 Mucositis oral (Gr 2) 
Nausea 
 
 
 Nausea (Gr 3) 
Vomiting 
 
 
 Vomiting (Gr 3) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
  
 
Edema limbs 
 
   
Fatigue 
 
 
 Fatigue (Gr 3) 
 
Fever 
 
 Fever (Gr 2) 
 
General disorders and 
administration site conditions - 
Other (mucosal inflammation) 
 
 General disorders and 
administration site conditions - 
Other (mucosal inflammation) 
(Gr 2) 
INFECTIONS AND INFESTATIONS 
  
 
Urinary tract infection 
 
 Urinary tract infection (Gr 2) 
INVESTIGATIONS 
  
 
Creatinine increased 
 
 Creatinine increased (Gr 2) 
 
 
Electrocardiogram QT corrected 
interval prolonged 
  
 
Platelet count decreased 
 
 Platelet count decreased (Gr 2) 
 
Weight loss 
 
 Weight loss (Gr 2) 
METABOLISM AND NUTRITION DISORDERS 
  
Anorexia 
 
 
 Anorexia (Gr 2) 
 
Dehydration 
 
 Dehydration (Gr 2) 
Hyperglycemia 
 
 
 Hyperglycemia (Gr 3) 
 
Hypokalemia 
 
 Hypokalemia (Gr 2) 
 
Hypomagnesemia 
 
 Hypomagnesemia (Gr 2) 
 
Hypophosphatemia 
 
 Hypophosphatemia (Gr 2) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
  
 
Arthralgia 
 
  
 
Back pain 
 
 Back pain (Gr 2) 
 
Pain in extremity 
 
  
NERVOUS SYSTEM DISORDERS 
  
 
Dizziness 
 
 Dizziness (Gr 2) 
 
Dysgeusia 
 
 Dysgeusia (Gr 2) 
 
Headache 
 
 Headache (Gr 2) 
PSYCHIATRIC DISORDERS 
  
 
Insomnia 
 
  

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40 
 
 Adverse Events with Possible  
 Relationship to MLN0128 (TAK-228) 
 (CTCAE 5.0 Term) 
[n= 390] 
 
 
 Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER)  
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
 
RENAL AND URINARY DISORDERS 
  
 
Acute kidney injury 
 
  
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
  
 
Cough 
 
 Cough (Gr 2) 
 
Dyspnea 
 
 Dyspnea (Gr 2) 
 
Oropharyngeal pain 
 
  
 
 
Pneumonitis 
  
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
  
Pruritus 
 
 
 Pruritus (Gr 2)  
Rash maculo-papular 
 
 
 Rash maculo-papular (Gr 2) 
 
1This table will be updated as the toxicity profile of the agent is revised.  Updates will be distributed to all 
Principal Investigators at the time of revision.  The current version can be obtained by contacting 
PIO@CTEP.NCI.NIH.GOV. Your name, the name of the investigator, the protocol and the agent should 
be included in the e-mail. 
 
 
Adverse events reported on MLN0128 (TAK-228) trials, but for which there is insufficient evidence 
to suggest that there was a reasonable possibility that MLN0128 (TAK-228) caused the adverse 
event: 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS - Blood and lymphatic system disorders - Other 
(hyperviscosity syndrome); Blood and lymphatic system disorders - Other (Raynaud's phenomenon); 
Febrile neutropenia 
CARDIAC DISORDERS - Heart failure; Pericardial effusion; Sinus tachycardia; Ventricular arrhythmia 
EYE DISORDERS - Blurred vision; Eye pain; Photophobia; Vision decreased 
GASTROINTESTINAL DISORDERS - Abdominal distension; Colitis; Dysphagia; Esophagitis; Gastritis; 
Gastroesophageal reflux disease; Gastrointestinal disorders - Other (intestinal obstruction); 
Gastrointestinal disorders - Other (intestinal perforation);  Gastrointestinal disorders - Other (salivary 
hypersecretion); Hemorrhoids; Ileus; Oral pain; Pancreatitis; Small intestinal obstruction; Small intestinal 
perforation; Toothache 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS - Chills; Flu like symptoms; Gait 
disturbance; General disorders and administration site conditions - Other (groin pain); Malaise; Non-
cardiac chest pain; Pain 
HEPATOBILIARY DISORDERS - Gallbladder obstruction 
IMMUNE SYSTEM DISORDERS - Allergic reaction 
INFECTIONS AND INFESTATIONS - Abdominal infection; Infections and infestations - Other (cystitis); 
Infections and infestations - Other (lower respiratory tract infection); Infections and infestations - Other 
(mucosal infection); Infections and infestations - Other (parotid gland); Kidney infection; Lung infection; 
Papulopustular rash; Sepsis; Skin infection; Upper respiratory infection 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS - Fall; Fracture; Injury, poisoning and 
procedural complications - Other (accidental overdose); Injury, poisoning and procedural complications - 
Other (postoperative fever); Injury, poisoning and procedural complications - Other (subdural 
hemorrhage); Tracheal obstruction 
INVESTIGATIONS - Alanine aminotransferase increased; Alkaline phosphatase increased; Aspartate 
aminotransferase increased; Blood bilirubin increased; Blood lactate dehydrogenase increased; 
Cholesterol high; GGT increased; Lipase increased; Lymphocyte count decreased; Neutrophil count 
decreased; White blood cell decreased 

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METABOLISM AND NUTRITION DISORDERS - Acidosis; Hypercalcemia; Hyperkalemia; 
Hypernatremia; Hypertriglyceridemia; Hyperuricemia; Hypoalbuminemia; Hypocalcemia; Hyponatremia; 
Metabolism and nutrition disorders - Other (severe chronic malnutrition); Metabolism and nutrition 
disorders - Other (vitamin D deficiency)  
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Bone pain; Chest wall pain; Flank 
pain; Generalized muscle weakness; Muscle cramp; Myalgia 
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) - Neoplasms 
benign, malignant and unspecified (incl cysts and polyps) - Other (non-hodgkin lymphoma); Treatment 
related secondary malignancy 
NERVOUS SYSTEM DISORDERS - Ataxia; Intracranial hemorrhage; Lethargy; Nervous system 
disorders - Other (carotid artery occlusion); Nervous system disorders - Other (neuropathy peripheral); 
Paresthesia; Radiculitis; Stroke; Tremor 
PSYCHIATRIC DISORDERS - Anxiety; Confusion; Depression; Psychiatric disorders - Other (mental 
status changes) 
RENAL AND URINARY DISORDERS - Dysuria; Hematuria; Proteinuria; Renal and urinary disorders - 
Other (strangury) 
REPRODUCTIVE SYSTEM AND BREAST DISORDERS - Vaginal hemorrhage 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Bronchopulmonary hemorrhage; 
Epistaxis; Hiccups; Hypoxia; Nasal congestion; Pleural effusion; Pleuritic pain; Pneumothorax; Postnasal 
drip; Productive cough 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Alopecia; Dry skin; Hyperhidrosis; Rash 
acneiform; Urticaria 
VASCULAR DISORDERS - Flushing; Hypertension; Hypotension; Thromboembolic event 
 
 
 
Note: MLN0128 (TAK-228) in combination with other agents could cause an exacerbation of any adverse 
event currently known to be caused by the other agent, or the combination may result in events never 
previously associated with either agent. 
 
7.2 
Adverse Event Characteristics  
 
x CTCAE term (AE description) and grade:  The descriptions and grading scales found in 
the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 4.0 
will be utilized until March 31, 2018 for AE reporting.  CTCAE version 5.0 will be utilized 
for AE reporting beginning April 1, 2018.  All appropriate treatment areas should have 
access to a copy of the CTCAE version 5.0.  A copy of the CTCAE version 5.0 can be 
downloaded from the CTEP web site  
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm 
 
x For expedited reporting purposes only:   
- 
AEs for the agent that are bold and italicized in the CAEPR (i.e., those listed in the 
SPEER column, Section 7.1.1) should be reported through CTEP-AERS only if the 
grade is above the grade provided in the SPEER. 
- 
Other AEs for the protocol that do not require expedited reporting are outlined in 
section 7.3.4. 
 
x Attribution of the AE: 
- 
Definite – The AE is clearly related to the study treatment. 
- 
Probable – The AE is likely related to the study treatment. 
- 
Possible – The AE may be related to the study treatment. 

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42 
- 
Unlikely – The AE is doubtfully related to the study treatment. 
- 
Unrelated – The AE is clearly NOT related to the study treatment. 
 
7.3 
Expedited Adverse Event Reporting 
 
7.3.1 Expedited AE reporting for this study must use CTEP-AERS (CTEP Adverse Event 
Reporting System), accessed via the CTEP Web site (https://eapps-
ctep.nci.nih.gov/ctepaers).  The reporting procedures to be followed are presented in the 
“NCI Guidelines for Investigators: Adverse Event Reporting Requirements for DCTD 
(CTEP and CIP) and DCP INDs and IDEs” which can be downloaded from the CTEP 
Web site 
(http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm
).  These requirements are briefly outlined in the tables below (Section 7.3.3). 
 
In the rare occurrence when Internet connectivity is lost, a 24-hour notification is to be 
made to CTEP by telephone at 301-897-7497.  Once Internet connectivity is restored, the 
24-hour notification phoned in must be entered electronically into CTEP-AERS by the 
original submitter at the site. 
 
7.3.2 Distribution of Adverse Event Reports 
 
CTEP-AERS is programmed for automatic electronic distribution of reports to the 
following individuals:  Principal Investigator and Adverse Event Coordinator(s) (if 
applicable) of the Corresponding Organization or Lead Organization, the local treating 
physician, and the Reporter and Submitter.  CTEP-AERS provides a copy feature for 
other e-mail recipients.  
 
The Coordinating Center of the Corresponding Organization is responsible for submitting 
to the CTSU documentation of AEs that they deem reportable for posting on the CTSU 
protocol web page and inclusion on the CTSU bi-monthly broadcast. 
 
