Clinical trial NCT01431209
Conditions: Recurrent Diffuse Large B-Cell Lymphoma Recurrent Mature T- and NK-Cell Non-Hodgkin Lymphoma Refractory Diffuse Large B-Cell Lymphoma Refractory Mature T-Cell and NK-Cell Non-Hodgkin Lymphoma
Sponsor: University of Nebraska
Start date: 2011-08-12; Completion date: 2021-05-26
Enrollment: 71 participants; Allocation: NA; Intervention model: SINGLE_GROUP

Brief summary:
This phase II trial studies how well ruxolitinib phosphate works in treating patients with diffuse large B-cell or peripheral T-cell non-Hodgkin lymphoma that has returned (relapsed) or that does not respond to treatment (refractory) after donor stem cell transplant. Ruxolitinib phosphate may stop the growth of cancer cells by blocking some of the enzymes needed for cell growth.

Detailed description:
PRIMARY OBJECTIVES:

I. Assess the overall response rate (ORR) of subjects with relapsed diffuse large B-cell lymphoma (DLBCL) and peripheral T-cell lymphoma (PTCL) who are relapsed or refractory to front-line treatment and ineligible for stem cell transplantation or have recurrent disease after stem cell transplantation to oral ruxolitinib (ruxolitinib phosphate).

SECONDARY OBJECTIVES:

I. Evaluate safety of oral ruxolitinib in subjects with DLBCL and PTCL. II. Determine progression-free survival (PFS), duration of response, and overall response (OS) in subjects with DLBCL and PTCL.

TERTIARY OBJECTIVES:

I. Explore the relationship between responses to oral ruxolitinib and alterations in gene expression profiling (GEP) signatures as well as biomarker immunophenotypic changes related to JAK2/STAT3, NF-kB, PI3K/AKT, and mTOR pathways.

II. Evaluate potential effect of oral ruxolitinib exposure on JAK2/STAT3 pathway inhibition in serial tumor samples.

OUTLINE:

Patients receive ruxolitinib phosphate orally (PO) twice daily (BID) on days 1-28. Courses repeat every 28 days in the absence of disease progression or unacceptable toxicity.

After completion of study treatment, patients are followed up every 3 months for 1 year and then every 6 months thereafter.

Arms: arm 1: Patients receive ruxolitinib phosphate PO BID on days 1-28. Courses repeat every 28 days in the absence of disease progression or unacceptable toxicity.
Interventions: intervention 1: Laboratory Biomarker Analysis intervention 2: Ruxolitinib Phosphate
Intervention descriptions: intervention 1: Correlative studies intervention 2: Given PO

Protocol documents:
Prot_SAP_000.pdf: 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 1 of 75 
Version Date 29 February 2016 
 
Clinical Study Protocol 
 
Title: 
A Phase 2 Multicenter, investigator initiated study of 
Oral Ruxolitinib Phosphate for the Treatment of 
Relapsed or Refractory Diffuse Large B-cell and 
Peripheral T-cell Non-Hodgkin Lymphoma 
 
IND Number: 
112445 
 
UNMC IRB Number: 
283-11 
 
NCT# 
01431209 
 
Product: 
Ruxolitinib Phosphate (also known as INCB018424 
and, INC424) 
 
 
Phase of Study: 
Phase 2 
 
 
Sponsor-Investigator: 
Julie Vose, M.D. 
 
987680 Nebraska Medical Center 
 
Omaha, NE  68198-7680 
United States 
 
Study Drug provided by: 
Incyte Corporation 
Route 141 & Henry Clay Road 
Building E336 
Wilmington, DE  19880 
United States 
 
 
Date of Protocol: 
5 May 2011 
 
 
Date(s) Revised: 
Amendment 2, date 5 December 2011 
 
Amendment 3, date 27 June 2012 
 
Amendment 4, date 23 January 2013 
 
 
 
 
 
Amendment 5, date 06 February 2014 
 
 
 
 
 
Amendment 6, date 16 February 2015 
 
 
 
 
 
Amendment 7, date 29 February 2016 
 
 
 
The information in this document is privileged and confidential.  No part of this information may be duplicated, 
referenced, or transmitted in any form or by any means (electronic, mechanical, photocopy, recording, or 
otherwise) without the prior written consent of Dr. Julie Vose. 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 2 of 75 
Version Date 29 February 2016 
 
STUDY CONTACT INFORMATION  
Lead Institution 
 
PI and Study Director:   
Julie M. Vose, M.D. 
Ph: 402-559-3848 
Fax:  402-559-8101 
jmvose@unmc.edu 
 
University of Nebraska Medical Center 
987680 Nebraska Medical Center 
Omaha, NE 68198-7680 
 
Sub-Investigators:   
James Armitage, M.D.,  
Philip Bierman, M.D.,  
R. Gregory Bociek, M.D. 
Matthew Lunning, D.O. 
 
Study Coordinator:   
Susan Blumel, R.N. 
Ph:  402-559-9183 
Fax:  402-559-8101 
sblumel@unmc.edu 
 
Participating Institution 
 
PI:   
Thomas Witzig, M.D. 
Ph:  507-266-2040 
Fax:  507-266-9277 
Witzig.thomas@mayo.edu 
 
Mayo Clinic 
Hem 
200 First St. SW 
Rochester, MN  55905-0001 
  
 
Participating Institution 
 
PI:   
Wyndam Wilson, M.D. 
Ph:  301-435-2415 
Fax:  301-480-4087 
wilsonw@mail.nih.gov 
 
National Cancer Institute 
9000 Rockville Pike, Rm 4n115 
Bldg 10 
Bethesda, MD  20892-0001 
 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 3 of 75 
Version Date 29 February 2016 
 
TABLE OF CONTENTS 
1.0 
PROTOCOL SYNOPSIS ........................................................................................6 
2.0 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS ........................10 
3.0 
INTRODUCTION .................................................................................................11 
3.1 
Background ......................................................................................................11 
3.2 
Trial Rationale .................................................................................................14 
3.3 
Potential Risks and Benefits ............................................................................16 
3.4 
Justification of Route, Dose Regimen and Treatment Period ..........................17 
4.0 
STUDY OBJECTIVES ..........................................................................................17 
4.1 
Primary Objectives...........................................................................................17 
4.2 
Secondary Objectives.......................................................................................17 
4.3 
Exploratory Objectives…………………………………………………….   17 
5.0 
INVESTIGATIONAL PLAN ................................................................................18 
5.1 
Trial Endpoints.................................................................................................18 
5.2 
Other Exploratory Evaluations ........................................................................18 
6.0 
SUBJECT ELIGIBILITY ......................................................................................20 
6.1 
Inclusion Criteria .............................................................................................20 
6.2 
Exclusion Criteria ............................................................................................21 
7.0 
SCHEDULE OF OBSERVATIONS .....................................................................23 
7.1 
Schedule of Observations Flowchart ...............................................................23 
7.2 
Screening and Enrollment ................................................................................25 
7.3 
On-Treatment Evaluations ...............................................................................26 
7.4 
End-of-treatment Evaluations ..........................................................................27 
7.5 
Follow-up Evaluations .....................................................................................28 
7.6 
Duration of Participation..................................................................................28 
8.0 
STUDY ASSESSMENTS .....................................................................................29 
8.1 
Demographic and Other Pre-Treatment Assessments .....................................29 
8.2 
Safety Assessments ..........................................................................................29 
8.2.1 
Adverse Events ........................................................................................29 
8.2.2 
Physical Examinations .............................................................................29 
8.2.3 
Vital Signs ...............................................................................................29 
8.2.4 
12-Lead ECG Interpretation ....................................................................30 
8.2.5 
Clinical Safety Laboratory Assessments .............................................30  
9.0 
TREATMENT OF SUBJECTS .............................................................................28 
9.1 
Investigational Product(s) Description ............................................................30 
9.1.1 
Dosage and Dose Regimen ......................................................................30 
9.1.2 
Packaging and Labeling ..........................................................................31 
9.1.3 
Storage/Stability ......................................................................................31 
9.1.4 
Drug Accountability ................................................................................31 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 4 of 75 
Version Date 29 February 2016 
 
9.2 
Administration of Study Medication(s)  ..........................................................32 
9.2.1 
Starting Dose Assignment .......................................................................32 
9.2.2 
Dose Increases for Inadequate Efficacy ..................................................32 
9.2.3 
Dose Adjustments for Safety ...................................................................33 
9.3 
Concomitant Medications / Measures ..............................................................36 
9.4 
Restricted and / or Prohibited Medications ......................................................37 
9.4.1 
Restricted Therapies ................................................................................37 
9.4.2 
Prohibited Therapies ................................................................................38 
9.5 
Discontinuation of Study Medication(s) ..........................................................38 
10.0 
WITHDRAWAL OF STUDY SUBJECTS ...........................................................38 
10.1 
Withdrawal Criteria and Procedures ................................................................38 
10.1.1 
Withdrawal of Subjects from Study ........................................................38 
10.2 
Replacement Subjects ......................................................................................39 
10.3 
Protocol Deviations ..........................................................................................39 
11.0 
ADVERSE EVENTS .............................................................................................40 
11.1 
Definitions and Reporting ................................................................................40 
11.2 
Laboratory Test Abnormalities ........................................................................41 
11.3 
Serious Adverse Events ...................................................................................42 
11.3.1 
Definitions ...............................................................................................42 
11.3.2 
Serious Adverse Events Reporting ..........................................................43 
11.4 
Pregnancies ......................................................................................................45 
11.5 
Warnings and Precautions................................................................................46 
12.0 
STATISTICS .........................................................................................................46 
12.1 
Study Populations ............................................................................................46 
12.2 
Efficacy Analysis .............................................................................................46 
12.2.1 
Primary Efficacy Analyses ..................................................................46 
12.2.2 
Secondary Efficacy Analyses ..............................................................48 
12.2.3 
Exploratory Analyses ...........................................................................49 
12.3 
Safety Analysis ................................................................................................49 
12.3.1 
Adverse Events ........................................................................................49 
13.0 
DATA MANAGEMENT........................................................................................... 
 
13.1 Data Collection ....................................................................................................50 
 
13.1 Data Management ................................................................................................50 
14.0 
STUDY ADMINISTRATION................................................................................... 
14.1 
Access to Source Documents ...........................................................................51 
14.2 
Statement of Good Clinical Practices ..............................................................52 
14.3 
Protocol Adherence ..........................................................................................52 
14.4 
Study Termination ...........................................................................................52 
14.5 
Financial Disclosure.........................................................................................53 
14.6 
Quality Control and Assurance ........................................................................53 
14.6.1 
Sponsor Audits ........................................................................................53 
14.6.2 
Inspection by Regulatory Authorities ......................................................54 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 5 of 75 
Version Date 29 February 2016 
 
15.0 
ETHICS...................................................................................................................... 
15.1 
Institutional Review Board or Independent Ethics Committee .......................54 
15.2 
Informed Consent.............................................................................................55 
15.2.1 
Data Privacy ............................................................................................56 
16.0 
RECORD KEEPING / RETENTION OF RECORDS .............................................. 
16.1 
Confidentiality ..................................................................................................... 
17.0 
REFERENCES .......................................................................................................... 
18.0 
INVESTIGATOR’S SIGNATURE PAGE............................................................61 
19.0 
LIST OF APPENDICES ........................................................................................62 
APPENDIX 1 – 
RESPONSE CRITERIA ......................................................................63 
 APPENDIX 2 – LABORATORY METHODS ..............................................................66 
APPENDIX 3 – 
GRADING OF ADVERSE EVENTS .................................................75 
 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 6 of 75 
Version Date 29 February 2016 
 
1.0 
PROTOCOL SYNOPSIS  
Title 
A Phase 2 study of Oral Ruxolitinib Phosphate for the Treatment of 
Relapsed or Refractory Diffuse Large B-cell and Peripheral T-cell Non-
Hodgkin Lymphoma 
Protocol IND Number 
112445 
Study Phase 
II 
Study Design 
This is an open-label, multicenter, Phase II study 
Planned Number of Study Sites 
and Planned Number of Subjects 
Four study sites will participate. 
Approximately 90 subjects will be enrolled 
Coordinating Investigator 
Julie Vose, M.D. 
Study Objectives  
Primary Objective:   
Assess the overall response rate (ORR) of subjects with diffuse large B-
cell BCL) and peripheral T-cell non-Hodgkin lymphoma (PTCL)  who 
are relapsed or refractory to front-line treatment and ineligible for stem 
cell transplantation or have recurrent disease after stem cell 
transplantation to oral ruxolitinib.  
 
Secondary Objectives: 
Evaluate safety of oral ruxolitinib therapy in subjects with DLBCL and 
PTCL 
 
Determine progression free survival (PFS), duration of response, and 
overall survival (OS) in subjects with DLBCL and PTCL 
 
Exploratory Objectives: 
Explore relationship between responses to oral ruxolitinib and 
alterations in GEP signatures as well as biomarker immunophenotypic 
changes related to JAK2/STAT3, NF-κB, BCR, PI3K/AKT, and mTOR 
pathways. 
 
Evaluate potential effect of oral ruxolitinib exposure on JAK2/STAT3 
pathway inhibition in serial tumor samples. 
 
