A Phase 1 Study of MLN0128 and Bevacizumab in Patients With Recurrent Glioblastoma and Other Solid Tumors
Phase: PHASE1
Conditions: Adult Glioblastoma, Endometrial Clear Cell Adenocarcinoma, Endometrial Serous Adenocarcinoma, Ovarian Clear Cell Cystadenocarcinoma, Ovarian Endometrioid Adenocarcinoma, Ovarian Mucinous Cystadenocarcinoma, Ovarian Serous Cystadenocarcinoma, Recurrent Fallopian Tube Carcinoma, Recurrent Malignant Uterine Corpus Neoplasm, Recurrent Ovarian Carcinoma, Recurrent Primary Peritoneal Carcinoma, Solid Neoplasm, Stage IIIA Fallopian Tube Cancer AJCC v7, Stage IIIA Ovarian Cancer AJCC v6 and v7, Stage IIIA Primary Peritoneal Cancer AJCC v7, Stage IIIB Fallopian Tube Cancer AJCC v7, Stage IIIB Ovarian Cancer AJCC v6 and v7, Stage IIIB Primary Peritoneal Cancer AJCC v7, Stage IIIC Fallopian Tube Cancer AJCC v7, Stage IIIC Ovarian Cancer AJCC v6 and v7, Stage IIIC Primary Peritoneal Cancer AJCC v7, Stage IV Fallopian Tube Cancer AJCC v6 and v7, Stage IV Ovarian Cancer AJCC v6 and v7, Stage IV Primary Peritoneal Cancer AJCC v7
Sponsor: National Cancer Institute (NCI)

i 
SUMMARY OF CHANGES 
 
For Protocol Amendment  
 
NCI Protocol #: 9552 
Local Protocol #: 14-079 
 
NCI Version Date: TBD 
Protocol v9.0 Date: 04-October-2016 
 
 
# 
Section 
Page(s) 
Change 
1. 
Title 
page 
3 
Protocol version date change to: 04-october-2016 
 
2. 
7.2.4 
54-61 
 Update CAEPR list v2.4  dated 5/23/16 for Bevacizumab 
 
 

1 
NCI Protocol #: 
9552 
Local Protocol #: 
14-079 
 
 
TITLE:  A Phase 1 study of MLN0128 and bevacizumab in patients with recurrent 
glioblastoma and other solid tumors 
 
 
Coordinating Center: 
 
 
Dana-Farber Cancer Institute 
 
 
Principal Investigator: 
Lakshmi Nayak, MD 
 
 
 
Dana-Farber Cancer Institute 
 
 
 
450 Brookline Avenue 
 
 
 
Boston, MA 02215 
 
Phone: 617-632-2166  
Fax: 617-632-4773 
Lakshmi_Nayak@DFCI.harvard.edu 
 
Co-Investigators:  
 
John L. Hays, MD, PhD 
The Ohio State University 
450 W 12th Avenue 
Columbus, OH 43210 
Phone: 614-685-5840 
Fax: 614-292-6356 
john.hays@osumc.edu  
 
Vinay K. Puduvalli, MD 
The Ohio State University 
320 W 10th Avenue 
Columbus, OH 43210 
Phone: 614-688-7592 
Fax: 614-366-5763 
Vinay.puduvalli@osumc.edu 
 
 
David Reardon, MD 
Dana-Farber Cancer Institute 
450 Brookline Avenue 
Boston, MA 02215 
 
Phone: 617-632-2166  
Fax: 617-632-4773 
David_Reardon@DFCI.harvard.edu 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
2 
Geoffrey Shapiro, MD, PhD 
Dana-Farber Cancer Institute 
450 Brookline Avenue 
Boston, MA 02215 
 
Phone: 617-632-4942 
Fax:  617-632-1977 
Geoffrey_Shapiro@DFCI.harvard.edu 
 
Andrew Chi, MD 
Massachusetts General Hospital 
55 Fruit Street 
Boston, MA 02114 
Phone: 617-724-8770 
Fax: 617-724-8769 
Email: chi.andrew@mgh.harvard.edu  

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
3 
 
 
 
Statistician: 
 
Study Coordinator:  
 
Alona Muzikansky 
Ketki Bhushan, MPH 
Massachusetts General Hospital 
Dana Farber Cancer Institute  
Phone: 617-724-6985 
Phone: 617-632-4270 
Fax: 617-724-9878 
Fax: 617-582-7922 
Email: AMuzikansky@partners.org  
Email: kbhushan@partners.org  
 
Responsible Research Nurse: 
  
Responsible Data Manager: 
Lisa Doherty, NP 
 Brendan Wrigley 
Dana Farber Cancer Institute 
 
            Dana Farber Cancer Institute 
 
Phone: 617-632-2166  
 
            Phone: 617-632-5396 
Fax: 617-632-4773 
Fax: 617-394-2683 
Email: Lisa_Doherty@DFCI.harvard.edu  
            Email: brendan_wrigley@dfci.harvard.edu  
  
 
 
NCI-Supplied Agent: MLN0128 (Millennium Pharmaceuticals, Inc.) 
Other Agent(s): Bevacizumab (commercial) 
IND #:  
IND Sponsor:  CTEP, DCTD 
Revision / Version3/ Version Date: Version 9.0/ 04-October-2016

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
4 
SCHEMA 
 
This study will involve 2 stages. 
                                                  
                                          Stage 1: Dose Escalation 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                         Stage 2: Dose Expansion 
 
 
 
 
 
 
 
 
MLN0128 
 
(Dose Level 1 MLN0128 oral 
daily) 
+ 
Bevacizumab 
(intravenously every 2 weeks) 
                    
Patient Population: 
Advanced Solid 
Tumors and Recurrent 
Glioblastoma 
n = 12-18 patients 
Declaration of MTD/RP2D or 
Recommendation for expansion 
MLN0128 
(MTD/RP2D or  
Recommendation for expansion) 
+ 
Bevacizumab 
(intravenously every 2 weeks) 
Patient Population: 
Recurrent Glioblastoma 
n = 10 patients 
 
Endometrial Cancer 
n = 10-15 patients* 
 
Ovarian Cancer 
n = 10-15 patients* 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
5 
Stage 1: Dose escalation to estimate MTD/RP2D. 
Approximately 12-18 patients with advanced solid tumors including recurrent glioblastoma 
(GBM) will be enrolled using a standard 3+3 design, including 3-6 patients in each cohort. 
Patients will start at dose level 1, 3mg daily of MLN0128, based on the recommended single 
agent daily dose of MLN0128 by Millennium. MTD for the current study will be defined as the 
highest dose at which <2/6 patients experience DLT. Bevacizumab will be administered at 
10mg/kg IV every 2 weeks. Should 2/6 patients at the initial dose level experience DLT, then 3 
patients will be enrolled at dose level -1 (MLN0128 3mg orally 5 out of 7 days with standard 
dose bevacizumab.) 
 
Stage 2: Expansion cohort at MTD.  
After the MTD/RP2D is determined, stage 2 will enroll and treat up to an additional 40 patients 
(10-15* patients with endometrial cancer, 10-15* patients with ovarian cancer and 10 patients 
with recurrent GBM) to:  1)better characterize the safety profile of MLN0128; 2)  evaluate 
plasma and CSF concentrations of MLN0128 when administered with and without bevacizumab; 
and 3) evaluate pharmacodynamic properties of MLN0128 in tumor tissue and plasma. Patients 
in stage 2 will receive MLN0128 daily starting with cycle 1 day 1 and bevacizumab 10mg/kg IV 
every 2 weeks starting with cycle 1 day 15. Bevacizumab will not be administered cycle 1 day 1.  
 
*may enroll up to 15 participants in these two dose expansion cohorts in order to obtain sufficient 
biopsy material from 10 patients per cohort for correlative study requirements  
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
6 
TABLE OF CONTENTS 
1. 
OBJECTIVES ......................................................................................................................9 
1.1 
Primary Objectives ...................................................................................................9 
1.2 
Secondary Objectives ...............................................................................................9 
1.3 
Exploratory Objectives ............................................................................................9 
2. 
BACKGROUND ...............................................................................................................10 
2.1 
Study Diseases .......................................................................................................10 
2.2 
CTEP IND Study Agent:  MLN 0128....................................................................11 
2.3 
Other Agent(s) .......................................................................................................20 
2.4 
Rationale ................................................................................................................21 
2.5 
Correlative Studies Background ............................................................................22 
3. 
PATIENT SELECTION ....................................................................................................23 
3.1 
Eligibility Inclusion Criteria ..................................................................................23 
3.2 
Eligibility Exclusion Criteria .................................................................................26 
3.3 
Inclusion of Women and Minorities ......................................................................29 
4. 
REGISTRATION PROCEDURES ...................................................................................29 
4.1 
General Guidelines .................................................................................................29 
4.2 
Registration Process ...............................................................................................29 
5. 
TREATMENT PLAN ........................................................................................................29 
5.1 
Agent Administration .............................................................................................29 
5.2 
Definition of Dose-Limiting Toxicity ....................................................................32 
5.3 
General Concomitant Medication and Supportive Care Guidelines ......................34 
5.4 
Duration of Therapy ...............................................................................................35 
5.5 
Duration of Follow Up ...........................................................................................35 
5.6 
Criteria for Removal from Study ...........................................................................36 
6. 
DOSING DELAYS/DOSE MODIFICATIONS................................................................36 
6.1 
Bevacizumab ..........................................................................................................36 
6.2 
MLN0128 ...............................................................................................................40 
6.3 
Management of Hematologic Toxicities and Use of Hematologic Growth 
Factors ....................................................................................................................49 
7. 
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................50 
7.1 
General Information ...............................................................................................50 
7.2 
Comprehensive Adverse Events and Potential Risks (CAEPR) Lists ...................51 
7.3 
Expedited Adverse Event Reporting to CTEP .......................................................59 
7.4 
Routine Adverse Event Reporting .........................................................................62 
7.5 
Secondary Malignancy ...........................................................................................62 
7.6 
Expedited Adverse Event Reporting to Local IRB ................................................62 
7.7 
Routine Adverse Event Reporting .........................................................................62 
8. 
PHARMACEUTICAL INFORMATION ..........................................................................62 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
7 
8.1 
Study Agent: MLN0128 ........................................................................................63 
8.2 
Commercial Agent: Bevacizumab .........................................................................65 
9. 
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES ........................................67 
9.1 
Correlative Studies for Stage 2 ..............................................................................68 
10. 
STUDY CALENDAR .......................................................................................................74 
11. 
MEASUREMENT OF EFFECT........................................................................................77 
11.1 
Antitumor Effect – Non-GBM  Solid Tumors .......................................................77 
11.2 
Antitumor Effect – Glioblastoma patients .............................................................83 
12. 
DATA REPORTING / REGULATORY REQUIREMENTS ...........................................87 
12.1 
Data Reporting .......................................................................................................87 
12.2 
CTEP Multicenter Guidelines ................................................................................88 
12.3 
Collaborative Agreements Language .....................................................................88 
13. 
STATISTICAL CONSIDERATIONS...............................................................................90 
13.1 
Study Design/Endpoints.........................................................................................90 
13.2 
Sample Size/Accrual Rate ......................................................................................91 
13.3 
Stratification Factors ..............................................................................................93 
13.4 
Analysis of Secondary and Exploratory Endpoints ...............................................93 
REFERENCES ..............................................................................................................................95 
APPENDIX A 
PERFORMANCE STATUS CRITERIA ................................................101 
APPENDIX B 
CTEP MULTICENTER GUIDELINES ..................................................102 
APPENDIX C 
STRONG INHIBITORS AND STRONG INDUCERS of CYP2c9, 
cyp2c19 and cype3a4 .......................................................................................................104 
APPENDIX D 
DATA AND SAFETY MONITORING PLAN ......................................105 
1.0 
INTRODUCTION..........................................................................................................107 
1.1 
Purpose................................................................................................................107 
1.2 
Multi-Center Data and Safety Monitoring Plan Definitions..........................107 
2.0 
GENERAL ROLES AND RESPONSIBILITIES .......................................................108 
2.1 
Protocol Chair ....................................................................................................108 
2.2 
Coordinating Center ..........................................................................................108 
2.3 
DF/HCC Quality Assurance Office for Clinical Trials (QACT) ...................109 
2.4 
Participating Institution ....................................................................................109 
3.0 
DF/HCC REQUIREMENTS FOR MULTI-CENTER PROTOCOLS ....................110 
3.1 
Protocol Distribution .........................................................................................110 
3.2 
Protocol Revisions and Closures .......................................................................110 
3.3 
Informed Consent Requirements .....................................................................111 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
8 
3.4 
IRB Documentation ...........................................................................................111 
3.5 
IRB Re-Approval ...............................................................................................111 
3.6 
Participant Confidentiality and Authorization Statement .............................111 
3.7 
DF/HCC Multi-Center Protocol Registration Policy ......................................112 
3.8 
DF/HCC Protocol Case Number ......................................................................114 
3.9 
Protocol Deviations, Exceptions and Violations ..............................................114 
3.10 
Safety Assessments and Toxicity Monitoring ..................................................115 
3.11 
Data Management ..............................................................................................116 
4.0 
Requisitioning Investigational Drug ............................................................................116 
4.1 
CTEP Trial Routine Drug Requisitions ...........................................................117 
5.0 
MONITORING: QUALITY CONTROL ....................................................................117 
5.1 
Monitoring by NCI/CTEP .................................................................................117 
5.2 
Monitoring by DFCI Coordinating Center .....................................................118 
5.3 
Evaluation of Participating Institution Performance .....................................119 
6.0 
AUDITING: QUALITY ASSURANCE .......................................................................119 
6.1 
NCI Sponsored Trials ........................................................................................119 
6.2 
Participating Institution ....................................................................................120 
6.3 
Protocol Chair and Coordinating Center ........................................................120 
6.4 
Sub-Standard Performance ..............................................................................120 
APPENDIX E 
DOSE LEVEL 1, 2 & 3 PILL DIARY FOR MLN0128 ..........................121 
APPENDIX F 
DOSE LEVEL 1a & -1 PILL DIARY FOR MLN0128 ..........................124 
APPENDIX G 
BIOASSAY PROCEDURES...................................................................127 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
9 
 
1. 
OBJECTIVES 
 
1.1 
Primary Objectives 
 
• To determine the maximum tolerated dose and recommended phase 2 dose 
(MTD/RP2D) of daily oral MLN0128 when administered with bevacizumab in 
patients with advanced solid tumors including recurrent glioblastoma (GBM). 
• To evaluate the overall safety and tolerability of the combination of MLN0128 and 
bevacizumab. 
 
1.2 
Secondary Objectives 
 
• To assess the preliminary anti-tumor activity of the combination of MLN0128 and 
bevacizumab, as determined by response rate (RR), progression-free survival (PFS) 
and overall survival (OS). 
• To assess tolerability throughout study therapy with MLN0128 and bevacizumab, 
including beyond the MTD interval with the following measures of cumulative 
treatment-related toxicities:  
o Frequency of toxicities leading to missed doses or delays 
o Percentage of cycles given or not within 7 days of their scheduled times 
o Percentage of actual planned dosage administration 
o Percentage of patients that discontinue study drugs due to treatment related 
toxicity. 
 
1.3 
Exploratory Objectives 
 
• To assess CSF penetration of MLN0128 in combination with bevacizumab in patients 
with recurrent GBM by evaluating the plasma and CSF concentrations of MLN0128 
in the absence and presence of bevacizumab. 
• To perform archival tumor analysis for markers of dysregulated cell signaling that 
may predict response to mTOR inhibitor therapy such as EGFR (expression by IHC 
and amplification by FISH), PTEN (expression by IHC and deletion by FISH), p-
AKT, p-S6K, p-4EBP, p-mTOR and p-Erk in patients with recurrent GBM.  
• To analyze select phosphorylated proteins (ERK, AKT, mTOR, 4EBP1, GSK3beta, 
p70S6K, rS6) from tumor biopsies obtained at baseline and after treatment with 
MLN0128 from endometrial and ovarian cancer patients enrolled in stage 2. 
• To analyze circulating plasma levels of angiogenic growth factors before, during and 
after treatment with MLN0128 and bevacizumab 
To perform genetic mutation analysis and proteomic analysis of tissue from biopsies 
of endometrial and ovarian cancer patients including analysis of KRAS, BRAF, 
PIK3CA, AKT1 and PTEN. 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
10 
2. 
BACKGROUND 
 
2.1 
Study Diseases 
 
2.1.1 
Glioblastoma 
 
Glioblastoma (GBM) is the most common type of malignant primary brain tumor with 
over 10,000 new cases diagnosed each year in the United States1. Despite optimal 
treatment with surgery, radiation therapy and temozolomide, most patients have tumor 
recurrence and the median survival is only approximately 15 months2. Following 
disease progression, most chemotherapeutic agents have minimal activity1. 
Bevacizumab, a monoclonal antibody targeting vascular endothelial growth factor 
(VEGF) has shown modest activity, producing a 26% response rate and a median 
survival of approximately 9 months from recurrence 3,4.  
 
In the past decade, there has been important progress in understanding the molecular 
pathogenesis of GBM 5,6. The phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR 
signaling axis plays a central role in cell growth, survival, motility, and metabolism 7 
in a variety of cancers including GBM5. Data from TCGA suggests that over 80% of 
GBM patients have activation of this pathway as a result of either PIK3Ca or PIK3R1 
mutations, inactivation of PTEN, or amplification or mutation of receptor tyrosine 
kinases such as EGFR, PDGFR and MET 5. Inhibition of this pathway represents an 
attractive therapeutic strategy. Prior clinical trials evaluating mTOR inhibitors have 
generated modest evidence of anti-tumor activity although assessment of effective 
penetration of these agents through the blood brain barrier was not carefully 
determined in the prior trials8,9.  
 
2.1.2 
Endometrial Cancer 
 
Endometrial cancer is diagnosed in approximately 40,000 women in the US every 
year, and long term outcomes for patients with advanced or recurrent disease are 
poor10. New therapeutic approaches and combinations are needed to improve 
outcomes in this patient population. There are limited treatment options with in the 
advanced disease setting. Inactivation of the PTEN (phosphatase with tensin 
homology) tumor-suppressor gene is the most common genetic defect in endometrial 
cancers, seen in up to 80% of endometrioid (type 1) tumors11. PIK3CA activating 
mutation are also seen in 36% of endometrial type 1 carcinomas, most frequently in 
those tumors that also bear PTEN mutation12. When PTEN is deleted, mutated or 
otherwise inactivated, activation of PI3K (phosphatidylinositol 3-kinase) effectors, 
particularly AKT and the downstream mTOR can occur in the absence of any 
exogenous stimulus 
 
Given the strong data supporting dysregulation of the PI3K/AKT/mTOR pathway, the 
rapalogs have generated significant interest in endometrial cancer. A single-agent, 
multi-institution trial of temsirolimus in patients with recurrent and/or metastatic 
endometrial cancer were recently reported13. The study had two investigational arms: 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
11 
Group A was chemotherapy naïve and Group B had been exposed to one prior line of 
chemotherapy. Four (14%) of 29 evaluable patients in Group A had a partial response, 
and 20 (69%) had a stable disease; the median PFS was 7.33 months for the group. Of 
25 evaluable patients in Group B, 1 (4%) patient had a partial response and 12 (48%) 
had stable disease. Median PFS was 3.25 months in Group B. Stable disease required a 
minimum of 4 weeks duration. Treatment was better tolerated in the chemotherapy 
naïve group; however sixteen of sixty patients in the combined arms discontinued 
therapy due to toxicity (26.6%). The combination of bevacizumab and temsirolimus 
was investigated in a phase 2 study for endometrial cancer patients having previously 
received 1-2 lines of chemotherapy and/or radiation.  This study reported a 24.5% 
response rate including one complete response and a 6-month progression-free 
survival (PFS6) of 46.9%.  The combination in this pretreated population was also 
associated with significant toxicities, including gastrointestinal-vaginal fistulas, 
intestinal perforations, epistaxis and thromboembolism14. 
 
2.1.3 
Ovarian Cancer   
 
There is an unmet need to develop effective and novel treatment strategies for 
epithelial ovarian cancer (EOC). It is the leading cause of death from gynecologic 
malignancies in the United States10. Targeted molecular therapies against the cancer 
cell and surrounding stromal cells such as fibroblasts, endothelial cells, and 
inflammatory cells, are being developed as the signaling pathways that drive tumor 
development and progression are elucidated.  EOCs induce extensive 
neovascularization that facilitates tumor growth and metastasis. Hollingsworth et al. 
demonstrated that increased vasculature correlates with higher grade EOC tumors and 
poor survival15.  Multiple therapies have been developed to target the interactions 
between tumor cells and the stroma, including anti-angiogenic agents, exemplified by 
bevacizumab, a monoclonal antibody against vascular endothelial growth factor 
(VEGF) that has some single agent phase II clinical activity in platinum-resistant 
EOC16.  However, this and other single biologic agents have not extended the 
progression-free or overall survival in EOC remarkably.  Combination of bevacizumab 
with other targeted agents has significantly increased its efficacy in early phase 1 and 
phase 2 trials in EOC.  
 
Approximately 40% of ovarian cancers have increased AKT2 activity17,18. 
Downstream of AKT, phosphorylated (p)mTOR and pGSK-3β correlate with AKT 
activation status in > 80% of ovarian cancers, validating activation of the PI3K/AKT 
pathway 17. Thus, pharmacologic agents that inhibit downstream targets of the 
PI3K/AKT signaling pathway such as mTOR might preferentially kill tumor cells 
having AKT dependence for survival not shared by normal cells19. A phase 2 trial of 
temsirolimus in recurrent EOC demonstrated a 9% response rate and a 24% PFS at six 
months indicating modest activity of this TORC1 inhibitor20.  
 
2.2 
CTEP IND Study Agent:  MLN 0128 
 
The phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
12 
signaling axis plays a central role in cell growth, survival, motility, and metabolism in a variety 
of cancers21,22. Several studies have examined the role of mTOR inhibitors, namely, rapamycin 
and its analogs (rapalogs) for the treatment of cancer including sirolimus, temsirolimus, 
everolimus, and ridaforolimus9,23-25. However, these agents have achieved limited efficacy for 
several reasons. First, all of these inhibitors selectively inhibit TORC1 but fail to block TORC2, 
and therefore may result in activation of Akt via the S6K-IRS1 feedback loop and via mTORC2-
mediated phosphorylation of AKT at serine 473 (Ser473)26. Additionally, TORC1 inhibition by 
rapalogs may lead to activation of the MAPK pathway27. In the brain, many of the rapalogs also 
have only limited penetration across the blood-brain barrier (BBB) and may fail to achieve 
effective intra-tumoral therapeutic concentrations.  
 
The TOR kinase-domain inhibitors of mTOR (TORKinibs) differ in their mode of action from 
rapalogs by binding to the ATP-binding site of the kinase domain of mTOR, thus resulting in 
inhibition of both mTOR complexes, TORC1 and TORC2. Inhibition of TORC2 has been shown 
to reverse the AKT activation induced by TORC1 inhibition28. 
 
MLN0128 is a potent, orally available ATP-competitive inhibitor of both TORC1 and TORC2 
complexes. It has been shown to inhibit phosphorylation of TORC1 downstream targets, 
including S6 and 4EBP1.  Additionally, it inhibits phosphorylation of AKT, a TORC2 target a 
variety of tumor cell lines, including HER2-amplified trastuzumab-sensitive and –resistant breast 
cancer cells, breast ductal T47D cells that harbor PI3KCA mutation, as well as metastatic renal 
cell cancer (RCC) and endometrial cell lines22,29-31.  
 
Summaries of Nonclinical and Clinical Studies 
The pharmacodynamics and antitumor activity of MLN0128 was studied in vivo in murine 
xenograft models of human glioblastoma, non-small cell lung cancer (NSCLC), breast cancer, 
renal cell cancer, endometrial adenocarcinoma, and castration-resistant prostate cancer (CPRC). 
Consistent with the mode of action, MLN0128 inhibited phosphorylation of downstream 
modulators of mTORC1 (namely 4EBP1 and S6) and mTORC2 (namely AKT [S473]) in human 
U87 glioblastoma tumor xenograft models in mice at doses as low as 0.1 mg/kg. Additionally, 
MLN0128 showed strong tumor growth inhibition (TGI) in all 8 xenograft models at tolerable 
oral (PO) doses from 0.15 mg/kg (daily [QD]; tested in MDA-MB-361 breast carcinoma) to 3.0 
mg/kg (every other day [Q2D] or once weekly [QW]; tested in all models). 
 
Single-agent MLN0128 is in clinical development in two phase 1 studies in subjects with 
advanced solid malignancies and hematologic malignancies (multiple myeloma [MM] and 
Waldenstrom macroglobulinemia [WM]), and in a third study in combination with paclitaxel 
with or without trastuzumab in subjects with advanced solid tumors. 
 
Study INK128-001 
Study INK128-001 is evaluating safety and anti-tumor activity of MLN0128 in subjects with 
advanced solid malignancies. As of 09 December 2012, 106 subjects have been treated in Study 
INK128-001. The most common adverse events (AEs) (≥ 20%), regardless of causality were 
hyperglycemia (64%), nausea (60%), vomiting (49%), decreased appetite (40%), diarrhea (37%), 
asthenia (35%), fatigue and mucosal inflammation (28% each), rash (27%), and pruritus (24%). 
Most commonly reported (> 3%) Grade ≥ 3 AEs, regardless of causality, include hyperglycemia 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
13 
(10%), asthenia (7%), anemia (6%), lymphopenia (6%), hypophosphatemia (5%), mucosal 
inflammation (5%), and rash (5%).  
 
In Study INK128-001, as of 09 December 2012, the maximum tolerated doses (MTD) for all 4 
schedules has been determined: for the QD dosing the MTD is 6 mg QD, for the QDx3dQW 
dosing, the MTD is 16 mg; for the QDx5dQW dosing, the MTD is 10 mg; and for the QW 
dosing schedule, the MTD is 40 mg. The MTDs for each of the 4 schedules was determined by 
evaluation of cohorts of 6 evaluable patients. At each MTD, up to 6 additional patients were 
enrolled to further evaluate safety and tolerability. A significant proportion of patients treated at 
the MTDs required dose modifications due to drug-related AEs beyond 1 or 2 cycles, and 
therefore were not representative of a recommended phase 2 dose. The study is currently further 
evaluating doses at less than the MTD for QDx3dQW and QDx5dQW, to determine a dose(s) 
and schedule(s) to be studied further in the expansion phase of the study, as well as in future 
phase 2 studies. The dose escalation portion of the study has evaluated dose regimens ranging 
from 2 to 7 mg QD, 7 to 40 mg QW, 6 to 20 mg QDx3dQW, and 7 to 13 mg QDx5dQW. 
 
Study INK128-002 
Study INK128-002 is evaluating safety and anti-tumor activity of MLN0128 in subjects with 
hematologic malignancies (MM and WM). As of 09 December 2012, 39 subjects have been 
treated in Study INK128-002. The most common AEs (≥ 20%), regardless of causality were 
fatigue and nausea (51% each), hyperglycemia (38%), thrombocytopenia (36%), diarrhea (26%), 
decreased appetite and vomiting (23% each), and stomatitis/anemia (21% each). Most commonly 
reported (at least 2 subjects) Grade ≥ 3 AEs, regardless of causality included thrombocytopenia 
(18%), fatigue (10%), neutropenia (8%), hypocalcemia (5%), hypophosphatemia (5%), mucosal 
inflammation (5%), and pneumonia (5%). 
 
In Study INK128-002, dose escalation is completed, with 4 mg determined as the MTD for the 
QD schedule, and 9 mg determined as the MTD for the QDx3dQW schedule. 
 
Study INK128-003 
Study INK128-003 is evaluating safety and anti-tumor activity of MLN0128 in subjects with 
advanced solid tumors in combination with paclitaxel (and trastuzumab for HER2+ subjects). As 
of 09 December 2012, 48 subjects have been treated in Study INK128-003; no subject has been 
treated with trastuzumab. The most common AEs (≥ 20%), regardless of causality were fatigue 
(67%); nausea (56%); diarrhea (50%); dehydration and hyperglycemia (44% each); anemia 
(40%); anorexia, mucosal inflammation, and vomiting (38% each); rash (35%); asthenia and 
neutropenia (31% each); hypokalemia (27%); hypophosphatemia and urinary tract infection 
(23% each); and constipation (21%). Most commonly reported (at least 2 subjects) Grade ≥ 3 
AEs, regardless of causality, include neutropenia (23%); hypophosphatemia (17%); diarrhea, 
fatigue, and hyperglycemia (15%); and dehydration (10%). 
 
In the dose expansion phase of this study, additional subjects were enrolled once the MTD was 
determined and evaluated for each of the dosing schedules. These subjects were enrolled into an 
arm of HER2- subjects receiving MLN0128 in combination with paclitaxel (n = 11) at the MTD 
or an arm of HER2+ subjects receiving MLN0128 in combination with paclitaxel plus weekly 
trastuzumab (n = 2) at the MTD. The most common AEs (≥ 20%), regardless of causality, were 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
14 
alopecia, fatigue, and nausea (23% each) and anorexia, asthenia, diarrhea, dyspepsia, mucosal 
inflammation, neutropenia, and vomiting (15% each). Most commonly reported (at least 2 
subjects) Grade ≥ 3 AEs in the dose expansion phase of INK128-003, regardless of causality, 
include mucosal inflammation, neutropenia, and pneumonia (reported by 1 subject each in the 
HER2- arm). 
 
In Study INK128-003, dose escalation is completed, with 8 mg of MLN0128 QDx3dQW being 
selected for the dose expansion phase of the study. The QDx5dQW and QW schedules were 
abandoned before MTDs were declared, as these schedules were viewed as less convenient 
relative to the QDx3dQW schedule, from the perspective of administering the paclitaxel and 
trastuzumab combination. The dose expansion portion of this study is ongoing, with HER2-
/unknown patients receiving 8 mg of MLN0128 QDx3dQW in combination with paclitaxel, and 
HER2+ patients receiving 8 mg of MLN0128 QDx3dQW in combination with paclitaxel and 
trastuzumab. 
 
Nonclinical and Clinical Pharmacokinetics 
MLN0128 is rapidly absorbed after oral administration to mice, rats, dogs, and monkeys, with 
high oral bioavailability. 
 
A study of the tissue distribution of [14C]MLN0128 showed that [14C]MLN0128 was rapidly and 
widely distributed throughout the body in Long-Evans rats; radioactivity was eliminated from 
most tissues at 48 hours postdose, and from all but the adrenal cortex, adrenal gland, adrenal 
medulla, eye, liver, and uveal tract at 168 hours. MLN0128 displayed dose proportional plasma 
exposures and a moderate propensity to cross the blood-brain barrier. MLN0128 was modestly 
bound to human plasma proteins (approximately 70%). MLN0128 inhibited breast cancer 
resistance protein (BCRP), organic cation transporter (OCT)1, and OCT2. 
 
M1, the single metabolite (monohydroxylation product) observed in human microsomal 
incubations, was also observed in rats and monkeys, the species used for the Good Laboratory 
Practice (GLP) toxicology studies. The main isozymes responsible for phase 1 metabolism 
appear to be cytochrome P450 (CYP) 2C9, 2C19, and 3A4. MLN0128 displayed low potential 
(IC50 > 30 μM) for inhibition of CYP1A2, 2C19, 2C8, 2C9, CYP2D6, and 3A4. MLN0128 did 
not induce CYP1A2, 2B6, and 3A4 activity and expression at concentrations up to 30 μM.  
 
Biliary and urinary excretion of MLN0128 and its monohydroxylation metabolite (M1) was 
investigated in bile duct-cannulated male Sprague-Dawley rats over 24 hours after administration 
of a single IV dose of 0.5-mg/kg MLN0128(38) The biliary elimination of MLN0128 and M1 
each represented less than 1% of the total MLN0128 dose. The urinary excretion of MLN0128 
and M1 represented less than 1% and 21%, respectively, of the total MLN0128 dose. 
 
Oral administration of MLN0128 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 single dose (total maximum plasma concentration [Cmax] of 0.64 
μM [free Cmax of 0.19 μM] at 40 mg QW). 
 
MLN0128 does not inhibit P-glycoprotein (P-gp). 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
15 
 
Preliminary pharmacokinetic (PK) data from phase 1 studies in humans indicate that MLN0128 
exhibits fast oral absorption (first time to maximum plasma concentration [Tmax] generally 
between 1 to 4 hours after dosing) and dose-linear pharmacokinetics with a mean plasma half-
life of ~8 hours and does not accumulate meaningfully in plasma on either dosing regimen. The 
pharmacokinetics of MLN0128 was generally consistent with no appreciable differences across 
the three phase 1 studies. Neither paclitaxel nor MLN0128 appeared to alter the PK of the other 
agent when co-administered.  
 
2.2.1 
Bevacizumab (rhuMAb VEGF) 
 
Bevacizumab is a humanized IgG1 monoclonal antibody (MAb) that binds all biologically active 
isoforms of human VEGF (or VEGF-A) with high affinity (kd = 1.1 nM). The antibody consists 
of a human IgG1 framework and the antigen-binding complementarity-determining regions from 
the murine anti-VEGF MAb A.4.6.1.16-18. Bevacizumab is commercially available and FDA 
approved as monotherapy for patients with recurrent glioblastoma. It is currently approved in 
combination therapy for certain solid tumors, such as advanced non-squamous non-small cell 
lung cancer, metastatic renal cell cancer, and metastatic colorectal cancer. 
 
Mechanism of Action 
 
VEGF is one of the most potent and specific angiogenic factors, and it has been identified as a 
crucial regulator of both normal and pathological angiogenesis. VEGF is a secreted, 
heparin-binding protein that exists in multiple isoforms. Action of VEGF is primarily mediated 
through binding to the receptor tyrosine kinases VEGFR-1 (Flt-1) and VEGFR-2 (KDR/Flk-1). 
The biologic effects of VEGF include endothelial cell mitogenesis and migration, increased 
vascular permeability, induction of proteinases leading to remodeling of the extracellular matrix, 
and suppression of dendritic cell maturation. Neutralization of VEGF by A.4.6.1 or bevacizumab 
has been shown to inhibit the VEGF-induced proliferation of human endothelial cells in vitro and 
to decrease microvessel density and interstitial pressure in tumor xenografts in vivo. 
 
Preclinical Studies 
 
The murine parent MAb of bevacizumab, A4.6.1, has demonstrated potent growth inhibition in 
vivo in a variety of human cancer xenograft and metastasis models, including those for SKLMS-
1 leiomyosarcoma, G55 glioblastoma multiforme, A673 rhabdomyosarcoma, Calu-6, and MCF-7 
cell lines 32-34. The antitumor activity was enhanced with the combination of A4.6.1 and 
chemotherapeutic agents compared to either agent alone. Furthermore, combined blockage of the 
VEGF pathway and other growth factor pathways (e.g., EGFR or PDGFR) has also demonstrated 
additive effects in vivo 35,36. Associated with the antitumor activity of anti-VEGF MAbs were 
findings of reduced intratumoral endothelial cells and microcapillary counts as well as reduced 
vascular permeability and interstitial pressure.  
 
Nonclinical toxicology studies have examined the effects of bevacizumab on female 
reproductive function, fetal development, and wound healing. Fertility may be impaired in 
Cynomolgus monkeys administered bevacizumab, which led to reduced uterine weight and 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
16 
endometrial proliferation as well as a decrease in ovarian weight and number of corpora lutea. 
Bevacizumab is teratogenic in rabbits, with increased frequency of fetal resorption as well as 
specific gross and skeletal fetal alterations. In juvenile Cynomolgus monkeys with open growth 
plates, bevacizumab induced epiphyseal dysplasia that was partially reversible upon cessation of 
therapy. Bevacizumab also delays the rate of wound healing in rabbits, and this effect appeared 
to be dose dependent and characterized by a reduction of wound tensile strength. 
 