7.3.3 Expedited Reporting Guidelines 
 
Use the NCI protocol number and the protocol-specific patient ID assigned during trial 
registration on all reports. 
 
Note: A death on study requires both routine and expedited reporting, regardless of 
causality. Attribution to treatment or other cause must be provided. 
 
Death due to progressive disease should be reported as Grade 5 “Disease progression” in 
the system organ class (SOC) “General disorders and administration site conditions.” 
Evidence that the death was a manifestation of underlying disease (e.g., radiological 
changes suggesting tumor growth or progression: clinical deterioration associated with a 
disease process) should be submitted.  
 
The Late Phase 2 and Phase 3 Studies: Expedited Reporting Requirements for Adverse 

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Events that Occur on Studies under an IND/IDE within 30 Days of the Last Administration 
of MLN0128 (TAK-228)1, 2 
FDA REPORTING REQUIREMENTS FOR SERIOUS ADVERSE EVENTS (21 CFR Part 312) 
NOTE:  Investigators MUST immediately report to the sponsor (NCI) ANY Serious Adverse Events, whether or not 
they are considered related to the investigational agent(s)/intervention (21 CFR 312.64) 
An adverse event is considered serious if it results in ANY of the following outcomes:   
1) 
Death 
2) 
A life-threatening adverse event  
3) 
$QDGYHUVHHYHQWWKDWUHVXOWVLQLQSDWLHQWKRVSLWDOL]DWLRQRUSURORQJDWLRQRIH[LVWLQJKRVSLWDOL]DWLRQIRU
hours  
4) 
A persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions  
5) 
A congenital anomaly/birth defect.  
6) 
Important Medical Events (IME) that may not result in death, be life threatening, or require hospitalization 
may be considered serious when, based upon medical judgment, they may jeopardize the patient or 
subject and may require medical or surgical intervention to prevent one of the outcomes listed in this 
definition. (FDA, 21 CFR 312.32; ICH E2A and ICH E6). 
 
ALL SERIOUS adverse events that meet the above criteria MUST be immediately reported to the NCI via AdEERS 
within the timeframes detailed in the table below. 
Hospitalization 
Grade 1 
Timeframes 
Grade 2 
Timeframes 
Grade 3 Timeframes 
Grade 4 & 5 
Timeframes 
Resulting in 
Hospitalization  
KUV 
10 Calendar Days 
24-Hour 5 
Calendar Days 
Not resulting in 
Hospitalization  
KUV 
Not required 
10 Calendar Days 
NOTE:  Protocol specific exceptions to expedited reporting of serious adverse events are found in the Specific 
Protocol Exceptions to Expedited Reporting (SPEER) portion of the CAEPR 
Expedited AE reporting timelines are defined as: 
o 
“24-Hour; 5 Calendar Days” - The AE must initially be reported via AdEERS within 24 hours of learning of 
the AE, followed by a complete expedited report within 5 calendar days of the initial 24-hour report. 
o 
“10 Calendar Days” - A complete expedited report on the AE must be submitted within 10 calendar days of 
learning of the AE. 
1Serious adverse events that occur more than 30 days after the last administration of investigational 
agent/intervention and have an attribution of possible, probable, or definite require reporting as follows:  
Expedited 24-hour notification followed by complete report within 5 calendar days for: 
x 
All Grade 4, and Grade 5 AEs 
Expedited 10 calendar day reports for: 
x 
Grade 2 adverse events resulting in hospitalization or prolongation of hospitalization  
x 
Grade 3 adverse events 
2For studies using PET or SPECT IND agents, the AE reporting period is limited to 10 radioactive half-lives, 
rounded UP to the nearest whole day, after the agent/intervention was last administered.  Footnote “1” above 
applies after this reporting period. 
Effective Date:  May 5, 2011 
 
 
7.4 
Routine Adverse Event Reporting 
 
All Adverse Events must be reported in routine study data submissions.  AEs reported through 
CTEP-AERS must also be reported in routine study data submissions. 
 

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Serious AE (SAE) means any untoward medical occurrence that at any dose: 
x Results in death. 
x Is life-threatening (refers to an AE in which the patient was at risk of death at the time of 
the event.  It does not refer to an event which hypothetically might have caused death if it 
were more severe). 
x Requires inpatient hospitalization or prolongation of an existing hospitalization (see 
clarification in the paragraph below on planned hospitalizations). 
x Results in persistent or significant disability or incapacity. (Disability is defined as a 
substantial disruption of a person’s ability to conduct normal life functions). 
x Is a congenital anomaly/birth defect. 
x Is a medically important event.  This refers to an AE that may not result in death, be 
immediately life threatening, or require hospitalization, but may be considered serious 
when, based on appropriate medical judgment, may jeopardize the patient, require 
medical or surgical intervention to prevent 1 of the outcomes listed above, or involves 
suspected transmission via a medicinal product of an infectious agent.   Examples of such 
medical events include allergic bronchospasm requiring intensive treatment in an 
emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse; any 
organism, virus, or infectious particle (eg, prion protein transmitting Transmissible 
Spongiform Encephalopathy), pathogenic or nonpathogenic, is considered an infectious 
agent.   
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. 
 
 
7.5 
Secondary Malignancy 
 
A secondary malignancy is a cancer caused by treatment for a previous malignancy (e.g., treatment 
with investigational agent/intervention, radiation or chemotherapy). A secondary malignancy is 
not considered a metastasis of the initial neoplasm.  
CTEP requires all secondary malignancies that occur following treatment with an agent under an 
NCI IND/IDE be reported via CTEP-AERS. Three options are available to describe the event:  

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x Leukemia secondary to oncology chemotherapy (e.g., acute myelocytic leukemia 
[AML])  
x Myelodysplastic syndrome (MDS)  
x Treatment-related secondary malignancy  
 
Any malignancy possibly related to cancer treatment (including AML/MDS) should also be 
reported via the routine reporting mechanisms outlined in each protocol.  
 
7.6 
Second Malignancy 
 
A second malignancy is one unrelated to the treatment of a prior malignancy (and is NOT a 
metastasis from the initial malignancy).  Second malignancies require ONLY routine AE 
reporting unless otherwise specified. 
 
7.7 
Pregnancy  
 
Although not an adverse event in and of itself, pregnancy as well as its outcome must be 
documented via CTEP-AERS.  In addition, the Pregnancy Information Form included within 
the NCI Guidelines for Adverse Event Reporting Requirements must be completed and 
submitted to CTEP.  Any pregnancy occurring in a patient or patient’s partner from the time of 
consent to 90 days after the last dose of study drug must be reported and then followed for 
outcome.  Newborn infants should be followed until 30 days old.  Please see the “NCI 
Guidelines for Investigators: Adverse Event Reporting Requirements for DCTD (CTEP and CIP) 
and DCP INDs and IDEs” (at http://ctep.cancer.gov/protocolDevelopment/adverse_effects.htm) 
for more details on how to report pregnancy and its outcome to CTEP.  
 
7.8 
Pregnancy loss 
 
x Pregnancy loss is defined in CTCAE as “Death in utero.”   
x Any Pregnancy loss should be reported expeditiously, as Grade 4 “Pregnancy loss” under the 
Pregnancy, puerperium and perinatal conditions SOC. 
x A Pregnancy loss should NOT be reported as a Grade 5 event under the Pregnancy, 
puerperium and perinatal conditions SOC, as currently CTEPAERS recognizes this event as 
a patient death. 
 
7.9 
Neonatal death 
 
A neonatal death should be reported expeditiously as Grade 4, “Death neonatal” under the 
General disorders and administration SOC. 
 
8. PHARMACEUTICAL INFORMATION 
 
A list of the adverse events and potential risks associated with the use of MLN0128 (TAK-228) 
can be found in Section 7.1. 
 

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8.1 
CTEP IND Agent(s) 
 
8.1.1 MLN0128 (TAK-228) 
 
Other Names: TAK-228, INK128 
 
Other Names: 
TAK-228, INK128 
 
Classification: 
mTOR inhibitor, TORC1/2  
 
CAS Registry Number: 
1224844 
 
Molecular Formula: C15H15N7O  
M.W.: 
 
309.3 
 
Approximate Solubility: 
MLN0128 exhibits a pH-dependant aqueous solubility: at 
physiological pH the solubility is approximately 0.1 mg/mL and at or below pH 3 the solubility 
is greater than 15 mg/mL. 
 
Mode of Action: 
MLN0128 is a non-rapamycin analog mTOR (mechanistic target of 
rapamycin) kinase inhibitor.  The mTOR kinase regulates cell growth, translational control, 
angiogenesis, and cell survival by integrating nutrient and hormonal signals.  The mTOR 
complex (TORC) is an intracellular point of convergence for a number of cellular signaling 
pathways.  ML0128 is a potent and selective adenosine tri-phosphate (ATP)-competitive 
inhibitor of mTOR complex 1 and 2 (TORC1/2). 
 
Description: 
 
MLN0128 drug substance is a white to off-white, crystalline 
powder. 
 
How Supplied: 
MLN0128 is supplied by Millennium Pharmaceuticals, Inc. and distributed 
by the Pharmaceutical Management Branch, CTEP/DCTD/NCI as size 2 hard gelatin capsules in 
the following strengths: 1 mg (white opaque color), and 3 mg (orange opaque color).  The 
composition of the drug product consists of a blend of MLN0128 drug substance, 
microcrystalline cellulose, and magnesium stearate.  Milled formulations will have a white label 
with a large watermark of the strength on the label.  
 
MLN0128 capsules are packaged in 30-count, 60-cc high-density polyethylene (HDPE), white, 
opaque, round, tamper- and child-resistant bottles.   
 
Storage: Capsules are to be stored in the original package between 15°C to 30°C, with allowed 
short-term excursions between 2°C and 40°C.   
 