Dose and Mode of Administration 
and Duration of Treatment 
Subjects will receive continuous dosing with oral ruxolitinib for 28 day 
cycles.  The study is comprised of 3 phases: 
Screening: up to 28 days 
On-Treatment Phase: participation may continue for subjects 
receiving benefit  and who have not met any reason for study 
discontinuation  
Follow-up: Subjects will be followed after discontinuation from the 
study to assess disease status, subsequent therapies and survival. 
Follow-up will occur by a clinic visit or telephone contact every 3 
months for the 1st year and every 6 months thereafter.  
 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 7 of 75 
Version Date 29 February 2016 
 
Evaluable subjects will include subjects who have received at least 2 
cycles of therapy, or subjects with documented progression of disease 
prior to completion of 2 cycles of therapy.  
 
Correlative Studies 
An initial mandatory tumor sample will be obtained for PY-STAT3 
activation, NF-kB activation (nuclear staining for p50/52, CARD 11 
mutation status, AKT pathway activations (pAKT IHC) 
An additional two tumor samples will also be obtained in subjects who 
consent to voluntary second biopsy to evaluate JAK2/STAT3 pathway 
inhibition and changes of other STAT3 targets after 2 cycles of therapy 
and at progression.  
An archived tumor sample collected at subjects’ initial diagnosis will be 
obtained for correlation between current and initial tumor samples. 
Summary of Entrance Criteria 
 
Subjects may be included in the study if they are: 
 
1. Subjects must have histologically documented relapsed, or 
refractory disease, with a diagnosis of one of the following 
lymphoid malignancies: Diffuse Large B-cell Lymphoma, 
Peripheral T-cell Lymphoma (any subtype). Subjects must 
have received at least one prior systemic chemotherapy and 
must have either received an autologous stem cell transplant, 
refused or been deemed ineligible for an autologous stem cell 
transplant; 
2. Subjects must be willing and able to have a fresh tumor biopsy 
prior to start of study treatment for research evaluations and 
cohort categorizing Note: if insufficient fresh tissue is obtained 
to provide sub-classification for cohorts, then tissue material 
from a previous relapse biopsy and/or original diagnostic 
block may be requested to meet this criterion. 
3. Subjects must have measurable lesions (at least one target 
lesion measuring 2 cm in diameter) by computerized 
tomography (CT) scan, and/or measurable lymphoma 
cutaneous lesions of any size; 
4. Adult Age as defined by the State where the study site is 
located ( ≥ 19 years old at UNMC;  > 18 years at MDACC, 
Mayo, NCI) 
5. Eastern Cooperative Oncology Group (ECOG) performance 
status 0-2; 
6. Adequate bone marrow, renal, and hepatic function, per local 
reference laboratory ranges (values must not be achieved with 
transfusions or growth factors) as follows: 
a. Absolute neutrophil count (ANC) ≥ 1,000/mm3; 
b. Platelet count ≥ 75,000/mm3; 
c. Hemoglobin ≥ 8.0 g/dL; 
d. Serum creatinine ≤ 2.0 g/dL or calculated creatinine 
clearance ≥ 60mL/min (Cockcroft-Gault Method); 
e. AST and ALT ≤ 2.5 x institutional upper limit of normal 
(ULN) or ≤ 5 x ULN if liver involved by lymphoma 
f. Bilirubin < 2.0 x ULN unless subject has Gilbert’s disease, 
low-grade hemolysis, or liver involvement with lymphoma. 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 8 of 75 
Version Date 29 February 2016 
 
7. At least 2 weeks since prior chemotherapy, biological therapy, 
radiation therapy, major surgery, other investigational, or anti-
cancer therapy that is considered disease-directed and 
recovered from prior toxicities to Grade 0-1 at least 2 weeks 
prior to investigational therapy;  
8. Females will be either postmenopausal for at least 1 year or 
surgically sterile for at least 3 months     
OR  
Females of child-bearing potential must have a negative 
pregnancy test at screening and agree to take appropriate 
precautions to avoid pregnancy from screening Until 3 months 
after their last dose of study medication. 
9. Males must agree to take appropriate precautions to avoid 
fathering a child from screening until 3 months after their last 
dose of study medication.  
10. Able to comprehend and willing to sign an Informed Consent 
Form (ICF).  
 
Subjects will be excluded from the study if they have: 
1. History of or active central nervous system (CNS) malignancy 
2. Allogeneic stem cell transplant within the last 6 months, or 
active graft versus host disease following allogeneic transplant, 
or subjects currently on immunosuppressive therapy following 
allogeneic transplant.  
3. Uncontrolled intercurrent illness including, but not limited to, 
ongoing active infection, symptomatic congestive heart failure, 
unstable angina pectoris, cardiac arrhythmia, or psychiatric 
illness/social situation that would limit compliance with study 
requirements as judged by treating physician; subjects 
receiving antibiotics that are under control  may be included in 
the study 
4. Pregnant or breastfeeding women. 
5. Clinically symptomatic and uncontrolled cardiovascular 
disease 
6. History of myocardial infarction, severe/unstable angina, or 
symptomatic congestive heart failure, within the 6 months prior 
to study drug administration 
7. Current or recent history (< 21 days prior to start of treatment) 
of a clinically significant bacterial, viral, fungal, parasitic or 
mycobacterial infection.  
8. History of other malignancy, with the exception of squamous 
cell carcinoma of the skin, basal cell carcinoma of the skin, 
cervical intraepithelial neoplasia, or other malignancies that 
have been in remission for at least 3 years 
9. Presence of a malabsorption syndrome possibly affecting drug 
absorption (eg, Crohn’s disease or chronic pancreatitis). 
10. Any prior or concomitant use of another JAK inhibitor. 
11. Known active hepatitis B or C, or HIV infection. 
12. Subjects who, in the opinion of the Investigator, are unable or 
unlikely to comply with the dosing schedule and study 
evaluations. 
 
Statistical Methods 
The study is  3-step design.  There will be 3 cohorts of subjects: Cohort 
1 - DLBCL ABC Cohort 2 -  DLBCL GCB and Cohort 3 - PTCL.  Each 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 9 of 75 
Version Date 29 February 2016 
 
cohort will have a minimum of 10 and a maximum of 30 subjects 
enrolled. There will be a maximum of 90 subjects enrolled in the study. 
Enrolled subjects who do not fit into the cohorts described above (i.e. 
non-GCB, primary mediastinal large b-cell, or other) will be placed into 
a 4th cohort. 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 10 of 75 
Version Date 29 February 2016 
 
2.0 
LIST OF ABBREVIATIONS AND DEFINITIONS OF TERMS  
 
 
AE 
Adverse event 
BMI 
Body Mass Index 
CFR 
Code of Federal Regulations 
eCRF 
Electronic Case Report Form 
CRO  
Contract Research Organization 
ECG 
Electrocardiogram 
HIPAA 
Health Insurance Portability and Accountability Act (in relation to the 
Privacy Rule implemented April 2003) 
ICH 
International Conference on Harmonization of Pharmaceuticals for 
Technical Use 
IRB/IEC 
Institutional Review Board or Independent Ethics Committee 
mcg 
Microgram 
mg 
milligram 
mL 
milliliter 
mmol 
millimol 
PK 
Pharmacokinetics 
SAE 
Serious Adverse Event 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 11 of 75 
Version Date 29 February 2016 
 
3.0 
INTRODUCTION 
3.1 
Background 
Non Hodgkin Lymphomas (NHLs) are the most common hematologic malignancy with 
annual US incidence of approximately 66,000 in the US 1.  NHLs are a heterogeneous 
group of lymphoproliferative malignancies with differing patterns of behavior and 
responses to treatment 2.  NHL is much less predictable than Hodgkin Lymphoma and has 
a far greater predilection to disseminate to extranodal sites.  NHLs can be divided into 2 
prognostic groups:  indolent and aggressive lymphomas.  Despite progress in lymphoma 
therapy, many patients with these diseases still die from relapse and disease progression 
or from complications associated with treatment; therefore, more selective and less toxic 
treatments are needed. Constitutive activation of the JAK-STAT pathway has been 
reported in various types of leukemias and lymphomas, suggesting that targeted therapies 
directed at this pathway may show clinical benefit in these malignancies. More recent 
reports have also identified activating mutations or gene amplification of JAK1 and JAK2 
in acute myeloid and lymphoblastic leukemias, lymphoma and in myelodysplastic 
syndrome 3-13.  As with many therapeutics, selective JAK inhibitors may be most 
beneficial when combined with other targeted or cytotoxic therapies.    
 
Ruxolitinib phosphate (also known as INCB018424 phosphate or INC424) is an inhibitor 
of the Janus kinase family of protein tyrosine kinases and will be referred to as ruxolitinib 
throughout this document.  Ruxolitinib is an investigational product that is in 
development for treatment of myeloproliferative neoplasms (MPNs), hematologic 
malignancies and solid tumors. JAKs play an important role in signal transduction 
following cytokine and growth factor binding to their receptors. Aberrant activation of 
JAKs has been associated with increased malignant cell proliferation and survival.   In 
particular, a pathologic role for JAK2 has recently been suggested for the majority of 
patients with Philadelphia chromosome negative MPNs. Therefore, JAK inhibitors 
represent potential therapeutic agents for these disease states. 
Clinical Summary 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 12 of 75 
Version Date 29 February 2016 
 
Ruxolitinibhas been administered to over 180 healthy volunteers as single, repeat single, 
or multiple doses of up to 10 days duration.  Ithas also been administered to 
approximately 450 subjects with MF for periods of up to > 24 months, and over 
100 subjects with prostate cancer, multiple myeloma, polycythemia vera or essential 
thrombocythemia for periods of up to > 24 months.   
 
In healthy volunteer studies, a transient, reversible decrease in neutrophil count has 
frequently been seen following dosing, which reverses after 12 to 24 hours off drug, 
suggestive that the neutropenia may reflect an effect of ruxolitininb blocking IL-6 
signaling and causing neutrophil margination on blood vessel walls.  In a repeat dose 
healthy volunteer study, neutropenia of any severity grade was seen in 22% of placebo 
subjects, 11% of subjects receiving 50 mg qd, 67% of subjects receiving 100 mg qd, 13% 
of subjects receiving 15 mg bid, 33% of subjects receiving 25 mg bid and 67% of 
subjects receiving 50 mg bid.  Importantly, these neutropenia events were of Grade 1 or 
Grade 2 severity with a single instance of severe Grade 4 neutropenia that led to 
discontinuation of ruxolitinib in 1 subject receiving a 50 mg bid dose (NOTE: This was 
the highest dose administered during any clinical study).  The maximum tolerated dose in 
healthy volunteers was determined to be 25 mg bid and no dose limiting toxicities (DLT) 
were seen at 100 mg qd.  (See the Investigator’s Brochure for additional details).  
Ruxolitinib was tolerated in patients with rheumatoid arthritis dosed up to 28 days.  
Adverse events were seen in similar frequency in patients receiving ruxolitinib as in 
patients receiving placebo.  One patient dosed with 25 mg bid exhibited Grade 3 
neutropenia, which improved with continued dosing, and one patient who had a prior 
history of thrombocytopenia developed Grade 3 platelet decline.  One subject dosed with 
25 mg bid was withdrawn due to nausea and vomiting.   (See the Investigator’s Brochure 
for additional details).  
 
In a study of patients with advanced prostate cancer, ruxolitinib was generally well 
tolerated.  Serious adverse events seen were generally related to the expected progression 
of the underlying disease of prostate cancer.  One patient, with a history of congestive 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 13 of 75 
Version Date 29 February 2016 
 
heart failure, hypertension, hypercholesterolemia and T-wave abnormality on ECG who 
was severely ill with progressive disease, was reported to have experienced sudden death 
while on study.  This death was attributed to cardiac arrest, which was felt by the 
investigator to be possibly related to ruxolitinib.   (See the Investigator’s Brochure for 
additional details).  
 
In a study of patients with advanced multiple myeloma, ruxolitinib was generally well 
tolerated.  Observed toxicities included thrombocytopenia and anemia.  SAE’s reported 
included disease progression, pneumonia, urinary tract infection, anemia, pyrexia and 
other cardiac and pulmonary complications.  Safety results were consistent with those 
observed in other  ruxolitinib studies.   (See the Investigator’s Brochure for additional 
details).  
 
In a study of patients with Advanced Polycythemia Vera (PV) or Essential 
Thrombocythemia (ET),  ruxolitinib was generally well tolerated.  The most commonly 
observed AEs were anemia in ET subjects and anemia and thrombocytopenia in PV 
subjects, and these were reversible with dose modifications.  Serious adverse events 
deemed at least possibly related to study medication included a case of atrial flutter in a 
PV subject which resolved; acute renal failure in an ET subject which resolved; and a 
renal tumor in a PV subject which was surgically resected and the subject recovered.   
(See the Investigator’s Brochure for additional details).  
 