Clinical Studies 
 
Bevacizumab has been studied in multiple Phase I, Phase II, and Phase III clinical trials and in 
multiple tumor types. The following discussion summarizes bevacizumab’s safety profile and 
presents some of the efficacy results pertinent to this particular trial. Clinical proof of principle 
for anti‐VEGF therapy with bevacizumab has been provided by the pivotal Phase III trial of 
bevacizumab (5 mg/kg every 2 weeks) in combination with bolus irinotecan/5‐
fluorouracil/leucovorin (IFL) in patients with untreated advanced colorectal cancer (AVF2107g) 
37. In that study, the addition of bevacizumab to IFL was associated with an increase in objective 
responses (45% vs. 35%) and significant prolongations of both time to progression (10.6 vs. 6.2 
months) and overall survival (20.3 vs. 15.6 months) compared with IFL.  
 
Based on the survival advantage, bevacizumab was approved in 2004 in the United States for 
first‐line treatment in combination with IV 5-FU-based chemotherapy for subjects with 
metastatic colorectal cancer. Additional data from Phase III trials in metastatic CRC 38, and non-
small cell lung cancer 39 have also demonstrated clinical benefit from bevacizumab when added 
to chemotherapy. 
 
Single agent bevacizumab received accelerated FDA approval in 2009 based on favorable results 
from two Phase II clinical trials in recurrent GBM 3,4. In these studies, PFS6 for bevacizumab 
monotherapy ranged from 29% to 42.6%. Compared to a historical PFS6 of 15% for recurrent 
GBM 40, these studies suggest that bevacizumab has significant clinical activity in this patient 
population. 
 
There is evidence that angiogenesis also plays a role in endometrial cancer progression and 
prognosis41. Fifty-two patients with one or two rounds of prior systemic therapy were treated 
with single agent bevacizumab in the GOG study 229E42. Seven patients (13.5%) had clinical 
responses (one complete response and six partial responses, with six months median response 
duration) and 21 patients (40.4%) survived progression free for at least six months. Median PFS 
and OS times were 4.2 and 10.5 months, respectively. 
 
In ovarian cancer, single agent bevacizumab has shown some clinical activity, but no impact on 
OS16,43. However, its combination with other targeted agents has shown promise in early phase I 
and II trials44,45.  
 
Safety Profile in Humans 
 
In the initial Phase I and II clinical trials, four potential bevacizumab-associated safety signals 
were identified: hypertension, proteinuria, thromboembolic events, and hemorrhage. Additional 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
17 
completed Phase II and Phase III studies of bevacizumab as well as spontaneous reports have 
further defined the safety profile of this agent. Bevacizumab‐associated adverse events identified 
in Phase III trials include congestive heart failure (CHF) primarily in metastatic breast cancer, 
gastrointestinal perforations, wound healing complications, and arterial thromboembolic events 
(ATE).  
 
Hypertension: An increased incidence of hypertension has been observed in patients treated 
with bevacizumab. Grade 4 and 5 hypertensive events are rare. Clinical sequelae of hypertension 
are rare but have included hypertensive crisis, hypertensive encephalopathy, and reversible 
posterior leukoencephalopathy syndrome (RPLS) 37,46. There is no information on the effect of 
bevacizumab in patients with uncontrolled hypertension at the time of initiating bevacizumab 
therapy. Therefore, caution should be exercised before initiating bevacizumab therapy in these 
patients. Monitoring of blood pressure is recommended during bevacizumab therapy. Optimal 
control of blood pressure according to standard public health guidelines is recommended for 
patients on treatment with or without bevacizumab. Temporary interruption of bevacizumab 
therapy is recommended in patients with hypertension requiring medical therapy until adequate 
control is achieved.  If hypertension cannot be controlled with medical therapy, bevacizumab 
therapy should be permanently discontinued. Bevacizumab should be permanently discontinued 
in patients who develop hypertensive crisis or hypertensive encephalopathy. 
 
Proteinuria: An increased incidence of proteinuria has been observed in patients treated with 
bevacizumab compared with control arm patients. In the bevacizumab‐containing treatment arms 
of clinical trials (across all indications), the incidence of proteinuria (reported as an adverse 
event) was up to 38% (metastatic CRC Study AVF2192g) 47. The severity of proteinuria has 
ranged from asymptomatic and transient events detected on routine dipstick urinalysis to 
nephrotic syndrome; the majority of proteinuria events have been Grade 1. NCI‐CTC Grade 3 
proteinuria was reported in up to 3% of bevacizumab‐treated patients, and Grade 4 in up to 1.4% 
of bevacizumab‐treated patients. The proteinuria seen in bevacizumab clinical trials was not 
associated with renal impairment and rarely required permanent discontinuation of bevacizumab 
therapy.  
 
Bevacizumab should be discontinued in patients who develop Grade 4 proteinuria (nephrotic 
syndrome). Patients with a history of hypertension may be at increased risk for the development 
of proteinuria when treated with bevacizumab. There is evidence from the dose‐finding, Phase II 
trials (AVF0780g, AVF0809s, and AVF0757g) suggesting that Grade 1 proteinuria may be 
related to bevacizumab dose. Proteinuria will be monitored by urine protein: creatinine (UPC) 
ratio at least every 4 weeks.  
 
Thromboembolic Events: Both venous and arterial thromboembolic (TE) events, ranging in 
severity from catheter‐associated phlebitis to fatal, have been reported in patients treated with 
bevacizumab in the colorectal cancer trials, the recurrent glioblastoma trial and, to a lesser 
extent, in patients treated with bevacizumab in NSCLC and breast cancer trials. Venous 
thromboembolic events (VTE) have also been observed in trials with bevacizumab and 
glioblastoma. To assess the overall risk of VTE associated with the use of bevacizumab, a 
systemic review and meta-analysis was performed and included prospective randomized 
controlled trials in which standard antineoplastic therapy was used with and without 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
18 
bevacizumab 48. A total of 7,956 patients with a variety of advanced solid tumors from 15 trials 
were indentified. Among the patients treated with bevacizumab, the rates of all-grade and high-
grade VTE were 11.9% and 6.3, respectively. Patients treated with bevacizumab had a 
significantly increased risk of VTE compared with controls (RR 1.31). Since TE events are very 
common in GBM independent of treatment 2, the relationship of thromboembolism to 
bevacizumab in this population is uncertain. Based on a Phase II clinical trial of bevacizumab 
with or without irinotecan in recurrent GBM, the rates of arterial thromboembolism were 2.4%-
2.5% and venous thromboembolism were 3.6%-8.9% 3. The first incidence of VTE will therefore 
not constitute a DLT.  
 
An increased incidence of arterial thromboembolic events (ATE) was observed in patients 
treated with bevacizumab compared with those receiving control treatment. ATE include 
cerebrovascular accidents, myocardial infarction, transient ischemic attacks (TIAs), and other 
ATE. The analysis of pooled data of 1,745 patients from five randomized trials using 
bevacizumab combined with chemotherapy showed an increased risk of ATE (3.8% in treatment 
arm vs. 1.7% in the control arm) but not VTE 49. Most ATE episodes described were myocardial 
or cerebrovascular events. Development of an ATE event was associated with a prior ATE event 
or age ≤ 65 years.  
 
Gastrointestinal perforation: Patients may be at increased risk for the development of 
gastrointestinal perforation and fistula when treated with bevacizumab and steroids or 
chemotherapy. Bevacizumab should be permanently discontinued in patients who develop 
gastrointestinal perforation. A causal association of intra‐abdominal inflammatory processes and 
gastrointestinal perforation to bevacizumab treatment has not been established. Nevertheless, 
caution should be exercised when treating patients with intra‐abdominal inflammatory processes 
with bevacizumab. A meta-analysis of 17 randomized controlled trials demonstrated a 
significantly increased risk of gastrointestinal perforation in patients treated with bevacizumab 
compared to control medication 50. The incidence was 0.9%, and the risks varied with tumor 
type, with colorectal cancer and renal cell cancer having the highest risk. In a Phase II clinical 
trial of bevacizumab with or without irinotecan for patients with recurrent GBM, 2.1%-2.5% 
experienced a Grade 3 gastrointestinal perforation 3,4. 
 
Fistula: Bevacizumab use has been associated with serious cases of fistulae including events 
resulting in death. Fistulae in the GI tract are common (1%–10% incidence) in patients with 
metastatic CRC, but uncommon (0.1% 1%) or rare (0.01%–0.1%) in other indications. In 
addition, fistulae that involve areas of the body other than the GI tract (e.g. tracheoesophageal, 
bronchopleural, urogenital, biliary) have been reported uncommonly (0.1%–1%) in patients 
receiving bevacizumab in clinical studies and postmarketing reports. Events were reported at 
various timepoints during treatment, ranging from 1 week to > 1 year following initiation of 
bevacizumab, with most events occurring within the first 6 months of therapy. 
 
Wound healing complications: Wound healing complications such as wound dehiscence have 
been reported in patients receiving bevacizumab. Most clinical trials with bevacizumab have 
required at least 28 days from any major surgery before starting treatment 51. In a retrospective 
analysis of randomized trials in metastatic colorectal cancer, for a subset of patients who had 
surgeries 28-60 days before initiating bevacizumab, the incidence of wound complications were 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
19 
low (1.3%) 52, indicating that the 28-day interval from colonic surgery might be appropriate. 
However, in the subset of patients undergoing emergent surgery while on study, 13% of the 
patients in the bevacizumab arm developed Grade 3 or Grade 4 postoperative wound 
complications compared to 3.4% of the patients in the chemotherapy arm. Surgery in patients 
currently receiving bevacizumab is not recommended. No definitive data are available to define a 
safe interval after bevacizumab exposure with respect to wound healing risk in patients receiving 
elective surgery; however, the estimated half-life of bevacizumab is 21 days. Bevacizumab 
should be discontinued in patients with severe wound healing complications. If patients receiving 
treatment with bevacizumab require elective major surgery, it is recommended that bevacizumab 
be held for 4–8 weeks prior to the surgical procedure. Patients undergoing a major surgical 
procedure should not begin or restart bevacizumab until 4 weeks after that procedure (in the case 
of high‐risk procedures such as liver resection, thoracotomy, or neurosurgery, it is recommended 
that bevacizumab be restarted no earlier than 4 weeks after surgery). In a Phase II clinical trial of 
bevacizumab with or without irinotecan in patients with recurrent GBM, Grade 3 or higher 
wound-healing complications were reported in 1.3-2.4% 3. 
 
Hemorrhage: Overall, grade 3 and Grade 4 bleeding events were observed in 4.0% of 1132 
patients treated with bevacizumab in a pooled database from eight Phase I, Phase II, and Phase 
III clinical trials in multiple tumor types 53. The hemorrhagic events that have been observed in 
bevacizumab clinical studies were predominantly tumor‐associated hemorrhage (See below: 
Tumor-Associated Hemorrhage) and minor mucocutaneous hemorrhage. 
 
Tumor-Associated Hemorrhage: Major hemorrhage has been observed primarily in patients with 
NSCLC. Life‐threatening and fatal hemoptysis was identified as a bevacizumab‐related adverse 
event in NSCLC trials. These events occurred suddenly and presented as major or massive 
hemoptysis. GI hemorrhages, including rectal bleeding and melena have been reported in 
patients with CRC, and have been assessed as tumor associated hemorrhages. Grades 1-4 tumor‐
associated hemorrhages were only very rarely seen in patients with GBM (less than 4%) 3. Two 
of the five patients who developed intracranial hemorrhage were anticoagulated at the time of the 
hemorrhage; both hemorrhages were Grade 1. 
 
Mucocutaneous Hemorrhage: Across all bevacizumab clinical trials, mucocutaneous 
hemorrhage has been seen in 20%‐40% of patients treated with bevacizumab 53. These were most 
commonly NCICTC Grade 1 epistaxis that lasted less than 5 minutes, resolved without medical 
intervention and did not require any changes in bevacizumab treatment regimen. There have also 
been less common events of minor mucocutaneous hemorrhage in other locations, such as 
gingival bleeding and vaginal bleeding. 
 
Reversible Posterior Leukoencephalopathy Syndrome: There have been rare reports of 
bevacizumab‐treated patients developing signs and symptoms that are consistent with RPLS, a 
rare neurologic disorder that can present with the following signs and symptoms (among others): 
seizures, headache, altered mental status, visual disturbance, or cortical blindness, with or 
without associated hypertension. Brain imaging is mandatory to confirm the diagnosis of RPLS. 
In patients who develop RPLS, treatment of specific symptoms, including control of 
hypertension, is recommended along with discontinuation of bevacizumab. The safety of 
reinitiating bevacizumab therapy in patients previously experiencing RPLS is not known. In a 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
20 
Phase II clinical trial of bevacizumab with or without irinotecan in patients with recurrent GBM, 
only one patient (1.3%) experienced serious reversible posterior leukoencephalopathy syndrome 
3. 
 
Congestive heart failure: In clinical trials CHF was observed in all cancer indications studied to 
date, but predominantly in patients with metastatic breast cancer. In the Phase III clinical trial of 
metastatic breast cancer (AVF2119g), 7 (3%) bevacizumab‐treated patients experienced CHF, 
compared with two (1%) control arm patients 54. These events varied in severity from 
asymptomatic declines in left ventricular ejection fraction (LVEF) to symptomatic CHF 
requiring hospitalization and treatment. All the patients treated with bevacizumab were 
previously treated with anthracyclines (doxorubicin cumulative dose of 240 360 mg/m2). Many 
of these patients also had prior radiotherapy to the left chest wall. Most of these patients showed 
improved symptoms and/or left ventricular function following appropriate medical therapy 54. No 
information is available on patients with preexisting CHF of New York Heart Association 
(NYHA) Class II-IV at the time of initiating bevacizumab therapy, as these patients were 
excluded from clinical trials. 
 
Adverse events in GBM studies from FDA labeling information: Bevacizumab is 
commercially available and FDA approved for patients with recurrent glioblastoma. For further 
details, see the bevacizumab FDA labeling information available at 
http://www.accessdata.fda.gov/drugsatfda_docs/label/2009/125085s0169lbl.pdf. 
 
All adverse events were collected in 163 patients enrolled in a non-comparative Phase II study 
who either received Bevacizumab alone or Bevacizumab plus irinotecan 3. All patients received 
prior radiotherapy and temozolomide. Bevacizumab was administered at 10 mg/kg every 2 
weeks alone or in combination with irinotecan. Bevacizumab was discontinued due to adverse 
events in 4.8% of patients treated with Bevacizumab alone. 
 
In patients receiving Bevacizumab alone (N=84), the most frequently reported adverse events of 
any grade were infection (55%), fatigue (45%), headache (37%), hypertension (30%), epistaxis 
(19%) and diarrhea (21%). Of these, the incidence of Grade ≥ 3 adverse events was infection 
(10%), fatigue (4%), headache (4%), hypertension (8%) and diarrhea (1%). Two deaths on study 
were possibly related to Bevacizumab: one retroperitoneal hemorrhage and one neutropenic 
infection. 
 
In patients receiving Bevacizumab alone or Bevacizumab plus irinotecan (N=163), the incidence 
of Bevacizumab-related adverse events (Grade 1−4) were bleeding/hemorrhage (40%), epistaxis 
(26%), CNS hemorrhage (5%), hypertension (32%), venous thromboembolic event (8%), arterial 
thromboembolic event (6%), wound-healing complications (6%), proteinuria (4%), 
gastrointestinal perforation (2%), and RPLS (1%). The incidence of Grade 3−5 events in these 
163 patients were bleeding/hemorrhage (2%), CNS hemorrhage (1%), hypertension (5%), 
venous thromboembolic event (7%), arterial thromboembolic event (3%), wound-healing 
complications (3%), proteinuria (1%), and gastrointestinal perforation (2%). 
 
2.3 
Other Agent(s) 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
21 
Not Applicable 
 
2.4 
Rationale 
 
MLN0128 was demonstrated to be efficacious in five human tumor cell-line xenograft mouse 
models, including glioblastoma (GBM) U87MG (mutant PTEN), non-small cell lung cancer 
(NSCLC) A549 (mutant KRAS/LKB-1), breast carcinoma ZR-75-1 (mutant PTEN), RCC 786-O 
(mutant PTEN/VHL), and endometrial adenocarcinoma AN3-CA (mutant PTEN), demonstrating 
strong inhibition of tumor growth in these models compared to controls (untreated animals).  
Depending on the tumor type, tumor growth inhibition ranged from 32%-57% at 0.3 mg/kg QD 
and 60%-94% at 1 mg/kg QD. Tumor inhibition achieved at 3 mg/kg QOD (45%-99%) was 
similar to that obtained at 1 mg/kg QD in all five xenograft models. In U87MG GBM xenografts, 
MLN0128 produced dose-dependent inhibition of phosphorylation of 4EBP1, S6K and AKT 22. 
Preclinical data have indicated that MLN0128 displays a low to moderate propensity to cross the 
BBB; steady-state plasma concentrations exceed brain concentrations by 5-fold in mice receiving 
a single 10-mg/kg oral dose of MLN012822.  
 
In a phase I dose escalation study of MLN0128 (INK128) given orally daily in patients with 
advanced solid tumors, the maximum tolerated dose (MTD) was 6mg with dose limiting toxicity 
(DLT) of grade 3 rash in 1 out of 6 patients55. In this study, pharmacodynamic (PD) biomarker 
measurements in peripheral blood mononuclear cells, skin, and tumor showed treatment-related 
changes, occurring even at low exposures, as evidenced by decreases in p4EBP1, pS6, and 
pPRAS40. 
 
The pharmacokinetic (PK) profile of MLN0128 has been evaluated in 130 patients in several 
ongoing studies22. MLN0128 is rapidly absorbed after oral administration achieving a Cmax 
within 2 to 4 hours post-dose. MLN0128 exhibited dose-linear PK with an elimination half-life 
(t1/2) of approximately 8 hours. The mean steady-state plasma Cmax ranged from 52-232 nM. 
No significant change in the PK parameters of MLN0128 was observed on repeat dosing; the 
mean accumulation index of MLN0128 ranged from 0.7-1.7-fold following multiple doses. 
 
Combinations of mTOR and tyrosine kinase or antibody VEGF/VEGFR inhibitors have been 
studied in a variety of cancers56.  A phase II trial of combination bevacizumab and temsirolimus 
was conducted in patients with recurrent or persistent endometrial cancer57. Twelve patients 
(24.5%) experienced a RECIST response including one complete response and 23 patients 
(46.9%) were progression free at six months. The increased response with the combination did 
come with a cost of increased toxicity including intestinal perforations (2), fistula formation (2) 
and a grade 4 thromboembolic event. The combination of bevacizumab with sorafenib had a 
remarkably high response rate (47%) in patients with EOC in a phase 1 trial5.  
Moreover, combining VEGF and mTOR inhibitors has demonstrated greater tumor growth 
inhibition and better survival compared to either agent alone in additional preclinical studies 
utilizing intra-cranial glioma models58.  
 
In xenograft models of breast cancer with transgenically elevated VEGF levels, the combination 
of INK128 and bevacizumab produced superior target inhibition and inhibition of tumor growth 
compared to either INK128 or bevacizumab alone22,59. Target (TORC1 and TORC2) inhibition 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
22 
was evidenced by reduced levels of S6pSer240/244, 4EBP1pThr37/45 and AKTpSer473. 
 
Based on these studies, dual inhibition of the VEGF/VEGFR pathway with effective inhibition of 
mTOR signaling represents an attractive combination for a study in advanced solid tumors 
including recurrent GBM, ovarian and endometrial cancers. 
 
The combination of MLN0128 with bevacizumab may have more antitumor activity than either 
agent alone. This phase I study will examine the safety and tolerability of the combination and 
determine the MTD and recommended phase II dose (RP2D) in patients with solid tumors, 
including GBM.  
 
2.5 
Correlative Studies Background 
 
Plasma and CSF MLN0128 concentrations: Stage 2 recurrent GBM patients 
We will assess plasma and CSF concentrations of MLN0128 in the presence or absence of 
bevacizumab in patients with recurrent GBM.  Evaluation of achievable drug levels particularly 
in presence of bevacizumab will provide critical insight into whether bevacizumab co-
administration should be considered in a follow-up Phase II study. The concentration of 
MLN0128 in study samples will be determined by validated LC-MS/MS assay. 
 
Archival tumor analysis: Stage 2 recurrent GBM patients 
Archival paraffin-embedded tumor will be analyzed for markers associated with dysregulated 
cell signaling that may predict response to mTOR inhibitor therapy such as EGFR (amplification 
by FISH), PTEN (expression by IHC and deletion by FISH), p-AKT, p-S6, p-4EBP, p-mTOR 
and p-ERK in patients with recurrent GBM.  
 
Tumor biopsies: Stage 2 endometrial and ovarian cancer patients 
Endometrial and ovarian cancer patients in stage 2 will undergo serial tumor biopsies to 
characterize the effects that MLN0128 has upon the tumor and associated stroma. Tumor 
biopsies will be obtained through Interventional Radiology only among patients considered at 
minimal surgical risk. Biopsies will be obtained before treatment, after 2 weeks of MLN0128 
monotherapy , and optionally at the time of progression on study therapy. This plan will allow 
the discovery of possible predictive biomarkers that can be queried in future trials with this 
therapeutic regimen and as well for pharmacodynamic endpoints associated with MLN0128 
therapy. 
 
Circulating cytokines in blood: Stage 2 endometrial and ovarian cancer patients 
We will assess plasma for the following cytokines, VEGFA, PIGF,  bFGF, , VEGFD, MMP2, 
MMP9, IL6, IL8, EGF and angiopoietin.  Cytokine selection is based upon published reports of 
proteins and growth factors believed to be important in vascular formation (VEGFA,VEGFD, 
IL6, IL8, Angiopoietin-1, bFGF), tumor aggressiveness and invasion (IL-6, IL-8, EGF, MMP2, 
MMP9), resistance/sensitivity to bevacizumab mediated therapy (VEGFA, VEGFD, IL-6, 
Angiopoietin-1), or linked with signaling through PI3K/AKT/mTOR pathway.  These angiogenic 
factors will be assessed as markers for response, resistance or progression. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
23 
 
3. 
PATIENT SELECTION 
 
Participants must meet the following eligibility criteria on screening examination to be eligible to 
participant in the study.  Screening evaluations are detailed in Section 10. 
 
Following registration, on Cycle 1, Day 1, participants should be evaluated for eligibility to treat 
based upon dose modification criteria outlined in Table 6.1 and 6.2 and not inclusion and 
exclusion criteria outlined here in Protocol Sections 3.1 and 3.2; these sections need only be met 
during screening for trial for registration.  
 
3.1 
Eligibility Inclusion Criteria  
 
3.1.1 Patients must have a histologically/cytologically confirmed diagnosis of recurrent 
glioblastoma or an advanced solid tumor in which bevacizumab has shown benefit in 
specific disease population and for which standard or curative measures do not exist or 
are no longer effective. 
 
3.1.2 Measurable or evaluable disease as assessed by RECIST 1.1 for non-GBM tumors and by 
RANO criteria for GBM60,61. 
 
3.1.3 For Stage 1 (all patients) and dose expansion (stage 2) endometrial and ovarian cancer 
cohorts, participants are allowed following unlimited prior therapy. For Stage 2 GBM 
participants, no more than 2 prior relapses are allowed.  For these patients, relapse is 
defined as progression following initial therapy (i.e. radiation +/- chemo if that was used 
as initial therapy) or a subsequent therapy. The intent therefore is that GBM  patients 
enrolling onto stage 2 had no more than 3 prior therapies (initial and treatment for 2 
relapses). If the patient had a surgical resection for relapsed disease and no anti-cancer 
therapy was instituted for up to 12 weeks, and the patient undergoes another surgical 
resection, this is considered to constitute 1 relapse.  
 
NOTE: For participants who had prior therapy for a low-grade glioma, the surgical 
diagnosis of glioblastoma will be considered the first relapse. Therefore, these 
participants may have had more than 3 prior therapies. 
 
3.1.4 Patients must have recovered from clinically significant toxicity of prior therapy to grade 
≤ 1 or pre-treatment baseline. The following intervals from previous treatments are 
required prior to day 1 of study therapy: 
• 12 weeks from the completion of radiation for recurrent GBM unless there is surgical 
diagnosis of recurrence or a new lesion that was not previously radiated 
• 6 weeks from a nitrosourea chemotherapy 
• 3 weeks from a non-nitrosourea chemotherapy 
• 4 weeks from an investigational agent (not FDA approved) (or 5 half lives, whichever 
is shorter) 
• 2 weeks from administration of a non-cytotoxic, FDA-approved agent (e.g., erlotinib, 
hydroxychloroquine, etc.) (or 5 half lives, whichever is shorter). 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
24 
 
3.1.5 Age ≥18 years. 
 
3.1.6 ECOG performance status ≤2 (Karnofsky ≥60%, see Appendix A). 
 
3.1.7 Patients must have normal organ and marrow function as defined below: 
• Absolute neutrophil count 
 
> 1,500/µL 
• Platelets  
 
 
> 100,000/µL 
• Hemoglobin 
 
 
> 9.0g/dL 
• Total bilirubin 
 
 
<1.5 x institutional upper limit of  
normal with direct bilirubin within     
normal limits except for participants  
with Gilbert’s disease 
• AST(SGOT)/ALT (SGPT) 
 
< 2.5 x institutional upper limit of  
normal (≤ 5 x ULN if liver metastases 
are present).   
• Creatinine 
 
 
< 1.5 x normal institutional limits 
OR 
• Creatinine clearance 
 
> 50mL/min/1.73m2 for patients with  
creatinine level above institutional 
normal based either on Cockroft-Gault 
estimate or based on urine collection (12 
or 24 hour). 
 
3.1.8 Metabolic: fasting serum glucose (≤ 130 mg/dL) and fasting triglycerides ≤ 300 mg/dL 
 
3.1.9 The effects of MLN0128 on the developing human fetus are unknown.  For this reason 
and because mTOR inhibitors as well as other therapeutic agents (bevacizumab) used in 
this trial are known to be teratogenic, women of child-bearing potential and men must 
agree to use adequate contraception (hormonal or barrier method of birth control; 
abstinence) prior to study entry, the duration of study participation and 6 months after 
completion of MLN 0128 or bevacizumab administration.  Should a woman become 
pregnant or suspect she is pregnant while she or her partner is participating in this study, 
she should inform her treating physician immediately.  Men treated or enrolled on this 
protocol must also agree to use adequate contraception prior to the study, for the duration 
of study participation, and 6 months after completion of MLN0128 or bevacizumab 
administration. 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
25 
3.1.10 Patients must have no concurrent malignancy except curatively treated basal or squamous 
cell carcinoma of the skin or carcinoma in situ of the cervix, breast, or bladder.  Patients 
with prior malignancies must be disease-free for  three years prior to registration. 
 
3.1.11 Solid tumor patients must be off corticosteroids prior to registration. If GBM patient is 
receiving corticosteroids, patient must be on a stable or decreasing dose of corticosteroids 
for at least 5 days prior to baseline MRI or CT.  If steroids are added or the steroids dose 
is increased between the date of the screening MRI or CT and the start of treatment, a 
new baseline MRI or CT is required. 
 
3.1.12 Patients must be able to swallow whole capsules. 
 
3.1.13 Ability to understand and the willingness to sign a written informed consent document. 
 
3.1.14 For Stage 2 GBM participants, a block of paraffin embedded tissue or 30 unstained slides 
at standard 4-5 um thickness from any prior surgery demonstrating GBM pathology must 
be available for submission. 
 
3.1.15 Stage 2 endometrial and ovarian cancer patients must have at least one lesion amenable to 
biopsy. This determination will be made by a member of the interventional radiology 
team or surgical associate investigator and an associate investigator. This requirement is 
not necessary for patients in stage 1. 
 
3.1.16  Solid tumor patients in stage 2 must have a diagnosis of papillary serous, endometrioid 
or clear cell endometrial carcinoma or, high grade serous, clear cell, endometrioid or 
mucinous ovarian, fallopian or primary peritoneal carcinoma. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
26 
3.2 
Eligibility Exclusion Criteria 
 
3.2.1 Concurrent administration of any other investigational agents. 
 
3.2.2 History of allergic reactions attributed to compounds of similar chemical or biologic 
composition to MLN0128 or bevacizumab. The MLN0128 or Bevacizumab Investigator 
Brochure can be referenced for more information. 
 
3.2.3 For all Stage 2 participants, no prior treatment with mTOR, PI3 kinase or Akt inhibitors. 
Prior treatment with mTOR, PI3 kinase or Akt inhibitors allowed in Stage 1 only.  
 
3.2.4 For Stage 2 GBM participants, no prior treatment with bevacizumab/VEGFR inhibitors. 
Prior treatment with bevacizumab/VEGFR inhibitors is allowed in Stage 1 for all 
participants, as well as Stage 2 endometrial and ovarian cancer participants. 
 
3.2.5 Stage 1 solid tumor and stage 2 endometrial and ovarian cancer participants with known 
CNS metastatic lesions which are symptomatic and/or growing. Patients previously 
treated for these conditions that are asymptomatic in the absence of corticosteroid therapy 
are allowed to enroll. Brain metastasis must be stable for 1 month with verification by 
imaging (brain MRI completed at screening demonstrating no current evidence of 
progressive brain metastases). CNS imaging will not be mandated for asymptomatic 
patients with no history of CNS metastases. 
 
3.2.6 Concurrent use of enzyme-inducing anti-epileptic drugs (EIAED). Patients may be on 
non-enzyme inducing anti-epileptic drugs or not be taking any anti-epileptic drugs. 
Patients previously treated with EIAED may be enrolled if they have been off the EIAED 
for 10 days or more prior to the first dose of MLN0128. (see Section 5.3, Prohibited 
Medication During Study). 
 
3.2.7 Subjects taking strong CYP3A4 and CYP2C19 inhibitors and/or inducers should be 
considered with caution. Alternative treatments that are less likely to affect MLN0128 
metabolism, if available, should be considered. If a subject requires treatment with 1 or 
more of the strong CYP3A4 and CYP2C19 inhibitors and/or inducers, the Principal 
Investigator should be consulted. Examples of the strong CYP3A4 and CYP2C19 
inhibitors and inducers included in Appendix C).   
 
3.2.8 Concurrent use of herbal supplements and other non-traditional medications.  All herbal 
supplements and other non-traditional medications must be stopped before time of 
registration.  
 
3.2.9 Concurrent use of anti-coagulants (warfarin, etc.) other than low-molecular weight 
heparin (LMWH). Medication must be stopped before time of registration. If patient has 
recently been on anti-coagulants other than LMWH, patient must have INR ≤ 2.  
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
27 
3.2.10 Evidence of any significant intracranial hemorrhage, as determined by the treating 
investigator, within 6 weeks from registration or as seen on most recent MRI prior to 
screening/baseline MRI.  
 
3.2.11 Uncontrolled intercurrent illness including, but not limited to, ongoing or active infection, 
symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, or 
psychiatric illness/social situations that would limit compliance with study requirements, 
are ineligible.  
 
3.2.12 History of any of the following within 6 months prior to start of MLN0128: 
 
• Left ventricular ejection fraction (LVEF) ≤ 55 % as determined by MUGA scan or 
ECHO 
• Heart failure ≥ NYHA grade 3 
• Significant ST depression of ≥ 1.5 mm in 2 or more leads and/or T wave inversions in 
≥ 2 leads 
• Complete left bundle branch block 
• Right bundle branch block + left anterior hemiblock (bi-fascicular block) 
• Congenital long QT syndrome 
• QTcF > 450 msec on screening ECG 
• Requirement of inotropic support (excluding digoxin) 
• History or presence of clinically significant ventricular or atrial tachyarrhythmias, or 
cardiac arrest 
• Clinically significant resting bradycardia 
• Presence of unstable atrial fibrillation (ventricular response >100 beats per minute). 
• Patients with stable atrial fibrillation are allowed in the study provided they do not 
meet the other cardiac exclusion criteria 
• History of arrhythmia requiring an implantable cardiac defibrillator 
• Angina pectoris ≤ 12 months prior to starting drug 
• Acute myocardial infarction ≤ 12 months prior to starting drug 
• Any valve disease CTCAE grade 
• Ischemic myocardial event including angina requiring therapy and artery 
revascularization procedures 
• Placement of a pacemaker for control of rhythm 
• Pulmonary embolism 
• Ischemic cerebrovascular event, including TIA and artery revascularization 
procedures 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
28 
 
3.2.13 Impairment of gastrointestinal (GI) function or GI disease that may significantly alter the 
absorption of oral MLN0128 (e.g., ulcerative diseases, uncontrolled nausea, vomiting, 
diarrhea, malabsorption syndrome, small bowel resection that requires nutritional 
support). 
 
3.2.14 Use of hematopoietic colony-stimulating growth factors (e.g. G-CSF, GMCSF, M-CSF) 
≤ 2 weeks prior to starting study drug. Erythropoietin, darbepoetin and Erythropoietin-
biosimilars are allowed for as long as they have been initiated at least 2 weeks prior to 
study enrollment. 
 
3.2.15 Pregnant or nursing women. MLN0128 has potential for teratogenic or abortifacients 
effects.  Because there is an unknown but potential risk for adverse events in nursing 
infants secondary to treatment of the mother with MLN0128, breastfeeding should be 
discontinued if the mother is treated with MLN0128. 
 
3.2.16 HIV-positive patients on combination antiretroviral therapy are ineligible because of the 
potential for pharmacokinetic interactions with MLN0128. In addition, these patients are 
at increased risk of lethal infections when treated with marrow-suppressive therapy. If an 
HIV-positive patient has adequate CD4 counts (CD4 above the lower limit of institutional 
normal) and is on antiretroviral therapy with newer agents, which are not strong CYP 
inhibitors (see Appendix C), they will be eligible.  
 
3.2.17  Uncontrolled high blood pressure (i.e., systolic blood pressure > 160 mmHg, diastolic       
blood pressure > 90mmHg) 
 
3.2.18  Pulmonary hypertension 
 
3.2.19  Uncontrolled asthma or O2 saturation < 90% by ABG (arterial blood gas) analysis or   
pulse oximetry on room air 
 
3.2.20   Participants with poorly controlled diabetes mellitus (defined as HbA1c >7%); subjects 
with a history of transient glucose intolerance due to corticosteroid administration are 
allowed in this study if all other inclusion/exclusion criteria are met. 
 
3.2.21 
Urine protein should be screened by urinalysis. If protein is 2+ or higher, 24 hour  
urine protein should be obtained and the level should be <1000mg for patient enrollment.  
 
3.2.22 
Serious or non-healing wound, ulcer or bone fracture. 
 
3.2.23 
History of abdominal fistula, gastrointestinal perforation, or intra-abdominal abscess 
within 6 months prior to day 1. 
 
3.2.24 
 Invasive procedures defined as follows: 
• Major surgical procedure, open biopsy or significant traumatic injury within 28 
days prior to day 1 therapy. 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
29 
• Anticipation of need for major surgical procedures during the course of the study. 
• Core biopsy within 7 days prior to day 1 therapy 
 
3.2.25 
Significant vascular disease (e.g. aortic aneurysm requiring surgical repair or recent 
peripheral arterial thrombosis) within 6 months prior to day 1. 
 
3.2.26 
Evidence of bleeding diathesis or coagulopathy. 
 
3.2.27 
 Patients with known hypersensitivity to Chinese Hamster ovary cell products or other 
recombinant human antibodies. 
 
 
3.3 
Inclusion of Women and Minorities 
 
Both men and women of all races and ethnic groups are eligible for this trial. 
 
 
4. 
REGISTRATION PROCEDURES 
 
4.1 
General Guidelines 
 
Eligible patients will be entered on study centrally at the Dana-Farber Cancer Institute by the 
Data Manager.  All sites should call the Data Manager, Katrina Smith at 617-632-3780 to verify 
dose level availabilities. Following registration, patients should begin protocol treatment within 5 
days.  Issues that would cause treatment delays should be discussed with the Principal 
Investigator, Dr. Lakshmi Nayak.  If a patient does not receive protocol therapy following 
registration, the patient’s registration on the study may be canceled.  The Coordinating Center 
should be notified of cancellations as soon as possible. 
 
4.2 
Registration Process 
 
To register patients onto this study please refer to Appendix D, Data and Safety Monitoring Plan 
(DSMP) Section 3.7.  
 
 
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. 
 
Stage 1: Dose escalation to estimate MTD/RP2D. 
Approximately 12-18 patients with advanced solid tumors including recurrent GBM will be 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
30 
enrolled using a standard 3+3 design, including 3-6 patients in each cohort. Patients will start at 
dose level 1, 3mg oral daily dosing of MLN0128 based on the MTD from a prior phase I study of 
single agent MLN012855. MTD will be defined as the highest dose at which <2/6 patients will 
experience a DLT. The dose of bevacizumab will be 10mg/kg every 2 weeks. 
 