Route of Administration: MLN0128 (TAK-228) should be taken orally on an empty stomach at 
least 2 hours after food and do not eat or drink (except water) for at least one hour after taking 
MLN0128 (TAK-228).  Do not chew, open or manipulate the capsule in any way prior to swallowing.  
Each dose should be taken with 8 ounces (240 mL) of water. 

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47 
 
Potential Drug Interactions: 
  Multiple human metabolizing enzymes are involved in the 
Phase I metabolism of MLN0128. When normalized for human liver content, the CYP isoforms 
CYP3A4, CYP2C9, and CYP2C19 appear to contribute to MLN0128 metabolism.  MLN0128 
displayed low potential (IC50 !ȝ0IRULQKLELWLRQRIWKHPDMRUKXPDQ&<3LVRIRUPV 
 
Patient Care Implications: 
Women of childbearing potential should use effective methods of contraception during and through 
90 days after the last dose of MLN0128. 
 
Men should use effective methods of contraception and not donate sperm during and through 120 
days after the last dose of MLN0128. 
 
 
8.1.2 Agent Ordering and Agent Accountability 
 
8.1.2.1 
NCI-supplied agents may be requested by the Principal Investigator (or their authorized 
designee) at each participating institution.  Pharmaceutical Management Branch (PMB) 
policy requires that agent be shipped directly to the institution where the patient is to 
be treated.  PMB does not permit the transfer of agents between institutions (unless 
prior approval from PMB is obtained).  The CTEP-assigned protocol number must be 
used for ordering all CTEP-supplied investigational agents.  The responsible 
investigator at each participating institution must be registered with CTEP, DCTD 
through an annual submission of FDA Form 1572 (Statement of Investigator), 
Curriculum Vitae, Supplemental Investigator Data Form (IDF), and Financial 
Disclosure Form (FDF).  If there are several participating investigators at one 
institution, CTEP-supplied investigational agents for the study should be ordered under 
the name of one lead investigator at that institution. 
 
Active CTEP-registered investigators and investigator-designated shipping designees 
and ordering designees can submit agent requests through the PMB Online Agent Order 
Processing 
(OAOP) 
application 
(https://eapps-
ctep.nci.nih.gov/OAOP/pages/login.jspx).  Access to OAOP requires the establishment 
of a CTEP Identity and Access Management (IAM) account (https://eapps-
ctep.nci.nih.gov/iam/) and the maintenance of an “active” account status and a 
“current” password.  For questions about drug orders, transfers, returns, or 
accountability, call (301) 496-5725 Monday through Friday between 8:30 am and 4:30 
pm (ET) or email PMBAfterHours@mail.nih.gov anytime. 
 
8.1.2.2 
Agent Inventory Records – The investigator, or a responsible party designated by the 
investigator, must maintain a careful record of the inventory and disposition of all 
agents received from DCTD using the NCI Oral Drug Accountability Record Form 
(DARF).  (See the NCI Investigator’s Handbook for Procedures for Drug 
Accountability and Storage.) 
 

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8.1.2.3 
Study drug will be administered or dispensed only to eligible patients under the 
supervision of the investigator or identified sub-investigator(s).  The appropriate 
study personnel will maintain records of study drug receipt and dispensing. 
 
8.1.2.4 
IB documents for agents on protocols where CTEP/DCTD sponsors the IND and 
PMB distributes the agent are available via PMB's Online Agent Order Processing 
(OAOP) application.  Access to OAOP requires an active CTEP IAM account with a 
current password. Once logged into OAOP, go to the "Investigator Brochures" tab 
and provide the required investigator, agent, and protocol information to search for 
the current IB documents. Refer to PMB's FAQs for more information about 
accessing OAOP and obtaining an investigator brochure.  
 
8.1.2.5 
Useful Links and Contacts 
x CTEP Forms, Templates, Documents:  http://ctep.cancer.gov/forms/ 
x NCI CTEP Investigator Registration:  PMBRegPend@ctep.nci.nih.gov 
x PMB policies and guidelines: 
http://ctep.cancer.gov/branches/pmb/agent_management.htm  
x PMB Online Agent Order Processing (OAOP) application: https://eapps-
ctep.nci.nih.gov/OAOP/pages/login.jspx  
x CTEP Identity and Access Management (IAM) account: https://eapps-
ctep.nci.nih.gov/iam/ 
x CTEP Associate Registration and IAM account help:  
ctepreghelp@ctep.nci.nih.gov  
x PMB email:  PMBAfterHours@mail.nih.gov 
PMB phone and hours of service: (240) 276-6575 Monday through Friday between 
8:30 am and 4:30 pm (ET) 
 
9. BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES 
 
9.1 
Biomarker Studies 
 
Hypotheses: MLN0128 (TAK-228) is active, safe and tolerable in patients with locally advanced 
or metastatic TCC harboring a TSC1 mutation 
 
This study will be using an integral biomarker by identifying bladder cancer patients whose 
tumors harbor a TSC1 and/or TSC2 mutation identified by a CLIA-certified laboratory. If the 
patient’s mutation status is unknown, this protocol screens patients’ TCC tumor for TSC-1 and/or 
TSC-2 mutation at the Yale Clinical Molecular Pathology Laboratory (YCMPL) under the 
direction of Dr. Jeffrey Sklar. Only patients whose TCC tumors are determined to be positive for 
TSC1 and/or TSC2 mutations will be treated with MLN0128 (TAK-228). Unless the 
prescreening was done at YCMPL, the participating site must submit an archival tissue prior to 
initiation of treatment in a form of 10 unstained slides, or a FFPE block to Dr. Jeffrey Sklar’s 
laboratory at Yale University. Contact the Study PI via email for the latest version of the Lab 
Manual for handling the specimen. This will be posted on the CTSU website.  
Background:  As previously noted, only those patients whose tumors harbor mutations in the 

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TSC1 and/or TSC2 and meet other eligibility criteria will be treated with MLN0128 (TAK-228). It 
is unknown if the biologic and clinical effects of TSC1 and TSC2 mutations in TCC are identical.  
The available literature supports a positive correlation between TSC1 mutation and clinical benefit 
with rapalog treatment; however, it is unknown if the same benefit is possible with TSC2 mutated 
TCC.  The primary objective will be to study the activity of MLN0128 (TAK-228) in TSC1 
mutated TCC. It is unknown if the biologic and clinical effects of TSC1 and TSC2 mutations are 
identical. We will evaluate the activity and tolerability of MLN0128 (TAK-228) in TSC2 mutated 
TCC in an exploratory fashion to gain experience as we accrue in the TSC1 cohort to meet its 
accrual objectives of evaluable patients. 
Facilities and methods: Dr. Jeffrey Sklar at Yale University will implement a clinically validated 
program for assessing somatic coding mutations in the TSC1 and TSC2 genes in bladder cancers.  
The profiling will be done at the YCMPL which operates under the auspices of CMS/CLIA. 
Paraffin embedded tissue blocks or slides will be provided by the clinical sites and shipped to Dr. 
Sklar’s laboratory using a standard operating procedure (SOP) developed and validated and 
currently being used for the NCI MATCH program.  Specimens will be histopathologically 
assessed and DNA will be subsequently extracted from each quality assessed tumor using Yale’s 
Molecular Profiling SOPs. 
 
 The above mentioned samples will be assessed for adequacy and DNA will be extracted. TSC1 
and TSC2 genes will be sequenced using a validated CLIA certified approach. To address 
reportable range, nucleotide variants of TSC1 and TSC2 will be counted in treatment decisions 
only if they meet all of the following criteria: 1) the specific nucleotide change is not found or at 
prevalence below 0.001 percent within the 1000 Genomes database; 2) the specific nucleotide 
change is not found within the NHLBI exome sequence variant database; 3) The specific 
nucleotide variant resides within an annotated coding exon of TSC1 and/or TSC2; 4) The specific 
nucleotide variant results in an amino acid change, stop codon, or a frameshift. 
 
9.1.1 Tissue Handling and Shipping:   
 
Contact the Study PI for the Lab Manual. This will be posted on the CTSU website.   
 
 

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10. STUDY CALENDAR 
In the event that the patient’s condition is deteriorating, laboratory evaluations should be repeated 
within 48 hours prior to initiation of the next cycle of therapy.  
 
For each of visits, there is +/- 3 business day window in case of scheduling conflicts.  
 
 
 
 
Cycle 1 
Cycle 2 
Cycle 3 and 
Subsequent 
Cycles 
 
Assessments1 
Pre- 
Screen9 
Screening 
Day -28 
to 
Day -1 
Cycle 1 
Day 1 
Cycle 1 
Day 15 
Cycle 2 
Day 1 
Cycle 2 
Day 15 
Day 1 
 
End of 
Treatment15 
Pre-Screening 
Consent 
X 
 
 
 
 
 
 
 
Archival 
Tissue submission for TSC1 
or TSC2 mutation testing  
X 
 
 
 
 
 
 
 
Buccal swab 
X 
 
 
 
 
 
 
 
Study Consent 
 
X 
 
 
 
 
 
 
Registration 
 
X13 
 
 
 
 
 
 
Concurrent meds 
 
X 
X 
X 
X 
X 
X 
X 
Performance Status check 
 
X 
X 
X 
X 
X 
X 
X 
Physical Exam2 
 
X 
X 
X 
X 
X 
X 
X 
Vitals 
 
X 
X 
X 
X 
X 
X 
X 
Hematology/ Chemistry3 
 
X 
X 
X 
X 
X 
X 
X 
Coagulation (PT/INR, 
aPTT) 
 
X 
X 
 
X 
 
X 
X 
Fasting serum glucose6 
 
X 
X 
X 
X 
X 
X 
X 
Fasting lipid profile4 
 
X 
X 
 
X 
 
X 
X 
Pregnancy test10 
 
X10 
X10 
 
X10 
 
X10 
X10 
Urinalysis 
 
X 
X 
X 
X 
X 
X 
X 
EKG5 
 
X 
 
 
 
 
 