In an ongoing study in subjects with myelofibrosis (MF) where median time on drug is 
~ 15 months (N=154),  ruxolitinib was well tolerated by this elderly population (median 
age 65) with advanced disease.  The DLT was thrombocytopenia.  Initial dose ranging 
established an MTD of 25 mg bid and 100 mg qd in the MF population.  Most adverse 
events were mild to moderate in severity and considered unrelated to administration of 
study drug.  Related adverse events occurring in at least 5% (8 subjects) of the 
154 subjects included in the safety database through December 31, 2009 were restricted 
to anemia (45 subjects), thrombocytopenia (66 subjects), weight increased (11 subjects), 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 14 of 75 
Version Date 29 February 2016 
 
diarrhea (10 subjects) and fatigue (8 subjects).  Both anemia and thrombocytopenia 
represent JAK-inhibitor induced myelosuppression.  Forty (40) subjects (26% of study 
population) had a Grade 3 or Grade 4 decline in platelet count during the study (31 Grade 
3 events, 9 Grade 4 events).  Subjects with Grade 3 or 4 thrombocytopenia entered the 
study, in general, with platelet counts less than 200 K/µL, although there are exceptions 
to this trend.  Twenty percent of Grade 3 + 4 thrombocytopenia events occurred in the 
first 4 weeks of dosing, just under half (48%) of Grade 3 + 4 events occurred in the first 
16 weeks of treatment.  The incidence of thrombocytopenia was dose dependent, as 
anticipated.  For most subjects, thrombocytopenia was rapidly reversible and manageable 
with  ruxolitinib dose interruption and/or dose reduction.  Anemia, in general, reflected 
the low hemoglobin status at baseline in this disease population.   
 
Ruxolitinib has demonstrated marked reduction in spleen size in the ongoing study in 
patients with MF, and without regard to presence of the JAK2 V617F mutation.  In 
addition to spleen size reduction, Eastern Cooperative Oncology Group (ECOG) scores 
and symptoms thought to be related to splenomegaly, as well as symptoms related to 
elevated cytokine levels, all show improvement with  ruxolitinib treatment.  As a 
surrogate marker for functional benefit, exercise capacity was assessed with a 
standardized six minute walk test (6MWT).   ruxolitinib therapy resulted in improved 
6MWT performance after 1, 3 or 6 months of therapy.  After an initial small weight loss 
likely due to resolution of ascites and/or reduction in splenomegaly, there is an increase 
in total body weight; importantly, there is weight gain in subjects with low body mass 
index at entry, i.e., cachectic subjects.   See the Investigator’s Brochure for additional 
details.  
 
In Study INCB 18424-256 in patients with advanced PV or ET, and after a median 
follow-up of 15 months (range 8-21), 97% of enrolled PV subjects achieved Hct control 
to < 45% in the absence of phlebotomy, and all continued to maintain phlebotomy-
independence at the time of last follow-up visit.   Prior to treatment with ruxolitinib, 
twenty-six subjects were phlebotomy-dependent with the majority being maintained on 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 15 of 75 
Version Date 29 February 2016 
 
cytoreductive therapy.  After treatment, all but one of the 26 have maintained 
phlebotomy-independence as of the third week of the study.  Rapid and sustained 
reductions in mean Hct %, WBC count, and platelet counts have been noted (Table 18).  
Leukocytosis > 15 x 109/L was present in 44% of subjects at baseline and improved (≤ 15 
x 109/L) or normalized (≤ upper limit of normal, ULN) in 87% and 67% of these subjects, 
respectively.  Thrombocytosis > 600 x 109/L was present in 38% of subjects at baseline 
and improved (≤ 600 x 109/L) or normalized (< ULN) in 92% and 69%, respectively.   
See the Investigator’s Brochure for additional details.  
 
Two Phase 3 registrations studies are ongoing with subject participation but the protocol-
specified criteria to allow the database to be locked and data analyzed has been met.  
Study INCB 18424-351 is a double blind, placebo controlled study of ruxolitinib in 
subjects with MF, and Study INCB 18424-352 is an open label comparative study of 
ruxolitinib versus best available therapy in subjects with MF.  In both Phase 3 studies, 
subjects begin dosing at 20 mg bid if their platelet count at study entry is > 200,000/µL 
and at 15 mg bid for a platelet count at study entry of 100,000 to 200,000/µL, inclusive. 
 
3.2 
Trial Rationale 
This study is designed to investigate potential benefits of ruxolitinib in patients with Non-
Hodgkin’s Lymphoma, DLBC subtype and PTCL.  This will be the first study of 
ruxolitinib in patients with lymphoma.   The pre-clinical data provide support for the use 
of ruxolitinib in targeting the JAK-STAT pathway for the treatment of lymphomas. 
For the potential treatment of neoplastic disease ruxolitinib was evaluated in two mouse 
models where either a cytokine-dependent multiple myeloma cell line, INA-6, or a BaF3 
cell line engineered to express JAK2V617F was inoculated. Ruxolitinib administration 
(oral, bid) inhibited JAK-STAT signaling and INA-6 tumor growth in a dose-dependent 
manner as demonstrated by the percent tumor growth inhibition (TGI) and reduction in 
pSTAT3 levels determined by ELISA. Based on the data obtained from this study, it 
appears that > 80% suppression of JAK-STAT signaling for a minimum of 8 h each day 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 16 of 75 
Version Date 29 February 2016 
 
(4 h following each of two daily doses), and not continuous JAK inhibition, is required 
for maximal suppression of tumor growth in this model. 
 Ruxolitinib is an inhibitor of the Janus kinase family of protein tyrosine kinases (JAKs).  
Subject eligibility criteria are consistent with those used in studies of this population.  
The multi-center nature of this study provides greater likelihood that the results will have 
general applicability.  
 
3.3 
Potential Risks and Benefits  
Potential Risks 
No specific findings in nonclinical repeat dose toxicity studies identify clinical risk other 
than noting that consequences of immunosuppression may occur.  Hypotension and 
increases in heart rate were noted at a high dose in a cardiovascular preclinical study. 
However, these findings have not been recapitulated in a clinical setting.   
The primary clinical risks with ruxolitinib treatment are the potential sequelae of 
decreased hematopoietic proliferation secondary to the inhibition of growth factor 
pathways by JAK2 inhibition.  Dose-dependent, reversible thrombocytopenia has been 
observed in the ongoing study in subjects with MF and represents the DLT.  Anemia and, 
less frequently, neutropenia have also been observed in the ongoing study in patients with 
MF. Increased rates of infection and anemia are potential risks of myelosuppression, and 
there are multiple sequelae of anemia including the burden and risks of transfusion.  A 
few subjects have had an apparent worsening of their pre-morbid disease symptoms 
following rapid cessation of ruxolitinib therapy and a gradual tapering and use of steroids 
in fragile subjects may be considered when stopping ruxolitinib therapy.  In healthy 
volunteers and patients with RA with greater bone marrow reserve, the effects on 
hematopoietic proliferation appear to be less pronounced. 
 
Pneumonias and herpes zoster infections have been observed in MF patients treated with 
ruxolitinib. These infections have, in general, ruxolitinib (See Investigator’s Brochure) 
been assessed as unrelated to study medication, and may reflect in large part the 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 17 of 75 
Version Date 29 February 2016 
 
heightened incidence of these infections in this diseased and elderly study population. In 
ongoing phase 2 and 3 studies, other opportunistic infections have been seen in MF 
patients, including a serious adverse event of extra-pulmonary tuberculosis.  
3.4 
Justification of Route, Dose Regimen and Treatment Period 
In prior studies evaluating treatment in patients with myelofibrosis, the maximum 
tolerated oral dose was 25 mg po BID.  Therefore, this dose will be the upper reference 
point in the current study.   Starting doses explored in polycythemia vera and 
myelofibrosis range from 10 mg po BID to 20 mg po BID.  Since patients on this study 
may have limited marrow reserves from prior therapies and since thrombocytopenia is the 
most prominent toxicity seen in earlier studies, the baseline platelet count will be used to 
guide the initial dose, either 15 mg po BID or 10 mg po BID (see section 9.2).  Doses 
may be decreased in the presence of toxicities, or may be increased in the absence of 
toxicity and lack of objective response to a maximum dose of 25 mg po BID.   
4.0 
STUDY OBJECTIVES 
4.1 
Primary Objective 
• Assess the overall response rate (ORR) of subjects with relapsed DLBCL and PTCL 
who are relapsed or refractory to front-line treatment and ineligible for stem cell 
transplantation or have recurrent disease after stem cell transplantation to oral 
ruxolitinib. 
4.2 
Secondary Objectives 
• Evaluate safety of oral ruxolitinib in subjects with DLBCL and PTCL 
• Determine progression free survival (PFS), duration of response, and overall survival 
(OS) in subjects with DLBCL and PTCL 
4.3 
Exploratory Objectives 
• Explore the relationship between responses to oral ruxolitinib and alterations in GEP 
signatures as well as biomarker immunophenotypic changes related to JAK2/STAT3, 
NF-κB, BCR, PI3K/AKT, and mTOR pathways. 
• Evaluate potential effect of oral ruxolitinib exposure on JAK2/STAT3 pathway 
inhibition in serial tumor samples 
 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 18 of 75 
Version Date 29 February 2016 
 
5.0 
INVESTIGATIONAL PLAN 
5.1 
Study Endpoints 
• Determination of response rates according to revised Cheson criteria. 
• Evaluate safety of oral ruxolitinib in subjects with DLBCL and PTCL according 
to NCI CTC v. 4.0 criteria. 
• Determine progression free survival (PFS), duration of response, and overall 
survival (OS) in subjects with DLBCL and PTCL 
• Explore relationship between responses to oral ruxolitinib (and alterations in GEP 
signatures as well as biomarker immunophenotypic changes related to 
JAK2/STAT3, NF-κB, BCR, PI3K/AKT, and mTOR pathways. 
• Evaluate potential effect of oral ruxolitinib exposure on JAK2/STAT3 pathway 
inhibition in serial tumor samples 
5.2 
Other Exploratory Evaluations 
5.2.1. Tumor Genotyping 
A mandatory tumor sample will be obtained from all subjects at screening for gene 
expression profiling studies to assess pathway activation (PY-STAT3 activation, NF-κB 
activation (nuclear staining for p50/52, CARD 11 mutation status, AKT pathway 
activations (pAKT IHC).  Either excisional or two 14 gauge or larger cores will be 
submitted to the central lab.  In addition, all diffuse large B-cell non-Hodgkin lymphoma 
tumor samples will be evaluated with immunohistochemistry to determine subtype 
(activated B-cell versus germinal center B-cell subtype versus other subtypes of DLBC). 
The central pathology review will be used to identify subject cohort assignment. (See 
appendix 2 for details).   
 
Should there not be sufficient tumor samples to evaluate and identify subject cohort 
assignment, then an archived tumor sample (paraffin blocks) from a relapsed or initial 
diagnostic biopsy may be requested.  These specimens would be submitted to the central 
lab for review. 
 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 19 of 75 
Version Date 29 February 2016 
 
Archived tumor sample from the time of initial diagnosis will be obtained from all 
subjects for RNA sequencing and comparison of gene expression between initial and 
current tumor tissue. A minimum of 5 unstained 10 µm slides will be submitted to the 
central lab. 
 
Additional, optional fresh tumor samples will also be evaluated in subjects who consent 
to voluntary biopsies to evaluate JAK2/STAT3 pathway inhibition and changes of other 
STAT3 targets while on therapy and post-treatment for subjects who have documented 
disease progression.  Either excisional biopsy or two 14 gauge or larger, > 2cm length 
cores will be obtained sometime after the completion of 2 cycles for the on therapy 
biopsy and within 6 weeks post treatment for the post treatment biopsy.  (See appendix 
2). 
 
5.2.2. Blood Sampling for Cytokine Profiling 
Serial blood samples will be collected before the first dose of study drug, at three hours 
after the first dose of study drug, and then weekly on Days 8, 15, and 22 during cycle 1 
and on Day 1 of Cycle 2 for a total of 5 time points.  Samples will be collected and 
shipped to the central laboratory at the University of Nebraska Medical Center for 
analysis to measure cytokines and chemokines using plasma and PBMC. (See appendix 
2). 
 
5.2.3 Blood Sampling for C-reactive protein 
Blood samples will be collected within 7 days prior to the first dose of study drug, and on 
Day 1 of Cycle 2, and at time of relapse.   Samples will be collected and shipped to the 
central laboratory at the University of Nebraska Medical Center.  (See appendix 2).  