Note: A pilot study evaluating perioperative MLN0128 dosing in recurrent GBM patients (NCI 
9546) will be ongoing to determine the optimal dosing for brain penetration. If that study 
determines that once-weekly dosing of MLN0128 leads to better CNS penetration among GBM 
patients, then the current study will be amended accordingly to include a separate dose escalation 
schema of weekly MLN0128 and bevacizumab among recurrent GBM patients. 
 
Table 5.1 
 
Stage 1 Dose Escalation Schedule 
Dose Level 
Dose 
 
MLN0128 
 
 
Bevacizumab 
 
Level -1 
3mg oral, daily for 5 
of 7 days 
10mg/kg intravenously, every 2 weeks 
Level 1* 
3mg oral, daily 
10mg/kg intravenously, every 2 weeks 
Level 1a** 
4mg oral, daily for 5 
of 7 days 
10mg/kg intravenously, every 2 weeks 
Level 2 
4mg oral, daily 
10mg/kg intravenously, every 2 weeks 
Level 3  
5mg oral, daily 
10mg/kg intravenously, every 2 weeks 
*Starting dose level 
**Enrollment will begin at Level 1 and then proceed to Level 2, if there are DLTs at Level 2 
then enrollment will proceed on Level 1a as defined in Section 6.2.  
 
Stage 2: Expansion cohort at MTD.  
After the MTD/RP2D is determined, up to 30 patients with ovarian and endometrial cancer, and 
10 patients with recurrent GBM will be enrolled and treated at the MTD/RP2D to: 1) better 
characterize the safety profile of MLN0128; 2) estimate plasma and CSF concentrations of 
MLN0128 when administered with and without bevacizumab; and 3) evaluate the 
pharmacodynamic properties of MLN0128 in tumor tissue and plasma.  
 
5.1.1 CTEP IND Agent: MLN0128 
 
MLN0128 is an oral drug. MLN0128 will be administered orally once (unless enrolled in 
dose level -1 or 1a as described above) in the morning after a light meal at approximately 
the same time of day.  MLN0128 may be taken later on particular clinic days, in order to 
accommodate for research related testing.  MLN0128 capsules should be swallowed with 
water without chewing or sucking the capsule. Capsules should not be opened. If the 
subject chews or sucks the capsule by error, the subject should drink a large glass of 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
31 
water (~8 oz.). 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 with a meal (subjects should not take 
2 consecutive daily doses within 12 hours of each other).  If subject misses a scheduled 
dose more than 12 hours following regular dosing time, the dose should be noted as 
missed in the pill diary (missed doses should not be made up for the 5 of 7 days dosing in 
doses level -1 or 1a).  Subjects who vomit shortly after receiving MLN0128 will not 
receive a replacement dose.  If confirmed that the study drug has been vomited, the dose 
should be noted as having been missed. 
 
On days of scheduled pharmacokinetic sampling, the MLN0128 dose must be taken in 
the outpatient clinic (prior to bevacizumab administration), to allow for the post-dosing 
PK sample.  
 
Grapefruit and grapefruit juice should be avoided while participating in this protocol. 
 
Compliance 
The participant will be requested to maintain a medication diary of each dose of the oral 
medication, MLN0128. The medication diary will be returned to clinic staff at the end of 
each course. See Appendix E. 
 
5.1.2 Bevacizumab 
 
Patients will be treated with bevacizumab at 10mg/kg intravenously (IV) on days 1 and 
15 (+/- 2 days of each 28-day cycle with no less than 10 days between bevacizumab 
administrations), except for patients enrolled in stage 2 of the trial who will not receive 
bevacizumab on cycle 1 day 1, and will start treatment with bevacizumab on cycle 1 day 
15.  
 
The calculated dose of bevacizumab should be placed in 100 mL of 0.9% Sodium 
Chloride for injection. Administration will be as a continuous IV infusion. Anaphylaxis 
precautions should be observed during study drug administration. It is not necessary to 
correct dosing based on ideal weight. Actual body weight at each clinic visit prior to 
bevacizumab dosing (on Days 1 and 15 of each 28 day cycle) will be used to calculate the 
dose of bevacizumab.  
 
The initial dose will be delivered over 90 ± 15 minutes. If the first infusion is tolerated 
without infusion‐associated adverse events (fever and/or chills), the second infusion may 
be delivered over 60 ± 10 minutes. If the 60‐minute infusion is well tolerated, all 
subsequent infusions may be delivered over 30 ± 10 minutes. If a subject experiences an 
infusion–associated adverse event, he or she will be monitored according to institutional 
guidelines and may be pre‐medicated for the next study drug infusion. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
32 
Special Precautions/Safety Issues: 
 
Prior to each treatment, the patient should be carefully assessed with special attention to 
BP, proteinuria, bleeding and cardiovascular events, as well as symptoms or signs of 
bowel perforation and RPLS.  Decisions for retreatment or dose modification/interruption 
should follow the dose modification guidelines in Section 6.1. 
 
Patients who have an ongoing study agent-related SAE upon study completion or at 
discontinuation from the study will be contacted by the investigator or his/her designee 
periodically until the event is resolved or determined to be irreversible. 
 
Infusional reactions:  Routine premedication is not required for the first dose of 
bevacizumab.  If infusional reactions occur, acetaminophen, diphenhydramine, steroids, 
or other medications may be given for symptom control and for premedication as needed.  
Anaphylactic precautions should be observed during bevacizumab administration. 
 
Hypertension:   Patients should have BP monitored prior to each infusion of 
bevacizumab.  Hypertensive mediation should be initiated or increased for optimal BP 
control according to standard public heath guidelines. 
 
Proteinuria:  Proteinuria should be monitored by dipstick at least every 6 weeks.    
 
Surgery and wound complication issues and surgery:  The appropriate interval from 
discontinuation of bevacizumab to subsequent elective surgery required to reduce the risk 
of impaired wound healing has not been determined.  Decision on such an interval should 
take into consideration the half-life of bevacizumab.  It is generally recommended that 
bevacizumab should be discontinued at least 4-8 weeks prior to major elective surgery.  
In addition, bevacizumab should not be restarted until at least 4 weeks after major 
surgery provided that the wound has adequately healed; in cases of high risk procedures 
such as liver resection, thoracotomy, or neurosurgery, it is recommended that 
bevacizumab be resumed no earlier than 8 weeks after surgery. 
 
5.2 Definition of Dose-Limiting Toxicity 
 
Dose-limiting toxicity (DLT) is based on the CTEP Active Version of the NCI Common 
Terminology Criteria for Adverse Events (CTCAE Version 4.0). A DLT is defined as an adverse 
event (AE) or abnormal laboratory value assessed as possibly, probably or definitely related to 
MLN0128 and/or bevacizumab study therapy that occurs during the initial 28 days of therapy 
and meets any of the following criteria: 
 
• Grade 3 non-hematologic toxicity:  
o The following will not be considered dose limiting unless they persist despite 
maximal medical treatment for more than 3 days: grade 3 nausea/vomiting, 
electrolyte imbalance, hypertension, and hyperglycemia;  
o The following grade 3 laboratory abnormalities will not be considered dose 
limiting if they return to baseline within 7 days: bilirubin, AST, ALT, cholesterol 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
33 
high, hypertriglyceridemia, amylase, lipase and creatinine. 
• Grade 4 non-hematologic toxicity despite maximal medical therapy;  
• Grade ≥ 3 thrombocytopenia, febrile neutropenia (ANC < 1.0 X 109/L or 1000/mm3 
and a single temperature of > 38.3°C (101°F) or a sustained temperature of ≥ 38°C 
(100.4°F) for more than one hour) or Grade 4 neutropenia; 
• Any treatment related AEs that lead to treatment delays or skipped doses for more 
than 14 days would be considered a DLT. 
 
Investigators, together with the Overall PI, Dr. Lakshmi Nayak and CTEP, can declare a DLT if 
a patient is experiencing increasing toxicity at any time during treatment, and it becomes clear 
that it is not going to be possible to complete the treatment without exposing the patient to 
excessive risk.  
 
After MTD/RP2D  is determined and patients are accrued in Stage 2 of the study, if 2 or more 
patients in each dose-expansion cohort develop unacceptable toxicity defined as grade 4 or 5 
non-hematological toxicity or ≥grade 2 intracranial hemorrhage (in recurrent GBM patients), 
then further accrual to that cohort will be stopped and the next dose level down will be 
considered the MTD for that particular cohort. At that time, Dr. Lakshmi Nayak (the overall 
principal investigator) will discuss with CTEP and Millennium to determine if further accrual 
needs to occur to obtain additional information regarding toxicity. 
 
Whenever a patient experiences toxicity that fulfills criteria for DLT, treatment with the study 
regimen will be interrupted and the toxicity will be followed up as described in Section 6. For the 
purposes of dose escalation and determination of MTD, DLTs that occur during the initial 28 
days of therapy will be necessarily considered, including those in which the event started in the 
initial 28 days of therapy and the confirmation of DLT occurs in a subsequent cycle. 
 
NOTE: If a Stage 1 participant comes off active study treatment for a reason other than toxicity 
before receiving a full cycle (28 days) of therapy, s/he is not considered evaluable for 
determination of the MTD.  Therefore, although a Stage 1 participant who comes off active study 
treatment for a reason other than toxicity before receiving a full cycle (28 days) of therapy will 
typically be considered otherwise evaluable for study analysis purposes, an additional participant 
should be accrued to that cohort to replace him/her only in determination of the MTD.  
 
Rules for re-initiation and dose modifications of MLN0128 and bevacizumab are outlined in 
Section 6. 
 
Dose escalation will proceed according to the following: 
 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
34 
Table 5.2 
Number of Patients with DLT at a 
Given Dose Level 
Escalation Decision Rule 
0 out of 3 
Enter 3 patients at the next dose level. 
>2 
Dose escalation will be stopped.  This dose level will be 
declared the maximally administered dose (highest dose 
administered).  Three (3) additional patients will be 
entered at the next lowest dose level if only 3 patients 
were treated previously at that dose. 
1 out of 3 
Enter at least 3 more patients at this dose level. 
• If 0 of these 3 patients experience DLT, proceed to 
the next dose level. 
• If 1 or more of this group suffer DLT, then dose 
escalation is stopped, and this dose is declared the 
maximally administered dose.  Three (3) additional 
patients will be entered at the next lowest dose level 
if only 3 patients were treated previously at that dose. 
≤1 out of 6 at highest dose level 
below the maximally administered 
dose 
This is the recommended phase 2 dose. At least 6 
patients must be entered at the recommended phase 2 
dose. 
 
 
5.3 
General Concomitant Medication and Supportive Care Guidelines 
 
Prohibited Concomitant Medications During Study 
Oral administration of MLN0128 in humans has a low potential for metabolic and transporter-
based drug-drug interactions. Therefore, except for EIAED and herbal / non-traditional 
medication, the use of any concomitant medication/therapies deemed necessary for the care of 
the patient is allowed. 
 
Corticosteroids 
GBM patients may be on stable or decreasing dose of corticosteroids (no increase for 5 days) at 
the time of study entry. Solid tumor, including endometrial and ovarian, cancer patients with 
known CNS metastatic lesions must be stable off corticosteroid therapy.  
 
Antiemetics 
The use of any antiemetic deemed necessary for the care of the patient is allowed. 
 
Anticonvulsants 
Patients may not be on enzyme-inducing anti-epileptic drugs (EIAED); patients who require anti-
epileptic drugs (AED) may be on non-enzyme inducing anti-epileptic drugs (NEIAED). If a 
patient on this study protocol needs to have an AED started or needs to have a second AED 
added then only NEIAED should be used.  There must be a ≥ 10 day period from discontinuation 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
35 
of an EIAED and initiation of therapy.  In the event that an enzyme-inducing anti-epileptic drug 
must be used for a patient on study the patient will be removed from the protocol. 
 
 
Herbal and Non-Traditional Medications 
No data exist regarding the interaction of MLN0128 with commonly used herbal or non-
traditional medications. Patients should be instructed not to use such medications while receiving 
MLN0128 therapy. 
  
Strong CYP3A4/CYP2C19 Inducers/Inhibitors 
If a subject requires treatment with 1 or more of the strong CYP3A4 and CYP2C19 inhibitors 
and/or inducers, the Principal Investigator should be consulted  (see Appendix C).  There are no 
known strong specific CYP2C9 inhibitor or inducers.  Examples of moderate inhibitors 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.  
 
 
5.4 
Duration of Therapy 
 
In the absence of treatment delays due to adverse event(s), study treatment may continue for until 
one of the following criteria applies: 
 
• 
Disease progression (Section 11), 
 
• 
Intercurrent illness that prevents further administration of treatment, 
 
• 
Unacceptable adverse event(s), 
 
• 
Patient decides to withdraw from the study, or 
 
• 
General or specific changes in the patient's condition render the patient unacceptable 
for further treatment in the judgment of the investigator. 
 
5.5 
Duration of Follow Up 
 
Patients will be followed after removal from study treatment up until the 30-day follow-up 
contact or until death, whichever occurs first.  Patients removed from study for unacceptable 
adverse event(s) will be followed until resolution or stabilization of the adverse event. 
 
Once participants complete the 30-day follow-up period, they will be followed annually for 
survival via telephone or medical record follow-up until patient either passes away or is lost to 
follow-up.  Progression information will be collected for those participants who do not progress 
while on study treatment. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
36 
5.6 
Criteria for Removal from Study 
 
Patients will be removed from study when any of the criteria listed in Section 5.4 applies.  The 
reason for study removal and the date the patient was removed must be documented in the Case 
Report Form. 
 
In the event of unusual or life-threatening complications, participating investigators must 
immediately notify the Principal Investigator, Dr. Lakshmi Nayak, at 617-632-2166 within 24 
hours when possible. 
 
 
 
6. 
DOSING DELAYS/DOSE MODIFICATIONS 
 
6.1 
Bevacizumab  
No dose modifications of bevacizumab are permitted. Bevacizumab dose will be based on actual 
weight at each clinic visit prior to bevacizumab administration on Days 1 and 15 (+/- 2 days) of 
each 28 day cycle. If adverse events occur that require holding bevacizumab, the dose will 
remain the same once treatment resumes. Patients who require bevacizumab discontinuation are 
permitted to continue to receive study treatment with MLN0128 alone. 
Any toxicities deemed at least possibly related to bevacizumab treatment should be managed 
according to Table 6.1. Bevacizumab has a terminal half-life of 2 to 3 weeks; therefore, its 
discontinuation results in slow elimination over several months. There is no available antidote 
for bevacizumab.  
Subjects should be assessed clinically for toxicity prior to, during, and after each infusion. If 
unmanageable toxicity occurs because of bevacizumab at any time during the study, treatment 
with bevacizumab should be discontinued.  
Infusion Reaction: Infusion of bevacizumab should be interrupted for subjects who develop 
dyspnea or clinically significant hypotension. Subjects who experience a NCI CTCAE v. 4.0 
Grade 3 or 4 allergic reaction / hypersensitivity, adult respiratory distress syndrome, or 
bronchospasm (regardless of grade) will be discontinued from bevacizumab treatment. 
The infusion should be slowed to 50% or less or interrupted for subjects who experience any 
infusion-associated symptoms not specified above. When the subject’s symptoms have 
completely resolved, the infusion may be continued at no more than 50% of the rate prior to the 
reaction and increased in 50% increments every 30 minutes if well tolerated. Infusions may be 
restarted at the full rate during the next cycle.  
Adverse events requiring delays or permanent discontinuation of bevacizumab are listed in Table 
6.1  
Patients who require discontinuation of study bevacizumab therapy due to toxicity will be 
allowed to continue to receive MLN0128 study therapy unless criteria specified in Section 5.4 
are met. The maximum length of bevacizumab interruption is 28 days.  
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
37 
Table 6.1: Bevacizumab Dose Management Due to Adverse Events 
 
Treatment Modification for Bevacizumab-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Allergic reactions  
Or  
Infusion-related 
reactions 
Or  
Anaphylaxis 
Grade 1-2  
• Infusion of bevacizumab should be interrupted for 
subjects who develop dyspnea or clinically significant 
hypotension.  
• For infusion-associated symptoms not specified above, 
infusion should be slowed to 50% or less or interrupted.  
Upon complete resolution of the symptoms, infusion may 
be continued at no more than 50% of the rate prior to the 
reaction and increased in 50% increments every 30 
minutes if well tolerated.  Infusions may be restarted at 
the full rate during the next cycle.  
• Subjects who experience bronchospasm (regardless of 
grade) should discontinue bevacizumab. 
Grade 3-4 
Discontinue bevacizumab 
Thromboembolic 
Event (Arterial), 
arterial  ischemia  
- Cardiac ischemia 
- Myocardial  
infraction 
- CNS ischemia 
(TIA, CVA) 
- Any peripheral or 
visceral arterial 
ischemia/thrombo
sis 
Grade 2 (new or 
worsening since 
bevacizumab) 
Discontinue bevacizumab. 
Grade 3-4 
Discontinue bevacizumab 
Thromboembolic 
Event (Venous) 
 
 
[Note:  Patients with primary lung cancer requiring therapeutic anticoagulation 
should discontinue bevacizumab] 
Grade 3 
OR 
asymptomatic 
Grade 4 
▪ Hold bevacizumab treatment.  If the planned duration of 
full-dose anticoagulation is <2 weeks, bevacizumab 
should be held until the full-dose anticoagulation period is 
over. 
▪ If the planned duration of full-dose anticoagulation is >2 
weeks, bevacizumab may be resumed during full-dose 
anticoagulation IF all of the criteria below are met: 
- The subject must not have pathological conditions 
that carry high risk of bleeding (e.g. tumor involving 
major vessels or other conditions) 
- The subject must not have had hemorrhagic events 
while on study 
- The subject must be on stable dose of heparin or have 
an in-range INR (usually 2-3) on a stable dose of 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
38 
Treatment Modification for Bevacizumab-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
warfarin prior to restarting bevacizumab. 
▪ If thromboemboli worsen/recur upon resumption of study 
therapy, discontinue bevacizumab 
Grade 4 
(symptomatic) 
Discontinue bevacizumab 
Hypertension 
[Treat with anti-hypertensive medication as needed.  The goal of BP control 
should be consistent with general medical practice] 
Grade 1 
(SBP 120-139 
mmHg or DBP 
80-89 mmHg) 
Consider increased BP monitoring; start anti-hypertensive 
medication if appropriate 
Grade 2 
asymptomatic 
(SBP 140-159 
mmHg or DBP 
90-99 mmHg) 
Start or adjust anti-hypertensive therapy and continue 
bevacizumab 
• Grade 2 
symptomatic 
(SBP 140-159 
mmHg or DBP 
90-99 mm Hg) 
• Grade 3 
(SBP >160 
mmHg or 
DBP >100 
mmHg) 
• Start or adjust anti-hypertensive medication 
• Hold bevacizumab until symptoms resolve AND BP < 
160/90mmHg 
• For hypertension that is refractory requiring delay of 
bevacizumab for > 4 weeks, discontinue bevacizumab  
 
 
Grade 4  
(Hypertensive 
crisis or 
malignant 
hypertension) 
Discontinue bevacizumab 
Heart Failure  
OR 
Left Ventricular 
(LV) dysfunction 
• Heart failure 
>Grade 2 
• LV dysfunction 
>Grade 3 
Discontinue bevacizumab 
Proteinuria 
Proteinuria will be 
monitored by urine 
analysis dipstick. If 
Dipstick >2+ 
proteinuria, 24-hour 
urine protein should 
Dipstick > 2+ 
Hold bevacizumab and obtain 24 hour urine protein 
If 24-h urine 
protein <2g 
Continue bevacizumab 
If 24-h urine 
protein >2 g 
• Hold bevacizumab until 24-hour urine protein <2.0 g   
• Discontinue bevacizumab if urine protein does not 
recover to < 2.0 g after 28 days of bevacizumab 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
39 
Treatment Modification for Bevacizumab-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
be obtained 
interruption 
Nephrotic 
syndrome 
Discontinue bevacizumab. 
Hemorrhage 
(intracranial or 
pulmonary)  
Grade 2-4 
• Discontinue bevacizumab 
Grade 1 
• Patients receiving full-dose anticoagulation should 
discontinue bevacizumab. 
• For patients not on full-dose anticoagulation, hold 
bevacizumab until ALL of the following criteria are met: 
- the bleeding has resolved and hemoglobin is stable 
- there is no bleeding diathesis that would increase the 
risk of therapy 
• there is no anatomic or pathologic condition that could 
increase the risk of hemorrhage recurrence 
Hemorrhage (not 
CNS or pulmonary) 
Grade 3  
 
• Patients receiving full-dose anticoagulation should 
discontinue bevacizumab. 
• For patients not on full-dose anticoagulation, hold 
bevacizumab until ALL of the following criteria are met: 
- the bleeding has resolved and hemoglobin is stable 
- there is no bleeding diathesis that would increase the 
risk of therapy 
- there is no anatomic or pathologic condition that 
could increase the risk of hemorrhage recurrence. 
• Patients who experience recurrence of grade 3 
hemorrhage should discontinue study therapy. 
Grade 4 
Discontinue bevacizumab 
RPLS (Reversible 
Posterior 
Leukoencephalopathy 
syndrome  
OR 
PRES (Posterior 
Reversible 
Encephalopathy 
Syndrome) 
Any Grade 
Discontinue bevacizumab upon diagnosis of RPLS/PRES.   
Wound dehiscence 
OR 
 Wound 
complications  
Grade 2 
Hold bevacizumab until healing  
Grade 3-4 
Discontinue bevacizumab 
Perforation (GI, or 
any other organ) 
Any Grade 
Discontinue bevacizumab 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
40 
Treatment Modification for Bevacizumab-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Fistula (GI, 
pulmonary or any 
other organ) 
Any Grade 
Discontinue bevacizumab 
Obstruction of GI 
tract 
Grade 2 
requiring 
medical 
intervention 
Hold bevacizumab until complete resolution  
 
Grade 3-4 
• Hold bevacizumab until complete resolution 
• If surgery is required, patient may restart bevacizumab 
after 28 days and full recovery from surgery, and at 
investigator’s discretion 
Other Unspecified 
bevacizumab-related 
AEs (except 
controlled 
nausea/vomiting). 
Grade 3 
• Hold bevacizumab until symptoms resolve to<Grade 1 
Grade 4 
• Discontinue bevacizumab 
• Upon consultation with the study chair, resumption of 
bevacizumab may be considered if a patient is benefiting 
from therapy, and the Grade 4 toxicity is transient, has 
recovered to <Grade 1 and unlikely to recur with 
retreatment. 
 
Note 1:  There will be no dose reduction for bevacizumab.  Treatment should be interrupted or 
discontinued for certain adverse events, as described below 
 
Note 2:  If bevacizumab is interrupted for ANY reasons for >4 weeks (unless otherwise 
specified), the patient should discontinue bevacizumab therapy on protocol. 
 
 
6.2 
MLN0128 
 
For patients who do not tolerate the protocol-specified dosing schedule of MLN0128, dose 
adjustments are permitted in order to allow the patient to continue study treatment. Patients who 
require MLN0128 discontinuation due to toxicity, will be permanently discontinued from study 
treatment.  
 
All dose modifications should be based on the worst preceding toxicity (CTCAE version 4.0). 
Dose modification of MLN0128 and/or withholding of bevacizumab will be made when toxicity 
is considered to be at least possibly related to the study drug. Once a dose has been reduced it 
will not be increased at a later time even if there is no toxicity. Adverse events (AEs) should be 
treated with the appropriate maximum supportive care. 
 
Before the start of each cycle or for any AE requiring study therapy interruption or modification, 
drug-related toxicities must resolve to either baseline or grade 1. If a patient requires a dose 
delay of > 28 days from the intended day of the next scheduled dose, , then the patient should be 
discontinued from the study treatment. In exceptional situations, if the patient is clearly 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
41 
benefiting from study drug treatment (i.e. stable disease, partial or complete response), and in the 
opinion of the investigator no safety concerns are present, continuation of study treatment must 
be discussed with the overall PI and the CTEP.  Patients who require dose modification below 
dose level -1 (3mg/day for 5 days out of 7) will be discontinued from study therapy.  
 
The MLN0128 dose should be reduced by one dose level* for subsequent therapy if the 
investigator determines that it is in the best interest of the patient or if the patient experienced at 
least one of the following events: 
a. DLT (as defined in section 5.2) 
b. DLT equivalent toxicity (cycle 2 or beyond) 
c. Greater than 14 day delay to meet re-treatment criteria  
 
*Note: Patients on dose level 2 will drop to dose level 1a if they meet any of the above 
criteria. 
 
Additional toxicity-specific dose interruption and modification guidelines are provided below in 
table 6.2: 
 
Table 6.2 MLN0128 Dose Management Due to Adverse Events 
 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
CARDIAC 
Cardiac general – Left 
ventricular systolic 
dysfunction (ejection 
fraction decrease) 
Grade 2 
asymptomatic, 
resting ejection 
fraction 40-50%; 
or 10-19% drop 
from baseline 
Maintain dose level of MLN0128 
Repeat LVEF within 4 weeks or as clinically 
appropriate 
Grade 3: 
symptomatic 
responsive to 
intervention, 
ejection fraction 
39-20% or > 20% 
drop from baseline 
Omit MLN0128 dose until resolved* to normal values,  
• If resolved in ≤ 7 days, maintain at same dose 
level of MLN0128 
• LVEF measurement to be repeated, if resolved 
* to normal values within>7 days,  resume at ↓1 
dose level of MLN0128. 
*the event is considered resolved when the patient is 
asymptomatic, has a resting ejection fraction ≥ 40% 
and ≤ 20% from baseline 
Grade 4: refractory 
or poorly 
controlled, ejection 
fraction < 20% 
Permanently discontinue patient from the study 
treatment  
 
QTc prolongation 
≥ Grade 3 or > 
60ms change from 
baseline on at least 
First Occurrence: 
• Omit MLN0128 dose  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
42 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
two separate ECGs 
• Perform an analysis of serum potassium and 
mangesium, and if below lower limit of normal, 
correct with supplements to within normal 
limits. Concomitant medication usage must be 
reviewed.  
• Perform a repeat ECG within one hour of the 
first QTcF of 500 ms  
• If QTcF remains > 500 ms, repeat ECG as 
clinically indicated, but at least once a day until 
the QTcF returns to < 480 ms. Seek cardiologist 
input  
• Once QTcF prolongation has resolved, 
MLN0128 may be restarted at a one lower dose 
level  
Second Occurrence: 
Permanently discontinue patient from the study 
treatment 
Other Cardiac Events 
Grade 1-2 
Maintain dose level of MLN0128 
Grade 3 
Omit dose of MLN0128 until resolved to ≤ Grade 1 
within 7 days, then resume at same dose level of 
MLN0128. If resolved in >7 days, resume at ↓1 dose 
level of MLN0128. 
Grade 4 
Permanently discontinue patient from the study 
treatment 
 
 
ENDOCRINE 
Fasting Plasma 
Glucose (FPG)  
(2 hrs fasting) 
Grade 1 
Maintain dose level of MLN0128, check FPG every 
week 
• Initiate or intensify with appropriate anti-
diabetic treatment as per investigator’s 
discretion 
• Instruct patient to follow dietary guidelines 
according to local and/or institutional standards 
for management of diabetes mellitus (such as 
those provided by the American Diabetes 
Association) during the study 
• Consider use of oral anti-hyperglycemic therapy 
such as metformin  
Check FGP weekly for 8 weeks, then continue 
checking at least every 2 weeks 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
43 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Grade 2 
First Occurrence: 
 
If signs or symptoms of hyperglycemia (for example, 
mental status changes, excessive thirst, polyuria), omit 
dose of MLN0128 immediately and manage as for 
Grade 3 hyperglycemia (below) 
 
If asymptomatic, maintain MLN0128 dose and re-
check FPG within 24 hours. If grade worsens or 
improves then follow specific grade recommendations. 
 
If FPG remains at Grade 2: 
• Maintain dose level of MLN0128 
• Initiate or intensify with appropriate anti-
diabetic treatment  
• Instruct patient to follow dietary guidelines 
according to local and/or institutional standards 
for management of diabetes mellitus (such as 
those provided by the American Diabetes 
Association) during the study 
• Consider use of oral anti-hyperglycemic 
therapy such as metformin 
 
If FPG does not resolve to ≤ Grade 1 within 7 days 
after initiation/intensifying anti-diabetic treatment: 
• Omit dose of MLN0128 if not already done 
• Monitor FPG at least weekly until FPG resolves 
to ≤ Grade 1  
• Then re-start MLN0128 and ↓1 dose level  
• Continue with anti-diabetic treatment  
• Check FPG weekly for 8 weeks, then continue 
checking every 2 weeks  
 
Second Occurrence:  
 
Maintain dose level of MLN0128, re-check FPG within 
24 hours. If grade worsens or improves then follow 
specific grade recommendations.  
 
If FPG remains at Grade 2: 
• Omit dose of MLN0128 
• Initiate or intensify with appropriate anti-
diabetic treatment 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
44 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
• Monitor FPG at least twice weekly until FPG 
resolves to ≤ Grade 1  
• Then re-start MLN0128 and ↓1 dose level  
• Continue with anti-diabetic treatment 
Check FPG at least weekly for 8 weeks, then continue 
checking at least every 2 weeks 
Grade 3 
Immediately omit MLN0128, initiate or intensify 
medication with appropriate anti-diabetic treatment, re-
check FPG within 24 hours. If grade worsens or 
improves then follow specific grade recommendations.  
 
If FPG remains at Grade 3: 
• Administer intravenous hydration and 
intervention for 
electrolyte/ketoacidosis/hyperosmolar 
disturbances as clinically appropriate 
• Continue to omit dose of MLN0128 
• Monitor FPG at least twice weekly until FPG 
resolves to ≤ Grade 1 
• If FPG resolves to ≤ Grade 1 in 7 days or less, 
then re-start MLN0128 at the same dose level 
If FPG remains greater than Grade 1 severity for more 
than 7 days, then discontinue patient from study 
treatment: 
• Initiate or continue anti-diabetic treatment as 
appropriate  
• Instruct patient to follow dietary guidelines 
according to local and/or institutional standards 
for management of diabetes mellitus (such as 
those provided by the American Diabetes 
Association) during the study  
• Consider use of oral anti-hyperglycemic therapy 
such as metformin  
• Check FPG at least weekly for 8 weeks, then 
continue checking at least every 2 weeks 
 
For non-fasting plasma glucose >250-500mg/dL (> 
13.9 – 27.8 mmol/L) accompanied by signs/symptoms 
of hyperglycemia (for example, mental status changes, 
excessive thirst, polyuria), or presence of blood or urine 
ketones, omit MLN0128 and follow guidance for 
management of Grade 3 fasting plasma glucose (FPG). 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
45 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Grade 4 
Immediately omit dose of MLN0128, initiate or 
intensify medication with appropriate anti-diabetic 
treatment, re-check within 24 hours, if confirmed 
Grade 4: 
• Administer intravenous hydration and 
intervention for 
electrolyte/ketoacidosis/hyperosmolar 
disturbances as clinically appropriate 
• Discontinue patient from the study. Instruct 
patient to follow dietary guidelines according to 
local and/or institutional standards for 
management of diabetes mellitus (such as those 
provided by the American Diabetes 
Association) during the study 
• Consider use of oral anti-hyperglycemic therapy 
such as metformin  
• Check FPG weekly for 8 weeks, then continue 
checking at least every 2 weeks if clinically 
indicated 
For non-fasting plasma glucose >500 mg/dL (> 27.8 
mmol/L) accompanied by signs/symptoms of 
hyperglycemia (for example, mental status changes, 
excessive thirst, polyuria), or presence of blood or urine 
ketones, discontinue MLN0128 and following guidance 
for management of Grade 4 fasting plasma glucose 
(FPG). 
 
GASTROINTESTINAL 
Mucositis oral 
Grade 1 
Maintain MLN0128 dose level 
Grade 2 
Maintain MLN0128 dose level if tolerable, if toxicity 
becomes intolerable omit dose of MLN0128 until 
resolved to Grade < 1, then restart at the same dose 
level  
Grade 3 
Omit dose of MLN0128 until resolved to Grade < 1, 
then restart at ↓1 dose level of MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
GENERAL DISORDERS 
Fatigue (asthenia) 
Grade 1-2 
Maintain MLN0128 dose level 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
46 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Grade 3 
Omit dose of MLN0128 until resolved to ≤ Grade 1, 
then:  
• If resolved in ≤ 7 days, maintain dose level of 
MLN0128 
• If resolved in > 7 days, ↓ 1 dose level of 
MLN0128 
 
Grade 4 
Omit dose of MLN0128 and discontinue patient from 
the study treatment 
HEMATOLOGIC 
Neutropenia (ANC) 
Grade 1-2  
Maintain dose level of MLN0128 
Grade 3 
Omit dose of MLN0128 until resolved to < Grade 1 or 
baseline, then: 
• If resolved in < 7 days, maintain dose level of 
MLN0128 
• If resolved in > 7 days, resume treatment at ↓1 
dose level of MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
Febrile Neutropenia 
Grade 3 
Omit dose of MLN0128 until resolved to Grade 1 or 
baseline, then: 
• If resolved in < 7 days, resume treatment at ↓1 
dose level of MLN0128 
• If resolved in > 7 days, discontinue MLN0128  
Thrombocytopenia 
 
 
Grade 1-2 
Maintain dose level of MLN0128 
Grade 3 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline then:  
• If resolved in ≤ 7 days, resume treatment at ↓ 1 
dose level of MLN0128 
• If resolved in > 7 days, discontinue MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
HEPATIC 
Bilirubin 
Grade 1 
 
Maintain dose level of MLN0128 
Grade 2 (with ALT 
or AST grade 1 or 
2) 
Omit dose of MLN0128 until resolved to < Grade 1 or 
baseline, then resume at the same dose level of 
MLN0128 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
47 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Grade 3 (with ALT 
or AST grade 1 or 
2) 
 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline, then:  
• If resolved in ≤ 7 days, maintain same dose 
level of MLN0128 
• If resolved in > 7 days, resume treatment at ↓ 1 
dose level of MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
AST or ALT 
Grade 1 or Grade 2 
(without total 
bilirubin elevation 
> grade 1) 
Maintain dose level of MLN0128 
Grade 3 (without 
total bilirubin 
elevation > grade 
1) 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline, then:  
• If resolved in ≤ 7 days, maintain dose level of 
MLN0128 
• If resolved in > 7 days, resume treatment at ↓1 
dose level of MLN0128 
Grade 4 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline, then resume at ↓1 dose level 
 
 
INVESTIGATIONS 
Cholesterol high 
and/or 
hypertriglyceridemia 
Grade 1 
Maintain MLN0128 dose level 
Grade 2 
Maintain dose if tolerable, if toxicity becomes 
intolerable, omit dose MLN0128 until resolved to < 1, 
then restart MLN0128 as the same dose level 
Grade 3 
Omit dose of MLN0128 until resolved to Grade  < 1, 
then restart at ↓1 dose level of MLN0128 
 
Grade 4 
 
Permanently discontinue patient from the study 
treatment 
PANCREATIC 
Amylase or Lipase  
Grade 1-2 
Maintain dose level of MLN0128 
Grade 3 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline, then:  
• If resolved in ≤ 7 days, maintain dose level of 
MLN0128 
• If resolved in > 7 days, resume treatment at ↓1 
dose level of MLN0128 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
48 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
Grade 4 
Permanently discontinue patient from the study 
treatment 
RENAL 
Serum Creatinine 
Grade 1 
Maintain dose level of MLN0128 
Grade 2 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline, then resume treatment at the same dose level. 
Patients will be instructed to increase their fluid intake 
until resolution to ≤ Grade 1 or baseline. 
Grade 3 
Omit dose of MLN0128 until resolved to ≤ Grade 1 or 
baseline then:  
• If resolved in ≤ 7 days, maintain dose level of 
MLN0128 
• If resolved in > 7 days, resume treatment at ↓ 1 
dose level of MLN0128 
RESPIRATORY 
Non-infectious 
Pneumonitis 
Grade 1 
Maintain dose level of MLN0128 
Grade 2 
Omit dose of MLN0128 until resolved to Grade < 1, 
then: 
• Restart at ↓1 dose level of MLN0128 
• Discontinue MLN0128 if failure to recover 
within 4 weeks 
Grade 3 
Omit dose of MLN0128 until resolved to Grade < 1, 
then: 
• Consider re-initiating MLN0128 at ↓1 dose 
level of MLN0128 
• If toxicity recurs at Grade 3, discontinue 
MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
Rash (maculo-papular) Grade 1 
Maintain dose level of MLN0128. Consider to initiate 
appropriate skin toxicity therapy (such as 
antihistamines, topical corticosteroids) 
Grade 2 
Maintain dose level of MLN0128. Initiate/intensify 
appropriate skin toxicity therapy  (such as 
antihistamines, topical corticosteroids) 
Grade 3 
Omit dose of MLN0128 until resolved to Grade ≤ 1, 
then: 
• If resolved in ≤ 7 days, maintain at same dose 
of MLN 0218 
• If resolved in > 7 days, resume at ↓1 dose level 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
49 
Treatment Modification for MLN0128-Related Adverse Events 
Event 
CTCAE. V4 
Grade 
Action to be Taken 
of MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment 
OTHER ADVERSE EVENTS 
Other AEs 
Grade 1-2 
Maintain MLN0128 
Grade 3 
Omit dose of MLN0128 until resolved to ≤Grade 1, 
then: 
• If resolved in ≤ 7 days, maintain at same dose 
of MLN 0218 
• If resolved in > 7 days, resume at ↓1 dose level 
of MLN0128 
Grade 4 
Permanently discontinue patient from the study 
treatment  
 
Note: Omit dose for ≥ Grade 3 vomiting or Grade 3 
nausea only if the vomiting or nausea cannot be 
controlled with optimal antiemetic therapy 
 
 
6.3 
Management of Hematologic Toxicities and Use of Hematologic Growth Factors 
 
Because of the increased risk of bleeding associated with bevacizumab, patients are encouraged 
to receive a transfusion when their platelets reach ≤ 30 x 109/L. 
 