X 
Archival tumor tissue 14 (or 
fresh tumor biopsy12a), and 
buccal swab  
 
X 
 
 
 
 
 
X12b 
MLN0128 (TAK-228) 
Admin 
 
 
X-----------------------------------------------------------------Æ 
 
AE assessment 
 
 
X 
X 
X 
X 
X 
X 
Tumor measurements7 (CT, 
MRI8) 
 
X 
Tumor measurements are repeated after every 8 weeks for the first 
24 weeks, then after every 12 weeks thereafter.  Confirmatory 
scans will also be obtained 4 to 8 weeks following initial 
documentation of an objective response 
 
Completed Diary11 Returned 
to Clinic 
 
 
 
X 
X 
X 
X 
X 
1. Assessments (safety labs including chemistry/hematology/coag, fasting lipid profiling, pregnancy test, urinalysis) may be done within 48 hours 
of dosing with MLN0128 (TAK-228) administration.  
2. Symptom directed. 
3. CBC with differential, electrolyte panel, BUN, Serum Creatinine, LFTs (AST, ALT, Alk Phos, Total and Direct bilirubin), Albumin, Calcium, 
Phosphate, Magnesium, LDH, total protein.  
4.  Total cholesterol, HDL-C, LDL-C, triglycerides. 
5. Single, 12-lead EKG will be collected as screening (within 28 of first dose) at the end of treatment and on therapy if clinically indicated.  
6.  Fasting serum glucose will be measured in the clinic. Patients are required to fast overnight (nothing except water and/or medications after 
midnight or for a minimum of 8 hours before the assessment) for each of these measurements.  
7. Tumor measurements will follow RECIST v1.1.  Standard of Care modalities will be utilized to collect tumor measurements for study subjects.  
The same modality used at screening will be followed throughout the study period. 
8. Brain MRI or CT head with IV contrast (if contraindication to MRI) should be considered in a patient with history of CNS metastasis or when 
clinically indicated. 
9.  Consent for Prescreening testing and the tissue submission can be done at any time in the subject’s metastatic disease status as long as the 
patient is potentially deemed eligible for the Main Study in the opinion of the treating investigator. 
10. Pregnancy Testing is required for women of childbearing potential.    While serum beta-HCG testing is required for screening, either serum or 
urine pregnancy test is required prior to the start of each cycle beginning cycle 1, at End of Treatment and End of Study. In a scenario where a 
beta-HCG elevation is noted as a serum tumor marker of TCC, a series of beta HCG levels must be documented to prove that the level and the 
trend of beta-HCG elevation are not consistent with pregnancy. A pelvic/pregnancy US should be considered if pregnancy is suspected.  

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11. Please return any diaries and pill bottles to each study visit, beginning with C1D15. Pill diary include DAILY glucose monitoring. Glucometer 
will be provided to the patient.  
12a. A tumor biopsy is mandatory for those patients who have no available tissue for submission.   
12b. A tumor biopsy is optional at the time of disease progression; recommended in patients with initial response to TAK-228.  
13. Patients should begin protocol treatment within 7 days following registration.  Issues that would cause treatment delays should be discussed 
with the Principal Investigator 
14. Archival tumor tissue submission is required unless the pre-screening was done at YCMPL. (i.e., if pre-screening for TSC mutation was done 
at YCMPL, then no additional tissue submission is needed).  If no archival tumor tissue available, a fresh tumor biopsy is required. (See criteria 
3.1.4) 
15. EOT visit will take place at 4 weeks after the last dose of the study drug (See the Section 5.4) 
 
 
 
 
 
 
 
 
 

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11. MEASUREMENT OF EFFECT 
 
Antitumor Effect – Solid Tumors 
 
For the purposes of this study, patients should be re-evaluated for response after every 8 weeks for 
the first 24 weeks, then after every 12 weeks thereafter.  In addition to a baseline scan, confirmatory 
scans should also be obtained in 4 to 8 weeks following initial documentation of objective 
response. 
 
Response and progression will be evaluated in this study using the new international criteria 
proposed by the revised Response Evaluation Criteria in Solid Tumors (RECIST) guideline 
(version 1.1) [Eur J Ca 45:228-247, 2009].  Changes in the largest diameter (unidimensional 
measurement) of the tumor lesions and the shortest diameter in the case of malignant lymph nodes 
are used in the RECIST criteria. 
 
11.1 
 Definitions 
 
Evaluable for toxicity.  All patients will be evaluable for toxicity from the time of their first 
treatment with MLN0128 (TAK-228) 
 
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.  
 
11.2 
Disease Parameters 
 
Measurable disease.  Measurable lesions are defined as those that can be accurately 
measured in at least one dimension (longest diameter to be recorded) as 20 mm by chest 
x-ray or as 10 mm with CT scan, MRI, or calipers by clinical exam.  All tumor 
measurements must be recorded in millimeters (or decimal fractions of centimeters). 
 
Note:  Tumor lesions that are situated in a previously irradiated area might or might not be 
considered measurable. 
 
Malignant lymph nodes.  To be considered pathologically enlarged and measurable, a 
lymph node must be 15 mm in short axis when assessed by CT scan (CT scan slice 
thickness recommended to be no greater than 5 mm).  At baseline and in follow-up, only 
the short axis will be measured and followed. 

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Non-measurable disease.  All other lesions (or sites of disease), including small lesions 
(longest diameter <10 mm or pathological lymph nodes with 10 to <15 mm short axis), 
are considered non-measurable disease.  Bone lesions, leptomeningeal disease, ascites, 
pleural/pericardial effusions, lymphangitis cutis/pulmonitis, inflammatory breast disease, 
and abdominal masses (not followed by CT or MRI), are considered as non-measurable. 
 
Note:  Cystic lesions that meet the criteria for radiographically defined simple cysts 
should not be considered as malignant lesions (neither measurable nor non-measurable) 
since they are, by definition, simple cysts. 
 
‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable 
lesions, if they meet the definition of measurability described above. However, if non-
cystic lesions are present in the same 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.  
 
11.3 
Methods for Evaluation of Measurable Disease 
 
All measurements should be taken and recorded in metric notation using a ruler or calipers.  
All baseline evaluations should be performed as closely as possible to the beginning of 
treatment and never more than 4 weeks before the beginning of the treatment. 
 
The same method of assessment and the same technique should be used to characterize 
each identified and reported lesion at baseline and during follow-up. Imaging-based 
evaluation is preferred to evaluation by clinical examination unless the lesion(s) being 
followed cannot be imaged but are assessable by clinical exam. 
 

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Clinical lesions Clinical lesions will only be considered measurable when they are 
superficial (e.g., skin nodules and palpable lymph nodes) and 10 mm diameter as assessed 
using calipers (e.g., skin nodules).  In the case of skin lesions, documentation by color 
photography, including a ruler to estimate the size of the lesion, is recommended.  
 
Chest x-ray Lesions on chest x-ray are acceptable as measurable lesions when they are 
clearly defined and surrounded by aerated lung.  However, CT is preferable.  
 
Conventional CT and MRI This guideline has defined measurability of lesions on CT scan 
based on the assumption that CT slice thickness is 5 mm or less.  If CT scans have slice 
thickness greater than 5 mm, the minimum size for a measurable lesion should be twice the 
slice thickness.  MRI is also acceptable in certain situations (e.g. for body scans).   
 
Use of MRI remains a complex issue.  MRI has excellent contrast, spatial, and temporal 
resolution; however, there are many image acquisition variables involved in MRI, which 
greatly impact image quality, lesion conspicuity, and measurement.  Furthermore, the 
availability of MRI is variable globally.  As with CT, if an MRI is performed, the technical 
specifications of the scanning sequences used should be optimized for the evaluation of the 
type and site of disease.  Furthermore, as with CT, the modality used at follow-up should 
be the same as was used at baseline and the lesions should be measured/assessed on the 
same pulse sequence.  It is beyond the scope of the RECIST guidelines to prescribe specific 
MRI pulse sequence parameters for all scanners, body parts, and diseases.  Ideally, the 
same type of scanner should be used and the image acquisition protocol should be followed 
as closely as possible to prior scans.  Body scans should be performed with breath-hold 
scanning techniques, if possible. 
 
PET-CT At present, the low dose or attenuation correction CT portion of a combined PET-
CT is not always of optimal diagnostic CT quality for use with RECIST measurements.  
However, if the site can document that the CT performed as part of a PET-CT is of identical 
diagnostic quality to a diagnostic CT (with IV and oral contrast), then the CT portion of 
the PET-CT can be used for RECIST measurements and can be used interchangeably with 
conventional CT in accurately measuring cancer lesions over time.  Note, however, that 
the PET portion of the CT introduces additional data which may bias an investigator if it 
is not routinely or serially performed.   
 
Ultrasound is not useful in assessment of lesion size and should not be used as a method of 
measurement.  Ultrasound examinations cannot be reproduced in their entirety for 
independent review at a later date and, because they are operator dependent, it cannot be 
guaranteed that the same technique and measurements will be taken from one assessment 
to the next.  If new lesions are identified by ultrasound in the course of the study, 
confirmation by CT or MRI is advised.  If there is concern about radiation exposure at CT, 
MRI may be used instead of CT in selected instances. 
 
Endoscopy, Laparoscopy The utilization of these techniques for objective tumor evaluation 
is not advised.  However, such techniques may be useful to confirm complete pathological 
response when biopsies are obtained or to determine relapse in trials where recurrence 

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following complete response (CR) or surgical resection is an endpoint. 
 
Tumor markers Tumor markers alone cannot be used to assess response.  If markers are 
initially above the upper normal limit, they must normalize for a patient to be considered 
in complete clinical response.  Specific guidelines for both CA-125 response (in recurrent 
ovarian cancer) and PSA response (in recurrent prostate cancer) have been published [JNCI 
96:487-488, 2004; J Clin Oncol 17, 3461-3467, 1999; J Clin Oncol 26:1148-1159, 2008].  
In addition, the Gynecologic Cancer Intergroup has developed CA-125 progression criteria 
which are to be integrated with objective tumor assessment for use in first-line trials in 
ovarian cancer [JNCI 92:1534-1535, 2000]. 
 