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 20 of 75 
Version Date 29 February 2016 
 
6.0 
SUBJECT ELIGIBILITY 
6.1 
Inclusion Criteria 
Subjects may be included in the study if they are: 
 
1. Subjects must have histologically documented relapsed or refractory disease, with 
a diagnosis of one of the following lymphoid malignancies: Diffuse Large B-cell 
Lymphoma, Peripheral T-cell Lymphoma (any subtype). Subjects must have 
received at least one prior systemic chemotherapy and must have either received 
an autologous stem cell transplant, refused or been deemed ineligible for an 
autologous stem cell transplant; 
2. Subjects must be willing and able to have a fresh tumor biopsy prior to start of 
study treatment for research evaluations and cohort categorizing.  Note: if 
insufficient fresh tissue is obtained to provide sub-classification for cohorts, then 
tissue material from a previous relapse biopsy and/or original diagnostic block 
may be requested to meet this criterion; 
3. Subjects must have measurable lesions (at least one target lesion measuring 2 cm 
in diameter) by computerized tomography (CT) scan, and/or measurable 
lymphoma cutaneous lesions of any size; 
4. Adult Age as defined by the State where the study site is located ( ≥ 19 years old 
at UNMC;  > 18 years at MDACC, Mayo, NCI) 
5. Eastern Cooperative Oncology Group (ECOG) performance status 0-2; 
6. Adequate bone marrow, renal, and hepatic function, per local reference laboratory 
ranges (values must not be achieved with transfusions or growth factors) as 
follows: 
a. Absolute neutrophil count (ANC) ≥ 1,000/mm3; 
b. Platelet count ≥ 75,000/mm3; 
c. Hemoglobin ≥ 8.0 g/dL; 
d. Serum creatinine ≤ 2.0 g/dL or calculated creatinine clearance ≥ 60mL/min 
(Cockcroft-Gault Method); 
e. AST and ALT ≤ 2.5 x institutional upper limit of normal (ULN) or ≤ 5 x ULN 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 21 of 75 
Version Date 29 February 2016 
 
if liver involved by lymphoma 
f. Bilirubin < 2.0 x ULN unless subject has Gilbert’s disease, low-grade 
hemolysis, or liver involvement with lymphoma. 
7. At least 2 weeks since prior chemotherapy, biological therapy, radiation therapy, 
major surgery, other investigational, or anti-cancer therapy that is considered 
disease-directed and recovered from prior toxicities to Grade 0-1 at least 2 weeks 
prior to investigational therapy;  
8. Females will be either postmenopausal for at least 1 year or surgically sterile for 
at least 3 months;  
OR  
Females of child-bearing potential must have a negative pregnancy test at 
screening and agree to take appropriate precautions to avoid pregnancy from 
screening until 3 months after their last dose of study medication.    
9. Males must agree to take appropriate precautions to avoid fathering a child from 
screening until 3 months after their last dose of study medication.  
10. Able to comprehend and willing to sign an Informed Consent Form (ICF).  
6.2 
Exclusion Criteria 
Subjects will be excluded from the study if they have:  
1. History of or active central nervous system (CNS) malignancy 
2. Allogeneic stem cell transplant within the last 6 months, or active graft versus 
host disease following allogeneic transplant, or subjects currently on 
immunosuppressive therapy following allogeneic transplant. 
3. Uncontrolled intercurrent illness including, but not limited to, ongoing active 
infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac 
arrhythmia, or psychiatric illness/social situation that would limit compliance with 
study requirements as judged by treating physician; subjects receiving antibiotics 
that are under control  may be included in the study 
4. Pregnant or breastfeeding women. 
5. Clinically symptomatic and uncontrolled cardiovascular disease 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 22 of 75 
Version Date 29 February 2016 
 
6. History of myocardial infarction, severe/unstable angina, or symptomatic 
congestive heart failure, within the 6 months prior to study drug administration 
7. Current or recent history (< 21 days prior to start of treatment) of a clinically 
significant bacterial, viral, fungal, parasitic or mycobacterial infection.  
8. History of other malignancy, with the exception of squamous cell carcinoma of 
the skin, basal cell carcinoma of the skin, cervical intraepithelial neoplasia, or 
other malignancies that have been in remission for at least 3 years 
9. Presence of a malabsorption syndrome possibly affecting drug absorption 
(eg, Crohn’s disease or chronic pancreatitis). 
10.  Any prior or concomitant use of another JAK inhibitor. 
11. Known active hepatitis B or C, or HIV infection. 
12. Subjects who, in the opinion of the Investigator, are unable or unlikely to comply 
with the dosing schedule and study evaluations. 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 23 of 75 
Version Date 29 February 2016 
 
7.0 
SCHEDULE OF OBSERVATIONS 
7.1 
Schedule of Observations Flowchart  
 
Screening 
Cycle 1 
 (+/- 2 days each time point) 
Cycle 2 
 
Every Cycle 
thereafter 
End of 
Treatment 
Follow-up 
 
<28 
days 
<14 
days 
Day 
1 
Day 
8 
Day 
15 
Day 
22 
Day 1 
(+/- 7 days) 
Day 1 
(+/- 7 days) 
(+/- 7 days) 
(each time point 
+/- 4 weeks) 
Evaluation 
 
 
 
 
 
 
 
 
 
 
Informed consent  
X 
 
 
 
 
 
 
 
 
 
Medical  history  
X 
 
 
 
 
 
 
 
 
 
Physical examination  
 
X 
 
 
 
 
X 
X 
X 
 
Vital Signs 
 
X 
 
 
 
 
X 
X 
 
 
ECOG performance score 
 
X 
 
 
 
 
X 
X 
 
 
Concomitant medications 
 
X 
X 
 
 
 
X 
X 
X 
 
12-lead ECG 
 
Xa 
 
 
 
 
 
 
 
 
Serum Pregnancy test  
 
Xa 
 
 
 
 
 
 
 
 
Hematology Lab 
 
X 
Xb 
X 
X 
X 
X 
X 
X 
 
Chemistry Lab 
 
X 
Xb 
X 
X 
X 
X 
X 
X 
 
PET scan 
Xc 
 
 
 
 
 
 
 
 
 
CT scan 
Xc 
 
 
 
 
 
 
Xc 
Xc 
 
Bone Marrow Biopsy 
 
 
 
 
 
 
 
(X)d 
 
 
Tumor Tissue collection for 
GEP,IHC or other subtype 
analysis 
Xe 
 
 
 
 
 
 
(X)e 
(X)e 
 
Archive Tissue collection 
X 
 
 
 
 
 
 
 
 
 
Blood Sampling for Cytokine 
Profilingf 
 
 
Xb,f 
Xf 
Xf 
Xf 
X 
 
 
 
Blood Sampling for CRPg 
 
 
X 
 
 
 
X 
 
X 
 
Study med dispensed 
 
 
X 
 
 
 
X 
X 
 
 
Adverse event reporting 
X 
 
X 
X 
X 
X 
X 
X 
Xh 
 
Compliance assessment – study 
med. 
 
 
 
X 
X 
X 
X 
X 
X 
 
Subject Status 
 
 
 
 
 
 
 
 
 
Xi 


Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 24 of 75 
Version Date 29 February 2016 
 
a.  Repeat ECG’s and pregnancy testing are not required but may be repeated throughout the study at the discretion of the investigator. 
b.  Cycle 1, day 1 Hematology and Chemistry labwork may be collected within 7 days prior to C1, D1 study drug dosing.  
c.  Baseline staging should include measurable disease by CT scan and a PET scan.  If sites can accomplish tumor measurements with one PET/CT scan, this will 
be acceptable.  CT scans will be done for restaging purposes.  In subjects with cutaneous lesions only, bidimensional measurements and photographs will be used 
for response assessment.   PET scan may be repeated to confirm PR or CR at the discretion of the investigator.  Disease restaging will occur after 2 cycles 
concurrent with the start of Cycle 3 and then every 2 cycles thereafter.  In subjects who are beyond the post cycle 6 response assessment AND have demonstrated 
objective resonse (PR or CR) restaging may be done every 3 cycles thereafter.  
d.  Bone marrow aspirate and biopsy will be performed to confirm complete remission unless the subject had a documented negative bone marrow biopsy 
evaluated with 45 days prior to treatment initiation. 
e.  Tumor excisional biopsy or 2 core biopsies are required at baseline and are optional during treatment at time of disease progression (post Cycle 2) and End of 
treatment. See appendix 2 for tumor tissue collection, processing and shipping instructions. 
f.  The Cycle 1, day 1 blood may be collected within 7 days prior to initiation of ruxolitinib.  On Cycle 1, Day 1 only, an additional blood for cytokine analysis 
will be drawn 3 hours after the first dose of ruxolitinib.  See appendix 2 for cytokine collection, processing and shipping instructions. Blood for cytokine analysis 
will be drawn prior to the morning dose of ruxolitinib on days 8, 15, 22 in Cycle 1 and on Cycle 2, day 1.   
g.  Blood for C-reactive protein (CRP) will be analyzed from blood collected for cytokine profling at pre-treatment (within 7 days prior to initiation of 
ruxolitinib) and at cycle 2, day 1.  An additional blood sample for CRP will be collect at time of progression or relapse. 
 
h. All subjects must be followed for safety for at least 30 days after study treatment has ended, or until study drug related toxicities resolve, return to Baseline or 
are deemed irreversible, whichever is longer. 
 
i.  Subjects will be followed every 3 months for the first year and every 6 months thereafter via clinic contact or telephone to obtain disease status and survival 
information (see section 7.6). 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 25 of 75 
Version Date 29 February 2016 
 
7.2 
Screening Evaluations and Subject Enrollment 
7.2.1 
The following procedures will be performed at the Screening visit within 
28 days prior to start of treatment unless noted otherwise:  
• Informed consent must be obtained before study-specific screening evaluations 
are performed, unless performed as standard of care.  The informed consent 
process should be documented in the subject’s medical chart. 
• Medical history; 
• Physical examination, including height, weight, and clinical signs and symptoms 
(within 14 days prior to cycle 1 day 1); 
• Vital signs, including pulse, systolic and diastolic blood pressure (BP), respiration 
rate, and body temperature(within 14 days prior to cycle 1 day 1); 
• ECOG performance status(within 14 days prior to cycle 1 day 1); 
• Single 12-lead ECG; 
• Hematology: CBC with differential within 14 days prior to cycle 1 day 1 (see 
section 8.2.5); 
• Blood chemistry within 14 days prior to cycle 1 day 1(see section8.2.5); 
• Serum pregnancy test for women of child-bearing potential (within 14 days prior 
to cycle 1 day 1); 
• Concomitant medications(within 14 days prior to cycle 1 day 1); 
• Whole body PET scan and CT of chest, abdomen and pelvis (may include neck at 
the discretion of the investigator).  
• Tumor tissue collection must be obtained on all subjects prior to start of treatment 
(see section 5.2.1 and appendix 2 for details) for research evaluation.   
• Archived tumor tissue from time of initial diagnosis of DLBC or PTCL must be 
obtained for research evaluation and correlation with the current tissue sample.   
7.2.2 
Subject Enrollment 
The results from the Screening visit evaluations will be reviewed to determine if the 
subject continues to meet the eligibility requirements as specified in the protocol. If a 
subject does not meet eligibility requirements or withdraws consent prior to treatment 
initiation, then that subject will be determined a screen failure and will not be eligible to 
receive treatment in the study. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 26 of 75 
Version Date 29 February 2016 
 
 
Subjects who have signed the informed consent and meet all the entry criteria (see 
Inclusion/Exclusion Criteria) will be enrolled in the study.  At the time of enrollment a 
subject study identifier will be assigned by the sponsor.   
 
7.3 
On-Treatment Evaluations 
Cycle 1, Day 1 Assessments: 
• Hematology and Chemistry laboratory assessments unless completed within 7 days 
prior (see section 8.2.5) to treatment.  If the screening laboratory assessments were 
collected within 7 days prior to treatment, these results may be also used for the Cycle 
1, day 1 assessment. 
• Vital Signs within 30 minutes prior to first dose 
• AE assessment 
• Con Meds 
• Subjects will be prescribed ruxolitinib orally twice daily. A cycle consists of 28 
consecutive days of BID dosing. (See section 9.0) 
• Blood Samples for Cytokine Profiling and C reactive protein analysis will be 
collected within 7 days before first dose and blood for cytokine profiling will be 
collected at 3 hours after the first dose of ruxolitinib.  (see appendix 2) 
• Vital Signs one hour after first dose. 
• Subjects will be instructed to take doses approximately 12 hours apart. 
• Subjects will be asked to complete a study drug dosing diary and to return all empty 
study drug bottles and completed diaries to the study center. 
 
Cycle 1, weekly assessments on Day 1, Day 8, Day 15, and Day 22: 
• Hematology and chemistry laboratory assessments (see section 8.2.5) 
• Blood Sample for Cytokine Profiling will be collected prior to the morning dose of 
ruxolitinib (see appendix 2) 
 
Cycle 2, and each subsequent Cycle assessments:   
• Hematology and Chemistry laboratory assessments (see section 8.2.5) 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 27 of 75 
Version Date 29 February 2016 
 
• Cycle 2, Day 1 only:  Blood Sample for Cytokine Profiling and C-reactive protein 
analysis will be collected prior to initiation of cycle 2 dosing (see appendix 2). 
• Vital Signs  
• AE assessment 
• Concomitant Medications 
• Physical Exam 
• ECOG performance status 
• Optional fresh tumor sample collection:  Either excisional biopsy or two 14 gauge or 
larger, > 2cm length cores will be obtained sometime after the completion of 2 cycles 
of treatment (see appendix 2).    
 