No growth factors (G-CSF or GM-CSF) are to be used prophylactically in this protocol.  
Clinicians caring for patients on this protocol are permitted to use these growth factors to 
provide optimal care for patients with severe neutropenia in accordance with the ASCO 
guidelines62. If these growth factors are used in the acute setting of neutropenia and infection 
(documented or suspected), they will not be utilized prophylactically in subsequent cycles and 
they will not subsequently be used in lieu of dose reduction of (study agent). 
 
Erythrocyte growth factors (e.g. erythropoietin) are not to be administered prophylactically but 
may be prescribed per institutional guidelines for anemia if this is 
thought to be appropriate. Transfusions are also permitted. 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
50 
7. 
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS  
 
7.1 
General Information 
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial.  Adverse 
events experienced by participants will be collected, recorded and reported from the point the 
participant starts taking study drug up until 30 days after the last dose of study medication. The 
period for collection and recording of adverse events is extended for participants with ongoing 
reportable adverse events at least possibly related to study agent; for such participants, adverse 
events will be followed until the reportable event has resolved, stabilized, or determined to be 
irreversible by the participating investigator.  
 
Participants should be instructed to report any serious post-study event(s) that might reasonably 
be related to participation in this study. The investigator should notify the local IRB, the Overall 
PI Dr. Lakshmi Nayak and any other applicable regulatory agency of any unanticipated death or 
adverse event occurring after a participant has discontinued or terminated study participation that 
may reasonably be related to the study.  
 
Each adverse event will be assessed to determine if it meets the criteria for reporting.  Adverse 
event reporting is to occur according the site’s specific IRB guidelines, and as outlined in this 
Section for CTEP-AERS.  
 
7.1.1 
Definitions 
 
7.1.1.1 Adverse Event (AE)  
 
An adverse event (AE) is any undesirable sign, symptom or medical condition or 
experience that develops or worsens in severity after starting study drug, even if the 
event is not considered to be related to the study.  
 
Abnormal laboratory values or diagnostic test results constitute adverse events only if 
they induce clinical signs or symptoms or require treatment or further diagnostic tests. 
 
7.1.1.2 Serious Adverse Event (SAE) 
 
A serious adverse event (SAE) is any adverse event, occurring at any dose and 
regardless of causality that: 
• Results in death. 
• Is life-threatening. Life-threatening means that the person was at immediate 
risk of death from the reaction as it occurred (i.e., it does not include a 
reaction which hypothetically might have caused death had it occurred in a 
more severe form).  
• Requires or prolongs inpatient hospitalization for ≥ 24 hours. Hospitalization 
admissions and/or surgical operations scheduled to occur during the stud 
period, but planned prior to signing the informed consent for the study are not 
considered SAEs if the illness or disease existed before the participant was 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
51 
enrolled in the trial, provided that it did not deteriorate in an unexpected 
manner during the trial (e.g., surgery performed earlier than planned).  
• Results in persistent or significant disability/incapacity. Disability is defined 
as a substantial disruption of a person’s ability to conduct normal life 
functions. 
• Is a congenital anomaly or birth defect. 
• Is an important medical event (IME) when, based upon appropriate medical 
judgment, it may jeopardize the participant and may require medical or 
surgical intervention to prevent one of the outcomes listed above.  
 
7.1.1.3 Expectedness 
 
Expected adverse events are those that have been previously identified as resulting 
from administration of the agent(s).  For the purposes of this study, refer to the 
CAEPR Lists in the following sections.   
 
− 
The Specific Protocol Exceptions to Expedited Reporting (SPEER) within 
each CAEPR list will determine whether the event requires expedited 
reporting via CTEP-AERS.   
 
7.1.2 
Adverse Event Characteristics 
 
CTCAE term (AE description) and grade:  The descriptions and grading scales found in the 
revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 4.0 will be 
utilized for AE reporting.  All appropriate treatment areas should have access to a copy of the 
CTCAE version 4.0.  A copy of the CTCAE version 4.0 can be downloaded from the CTEP web 
site http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 
 
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) should be reported through CTEP-AERS only if the grade is above the grade provided 
in the SPEER. 
 
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. 
− 
Unlikely – The AE is doubtfully related to the study treatment. 
− 
Unrelated – The AE is clearly NOT related to the study treatment. 
 
7.2 
Comprehensive Adverse Events and Potential Risks (CAEPR) Lists  
 
The Comprehensive Adverse Event 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 of AEs, 
the Specific Protocol Exceptions to Expedited Reporting (SPEER), appears in a separate column 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
52 
and is identified with bold and italicized text.  The SPEER is a list of events that are protocol-
specific exceptions to expedited reporting to NCI via CTEP-AERS (except as noted below).   
 
Refer to the 'CTEP, NCI Guidelines: Adverse Event Reporting Requirements' 
http://ctep.cancer.gov/protocolDevelopment/default.htm#adverse_events_adeers for further 
clarification.  
 
NOTE:  The highest grade currently reported is noted in parentheses next to the AE in the 
SPEER.  Report ONLY AEs higher than this grade expeditiously via CTEP-AERS .  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. 
 
7.2.3 CAEPR for MLN0128 
 
Adverse events that have a reasonably causal relationship to treatment with MLN0128 are 
indicated in the table below. Frequency is provided based on 252 patients. 
Version 2.1, June 1, 20151 
 
 Adverse Events with Possible  
 Relationship to MLN0128 (INK128) 
 (CTCAE 4.0 Term) 
[n= 252] 
 
 
 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) 
Mucositis oral 
 
 
 Mucositis oral (Gr 2) 
Nausea 
 
 
 Nausea (Gr 2) 
Vomiting 
 
 
 Vomiting (Gr 2) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
  
Fatigue 
 
 
 Fatigue (Gr 2) 
 
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 
  
 
Lung infection 
 
  
 
Urinary tract infection 
 
 Urinary tract infection (Gr 2) 
INVESTIGATIONS 
  
 
Creatinine increased 
 
 Creatinine increased (Gr 2) 
 
 
Electrocardiogram QT corrected 
interval prolonged 
  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
53 
 
 Adverse Events with Possible  
 Relationship to MLN0128 (INK128) 
 (CTCAE 4.0 Term) 
[n= 252] 
 
 
 Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER)  
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
 
 
Lymphocyte count decreased 
 
  
 
Neutrophil count decreased 
 
  
 
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 2) 
 
Hypocalcemia 
 
  
 
Hypokalemia 
 
 Hypokalemia (Gr 2) 
 
Hypomagnesemia 
 
 Hypomagnesemia (Gr 2) 
 
Hypophosphatemia 
 
 Hypophosphatemia (Gr 2) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
  
 
Back pain 
 
 Back pain (Gr 2) 
 
Pain in extremity 
 
  
NERVOUS SYSTEM DISORDERS 
  
 
Dizziness 
 
 Dizziness (Gr 2) 
 
Dysgeusia 
 
 Dysgeusia (Gr 2) 
 
Headache 
 
 Headache (Gr 2) 
RENAL AND URINARY DISORDERS 
  
 
Acute kidney injury 
 
  
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
  
 
Cough 
 
 Cough (Gr 2) 
 
Dyspnea 
 
 Dyspnea (Gr 2) 
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. 
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. 
Also reported on MLN0128 (INK128) trials but with the relationship to MLN0128 (INK128) still 
undetermined: 
 
 
EYE DISORDERS - Photophobia 
GASTROINTESTINAL DISORDERS - Dyspepsia; Esophagitis; Gastroesophageal reflux disease 
INFECTIONS AND INFESTATIONS - Sepsis; Skin infection 
INVESTIGATIONS - Alanine aminotransferase increased; Aspartate aminotransferase increased; 
Cholesterol high; White blood cell decreased 
METABOLISM AND NUTRITION DISORDERS - Hypoalbuminemia; Hyponatremia 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Arthralgia; Musculoskeletal and 
connective tissue disorder - Other (muscle spasms); Myalgia 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
54 
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) - Treatment 
related secondary malignancy 
PSYCHIATRIC DISORDERS - Anxiety; Depression; Insomnia; Personality change 
RENAL AND URINARY DISORDERS - Hematuria 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Epistaxis; Hypoxia; Pleural effusion 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Rash acneiform; Urticaria 
VASCULAR DISORDERS - Flushing; Hypotension; Thromboembolic event 
Note: MLN0128 (INK128) 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. 
 
 
 
 
 
 
 
 
 
7.2.4 
CAEPR for Bevacizumab 
 
Comprehensive Adverse Events and Potential Risks list (CAEPR) 
for 
Bevacizumab (rhuMAb VEGF, NSC 704865) 
 
The Comprehensive Adverse Event 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 3540 patients. Below is the CAEPR for 
bevacizumab (rhuMAb VEGF). 
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. 
 
 
 
 
 
 
Version 2.4, May 23, 20161 
 
 Adverse Events with Possible  
 Relationship to Bevacizumab (rhuMAb VEGF) 
 (CTCAE 4.0 Term) 
[n= 3540] 
 
 
 Specific Protocol Exceptions to 
Expedited Reporting (SPEER)  
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
  
 
Anemia 
 
 Anemia (Gr 3) 
 
 
Blood and lymphatic system 
disorders - Other (renal thrombotic 
microangiopathy) 
  
 
Febrile neutropenia 
 
 Febrile neutropenia (Gr 3) 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
55 
CARDIAC DISORDERS 
  
 
 
Acute coronary syndrome2 
  
 
Cardiac disorders - Other 
(supraventricular 
arrhythmias)3 
 
 Cardiac disorders - Other 
(supraventricular arrhythmias)3 (Gr 3) 
 
 
Heart failure 
  
 
 
Left ventricular systolic dysfunction   
 
 
Myocardial infarction2 
  
 
 
Ventricular arrhythmia 
  
 
 
Ventricular fibrillation 
  
GASTROINTESTINAL DISORDERS 
  
 
Abdominal pain 
 
 Abdominal pain (Gr 3) 
 
Colitis 
 
 Colitis (Gr 3) 
 
Constipation 
 
 Constipation (Gr 3) 
 
Diarrhea 
 
 Diarrhea (Gr 3) 
 
Dyspepsia 
 
 Dyspepsia (Gr 2) 
 
 
Gastrointestinal fistula4 
  
 
Gastrointestinal hemorrhage5  
 Gastrointestinal hemorrhage5 (Gr 2) 
 
 Gastrointestinal obstruction6 
 
  
 
 
Gastrointestinal perforation7 
  
 
 
Gastrointestinal ulcer8 
  
 
Ileus 
 
  
 
Mucositis oral 
 
 Mucositis oral (Gr 3) 
 
Nausea 
 
 Nausea (Gr 3) 
 
Vomiting 
 
 Vomiting (Gr 3) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
  
 
Fatigue 
 
 Fatigue (Gr 3) 
 
Infusion related reaction 
 
 Infusion related reaction (Gr 2) 
 
Non-cardiac chest pain 
 
 Non-cardiac chest pain (Gr 3) 
 
Pain 
 
 Pain (Gr 3) 
IMMUNE SYSTEM DISORDERS 
  
 
Allergic reaction 
 
 Allergic reaction (Gr 2) 
 
 
Anaphylaxis 
  
INFECTIONS AND INFESTATIONS 
  
 
Infection9 
 
 Infection9 (Gr 3) 
 
 
Infections and infestations - Other 
(necrotizing fasciitis) 
  
 
Infections and infestations - 
Other (peri-rectal abscess) 
 
  
INJURY, POISONING AND PROCEDURAL COMPLICATIONS 
  
 
 
Injury, poisoning and procedural 
complications – Other 
(anastomotic leak)10 
  
 
Wound complication 
 
 Wound complication (Gr 2) 
 
Wound dehiscence 
 
 Wound dehiscence (Gr 2) 
INVESTIGATIONS 
  
 
Alanine aminotransferase 
increased 
 
 Alanine aminotransferase increased 
(Gr 3) 
 
Alkaline phosphatase 
increased 
 
 Alkaline phosphatase increased (Gr 3) 
 
Aspartate aminotransferase 
increased 
 
 Aspartate aminotransferase increased 
(Gr 3) 
 
Blood bilirubin increased 
 
 Blood bilirubin increased (Gr 2) 
 
Cardiac troponin I increased  
  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
56 
Neutrophil count 
decreased 
 
 
 Neutrophil count decreased (Gr 3) 
 
Platelet count decreased 
 
 Platelet count decreased (Gr 4) 
 
Weight loss 
 
 Weight loss (Gr 3) 
 
White blood cell decreased 
 
 White blood cell decreased (Gr 3) 
METABOLISM AND NUTRITION DISORDERS 
  
 
Anorexia 
 
 Anorexia (Gr 3) 
 
Dehydration 
 
 Dehydration (Gr 3) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
  
 
Arthralgia 
 
 Arthralgia (Gr 3) 
 
Musculoskeletal and 
connective tissue disorder -  
Other (bone metaphyseal 
dysplasia)11 
 
  
 
Myalgia 
 
 Myalgia (Gr 3) 
 
Osteonecrosis of jaw12 
 
  
NERVOUS SYSTEM DISORDERS 
  
 
Dizziness 
 
 Dizziness (Gr 2) 
 
Headache 
 
 Headache (Gr 3) 
 
 
Intracranial hemorrhage 
  
 
 
Ischemia cerebrovascular2 
  
 
Peripheral sensory 
neuropathy13 
 
  
 
 
Reversible posterior 
leukoencephalopathy syndrome 
  
 
Syncope 
 
  
RENAL AND URINARY DISORDERS 
  
 
 
Acute kidney injury 
  
 
Hematuria 
 
 Hematuria (Gr 3) 
 
Proteinuria 
 
 Proteinuria (Gr 2) 
 
 
Renal and urinary disorders - 
Other (Nephrotic Syndrome) 
  
 
 
Urinary fistula 
 
  
REPRODUCTIVE SYSTEM AND BREAST DISORDERS 
  
Reproductive system 
and breast disorders - 
Other (ovarian 
failure)14 
 
 
  
 
 
Vaginal fistula 
  
 
Vaginal hemorrhage 
 
 Vaginal hemorrhage (Gr 3) 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
  
 
Allergic rhinitis 
 
 Allergic rhinitis (Gr 3) 
 
 
Bronchopleural fistula 
  
 
 
Bronchopulmonary hemorrhage 
  
 
Cough 
 
 Cough (Gr 3) 
 
Dyspnea 
 
 Dyspnea (Gr 2) 
 
Epistaxis 
 
 Epistaxis (Gr 3) 
 
Hoarseness 
 
 Hoarseness (Gr 3) 
 
 
Respiratory, thoracic and 
mediastinal disorders - Other 
(nasal-septal perforation) 
  
 
 
Respiratory, thoracic and 
mediastinal disorders - Other 
(tracheo-esophageal fistula) 
  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
57 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
  
 
Pruritus 
 
 Pruritus (Gr 2) 
 
Rash maculo-papular 
 
 Rash maculo-papular (Gr 2) 
 
Urticaria 
 
 Urticaria (Gr 2) 
VASCULAR DISORDERS 
  
Hypertension 
 
 
 Hypertension (Gr 3) 
 
Thromboembolic event 
 
 Thromboembolic event (Gr 3) 
 
 
Vascular disorders - Other (arterial 
thromboembolic event)2,15 
  
  
 
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. 
 
2The risks of arterial thrombosis such as cardiac or CNS ischemia are increased in elderly patients and in 
patients with a history of diabetes. 
 
3Supraventricular arrhythmias may include supraventricular tachycardia, atrial fibrillation and atrial flutter. 
 
4Gastrointestinal fistula may include: Anal fistula, Colonic fistula, Duodenal fistula, Esophageal fistula, 
Gastric fistula, Gastrointestinal fistula, Rectal fistula, and other sites under the GASTROINTESTINAL 
DISORDERS SOC. 
 
5Gastrointestinal hemorrhage may include: Colonic hemorrhage, Duodenal hemorrhage, Esophageal 
hemorrhage, Esophageal varices hemorrhage, Gastric hemorrhage, Hemorrhoidal hemorrhage, Intra-
abdominal hemorrhage, Oral hemorrhage, Rectal hemorrhage, and other sites under the 
GASTROINTESTINAL DISORDERS SOC. 
 
6Gastrointestinal obstruction may include: Colonic obstruction, Duodenal obstruction, Esophageal 
obstruction, Ileal obstruction, Jejunal obstruction, Rectal obstruction, Small intestinal obstruction, and 
other sites under the GASTROINTESTINAL DISORDERS SOC. 
 
7Gastrointestinal perforation may include: Colonic perforation, Duodenal perforation, Esophageal 
perforation, Gastric perforation, Jejunal perforation, Rectal perforation, Small intestinal perforation, and 
other sites under the GASTROINTESTINAL DISORDERS SOC. 
 
8Gastrointestinal ulcer may include: Duodenal ulcer, Esophageal ulcer, Gastric ulcer, and other sites 
under the GASTROINTESTINAL DISORDERS SOC. 
 
9Infection may include any of the 75 infection sites under the INFECTIONS AND INFESTATIONS SOC. 
 
10Anastomotic leak may include Gastric anastomotic leak; Gastrointestinal anastomotic leak; Large 
intestinal anastomotic leak; Rectal anastomotic leak; Small intestinal anastomotic leak; Urostomy leak; 
Vaginal anastomotic leak 
 
11Metaphyseal dysplasia was observed in young patients who still have active epiphyseal growth plates. 
 
12Cases of osteonecrosis of the jaw (ONJ) have been reported in cancer patients in association with 
bevacizumab treatment, the majority of whom had received prior or concomitant treatment with i.v. 
bisphosphonates. 
 
13Increased rate of peripheral sensory neuropathy has been observed in trials combining bevacizumab 
and chemotherapy compared to chemotherapy alone.  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
58 
 
14Ovarian failure, defined as amenorrhea lasting 3 or more months with follicle-stimulating hormone 
(FSH) elevation (≥30 mIU/mL), was increased in patients receiving adjuvant bevacizumab plus 
mFOLFOX compared to mFOLFOX alone (34% vs. 2%).  After discontinuation of bevacizumab, 
resumption of menses and an FSH level <30 mIU/mL was demonstrated in 22% (7/32) of these 
women.  Long term effects of bevacizumab exposure on fertility are unknown. 
 
15Arterial thromboembolic event includes visceral arterial ischemia, peripheral arterial ischemia, heart 
attack and stroke. 
 
 
Also reported on bevacizumab (rhuMAb VEGF) trials but with the relationship to bevacizumab 
(rhuMAb VEGF) still undetermined: 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS - Blood and lymphatic system disorders - Other 
(idiopathic thrombocytopenia purpura); Bone marrow hypocellular; Disseminated intravascular 
coagulation; Hemolysis 
CARDIAC DISORDERS - Atrioventricular block complete; Atrioventricular block first degree; Cardiac 
arrest; Myocarditis; Pericardial effusion; Restrictive cardiomyopathy; Right ventricular dysfunction 
EAR AND LABYRINTH DISORDERS - Ear and labyrinth disorders - Other (tympanic membrane 
perforation); Hearing impaired; Tinnitus; Vertigo 
ENDOCRINE DISORDERS - Hyperthyroidism; Hypothyroidism 
EYE DISORDERS - Blurred vision; Cataract; Dry eye; Extraocular muscle paresis; Eye disorders - Other 
(blindness); Eye disorders - Other (conjunctival hemorrhage); Eye disorders - Other (corneal epithelial 
defect); Eye disorders - Other (floaters); Eye disorders - Other (ischemic CRVO); Eye disorders - Other 
(macular pucker); Eye disorders - Other (transient increased IOP > or =30 mm Hg); Eye disorders - Other 
(vitreous hemorrhage); Eye pain; Keratitis; Optic nerve disorder; Photophobia; Retinal detachment; 
Retinal tear; Retinopathy; Watering eyes 
GASTROINTESTINAL DISORDERS - Ascites; Chelitis; Colonic stenosis; Dry mouth; Dysphagia; 
Enterocolitis; Esophageal pain; Esophageal stenosis; Flatulence; Gastrointestinal disorders - Other 
(peritonitis); Oral pain; Pancreatitis; Proctitis; Rectal mucositis; Rectal stenosis;Typhlitis 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS - Death NOS; Edema face; 
Edema limbs; Edema trunk; Facial pain; Fever; Flu like symptoms; Gait disturbance; Injection site 
reaction; Localized edema; Multi-organ failure; Sudden death NOS 
HEPATOBILIARY DISORDERS - Cholecystitis; Gallbladder necrosis; Gallbladder obstruction; Hepatic 
failure; Hepatic necrosis 
INFECTIONS AND INFESTATIONS - Infections and infestations - Other (aseptic meningitis) 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS - Arterial injury; Bruising; Burn; 
Dermatitis radiation; Fracture 
INVESTIGATIONS - Activated partial thromboplastin time prolonged; Blood antidiuretic hormone 
abnormal; CD4 lymphocytes decreased; CPK increased; Carbon monoxide diffusing capacity decreased; 
Electrocardiogram QT corrected interval prolonged; Forced expiratory volume decreased; GGT 
increased; INR increased; Lipase increased; Lymphocyte count decreased; Serum amylase increased; 
Weight gain 
METABOLISM AND NUTRITION DISORDERS - Acidosis; Hypercalcemia; Hyperglycemia; 
Hyperkalemia; Hypermagnesemia; Hypernatremia; Hypertriglyceridemia; Hyperuricemia; 
Hypoalbuminemia; Hypocalcemia; Hypokalemia; Hypomagnesemia; Hyponatremia; Hypophosphatemia 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Arthritis; Back pain; Bone pain; 
Chest wall pain; Fibrosis deep connective tissue; Generalized muscle weakness; Head soft tissue 
necrosis; Joint effusion; Muscle weakness lower limb; Muscle weakness upper limb; Musculoskeletal and 
connective tissue disorder - Other (aseptic necrotic bone); Musculoskeletal and connective tissue 
disorder - Other (myasthenia gravis); Musculoskeletal and connective tissue disorder - Other (polymyalgia 
rheumatica); Neck pain; Pain in extremity; Pelvic soft tissue necrosis; Soft tissue necrosis lower limb 
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) - Tumor pain 
NERVOUS SYSTEM DISORDERS - Arachnoiditis; Ataxia; Central nervous system necrosis; 
Cerebrospinal fluid leakage; Cognitive disturbance; Depressed level of consciousness; Dysesthesia; 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
59 
Dysgeusia; Dysphasia; Encephalopathy; Extrapyramidal disorder; Facial nerve disorder; Hydrocephalus; 
Leukoencephalopathy; Memory impairment; Nervous system disorders - Other (increased intracranial 
pressure); Paresthesia; Peripheral motor neuropathy; Pyramidal tract syndrome; Seizure; Somnolence; 
Tremor; Vasovagal reaction 
PSYCHIATRIC DISORDERS - Agitation; Anxiety; Confusion; Depression; Insomnia; Libido decreased; 
Psychosis 
RENAL AND URINARY DISORDERS - Bladder spasm; Chronic kidney disease; Cystitis noninfective; 
Renal and urinary disorders - Other (dysuria); Renal and urinary disorders - Other (ureterolithiasis); Renal 
hemorrhage; Urinary frequency; Urinary incontinence; Urinary retention; Urinary tract obstruction; Urinary 
tract pain 
REPRODUCTIVE SYSTEM AND BREAST DISORDERS - Breast pain; Erectile dysfunction; Irregular 
menstruation; Pelvic pain; Vaginal discharge 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Adult respiratory distress syndrome; 
Atelectasis; Hypoxia; Nasal congestion; Pulmonary fibrosis; Pulmonary hypertension; Respiratory failure; 
Respiratory, thoracic and mediastinal disorders - Other (dry nares); Respiratory, thoracic and mediastinal 
disorders - Other (pulmonary infarction) 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Alopecia; Dry skin; Hyperhidrosis; Nail loss; Pain 
of skin; Palmar-plantar erythrodysesthesia syndrome; Photosensitivity; Purpura; Rash acneiform; Skin 
and subcutaneous tissue disorders - Other (diabetic foot ulcer); Skin and subcutaneous tissue disorders - 
Other (skin breakdown/ decubitus ulcer); Skin hyperpigmentation; Skin induration; Skin ulceration; 
Stevens-Johnson syndrome 
VASCULAR DISORDERS - Flushing; Hot flashes; Hypotension; Lymphocele; Phlebitis; Vasculitis  
 
 
 
Note: Bevacizumab (rhuMAb VEGF) 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. 
 
7.3 
Expedited Adverse Event Reporting to CTEP 
 
7.3.1 Expedited AE reporting for this study must use CTEP-AERS (CTEP Adverse Event 
Reporting System), accessed via the CTEP Web site (http://ctep.cancer.gov).  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).  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 CTEP-AERS is programmed for automatic electronic distribution of reports to the 
following individuals:  Study Coordinator of the Lead Organization, Principal 
Investigator, and the local treating physician.  CTEP-AERS provides a copy feature for 
other e-mail recipients.  
 
7.3.3 Expedited Reporting Guidelines 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
60 
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, unless as noted below.  Attribution to treatment or other cause must be 
provided. 
 
Death due to progressive disease should be reported as Grade 5 “Neoplasms benign, 
malignant and unspecified (incl cysts and polyps) - Other (Progressive Disease)” 
under the system organ class (SOC) of the same name.  Evidence that the death was a 
manifestation of underlying disease (e.g., radiological changes suggesting tumor growth 
or progression: clinical deterioration associated with a disease process) should be 
submitted.  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Phase 1 and Early Phase 2 Studies:  Expedited Reporting Requirements for Adverse 
Events that Occur on Studies under an IND/IDE within 30 Days of the Last Administration 
of the Investigational Agent/Intervention 1, 2 
FDA REPORTING REQUIREMENTS FOR SERIOUS ADVERSE EVENTS (21 CFR Part 312) 
NOTE:  Investigators MUST immediately report to the sponsor (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) 
An adverse event that results in inpatient hospitalization or prolongation of existing hospitalization for ≥ 24 
hours  
4) 
A persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions  
5) 
A congenital anomaly/birth defect.  
6) 
Important Medical Events (IME) that may not result in death, be life threatening, or require hospitalization 
may be considered serious when, based upon medical judgment, they may jeopardize the patient or 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
61 
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 CTEP-
AERS within the timeframes detailed in the table below. 
Hospitalization 
Grade 1 and Grade 2 Timeframes 
Grade 3-5 
Timeframes 
Resulting in 
Hospitalization  
≥ 24 hrs 
10 Calendar Days 
24-Hour 5 Calendar 
Days 
Not resulting in 
Hospitalization  
≥ 24 hrs 
Not required 
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 CTEP-AERS 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: 
• 
All Grade 3, 4, and Grade 5 AEs 
Expedited 10 calendar day reports for: 
• 
Grade 2 AEs resulting in hospitalization or prolongation of hospitalization 
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 
 
 
 
 
 
7.3.4 Additional Protocol-Specific Expedited Adverse Event Reporting Exclusions 
 
For this protocol only, the AEs/grades listed below do not require expedited reporting via 
CTEP-AERS .  However, they still must be reported through the routine reporting 
mechanism (Section 7.4): 
 
CTCAE 
SOC 
Adverse 
Event 
Grade 
Hospitalization/ 
Prolongation of 
Hospitalization 
Attribution 
Comments 
10025256 
Lymphopenia 
1-4 
Hospitalization/ 
Prolongation of 
Hospitalization 
Any 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
62 
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. 
 
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:  
 
• Leukemia secondary to oncology chemotherapy (e.g., acute myelocytic leukemia 
[AML])  
• Myelodysplastic syndrome (MDS)  
• 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 
Expedited Adverse Event Reporting to Local IRB 
 
Sites within DF/HCC and DF/PCC will submit reportable adverse events directly to the DFCI 
Office for Human Research Studies (OHRS) per the DFCI IRB reporting policy.  
 
External participating sites will report SAEs to their respective IRB according to the local IRB’s 
policies and procedures in reporting adverse events.  
 
7.7 
Routine Adverse Event Reporting  
 
All Adverse Events must be reported in routine study data submissions to the Overall PI on the 
toxicity case report forms.  AEs reported through expedited processes (e.g., reported to the IRB, 
CTEP-AERS , etc.) must also be reported in routine study data submissions.  
 
 
8. 
PHARMACEUTICAL INFORMATION 
 
A list of the adverse events and potential risks associated with the investigational or commercial 
agents administered in this study can be found in Section 7.2. 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
63 
8.1 
Study Agent: MLN0128 
 
Other Names: 
 
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 (mammalian 
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 will be supplied in tamper-resistant bottles as 
capsules containing 1 of 3 dose strengths. 
 
MLN0128 capsules, 1mg – white opaque color 
MLN0128 capsules, 3mg – orange opaque color 
MLN0128 capsules, 5mg – grey opaque color 
 
Each 1-, 3-, and 5-mg capsule for oral administration contain 1, 
3, and 5 mg of MLN0128, respectively in addition to the 
following inactive ingredients: microcrystalline cellulose (solid 
filler/diluents), magnesium stearate (lubricant), and hard 
gelatin capsule. 
 
Bottles of MLN0128 will contain 30 capsules each.  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
64 
 
Storage:  
Bottles are to be stored at room temperature (15C to 30C [59F 
to 85F]).   
 
Route of Administration: Oral 
 
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 > 25 μM) for 
inhibition of the major human CYP isoforms. 
 
Please refer to the MLN0128 Investigator’s Brochure for more 
information. 
 
Availability: 
MLN0128 is an investigational agent supplied to investigators 
by the Division of Cancer Treatment and Diagnosis (DCTD), 
NCI. 
 
MLN0128 is provided to the NCI under a Collaborative 
Agreement between the Millennium Pharmaceuticals, Inc. and 
the DCTD, NCI (see Section 12.3). 
 
 
 
 
 
 
 
 
 
 
 
 
 
8.1.1 
Agent Ordering and Agent Accountability 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
65 
8.1.1.1      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 (240) 276-6575 Monday through Friday between 8:30 am and 
4:30 pm (ET) or email PMBAfterHours@mail.nih.gov anytime. 
 
8.1.1.2       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 Drug Accountability Record Form 
(DARF).  (See the NCI Investigator’s Handbook for Procedures for Drug 
Accountability and Storage.) 
 
 
8.2 
Commercial Agent: Bevacizumab 
 
Other Names:  
rhuMAb VEGF, Avastin® 
 
Classification:  
Recombinant humanized monoclonal antibody 
 
Molecular Weight: 
Approximate molecular weight is 149,000 daltons 
 
Mode of Action:  
Bevacizumab blocks the binding of vascular endothelial 
growth factor (VEGF) to its receptors resulting in inhibition 
of angiogenesis. 
 
Description:  
Bevacizumab is a recombinant humanized anti-VEGF 
monoclonal antibody consisting of 93% human and 7% 
murine amino acid sequences. The agent is composed of 
human IgG framework and murine antigen-binding 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
66 
complementarity-determining regions 
 
How Supplied:  
Bevacizumab is supplied as a clear to slightly opalescent, 
sterile liquid for parenteral administration.    Each 400 mg 
(25mg/ml – 16 mL fill) glass vial contains bevacizumab 
with phosphate, trehalose, polysorbate 20, and Sterile 
Water for Injection, USP. 
   
Preparation:   
Vials contain no preservatives and are intended for single 
use only. Place the calculated dose in 100 mL of 0.9% 
sodium chloride for injection.  
 
Storage:  
Upon receipt, refrigerate bevacizumab (2˚ to 8˚ C).  Do not 
freeze.  Do not shake. 
 
Stability:  
Shelf-life studies of rhuMAb VEGF are ongoing.  The 
sterile single use vials contain no antibacterial 
preservatives.  Discard vials 8 hours after initial entry. 
 
Once diluted in 0.9% sodium chloride, administer solutions 
of bevacizumab within 8 hours. 
   
Route of Administration:  Intravenous 
 
Method of Administration: Administer the initial dose over a minimum of 90 minutes.  
If no adverse reactions occur, administer the second dose 
over a minimum of 60 minutes. If no adverse reactions 
occur after the second dose, administer subsequent doses 
over a minimum of 30 minutes. If infusion-related adverse 
reactions occur, all subsequent infusions should be 
administered over the shortest period that was well 
tolerated.  
 
To insure complete delivery of bevacizumab, flush the IV 
infusion line with 0.9% sodium chloride. The following are 
two recommended methods for flushing the bevacizumab 
IV infusion line: 
 
1.  When the bevacizumab infusion is complete, add an 
additional 50 mL of 0.9% sodium chloride for injection 
to the bevacizumab infusion bag. Continue the infusion 
until a volume equal to that of the volume contained in 
the tubing has been administered. 
 
2.  Replace the empty bevacizumab infusion bag with a 50 
mL bag of 0.9% sodium chloride for injection and 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
67 
infuse a volume equal to the volume contained in the 
tubing.  
 
Please note: the flush is not included in the total 
recommended infusion times. 
 
Agent Ordering:    
Bevacizumab is commercially available. The investigator 
or designated study personnel are responsible for 
maintaining dispensing records of bevacizumab per 
institutional standards.  
 
 
9. 
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES 
 
All biomarker and correlative studies will be performed only in patients participating in stage 2 
or the dose expansion cohort of the study. These studies will be exploratory.  
 