Cytology, Histology These techniques can be used to differentiate between partial 
responses (PR) and complete responses (CR) in rare cases (e.g., residual lesions in tumor 
types, such as germ cell tumors, where known residual benign tumors can remain). 
 
The cytological confirmation of the neoplastic origin of any effusion that appears or 
worsens during treatment when the measurable tumor has met criteria for response or stable 
disease is mandatory to differentiate between response or stable disease (an effusion may 
be a side effect of the treatment) and progressive disease. 
 
FDG-PET  While FDG-PET response assessments need additional study, it is sometimes 
reasonable to incorporate the use of FDG-PET scanning to complement CT scanning in 
assessment of progression (particularly possible 'new' disease).  New lesions on the basis 
of FDG-PET imaging can be identified according to the following algorithm:  
a. Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of PD 
based on a new lesion. 
b. No FDG-PET at baseline and a positive FDG-PET at follow-up:  If the positive FDG-
PET at follow-up corresponds to a new site of disease confirmed by CT, this is PD.  If 
the positive FDG-PET at follow-up is not confirmed as a new site of disease on CT, 
additional follow-up CT  scans are needed to determine if there is truly progression 
occurring at that site (if so, the date of PD will be the date of the initial abnormal FDG-
PET scan).  If the positive FDG-PET at follow-up corresponds to a pre-existing site of 
disease on CT that is not progressing on the basis of the anatomic images, this is not 
PD. 
c. FDG-PET may be used to upgrade a response to a CR in a manner similar to a biopsy 
in cases where a residual radiographic abnormality is thought to represent fibrosis or 
scarring.  The use of FDG-PET in this circumstance should be prospectively described 
in the protocol and supported by disease-specific medical literature for the indication.  
However, it must be acknowledged that both approaches may lead to false positive CR 
due to limitations of FDG-PET and biopsy resolution/sensitivity.  mTOR inhibitors 
inhibit GLUT1 and other cellular glucose transporters, and MLN0128 (TAK-228) 
might potentially decrease FDG uptake in a residual mass as a pharmacokinetic effect 
separate from an antitumor effect.  Therefore, FDG PET scans taken concurrent with 
MLN0128 (TAK-228) treatment may potentially give a false negative reading.   
 
Note:  A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake 

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greater than twice that of the surrounding tissue on the attenuation corrected image. 
 
11.4 
Response Criteria 
 
11.4.1 Evaluation of Target Lesions 
 
Complete Response (CR):  Disappearance of all target lesions.  Any pathological lymph 
nodes (whether target or non-target) must have reduction in short axis to <10 mm. 
 
Partial Response (PR):  At least a 30% decrease in the sum of the diameters of target 
lesions, taking as reference the baseline sum diameters. 
 
Progressive Disease (PD):  At least a 20% increase in the sum of the diameters of target 
lesions, taking as reference the smallest sum on study (this includes the baseline sum if 
that is the smallest on study).  In addition to the relative increase of 20%, the sum must 
also demonstrate an absolute increase of at least 5 mm.  (Note:  the appearance of one 
or more new lesions is also considered progressions). 
 
Stable Disease (SD):  Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD, taking as reference the smallest sum diameters while on 
study. 
 
11.4.2 Evaluation of Non-Target Lesions 
 
Complete Response (CR):  Disappearance of all non-target lesions and normalization 
of tumor marker level.  All lymph nodes must be non-pathological in size (<10 mm 
short axis). 
 
Note:  If tumor markers are initially above the upper normal limit, they must normalize 
for a patient to be considered in complete clinical response. 
 
Non-CR/Non-PD:  Persistence of one or more non-target lesion(s) and/or maintenance 
of tumor marker level above the normal limits. 
 
Progressive Disease (PD):  Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions.  Unequivocal progression should not 
normally trump target lesion status.  It must be representative of overall disease status 
change, not a single lesion increase.     
 
Although a clear progression of “non-target” lesions only is exceptional, the opinion of 
the treating physician should prevail in such circumstances, and the progression status 
should be confirmed at a later time by the review panel (or Principal Investigator). 
 
11.4.3 Evaluation of Best Overall Response 
 
The best overall response is the best response recorded from the start of the treatment 

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until disease progression/recurrence (taking as reference for progressive disease the 
smallest measurements recorded since the treatment started).  The patient's best 
response assignment will depend on the achievement of both measurement and 
confirmation criteria. 
 
For Patients with Measurable Disease (i.e., Target Disease) 
 
Target 
Lesions 
Non-Target 
Lesions 
New 
Lesions 
Overall 
Response 
Best Overall Response when 
Confirmation is Required* 
CR 
CR 
No 
CR 
>4 wks. Confirmation** 
CR 
Non-CR/Non-
PD 
No 
PR 
>4 wks. Confirmation** 
CR 
Not evaluated 
No 
PR 
PR 
Non-CR/Non-
PD/not 
evaluated 
No 
PR 
SD 
Non-CR/Non-
PD/not 
evaluated 
No 
SD 
Documented at least once >4 
wks. from baseline** 
PD 
Any 
Yes or No 
PD 
no prior SD, PR or CR 
Any 
PD*** 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
 
See RECIST 1.1 manuscript for further details on what is evidence of a new lesion. 
**        Only for non-randomized trials with response as primary endpoint. 
***      In exceptional circumstances, unequivocal progression in non-target lesions may be 
            accepted as disease progression. 
 
Note:  Patients with a global deterioration of health status requiring discontinuation of 
treatment without objective evidence of disease progression at that time should be 
reported as “symptomatic deterioration.”  Every effort should be made to document the 
objective progression even after discontinuation of treatment. 
 
For Patients with Non-Measurable Disease (i.e., Non-Target Disease) 
 
Non-Target Lesions 
New Lesions 
Overall Response 
CR 
No 
CR 
Non-CR/non-PD 
No 
Non-CR/non-PD* 
Not all evaluated 
No 
not evaluated 
Unequivocal PD 
Yes or No 
PD 
Any 
Yes 
PD 
 
‘Non-CR/non-PD’ is preferred over ‘stable disease’ for non-target disease since SD is 
increasingly used as an endpoint for assessment of efficacy in some trials so to assign 
this category when no lesions can be measured is not advised 
 
11.4.4 Duration of Response 
 

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Duration of overall response:  The duration of overall response is measured from the time 
measurement criteria are met for CR or PR (whichever is first recorded) until the first date 
that recurrent or progressive disease is objectively documented (taking as reference for 
progressive disease the smallest measurements recorded since the treatment started). 
 
The duration of overall CR is measured from the time measurement criteria are first met 
for CR until the first date that progressive disease is objectively documented. 
 
 
Duration of stable disease:  Stable disease is measured from the start of the treatment until 
the criteria for progression are met, taking as reference the smallest measurements recorded 
since the treatment started, including the baseline measurements.  
 
11.4.5 Progression-Free Survival 
 
Progression-free survival (PFS) is defined as the duration of time from start of treatment 
to date of progression or death, whichever occurs first.   Patients not known to have 
progressed will be censored for PFS as of the date of their last tumor assessment 
performed via the methods described in Section 11.1. 
 
  
11.4.6 Overall Survival 
 
Overall survival (OS) is defined as the duration of time from start of treatment to time of   
death from any cause.   Patients not known to have expired will be censored for OS as of 
the most recent date of verification of their being still alive. 
 
 
 
12.  
STUDY OVERSIGHT AND DATA REPORTING / REGULATORY 
REQUIREMENTS 
 
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 7.0 
(Adverse Events: List and Reporting Requirements). 
 
12.1 
Study Oversight 
 
This protocol is monitored at several levels, as described in this section.  The Protocol Principal 
Investigator is responsible for monitoring the conduct and progress of the clinical trial, including 
the ongoing review of accrual, patient-specific clinical and laboratory data, and routine and 
serious adverse events; reporting of expedited adverse events; and accumulation of reported 
adverse events from other trials testing the same drug(s).  The Protocol Principal Investigator and 
statistician have access to the data at all times through the CTMS web-based reporting portal.   
 
 
For this Phase 2 study, the Protocol Principal Investigator will have, at a minimum, quarterly 
conference calls with the Study Investigators and the CTEP Medical Officer(s) to review accrual, 

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progress, and pharmacovigilance.  Decisions to proceed to the second stage of a Phase 2 trial will 
require sign-off by the Protocol Principal Investigator and the Protocol Statistician. 
 
All Study Investigators at participating sites who register/enroll patients on a given protocol are 
responsible for timely submission of data via Medidata Rave and timely reporting of adverse 
events for that particular study.  This includes timely review of data collected on the electronic 
CRFs submitted via Medidata Rave. 
 
All studies are also reviewed in accordance with the enrolling institution’s data safety monitoring 
plan. 
 
12.2 
Data Reporting 
 
Data collection for this study will be done exclusively through Medidata Rave.  Access to the 
trial in Rave is granted through the iMedidata application to all persons with the appropriate 
roles assigned in the Regulatory Support System (RSS).  To access Rave via iMedidata, the site 
user must have an active CTEP IAM account (check at < https://ctepcore.nci.nih.gov/iam  >) and 
the appropriate Rave role (Rave CRA, Read-Only, CRA, Lab Admin, SLA or Site Investigator) 
on either the LPO or participating organization roster at the enrolling site. To the hold Rave CRA 
role or CRA Lab Admin role, the user must hold a minimum of an AP registration type.  To hold 
the Rave Site Investigator role, the individual must be registered as an NPIVR or IVR.  
Associates can hold read-only roles in Rave.  If the study has a DTL, individuals requiring write 
access to Rave must also be assigned the appropriate Rave tasks on the DTL.   
 