Disease restaging will occur after 2 cycles concurrent with the start of Cycle 3 and then 
every 2 cycles thereafter.  In subjects who are beyond the post cycle 6 response 
assessment AND have demonstrated objective resonse (PR or CR) restaging may be done 
every 3 cycles thereafter.   The following tests will be completed: 
• CT  scan chest, abdomen, pelvis.  However, in subjects with measureable cutaneous 
lesions only, photographs and bidimensional measurements of skin lesions may be 
utilized for response assessment.  The Investigator should take care to ensure 
consistency in response assessment evaluation throughout the study.    
• PET scan may be performed at the discretion of the investigator to confirm CR or PR  
• If subject has complete remission by CT or CT/PET scan perform a bone marrow 
biopsy for confirmation of complete response unless the patient had a documented 
negative bone marrow biopsy within 45 days prior to treatment initiation. 
7.4 
Duration of Participation 
Subjects who are demonstrating benefit may continue to receive treatment with 
ruxolitinib unless a criterion for discontinuation from the study has been met. The criteria 
for study discontinuation are listed below: 
• unacceptable toxicity; 
• disease progression or relapse 
• investigator discretion 
• withdrawal of consent 
• pregnancy 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 28 of 75 
Version Date 29 February 2016 
 
If a subject is withdrawn from the study treatment for any reason, the study sponsor-
investigator must be notified and an end-of-treatment visit should be performed. Follow-
up evaluations will also be performed in accordance with the protocol requirements. 
7.5 
End-of-treatment Evaluations 
Subjects who are withdrawn from the study treatment for any reason will have 
evaluations performed at End-of-Treatment.  The following evaluations and procedures 
will be performed at this visit. 
• AE assessment 
• Concomitant Medications 
• Physical Exam 
• ECOG performance status 
• Hematology and Chemistry laboratory assessments 
• Documentation of response 
• All subjects must be followed for safety for at least 30 days after ruxolitinib treatment 
has ended, or ruxolitinib related toxicities resolve or return to Baseline or are deemed 
irreversible, whichever is the longer duration.  
• At time of relapse subjects will have a blood sample collected for C-reactive protein 
evaluation (see appendix 2. II. C) 
• Optional fresh tumor sample collection: subjects who have documented disease 
progression will have either excisional biopsy or two 14 gauge or larger, > 2cm 
length cores within 6 weeks post treatment (see appendix 2). 
7.6 
Follow-up Evaluations  
Subjects will be followed every 3 months for the first year and every 6 months thereafter 
via a clinic visit or contact by telephone by research staff personnel to obtain the 
following information:  
• Disease Status will be collected until first documented relapse or progression of the 
disease under study; 
• Date last alive or date of death 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 29 of 75 
Version Date 29 February 2016 
 
8.0 
STUDY ASSESSMENTS 
8.1 
Demographic and Other Pre-Treatment Assessments 
After written informed consent is obtained, demographic data and a complete medical 
and medication history will be collected at Screening. Height, body weight and BMI 
measurements will be done.  Medical history will be updated up through the first dose of 
study medication, after which adverse events will be recorded.  Disease staging, 
laboratory assessments, physical exam, performance status will be completed as outlined 
in the study flowchart.  In addition, all subjects will undergo tumor biopsy for exploratory 
tumor GEP and IHC studies. 
8.2 
Safety Assessments 
8.2.1 
Adverse Events 
Adverse events will be monitored continuously during the study after the first dose of 
study medication.  Subjects will be instructed to report all AEs during the study and 
subjects will be assessed for the occurrence of AEs throughout the study.  All AEs 
(serious and nonserious) must be recorded on the source documents and case report forms 
regardless of the assumption of a causal relationship with the study medication.  The 
definition, reporting, and recording requirements for AEs are described in Section 11. 
8.2.2 
Physical Examinations 
A comprehensive physical examination will be performed at the times indicated on the 
Schedule of Observations.  The comprehensive physical examination will include the 
following organ or body system assessments: skin; head, eyes, ears, nose, and throat; 
thyroid; lungs; cardiovascular; abdomen (liver, spleen); extremities, lymph nodes, and a 
brief neurological exam. 
8.2.3 
Vital Signs 
Vital sign measurements (blood pressure, heart rate, and body temperature) will be 
collected on the days and times noted in the Schedule of Observations.   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 30 of 75 
Version Date 29 February 2016 
 
8.2.4 
12-Lead ECG Interpretation 
The baseline 12-lead ECG will be interpreted by the Investigator at the site and will be 
used for immediate subject management. Subsequent ECG evaluations  may be 
performed at the discretion of the investigator.  The decision to include/exclude a subject 
or discontinue a subject’s participation in the study based on an ECG flagged as 
“Abnormal, Clinically Significant” is the responsibility of the Investigator.  
8.2.5 
Clinical Safety Laboratory Assessments 
All subjects will have samples of blood collected on the days and times noted in the 
Schedule of Observations for analysis of serum chemistry, hematology, and pregnancy 
status.   The hematology panel will include:  hematocrit, hemoglobin, platelet count, red 
blood cell count, white blood cell count, absolute basophils, absolute eosinophils, 
absolute lymphocytes, absolute monocytes, absolute neutrophils, blasts.  The chemistry 
panel will include: sodium, potassium, calcium, blood urea nitrogen (BUN), creatinine, 
total (unconjugated) bilirubin, glucose, total protein, albumin, alanine aminotransferase 
(ALT), aspartate aminotransferase (AST), lactic dehydrogenase (LDH), alkaline 
phosphate. 
 
9.0 
TREATMENT OF SUBJECTS 
9.1 
Investigational Product(s) Description  
9.1.1 
Dosage and Dose Regimen 
Open label ruxolitinib will be supplied by Incyte Corporation.   Ruxolitinib tablets (5 mg) 
will be administered as oral doses without regard to food in an outpatient setting.  
Starting doses will be either 15 mg BID or 10 mg BID as described in Section 9.2.  
Maximum dose will not exceed 25 mg BID.   A cycle consists of 28 consecutive days of 
BID dosing.  Dosing is continuous without planned interruptions between cycles. Dosing 
may be interrupted or modified due to toxicities (see section 9.2).   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 31 of 75 
Version Date 29 February 2016 
 
9.1.2 
Packaging and Labeling 
Ruxolitinib 5 mg tablets are packaged as 60-count in high-density polyethylene (HDPE) 
bottles. The bottles will include labeling “New Drug - Limited by Federal (USA) Law to 
Investigational Use”.  
9.1.3 
Storage/Stability  
The bottles of tablets should be stored at room temperature, 15°C to 30°C (59°F to 86°F). 
Stability studies will be conducted on all clinical batches to support the clinical trial. 
9.1.4 
Drug Accountability 
Responsibility for drug accountability at the study site rests with the Investigator; 
however, the Investigator may assign some of the drug accountability duties to an 
appropriate pharmacist or designee.  Inventory and accountability records must be 
maintained and readily available for inspection by the study monitor and are open to 
inspection at any time by any applicable regulatory authorities. 
 
The Investigator or designee will be expected to collect and retain all used, unused, and 
partially used containers of study medication until the end of the study.  The Investigator 
or designee must maintain records that document: 
• 
investigational product delivery to the study site 
• 
the inventory at the site 
• 
use by each subject including pill/unit counts from each supply dispensed 
• 
product returned to the Investigator or designee.   
 
These records should include dates, quantities, batch/serial numbers (if available), and the 
unique code numbers (if available) assigned to the investigational product and study 
subjects.   
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 32 of 75 
Version Date 29 February 2016 
 
The investigational product must be used only in accordance with the protocol.  The 
Investigator will also maintain records adequately documenting that the subjects were 
provided the study medication specified. 
  
Completed accountability records will be archived by the site.  If any unused ruxolitinib 
bottles remain at the end of the study, they will be accounted for at the site close-out visit.  
If a site is able to destroy ruxolitinib at their premises, or through a certified vendor, they 
may do so upon authorization by the Sponsor, provided their destruction policy is made 
available to the Sponsor. 
 
9.2 
Administration of Study Medication 
9.2.1     
Starting Dose Assignment 
Continuous BID dosing is planned.  A cycle is 28 days of BID dosing. The starting dose 
of ruxolitinib tablets will be determined based on Baseline platelet count as follows: 
• Subjects with Baseline platelet count > 100,000/μL will begin dosing at 15 mg BID 
(three 5 mg tablets BID).   
• Subjects with Baseline platelet count of 75,000/μL to <100,000/μL will begin dosing at 
10 mg BID (two 5 mg tablets BID). 
A standardized dosing paradigm will be used to determine dose adjustments for safety 
and efficacy so that each subject is titrated to their most appropriate dose. Doses will not 
exceed 25 mg BID.  
 
9.2.2      
Dose Increases  
The initial dose of ruxolitinib will be determined by the Baseline platelet count value.  
After every 2 cycles  (post cycle 2,  4, 6, etc.) of therapy, at the discretion of the 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 33 of 75 
Version Date 29 February 2016 
 
investigator, the dose may be increased in 5 mg BID increments, to a maximum dose of 
25 mg BID for subjects who meet all three of the following conditions: 
1. Inadequate efficacy is demonstrated by no response or stable disease relative to 
baseline.  
2. Platelet count is ≥ 50,000/μL and platelet count has never been below 50,000/μL at a 
prior laboratory evaluation since Baseline. 
3. Absolute neutrophil count levels have remained at or above 1000/μL since baseline. 
4. No grade 4 anemia has been observed since baseline. 
 
9.2.3     
Dose Adjustments for Safety 
Dosing must be held for toxicities according to Table 1.  In order to provide sufficient 
data to make the dose adjustment decisions, it is recommended that hematology 
parameters be obtained at least weekly for platelet count < 50,000/μL or ANC < 1000/μL 
and at least two times weekly for platelet count < 25,000/μL or ANC < 500/μL.  Dosing 
may be restarted or increased following recovery of toxicities to acceptable levels. 
Subjects with hematologic toxicities requiring dose holds for 3 weeks or longer will be 
removed from the study.   
 
The objective for restarting or escalating after a reduction for safety is to find the highest 
safe dose of ruxolitinib for each subject, with increases in dose not more than in 
increments of 5 mg BID and not more often than every 2 cycles.   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 34 of 75 
Version Date 29 February 2016 
 
Table 1   Dose Modification Guidelines 
NCI CTCAE Toxicity 
Grade 
Action Required 
Thrombocytopenia: 
Platelets < 35,000 /uL  
• Hold (interrupt dosing) 
• Follow CBC at least twice weekly 
• If thrombocytopenia resolved to < Grade 2 
(50,000/uL, may restart at next lower dose level) 
• Subjects in whom benefit is seen and who 
recover to at least 40,000/uL platelets, may be 
considered for retreatment with a dose reduction 
after consultation with the study PI on a case by 
case basis.  
Grade 3 or 4 Neutropenia 
(ANC <1000/uL)  
• Hold (interrupt dosing) 
• Follow CBC at least weekly 
• If neutropenia resolves to < Grade 2, may restart 
at next lower dose level 
• Use of growth factors is permitted at the 
discretion of the investigator 
• Subjects in whom benefit is seen and who 
recover to at least grade 3 ANC, may be 
considered for retreatment with a dose reduction 
after consultation with the study PI on a case by 
case basis. 
Grade 4 Anemia 
(life-threatening, urgent 
intervention indicated) 
• Hold (interrupt dosing) 
• Follow CBC at least weekly 
• If anemia resolves to < Grade 2, may restart at 
next lower dose level 
• Use of transfusions and/or erythropoietin is 
permitted at the discretion of the investigator 
Related Grade 3 non-
hematologic Toxicities  
• Hold (interrupt dosing) 
• Manage toxicity according to institutional 
guidelines 
• If  toxicity resolves to < Grade 2 within 2 weeks, 
the subject may restart at next lower dose level 
or maintain per the investigator discretion 
Related Grade 4 non-
hematologic toxicities 
• Discontinue dosing 
• Remove subject from the study 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 35 of 75 
Version Date 29 February 2016 
 
 
NOTE: Whether the dose interruption occurred because of neutropenia, 
thrombocytopenia, anemia or any combination of cytopenias, all cytopenias must be 
considered to determine the ‘new’ dose that the subject will receive. The lowest 
calculated dose will be used and in all cases the maximum dose must not exceed 5 
mg BID LESS than the dose that resulted in the toxicity that required the dose 
interruption.  Subjects with hematologic toxicities requiring dose holds for 3 weeks 
or longer will be removed from the study, unless permission is granted from the 
study PI on a case by case basis.  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 36 of 75 
Version Date 29 February 2016 
 
Table 2    Optional Dose Increase or Mandatory Reduction Levels for Subjects 
initiating treatment at 15 mg daily 
+2 Dose Level 
25 mg BID daily for 28 days per cycle 
+1 Dose Level 
20 mg BID daily for 28 days per cycle 
Starting Dose 
15 mg BID daily for 28 days per cycle 
-1 Dose Level 
10 mg BID daily for 28 days per cycle 
-2 Dose Level 
5 mg BID daily for 28 days per cycle 
 
Table 3    Optional Dose Increase or Mandatory Reduction Levels for Subjects 
initiating treatment at 10 mg daily 
+3 Dose Level 
25 mg BID daily for 28 days per cycle 
+2 Dose Level 
20 mg BID daily for 28 days per cycle 
+1 Dose Level  
15 mg BID daily for 28 days per cycle 
Starting Dose 
10 mg BID daily for 28 days per cycle 
-1 Dose Level 
5 mg BID daily for 28 days per cycle 
 