Table 9.1 Synopsis of Correlative Studies 
Purpose 
Technique 
Participants 
Timing of 
collection 
Collection 
requirements 
When 
requested by 
DFCI 
Coordinating 
Center, ship 
to: 
Blood PK 
studies 
Mass 
spectrometry 
on whole 
blood 
Recurrent 
GBM 
 
C1D15 and 
C2D1: 2-3 
hours post 
MLN0128 
dosing, prior 
to 
bevacizumab 
dose 
3 mL blood 
into a plastic 
plasma 
collection 
tube with 
spray coated 
sodium 
heparin 
Frozen at -70C 
and shipped 
overnight on 
dry ice: 
 
Jeffrey 
Supko, MD 
CSF PK 
studies 
Mass 
spectrometry 
on CSF 
Recurrent 
GBM 
C1D15 and 
C2D1: 2-3 
hours post 
MLN0128 
dosing, prior 
to 
bevacizumab 
dose 
2 mL of CSF 
into a 
cryotube 
Frozen at -70C 
and shipped 
overnight on 
dry ice: 
 
Jeffrey 
Supko, MD 
Biomarker 
Studies 
on 
Archival 
Tissue 
IHC on FFPE 
Recurrent 
GBM 
Archival 
Tissue 
30 unstained 
slides 
of 
standard (4 or 
5 micrometer) 
thickness 
Keith Ligon, 
MD, PhD 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
68 
from archival 
tissue 
Tissue 
Biopsy 
Radiological 
guided core 
needle biopsy. 
RPPA 
analysis and 
genomics 
studies 
Ovarian and 
endometrial 
expansion 
cohorts 
Before MLN 
0128 therapy, 
on C1D15 
prior to 
bevacizumab 
infusion and 
optional 
biopsy to be 
done at time 
of 
progression.  
As indicated 
below 
Frozen at -
70C and 
shipped on 
dry ice to 
John L. Hays 
MD, PhD 
Research 
blood draw 
for cytokines 
Illumna 
Multiplex 
assay on 
plasma and 
genomics 
studies 
Ovarian and 
endometrial 
expansion 
cohorts 
 Before 
MLN0128 
therapy and 
on C1D15 
prior to 
bevacizumab 
infusion, 
C2D1 and on 
the first day 
of each 
subsequent 
cycle 
7 mL blood 
into a plastic 
plasma 
collection 
tube with 
spray coated 
sodium 
heparin 
Shipped at 4C 
to John L. 
Hays MD, 
PhD 
 
 
9.1 
Correlative Studies for Stage 2 
 
9.1.1 
Plasma and CSF MLN0128 concentrations 
 
9.1.1.1 
Collection of the Specimens: 
 
The plasma and CSF concentrations of MLN0128 will be characterized in all patients 
with recurrent GBM enrolled in Stage 2 of the study. Blood and CSF samples will be 
collected 2 hours after the dose is taken by the patient, on cycle 1, day 15 and cycle 2, 
day 1. 
 
9.1.1.2 
Handling of the Specimens: 
 
For all pharmacokinetic plasma samples, draw 3 mL of blood into a plastic plasma 
collection tube with spray-coated sodium heparin at each of the time points 
specified above. Promptly mix the specimen by gently inverting the collection tube 
several times and then place it on wet ice. Centrifuge the sample at 1,100-1,300 x g 
for 10 min at 4°C within 30 min after collection. Remove the plasma from the 
blood cells using a pipette and distribute it in equal volumes into two self-standing 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
69 
polypropylene cryogenic tubes with external threads. Affix a computer-printed 
label (protocol no., patient no., sample no., scheduled sample time) to each 
cryotube. Completely cover the label with protective cryogenic freezer tape (Fisher 
catalog no. 11-867B). Place the tubes on crushed dry ice until stored in a freezer 
maintained at -70°C.  
 
For all pharmacokinetic CSF samples, collect 2 mL of CSF (obtained by performing 
lumbar puncture under provisions that the treating physician considers to be safe) in 
Nunc cryotubes. CSF studies will be omitted in participants with an increased risk of 
herniation. In those participants who have developed new or worsening neurologic 
signs and symptoms concerning for raised intracranial pressure, repeat head imaging 
in the form of head CT or brain MRI is recommended prior to lumbar puncture to rule 
out herniation. Affix a computer-printed label (protocol no., patient no., sample no., 
scheduled sample time) to each cryotube. Completely cover the label with protective 
cryogenic freezer tape (Fisher catalog no. 11-867B). Place the tubes on crushed dry ice 
until stored in a freezer maintained at -70°C. 
 
The concentration of MLN0128 in study samples will be determined by using an LC-
MS/MS assay.  The analytical method will be validated and applied to the analysis of 
study samples as recommended by the FDA Guidance for Industry: Bioanalytical 
Method Validation, May 2001 
(http://www.fda.gov/downloads/Drugs/Guidances/ucm070107.pdf). 
 
9.1.1.3 
Specimen Packaging and Shipping: 
 
Send complete sets of samples from each patient (pharmacokinetic plasma, 
pharmacokinetic CSF) by overnight courier to the address listed below. Place the 
sample tubes within a zip lock plastic bag. Fill a seamless Styrofoam container with at 
least 3 inches of dry ice, place the plastic bag containing the samples on top of the dry 
ice, and completely cover the bag with an additional 3 inches or more of dry-ice. Seal 
the Styrofoam container within a tight-fitting cardboard shipping box. Seal a copy of 
the sample collection time form for each set of samples within a zip-lock plastic bag 
and place the bag on top of the styrofoam container before the external shipping box is 
sealed.  Send the samples on a Monday, Tuesday, or Wednesday by overnight courier 
for delivery by 10:00 AM on the following day. Notification of the delivery must be 
made by e-mail to both Dr. Jeffrey G. Supko (email: jsupko@partners.org) and Sarah 
Hilderbrand (e-mail: slhilderbrand@partners.org). Include the name of the courier and 
the tracking no. in the email.   
 
Dr. Jeffrey G. Supko 
Massachusetts General Hospital 
55 Fruit St., GRJ 1025 
Boston, MA 02114 
Tel: 617-724-1970 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
70 
9.1.2 
Archival Tumor Samples for biomarkers 
 
9.1.2.1 
Collection and Handling of the Specimens: 
 
Archived tumor tissue from a prior resection of glioblastoma (pre-treatment, most 
recent surgery preferred but any other prior surgery tissue if most recent is not 
available) will be collected on all recurrent GBM patients enrolled in Stage 2 of the 
study. At the time of registration, prior to beginning treatment, a tumor tissue form 
indicating availability will need to be completed and signed by a pathologist.  This 
form provides written documentation of the availability of tissue for this study and the 
pathologist’s agreement to send it as described below. There will be central review of 
pathology by Dr. Keith Ligon at Dana-Farber Cancer Institute. The amount of tissue 
required for this study and registration of patients will be 30 unstained slides (standard 
4-5um, no heat treatment) from the initial resection from a block selected by the local 
pathologist to contain >70% tumor nuclei and <10% necrosis. Size of tumor tissue 
should be approximately 0.5cm in diameter or greater.  
 
The associated histopathology report as well as ALL ancillary testing reports for 
molecular or IHC studies (e.g. MGMT status, IDH1(R132H) mutation status, 
sequencing studies, and copy number analyses by FISH, arrays, or other methods) 
from the institution of collection should be shipped with the slides. 
 
9.1.2.2 
Shipping of the Specimens: 
 
Ship archival tumor tissue and associated report(s) to Dr. Ligon below. Notification of 
the delivery must be made by e-mail to Dr. Keith Ligon (email: 
Keith_Ligon@dfci.harvard.edu). Include the name of the courier and the tracking no. 
in the email.   
 
Keith L. Ligon, MD, PhD 
ATTN: Adult Neuropathology CRC 
Center for Molecular Oncologic Pathology 
Dana-Farber Cancer Institute 
450 Brookline Ave, JF215 
Boston, MA 02215 
Phone: 1-617-582-8764 
Fax: 
1-617-582-8761 
 
      Email: Keith_Ligon@DFCI.harvard.edu 
   
9.1.3 
Endometrial and ovarian cancer patient tumor biopsies 
 
9.1.3.1 
Collection, Handling and Shipping of Specimens: 
 
At least three core biopsies, not less than 18-gauge in diameter and at least 1cm in 
length will be obtained. Inability to get tissue with a reasonable attempt will not 
preclude treatment and the patient will remain eligible for all other translational 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
71 
components, including imaging. The use of imaging to facilitate biopsies will be 
decided upon by members of the interventional radiology team. We have optimized an 
SOP for reliable acquisition of tumor biopsies and quantification of cellular proteins 
and have recently reported the success and safety of obtaining serial biopsies in patient 
on clinical trials63. 
 
Upon acquisition, biopsy cores will be snap frozen in OCT on dry ice according to 
SOP in Appendix D and samples will mailed on dry ice to Dr. John Hays. Notification 
of the delivery must be made by e-mail to Dr. Hays (john.hays@osumc.edu) and 
please include the name of the shipping company and the tracking number in the e-
mail. 
 
For all research blood samples, draw 7 mL of blood into a plastic green top (Heparin 
containing) vacutainer at each of the time points specified in the research calendar. 
Promptly mix the specimen by gently inverting the collection tube several times and 
then place it on wet ice. Centrifuge the sample at 1,100-1,300 x g for 10 min at 4°C 
within 30 min after collection. Remove the plasma from the blood cells using a pipette 
and distribute it in equal volumes into 6 self-standing polypropylene cryogenic tubes 
(Sigma, Cat #V5007) with external threads. Remove the buffy coat layer and place 
into 1 self-standing polypropylene cryogenic tubes with external threads (Sigma, Cat 
#V5007).  Affix a computer-printed label (protocol no., patient no., sample no., 
scheduled sample time) to each cryotube. Completely cover the label with protective 
cryogenic freezer tape (Fisher catalog no. 11-867). Place the tubes on crushed dry ice 
until stored in a freezer maintained at -70°C until shipment.  
 
 
John L. Hays MD, PhD 
 
Biomedical Research Tower, Rm 560 
 
460 W. 12th Avenue, 
 
Columbus, OH 43210 
 
9.1.3.2 
Genomics Analysis 
 
Mutational analysis and sequencing will be performed on the first biopsy specimen 
and research blood draw (prior to therapy) and an optional third biopsy specimen at 
progression of disease.  We will employ clinical sequencing in for a custom cancer 
panel of 220 genes in a CLIA certified lab (Roychowdhury Lab). We have previously 
demonstrated feasibility for utilizing small tumor biopsy specimens and have a 95% 
success rate64. The custom cancer panel includes assessment of both DNA and RNA 
for 220 oncogenes and tumor suppressors (including PTEN, AKT1, KRAS, BRAF, 
FLT3, SRC, TP53, EGFR, NRAS, and PIK3CA) and is designed to detect point 
mutations, copy number changes, and gene fusions. Targeted gene sequencing is 
accomplished by solution-based hybridization capture with custom baits (Agilent) of 
both tumor (biopsy) and normal DNA (buffy coat isolate from blood obtained for 
circulating cytokines). This is used to generate somatic point mutations and copy 
number changes using published tools (Varscan2, MuTect). Targeted gene sequencing 
from RNAseq libraries is utilized to identify gene fusions and analyzed using 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
72 
published fusion tools (Tophat2, Chimerscan). All sample processing sequencing, and 
analysis will be completed in Dr. Roychowdhury’s lab and are standardized locked-
down procedures.  
 
9.1.3.3 
Proteomics Analysis 
 
Reverse phase protein arrays will be performed on patient biopsies to monitor the 
amount and phosphorylation states of the following proteins: MEK1/2 (S217/221), 
AKT (S473, T308), PI3K, p70S6K (T389), MAPK1/2 (T202/204), 
GSK3beta(S21/S9), p27 (T157, T198), p38MAPK (T180/182), rS6K (S235/236, 
S240/244), and 4E-BP1 (S65). These proteins represent a sample across multiple 
canonical pathways that have demonstrated importance in VEGF and PI3K  mediated 
signaling in various cancers7,65 and tumor microenvironment interactions66. RPPA 
assesses the qualitative and quantitative changes in defined endpoints using a 
microarray platform67. Clinical samples will be sliced and then lysed with total protein 
quantitated using BCA assay (Thermo Scientific, Rockford, IL). Sample analysis will 
take place at the MD Anderson Proteomics Core Facility. Samples will serially diluted 
and then arrayed on slides using an Auschon 2470 Arrayer (Auschon Biosystems, 
Billerica, MA). Each slide will be probed with a titer optimized primary antibody as 
we have done previously with clinical samples67. The signal will be analyzed using a 
DAKO CSA tyramide-amplification approach and visualized by DAB colorimetric 
reaction 68. Spots will be identified and their densities quantified by MicroVigene. 
Relative protein levels for each sample will be determined by interpolation of each 
dilution curve from the "standard curve" of the slide/antibody (MD Anderson 
Bioinformatics core facility).  Our studies have previously demonstrated that RPPAs 
provide an efficient method for quantifying protein expression of multiple protein 
endpoints from the same sample. Previous results in our laboratory have shown >30 
printings per sample is achievable with good reproducibility67.  Please refer to 
Appendix F for details regarding reverse phase protein arrays.  
 
9.1.3.4 
Circulating Cytokines 
 
Blood samples will also be obtained as described above (in section 9.1.1.2)  to 
measure levels of circulating cytokines by standard ELISA. Levels of VEGFA, PIGF,  
bFGF , VEGFD, MMP2, MMP9, IL6, IL8, EGF and angiopoietin will be determined 
at the specified time points.  Briefly, we will be using a multiplexed bead based array 
system (EMD Millipore with R&D Systems multiplexed performance assays bead 
panels).  Cytokine selection is based upon published reports of proteins and growth 
factors believed to be important in vascular formation (VEGFA,VEGFD, IL6, IL8, 
Angiopoietin-1, bFGF), tumor aggressiveness and invasion (IL-6, IL-8, EGF, MMP2, 
MMP9), resistance/sensitivity to bevacizumab mediated therapy (VEGFA, VEGFD, 
IL-6, Angiopoietin-1), or linked with signaling through PI3K/AKT/mTOR pathway.  
Seven milliliters of blood will be collected in a heparinized tube (BD Green top) for 
cytokine analysis and buffycoat isolation.  Sample will be drawn and stored on ice 
until centrifugation.  Samples will be centrifuged within 60 minutes of collection.  
Using a Pasteur pipette, plasma will be collected and placed in 5ml Nunc tube, labeled 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
73 
with subject ID and collection time, and stored at -70 degrees until shipment or 
analysis. Using a fresh Pasteur pipette, transfer buffy coat into 2ml Nunc tube, label 
with patient ID and collection time, and store at -70 degrees until shipment or analysis. 
The analytes can be covered with three different multiplexed arrays, each needing 
<100 microliters of plasma. 
 
9.1.3.5 
Apoptosis Assay 
 
Apoptosis assays will be performed with the validated triplex Rx1-IFA4 assay 
(γH2AX, Ki67, cleaved caspase 3, DAPI), through the DCTD laboratories after 
appropriate training of the PI through the DCTD 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
74 
 
 
10. 
STUDY CALENDAR 
Baseline evaluations are to be conducted within 14 days of registration.  GBM participants must have baseline scan performed within 
14 days of registrations; scans for all other patients must be done <4 weeks prior to registration.   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. 
 
Assessments 
Screening a 
Cycle 1  
Cycle 2  
Subsequent 
Cycles 
End of Tx e 
30-day post 
drug f 
Long Term 
Follow Up g 
D1b 
D8c 
D15 c 
D22 c 
D1d   
D8 c 
D15 c 
D22 c 
D1d   D15 c 
Informed consent h 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Background information/history i 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/exclusion criteria j 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Vital signs k 
X 
X 
X 
X 
X 
X 
 
X 
 
X 
X 
X 
 
 
Physical exam l 
X 
X 
X 
X 
X 
X 
 
X 
 
X 
X 
X 
 
 
Neurologic Exam m 
X 
X 
X 
X 
X 
X 
 
X 
 
X 
X 
X 
 
 
Performance Status n 
X 
X 
X 
X 
X 
X 
 
X 
 
X 
X 
X 
X 
 
Concomitant medications o 
X p 
----------------------------------------------------------------X o---------------------------------------------------------------- 
 
Adverse event assessment q 
 
----------------------------------------------------------------X q------------------------------------------------------------------ 
 
12-lead ECG r  
X 
X r 
 
 
 
X r 
 
 
 
X r 
 
X 
 
 
MUGA or ECHO  
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Imaging – CT or MRI s 
X 
 
 
 
 
 
 
 
 
X t 
 
X 
 
 
Response assessment t 
 
 
 
 
 
 
 
 
 
X t 
 
X 
 
 
Hematology u 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
 
Serum Chemistry v 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
 
Fasting serum glucose w 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
 
 
 HbA1c ff 
X 
 
 
 
 
 
 
 
 
Xff 
 
 
 
 
Fasting lipid profile w 
X 
X 
 
 
 
X 
 
 
 
X 
 
X 
 
 
Coagulation PT/INR- x 
X 
 
 
X 
 
X 
 
 
 
 
 
Xee 
 
 
Urinalysis y 
X 
X 
 
X 
 
X 
 
 
 
X 
 
X 
 
 
Serum Pregnancy Test z 
X 
 
 
 
 
X 
 
 
 
X 
 
X 
 
 
MLN0128 aa 
 
--------------------------------------------X cc-------------------------------------------- 
 
 
 
Bevacizumab bb 
 
X bb 
 
X bb 
 
X bb 
 
X bb 
 
X bb 
Xbb 
 
 
 
Blood PK cc 
 
 
 
X  
 
X 
 
 
 
 
 
 
 
 
CSF PK cc 
 
 
 
X 
 
X 
 
 
 
 
 
 
 
 
Biopsy cc 
 
X 
 
X 
 
 
 
 
 
 
 
X 
 
 
Blood for cytokines cc 
 
X 
 
X 
 
X 
 
 
 
X 
 
 
 
 
Submission of archival tissue ff 
 
X ff 
 
 
 
 
 
 
 
 
 
 
 
 
Survival g 
 
 
 
 
 
 
 
 
 
 
 
 
X 
X 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
75 
 
a. All screening procedures to be performed within 14 days of registration, except imaging within 14 days from start of study treatment for GBM participants 
and within 28 days from start of study treatment for all other participants.  
b. Cycle 1, Day 1 assessments to be performed within 2 days prior to MLN0128 
c. 
Mid cycle assessments have a +/- 2 days window. 
d. Within 2 days (48 hours) prior to Day 1 drug, except imaging which are within 7 days prior to Day 1 drug.  
e. End of treatment assessments to be performed within 7 days after last study drug or within 7 days after decision to end treatment.  
f. 
A contact/visit for review of adverse events, KPS, and vital status is to be performed at 30 days (+/- 5 days) after the last study drug is given (may be 
performed by documented clinician telephone call, if visit is not feasible).  This may be performed via documented phone conversation with a study nurse 
or clinician. Participants with ongoing reportable adverse events may require additional follow-up per section 11.1.    
g. Long-term Follow-Up: Per Section 5.6, participants will be following annually for survival via telephone or medical record following until patient either 
passes away or is lost to long-term follow-up.  Progression information will be collected for participants who do not progress while on study treatment. 
h. Informed Consent: performed by MD attending only. Informed consent process to be fully documented: e.g. prospective participant had sufficient time for 
deliberation, all questions were answered, treatment options provided by MD, full study reviewed including risks, and a copy of signed and dated consent 
given to participant. 
i. 
Background/history: to review treatment history for treated cancer, any ongoing medical conditions and medical history pertaining to eligibility on study 
and involvement during study. 
j. 
Inclusion/exclusion criteria: source documentation providing Investigator’s confirmation that patient has met all eligibility criteria must be available prior 
to registration.  
k. 
Vital signs:  weight, heart rate, blood pressure, respiration rate, temp, oxygen saturation.  Height required only at baseline. 
l. 
Physical Exam: physical exam. 
m. Neurologic exam required for recurrent GBM participants only.  
n. For all non-GBM participants, the performance status will be assessed according to the ECOG (WHO) performance status scale.  For all GBM participants, 
the performance status will be assessed according to the Karnofsky Performance Status (KPS) scale. See Appendix A for scales.  
o. Concomitant medications and reason for administration should be documented in the case history.  All medications taken within 30 days of screening  up 
until 30-day post drug visit should be recorded 
p. At baseline/screening, specific start dates are requested for steroids, AEDs, anti-coagulants, and drugs for hypertension. For all other concomitant 
medications at baseline/screening, knowledge of whether or not agent began within last thirty days will be requested for the eDC.  
q. Adverse events (AEs) experienced by participants will be collected and recorded from first dose of study drug up to 30 days of the last dose of study 
medication. The period for collection and recording of AEs is extended for participants with ongoing reportable adverse events that are related to study 
agent (see Section 7.1).  Adverse event reporting begins for events that occur after registration. 
r. 
ECG: C1D1 pre-dose, C1D1 2 hour post MLN0128 dose (+/- 10 minutes), C1D1 4 hours post MLN0128 dose (+/- 10 minutes); C2D1 pre-dose, C2D1 2 hours 
post MLN0128 dose (+/-10 minutes); subsequent day 1 ECGs to be done 2 hours post MLN0128 dose (+/- 10 minutes).  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
76 
s. 
CT with or without contrast or MRI with and without contrast. 
t. 
Within 7 days prior to day 1 of odd cycles (3, 5, 7, etc.).  
u. Hematology – erythrocytes (RBC), hemoglobin, hematocrit, platelets, total WBC plus absolute differential counts (neutrophils, lymphocytes, monocytes, 
eosinophils, basophils).   
v. 
Chemistry - albumin, alkaline phosphatase (ALP), bicarbonate (HCO3), BUN, calcium, chloride, creatinine, magnesium,(GBM patients only), phosphorous, 
LDH, potassium, SGOT (AST), SGPT (ALT), sodium, total protein, and total bilirubin.  If total bilirubin is greater than the upper limit of normal, direct and 
indirect bilirubin should be performed.   
w. Fasting lipid profile: total cholesterol, HDL-C, LDL-C, triglycerides (8 hours fasting).  
x. 
Coagulation: PT/INR,   
y. 
Urinalysis: specific gravity, pH, glucose, protein, bilirubin, ketones, leukocytes, and blood.  Per Table 6.1, if protein is ≥ 2+, obtain 24-hour urine protein.   
z. 
Serum pregnancy test only for women of child bearing potential.  
aa. MLN0128 to be taken in clinic on days of scheduled pharmacokinetic sampling and pre/post MLN0128 dose ECGs.  
bb. Bevacizumab to be administered on C1D1 on days 1 and 15 (+/- 2 days) for each 28-day cycle, except for participants enrolled in Stage 2 who will not 
receive bevaizumab on C1D1 and will start treatment with bevacizumab on C1D15. Please refer to Section 5.1.2 for timing of bevacizumab infusions.  
cc. All biomarker and correlative studies will be performed only in participants enrolled in the dose expansion cohort of stage 2 of this study.  Please refer to 
Section 9 for more details.  
dd. Submission of archival tissue required for GBM participants to be submitted within 60 days after registration.  See Section 9.1.2 for details.  
ee. Coagulation tests to be done at end of treatment visit only for participants undergoing biopsy. 
ff. HbA1c is required at screening and prior to initiation of odd cycles (C3D1, C5D1, etc) only. 
 
 
 
 
 
 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
77 
 
 
 
11. 
MEASUREMENT OF EFFECT 
 
Although response is not the primary endpoint of this trial, patients with measurable disease will 
be assessed by standard criteria.  For the purposes of this study, patients should be re-evaluated 
every 8 weeks.  In addition to a baseline scan, confirmatory scans will also be obtained 8 weeks 
following initial documentation of an objective response. 
 
11.1 
Antitumor Effect – Non-GBM  Solid Tumors 
 
For the purposes of this study, patients should be re-evaluated for response every 8 weeks.  In 
addition to a baseline scan, confirmatory scans should also be obtained 8 (not less than 4) 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)60.  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. 
 
11.1.1 Definitions 
 
Evaluable for toxicity.  All patients will be evaluable for toxicity from the time of their 
first treatment with MLN0128. 
 
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.  
 
11.1.2 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 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
78 
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. 
 
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.  
 
11.1.3 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 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
79 
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. 
 
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  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 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
80 
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 following complete response (CR) or surgical resection is an endpoint. 
 
Tumor markers  Tumor markers alone cannot be used to assess response.   
 
Cytology, Histology  These techniques can be used to differentiate between partial 
responses (PR) and complete responses (CR) in rare cases (e.g., residual lesions in tumor 
types, such as germ cell tumors, where known residual benign tumors can remain). 
 
The cytological confirmation of the neoplastic origin of any effusion that appears or 
worsens during treatment when the measurable tumor has met criteria for response or 
stable disease is mandatory to differentiate between response or stable disease (an 
effusion may be a side effect of the treatment) and progressive disease. 
 
FDG-PET  While FDG-PET response assessments need additional study, it is sometimes 
reasonable to incorporate the use of FDG-PET scanning to complement CT scanning in 
assessment of progression (particularly possible 'new' disease).  New lesions on the basis 
of FDG-PET imaging can be identified according to the following algorithm:  
a. Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of 
PD based on a new lesion. 
b. No FDG-PET at baseline and a positive FDG-PET at follow-up:  If the positive FDG-
PET at follow-up corresponds to a new site of disease confirmed by CT, this is PD.  If 
the positive FDG-PET at follow-up is not confirmed as a new site of disease on CT, 
additional follow-up CT  scans are needed to determine if there is truly progression 
occurring at that site (if so, the date of PD will be the date of the initial abnormal 
FDG-PET scan).  If the positive FDG-PET at follow-up corresponds to a pre-existing 
site of disease on CT that is not progressing on the basis of the anatomic images, this 
is not PD. 
c. Due to the complexity of interpreting FDG-PET results with mTORC1/2 inhibitors, 
FDG-PET will not be used to upgrade a response to CR.  
Note:  A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake 
greater than twice that of the surrounding tissue on the attenuation corrected image. 
 
11.1.4 Response Criteria 
 
11.1.4.1 
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. 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
81 
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. 
 
11.1.4.2 
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). 
 
11.1.4.3 
Evaluation of Best Overall Response 
 
The best overall response is the best response recorded from the start of the treatment 
until disease progression/recurrence (taking as reference for progressive disease the 
smallest measurements recorded since the treatment started).  The patient's best 
response assignment will depend on the achievement of both measurement and 
confirmation criteria. 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
82 
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 
 
11.1.5 Duration of Response 
 
Duration of overall response:  The duration of overall response is measured from the time 
measurement criteria are met for CR or PR (whichever is first recorded) until the first 
date that recurrent or progressive disease is objectively documented (taking as reference 
for progressive disease the smallest measurements recorded since the treatment started). 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
83 
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.  
 
11.1.6 Progression-Free Survival 
 
From date of first dose to date of progression or death. Participants who stop treatment 
for causes other than progression may be censored if other therapy is initiated or if 
regular assessments for assessing progression are no longer available.  
 
 
11.2 
Antitumor Effect – Glioblastoma patients 
 
This trial will utilize the criteria recently proposed by the Response Assessment in Neuro-
Oncology (RANO) working group61. The RANO Criteria updates its established predecessor, the 
Macdonald Criteria. 
 
11.2.1 Antitumor Effect – Definitions 
 
Evaluable for toxicity. All participants who receive at least one dose of study treatment will be 
evaluable for toxicity from the time of their first treatment. 
 
Evaluable for objective response. Only those participants who have measurable disease present 
at baseline and have received at least one cycle of study therapy will be considered evaluable for 
response. These participants will have their response classified according to the definitions stated 
below. (Note: Participants who exhibit objective disease progression or die prior to the end of 
cycle 1 will also be considered evaluable.) 
 
Measurable disease. Bidimensionally, contrast-enhancing, measurable lesions with clearly 
defined margins by CT or MRI scan, with a minimal diameter of 1 cm, and visible on 2 axial 
slices which are at least 5 mm apart with 0 mm skip. Measurement of tumor around a cyst or 
surgical cavity, if necessary, requires a minimum thickness of 3 mm. If there are too many 
measurable lesions to measure at each evaluation, the investigator must choose the largest two to 
be followed before a participant is entered on study.  The remaining lesions will be considered 
non-measureable for the purpose of objective response determination.  Unless progression is 
observed, objective response can only be determined when all measurable and non-measurable 
lesions are assessed. 
 
Non-measurable evaluable disease. Unidimensionally measurable lesions, masses with margins 
not clearly defined, lesions with maximal diameter < 1cm. 
 
11.2.2 Response/Progression Categories 
 
Complete response (CR).  

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
84 
All of the following criteria must be met:   
a. Complete disappearance of all enhancing measurable and non-measurable disease 
sustained for at least 4 weeks.  In the absence of a confirming scan 4 weeks later, 
this scan will be considered only stable disease. 
b. No new lesions. 
c. All measurable and non-measurable lesions must be assessed using the same 
techniques as baseline. 
d. Participants must be on no steroids or on physiologic replacement doses only. 
e. Stable or improved non-enhancing (T2/FLAIR) lesions  
f.  Stable or improved clinically, for clinical signs and symptoms present at baseline 
and  recorded to be disease related. 
g. Participants with non-measurable disease cannot have a complete response. The best 
response possible is stable disease. 
 
Partial response (PR).   
All of the following criteria must be met: 
a. Greater than or equal to 50% decrease compared to baseline in the sum of products 
of perpendicular diameters of all measurable enhancing lesions sustained for at 
least 4 weeks. In the absence of a confirming scan 4 weeks later, this scan will be 
considered only stable disease.  
b. No progression of non-measurable disease. 
c. No new lesions.  
d. All measurable and non-measurable lesions must be assessed using the same 
techniques as baseline.  
e. The steroid dose at the time of the scan evaluation should be no greater than the 
dose at time of baseline scan. 
f.     Stable or improved non-enhancing (T2/FLAIR) lesions on same or lower dose 
of corticosteroids compared to baseline scan. 
g. Stable or improved, for clinical signs and symptoms present at baseline and 
recorded to be disease related clinically.  
 
Participants with non-measurable disease cannot have a partial response. The best 
response possible is stable disease. 
 
 
Progressive disease (PD).  
The following criterion must be met: 
a. > 25% increase in sum of the products of perpendicular diameters of enhancing 
lesions (over best response or baseline if no decrease) on stable or increasing doses 
of corticosteroids and/or one or more of the of the following: 
b. Significant increase in T2/FLAIR non-enhancing lesion on stable or increasing 
doses of corticosteroids steroids compared to baseline scan or best response 
following initiation of therapy, not due to co-morbid events (radiation therapy, 
demyelination, ischemic injury, infection, seizures, post-operative changes, or 
other treatment effects). 
c. Any new lesion 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
85 
d. Clear clinical deterioration not attributable to other causes apart from the tumor 
(e.g. seizures, medication side effects, complications of therapy, cerebrovascular 
events, infection, etc.). The definition of clinical deterioration is left to the 
discretion of the investigator but it is recommended that a decline in the Karnofsky 
Performance Score (KPS) from 100 or 90 to 70 or less, a decline in KPS of at least 
20 from 80 or less, or a decline in KPS from any baseline to 50 or less, for at least 
7 days, be considered neurologic deterioration, unless attributable to co-morbid 
events or changes in corticosteroid dose. 
e. Failure to return for evaluation due to death or deteriorating condition 
 
Stable disease (SD).  
All of the following criteria must be met: 
a. Does not qualify for CR, PR, or progression. 
b. All measurable and non-measurable sites must be assessed using the same 
techniques as baseline. 
c. Stable non-enhancing (T2/FLAIR) lesions on same or lower dose of 
corticosteroids compared to baseline scan. In the event that the corticosteroid dose 
has been increased, the last scan considered to show stable disease will be the scan 
obtained when the corticosteroid dose was equivalent to the baseline dose. 
d. Stable clinically. 
 
Unknown response status.  
Progressive disease has not been documented and one or more measurable or non-
measurable lesions have not been assessed. 
 
Table 10.2 Summary of the RANO Response Criteria 
 
 
CR 
PR 
SD 
PD# 
T1-Gd + 
None 
≥50% decrease 
<50% decrease- 
<25% increase 
≥25% increase* 
T2/FLAIR 
Stable or 
decrease 
Stable or 
decrease 
Stable or decrease Increase* 
New Lesion 
None 
None 
None 
Present* 
Corticosteroids 
None 
Stable or 
decrease 
Stable or decrease NA 
Clinical Status 
Stable or 
increase 
Stable or 
increase 
Stable or increase 
Decrease* 
Requirement for 
Response  
All 
All 
All 
Any* 
CR=complete response;   PR=partial response;   SD=stable disease;   PD=progressive disease 
#:    Progression occurs when any of the criteria with * is present 
NA: Increase in corticosteroids alone will not be taken into account in determining progression 
in the absence of persistent clinical deterioration 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
86 
11.2.3 Methods for Evaluation of Measurable Disease 
 
All measurements should be taken and recorded in metric notation, using a ruler, calipers, or 
digital measurement tool. All baseline evaluations should be performed as closely as possible to 
the beginning of treatment and ideally within 14 days 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.  
 
11.2.4 Evaluation of Best Response 
 
The best overall response is the best response recorded from the start of the post-surgical 
treatment until disease progression (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started). If a response recorded at one scheduled MRI 
does not persist at the next regular scheduled MRI, the response will still be recorded based on 
the prior scan, but will be designated as a non-sustained response.  If the response is sustained, 
i.e. still present on the subsequent MRI, it will be recorded as a sustained response, lasting until 
the time of tumor progression. Participants without measurable disease may only achieve SD or 
PD as their best “response.” 
 
11.2.5 Other Effect Measures 
 
Neurological Exam 
Although not used for determining response, it is useful to evaluate changes in the neurological 
exam compared to the previous exam.  The following scale may be used:  
+2 
Definitely better 
+1 
Possibly better 
0 
Unchanged 
-1 
Possibly worse 
-2 
Definitely worse 
 
Performance Status 
Participants will be graded according to KPS score  
 
Overall survival time 
From date of first dose to date of death due to any cause. 
 
Progression-free survival time 
From date of first dose to date of progression or death. Participants who stop treatment for causes 
other than progression may be censored if other therapy is initiated or if regular assessments for 
assessing progression are no longer available. 
 
 
 
11.2.6 Response Review 
 
Central review of MRI or CT scans is planned for participants who achieve CR, PR, or PFS6.   
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
87 
Central review will be performed at Brigham and Women’s Hospital on registered participants 
who have been determined by the enrolling institution as having achieved PFS6, complete 
radiographic response, or partial radiographic response. When a participant’s films are requested, 
all films of all views from pre-registration and subsequent scans must be submitted for central 
review. Once the Central Review is complete, the central review results will be made available to 
the local PI. 
 
 
12. 
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 
Data Reporting 
 
12.1.1 Method 
 
The QACT will collect, manage, and monitor data for this study. 
 
This study will also be monitored by the Clinical Data Update System (CDUS).  Cumulative 
CDUS data will be submitted quarterly to CTEP via electronic means by the Coordinating Center 
for all participants. Reports are due January 31, April 30, July 31, and October 31. Instructions 
for submitting data using the Clinical Data Update System can be found on the CTEP website at: 
http://ctep.cancer.gov/protocoldevelopment.  
 
Note: All adverse events that are reported through CTEP-AERS must also be reported via 
CDUS. 
 
12.1.2 Data Submission 
 
The schedule for completion of submission of case report forms (paper or electronic) to the 
QACT is as follows: 
 
Form 
Suggested Submission Timeline 
Eligibility Checklist 
Complete prior to registration with QACT 
On Study and Baseline Forms 
Within 14 days of registration 
Treatment Forms 
Within 10 days of the last day of the cycle 
Adverse Event Report Forms 
Within 10 days of the last day of the cycle 
Response Assessment Forms 
Within 10 days of the last day of the cycle 
required for response evaluation 
Off Treatment/Off Study Forms 
Within 14 days of completing treatment or 
being taken off study for any reason 
Follow Up/Survival Forms 
Within 14 days of the protocol defined follow 
up visit date or contact  
 
Participating Institutions are responsible for submitting CDUS data and/or data forms to the 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
88 
Coordinating Center on the study quarterly to allow time for Coordinating Center compilation.  
The date for submission to the Coordinating Center will be set by the Overall PI.  CDUS does 
not accept data submissions from the participants on the study.  When setting the dates, allow 
time for Coordinating Center compilation, Principal Investigator review, and timely submission 
to CTEP by the quarterly deadlines (see Section 12.1.1).   
 
The Coordinating Center is responsible for compiling and submitting CDUS data to CTEP for all 
participants and for providing the data to the Principal Investigator for review.   
12.2 
CTEP Multicenter Guidelines 
 
This protocol will adhere to the policies and requirements of the CTEP Multicenter Guidelines.  
The specific responsibilities of the Principal Investigator and the Coordinating Center (Study 
Coordinator) and the procedures for auditing are presented in Appendix B. 
• The Principal Investigator/Coordinating Center is responsible for distributing all IND 
Action Letters or Safety Reports received from CTEP to all participating institutions for 
submission to their individual IRBs for action as required. 
 