Upon initial site registration approval for the study in RSS, all persons with Rave roles assigned 
on the appropriate roster will be sent a study invitation e-mail from iMedidata.  To accept the 
invitation, site users must log into the Select Login (https://login.imedidata.com/selectlogin) 
using their CTEP-IAM user name and password, and click on the “accept” link in the upper 
right-corner of the iMedidata page.  Please note, site users will not be able to access the study in 
Rave until all required Medidata and study specific trainings are completed.  Trainings will be in 
the form of electronic learnings (eLearnings), and can be accessed by clicking on the link in the 
upper right pane of the iMedidata screen.   
 
Users that have not previously activated their iMedidata/Rave account at the time of initial site 
registration approval for the study in RSS will also receive a separate invitation from iMedidata 
to activate their account. Account activation instructions are located on the CTSU website, Rave 
tab under the Rave resource materials (Medidata Account Activation and Study Invitation 
Acceptance).  Additional information on iMedidata/Rave is available on the CTSU members’ 
website under the Rave tab or by contacting the CTSU Help Desk at 1-888-823-5923 or by e-
mail at ctsucontact@westat.com. 
 
12.2.1 Method 
This study will be monitored by the Clinical Trials Monitoring Service (CTMS).  Data 
will be submitted to CTMS at least once every two weeks via Medidata Rave (or other 
modality if approved by CTEP).  Information on CTMS reporting is available at:  
http://www.theradex.com/clinicalTechnologies/?National-Cancer-Institute-NCI-11.  On-

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site audits will be conducted on an 18-36 month basis as part of routine cancer center site 
visits. More frequent audits may be conducted if warranted by accrual or due to concerns 
regarding data quality or timely submission.  For CTMS monitored studies, after users 
have activated their accounts, please contact the Theradex Help Desk at (609) 799-7580 
or by email at CTMSSupport@theradex.com for additional support with Rave and 
completion of CRFs 
 
12.2.2 Responsibility for Data Submission 
For ETCTN trials, it is the responsibility of the PI(s) at the site to ensure that all 
investigators at the ETCTN Sites understand the procedures for data submission for each 
ETCTN protocol and that protocol specified data are submitted accurately and in a timely 
manner to the CTMS via the electronic data capture system, Medidata Rave.   
 
Data are to be submitted via Medidata Rave to CTMS on a real-time basis, but no less 
than once every 2 weeks.  The timeliness of data submissions and timeliness in resolving 
data queries will be tracked by CTMS.  Metrics for timeliness will be followed and 
assessed on a quarterly basis.  For the purpose of Institutional Performance Monitoring, 
data will be considered delinquent if it is greater than 4 weeks past due. 
 
Data from Medidata Rave and CTEP-AERS is reviewed by the CTMS on an ongoing 
basis as data is received.  Queries will be issued by CTMS directly within Rave.  The 
queries will appear on the Task Summary Tab within Rave for the CRA at the ETCTN to 
resolve.  Monthly web-based reports are posted for review by the Drug Monitors in the 
IDB, CTEP.  Onsite audits will be conducted by the CTMS to ensure compliance with 
regulatory requirements, GCP, and NCI policies and procedures with the overarching 
goal of ensuring the integrity of data generated from NCI-sponsored clinical trials, as 
described in the ETCTN Program Guidelines, which may be found on the CTEP 
(http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm
)  and CTSU websites. 
 
An End of Study CRF is to be completed by the PI, and is to include a summary of study 
endpoints not otherwise captured in the database, such as (for phase 1 trials) the 
recommended phase 2 dose (RP2D), and a description of any dose-limiting toxicities 
(DLTs).  CTMS will utilize a core set of eCRFs that are Cancer Data Standards Registry 
and Repository (caDSR) compliant (http://cbiit.nci.nih.gov/ncip/biomedical-informatics-
resources/interoperability-and-semantics/metadata-and-models).  Customized eCRFs will 
be included when appropriate to meet unique study requirements.  The PI is encouraged 
to review the eCRFs, working closely with CTMS to ensure prospectively that all 
required items are appropriately captured in the eCRFs prior to study activation.  CTMS 
will prepare the eCRFs with built-in edit checks to the extent possible to promote data 
integrity. 
 
CDUS data submissions for ETCTN trials activated after March 1, 2014, will be carried 
out by the CTMS contractor, Theradex.  CDUS submissions are performed by Theradex 
on a monthly basis.  The trial’s lead institution is responsible for timely submission to 

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CTMS via Rave, as above. 
 
Further information on data submission procedures can be found in the ETCTN Program 
Guidelines 
(http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm
). 
 
12.3 CTEP Multicenter Guidelines 
 
12.4 Collaborative Agreements Language 
 
The agent(s) supplied by CTEP, DCTD, NCI used in this protocol is/are provided to the NCI 
under a Collaborative Agreement (CRADA, CTA, CSA) between the Pharmaceutical 
Company(ies) (hereinafter referred to as “Collaborator(s)”) and the NCI Division of Cancer 
Treatment and Diagnosis.  Therefore, the following obligations/guidelines, in addition to the 
provisions in the “Intellectual Property Option to Collaborator”  
(http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm) contained within the 
terms of award, apply to the use of the Agent(s) in this study: 
 
1. Agent(s) may not be used for any purpose outside the scope of this protocol, nor can 
Agent(s) be transferred or licensed to any party not participating in the clinical study.  
Collaborator(s) data for Agent(s) are confidential and proprietary to Collaborator(s) and shall 
be maintained as such by the investigators.  The protocol documents for studies utilizing 
Agents contain confidential information and should not be shared or distributed without the 
permission of the NCI.  If a copy of this protocol is requested by a patient or patient’s family 
member participating on the study, the individual should sign a confidentiality agreement.  A 
suitable model agreement can be downloaded from: http://ctep.cancer.gov. 
 
2. For a clinical protocol where there is an investigational Agent used in combination with 
(an)other Agent(s), each the subject of different Collaborative Agreements, the access to and 
use of data by each Collaborator shall be as follows (data pertaining to such combination use 
shall hereinafter be referred to as "Multi-Party Data”): 
 
a. NCI will provide all Collaborators with prior written notice regarding the existence and 
nature of any agreements governing their collaboration with NCI, the design of the 
proposed combination protocol, and the existence of any obligations that would tend to 
restrict NCI's participation in the proposed combination protocol. 
 
b. Each Collaborator shall agree to permit use of the Multi-Party Data from the clinical trial 
by any other Collaborator solely to the extent necessary to allow said other Collaborator 
to develop, obtain regulatory approval or commercialize its own Agent. 
 
c. Any Collaborator having the right to use the Multi-Party Data from these trials must 

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agree in writing prior to the commencement of the trials that it will use the Multi-Party 
Data solely for development, regulatory approval, and commercialization of its own 
Agent. 
 
3. Clinical Trial Data and Results and Raw Data developed under a Collaborative Agreement 
will be made available to Collaborator(s), the NCI, and the FDA, as appropriate and unless 
additional disclosure is required by law or court order as described in the IP Option to 
Collaborator (http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm).  
Additionally, all Clinical Data and Results and Raw Data will be collected, used and 
disclosed consistent with all applicable federal statutes and regulations for the protection of 
human subjects, including, if applicable, the Standards for Privacy of Individually 
Identifiable Health Information set forth in 45 C.F.R. Part 164. 
 
4. When a Collaborator wishes to initiate a data request, the request should first be sent to the 
NCI, who will then notify the appropriate investigators (Group Chair for Cooperative Group 
studies, or PI for other studies) of Collaborator's wish to contact them. 
 
5. Any data provided to Collaborator(s) for Phase 3 studies must be in accordance with the 
guidelines and policies of the responsible Data Monitoring Committee (DMC), if there is a 
DMC for this clinical trial. 
 
6. Any manuscripts reporting the results of this clinical trial must be provided to CTEP by the 
Group office for Cooperative Group studies or by the principal investigator for non-
Cooperative Group studies for immediate delivery to Collaborator(s) for advisory review and 
comment prior to submission for publication.  Collaborator(s) will have 30 days from the 
date of receipt for review.  Collaborator shall have the right to request that publication be 
delayed for up to an additional 30 days in order to ensure that Collaborator’s confidential and 
proprietary data, in addition to Collaborator(s)’s intellectual property rights, are protected.  
Copies of abstracts must be provided to CTEP for forwarding to Collaborator(s) for courtesy 
review as soon as possible and preferably at least three (3) days prior to submission, but in 
any case, prior to presentation at the meeting or publication in the proceedings.  Press 
releases and other media presentations must also be forwarded to CTEP prior to release.  
Copies of any manuscript, abstract and/or press release/ media presentation should be sent to: 
 
Email:  ncicteppubs@mail.nih.gov 
 
The Regulatory Affairs Branch will then distribute them to Collaborator(s).  No publication, 
manuscript or other form of public disclosure shall contain any of Collaborator’s confidential/ 
proprietary information. 
 
 
13. STATISTICAL CONSIDERATIONS 
 
13.1 
Study Design/Endpoints 
 
The study design is a single arm 2-stage Phase II pilot study of MLN0128 (TAK-228) in bladder 

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cancer patients whose tumors harbor a TSC1   mutation. 
   
 As per Section 1.1, the primary objective is to estimate the overall response rate (ORR) observed 
among TSC1 patients.      Hence, the primary statistical endpoint is the ORR among TSC1 patients. 
 
As per Section 1.2, the secondary endpoints are: 
a) Toxicity among TSC1 patients; 
b) PFS and OS among TSC1 patients.    
 
 
As per Section 1.3, the exploratory endpoints are: 
a) ORR among TSC2 patients; 
b) Toxicity among TSC2 patients; 
c) PFS and OS among TSC2 patients.    
 