 
In summary, it is the intention to identify the optimal dose for each individual subject 
over the first several weeks of therapy as follows: 
• Starting dose determined by baseline platelet count level. 
• Optional dose increase after every 2 cycles if an objective response (PR or CR) was not 
achieved and no significant thrombocytopenia or neutropenia was observed. 
• Frequent monitoring of hematology parameters, with mandatory dose decreases for 
toxicities.  
9.3 
Concomitant Medications / Measures 
All concomitant medications and treatments must be recorded in the eCRF.  Any prior 
medication received up to 30 days prior to randomization will be recorded in the eCRF.  
Concomitant treatments that are required to manage a subject’s medical condition during 
the trial will also be recorded in the eCRF.   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 37 of 75 
Version Date 29 February 2016 
 
9.4 
Restricted and / or Prohibited Medications and Therapies 
9.4.1 
Restricted Therapies 
The following medications have restrictions on use or doses or require changes to the 
way in which study drug is administered during the study: 
∙ Systemic corticosteroid doses should not be given except when necessary for non-
lymphoma related conditions and must not exceed a daily dose of prednisolone 
10mg/day; 
∙ Aspirin in doses exceeding 150 mg per day is not permitted. Low dose aspirin (≤ 150 
mg/day) and non steroidal anti-inflammatory agents (acetaminophen, ibuprofen) may be 
used; 
∙ Potent systemic inhibitors of CYP3A4 metabolizing enzymes (ketoconazole, 
clarithromycin, itraconazole, nefazodone and telithromycin should not be given.  When 
concomitant administration of a potent systemic inhibitor of CYP3A4 is required for 
subject management, and no alternative therapies are available, the sponsor must be 
contacted for discussion on a case by case basis.  Subjects may not receive ruxolitinib 
concurrently with potent systemic inhibitors of CYP3A4 without prior approval by the 
sponsor, and in most cases ruxolitinib dose adjustments will be necessary. 
∙ When concomitant administration of an anticoagulant/antiplatelet medication is required 
for subject management, the platelet count history, and any observations of 
thrombocytopenia during the study while on ruxolitinib should be considered. 
∙ During the study, use of CYP3A4 inducers is discouraged, and investigators should 
consider alternative therapies wherever possible. No dose adjustment will be used when 
moderate CYP3A4 inducers are co-administered with study drug. Any concomitant use 
of moderate CYP3A4 inducers (rifabutin, carbamazepine, phenytoin) must be 
documented. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 38 of 75 
Version Date 29 February 2016 
 
9.4.2 
Prohibited Therapies 
The following medications are prohibited during the study: 
∙ Concurrent anti-cancer medications or therapies, including radiation therapy; 
∙ Any prior or concomitant use of another JAK inhibitor. 
∙ Any investigational medication other than the study drug. Use of such medications 
within 14 days or 6 half-lives, whichever is longer, prior to the first dose of study drug 
and during the study through the Follow-up Visit is prohibited. 
9.5 
Discontinuation of Study Medication(s) 
 In the event that any subject discontinues the study medication and subsequently the 
study prior to completion, regardless of reason, reasonable efforts should be made to have 
the subject return for an early termination visit and have the End-of-treatment procedures 
completed as described in Section 7.4. 
 
The date the subject discontinued the study medication and the specific reason for 
discontinuation will be recorded in the eCRF.  This will include reasons such as 
discontinued due to treatment failure or withdrawn due to adverse event.  This 
information will be used to summarize the reasons for study discontinuation and 
treatment failure.  
10.0 WITHDRAWAL OF STUDY SUBJECTS 
10.1 
Withdrawal Criteria and Procedures 
10.1.1 
Withdrawal of Subjects from Study 
Subjects will be withdrawn from the study for any of the following reasons: 
• In the Investigator’s medical judgment, further participation would be injurious to 
the subject’s health or well being 
• Positive urine pregnancy test, confirmed by positive serum pregnancy (serum 
human chorionic gonadotropin) test results 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 39 of 75 
Version Date 29 February 2016 
 
• Consent is withdrawn 
• Termination of the study by the Sponsor. 
• Termination of the study by the local health authority or IRB/IEC  
 
If a subject is withdrawn from the study:   
• The study monitor or Sponsor must be notified.   
• The reason(s) for withdrawal must be documented in the subject’s medical record 
and eCRF.   
• An End-of-treatment visit should be performed. 
• All subjects must be followed for safety for at least 30 days after study treatment 
has ended, or until study drug related toxicities resolve, return to Baseline or are 
deemed irreversible, whichever is longer.  
  
If a subject is non-compliant in the opinion of the Investigator, the Sponsor-Investigator 
should be consulted for instruction on handling the subject. 
 
Criteria for discontinuation of study therapy are provided in Section 7.4. 
10.2 
Replacement Subjects 
Non-evaluable subjects will be replaced, at the Sponsor-Investigator’s discretion, to 
assure that a statistically appropriate number of subjects complete the study. 
10.3 
Protocol Deviations 
Subjects must meet eligibility requirements to be enrolled in the study. Major deviations 
must be reported to the IRB/IEC in accordance with the IRB/IEC requirements. During 
the course of the study the monitor must notify the Sponsor-Investigator of subjects 
found not to have met eligibility criteria.  The Sponsor-Investigator in collaboration with 
the Investigator will determine if the subject should be withdrawn from the study. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 40 of 75 
Version Date 29 February 2016 
 
11.0 ADVERSE EVENTS 
11.1 
Definitions and Reporting 
An Adverse Event for the purposes of this protocol is defined as the appearance of (or 
worsening of any pre-existing) undesirable sign(s), symptom(s), or medical condition(s) 
that occur after subject’s signed informed consent has been obtained. Abnormal 
laboratory values or test results occurring after informed consent constitute Adverse 
Events only if they induce clinical signs or symptoms, are considered clinically 
significant, require therapy (e.g., hematologic abnormality that requires transfusion), or 
require changes in study medication(s). 
Adverse Events that begin or worsen after informed consent should be recorded in the 
Adverse Events section of the eCRF. Conditions that were already present at the time of 
informed consent should be recorded in the Medical History section of the eCRF. 
Adverse Event monitoring should be continued for at least 30 days following the last 
dose of study treatment. Adverse Events (including lab abnormalities that constitute AEs) 
should be described using a diagnosis whenever possible, rather than individual 
underlying signs and symptoms. When a clear diagnosis cannot be identified, each sign 
or symptom should be reported as a separate Adverse Event. 
Adverse Events will be assessed according to the Common Terminology Criteria for 
Adverse Events (CTCAE) version 4.0).  If CTCAE grading does not exist for an Adverse 
Event, the severity of mild, moderate, severe, and life-threatening, or grades 1 - 4, will be 
used. CTCAE grade 5 (death) will not be used in this study; rather, information about 
deaths will be collected as an outcome of the event. The occurrence of Adverse Events 
should be sought by non-directive questioning of the subject during the screening process 
after signing informed consent and at each visit during the study. Adverse Events also 
may be detected when they are volunteered by the subject during the screening process or 
between visits, or through physical examination, laboratory test, or other assessments. As 
far as possible, each Adverse Event should be evaluated to determine:  
• The severity grade (CTCAE grade 1-4) 
• Reasonable possibility that AE is related to the study treatment: (no, yes) 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 41 of 75 
Version Date 29 February 2016 
 
• Start and end dates, unless unresolved at final exam 
• Action taken with respect to study drug (none, dose adjusted, temporarily 
interrupted, permanently discontinued, unknown, not applicable) 
• Outcome (not recovered/not resolved, recovered/resolved, recovering/resolving, 
recovered/resolved with sequelae, fatal, unknown) 
• Whether it is serious, as per SAE definition provided in Section 11.3.1. 
Unlike routine safety assessments, SAEs are monitored continuously and have special 
reporting requirements, see Section 11.3.2. 
All Adverse Events should be treated appropriately. If a concomitant medication or non-
drug therapy is given, this action should be recorded on the Adverse Event eCRF. 
Once an Adverse Event is detected, it should be followed until its resolution or until it is 
judged to be permanent, and assessment should be made at each visit (or more frequently, 
if necessary) of any changes in severity, the suspected relationship to the study drug, the 
interventions required to treat it, and the outcome. 
Disease progression should not be regarded or reported as an Adverse Event itself unless 
associated with a separate Adverse Event. 
Participating sites must agree to comply by UNMC Data and Safety Monitoring 
Committee (DSMC) procedures. The DSMC will monitor the protocol on at least a 
quarterly basis and as requested.  Sites must also comply with their local IRB 
requirements. All grade 3 and grade 4 adverse events and all Serious Adverse Events will 
be reported to the UNMC Eppley Cancer Center Data and Safety Monitoring Committee 
(DSMC) via the UNMC study coordinator. Sites will be provided with applicable policies 
and are required to enter all adverse events into the eCRF.  Adverse Event information 
will be collected from the eCRF database and reported to the UNMC DSMC. 
11.2 
Laboratory Test Abnormalities 
Definitions and Reporting 
Laboratory abnormalities that constitute an Adverse Event in their own right (are 
considered clinically significant, induce clinical signs or symptoms, require concomitant 
therapy or require changes in study treatment), should be recorded on the Adverse Events 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 42 of 75 
Version Date 29 February 2016 
 
eCRF. Whenever possible, a diagnosis, rather than a symptom should be provided (e.g. 
anemia instead of low hemoglobin). Laboratory abnormalities that meet the criteria for 
Adverse Events should be followed until they have returned to normal or an adequate 
explanation of the abnormality is found. When an abnormal laboratory or test result 
corresponds to a sign/symptom of an already reported Adverse Event, it is not necessary 
to separately record the lab/test result as an additional event. 
Laboratory abnormalities, that do not meet the definition of an Adverse Event, should not 
be reported as Adverse Events. A grade 3 or 4 event (severe) as per CTCAE does not 
automatically indicate a SAE unless it meets the definition of serious as defined below 
and/or as per investigator’s discretion. A dose hold or medication for the lab abnormality 
may be required by the protocol in Section 8.6 and should not contribute to designation of 
a lab parameter abnormality as a SAE: 
11.3 
Serious Adverse Events 
11.3.1   Definitions 
Serious Adverse Event (SAE) is defined as one of the following:  
• Is fatal or life-threatening (that is, immediate risk of dying) 
• Results in persistent or significant disability/incapacity 
• Constitutes a congenital anomaly/birth defect 
• Is medically significant, i.e., defined as an event that jeopardizes the subject or 
may require medical or surgical intervention to prevent one of the outcomes listed 
above. Considered significant by the investigator as an important medical event 
(s) that may not result in death, be life-threatening, or require hospitalization but 
may be considered a serious adverse event (s ) when, based upon appropriate 
medical judgment, they may jeopardize the subject and may require medical or 
surgical intervention to prevent one of the outcomes listed in this definition. 
• Requires inpatient hospitalization or prolongation of existing hospitalization, 
unless hospitalization is for:  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 43 of 75 
Version Date 29 February 2016 
 
o Routine treatment or monitoring of the studied indication, not associated 
with any deterioration in condition (specify what this includes) 
o Elective or pre-planned treatment for a pre-existing condition that is 
unrelated to the indication under study and has not worsened since signing 
the informed consent 
o Treatment on an emergency outpatient basis for an event not fulfilling any 
of the definitions of a SAE given above and not resulting in hospital 
admission 
o Social reasons and respite care in the absence of any deterioration in the 
subject’s general condition 
o Any SAEs that are expected due to the condition being treated, including 
if the SAE is a primary outcome measure, and whether there has been a 
clear agreement with regulators not to consider these as SAEs, provided 
the information is collected elsewhere 
11.3.2  Reporting 
To ensure subject safety, every SAE, regardless of suspected causality, occurring after 
the subject has provided informed consent and until at least 30 days after the subject has 
stopped study treatment must be reported to the Sponsor-Investigator or designee within 
24 hours of learning of its occurrence. Any SAEs experienced after this at least 30 day 
period should only be reported to the Sponsor-Investigator or designee if the investigator 
suspects a causal relationship to the study drug. Recurrent episodes, complications, or 
progression of the initial SAE must be reported as follow-up to the original episode 
within 24 hours of the investigator receiving the follow-up information. An SAE 
occurring at a different time interval or otherwise considered completely unrelated to a 
previously reported one should be reported separately as a new event. Serious adverse 
event collection begins after the subject has signed informed consent and has received 
study drug.  If a subject experiences a SAE after signing informed consent, but prior to 
receiving ruxolitinib, the event will NOT be collected unless the investigator feels the 
event may have been caused by a protocol procedure.  Previously planned (prior to 
signing the informed consent document) surgeries should not be reported as SAEs unless 
the underlying medical condition has worsened during the course of the study. 
Information about all SAEs is collected and recorded on the Serious Adverse Event 
Report Form. The investigator must assess and record the relationship of each SAE to the 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 44 of 75 
Version Date 29 February 2016 
 
study drug, complete the SAE Report Form in English, and send the completed, signed 
form by fax within 24 hours to the Sponsor-Investigator via a Sponsor-approved 
method.  The investigator must assess if there is a Reasonable possibility that SAE is 
related to the study treatment: (no, yes) 
All serious adverse events regardless of severity or relationship must be reported to the 
sponsor-investigator within 24 hours of the investigational staff’s knowledge. Please send 
a completed SAE form to: 
UNMC, ATTN: Susan Blumel 
 
 
Sentryx 
Fax:  402-559-8101 
 
 
AND  
Fax:  1-866-726-9234 
Phone:  402-559-9183 
 
 
 
Helpdesk:  1-866-278-6759, ext 250 
 
The Sponsor-Investigator will follow UNMC IRB and DSMC safety reporting 
requirements.  Participating sites must follow their local IRB and safety reporting 
requirements.  
The original copy of the SAE Report Form and the fax confirmation sheet must be kept 
with the case report form documentation at the study site. 
Follow-up information is sent to the same person to whom the original SAE Report Form 
was sent, using a new SAE Report Form stating that this is a follow-up to the previously 
reported SAE and giving the date of the original report. Each re-occurrence, 
complication, or progression of the original event should be reported as a follow-up to 
that event regardless of when it occurs. The follow-up information should describe 
whether the event has resolved or continues, if and how it was treated and whether the 
subject continued or withdrew from study participation. 
If the SAE is not previously documented in the Investigator’s Brochure for study 
medication (new occurrence) and is thought to be related to the study drug, a Sponsor’s 
associate may urgently require further information from the investigator for Health 
Authority reporting.   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 45 of 75 
Version Date 29 February 2016 
 
The Sponsor-Investigator may need to issue an Investigator Notification (IN), to inform 
all investigators involved in any study with the same drug that this SAE has been 
reported. Suspected Unexpected Serious Adverse Reactions (SUSARs) will be collected 
and reported to the competent authorities and relevant ethics committees in accordance 
regulatory requirements. 
 