• Except in very unusual circumstances, each participating institution will order DCTD-
supplied agents directly from CTEP.  Agents may be ordered by a participating site only 
after the initial IRB approval for the site has been forwarded by the Coordinating Center 
to the CTEP PIO (PIO@ctep.nci.nih.gov) except for Group studies. 
 
12.3 
Collaborative Agreements Language 
 
The agent supplied by CTEP, DCTD, NCI used in this protocol is 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”): 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
89 
 
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 
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 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
90 
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 
 
General considerations: 
 
Patients will be enrolled in this multicenter, open-label phase I study with dose escalation in a 
3+3 design followed by dose confirmation in 3 tumor types.  During dose escalation, patients 
will be enrolled in to sequential cohorts; the total number patients in a specific cohort will be 
determined based on the occurrence of DLTs at that dose level (refer to Section 5.1 and 5.5) with 
a range of 2-6 patients per cohort. During dose confirmation, 10 patients will be enrolled in each 
of the 3 tumor-specific cohort expansions, except in ovarian and endometrial cancer cohorts in 
which a maximum of 15 patients each may be enrolled.  
 
Primary Endpoints:  
 
• To determine the MTD/RP2D and dose limiting toxicity (DLT) of daily oral MLN0128 when 
administered with bevacizumab in patients with advanced solid tumors including recurrent 
GBM. 
• To evaluate the safety and tolerability of the combination of MLN0128 and bevacizumab. 
 
Enrollment, major protocol violations, and discontinuations from the study will be summarized 
by dose level. 
 
Demographic and baseline characteristics, such as age, sex, race, weight, type of malignancy, 
duration of malignancy, and baseline Karnofksy Performance Status, will be summarized using 
means, standard deviations, medians, and ranges for continuous variables, and proportions for 
categorical variables. All summaries will be presented overall and by dose level. Study drug 
administration data will be listed by dose level, and any dose modifications will be flagged. 
Means and standard deviations will be used to summarize the total dose of MLN0128 and 
bevacizumab received. 
 
Safety will be assessed through summaries of adverse events, changes in selected laboratory test 
results, changes in vital signs, and MLN0128 and bevacizumab exposure. All patients who 
receive any amount of study treatment will be included in the safety analysis. 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
91 
For the dose escalation portion, the following table shows the probability of escalating the 
dose for various true, but unknown, rates of unacceptable toxicity. 
 
True DLT Rate 
Probability of Dose 
Escalation 
10% 
91% 
20% 
71% 
30% 
49% 
40% 
31% 
50% 
17% 
60% 
8% 
 
13.2 
Sample Size/Accrual Rate 
 
13.2.1 
Sample Size Calculation 
 
Stage 1: 
 
Standard cohorts of three designs will be applied.  Patients will be accrued in cohorts of 3 
starting at dose level 1. 
 
The MTD will be based on the assessment of DLT during the first 4 weeks of treatment only (i.e. 
following the first 2 treatment cycles), and will be defined as the dose at which fewer than one-
third of patients experience a DLT to study treatment. The MTD is the dose level at which 0/6 or 
1/6 patients experience DLT with the next higher dose having at least 2 out of 3 or 2 out of 6 
patients encountering DLT.  
 
Three patients will be treated at each dose level, and can be enrolled simultaneously. If one DLT 
is encountered, an additional 3 patients will be added to that dose level. If at any point two DLTs 
are encountered within a given dose level, then the MTD has been exceeded and if only three 
patients have been treated at the next lower dose three more patients are treated at the next lower 
dose. 
 
If it is determined that dose level 1 exceeds the MTD, then additional reduced dose level (-1) will 
be discussed.  No dose levels above dose level 3 will be explored.  
 
A minimum of 12 and a maximum of 18 patients will be accrued in this part of the study. 
 
Stage 2:  
 
After the MTD/RP2D is established, a maximum of 40 patients; 10 (maximum of 15) with 
recurrent or advanced ovarian cancer, 10 (maximum of 15) with recurrent endometrial cancer 
(depending on biopsies, accrual will stop as soon as 10 adequate tissue are obtained but no more 
than 5 failures will be covered by additional enrollment in these expansion cohorts) and 10 with 
recurrent GBM will be accrued. The dose expansion part is primarily conducted and sized for 
continued safety evaluation If 2 or more patients in each dose-expansion cohort develop 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
92 
unacceptable toxicity defined as grade 4 or 5 non-hematological toxicity or ≥grade 2 intracranial 
hemorrhage (in recurrent GBM patients), then further accrual to that cohort will be stopped and 
the next dose level down will be considered the MTD for that particular cohort. If the true 
unacceptable toxicity rate is as low as 0.05 then the probability of observing 2 or more of the 
above adverse events in the expansion cohort is 0.08, while if it is as high as 0.3 then this 
probability is 0.85. The stopping rule will be assessed separately in each cohort. 
 
For the ovarian and endometrial cancer cohorts, we estimate that 10 patients per arm will provide 
power for exploratory translational analyses examining target presence, activation, modulation, 
and relationship to clinical outcome. This plan will allow the discovery of possible predictive 
biomarkers that can be queried in future trials with this combination. To be conservative, the 
sample size required was calculated under the assumption that a Bonferroni adjustment is 
required for the 10 primary evaluations to be performed during the RPPA analysis (MEK1/2 
(S217/221), AKT (S473, T308), PI3K, p70S6K (T389), MAPK1/2 (T202/204), 
GSK3beta(S21/S9), p27 (T157, T198), p38MAPK (T180/182), rS6K (S235/236, S240/244), and 
4E-BP1 (S65)). Thus, requiring a two-tailed p-value <0.005 (=0.05/10) for each test to be 
considered statistically significant will be used to estimate the desired number of subjects. In 
practice, a Hochberg adjustment will be used to evaluate the significance of the multiple 
comparisons, which is not as stringent as a Bonferroni adjustment, but will still maintain an 
overall 0.05 significance level for the comparisons performed.   Furthermore, since this study is 
mainly pilot in intent, the findings will be reported in that context. With 10 patients in a cohort, 
for each such comparison, there is 90% power to detect a difference from baseline equal to 20% 
change from baseline for each of the 10 parameters (assuming a mean CV of 6.7%), with an 
overall alpha=0.005 as stated above. This calculation assumes that a paired t-test will be used to 
test the difference in time for each parameter. If these changes are not normally distributed 
(p<0.05 by Shapiro-Wilks test), then a Wilcoxon signed rank test will be used instead of a t-test.  
In addition, a paired t-test or Wilcoxon signed rank test will be used to evaluate the significance 
of changes for each correlative end point. 
 
In an exploratory fashion, we hypothesize that patients harboring tumors with activating genomic 
alterations in PTEN, PIK3CA and AKT1 will show increased sensitivity and tumor response to 
use of MLN0128.  To evaluate this hypothesis we will test an expansion cohort of 10 
endometrial cancer patients. A recent study in patients with recurrent endometrial cancer patients 
indicated 17/31 patients harbored a genetic alteration in PTEN. The actual amount of PIK3CA 
mutation in this cohort is unknown, but activation of AKT (by measurement of pAKT) has 
generally demonstrated approximately 50% of patients with activation of this pathway. 10 
patients overall would provide 80% power (with an alpha = 10%) to detect a difference in 
progression free rate of about 50%, at three months between those harboring activating genomic 
alterations and those who do not using one-sided Z test with pooled variances.   
 
13.2.2 
Accrual rate: 
 
We estimate accrual of 2 patients per month for stage 1, with target goal for completion of 
accrual in 6 months. We estimate accrual of 2 patients per months for each cohort of stage 2, 
with target goal for completion of accrual in 6 months. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
93 
Accrual of Women and Minorities: 
 
For stage 2, patients accrued to ovarian and endometrial cancers, will be all women. 
 
 
Accrual Targets 
Ethnic Category 
Sex/Gender 
Females 
 
Males 
 
Total 
Hispanic or Latino 
3 
+ 
1 
= 
4 
Not Hispanic or Latino 
28 
+ 
10 
= 
38 
Ethnic Category: Total of all subjects 
31 
(A1) + 
11 
(B1) = 
42 
(C1) 
Racial Category 
 
American Indian or Alaskan Native 
0 
+ 
0 
= 
0 
Asian 
1 
+ 
1 
= 
2 
Black or African American 
3 
+ 
1 
= 
4 
Native Hawaiian or other Pacific 
Islander 
0 
+ 
0 
= 
0 
White 
27 
+ 
9 
= 
36 
Racial Category: Total of all subjects 
31 
(A2) + 
11 
(B2) = 
42 
(C2) 
 
(A1 = A2) 
 
(B1 = B2) 
 
(C1 = C2) 
 
 
13.3 
Stratification Factors 
 
None planned. 
 
 
13.4 
Analysis of Secondary and Exploratory Endpoints 
 
13.4.1 
Secondary Endpoints 
 
To assess the preliminary anti-tumor activity the combination of MLN0128 and bevacizumab, as 
determined by progression-free survival (PFS6), response rate (RR) and overall survival (OS). 
 
Response assessment data, PFS, and duration of response will be listed for all patients by dose 
level. 
 
Objective response rate will be estimated for patients, with disease measurable by RECIST or 
RANO (for recurrent GBM) guidelines. Objective response is defined as a complete or partial 
response, as determined by investigator assessment using RECIST or RANO. Patients with 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
94 
missing or no response assessments will be classified as non-responders. Among patients with an 
objective response, duration of response will be defined as the time from the initial complete or 
partial response to the time of disease progression or death. If a patient does not experience 
disease progression or death before the end of the study, duration of response will be censored at 
the day of the last tumor assessment. 
 
• To assess tolerability throughout study therapy with MLN0128 and bevacizumab, 
including beyond the MTD interval with the following measures of cumulative 
treatment-related toxicities:  
o Frequency of toxicities leading to missed doses or delays 
o Percentage of cycles given or not within 7 days of their scheduled times 
o Percentage of actual planned dosage administration 
o Percentage of patients that discontinue study drugs due to treatment related 
toxicity. 
 
The above percentages will be summarized. 
 
13.4.2 
Exploratory Endpoints 
 
• To assess CSF penetration of MLN0128 in combination with bevacizumab in patients with 
recurrent GBM by evaluating the plasma and CSF pharmacokinetic profile of MLN0128 in 
the absence and presence of bevacizumab. 
• To perform archival tumor analysis for markers associated with dysregulated cell signaling 
that may predict response to mTOR inhibitor therapy such as EGFR (expression by IHC and 
amplification by FISH), PTEN (expression by IHC and deletion by FISH), p-AKT, p-S6K, p-
4EBP, p-mTOR and p-Erk in patients with recurrent GBM.  
 
 
Plasma and CSF PK levels of MLN0128 obtained before and after bevacizumab administration 
will be evaluated and summarized. The ratio of plasma to CSF PK levels will also be 
summarized. 
 
The biomarkers predicting response to mTOR inhibitor activity will be resulted by dose level and 
response status. 
 
• Analysis of phosphorylated proteins (MEK1/2 (S217/221), AKT (S473, T308), PI3K, 
p70S6K (T389), MAPK1/2 (T202/204), GSK3beta(S21/S9), p27 (T157, T198), p38MAPK 
(T180/182), rS6K (S235/236, S240/244), and 4E-BP1 (S65)) at baseline and the change in 
these proteins after treatment with MLN0128 within tumor biopsies from patients with 
ovarian and endometrial cancers. 
• Analysis of circulating plasma levels of angiogenic growth factors before, during and after 
treatment with MLN0128 and bevacizumab in patients with ovarian and endometrial cancers. 
• Mutation analysis of tissue from biopsies of patients with ovarian and endometrial cancers 
including analysis of KRAS, BRAF, PIK3CA, AKT1 and PTEN. 
 
Please refer to section 13.2.1 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
95 
REFERENCES 
 
1. 
Wen PY, Kesari S. Malignant gliomas in adults. The New England journal of 
medicine 2008;359:492-507. 
 
2. 
Stupp R, Mason WP, van den Bent MJ, et al. Radiotherapy plus concomitant and 
adjuvant temozolomide for glioblastoma. The New England journal of medicine 
2005;352:987-96. 
 
3. 
Friedman HS, Prados MD, Wen PY, et al. Bevacizumab alone and in combination 
with irinotecan in recurrent glioblastoma. Journal of clinical oncology : official 
journal of the American Society of Clinical Oncology 2009;27:4733-40. 
 
4. 
Kreisl TN, Kim L, Moore K, et al. Phase II trial of single-agent bevacizumab 
followed by bevacizumab plus irinotecan at tumor progression in recurrent 
glioblastoma. Journal of clinical oncology : official journal of the American Society 
of Clinical Oncology 2009;27:740-5. 
 
5. 
Network CGAR. Comprehensive genomic characterization defines human 
glioblastoma genes and core pathways. Nature 2008;455:1061-8. 
 
6. 
Dunn GP, Rinne ML, Wykosky J, et al. Emerging insights into the molecular and 
cellular basis of glioblastoma. Genes & development 2012;26:756-84. 
 
7. 
Courtney KD, Corcoran RB, Engelman JA. The PI3K pathway as drug target in 
human cancer. Journal of clinical oncology : official journal of the American Society 
of Clinical Oncology 2010;28:1075-83. 
 
8. 
Galanis E, Buckner JC, Maurer MJ, et al. Phase II trial of temsirolimus (CCI-779) in 
recurrent glioblastoma multiforme: a North Central Cancer Treatment Group Study. 
Journal of clinical oncology : official journal of the American Society of Clinical 
Oncology 2005;23:5294-304. 
 
9. 
Reardon DA, Wen PY, Alfred Yung WK, et al. Ridaforolimus for patients with 
progressive or recurrent malignant glioma: a perisurgical, sequential, ascending-dose 
trial. Cancer Chemother Pharmacol 2012;69:849-60. 
 
10. 
Jemal A, Siegel R, Ward E, Hao Y, Xu J, Thun MJ. Cancer statistics, 2009. CA: a 
cancer journal for clinicians 2009;59:225-49. 
 
11. 
Mutter GL, Lin MC, Fitzgerald JT, et al. Altered PTEN expression as a diagnostic 
marker for the earliest endometrial precancers. Journal of the National Cancer 
Institute 2000;92:924-30. 
 
12. 
Oda K, Stokoe D, Taketani Y, McCormick F. High frequency of coexistent mutations 
of PIK3CA and PTEN genes in endometrial carcinoma. Cancer research 
2005;65:10669-73. 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
96 
 
13. 
Oza AM, Elit L, Tsao MS, et al. Phase II study of temsirolimus in women with 
recurrent or metastatic endometrial cancer: a trial of the NCIC Clinical Trials Group. 
Journal of clinical oncology : official journal of the American Society of Clinical 
Oncology 2011;29:3278-85. 
 
14. 
Alvarez EA, Brady WE, Walker JL, et al. Phase II trial of combination bevacizumab 
and temsirolimus in the treatment of recurrent or persistent endometrial carcinoma: a 
Gynecologic Oncology Group study. Gynecologic oncology 2013;129:22-7. 
 
15. 
Hollingsworth HC, Kohn EC, Steinberg SM, Rothenberg ML, Merino MJ. Tumor 
angiogenesis in advanced stage ovarian carcinoma. Am J Pathol 1995;147:33-41. 
 
16. 
Cannistra SA, Matulonis UA, Penson RT, et al. Phase II study of bevacizumab in 
patients with platinum-resistant ovarian cancer or peritoneal serous cancer. Journal of 
clinical oncology : official journal of the American Society of Clinical Oncology 
2007;25:5180-6. 
 
17. 
Altomare DA, Wang HQ, Skele KL, et al. AKT and mTOR phosphorylation is 
frequently detected in ovarian cancer and can be targeted to disrupt ovarian tumor cell 
growth. Oncogene 2004;23:5853-7. 
 
18. 
Sun M, Wang G, Paciga JE, et al. AKT1/PKBalpha kinase is frequently elevated in 
human cancers and its constitutive activation is required for oncogenic transformation 
in NIH3T3 cells. Am J Pathol 2001;159:431-7. 
 
19. 
Brognard J, Clark AS, Ni Y, Dennis PA. Akt/protein kinase B is constitutively active 
in non-small cell lung cancer cells and promotes cellular survival and resistance to 
chemotherapy and radiation. Cancer research 2001;61:3986-97. 
 
20. 
Behbakht K, Sill MW, Darcy KM, et al. Phase II trial of the mTOR inhibitor, 
temsirolimus and evaluation of circulating tumor cells and tumor biomarkers in 
persistent and recurrent epithelial ovarian and primary peritoneal malignancies: a 
Gynecologic Oncology Group study. Gynecologic oncology 2011;123:19-26. 
 
21. 
Courtney KD, Corcoran RB, Engelman JA. The PI3K pathway as drug target in 
human cancer. Journal of clinical oncology : official journal of the American Society 
of Clinical Oncology 2010;28:1075-83. 
 
22. 
Bjornsti MA, Houghton PJ. The TOR pathway: a target for cancer therapy. Nat Rev 
Cancer 2004;4:335-48. 
 
23. 
O'Donnell A, Faivre S, Burris HA, 3rd, et al. Phase I pharmacokinetic and 
pharmacodynamic study of the oral mammalian target of rapamycin inhibitor 
everolimus in patients with advanced solid tumors. Journal of clinical oncology : 
official journal of the American Society of Clinical Oncology 2008;26:1588-95. 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
97 
24. 
Cloughesy TF, Yoshimoto K, Nghiemphu P, et al. Antitumor activity of rapamycin in 
a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med 
2008;5:e8. 
 
25. 
Hudes G, Carducci M, Tomczak P, et al. Temsirolimus, interferon alfa, or both for 
advanced renal-cell carcinoma. The New England journal of medicine 
2007;356:2271-81. 
 
26. 
Markman B, Dienstmann R, Tabernero J. Targeting the PI3K/Akt/mTOR pathway--
beyond rapalogs. Oncotarget 2010;1:530-43. 
 
27. 
Carracedo A, Ma L, Teruya-Feldstein J, et al. Inhibition of mTORC1 leads to MAPK 
pathway activation through a PI3K-dependent feedback loop in human cancer. J Clin 
Invest 2008;118:3065-74. 
 
28. 
Nardella C, Carracedo A, Alimonti A, et al. Differential requirement of mTOR in 
postmitotic tissues and tumorigenesis. Sci Signal 2009;2:ra2. 
 
29. 
De PKR, Sun Y, Wu H, al. e. Pre-clinical potency of INK128, a highly potent 
TORC1/2 kinase inhibitor in the HER2 amplified breast cancer model. Cancer 
Research (abstract) 2012;72:2240. 
 
30. 
Kessler L, Jessen K, Janes M, al e. INK128, a TORC1/2 kinase inhibitor, enhances 
the efficacy of cytotoxic therapies in endometrial tumor models. Cancer Research 
(abstract) 2012;72:2745. 
 
31. 
Wang S, Jessen K, Kessler L, al. e. INK128, a novel TORC1/2 inhibitor with potent 
oral antitumor activity in preclinical models of renal cancer. Cancer research 
2011;71:4486. 
 
32. 
Kim KJ, Li B, Winer J, et al. Inhibition of vascular endothelial growth factor-induced 
angiogenesis suppresses tumour growth in vivo. Nature 1993;362:841-4. 
 
33. 
Presta LG, Chen H, O'Connor SJ, et al. Humanization of an anti-vascular endothelial 
growth factor monoclonal antibody for the therapy of solid tumors and other 
disorders. Cancer research 1997;57:4593-9. 
 
34. 
Borgstrom P, Gold DP, Hillan KJ, Ferrara N. Importance of VEGF for breast cancer 
angiogenesis in vivo: implications from intravital microscopy of combination 
treatments with an anti-VEGF neutralizing monoclonal antibody and doxorubicin. 
Anticancer research 1999;19:4203-14. 
 
35. 
Bergers G, Song S, Meyer-Morse N, Bergsland E, Hanahan D. Benefits of targeting 
both pericytes and endothelial cells in the tumor vasculature with kinase inhibitors. J 
Clin Invest 2003;111:1287-95. 
 
36. 
Shaheen RM, Ahmad SA, Liu W, et al. Inhibited growth of colon cancer 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
98 
carcinomatosis by antibodies to vascular endothelial and epidermal growth factor 
receptors. Br J Cancer 2001;85:584-9. 
 
37. 
Hurwitz H, Fehrenbacher L, Novotny W, et al. Bevacizumab plus irinotecan, 
fluorouracil, and leucovorin for metastatic colorectal cancer. The New England 
journal of medicine 2004;350:2335-42. 
 
38. 
Giantonio BJ, Catalano PJ, Meropol NJ, et al. Bevacizumab in combination with 
oxaliplatin, fluorouracil, and leucovorin (FOLFOX4) for previously treated metastatic 
colorectal cancer: results from the Eastern Cooperative Oncology Group Study 
E3200. Journal of clinical oncology : official journal of the American Society of 
Clinical Oncology 2007;25:1539-44. 
 
39. 
Sandler A, Gray R, Perry MC, et al. Paclitaxel-carboplatin alone or with bevacizumab 
for non-small-cell lung cancer. The New England journal of medicine 
2006;355:2542-50. 
 
40. 
Wong ET, Hess KR, Gleason MJ, et al. Outcomes and prognostic factors in recurrent 
glioma patients enrolled onto phase II clinical trials. Journal of clinical oncology : 
official journal of the American Society of Clinical Oncology 1999;17:2572-8. 
 
41. 
Sivridis E. Angiogenesis and endometrial cancer. Anticancer research 2001;21:4383-
8. 
 
42. 
Aghajanian C, Sill MW, Darcy KM, et al. Phase II trial of bevacizumab in recurrent 
or persistent endometrial cancer: a Gynecologic Oncology Group study. Journal of 
clinical oncology : official journal of the American Society of Clinical Oncology 
2011;29:2259-65. 
 
43. 
Burger RA, Sill MW, Monk BJ, Greer BE, Sorosky JI. Phase II trial of bevacizumab 
in persistent or recurrent epithelial ovarian cancer or primary peritoneal cancer: a 
Gynecologic Oncology Group Study. Journal of clinical oncology : official journal of 
the American Society of Clinical Oncology 2007;25:5165-71. 
 
44. 
Vlahovic G, Meadows KL, Uronis HE, et al. A phase I study of bevacizumab, 
everolimus and panitumumab in advanced solid tumors. Cancer Chemother 
Pharmacol 2012;70:95-102. 
 
45. 
Moroney J, Fu S, Moulder S, et al. Phase I study of the antiangiogenic antibody 
bevacizumab and the mTOR/hypoxia-inducible factor inhibitor temsirolimus 
combined with liposomal doxorubicin: tolerance and biological activity. Clin Cancer 
Res 2012;18:5796-805. 
 
46. 
Glusker P, Recht L, Lane B. Reversible posterior leukoencephalopathy syndrome and 
bevacizumab. The New England journal of medicine 2006;354:980-2; discussion -2. 
 
47. 
Kabbinavar F, Hurwitz HI, Fehrenbacher L, et al. Phase II, randomized trial 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
99 
comparing bevacizumab plus fluorouracil (FU)/leucovorin (LV) with FU/LV alone in 
patients with metastatic colorectal cancer. Journal of clinical oncology : official 
journal of the American Society of Clinical Oncology 2003;21:60-5. 
 
48. 
Nalluri SR, Chu D, Keresztes R, Zhu X, Wu S. Risk of venous thromboembolism 
with the angiogenesis inhibitor bevacizumab in cancer patients: a meta-analysis. 
JAMA  
2008;300:2277-85. 
 
49. 
Scappaticci FA, Skillings JR, Holden SN, et al. Arterial thromboembolic events in 
patients with metastatic carcinoma treated with chemotherapy and bevacizumab. 
Journal of the National Cancer Institute 2007;99:1232-9. 
 
50. 
Hapani S, Chu D, Wu S. Risk of gastrointestinal perforation in patients with cancer 
treated with bevacizumab: a meta-analysis. Lancet Oncol 2009;10:559-68. 
 
51. 
Chen HX, Cleck JN. Adverse effects of anticancer agents that target the VEGF 
pathway. Nat Rev Clin Oncol 2009;6:465-77. 
 
52. 
Scappaticci FA, Fehrenbacher L, Cartwright T, et al. Surgical wound healing 
complications in metastatic colorectal cancer patients treated with bevacizumab. J 
Surg Oncol 2005;91:173-80. 
 
53. 
Genentech. Bevacizumab Investigator's Brochure. 2005:South San Francisco, CA. 
 
54. 
Miller KD, Chap LI, Holmes FA, et al. Randomized phase III trial of capecitabine 
compared with bevacizumab plus capecitabine in patients with previously treated 
metastatic breast cancer. Journal of clinical oncology : official journal of the 
American Society of Clinical Oncology 2005;23:792-9. 
 
55. 
Infante JR, Taberno J, H.A. B, et al. A phase I, open label, dose escalation study of an 
oral mammalian target of rapamycin inhibitor INK128 administered once daily in 
patients with advanced malignancies. Cancer Research (abstract) 2012;72. 
 
56. 
Gangadhar TC, Cohen EE, Wu K, et al. Two drug interaction studies of sirolimus in 
combination with sorafenib or sunitinib in patients with advanced malignancies. Clin 
Cancer Res 2011;17:1956-63. 
 
57. 
Alvarez EA, Brady WE, Walker J, et al. Phase II trial of combination bevacizumab 
and temsirolimus in the treatment of recurrent or persistent endometrial carcinoma: A 
Gynecologic Oncology Group study. Gynecologic oncology 2012. 
 
58. 
Goudar RK, Shi Q, Hjelmeland MD, et al. Combination therapy of inhibitors of 
epidermal growth factor receptor/vascular endothelial growth factor receptor 2 
(AEE788) and the mammalian target of rapamycin (RAD001) offers improved 
glioblastoma tumor growth inhibition. Mol Cancer Ther 2005;4:101-12. 
 
59. 
Gokmen-Polar Y, Liu Y, Toroni RA, et al. Cancer Research (abstract) 2010;70. 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
100 
 
60. 
Eisenhauer EA, Therasse P, Bogaerts J, et al. New response evaluation criteria in 
solid tumours: revised RECIST guideline (version 1.1). Eur J Cancer 2009;45:228-47. 
 
61. 
Wen PY, Macdonald DR, Reardon DA, et al. Updated response assessment criteria 
for high-grade gliomas: response assessment in neuro-oncology working group. 
Journal of clinical oncology : official journal of the American Society of Clinical 
Oncology 2010;28:1963-72. 
 
62. 
American Society of Clinical Oncology. Recommendations for the use of 
hematopoietic colony-stimulating factors: evidence-based, clinical practice 
guidelines. Journal of clinical oncology : official journal of the American Society of 
Clinical Oncology 1994;12:2471-508. 
 
63. 
Lee JM, Hays JL, Noonan AM, et al. Feasibility and safety of sequential research-
related tumor core biopsies in clinical trials. Cancer 2013;119:1357-64. 
 
64. 
Roychowdhury S, Iyer MK, Robinson DR, et al. Personalized oncology through 
integrative high-throughput sequencing: a pilot study. Science translational medicine 
2011;3:111ra21. 
 
65. 
Nicosia SV, Bai W, Cheng JQ, Coppola D, Kruk PA. Oncogenic pathways implicated 
in ovarian epithelial cancer. Hematol Oncol Clin North Am 2003;17:927-43. 
 
66. 
Al-Ayoubi A, Tarcsafalvi A, Zheng H, Sakati W, Eblen ST. ERK activation and 
nuclear signaling induced by the loss of cell/matrix adhesion stimulates anchorage-
independent growth of ovarian cancer cells. J Cell Biochem 2008;105:875-84. 
 
67. 
Winters M, Dabir B, Yu M, Kohn EC. Constitution and quantity of lysis buffer alters 
outcome of reverse phase protein microarrays. Proteomics 2007;7:4066-8. 
 
68. 
Posadas EM, Kwitkowski V, Kotz HL, et al. A prospective analysis of imatinib-
induced c-KIT modulation in ovarian cancer: a phase II clinical study with proteomic 
profiling. Cancer 2007;110:309-17. 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
101 
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. 
 
 
 
 
 
 
 
 
 
 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
102 
APPENDIX B 
CTEP MULTICENTER GUIDELINES 
 
If an institution wishes to collaborate with other participating institutions in performing a 
CTEP sponsored research protocol, then the following guidelines must be followed. 
 
Responsibility of the Protocol Chair  
• The Protocol Chair will be the single liaison with the CTEP Protocol and Information 
Office (PIO).  The Protocol Chair is responsible for the coordination, development, 
submission, and approval of the protocol as well as its subsequent amendments.  The 
protocol must not be rewritten or modified by anyone other than the Protocol Chair.  
There will be only one version of the protocol, and each participating institution will use 
that document.  The Protocol Chair is responsible for assuring that all participating 
institutions are using the correct version of the protocol. 
• The Protocol Chair is responsible for the overall conduct of the study at all participating 
institutions and for monitoring its progress.  All reporting requirements to CTEP are the 
responsibility of the Protocol Chair.  
• The Protocol Chair is responsible for the timely review of Adverse Events (AE) to assure 
safety of the patients. 
• The Protocol Chair will be responsible for the review of and timely submission of data 
for study analysis. 
 
Responsibilities of the Coordinating Center 
• Each participating institution will have an appropriate assurance on file with the Office 
for Human Research Protection (OHRP), NIH.  The Coordinating Center is responsible 
for assuring that each participating institution has an OHRP assurance and must maintain 
copies of IRB approvals from each participating site.  
• Prior to the activation of the protocol at each participating institution, an OHRP form 310 
(documentation of IRB approval) must be submitted to the CTEP PIO. 
• The Coordinating Center is responsible for central patient registration.  The Coordinating 
Center is responsible for assuring that IRB approval has been obtained at each 
participating site prior to the first patient registration from that site. 
• The Coordinating Center is responsible for the preparation of all submitted data for 
review by the Protocol Chair. 
• The Coordinating Center will maintain documentation of AE reports.  There are two 
options for AE reporting: (1) participating institutions may report directly to CTEP with a 
copy to the Coordinating Center, or (2) participating institutions report to the 
Coordinating Center who in turn report to CTEP.  The Coordinating Center will submit 
AE reports to the Protocol Chair for timely review. 
• Audits may be accomplished in one of two ways:  (1) source documents and research 
records for selected patients are brought from participating sites to the Coordinating 
Center for audit, or (2) selected patient records may be audited on-site at participating 
sites.  If the NCI chooses to have an audit at the Coordinating Center, then the 
Coordinating Center is responsible for having all source documents, research records, all 
IRB approval documents, NCI Drug Accountability Record forms, patient registration 
lists, response assessments scans, x-rays, etc. available for the audit. 
 

NCI Protocol #: 9552 
Version 9.0 Date:  04-October-2016 
103 
Inclusion of Multicenter Guidelines in the Protocol 
• The protocol must include the following minimum information:  
➢ The title page must include the name and address of each participating institution and 
the name, telephone number and e-mail address of the responsible investigator at each 
participating institution. 
➢ The Coordinating Center must be designated on the title page. 
➢ Central registration of patients is required.  The procedures for registration must be 
stated in the protocol. 
➢ Data collection forms should be of a common format.  Sample forms should be 
submitted with the protocol.  The frequency and timing of data submission forms to 
the Coordinating Center should be stated. 
➢ Describe how AEs will be reported from the participating institutions, either directly 
to CTEP or through the Coordinating Center. 
➢ Describe how Safety Reports and Action Letters from CTEP will be distributed to 
participating institutions. 
 
Agent Ordering 
• Except in very unusual circumstances, each participating institution will order DCTD-
supplied investigational agents directly from CTEP.  Investigational agents may be 
ordered by a participating site only after the initial IRB approval for the site has been 
forwarded by the Coordinating Center to the CTEP PIO.  
 
 
 

 
104 
 
APPENDIX C 
STRONG INHIBITORS AND STRONG INDUCERS OF CYP2C9, CYP2C19 
AND CYPE3A4 
 
 
Strong Inhibitors 
Strong Inducers 
indinavir 
carbamazepine 
nelfinavir 
phenobarbital 
ritonavir 
phenytoin 
clarithromycin 
rifabutin 
itraconazole 
St. John’s wort 
ketoconazole 
troglitazone 
nefazodone 
secobarbital 
fluconazole 
rifampin 
saquinavir 
 
telithromycin 
 
fluvoxamine 
 
telithromycin 
 
fluvoxamine 
 
mibefradil 
 
omeprazole 
 
Ticlopidine 
 
 
Fruits and juice 
 
Star fruit and juice 
 
pomegranate fruit and juice 
 
grapefruit and juice 
 
Seville oranges and juice 
 
papaya fruit and juice 
 
 
Sources: ganfyd.org/index.php?title=Inhibitors_of_CYP3A4 and medicine.iupui.edu/clinpharm/ddis/ 
 
 
 
 
 
 
 
 
 
 
 
 

 
105 
 
APPENDIX D 
DATA AND SAFETY MONITORING PLAN 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 DFCI IRB Protocol #: 14-079 
 
Dana-Farber/Harvard Cancer Center 
Multi-Center Data and Safety Monitoring Plan 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 
106 
 
 
 
Table of Contents 
1.0 
INTRODUCTION 
1.1 
Purpose 
1.2 
Multi-Center Data and Safety Monitoring Plan Definitions 
2.0 
GENERAL ROLES AND RESPONSIBILITIES 
2.1 
Protocol Chair 
2.2 
Coordinating Center 
2.3 
DF/HCC Quality Assurance Office for Clinical Trials (QACT) 
2.4 
Participating Institution 
3.0 
DF/HCC REQUIREMENTS FOR MULTI-CENTER PROTOCOLS 
3.1 
Protocol Distribution 
3.2 
Protocol Revisions and Closures 
3.3 
Informed Consent Requirements 
3.4 
IRB Documentation 
3.5 
IRB Re-Approval 
3.6 
Participant Confidentiality and Authorization Statement 
3.7 
DF/HCC Multi-Center Protocol Registration Policy 
3.8 
DF/HCC Protocol Case Number 
3.9 
Protocol Deviations, Exceptions and Violations 
3.10 
Safety Assessments and Toxicity Monitoring 
3.11 
Data Management 
4.0 
Requisitioning Investigational Drug 
4.1 
CTEP Trial Routine Drug Requisitions 
5.0 
MONITORING: QUALITY CONTROL 
5.1 
Monitoring by NCI/CTEP 
5.2 
Monitoring by DFCI Coordinating Center 
5.3 
Evaluation of Participating Institution Performance 
6.0 
AUDITING: QUALITY ASSURANCE 
6.1 
NCI Sponsored Trials 
6.2 
DF/HCC Sponsored Trials 
6.3 
Participating Institution 
6.4 
Protocol Chair and Coordinating Center 
6.5 
Sub-Standard Performance 
 
 
 
 
 

 
107 
 
 
1.0 INTRODUCTION 
 
The Dana-Farber/Harvard Cancer Center Multi-Center Data and Safety Monitoring Plan (DF/HCC 
DSMP) outlines the procedures for conducting a DF/HCC Multi-Center research protocol. The 
DF/HCC DSMP should serve as a reference for any sites external to DF/HCC that will be 
participating in the research protocol. 
 
1.1 Purpose 
 
To establish standards that will ensure that a Dana-Farber/Harvard Cancer Center Multi-Center 
protocol will comply with Federal Regulations, Health Insurance Portability and Accountability Act 
(HIPAA) requirements and applicable DF/HCC Standard Operating Procedures, and Cancer 
Therapy Evaluation  Program (CTEP) Multi-Center Guidelines.        
 
1.2 Multi-Center Data and Safety Monitoring Plan Definitions 
 
DF/HCC Multi-center Protocol:  A research protocol in which one or more outside institutions are 
collaborating with Dana-Farber/Harvard Cancer Center where a DF/HCC investigator is the sponsor. 
DF/HCC includes Dana-Farber/Partners Cancer Care (DF/PCC) Network Clinical Trial Affiliates.  
 