13.2 
Sample Size/Accrual Rate 
 
13.2.1 To minimize the total number of patients with TSC1 mutant urothelial carcinomas  (TSC1 
patients) potentially needed for the planned 1-sample, 2-stage Phase 2 trial, a Simon minimax 
study design will be used.   We have assumed an ORR 0.10 (10%) for current therapy.  We believe 
that an improvement to 0.30 (30%) with MLN0128 (TAK-228) treatment would be clinically 
meaningful.   We have also assumed alpha = 0.10 and power = 0.90.  Under those assumptions a 
maximum of 25 eligible TSC1 patients would be required, 16 in Stage 1 and an additional 9 in 
Stage 2 (if needed), as determined by PASS 12 software. 
 
Assuming an approximate rate of 12% TSC1 incidence, it is estimated that 134 patients would 
need to be enrolled and screened in order to obtain the Stage 1 statistical design requirement of 16 
eligible TSC1 patients.  
 
If Stage 2 were required, it is estimated that 75 additional patients would need to be enrolled and 
screened in order to find 9 more TSC1 patients. That would mean screening a total of 209 patients 
to find the maximum statistical design requirement of 25 eligible TSC1 patients. 
 
13.2.2 Stopping Rules 
In Stage 1, 16 eligible TSC1 patients will be accrued.  A minimum follow-up period of 12 weeks 
will be required to assess clinical response. As per 11.4.3, all the responses will be confirmed with 
a subsequent scan obtained > 4 weeks.  If d 1 response is observed among them, stop the study 
and conclude that MLN0128 (TAK-228) is not worthy of further evaluation in this patient 
population.   If  t 2 responses are observed, accrue an additional 9 eligible TSC1 patients (i.e., 
begin Stage 2 of patient accrual).  If d 4 responses are observed in the final set of 25 eligible TSC1 
patients, conclude that MLN0128 (TAK-228) is not worthy of further study in TSC1 patients.   If  
t 5 responses are observed, conclude that MLN0128 (TAK-228) is promising. 
 
 The Type I error (i.e., the probability of concluding that MLN0128 (TAK-228) is promising when 

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that is not true) is 0.095 if the true response rate is 10%.  The power (i.e., the probability of correctly 
concluding that the regimen is active) of this procedure is 0.903 when the true response rate is 
30%.   The probability of early termination (PET) with this design is 0.515 when the true response 
rate is 10%, and the average total sample size for this design is 20.1 eligible TSC1 patients. 
 
13.2.3 These assumptions have been made regarding TSC1 (and TSC2) patient accrual rate. 
TSC1:    Metastatic bladder cancer patients will be recruited through the ETCTN.  Accessibility of these 
patients will come from both the UM-1 and N01 holders.  We do not anticipate a recruitment deficiency.  
Additionally, there were 4 lead institutions initially involved in the design and development of this 
protocol.  Those institutions are still interested and are:  Karmanos, Dana Farber Cancer Institute, 
Vanderbilt and Yale.  These 4 institutions see approximately 14, 150, 30 and 60 metastatic bladder cancer 
patients per year respectively, for a total of 254 such patients/year.    Conservatively, we expect that about 
15% of them will have a TSC1 (12%) and/or TSC2 (3%) gene mutation, making them study eligible.   
That 12% TSC1 incidence yields an estimated combined accrual rate of about 30 eligible TSC1 
patients/year. 
Allowing for up to 10% attrition of patients who do not become eligible, we may have to enroll 28 eligible 
TSC1 patients in order to have the potential maximum of 25 who are eligible for our planned 2-stage 
Simon minimax design.   At the expected accrual rate of 30 eligible TSC1 patients/year, it would take 
~12 months to accrue 25 eligible TSC1 patients for Stage 2 (should Stage 2 be needed).   
 
TSC2:      Since TSC2 patients only appear in our Exploratory Objectives, their accrual will be 
halted whenever the appropriate number of eligible TSC1 patients have been accrued, as per the 
planned 2-stage Simon minimax design. 
 Hence, it is uncertain how many TSC2 patients will be accrued, although the 3% incidence rate 
mentioned above might be a guideline.   That is about ¼ of the expected incidence rate of TSC1 
patients.   So, if 25 eligible TSC1 patients are eventually enrolled, then about 6-7 TSC2 patients 
would be expected to have been enrolled in parallel.    
  If any patients are enrolled who have both TSC1 and TSC2 mutations, they will be included with 
the exploratory cohort of patients who have only TSC2 mutations.   In this way, all interpretations 
of study results for the Primary and Secondary Objectives can be restricted to patients who have 
only a TSC1 mutation. 
 
 
 
Accrual Targets 
Ethnic Category 
Sex/Gender 
Females 
 
Males 
 
Total 
Hispanic or Latino 
2 
+ 
7 
= 
9 
Not Hispanic or Latino 
3 
+ 
13 
= 
16 
Ethnic Category: Total of all subjects 
5 
+ 
20 
= 
25                
(C1) 

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Racial Category 
 
American Indian or Alaskan Native 
1 
+ 
3 
= 
4 
Asian 
1 
+ 
3 
= 
4 
Black or African American 
1 
+ 
4 
= 
5 
Native Hawaiian or other Pacific 
Islander 
0 
+ 
3 
= 
3 
White 
2 
+ 
7 
= 
9 
Racial Category: Total of all subjects 
5 
(A2) 
+ 
20 
(B2) 
= 
25 
(C2) 
 
(A1 = A2) 
 
(B1 = B2) 
 
(C1 = C2) 
 
 
13.3 
Stratification Factors 
 
Not applicable since this is a 1-arm study.   Any stratification of interest can be performed after 
accrual is completed and the data are collected. 
 
 
13.4 
Analysis of Secondary Endpoints 
 
As per Section 1.2, the secondary objectives are: 
 
1) To evaluate the safety and tolerability of MLN0128 (TAK-228) in patients with locally 
advanced or metastatic TCC harboring a TSC1    mutation. 
 
2) To evaluate progression free survival (PFS) and overall survival (OS). 
 
 
For Secondary Objective 1, the occurrence rate of each specific type of toxicity at a certain severity 
grade will be described by point estimates and Wilson type 90% (2-sided) confidence intervals 
(CIs). 
. 
 
For Secondary Objective 2, the censored PFS and OS distributions will each be estimated by the 
Kaplan-Meier (K-M) survivorship function. Point estimates and 90% (2-sided) CIs will be 
computed for all estimable summary statistics, e.g, the median, 6-month rate, 12-month rate, etc. 
 
13.5 
Analysis of Exploratory Endpoints 
 
As per Section 1.3, the exploratory objectives are: 
 
1) To determine the ORR in patients with locally advanced or metastatic TCC harboring 
a TSC2 mutation. 
 
2) To evaluate toxicity, PFS, and OS in TSC2 mutation patients. 

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  The analysis of the endpoints for Exploratory Objectives 1 and 2 will be similar to that proposed 
for Secondary Objectives 1 and 2, respectively. 
 
 
13.6 
Reporting and Exclusions 
 
13.6.1 Evaluation of Toxicity 
 
All patients will be evaluable for toxicity from the time of their first treatment with 
MLN0128 (TAK-228) 
 
13.6.2 Evaluation of Response 
 
All patients included in the study will be assessed for response to treatment, even if there 
are major protocol treatment deviations or if they are ineligible.  Each patient will be 
assigned one of the following categories:  1) complete response, 2) partial response, 3) 
stable disease, 4) progressive disease, 5) early death from malignant disease, 6) early death 
from toxicity, 7) early death because of other cause, or 9) unknown (not assessable, 
insufficient data).   
 
All eligible patients (with the possible exception of those who received no study 
medication) will be included in the main analysis of the response rate.  Patients in response 
categories 4-9 will be considered to have a treatment failure (disease progression).  Thus, 
an incorrect treatment schedule or drug administration will not result in exclusion from the 
analysis of the response rate.   
 
All conclusions will be based on all eligible patients.  Subanalyses may be performed on 
the basis of a subset of patients, excluding those for whom major protocol deviations have 
been identified (e.g., early death due to other reasons, early discontinuation of treatment, 
major protocol violations, etc.).  However, these subanalyses will not serve as the basis for 
drawing conclusions concerning treatment efficacy, and the reasons for excluding patients 
from the analysis should be clearly reported.   
 
 

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Hintze, J. (2011).  PASS 11.  NCSS, LLC.  Kaysville, Utah, USA.   www.ncss.com 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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APPENDIX A 
PERFORMANCE STATUS CRITERIA 
 
ECOG Performance Status Scale 
Karnofsky Performance Scale 
Grade 
Descriptions 
Percent 
Description 
0 
Normal activity.  Fully active, able 
to carry on all pre-disease 
performance without restriction. 
100 
Normal, no complaints, no evidence 
of disease. 
90 
Able to carry on normal activity; 
minor signs or symptoms of disease. 
1 
Symptoms, but ambulatory.  
Restricted in physically strenuous 
activity, but ambulatory and able 
to carry out work of a light or 
sedentary nature (e.g., light 
housework, office work). 
80 
Normal activity with effort; some 
signs or symptoms of disease. 
70 
Cares for self, unable to carry on 
normal activity or to do active work. 
2 
In bed <50% of the time.  
Ambulatory and capable of all 
self-care, but unable to carry out 
any work activities.  Up and about 
more than 50% of waking hours. 
60 
Requires occasional assistance, but 
is able to care for most of his/her 
needs. 
50 
Requires considerable assistance and 
frequent medical care. 
3 
In bed >50% of the time.  Capable 
of only limited self-care, confined 
to bed or chair more than 50% of 
waking hours. 
40 
Disabled, requires special care and 
assistance. 
30 
Severely disabled, hospitalization 
indicated.  Death not imminent. 
4 
100% bedridden.  Completely 
disabled.  Cannot carry on any 
self-care.  Totally confined to bed 
or chair. 
20 
Very sick, hospitalization indicated. 
Death not imminent. 
10 
Moribund, fatal processes 
progressing rapidly. 
5 
Dead. 
0 
Dead. 
 