11.4         Pregnancies 
Pregnancy, in and of itself, is not regarded as an adverse event, unless there is suspicion 
that study medication may have interfered with the effectiveness of a contraceptive 
medication or method.  The procedures that will be followed based on whether a 
pregnancy is confirmed by a positive serum test result are listed below: 
• Investigator and subject must notify each other immediately 
• Investigator must notify the Sponsor immediately  
• Discontinue study medication immediately 
• Perform the required End-of-treatment visit study evaluations 
• Investigator must complete and submit the Pregnancy Initial and Follow-up report 
forms to the Sponsor 
 
To ensure subject safety, each pregnancy in a subject during maternal or paternal 
exposures to study drug must be reported within 24 hours of learning of its 
occurrence.  Data on fetal outcome and breast-feeding are collected for regulatory 
reporting and drug safety evaluation.  The pregnancy should be followed up to determine 
outcome, including spontaneous or voluntary termination, details of the birth, and the 
presence or absence of any birth defects, congenital abnormalities, or maternal and/or 
newborn complications by following until the first well-baby visit. Pregnancy should be 
recorded on a Clinical Study Pregnancy Form and reported by the investigator to the 
Sponsor-Investigator. Pregnancy follow-up should be recorded on the same form and 
should include an assessment of the possible relationship to the study drug of any 
pregnancy outcome and follow-up to the first well-baby visit. Any SAE experienced 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 46 of 75 
Version Date 29 February 2016 
 
during pregnancy must be reported on the SAE Report Form and needs to be 
reported to the Sponsor. 
11.5        Warnings and Precautions 
No evidence available at the time of the approval of this study protocol indicated that 
special warnings or precautions were appropriate, other than those noted in the provided 
Investigator Brochure. Additional safety information collected between IB updates will 
be communicated in the form of Investigator Notifications. This information will be 
included in the subject informed consent and should be discussed with the subject during 
the study as needed. 
12.0 STATISTICS  
12.1 
Study Populations 
The populations to be analyzed include the following:  
Intent-to-treat (ITT) population - Subjects enrolled in the study. 
Evaluable population – Subjects who had completed 2 cycles of therapy with response 
assessments or progressed before the evaluation of the primary endpoint.   
Safety evaluable population. - Subjects who received at least one dose of study 
medication.  
 
12.2 
Efficacy Analysis  
Primary efficacy analyses will be based on both the ITT and evaluable populations. 
Secondary efficacy analyses will be based on ITT population only.  
12.2.1 
Primary Efficacy Analyses 
Primary endpoint   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 47 of 75 
Version Date 29 February 2016 
 
The primary objective of the study is to evaluate subject overall response rate (ORR) 
after 6 cycles for each of the subject cohorts.  The description provided in this section 
includes the primary analyses for the primary objective. 
Statistical hypothesis and sample size justification  
Subjects meeting the stated eligibility requirements will be enrolled onto the study. 
Subjects will be grouped into cohorts 1) DLBCL ABC 2) DLBCL GCB 3) PTCL and 4) 
OTHER SUBTYPES (subjects who are not able to be placed into cohorts 1, 2, and 3),  
based upon a central determination of immunohistochemistry and gene-expression 
profile.  A target sample size of 30 is planned for cohorts 1, 2, and 3.   Cohorts 1, 2, and 3 
will have a minimum of 10 and a maximum of 30 subjects. There is no minimum or 
maximum requirement for Cohort 4, since there is a very low number of subjects 
anticipated for this cohort. (Maximum in all cohorts is 90 subjects). 
 
These sample sizes are based on a 3-stage design of alpha=0.07 with power of 77% 
(beta=0.23) to test the null hypothesis that ORR after 6 cycles will be ≤ 10% (not 
considered clinically compelling) versus the alternative hypothesis that ORR will be ≥ 
25% (considered clinically meaningful in this patient population) within each cohort. 
Based on the simulation study, to maintain the above type I and II errors, two interim 
analyses for futility will be performed for each cohort separately according to the 
following stopping rule: 
1) The first interim analysis will occur when 10 subjects have been enrolled in the 
cohort.  If there are any responders (CR+PR) observed among the 10 subjects, 
enrollment will continue; otherwise, enrollment will be suspended and these 10 
subjects will be followed to further assess their responses. During this follow-up 
period, as soon as one response is observed, enrollment will resume. If no 
response is observed after the 10 subjects have been fully assessed after 6 cycles, 
the trial will be terminated for futility.  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 48 of 75 
Version Date 29 February 2016 
 
2) The second interim analysis will occur when 20 subjects have been enrolled in 
the cohort. If there are 3 or more responders (CR+PR) observed among the 
20 subjects, enrollment will continue; otherwise, enrollment will be suspended 
and these 20 subjects will be followed to further assess their responses. During 
this follow-up, as soon as 3 or more responders are observed, enrollment will 
resume. If there are < 3 responders observed after the 20 subjects have been fully 
assessed, the trial will be terminated for futility. 
3) At the end of the trial, if there are ≥ 6 responders (CR+PR) observed among the 
30 subjects, the null hypothesis will be rejected and the drug is valuable to pursue 
further research; otherwise we fail to reject the null hypothesis and futility of the 
drug will be claimed. 
12.2.2 
Secondary Efficacy Analyses 
Secondary endpoints 
Safety endpoint 
All adverse events recorded during the study will be summarized by each subject cohort.  
The incidence of treatment-emergent adverse events (new or worsening from baseline) 
will be summarized by severity and type of adverse event. Listings of deaths, SAEs, and 
AEs leading to early termination of study treatment or premature withdrawal from study 
will also be provided. 
Duration of response (DOR) 
Duration of response is defined as the interval from the date of complete or partial 
remission documented to date of recurrence/progression, death due to any cause, or lost 
to follow-up. The Kaplan-Meier method will be used to estimate the median duration of 
response and its 95% confidence interval (CI). 
 
Progression-free survival (PFS) 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 49 of 75 
Version Date 29 February 2016 
 
PFS is defined as the time from the date of start of treatment to the date of event defined 
as the first documented progression or death due to any cause.  If a subject has not had an 
event, progression-free survival is censored at the date of last adequate assessment or 
start of another therapy, whichever occurs first.  The Kaplan-Meier method will be used 
to estimate PFS and its 95% CI.   
Overall survival (OS) 
OS is defined as the time from date of start of treatment to date of death due to any cause.  
If a subject is not known to have died, survival will be censored at the date of last contact.  
The Kaplan-Meier method will be used to estimate the median OS time and its 95% CI. 
12.2.3  
Exploratory Analyses 
Exploratory endpoints 
The exploratory aspect of the study is to explore relationship between responses to oral 
ruxolitinib and alterations in GEP signatures as well as biomarker immunophenotypic 
changes related to JAK2/STAT3, NF-κB, BCR, PI3K/AKT, and mTOR pathways, and to 
evaluate potential effect of oral ruxolitinib exposure on JAK2/STAT3 pathway inhibition 
in serial tumor samples.  Descriptive statistics will be used.  Mean, standard deviation 
(STD), median and range will be reported for markers pre- and post-treatment as well as 
for the marker changes between pre- and post-treatment. Paired t-test will be used to 
evaluate the marker changes between pre- and post-treatment.  Spearman or Pearson 
correlation coefficients will be calculated to evaluate the correlations among markers.  
Logistic regression will be utilized to assess the effects of markers at baseline on 
response to therapy. 
12.3 
Safety Analysis 
12.3.1 
Adverse Events 
Adverse events will be tabulated by the Medical Dictionary for Regulatory Activities 
(MedDRA®) preferred term and by body system.  Severity of adverse events will be 
based on the scale as indicated in Section 11.2.2. 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 50 of 75 
Version Date 29 February 2016 
 
The subset of adverse events that are considered by the Investigator to have a possible or 
probable relationship to study medication will be considered to be treatment-related 
adverse events.  If the Investigator does not specify the relationship of the adverse event 
to study medication, the adverse event will be considered to be treatment-related.  The 
incidence of adverse events and treatment-related adverse events will be tabulated.  
 
13.0 DATA MANAGEMENT 
13.1 
Data Collection 
The Investigator will be provided with a eCRF for each subject.   
 
Entries made in the eCRF must be verifiable against source documents, or, as directed by 
the Sponsor, directly entered into the eCRF, in which case the entry in the eCRF will be 
considered source documentation. Data reported in the eCRF  derived from source 
documents should be consistent with the source documents. The investigator must 
explain any discrepancies between the eCRF and the source documents. 
The Investigator will be responsible for reviewing all data and eCRF entries in each 
subject’s eCRF, verifying the information is true and correct.   
13.2 
Data Management 
Data management will be performed using electronic case report forms (eCRFs). 
 
All eCRF data will be entered into a validated database.   
 
All data entry, verification and validation will be performed in accordance with the 
current standard operating procedures of the Data Management Department at the 
sponsor or its designee.   The sponsor will authorize the database for lock once all data 
queries are complete, all study data are considered clean, and all defined procedures 
completed by the investigator.  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 51 of 75 
Version Date 29 February 2016 
 
14.0 STUDY ADMINISTRATION 
14.1 
Access to Source Documents 
    14.1.1 
Scientific Review Committee Audit Procedures 
The UNMC Eppley Cancer Center Scientific Review Committee will review this 
protocol on at least an annual basis. This study will not be audited by the UNMC 
Audit Committee, however monitoring updates will be provided to the Audit 
Committee as required.  
 
    14.1.2 
Monitoring Visits 
Monitoring visits provide the Sponsor-Investigator with the opportunity to: 
• Evaluate the progress of the study 
• Verify the accuracy and completeness of eCRFs 
 
• Assure that all protocol requirements, applicable laws and/or regulations, and 
Investigator’s obligations are being fulfilled 
• Resolve any inconsistencies in the study records.   
 
The Investigator must allow study monitors to periodically review, all eCRFs and 
office, hospital, and laboratory records supporting the participation of each subject in 
the study, at mutually convenient times, during the study and after the study has been 
completed.  The eCRFs and other documentation supporting the study must be kept 
up-to-date by the Investigator and the research staff at the investigative site.  These 
study materials must be available for review by the study monitor, and/or other 
qualified representatives of the Sponsor, at each monitoring visit. 
 
The study monitor will review the various records of the study (eCRFs, subject 
medical and laboratory records, and other pertinent data).  The study monitor will 
verify the eCRF data against original source documentation for accuracy and 
completeness.  The study monitor will identify data discrepancies and collaborate with 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 52 of 75 
Version Date 29 February 2016 
 
the Investigator and research staff to resolve the discrepancies in a timely manner.  
Protocol deviations will also be identified and recorded on a “Protocol Deviation 
Log.”  The study monitor will follow an “Issue Escalation” plan in order to ensure 
each issue identified during a monitoring visit is appropriately documented, reported, 
and resolved in a timely manner in accordance with the plan’s requirements.   
14.2 
Statement of Good Clinical Practices  
This trial will be conducted in adherence to the study protocol, Good Clinical Practices as 
defined in Title 21 of the US Code of Federal Regulations Parts 50, 54 56, 312 and 
Part 11 as well as ICH GCP consolidated guidelines (E6) and applicable regulatory 
requirements. http://www.fda.gov/cder/guidance/index.htm 
14.3 
Protocol Adherence 
Each Investigator must adhere to the protocol as described in this document and agree 
that deviations to the protocol, with the exception of medical emergencies, must be 
discussed and approved by the Sponsor-Investigator prior to seeking approval from the 
IRB/IEC.  Each Investigator is responsible for enrolling subjects who have met the 
protocol inclusion and exclusion criteria or must have obtained prior documented 
approval from the Sponsor prior to enrollment in the study.  The IRB/IEC that granted 
original approval, or the IRB/IEC currently responsible for overseeing the conduct of the 
study, must be notified of all changes in and deviations from the protocol that may 
increase risk to the subject, and/or that may adversely affect the rights of the subject or 
validity of the investigation.  The Investigator must send a copy of the approval letter 
from the IRB/IEC to the Sponsor or CRO and retain the original in the site study 
regulatory file. 
14.4 
Study Termination 
Both the Sponsor-Investigator and the Investigator reserve the right to terminate the 
study, according to the terms specified in the study contract.  The Investigator is to notify 
the IRB/IEC in writing of the study’s completion or early termination, and send a copy of 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 53 of 75 
Version Date 29 February 2016 
 
the notification to the Sponsor or CRO and retain one copy for the site study regulatory 
file. 
14.5 
Financial Disclosure 
All clinical Investigators participating in clinical studies subject to FDA Regulation Title 
21 Code of Federal Regulations (CFR) Part 54 – Financial Disclosure by Clinical 
Investigators are required prior to study initiation to submit a completed Clinical 
Investigator Financial Certification/Disclosure Request Form that sufficiently details any 
financial interests and arrangements that apply.  For the purpose of this regulation, 
clinical Investigator is defined as any Investigator or Sub-Investigator who is directly 
involved in the treatment or evaluation of research subjects, including the spouse and any 
dependent child of the Investigator, but not that of any Sub-Investigators.  These 
requirements apply to both US and foreign clinical Investigators conducting covered 
clinical studies. 
 