Lead Institution:  One of the Dana-Farber/Harvard Cancer Center consortium members (Dana-
Farber Cancer Institute (DFCI), Massachusetts General Hospital (MGH), Beth Israel Deaconess 
Medical Center (BIDMC), Children’s Hospital Boston (CHB), Brigham and Women’s Hospital 
(BWH)) responsible for the coordination, development, submission, and approval of a protocol as 
well as its subsequent amendments per the DFCI IRB and applicable regulatory guidelines (CTEP, 
Food and Drug Administration (FDA), etc.).  The Lead Institution is typically the home of the 
Protocol Chair. The Lead Institution also typically serves as the Coordinating Center for the 
DF/HCC Multi-Center Protocol.   
 
Protocol Chair:  The person sponsoring the submitted Multi-Center protocol.  Within DF/HCC, this 
person is the Overall Principal Investigator who takes responsibility for initiation, management and 
conduct of the protocol at all research locations. In this protocol, the Protocol Chair will serve as the 
single liaison with any regulatory agencies (i.e. CTEP Protocol and Information Office (PIO), etc.). 
The Protocol Chair has ultimate authority over the protocol and is responsible for the conduct of the 
study at DF/HCC and all Participating Institutions. In this case the Protocol Chair is the same person 
as the DF/HCC Principal Investigator; however, both roles can be filled by two different people.  
 
Participating Institution:  An institution that is outside the DF/HCC and DF/PCC consortium that 
is collaborating with DF/HCC on a protocol where the sponsor is a DF/HCC Investigator.  The 
Participating Institution acknowledges the Protocol Chair as having the ultimate authority and 
responsibility for the overall conduct of the study.    
 
 
Coordinating Center: The entity (i.e. Lead Institution, Medical Monitor, Contract Research 
Organization (CRO), etc) that provides administrative support to the Protocol Chair in order that 
he/she may fulfill the responsibilities outlined in the protocol document and DSMP, and as specified 
in applicable regulatory guidelines (i.e. CTEP Multi-Center Guidelines). In general, the Lead 
Institution is the Coordinating Center for the DF/HCC Multi-Center Protocol. Should the Protocol 
Chair decide to use a CRO, the CRO will be deemed the Coordinating Center.   
 

 
108 
 
DF/HCC Quality Assurance Office for Clinical Trials: A unit within DF/HCC developed to 
computerize and manage data, and to provide a Quality Control and Quality Assurance function for 
DF/HCC trials.   
 
2.0 GENERAL ROLES AND RESPONSIBILITIES 
 
In accordance with CTEP Multi-Center Guidelines, the Protocol Chair, Coordinating Center, and the 
Participating Institutions are expected to adhere to the following general responsibilities:  
 
2.1 Protocol Chair 
 
The Protocol Chair, Lakshmi Nayak, MD, will accept responsibility for all aspects of conducting a 
DF/HCC Multi-Center protocol which includes but is not limited to:  
• Oversee the coordination, development, submission, and approval of the protocol as well as 
subsequent amendments.  
• Ensure that the investigators, study team members, and Participating Institutions are 
qualified and appropriately resourced to conduct the protocol.   
• Submit the Multi-Center Data and Safety Monitoring Plan as an appendix to the protocol. 
• Assure all Participating Institutions are using the correct version of the protocol. 
• Ensure that each participating investigator and study team receives adequate protocol 
training and/or a Site Initiation Visit prior to enrolling participants and throughout trial’s 
conduct as needed. 
• Monitor progress and overall conduct of the study at all Participating Institutions.  
• Ensure all DFCI Institutional Review Board (IRB), DF/HCC and other applicable (i.e. CTEP, 
FDA) reporting requirements are met.  
• Review data and maintain timely submission of data for study analysis.  
• Act as the single liaison with CTEP/PIO Office (CTEP trials). 
• Ensure compliance with all requirements as set forth in the Code of Federal Regulations, 
applicable DF/HCC requirements, HIPAA requirements, and the approved protocol. 
• Commit to the provision that the protocol will not be rewritten or modified by anyone other 
than the Protocol Chair. 
• Identify and qualify Participating Institutions and obtain accrual commitments prior to 
extending the protocol to that site.  
 
2.2 Coordinating Center  
 
The Coordinating Center will assume the following general responsibilities: 
• Assist in protocol development  
• Maintain copies of Federal Wide Assurance and Institutional Review Board (IRB) approvals 
from all Participating Institutions. 
• Maintain CTEP correspondence. 
• Maintain updated roster of participants.  
• Verify eligibility. 
• Verify response. 
• Collect data on protocol specific CRFs. 
• Maintain documentation of Serious Adverse Event (SAE) reports submitted by Participating 
Institutions to CTEP.   
• Provide Participating Institutions with information regarding DF/HCC requirements that they 
will be expected to comply with. 
 
 
• Monitor Participating Institutions either by on-site or virtual monitoring.  

 
109 
 
• Maintain Regulatory documents of all Participating Institutions.  
• Conduct regular communications with all Participating Institutions (conference calls, emails, 
etc).  
• Maintain documentation of all communications. 
• Ensure that each Participating Institution has the appropriate assurance on file with the 
Office of Human Research Protection (OHRP).     
• Compile and submit a complete report via the Clinical Data Update System (CDUS) 
quarterly for all participants.   
 
2.2.1 Coordinating Center Contact Information 
 
The DF/HCC Coordinating Center will consist of designees from both the Neuro-
Oncology Department, as well as the Early Drug Development Center (Phase I).  
Responsibilities will be split within the departments as specified below, although 
may be updated based on Protocol Chair discretion. 
 
➢ Central email addresses to be used for general site questions: 
dfcieddc_regulatory@dfci.harvard.edu, 
and 
NeuroOnc_Coor@dfci.harvard.edu  
➢ EDDC: Regulatory functions including but not limited to amendments, 
teleconferences, INDSR and SAE review and circulation, overall 
coordination of accrual, etc.  
o Study Coordinator: Ketki Bhushan 
▪ Phone: (617) 632-4270 
▪ Email: kbhushan@partners.org  
➢ Neuro-Onc: Monitoring functions including but not limited to site initiation 
visits, monitoring plan development and maintenance, eligibility review 
and registration, interim monitoring visits, violation tracking, etc.  
o Responsible Data Manager (Monitor): Katrina Smith 
▪ Phone: (617) 632-3780 
▪ Email: khsmith@partners.org  
 
2.3 DF/HCC Quality Assurance Office for Clinical Trials (QACT) 
 
In addition to the Coordinating Center, the DF/HCC QACT provides the following support services 
to assist the Protocol Chair: 
• Develop protocol specific case report forms (CRF/eCRFS). 
• QA/QC data of protocol specific CRFs.  
• Provide a central participant registration, which includes review of consent and eligibility. 
• Provide auditing services (funding and QACT approval required). 
 
2.4 Participating Institution 
 
Each Participating Institution is expected to comply with all applicable Federal Regulations and 
DF/HCC requirements, the protocol and HIPAA requirements. All Participating Institutions will 
provide a list of personnel assigned to the role for oversight of data management at their site to the 
Coordinating Center.  
 
The general responsibilities for each Participating Institution are as follows: 
• Commit to the accrual of participants to the protocol. 
• Submit protocol and/or amendments to their local IRB. 

 
110 
 
• Maintain a regulatory binder in accordance with DF/HCC requirements. 
• Provide the Coordinating Center with regulatory documents as requested. 
• Participate in protocol training prior to enrolling participants and throughout the trial as 
needed (i.e. teleconferences). 
• Update Coordinating Center with research staff changes on a timely basis. 
• Register participants through the Coordinating Center.  
• Submit source documents, research records, and CRFs per protocol specific submission 
guidelines to the Coordinating Center. 
• Submit Serious Adverse Event (SAE) reports to local IRB per local requirements and 
provide copies to the Coordinating Center, in accordance with DF/HCC requirements.  
• Submit SAE reports directly to CTEP and provide copies to the Coordinating Center  
• Submit protocol deviations and violations to local IRB per local requirements and provide 
copies to the Coordinating Center, in accordance with DF/HCC requirements. 
▪ Deviations should be prospectively approved by the Protocol Chair as per DFCI 
guidelines.  
• Secure and store investigational agents and other protocol mandated drugs per federal 
guidelines and protocol requirements. 
• Have office space, office equipment, and internet access that meet HIPAA standards. 
• Order their own investigational agents regardless of the supplier (i.e. National Cancer 
Institute [NCI]). 
 
3.0 DF/HCC REQUIREMENTS FOR MULTI-CENTER PROTOCOLS 
 
The following section will clarify DF/HCC Requirements and further detail the expectations for 
participating in a DF/HCC Multi-Center protocol.  
 
3.1 Protocol Distribution 
 
The Coordinating Center will distribute the final DFCI IRB approved protocol and any subsequent 
amended protocols to all Participating Institutions.    
 
3.2 Protocol Revisions and Closures 
 
The Participating Institutions will receive notification of protocol revisions and closures from the 
Coordinating Center.  It is the individual Participating Institution’s responsibility to notify its IRB of 
these revisions. 
 
• Non life-threatening revisions: Participating Institutions will receive written notification of 
protocol revisions regarding non life-threatening events from the Coordinating Center. Non-
life-threatening protocol revisions must be IRB approved and implemented within 90 days 
from receipt of the notification. 
 
• Revisions for life-threatening causes: Participating Institutions will receive immediate 
notification from the Coordinating Center concerning protocol revisions required to protect 
lives with follow-up by fax, mail, e-mail, etc.  Life-threatening protocol revisions will be 
implemented immediately followed by IRB request for approval. 
 
• Protocol closures and temporary holds: Participating Institutions will receive notification 
of protocol closures and temporary holds from the Coordinating Center. Closures and holds 
will be effective immediately.  In addition, the Coordinating Center, will update the 

 
111 
 
Participating Institutions on an ongoing basis about protocol accrual data so that they will be 
aware of imminent protocol closures. 
 
3.3 Informed Consent Requirements 
 
The DF/HCC approved informed consent document will serve as a template for the informed 
consent for Participating Institutions. The Participating Institution consent form must follow the 
consent template as closely as possible and should adhere to specifications outlined in the DF/HCC 
Guidance Document on Model Consent Language for PI-Initiated Multi-Center Protocols.  This 
document will be provided separately to each Participating Institution. 
 
Participating Institutions are to send their version of the informed consent document and HIPAA 
authorization, if a separate document, to the Coordinating Center for review and approval prior to 
submission to their local IRB. The approved consent form must also be submitted to the 
Coordinating Center after approval by the local IRB. 
 
The Principal Investigator (PI) at each Participating Institution will identify the physician members 
of the study team who will be obtaining consent and signing the consent form for therapeutic 
protocols. Participating institutions must follow the DF/HCC requirement that only attending 
physicians obtain informed consent and re-consent to interventional trials (i.e. drug and/or device 
trials).   
 
3.4 IRB Documentation 
 
The following must be on file with the Coordinating Center: 
• Approval letter of the Participating Institution's IRB  
• Copy of the Informed Consent Form approved by the Participating Institution’s IRB  
• Participating IRB’s approval for all amendments 
 
It is the Participating Institution's responsibility to notify its IRB of protocol amendments.  
Participating Institutions will have 90 days from receipt to provide the Coordinating Center their 
IRB approval for amendments to a protocol.    
 
3.5 IRB Re-Approval 
 
Verification of IRB re-approval from the Participating Institutions is required in order to continue 
research activities.  There is no grace period for continuing approvals. 
 
The Coordinating Center will not register participants if a re-approval letter is not received from the 
Participating Institution on or before the anniversary of the previous approval date.   
 
 
3.6 Participant Confidentiality and Authorization Statement 
 
In 1996, congress passed the first federal law covering the privacy of health information known as 
the Health Insurance Portability and Accountability Act (HIPAA). Any information, related to the 
physical or mental health of an individual is called Protected Health Information (PHI). HIPAA 
outlines how and under what circumstances PHI can be used or disclosed.  
 
In order for covered entities to use or disclose protected health information during the course of a 
study, the study participant must sign an Authorization.  This Authorization may or may not be 

 
112 
 
separate from the informed consent document.  The Coordinating Center, with the approval from the 
DFCI IRB and CTEP, will provide a consent template, which covered entities (Participating 
Institutions) must use.  
 
The Protocol Chair will use all efforts to limit its use of protected health information in its trials.  
However, because of the nature of these trials, certain protected health information must be collected 
per NCI requirements. These are the primary reasons why DF/HCC has chosen to use 
Authorizations, signed by the participant in the trial, rather than limited data sets with data use 
agreements. 
 
3.6.1 DF/HCC Multi-Center Protocol Confidentiality 
 
All documents, investigative reports, or information relating to the participant are strictly 
confidential. Whenever reasonably feasible, any participant specific reports (i.e. Pathology Reports, 
MRI Reports, Operative Reports, etc.) submitted to the Coordinating Center must have the 
participant’s full name & social security number “blacked out” and the assigned DF/HCC QACT 
case number (as described below) and DF/HCC protocol number written in (with the exception of 
the signed informed consent document). Participant initials may only be included or retained for 
cross verification of identification 
 
3.7 DF/HCC Multi-Center Protocol Registration Policy 
 
3.7.1 Participant Registration and Randomization  
 
Eligible participants will be registered onto the trial with the DF/HCC Quality 
Assurance Office for Clinical Trials (QACT) central registration system.  
Registration must occur prior to the initiation of therapy. Registration should 
occur during QACT’s normal business hours, Monday through Friday from 8:00 
AM to 5:00 PM Eastern Time. Same day treatment registrations and off-hours 
registrations for a participant at a non-DF/HCC site will only be accepted with 
prior notice and discussion with the Coordinating Center.  
 
3.7.1.1 Participant Registration at a non-DF/HCC site 
 
Eligibility participants will be entered on study centrally at the Coordinating 
Center by the Study Coordinator.  All sites should call the Study Coordinator to 
verify dose level availabilities.  The required forms mentioned below will be 
provided to sites by the Coordinating Center during site activation. Issues that 
would cause treatment delays should be discussed with the Overall Principal 
Investigator (PI).  If a participant does not receive protocol therapy following 
registration, the participant’s registration on the study must be cancelled.  The 
Study Coordinator should be notified of cancellations as soon as possible.  
 
To register a participant at any non-DF/HCC site, the subsequent procedures must 
be followed.  Contact information for the Coordinating Center is located in section 
2.2.1. 
 
1. The Participant Site should contact the Coordinating Center to –  
➢ Notify regarding the potential participant  
➢ Confirm the methods of sending documents and communication for the 
registration 

 
113 
 
➢ Communicate desired timeline of the registration and start date 
2. The Participating Site should then send the following documents to the 
Coordinating Center –  
➢ Completed DF/HCC Eligibility Source Worksheet (ESW), which will be 
provided to each site separately  
➢ Copy of all protocol required screening test results, as requested on the 
ESW 
➢ Copy of the pathology and surgical reports, as requested on the ESW 
➢ List of all concomitant medications with review by a clinician 
➢ Copy of the signed informed consent document 
➢ Copy of the signed HIPAA authorization form (if separate from the 
informed consent document) 
3. After having received all documentation, the Coordinating Center will review 
the documents to verify eligibility. 
4. The Coordinating Center will register the participant with QACT, and 
subsequently inform the participating site of the successful registration via fax 
or email, to include 
➢ Participant case number 
➢ Applicable dose treatment level 
5. Treatment may not begin without confirmation from the Coordinating 
Center that the participant has been registered.  
6. After the participant is registered, additional documentation is to be sent to the 
Coordinating Center if it was not included in the upfront submission. The 
specifics and timeline of this will be specified by the Coordinating Center 
within the instructions for the Eligibility Source Worksheet.  
 
NOTE: Registration and randomization with the QACT can only be conducted 
during the business hours of 8:00 AM and 5:00 PM Eastern Standard Time 
Monday through Friday. Same day treatment registrations will only be accepted 
with prior notice and discussion with the DF/HCC Lead Institution.  
 
3.7.1.2 Participant Registration at a DF/HCC site 
 
The QACT registration staff is accessible on Monday through Friday, from 8:00 
AM to 5:00 PM Eastern Standard Time.  In emergency situations when a 
participant must begin protocol therapy during off-hours or holidays, call the 
QACT registration line at 617-632-3761 and follow the instructions for registering 
participants after hours.  
 
An investigator will confirm eligibility crtieria and a member of the study team 
will complete the QACT protocol-specific eligibility cehcklist.   
 
Following registration, participants may begin protocol therapy.  Issues that would 
cause treatment delays should be discussed with the Overall Principal Investigator 
(PI).  If a participant does not receive protocol therapy following registration, the 
participant’s registration on the study must be cancelled. Notify the QACT 
Registrar of registration cancellations as soon as possible.  
 
To register a participant at a DF/HCC site, the subsequent procedures must be 
followed.  Contact information for the Coordinating Center is located in section 
2.2.1.  

 
114 
 
 
• Obtain written informed consent from the participant prior to the 
performance of any protocol specific procedures or assessments 
• Complete the QACT protocol-specific eligibility checklist using the 
eligibility assessment document in the participant’s medical record and/or 
research chart.  To be eligible for registration to the protocol, the 
participant must meet all inclusion and exclusion criterion as 
described in the protocol and reflected on the eligibility checklist.  
• Fax the eligibility checklist and all pages of the consent form to the QACT 
at 617-632-2229.   
• The QACT Registrar will (a) review the eligibility checklist, (b) register 
the participant on the protocol, and (c) randomize the participant when 
applicable.  
• An email confirmation of the registration and/or randomization will be sent 
to the Overall PI, study coordinator(s) from the Lead Site, treating 
investigator and registering person immediately following the registration 
and/or randomization. 
 
3.7.2 Initiation of Therapy 
 
Participants must be registered with the DF/HCC QACT before receiving treatment.  Treatment may 
not be initiated until the Participating Institution receives a faxed or e-mailed copy of the 
participant’s registration confirmation memo from the Coordinating Center. Therapy must be 
initiated per protocol guidelines.  The Coordinating Center and DFCI IRB must be notified of any 
exceptions to this policy. 
 
3.7.3 Eligibility Exceptions 
 
CTEP specifically prohibits registration of a participant on any NCI Sponsored protocol that does 
not fully and completely meet all eligibility requirements. The DF/HCC QACT will make no 
exceptions to the eligibility requirements for a protocol without DFCI IRB approval. The DF/HCC 
QACT requires each institution to fully comply with this requirement. 
 
3.7.4 Verification of Registration, Dose Levels, and Arm Designation 
 
A registration confirmation memo for participants registered to DF/HCC Multi-Center Protocol 
will be faxed or emailed to the registering institution within one business day of the registration. 
Treatment may not be initiated until the site receives a faxed or e-mailed copy of the registration 
confirmation memo. 
 
3.8 DF/HCC Protocol Case Number 
 
Once eligibility has been established and the participant successfully registered, the participant is 
assigned a five digit protocol case number.  This number is unique to the participant on this trial and 
must be used for QACT CRF/eCRF completion and correspondence, and correspondence with the 
Coordinating Center.   
 
3.9 Protocol Deviations, Exceptions and Violations 
 
Federal Regulations require an IRB to review proposed changes in a research activity to ensure that 
researchers do not initiate changes in approved research without IRB review and approval, except 

 
115 
 
when necessary to eliminate apparent immediate hazards to the participant. DF/HCC requires all 
departures from the defined procedures set forth in the IRB approved protocol to be reported to the 
Protocol Chair, who in turn is responsible for reporting to the DFCI IRB. 
 
 
For reporting purposes, DF/HCC uses the terms “violation”, “deviation” and “exception” to 
describe derivations from a protocol. All Participating Institutions must adhere to these 
requirements for reporting to the Protocol Chair and will follow their institutional policy for 
reporting to their local IRB. 
 
3.9.1 Definitions 
 
Protocol Deviation: Any departure from the defined procedures set forth in the IRB-approved 
protocol which is prospectively approved prior to its implementation. 
 
Protocol Exception:  Any protocol deviation that relates to the eligibility criteria, e.g. 
enrollment of a participant who does not meet all inclusion/exclusion criteria. 
 
 
 
Protocol Violation: Any protocol deviation that was not prospectively approved by the IRB prior to 
its initiation or implementation.  
 
 
3.9.2 Reporting Procedures 
 
Protocol Chair: is responsible for ensuring that clear documentation is available in the medical 
record and/or regulatory documents to describe all protocol exceptions, deviations and violations.  
 
All protocol violations must be sent to the Protocol Chair and Coordinating Center in a timely 
manner.  
 
3.10 Safety Assessments and Toxicity Monitoring 
 
The study teams at all participating institutions are responsible for protecting the safety, rights and 
well-being of study participants. Recording and reporting of adverse events that occur during the 
course of a study help ensure the continuing safety of study participants.  
 
All participants receiving investigational agents and/or other protocol mandated treatment will be 
evaluated for safety.   The safety parameters include all laboratory tests and hematological 
abnormalities, physical examination findings, and spontaneous reports of adverse events reported by 
participants.  All toxicities encountered during the study will be evaluated according to the NCI 
criteria specified in the protocol. Life-threatening toxicities must be reported immediately to the 
Protocol Chair via the Coordinating Center. These toxicities must also be reported via the CTEP-
AERS system as outlined in the protocol. 
 
Additional safety assessments and toxicity monitoring will be outlined in the protocol. 
 
3.10.1   Guidelines for Reporting Serious Adverse Events  
 
Guidelines for reporting Adverse Events (AEs) and Serious Adverse Events (SAEs) are detailed in 
protocol section 7. 
 
 
 
 
 
 
The Coordinating Center will maintain documentation of all Participating Institution Adverse Event 
reports that are reported to CTEP via CTEP-AERS.  The Coordinating Center will also be 

 
116 
 
responsible for communicating all relevant CTEP SAEs reported via CTEP-AERS to all participant 
sites.   
 
3.10.2 Guidelines for Processing IND Safety Reports  
 
FDA regulations require sponsors of clinical studies to notify the FDA and all participating 
investigators of any adverse experience associated with the use of the investigational agent that is 
both serious and unexpected. The Protocol Chair will review all IND Safety Reports and ensure that 
all IND Safety Reports are distributed to the Participating Institutions.  The Participating 
Investigators are to review, send a copy to their IRB according to their local IRB’s policies and 
procedures, and file a copy with their regulatory documents. 
 
 
 
 
3.11 Data Management 
 
The DF/HCC QACT develops a set of either paper or electronic case report forms (CRF/eCRFs), for 
use with the protocol.  These forms are designed to collect data for each study. The DF/HCC QACT 
provides a web based training for eCRF users. 
   
3.11.1 Data Forms Review 
 
When data forms arrive at the DF/HCC QACT, they are reviewed for completeness, protocol 
treatment compliance, adverse events (toxicities) and response. Data submissions are monitored for 
timeliness and completeness of submission. Participating Institutions are notified of their data 
submission delinquencies in accordance with the following: 
 
Incomplete or Questionable Data 
If study forms are received with missing or questionable data, the submitting institution will receive 
a written or electronic query from the DF/HCC QACT Data Analyst or study monitor.  Responses to 
all queries should be completed and submitted within 14 calendar days.  Responses may be returned 
on the written query or on an amended paper case report form, or in the case of electronic queries, 
within the electronic data capture (eDC) system. In the case of a written query for data submitted on 
a paper case report form, the query must be attached to the specific data being re-submitted in 
response.   
 
Missing Forms 
If study forms are not submitted on schedule, the Participating Institution will receive a Missing 
Form Report from the Coordinating Center noting the missing forms.  These reports are compiled by 
the DF/HCC QACT and distributed a minimum of four times a year.  
 
4.0 Requisitioning Investigational Drug 
 
 
The ordering of investigational agent is specified in protocol section 8.  
 
Participating Institutions should order their own agent. 
 
For commercially available agents (bevacizumab), participant institutions should check with the 
Research Pharmacy to ensure that the agent is in stock. If the agent is not stocked, ensure that the 
agent can be ordered once the protocol is approved by the local IRB.  
 
For investigational agents (MLN0128), participating institutions should ensure that the pharmacy will 
be able to receive and store the agent according to state and federal requirements. The local IRB 

 
117 
 
should be kept informed of who will supply the agent (NCI) so that any regulatory responsibilities 
can be met in a timely fashion.  
 
4.1 CTEP Trial Routine Drug Requisitions 
 
Investigational drugs for use in Cancer Therapy Evaluation Program’s (CTEP) approved protocols 
are obtained through the Pharmaceutical Management Branch at CTEP in accordance with the 
guidelines provided in the NCI’s Investigator Handbook. Participating Institutions should order 
drugs directly from Division of Cancer Treatment and Diagnosis (DCTD) by completing a Clinical 
Drug Request (CDR) Form NIH-986.  
 
4.1.1 Guidelines for Clinical Drug Request Submission 
 
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 
agents 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 Form FDA 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 (240) 276-6575 Monday 
through Friday between 8:30 am and 4:30 pm (ET) or email PMBAfterHours@mail.nih.gov 
anytime. 
 
5.0 MONITORING: QUALITY CONTROL 
 
The quality control process for a clinical trial requires verification of protocol compliance and data 
accuracy. NCI/CTEP, the DFCI Coordinating Center, and DF/HCC QACT provide quality control 
oversight for the protocol. 
 
5.1 Monitoring by NCI/CTEP 
 
The NCI will utilize a variety quality control procedures: 
• Built-in edit checks within the Electronic Data Capture System 
• Cross check of data between various electronic reporting systems 
• Site performance evaluations 
• Special Response reviews to verify outcome data 
• Committees for central review of major elements that impact on the outcome of clinical 
trials, e.g., pathology, radiotherapy, surgery, and administration of investigational agents; 
and 
• Educational functions which address data collection, data management, and overall data 
quality 

 
118 
 
 
5.2 Monitoring by DFCI Coordinating Center 
 
The Participating Institutions are to submit participant source documents to the Coordinating Center 
for virtual monitoring upon request. Participating Institution may also be subject to on-site 
monitoring conducted by the Coordinating Center. In addition, participating DF/HCC sites, 
including the lead institution, will be subject to monitoring as well.   
 
The Coordinating Center will implement ongoing monitoring activities to ensure that sites are 
complying with regulatory and protocol requirements, data quality, and participant safety. 
Monitoring will occur before the clinical phase of the protocol begins, continue during protocol 
performance and through study completion. Additional monitoring practices may include but are not 
limited to; source verification, review and analysis of the following: eligibility requirements of all 
participants , informed consent procedures, adverse events and all associated documentation, study 
drug administration/treatment, regulatory files, protocol deviations, pharmacy records, response 
assessments, and data management.  
 
Additionally, sites will be required to participate in Coordinating Center initiated teleconferences. 
These will be planned for bi-weekly during Stage 1 of the protocol and monthly during Stage 2, 
although they may be more/less frequent at the discretion of the Protocol Chair. During the 
teleconferences, sites will be expected to convey the following information: 
− 
Updates on participants taking agent: holds, dose reductions, significant events, how the 
participant is doing, whether or not underwent re-consenting 
− 
Protocol status – which version is being used, and the status of any amendments 
− 
Any reportable adverse events or deviations/violations that have yet to be submitted  
− 
Review of prospective patients 
 
If sites are not able to have a representative participant, they should email this information to the 
Coordinating Center.  
 
Virtual Monitoring will be the primary mode of monitoring, although on-site monitoring may occur 
if felt to be necessary by the Coordinating Center and Protocol Chair.  Upon request, sites will be 
required to forward de-identified copies of participants’ medical record and source documents to the 
Coordinating Center to aid in source data verification.  
− 
Virtual monitoring of participant eligibility, human subject’s protection via the initial informed 
consent document and process, and screening evaluation completion will occur, if feasible, 
within 2 weeks of the first participant registration.  
− 
Interim monitoring visits will occur on the following schedule:  
− 
Once a site has registered a participant, up until all participants have discontinued taking 
study agent (may be in follow-up), interim monitoring visits will occur approximately 
every 6 months, with the primary mode being virtual visits. This frequency may be 
adjusted depending on accrual, site compliance and Protocol Chair discretion.  The first 
interim monitoring visit will occur approximately two months after the registration of 
the site’s first participant.  
− 
Once a site is closed to accrual and all participants have discontinued study agent, 
interim monitoring visits will occur approximately annually until study completion. 
− 
Monitoring visits will focus on reviewing some or all of the following: 
− 
Adverse events and altered results 
− 
Response assessment including measurements and clinical assessments 
− 
Study drug administration and accountability 
− 
Concomitant medications 

 
119 
 
− 
Consent and re-consenting 
− 
Presence of key documents: original consent, eligibility and screening source 
information, registration confirmation, off treatment and off study forms, collection and 
transfer of samples 
− 
Reason off treatment and reason off study 
− 
Timeliness of data completion 
− 
Completion of study procedures per protocol 
− 
Agreement between recorded results and source documentation 
− 
Analysis of data for any events that meet criteria for reportable adverse events, dose 
holds, dose reductions, or discontinuation of treatment 
− 
Regulatory binder: accessibility, organization, random sampling for relevant documents 
and agreement with the trial master file 
− 
Collection of research samples per protocol and appropriately entered onto CRFs, as this 
will be the primary mode of tracking samples across sites 
 
The Coordinating Center will be available to all sites’ study team members for resolving questions 
and concerns and facilitating compliance. 
 
All data submitted to the DF/HCC QACT will be monitored for timeliness of submission, 
completeness, and adherence to protocol requirements. The Coordinating Center and if applicable, 
QACT Data Analysts assigned to the protocol, will perform the ongoing protocol data compliance 
monitoring. 
 
5.3 Evaluation of Participating Institution Performance 
 
5.3.1 Monitoring Reports 
 
The Protocol Chair will review all monitoring reports for on-site and virtual monitoring of sites to 
ensure protocol compliance and ability to fulfill responsibilities of participating in the study. The 
Protocol Chair may increase the monitoring activities at a particular site that is unable to comply 
with the protocol, DF/HCC or CTEP requirements or federal and local regulations. Participating 
sites may also be subject to an audit as determined by the Protocol Chair. 
 
6.0 AUDITING: QUALITY ASSURANCE 
 
Auditing is a method of Quality Assurance. Its main focus is to measure whether standards and 
procedures were followed. Auditing is the systematic and independent examination of all trial 
related activities and documents.  Audits determine if evaluated activities were appropriately 
conducted and whether data was generated, recorded and analyzed, and accurately reported per the 
protocol, Standard Operating Procedures (SOPs), and the Code of Federal Regulations (CFR). 
 
6.1 NCI Sponsored Trials 
 
The Clinical Trials Monitoring Branch (CTMB) of the National Cancer Institute may arrange on-site 
auditing for this study. Therefore, in some cases the Protocol Chair funded audits may not occur on-
site.    
 
Audits may be accomplished in one of two ways:  (1) source documents and research records for 
selected patients are brought from participating sites to the Coordinating Center for audit, or (2) 
selected patient records may be audited on-site at participating sites.  If the NCI chooses to have an 
audit at the Coordinating Center, then the Coordinating Center is responsible for having all source 

 
120 
 
documents, research records, all IRB approval documents, NCI Drug Accountability Record forms, 
patient registration lists, response assessments scans, x-rays, etc. available for the audit. 
 
Participating Institutions that are not a part of a major cancer center may not undergo the routine 
NCI/Theradex audits.  In those cases, the Participating Institution may be subject to on-site auditing 
conducted by the Coordinating Center. 
 
6.2 Participating Institution 
 
It is the Participating Institution’s responsibility to notify the Coordinating Center of all scheduled 
audit dates (internal or NCI) and re-audit dates (if applicable), which involve this protocol. All 
institutions will forward a copy of final audit and/or re-audit reports and corrective action plans (if 
applicable) to the Coordinating Center, within 12 weeks after the audit date.  
 
6.3 Protocol Chair and Coordinating Center  
 
The Protocol Chair will review all final audit reports and corrective action plans if applicable. The 
Coordinating Center, must forward these reports to the DF/HCC QACT per DF/HCC policy for 
review by the DF/HCC Audit Committee. Based upon the audit assessments the DF/HCC Audit 
Committee could accept or conditionally accept the audit rating and final report. Conditional 
approval could require the Protocol Chair to implement recommendations or require further follow-
up.   
 
6.4 Sub-Standard Performance 
 
The Protocol Chair, DFCI IRB and the NCI for CTEP trials, is charged with considering the totality 
of an institution’s performance in considering institutional participation in the protocol. 
 
6.4.1 Corrective Actions 
 
Participating Institutions that fail to meet the performance goals of accrual, submission of timely 
accurate data, adherence to protocol requirements, and compliance with state and federal regulations, 
will be recommended for a six-month probation period. Such institutions must respond with a 
corrective action plan and must demonstrate during the probation period that deficiencies have been 
corrected, as evidenced by the improved performance measures. Participating Institutions that fail to 
demonstrate significant improvement will be considered by the Protocol Chair for revocation of 
participation. 
 
 

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
121 
 
APPENDIX E 
DOSE LEVEL 1, 2 & 3 PILL DIARY FOR MLN0128 
 
 
 
Completed by study personnel:  Participant ID #_______   Participant Initials: _______  Cycle #: ______ 
Month & Year: _________ 
MLN0128 Daily Dose________mg/day 
To be completed by Participant or Guardian:      
 
Number of Pill Bottles Received:______ with 1 mg capsules;  _______with 3 mg capsules; :______ with 5 mg capsules 
 
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 

 
122 
 
 
Participant/Guardian Signature: _________________________________     Date: ________________   
 
To be completed by study personnel:  
Bottles Returned: ___with 1 mg capsules;  ___with 3 mg capsules;  ___with 5 mg capsules  
 
                                   Pills Returned: ___ 1 mg; ___3 mg; ___5 mg    
Compare w/ drug diary entries made by participant or guardian.  If discrepancy (in the # of bottles or the # of pills returned), please reconcile: 
 
 
Study Personnel Signature:________________________________  Date: _________________ 
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
No. of 5 mg pills 
_____ 
 
Participant Initials 
_________ 

 
123 
 
MLN0128 Dosing Instruction Sheet  
to Be Given to Study Participants with Participant Pill Diary 
 
MLN0128 Instructions – When and How: 
• 
MLN0128 is an oral drug. 
• 
Take MLN0128 every morning after a light meal at approximately the same time each day. 
• 
Take the capsule(s) with a glass of water and swallow your dose whole.  Do not chew them or suck on the capsules. 
Capsules should not be opened.  If you chew, suck or the capsule(s) open in your mouth, you should drink a large 
glass of water (about 8 ounces).  
• 
Please try to drink at least 18-24 ounces of liquids a day to stay well-hydrated. 
• 
If you vomit your dose, do not take another dose; you will take your next dose on the next day as usual.  You should 
write down in your pill diary that you vomited the pills. 
• 
If you forget to take your dose at your normal dosing time, you may still take the dose within 12 hours of the regular 
dosing time with a meal (you should not take 2 consecutive daily doses within less than 12 hours of each other).    
• 
If you miss your dose more than 12 hours after your regular dosing time you should write down in your pill diary 
that you missed the dose. 
           
Additional Instructions: 
• 
You must avoid eating or drinking any foods with Seville oranges (like marmalade), grapefruit or foods or drink with 
grapefruit, and any exotic fruits during the entire treatment period.   
• 
Keep your study drug in the original container.  
• 
Do not throw away empty pill bottles. 
• 
Bring this diary, all pill bottles, and any unused pills to all scheduled clinic visits. 
• 
Contact your study doctor or nurse if you are having any new or worsening side effects. 
 
 
Please note that on days that you are coming to clinic or having blood tests, you may need to take your pills in clinic visit because of 
required study tests. 

 
124 
 
APPENDIX F 
DOSE LEVEL 1A & -1 PILL DIARY FOR MLN0128 
 
 
 
Completed by study personnel:  Participant ID #_______   Participant Initials: _______  Cycle #: ______ 
Month & Year: _________ 
MLN0128 Dose________mg/day 5 of 7 days 
To be completed by Participant or Guardian:      
 
Number of Pill Bottles Received:______ with 1 mg capsules;  _______with 3 mg capsules 
 
 
 
 
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
No pills taken today. 
 
 
Date: 
No pills taken today. 
 
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
No pills taken today. 
 
 
 
 
Date: 
 
No pills taken today. 
 
 
 
 

 
125 
 
 
 
Participant/Guardian Signature: _________________________________     Date: ________________   
 
To be completed by study personnel:  Bottles Returned: __with 1 mg capsules;  __with 3 mg capsules;   Pills Returned: ___ 3 mg; ___4 mg 
Compare w/ drug diary entries made by participant or guardian.  If discrepancy (in the # of bottles or the # of pills returned), please reconcile: 
 
 
Study Personnel Signature:________________________________  Date: _________________ 
 
 
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
DAY:  
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
No pills taken today. 
 