 
 
 
 
 
 
      
 
 

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APPENDIX B 
CTEP MULTICENTER GUIDELINES 
 
Not applicable.  
 
 
 
 
 

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APPENDIX C 
INFORMATION ON POSSIBLE DRUG INTERACTIONS 
 
Information on Possible Interactions with Other Agents for Patients and Their Caregivers 
and Non-Study Healthcare Team 
 
The patient ____________________________ is enrolled on a clinical trial using the 
experimental agent MLN0128 (TAK-228).   This clinical trial is sponsored by the National 
Cancer Institute.  This form is addressed to the patient, but includes important information for 
others who care for this patient.  
 
MLN0128 (TAK-228) may interact with many drugs that are processed by your liver.  Because of 
this, it is very important to tell your study doctors about all of your medicine before you start this 
study.  It is also very important to tell them if you stop taking any regular medicine, or if you start 
taking a new medicine while you take part in this study.  When you talk about your medicine with 
your study doctor, include medicine you buy without a prescription at the drug store (over-the-
counter remedy), or herbal supplements such as St. John’s wort.  
 
Many health care prescribers can write prescriptions.  You must also tell your other prescribers 
(doctors, physicians’ assistants or nurse practitioners) that you are taking part in a clinical trial. 
Bring this paper with you and keep the attached information card in your wallet.  These are 
the things that you and they need to know:  
 
MLN0128 (TAK-228) may interact with (a) certain specific enzyme(s) in your liver.  
x The enzyme(s) in question are CYP3A4, CYP2C9, and CYP2C19. MLN0128 (TAK-228) is 
broken down by this enzyme in order to be cleared from your system.  
x MLN0128 (TAK-228) must be used very carefully with other medicines that need these liver 
enzymes to be effective or to be cleared from your system.   
x Other medicines may also affect the activity of the enzyme.   
o Substances that increase the enzyme’s activity (“inducers”) could reduce the 
effectiveness of the drug, while substances that decrease the enzyme’s activity 
(“inhibitors”) could result in high levels of the active drug, increasing the chance 
of harmful side effects. 
 
x You and healthcare providers who prescribe drugs for you must be careful about adding or 
removing any drug in this category.  
x Before you start the study, your study doctor will work with your regular prescriber to switch 
any medicines that are considered “strong inducers/inhibitors or substrates of CYP3A4, 
CYP2C9, and CYP2C19  
x Your 
prescribers 
should 
look 
at 
this 
web 
site 
http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugIn
teractionsLabeling/ucm093664.htm#cypEnzymes)  or consult a medical reference to see if 
any medicine they want to prescribe is on a list of drugs to avoid.   
x Please be very careful!  Over-the-counter drugs have a brand name on the label—it’s usually 
big and catches your eye.  They also have a generic name—it’s usually small and located 
above or below the brand name, and printed in the ingredient list.  Find the generic name 
and determine, with the pharmacist’s help, whether there could be an adverse interaction.   

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x Be careful: 
x
If you take acetaminophen regularly:  You should not take more than 3 grams a day 
if you are an adult or 2.4 grams a day if you are older than 65 years of age.  Read 
labels carefully!  Acetaminophen is an ingredient in many medicines for pain, flu, 
and cold.
x
If you drink grapefruit juice or eat grapefruit:  Avoid these until the study is over. 
x
If you take herbal medicine regularly:  You should not take St. John’s wort while 
you are taking MLN0128 (TAK-228)
x
You should not take proton pump inhibitors, a class of medicines to reduce stomach 
acid, while taking MLN0128 (TAK-228). Examples include omeprazole, esomeprazole, 
or pantoprazole. 
x
Unless started more than 30 days ago, you should not start taking any bisphosphonate 
therapy, a class of medications to prevent of bone fractures, while taking MLN0128 
(TAK-228).
Other medicines can be a problem with your study drugs. 
x
You should check with your doctor or pharmacist whenever you need to use 
an over-the-counter medicine or herbal supplement. 
x
Your regular prescriber should check a medical reference or call your study 
doctor before prescribing any new medicine for you.  Your study doctor’s 
name is 
____________________________________ 
and he or she can be contacted at 
_____________________________________
INFORMATION ON POSSIBLE DRUG INTERACTIONS 
You are enrolled on a clinical trial using the experimental agent 
MLN0128 (TAK-228). 
This clinical trial is sponsored by the NCI.  
MLN0128 (TAK-228) may interact with drugs that are processed by 
your liver.  Because of this, it is very important to:
¾ Tell your doctors if you stop taking regular medicine or if you start 
taking a new medicine.
¾ Tell all of your prescribers (doctor, physicians’ assistant, nurse 
practitioner, pharmacist) that you are taking part in a clinical trial.
¾ Check with your doctor or pharmacist whenever you need to use an 
over-the-counter medicine or herbal supplement.
MLN0128(TAK-228) is metabolized by specific liver enzymes called 
CYP3A4, CYP2C9, and CYP2C19, and must be used very carefully with 
other medicines that interact with these enzymes. 
¾ Before you start the study, your study doctor will work with your 
regular prescriber to switch any medicines that are considered 
“strong inducers/inhibitors or substrates of called CYP3A4, CYP2C9, 
and CYP2C19.
¾
Before prescribing new medicines, your regular prescribers 
should 
go 
to 
http://www.fda.gov/Drugs/DevelopmentApprovalProcess/Dev
elopmentResources/DrugInteractionsLabeling/ucm093664.htm
#cypEnzymes) for a list of drugs to avoid, or contact your study 
doctor.  

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APPENDIX D: DIARY FOR MLN0128 (TAK-228)     
Date: _____________Cycle: ______ Subject ID: ___________________________Subject Initials:   ____ ____ 
 
* Please take capsule(s) approximately the same time on each scheduled day.  You will take ______ 
capsule(s) each day. Swallow capsules whole with water. Refrain from eating and drinking (except water 
and prescribed medications) for 2 hours before and 1 hour after each dose. Stay hydrated by drinking at 
least 2-3 cups of water each day.   
* Please bring this diary and capsule bottle with you to each appointment. 
* If you miss a dose and realize it within 12 hours, please take the dose on an empty stomach.  Do not 
take 2 doses 12 hours or less apart.  If you vomit after dosing, please note in the Comment column below, 
do not take another dose. 
* Always contact your study doctor before taking any new medications.  
* Do not 
eat 
grapefruit 
or drink 
grapefruit 
juice 
while 
you are 
on study.  
Day in 
Cycle 
Date of 
Dosing 
 
Time of 
Dosing 
 
Number of 
capsules taken 
Did you vomit after 
dosing?  If so, please note 
the time. Other comments: 
Fasting Blood Glucose 
D1 
 
 
 
 
 
D2 
 
 
 
 
 
D3 
 
 
 
 
 
D4 
 
 
 
 
 
D5 
 
 
 
 
 
D6 
 
 
 
 
 
D7 
 
 
 
 
 
D8 
 
 
 
 
 
D9 
 
 
 
 
 
D10 
 
 
 
 
 
D11 
 
 
 
 
 
D12 
 
 
 
 
 
D13 
 
 
 
 
 
D14 
 
 
 
 
 
D15 
 
 
 
 
 
D16 
 
 
 
 
 
D17 
 
 
 
 
 
D18 
 
 
 
 
 
D19 
 
 
 
 
 
D20 
 
 
 
 
 
D21 
 
 
 
 
 
D22 
 
 
 
 
 
D23 
 
 
 
 
 
D24 
 
 
 
 
 
D25 
 
 
 
 
 
D26 
 
 
 
 
 
D27 
 
 
 
 
 
D28 
 
 
 
 
 
 

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Patient’s Signature or Initials: ________________________________________ Date: _______________________ 
 
This diary has been reviewed by: 
 
Signature: ____________________________________________________Date _____________________________ 
 
Printed Name:  _________________________________________________________________________________ 
 
 

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APPENDIX E: NEW YORK HEART ASSOCIATION (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.  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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APPENDIX F: LIST OF RELEVANT CYTOCHROME P450 INHIBITORS AND 
INDUCERS 
MLN0128 (TAK-228) is metabolized by CYP2C19, CYP3A4, and CYP2C9. Thus, strong 
inhibitors and/or inducers of CYP2C19, CYP3A4 or CYP2CP are prohibited on study. Strong 
inhibitors and inducers of CYP2C19 and CYP3A4 are listed in the table below. There are no 
known strong specific inhibitors or inducers of CYP2C9.  Investigators must check the link to the 
FDA website below for any updates. Note the list of these medications is from the Tables 3-2 and 
3-3 of the FDA website. They were updated on 9/26/2016.  
http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractio
nsLabeling/ucm093664.htm#cypEnzymes 
Moderate inhibitors and/or inducers of CYP2C19, CYP3A4 and CYP2C9 may be used on study 
with caution unless they are strong inhibitors and/or inhibitors of these isozymes. Check the FDA 
website link above for the information. 
 
Strong Inhibitors and Strong Inducers of CYP2C9, CYP2C19, and CYP3A4 
Strong Inhibitors 
Strong Inducers 
boceprevir 
cobicistat 
conivaptan 
clarithromycin 
danoprevir and ritonavir 
diltiazem 
elvitegravir and ritonavir 
fluconazole 
fluoxetine 
fluvoxamine 
idelalisib 
indinavir and ritonavir 
itraconazole 
ketoconazole 
lopinavir and ritonavir 
nefazodone 
nelfinavir 
paritaprevir and ritonavir and (ombitasvir 
and/or dasabuvir) 
posaconazole 
ritonavir 
saquinavir and ritonavir 
telaprevir 
tipranavir and ritonavir 
troleandomycin 
carbamazepine 
enzalutamide  
mitotane 
phenytoin  
Rifampin 
Ritonavir 
St. John’s wort 

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voriconazole 
ticlopidine 
Fruits and juice 
 
grapefruit and juice 
 
Sources: 
http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/DrugInteractio
nsLabeling/ucm093664.htm#cypEnzymes