 
 
Date: 
No pills taken today. 
 
 
 
 
 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
Time: 
 
No. of 1 mg pills 
_____ 
 
No. of 3 mg pills 
_____ 
 
Participant Initials 
_________ 
Date: 
No pills taken today. 
 
 
 
Date: 
 
No pills taken today. 
 
 
 
 

 
126 
 
MLN0128 Dosing Instruction Sheet  
to Be Given to Study Participants with Participant Pill Diary 
MLN0128 Instructions – When and How: 
• 
MLN0128 is an oral drug. 
• 
Take MLN0128 every morning after a light meal at approximately the same time each day. 
• 
Take the capsule(s) with a glass of water and swallow your dose whole.  Do not chew them or suck on the capsules. Capsules should 
not be opened.  If you chew, suck or the capsule(s) open in your mouth, you should drink a large glass of water (about 8 ounces).  
• 
Please try to drink at least 18-24 ounces of liquids a day to stay well-hydrated. 
• 
If you vomit your dose, do not take another dose; you will take your next dose on the next day as usual.  You should write down in 
your pill diary that you vomited the pills. 
• 
If you forget to take your dose at your normal dosing time, you may still take the dose within 12 hours of the regular dosing time with 
a meal (you should not take 2 consecutive daily doses within less than 12 hours of each other).    
• 
If you miss your dose more than 12 hours after your regular dosing time you should write down in your pill diary that you missed the 
dose. Do not take your missed dose on your rest days, the shaded days of your diary. 
Additional Instructions: 
• 
You must avoid eating or drinking any foods with Seville oranges (like marmalade), grapefruit or foods or drink with grapefruit, and 
any exotic fruits during the entire treatment period.   
• 
Keep your study drug in the original container.  
• 
Do not throw away empty pill bottles. 
• 
Bring this diary, all pill bottles, and any unused pills to all scheduled clinic visits. 
• 
Contact your study doctor or nurse if you are having any new or worsening side effects. 
 
Please note that on days that you are coming to clinic or having blood tests, you may need to take your pills in clinic visit because of 
required study tests. 
 
 
 

 
127 
 
 
 
APPENDIX G 
BIOASSAY PROCEDURES 
 
Proteomics Program Standard Operating Procedure for Tissue Core Collection- Needle Biopsy – 
Cryopreservation in OCT 
 
Principle: 
Core needle biopsies are used to sample tissue from a specific, defined location. These biopsies may 
consist of normal, pre-malignant and malignant tissue due to the multi-level tissue sample that is obtained. 
This type of sample is ideal for studying the micro-tumor environment. Rapid freezing of the sample is 
required to prevent degradation of the proteins or RNA. Optimal Cutting Temperature (OCT) compound is 
an alcohol polymer that is liquid at room temperature and a solid at –20C. This polymer is used to cryo-
protect the tissue and provide a medium for cryo-sectioning. The goal for time of tissue acquisition to 
freezing is <10 minutes. 
Materials: 
Cryomolds (Sakura Finetek Cat. # 4728) 
OCT (Sakura Finetek Cat. # 4583) 
Dry ice 
Ultra cold freezer (-700 to -800C) 
Needle: 16 or 18 gauge 
Permanent marker 
Sterile forceps 
Sterile Glass slides 
Aluminum foil or 50ml Falcon tubes 
Procedure: 
1. Prepare all supplies prior to the biopsy procedure to avoid delay once the specimen has been obtained. 
2. Label the handle and the front surface of the cryomold with the sample or patient’s identifying 
information. 
3. Perform core needle biopsy. 
4. Pick the core from the biopsy needle onto a sterile glass slide. 
5. Fill cryomold about 1/3 full with OCT. Place the cryomold in dry ice to partially freeze the OCT. The 
OCT should be jelly-like, not completely frozen. 
6. Carefully lift the core biopsy by both ends with sterile forceps. Do not stretch the biopsy or it will 
break. 
7. Lay the biopsy as straight as possible in the OCT. Once the sample touches the OCT, you cannot 
reposition it or the sample will break apart. 
8. Quickly add OCT on top of the biopsy, completely covering the sample. 
9. Ensure the sample is level and freeze immediately in dry ice. 
10. Store wrapped in aluminum foil or in a 50ml Falcon tube at –70C. 
Note: 
Do not lay the biopsy on frozen OCT and cover it with liquid OCT. The OCT will not fuse and will split 
into two sections when cutting the frozen tissue sections. 
Frozen Section Slides 
1. Frozen sections for proteomic analysis should be cut at 5-8um on plain, uncoated glass microscope 
slides. 
2. The tissue section should be placed as close as possible to the center of the slide. Do not place 
the frozen section at the end of the slide. 
3. Two tissue sections from the same biopsy may be placed on the same glass slide if space permits. 
4. Do not allow the tissue section to air on the slide. Freeze immediately on dry ice or at –80C. 
 

 
128 
 
 
 
 
REVERSE PHASE PROTEIN MICROARRAY 
 
Rationale 
Molecular therapeutics is a relatively novel approach that targets abnormalities in signaling pathways that 
play critical roles in tumor development and progression. Kinases and phosphatases control the reversible 
process of phosphorylation and are dysregulated in many diseases including cancer. Protein and lipid 
phosphorylation regulates cell survival signaling. Targeting kinases and phosphatases are paramount for 
improving therapeutic intervention. In this regard, it is critical to define qualified cellular targets for cancer 
diagnoses and prognoses, as well as accurately predict and monitor responsiveness to therapies. 
 
The reverse phase protein microarray (RPPA) is a recently developed quantitative assay that analyzes 
nanoliter amounts of sample for potentially hundreds of proteins.  This antibody-based assay determines 
levels of protein expression, as well as protein modifications such as phosphorylation, cleavage, and fatty 
acid modification.  RPPAs allow concordant interrogation of multiple signaling molecules and their 
functional status.  RPPAs have been utilized to profile and validate signaling networks in human cancer 
cell lines and tumor tissue1-3. 
 
In essence, the RPPA study has major strengths in identification and validation of cellular targets, 
characterization of signaling pathways and networks, as well as determination of on and off target activity 
of novel drugs. The integrated information will display the potential therapeutic targets or biomarkers to 
accurately predict or rapidly define intracellular signaling networks and functional outcomes affected by 
therapeutics. Thus, the RPPA approach provides a method to assess multiple markers in a global 
manner. Linking robust pathway mapping approaches to molecular therapeutics should provide an 
expanding repertoire of validated biomarkers and targeted therapeutics for clinical evaluation. 
 
Availability of key reagents required for execution of the high throughput RPPA project 
 
We have extensively validated antibodies suitable for RPPA (please refer to the attached list of RPPA-
validated antibodies). Only antibodies with a single or 
dominant band on western blotting are further assessed by 
direct comparison to RPPA using cell lines with differential 
protein expression or modulated with ligands/inhibitors or 
siRNA for phospo- or structural proteins, respectively. Only 
antibodies with a Pearson correlation coefficient greater 
than 0.7 between RPPA and western blotting as well as 
wide dynamic range will be used. Further, these antibodies 
are assessed for specificity and quantification using 
phospho- and non-phosphopeptides arrayed on 
nitrocellulose-coated slides. Interslide reproducibility is 
high with average coefficient of variation for individual 
antibodies across multiple cell lines ranging from 1.5 - 
36.1%, median 6.7% (figure 1).  
 
 
We have full access to a Tecan robotic liquid handling system for serial dilution of cell lysates and sample 
transfer; a G3 GeneTac arrayer and an Aushon 2470 arrayer for printing of up to 24 (G3) or 100 slides 
(2470) per run with several automated runs feasible in a day; a Biogenix i600TM and two DAKO Universal 
Staining systems that probes each slide with a different antibody. Each autostainer is capable of staining 
approximately 60 slides per day under conditions that are specific for each individual antibody. 
 
 
 
 
Ln(Mean Sample Concentration)
Mean Coefficient of Variation (%)
-2
-1
0
1
2
3
0
10
20
30
40

 
129 
 
Approach 
 
For tumor tissue, we will extract proteins from 8-10 mg of snap frozen tissue by homogenizer or ceramic 
beads (See appendix D for description of biopsy handling and below for lysis procedure). We will also 
include one ovarian and one endometrial cancer cell line (untreated and treated with multiple 
concentrations of MLN0128) that will be handled identically.  Protein concentration will be determined and 
adjusted to 1ug/ul. Protein will be denatured by SDS.  
 
Tissue lysates will be serial diluted to define the linear range of each antigen-antibody reaction. Lysates 
will be printed on nitrocellulose-coated slides and probed with validated antibodies that recognize 
signaling molecules or their activated forms. Signals will be captured by tyramide dye deposition (CSA 
System, DAKO).  
 
Data will be collected and analyzed using quantification software specifically developed for this approach 
(http://www.vigenetech.com); this software has multiple features that have been developed by the 
company in collaboration with the MDACC RPPA Core Laboratory including automated spot identification, 
background correction, controlling for location, serial dilution-signal intensity curve construction and 
concentration determination. The values derived from the slope and intercept will be expressed relative to 
standard control cell lysates or control peptides on the array.  
 
Relative protein levels for each sample will be determined by interpolation of each dilution curve from the 
"standard curve" (supercurve) of the slide (antibody).  Each dilution curve will be fitted with a logistic 
model (“Supercurve Fitting” developed by the Department of Bioinformatics and Computational Biology in 
MD Anderson Cancer Center, “http://bioinformatics.mdanderson.org/OOMPA”). This fits a single curve 
using all the samples (i.e., dilution series) on a slide with the signal intensity as the response variable and 
the dilution steps are independent variable. The fitted curve is plotted with the signal intensities – both 
observed and fitted - on the y-axis and the log2-concentration of proteins on the x-axis for diagnostic 
purposes. The protein concentrations of each set of slides will then be normalized by median polish, which 
is corrected across samples by the linear expression values using the median expression levels of all 
antibody experiments to calculate a loading correction factor for each sample. These values (given as 
log2 values) will be reported in the "SprCrvRaw (log2)" data set. All of the data points will be normalized 
for protein loading and transformed to linear values as indicated in the "Normalized Linear" data set. For 
antibodies with replicated slides, we will choose the one with the highest QC Scores.  The QC Scores and 
antibody correlations will be included in the data set for reference. 
 
 
 
 
 
 
 
1. 
Yang JY, Yoshihara K, Tanaka K, et al. Predicting time to ovarian carcinoma recurrence using 
protein markers. J Clin Invest 2013;123:5410. 
2. 
Cardnell RJ, Feng Y, Diao L, et al. Proteomic Markers of DNA Repair and PI3K Pathway 
Activation Predict Response to the PARP Inhibitor BMN 673 in Small Cell Lung Cancer. Clin Cancer Res 
2013;19:6322-8. 
3. 
Sohn J, Do KA, Liu S, et al. Functional proteomics characterization of residual triple-negative 
breast cancer after standard neoadjuvant chemotherapy. Annals of oncology : official journal of the 
European Society for Medical Oncology / ESMO 2013;24:2522-6. 
 
 
 
 
 

 
130 
 
Core Standard Antibody List (as of 11/2013) 
 
# 
Ab Name  
Gene Name 
Company 
Catalog # 
Internal Ab ID 
Species 
Validation Status* 
1 
14_3_3_beta 
YWHAB 
Santa Cruz 
sc-628 
882 
Rabbit 
Validated 
2 
14_3_3_epsilon 
YWHAE 
Santa Cruz 
sc-23957 
913 
Mouse 
Use with Caution 
3 
14_3_3_zeta 
YWHAZ 
Santa Cruz 
sc-1019 
883 
Rabbit 
Validated 
4 
4E BP1 
EIF4EBP1 
CST 
9452 
2 
Rabbit 
Validated 
5 
4E BP1_pS65 
EIF4EBP1 
CST 
9456 
3 
Rabbit 
Validated 
6 
4E BP1_pT37/T46 
EIF4EBP1 
CST 
9459 
6 
Rabbit 
Validated 
7 
53BP1 
TP53BP1 
CST 
4937 
985 
Rabbit 
Validated 
8 
A Raf 
ARAF 
CST 
4432 
1217 
Rabbit 
Validated 
9 
ACC_pS79 
ACACA 
ACACB 
CST 
3661 
13 
Rabbit 
Validated 
10 
ACC1 
ACACA 
Epitomics 
1768-1 
14 
Rabbit 
Under Evaluation 
11 
ACVRL1 
ACVRL1 
Abcam 
ab108207 
1086 
Rabbit 
Use with Caution 
12 
ADAR1 
ADAR1 
Abcam 
ab88574 
1198 
Mouse 
Validated 
13 
Akt 
AKT1 AKT2 
AKT3 
CST 
4691 
1084 
Rabbit 
Validated 
14 
Akt_pS473 
AKT1 AKT2 
AKT3 
CST 
9271 
230 
Rabbit 
Validated 
15 
Akt_pT308 
AKT1 AKT2 
AKT3 
CST 
2965 
1154 
Rabbit 
Validated 
16 
AMPK_alpha 
PRKAA1 
CST 
2532 
39 
Rabbit 
Use with Caution 
17 
AMPK_pT172 
PRKAA1 
CST 
2535 
40 
Rabbit 
Validated 
18 
Annexin I 
ANXA1 
BD Biosciences 
610066 
1208 
Mouse 
Validated 
19 
Annexin VII 
ANXA7 
BD Biosciences 
610668 
1142 
Mouse 
Validated 
20 
AR 
AR 
Epitomics 
1852-1 
756 
Rabbit 
Validated 
21 
ARHI 
DIRAS3 
MDACC Laboratory 
Bast Lab 
1273 
Mouse 
Use with Caution 
22 
ATM 
ATM 
CST 
2873 
1363 
Rabbit 
Validated 
23 
ATM_pS1981 
ATM 
CST 
5883 
1364 
Rabbit 
Validated 
24 
ATP5H 
ATP5H 
Abcam 
ab110275 
1252 
Mouse 
Use with Caution 
25 
B Raf 
BRAF 
Santa Cruz 
sc-5284 
96 
Mouse 
Use with Caution 
26 
B Raf_pS445 
BRAF 
CST 
2696 
94 
Rabbit 
Validated 
27 
Bad_pS112 
BAD 
CST 
9291 
63 
Rabbit 
Validated 
28 
Bak 
BAK1 
Epitomics 
1542-1 
71 
Rabbit 
Use with Caution 
29 
BAP1 
BAP1 
Santa Cruz 
sc-28383 
1207 
Mouse 
Validated 
30 
Bax 
BAX 
CST 
2772 
73 
Rabbit 
Validated 
31 
Bcl 2 
BCL2 
Dako 
M0887 
80 
Mouse 
Validated 
32 
Bcl xL 
BCL2L1 
CST 
2762 
85 
Rabbit 
Validated 
33 
Beclin 
BECN1 
Santa Cruz 
sc-10086 
87 
Goat 
Use with Caution 
34 
Beta_catenin 
CTNNB1 
CST 
9562 
75 
Rabbit 
Validated 
35 
Beta_catenin_pT41/S45 
CTNNB1 
CST 
9565 
1170 
Rabbit 
Validated 
36 
Bid 
BID 
Abcam 
ab32060 
88 
Rabbit 
Use with Caution 
37 
Bim 
BCL2L11 
Abcam 
ab32158 
90 
Rabbit 
Validated 
38 
BRcA2 
BRCA2 
CST 
9012 
761 
Rabbit 
Use with Caution 
39 
c Jun_pS73 
JUN 
CST 
9164 
155 
Rabbit 
Validated 
40 
c Kit 
KIT 
Abcam 
ab32363 
157 
Rabbit 
Validated 
41 
c Met_pY1235 
MET 
CST 
3129 
727 
Rabbit 
Validated 
42 
c Myc 
MYC 
Santa Cruz 
sc-764 
1143 
Rabbit 
Use with Caution 
43 
c Raf 
RAF1 
Millipore 
04-739 
1201 
Rabbit 
Validated 
44 
c Raf_pS338 
RAF1 
CST 
9427 
179 
Rabbit 
Validated 
45 
Caspase 7_cleavedD198 
CASP7 
CST 
9491 
109 
Rabbit 
Use with Caution 
46 
Caveolin 1 
CAV1 
CST 
3238 
114 
Rabbit 
Validated 
47 
CD29 
CD29 
BD Biosciences 
610467 
1206 
Mouse 
Validated 
48 
CD31 
PECAM1 
Dako 
M0823 
127 
Mouse 
Validated 
49 
CD49b 
ITGA2 
BD Biosciences 
611016 
937 
Mouse 
Validated 
50 
CDK1 
CDC2 
CST 
9112 
1007 
Rabbit 
Validated 
51 
CDKN2A/p16INK4a 
CDKN2A 
Abcam 
ab81278 
1231 
Rabbit 
Validated 
52 
Chk1 
CHEK1 
CST 
2360 
1203 
Mouse 
Use with Caution 
53 
Chk1_pS345 
CHEK1 
CST 
2348 
903 
Rabbit 
Use with Caution 
54 
Chk2 
CHEK2 
CST 
3440 
146 
Mouse 
Validated 
55 
Chk2_pT68 
CHEK2 
CST 
2197 
147 
Rabbit 
Use with Caution 
56 
cIAP 
BIRC2 
Millipore 
07-759 
930 
Rabbit 
Use with Caution 
57 
Claudin 7 
CLDN7 
Novus 
NB100-91714 
852 
Rabbit 
Validated 
58 
Collagen VI 
COL6A1 
Santa Cruz 
sc-20649 
171 
Rabbit 
Validated 

 
131 
 
 
 
59 
Complex II_Subunit 30 
MED30 
Invitrogen 
459230 
1069 
Mouse 
Validated 
60 
Cox 2 
CMC2 
CST 
4842 
1218 
Rabbit 
Use with Caution 
61 
Cox IV 
PTGS3 
Abcam 
ab14744 
1253 
Mouse 
Use with Caution 
62 
Cyclin B1 
CCNB1 
Epitomics 
1495-1 
192 
Rabbit 
Validated 
63 
Cyclin D1 
CCND1 
Santa Cruz 
sc-718 
194 
Rabbit 
Validated 
64 
Cyclin E1 
CCNE1 
Santa Cruz 
sc-247 
201 
Mouse 
Validated 
65 
Cyclophilin F 
PPIF 
Abcam 
ab110324 
1257 
Mouse 
Validated 
66 
DJ 1 
PARK7 
Abcam 
ab76008 
891 
Rabbit 
Validated 
67 
Dvl 3 
DVL3 
CST 
3218 
940 
Rabbit 
Validated 
68 
E cadherin 
CDH1 
CST 
3195 
1099 
Rabbit 
Validated 
69 
E2F1 
E2F1 
Santa Cruz 
sc-251 
1261 
Mouse 
Validated 
70 
eEF2 
EEF2 
CST 
2332 
1060 
Rabbit 
Use with Caution 
71 
eEF2K 
EEF2K 
CST 
3692 
1061 
Rabbit 
Validated 
72 
EGFR 
EGFR 
CST 
2232 
1120 
Rabbit 
Validated 
73 
EGFR_pY1068 
EGFR 
CST 
2234 
217 
Rabbit 
Use with Caution; 
also sees pHer2 
74 
EGFR_pY1173 
EGFR 
Abcam 
ab32578 
221 
Rabbit 
Validated 
75 
eIF4E 
EIF4E 
CST 
9742 
722 
Rabbit 
Validated 
76 
eIF4G 
EIF4G1 
CST 
2498 
1124 
Rabbit 
Use with Caution 
77 
ER alpha 
ESR1 
Lab Vision 
RM-9101-S 
238 
Rabbit 
Validated 
78 
ER alpha_pS118 
ESR1 
Epitomics 
1091-1 
241 
Rabbit 
Validated 
79 
ETS 1 
ETS1 
Bethyl 
A303-501A 
1200 
Rabbit 
Validated 
80 
FAK 
FAK 
CST 
3285 
1228 
Rabbit 
Under Evaluation 
81 
FAK_pT397 
PTK2 
CST 
3283 
1227 
Rabbit 
Validated 
82 
FASN 
FASN 
Cell Signaling 
3180 
1156 
Rabbit 
Validated 
83 
Fibronectin 
FN1 
Epitomics 
1574-1 
262 
Rabbit 
Validated 
84 
Fox03a 
FOXO3 
CST 
2497 
1122 
Rabbit 
Use with Caution 
85 
FoxM1 
FOXM1 
CST 
5436 
1123 
Rabbit 
Validated 
86 
FoxO3a_pS318/S321 
FOXO3 
CST 
9465 
270 
Rabbit 
Use with Caution 
87 
G6PD 
G6PD 
Santa Cruz 
sc-373887 
1155 
Mouse 
Validated 
88 
Gab2 
GAB2 
CST 
3239 
943 
Rabbit 
Validated 
89 
GAPDH 
GAPDH 
Ambion 
AM4300 
274 
Mouse 
Use with Caution 
90 
GATA3 
GATA3 
BD Biosciences 
558686 
764 
Mouse 
Validated 
91 
GCN5L2 
KAT2A 
CST 
3305 
1263 
Rabbit 
Validated 
92 
GPBB 
PYGM 
Novus Biologicals 
NBP1-32799 
1248 
Rabbit 
Validated 
93 
GSK3_alpha/beta 
GSK3A 
GSK3B 
Santa Cruz 
sc-7291 
284 
Mouse 
Validated 
94 
GSK3_alpha/beta_pS21/S9 
GSK3A 
GSK3B 
CST 
9331 
285 
Rabbit 
Validated 
95 
GSK3_pS9 
GSK3A 
GSK3B 
CST 
9336 
1082 
Rabbit 
Validated 
96 
GYS 
GYS 
CST 
3886 
1035 
Rabbit 
Validated 
97 
GYS_pS641 
GYS 
CST 
3891 
1036 
Rabbit 
Validated 
98 
HER2 
ERBB2 
Lab Vision 
MS-325-P1 
1038 
Mouse 
Validated 
99 
HER2_pY1248 
ERBB2 
R&D Systems 
AF1768 
1075 
Rabbit 
Use with Caution; 
likely sees pEGFR 
100 
HER3 
ERBB3 
Santa Cruz 
sc-285 
911 
Rabbit 
Validated 
101 
HER3_pY1289 
ERBB3 
CST 
4791 
728 
Rabbit 
Use with Caution 
102 
Heregulin 
NRG1 
CST 
2573 
890 
Rabbit 
Validated 
103 
Histone H3 
HIST3H3 
Abcam 
ab1791 
1250 
Rabbit 
Validated 
104 
IGF1R 
IGF1R 
CST 
3018 
1220 
Rabbit 
Validated 
105 
IGFBP2 
IGFBP2 
CST 
3922 
335 
Rabbit 
Validated 
106 
INPP4B 
INPP4B 
CST 
4039 
1065 
Rabbit 
Validated 
107 
IRS1 
IRS1 
Millipore 
06-248 
802 
Rabbit 
Validated 
108 
JNK_pT183/Y185 
MAPK8 
CST 
4668 
888 
Rabbit 
Validated 
109 
JNK2 
MAPK9 
CST 
4672 
380 
Rabbit 
Use with Caution 
110 
Lck 
LCK 
CST 
2752 
397 
Rabbit 
Validated 
111 
MAPK_pT202/Y204 
MAPK1 
MAPK3 
CST 
4377 
405 
Rabbit 
Validated 
112 
Mcl 1 
MCL1 
CST 
5453 
1222 
Rabbit 
Validated 
113 
MDM2_pS166 
MDM2 
CST 
3521 
1164 
Rabbit 
Validated 
114 
MEK1 
MAP2K1 
Epitomics 
1235-1 
417 
Rabbit 
Validated 
115 
MEK1_pS217/S221 
MAP2K1 
CST 
9154 
1076 
Rabbit 
Validated 
116 
MEK2 
MAP2K2 
CST 
9125 
1243 
Rabbit 
Validated 

 
132 
 
 
 
117 
MIG 6 
ERRFI1 
Sigma Aldrich 
WH0054206M1 
1062 
Mouse 
Validated 
118 
MSH2 
MSH2 
CST 
2850 
905 
Mouse 
Validated 
119 
MSH6 
MSH6 
Novus Biologicals 
22030002 
1063 
Rabbit 
Use with Caution 
120 
mTOR 
FRAP1 
CST 
2983 
444 
Rabbit 
Validated 
121 
mTOR_pS2448 
FRAP1 
CST 
2971 
446 
Rabbit 
Use with Caution 
122 
MYH11 
MYH11 
Novus Biologicals 
21370002 
1139 
Rabbit 
Validated 
123 
Myosin Iia_pS1943 
MYH9 
CST 
5026 
1160 
Rabbit 
Validated 
124 
N cadherin 
CDH2 
CST 
4061 
452 
Rabbit 
Validated 
125 
N Ras 
NRAS 
Santa Cruz 
sc-31 
1136 
Mouse 
Validated 
126 
Napsin 
NAPSA 
Abcam 
ab129189 
1274 
Rabbit 
Use with Caution 
127 
NDRG1_pT346 
NDRG1 
CST 
3217 
1126 
Rabbit 
Validated 
128 
NF2 
NF2 
Novus Biologicals 
22710002 
1046 
Rabbit 
Use with Caution 
129 
NF-kBp65_pS536 
NFKB1 
CST 
3033 
457 
Rabbit 
Use with Caution 
130 
Notch1 
NOTCH1 
CST 
3268 
1064 
Rabbit 
Validated 
131 
p21 
CDKN1A 
Santa Cruz 
sc-397 
470 
Rabbit 
Validated 
132 
p27 
CDKN1B 
Abcam 
ab32034 
897 
Rabbit 
Validated 
133 
p27_pT157 
CDKN1B 
R&D 
AF1555 
842 
Rabbit 
Use with Caution 
134 
p27_pT198 
CDKN1B 
Abcam 
ab64949 
878 
Rabbit 
Validated 
135 
p38 alpha MAPK 
MAPK1 
CST 
9228 
1175 
Mouse 
Validated 
136 
p38 MAPK 
MAPK14 
CST 
9212 
478 
Rabbit 
Validated 
137 
p38_pT180/Y182 
MAPK14 
CST 
9211 
479 
Rabbit 
Validated 
138 
p53 
TP53 
CST 
9282 
481 
Rabbit 
Use with Caution 
139 
p70S6K 
RPS6KB1 
Epitomics 
1494-1 
493 
Rabbit 
Validated 
140 
p70S6K_pT389 
RPS6KB1 
CST 
9205 
494 
Rabbit 
Validated 
141 
p90RSK 
RPS6KA1 
CST 
9347 
759 
Rabbit 
Use with Caution 
142 
PAI 1 
PAI1 
BD Biosciences 
612024 
499 
Mouse 
Validated 
143 
Paxillin 
PXN 
Epitomics 
1500-1 
505 
Rabbit 
Use with Caution 
144 
PCNA 
PCNA 
Abcam 
ab29 
511 
Mouse 
Use with Caution 
145 
PDCD 1L1 
PDCD1 
Santa Cruz 
sc-19090 
1234 
Goat 
Use with Caution 
146 
PDCD4 
PDCD4 
Rockland 
600-401-965 
816 
Rabbit 
Use with Caution 
147 
PDGFR_beta 
PDGFR 
CST 
3169 
1225 
Rabbit 
Validated 
148 
PDK1 
PDK1 
CST 
3062 
515 
Rabbit 
Validated 
149 
PDK1_pS241 
PDK1 
CST 
3061 
516 
Rabbit 
Validated 
150 
PEA15 
PEA15 
CST 
2780 
1017 
Rabbit 
Validated 
151 
PEA15_pS116 
PEA15 
Invitrogen 
44-836G 
1018 
Rabbit 
Validated 
152 
PI3K_p110_alpha 
PIK3CA 
CST 
4255 
808 
Rabbit 
Use with Caution 
153 
PI3K_p85 
PIK3R1 
Millipore 
06-195 
523 
Rabbit 
Validated 
154 
PKC_alpha 
PRKCA 
Millipore 
05-154 
529 
Mouse 
Validated 
155 
PKC_alpha_pS657 
PRKCA 
Millipore 
06-822 
530 
Rabbit 
Use with Caution 
156 
PKC_delta_pS664 
PRKCD 
Millipore 
07-875 
932 
Rabbit 
Validated 
157 
PKCpan BetaII_pS660 
PKC 
CST 
9371 
1137 
Rabbit 
Validated 
158 
PMS2 
PMS2 
Novus Biologicals 
22510002 
1246 
Rabbit 
Validated 
159 
PR 
PGR 
Abcam 
ab32085 
549 
Rabbit 
Validated 
160 
PRAS40_pT246 
AKT1S1 
Biosource 
441100G 
739 
Rabbit 
Validated 
161 
PREX1 
PREX1 
Abcam 
ab102739 
1204 
Rabbit 
Validated 
162 
PTEN 
PTEN 
CST 
9552 
566 
Rabbit 
Validated 
163 
Rab11 
RAB11A 
RAB11B 
CST 
3539 
1083 
Rabbit 
Under Evaluation 
164 
Rab25 
RAB25 
CST 
4314 
1150 
Rabbit 
Validated 
165 
Rad50 
RAD50 
Millipore 
05-525 
987 
Mouse 
Validated 
166 
Rad51 
RAD51 
CST 
8875 
1262 
Rabbit 
Validated 
167 
Raptor 
RPTOR 
CST 
2280 
1128 
Rabbit 
Validated 
168 
Rb_pS807/811 
RB1 
CST 
9308 
557 
Rabbit 
Validated 
169 
RBM15 
RBM15 
Novus Biologicals 
21390002 
1138 
Rabbit 
Validated 
170 
Rictor 
RICTOR 
CST 
2114 
1129 
Rabbit 
Use with Caution 
171 
Rictor_pT1135 
RICTOR 
CST 
3806 
1130 
Rabbit 
Validated 
172 
S6_pS235/236 
RPS6 
CST 
2211 
600 
Rabbit 
Validated 
173 
S6_pS240/244 
RPS6 
CST 
2215 
601 
Rabbit 
Validated 
174 
SCD1 
SCD1 
Santa Cruz 
sc-58420 
1127 
Mouse 
Validated 
175 
SF2 
SFRS1 
Invitrogen 
32-4500 
1131 
Mouse 
Validated 
176 
SHC_pY317 
SHC1 
CST 
2431 
1031 
Rabbit 
Validated 
177 
Smad1 
SMAD1 
Epitomics 
1649-1 
922 
Rabbit 
Validated 
178 
Smad3 
SMAD3 
Abcam 
ab40854 
796 
Rabbit 
Validated 
179 
Smad4 
SMAD4 
Santa Cruz 
sc-7966 
920 
Mouse 
Validated 

NCI Protocol #: 9552 
Version 9.0 Date: 04-October-2016 
133 
 
 
 
180 
Src 
SRC 
Millipore 
05-184 
621 
Mouse 
Validated 
181 
Src_pY416 
SRC 
CST 
2101 
623 
Rabbit 
Use with Caution 
182 
Src_pY527 
SRC 
CST 
2105 
626 
Rabbit 
Validated 
183 
STAT3_pY705 
STAT3 
CST 
9131 
637 
Rabbit 
Validated 
184 
STAT5_alpha 
STAT5A 
Abcam 
ab32043 
638 
Rabbit 
Validated 
185 
Stathmin 
STMN1 
Abcam 
ab52630 
718 
Rabbit 
Validated 
186 
Syk 
SYK 
Santa Cruz 
sc-1240 
1033 
Mouse 
Validated 
187 
TAZ 
WWTR1 
CST 
2149 
777 
Rabbit 
Validated 
188 
TIGAR 
C12ORF5 
Abcam 
ab137573 
1107 
Rabbit 
Validated 
189 
Transglutaminase 
TGM2 
Lab Vision 
MS-224-P1 
908 
Mouse 
Validated 
190 
TRFC 
TRFC 
Novus Biologicals 
22500002 
1140 
Rabbit 
Validated 
191 
TSC1 
TSC1 
CST 
4906 
1125 
Rabbit 
Use with Caution 
192 
TTF1 
TTF1 
Abcam 
ab76013 
1081 
Rabbit 
Validated 
193 
Tuberin 
TSC2 
Epitomics 
1613-1 
670 
Rabbit 
Validated 
194 
Tuberin_pT1462 
TSC2 
CST 
3617 
671 
Rabbit 
Validated 
195 
TYRO3 
TYRO3 
CST 
5585 
1080 
Rabbit 
Validated 
196 
UBAC1 
UBAC1 
Sigma Aldrich 
HPA005651 
1270 
Rabbit 
Validated 
197 
UGT1A 
UGT1A 
Santa Cruz 
sc-271268 
1267 
Mouse 
Validated 
198 
UQCRC2 
UQCRC2 
Abcam 
ab14745 
1256 
Mouse 
Use with Caution 
199 
VDAC1/Porin 
VDAC1 
Abcam 
ab14734 
1254 
Mouse 
Validated 
200 
VEGFR2 
KDR 
CST 
2479 
688 
Rabbit 
Validated 
201 
XRCC1 
XRCC1 
CST 
2735 
906 
Rabbit 
Use with Caution 
202 
YAP 
YAP1 
Santa Cruz 
sc-15407 
780 
Rabbit 
Under Evaluation 
203 
YAP_pS127 
YAP1 
CST 
4911 
782 
Rabbit 
Under Evaluation 
204 
YB 1 
YBX1 
Novus Biologicals 
1725.00.02 
700 
Rabbit 
Validated 
205 
YB 1_pS102 
YBX1 
CST 
2900 
835 
Rabbit 
Validated 
 
Validation Status* 
Valid = RPPA and WB correlation > 0.7 
Use with caution = RPPA and WB correlation < 0.7 
Under Evaluation = Antibody has given mixed results and / or evaluated by another lab; We are in the 
process of (re)validating 
 
 
 

 
134 
 
Preparation of tumor lysates from frozen tissue 
(By Precellys homogenizer) 
for Reverse Phase Protein Array 
 
1.  Reagents and material: Frozen tumor tissue set on dry ice, Scalper, Weighing dish, 
Tweezers, Lysis buffer with protease inhibitors set on ice, tubes from Precellys Ceramic 
Beads Kit (1.4 mm, Cat # 10011152, from Cayman Chemical, www.caymanchem.com, 
Phone 800-364-9897 or 734-971-3335), 1.5ml microcentrifuge tubes labeled with sample 
number and set on ice. 
 
Lysis Buffer: 1% Triton X-100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 
1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, 
containing freshly added protease and phosphatase inhibitors from Roche Applied 
Science Cat. # 05056489001 and 04906837001, respectively 
 
4X SDS Sample Buffer: 40% Glycerol, 8% SDS, 0.25M Tris.HCL, pH 6.8. Before use, 
add beta-mercaptoethanol at 1/10 of volume. 
 
2.  Remove the tumor tissue from cryovials and wash out OCT medium.  Cut a small piece 
of tumor tissue (approximately the size of a grain of rice, 20mg) and place in 2ml tubes 
with Ceramic Beads(for Precellys homogenizer). We can work with small volume by 
Precellys homogenizer. We estimate protein yield at 60ug from 1mg of tumor tissue. 
 
3.  Add ice-cold lysis buffer to the tube. The volume of lysis buffer is calculated as 40mg of 
tumor /ml. 
 
4.  For using Precellys, place the tubes on the rack, put the white lid on, and choose from 
program 1 or 2, click valid to start. Program 1 sets at 30 second per cycle for 2 cycles 
and Program 2 sets at 45 seconds per cycle for 2 cycles. 
 
5.  Centrifuge at 4o C for 15 minutes at maximum speed (13,000~14,000 rpm). 
 
6.  Collect supernatant (tumor lysates) and transfer to another set of microcentrifuge tubes. 
 
7.  Determine protein concentration by BCA or Bradford reaction and adjust protein 
concentration to 1-1.5mg/ml by lysis buffer. 
 
8.  Mix the cell lysate with 4X SDS sample buffer without Bromophenol Blue (3 parts of cell 
lysate plus one part of 4X SDS sample buffer). Boil the samples for 5 minutes. The 
samples are ready for RPPA processing. If the samples need to be stored for later use, 
store them in –80oC.