Any new Investigators or Sub-Investigators added to the covered clinical study during its 
conduct must also submit a completed Clinical Investigator Financial Disclosure Request 
Form.  At the conclusion of the covered clinical study, the Investigators will be reminded 
of their obligation to report to the Sponsor/designee any changes to the financial 
disclosure information previously reported.  The clinical Investigators will also be 
reminded that they must report any changes in their financial information regarding 
significant equity interests and significant payments for a period of 1 year after 
completion of their participation in the covered clinical study.   
14.6 
Quality Control and Assurance 
14.6.1 
Sponsor Audits 
At some point during the study, individuals from the Sponsor’s Quality Assurance 
department and/or their authorized representative may visit the Investigator’s site to 
conduct an audit of the study.  The purpose of this visit will be to determine the 
Investigator’s adherence to the protocol, applicable regulations, and the Sponsor’s 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 54 of 75 
Version Date 29 February 2016 
 
procedures, in addition to assessing the accuracy of the study data.  Prior to initiating this 
audit, the Investigator will be contacted by the Sponsor to arrange a convenient time for 
this visit.  The Investigator and staff are expected to cooperate with the auditors and 
allow access to all subject records supporting the eCRFs and other study-related 
documents. 
14.6.2 
Inspection by Regulatory Authorities 
At some point during the investigational product’s development program, a regulatory 
authority may visit the Investigator to conduct an inspection of the study and the site.  
The Investigator and staff are expected to cooperate with the inspectors and allow access 
to all source documents supporting the eCRFs and other study-related documents.  The 
Investigator must immediately notify the Sponsor when contacted by any regulatory 
authority for purposes of conducting an inspection. 
15.0 ETHICS 
15.1 
Institutional Review Board or Independent Ethics Committee 
It is the responsibility of the Investigator to assure that all aspects of the ethics review are 
conducted in accordance with the Declaration of Helsinki as described in the 
International Conference on Harmonisation (ICH) E6: Guideline for Good Clinical 
Practice (GCP), and/or local laws, whichever provides the greatest level of protection for 
the study participants 14.  The protocol and any information supplied to the subject to 
obtain informed consent, including written informed consent form(s), subject recruitment 
procedures (eg, advertisements), and written information to be provided to subjects 
(information leaflets), must be reviewed and approved by a qualified IRB/IEC prior to 
enrollment of participants in the study.  Prior to initiation of the study, the Sponsor-
Investigator must receive documentation of the IRB/IEC approval, which specifically 
identifies the study/protocol, and a list of the committee members. 
 
Amendments to the protocol and revisions to the informed consent must also be 
submitted to and, if required, approved by the IRB/IEC. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 55 of 75 
Version Date 29 February 2016 
 
 
Investigators must submit progress reports to the IRB/IEC in accordance with the 
IRB/IEC requirements. Annual re-approval of the study must be obtained. Copies of 
progress reports and Annual re-approvals must be sent to the Sponsor-Investigator. 
 
When the Sponsor-Investigator provides the Investigator with a safety report, the 
Investigator must promptly forward a copy to the IRB/IEC, according to site IRB/IEC 
reporting requirements. 
 
After completion or termination of the study, the Investigator must submit a final report 
to the IRB/IEC and to the Sponsor-Investigator.   
 
The Investigator, as part of the records retention requirements for the study, must 
maintain documentation of all submissions, correspondence, and approvals to and from 
the IRB/IEC. 
 
Each clinical Investigator is responsible to conduct the study in accordance with the 
protocol, all applicable laws, regulations, and GCP according to ICH guidelines. 
15.2 
Informed Consent  
Preparation of the consent form is the responsibility of the Investigator and the Sponsor-
Investigator and must include all elements required by the ICH, GCP, and applicable 
regulatory requirements, and must adhere to GCP and to the ethical principles that have 
their origin in the Declaration of Helsinki.   
 
A template will be provided by the Sponsor-Investigator.  The Sponsor-Investigator or 
designee must review and approve all changes to site-specific Informed Consent forms.  
 
The consent form must include a statement that the Sponsor-Investigator or designee and 
regulatory authorities have direct access to subject records.  Prior to the beginning of the 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 56 of 75 
Version Date 29 February 2016 
 
study, the Investigator must have the IRB/IEC’s written approval/favorable opinion of the 
written informed consent form and any other information to be provided to the subjects. 
Before being enrolled in the clinical study, subjects must consent to participate after the 
nature, scope, and possible consequences of the study have been explained in a form 
understandable to them.   
 
An informed consent document that includes both information about the study and the 
consent form will be prepared and given to the subject.  This document will contain all 
the elements required by the ICH E6 Guideline for Good Clinical Practice and any 
additional elements required by local regulations.  The document must be in a language 
understandable to the subject and must specify who informed the subject.  Where 
required by local law, the person who informs the subject must be a physician. 
A copy of the signed consent document must be given to the subject.  The original signed 
consent document will be retained by the Investigator. 
 
The Investigator will not undertake any measures specifically required only for the 
clinical study until valid consent has been obtained. 
 
The Investigator must inform the subject’s primary physician about the subject’s 
participation in the trial if the subject has a primary physician and if the subject agrees to 
the primary physician being informed. 
15.2.1 
Data Privacy 
Applicable data privacy laws and regulations must be adhered to. The Investigator and 
the Sponsor are responsible for ensuring that sensitive information is handled in 
accordance with local requirements (eg, HIPAA).  Appropriate consent and 
authorizations for use and disclosure and/or transfer (if applicable) of protected 
information must be obtained. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 57 of 75 
Version Date 29 February 2016 
 
16.0 RECORD KEEPING / RETENTION OF RECORDS 
The Investigator must ensure that all records pertaining to the conduct of the clinical 
study, informed consent forms, drug accountability records, source documents, and other 
study documentation are adequately maintained for a period of 2 years after the last 
approval of a marketing application in an ICH region and until there are no pending or 
contemplated marketing applications in an ICH region or at least 2 years have elapsed 
since the formal discontinuation of clinical development of the investigational product.  
 
The Investigator must not destroy any records associated with the study without receiving 
approval from the Sponsor-Investigator.  The Investigator must notify the Sponsor-
Investigator in the event of accidental loss or destruction of any study records.  If the 
Investigator leaves the institution where the study was conducted, the Sponsor-
Investigator must be contacted to arrange alternative record storage options. 
 
Whenever possible, an original recording of an observation must be retained as the source 
document.  However, a photocopy of a record is acceptable provided it is legible and is a 
verified copy of the original document. 
 
All eCRF data entered by the site (including audit trail), as well as computer hardware 
and software (for accessing the data), will be maintained or made available at the site in 
compliance with applicable record retention regulations.  The Sponsor-Investigator will 
retain the original eCRF data and audit trail.   
16.1 
Confidentiality 
Subject names will not be supplied to the Sponsor.  Only the subject number and subject 
initials will be recorded in the eCRF, and if the subject name appears on any other 
document (eg, laboratory report), it must be obliterated on the copy of the document to be 
supplied to the Sponsor-Investigator.  Study findings stored on a computer will be stored 
in accordance with local data protection laws.  The subjects will be informed that 
representatives of the Sponsor-Investigator, IRB/IEC, or regulatory authorities may 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 58 of 75 
Version Date 29 February 2016 
 
inspect their medical records to verify the information collected, and that all personal 
information made available for inspection will be handled in strictest confidence and in 
accordance with local data protection laws. 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 59 of 75 
Version Date 29 February 2016 
 
17.0 REFERENCES 
 
1. 
Jemal, A., et al., Cancer statistics, 2010. CA Cancer J Clin, 2010. 60(5): p. 277-
300. 
2. 
World Health Organization, WHO Classification of Tumours of Haematopoietic 
and Lymphoid Tissues. Geneva, Switzerland: WHO Press, 2008. 
3. 
Rosenwald, A., et al., The use of molecular profiling to predict survival after 
chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med, 2002. 346(25): 
p. 1937-47. 
4. 
Mottok, A., et al., Inactivating SOCS1 mutations are caused by aberrant somatic 
hypermutation and restricted to a subset of B-cell lymphoma entities. Blood, 
2009. 114(20): p. 4503-6. 
5. 
Ritz, O., et al., Recurrent mutations of the STAT6 DNA binding domain in 
primary mediastinal B-cell lymphoma. Blood, 2009. 114(6): p. 1236-42. 
6. 
Lam, L.T., et al., Cooperative signaling through the signal transducer and 
activator of transcription 3 and nuclear factor-{kappa}B pathways in subtypes of 
diffuse large B-cell lymphoma. Blood, 2008. 111(7): p. 3701-13. 
7. 
Chiarle, R., et al., Stat3 is required for ALK-mediated lymphomagenesis and 
provides a possible therapeutic target. Nat Med, 2005. 11(6): p. 623-9. 
8. 
van Kester, M.S., et al., Cucurbitacin I inhibits Stat3 and induces apoptosis in 
Sezary cells. J Invest Dermatol, 2008. 128(7): p. 1691-5. 
9. 
Zhang, C., et al., Curcumin selectively induces apoptosis in cutaneous T-cell 
lymphoma cell lines and patients' PBMCs: potential role for STAT-3 and NF-
kappaB signaling. J Invest Dermatol, 2010. 130(8): p. 2110-9. 
10. 
Verma, N.K., et al., STAT3 knockdown by siRNA induces apoptosis in human 
cutaneous T-cell lymphoma line Hut78 via downregulation of Bcl-xL. Cell Mol 
Biol Lett, 2010. 15(2): p. 342-55. 
11. 
Burger, R., et al., Janus kinase inhibitor INCB20 has antiproliferative and 
apoptotic effects on human myeloma cells in vitro and in vivo. Mol Cancer Ther, 
2009. 8(1): p. 26-35. 
12. 
Ding, B.B., et al., Constitutively activated STAT3 promotes cell proliferation and 
survival in the activated B-cell subtype of diffuse large B-cell lymphomas. Blood, 
2008. 111(3): p. 1515-23. 
13. 
Verstovsek, S., et al., Safety and efficacy of Ruxolitinib, a JAK1 and JAK2 
inhibitor, in myelofibrosis. N Engl J Med, 2010. 363(12): p. 1117-27. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 60 of 75 
Version Date 29 February 2016 
 
14. 
WORLD MEDICAL ASSOCIATION DECLARATION OF HELSINKI Ethical 
Principles for Medical Research Involving Human Subjects.  Adopted by the 18th 
WMA General Assembly, Helsinki, Finland, June 1964, and amended by the 29th 
WMA General Assembly, Tokyo, Japan, October 1975, 35th WMA General 
Assembly, Venice, Italy, October 1983, 41st WMA General Assembly, Hong 
Kong, September 1989, 48th WMA General Assembly, Somerset West, Republic 
of South Africa, October 1996, and the 52nd WMA General Assembly, 
Edinburgh, Scotland, October 2000.  Note of Clarification on Paragraph 29 added 
by the WMA General Assembly, Washington 2002. Note of Clarification on 
Paragraph 30 added by the WMA General Assembly, Tokyo 2004.  Available at 
http://www.wma.net/e/policy/b3.htm. 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 61 of 75 
Version Date 29 February 2016 
 
18.0 INVESTIGATOR’S SIGNATURE PAGE 
 
A Phase 2 Multicenter, investigator initiated study of Oral Ruxolitinib Phosphate 
for the Treatment of Relapsed or Refractory Diffuse Large B-cell and Peripheral T-
cell Non-Hodgkin Lymphoma 
Protocol IND number :  
112445 
Protocol Version/Date: 
Amendment 7, version date 29 February 2016 
 
 
I have read, understand, and agree to follow the attached Protocol. 
 
 
 
 
 
 
 
 
(Investigator Signature) 
 
(Date) 
 
 
 
 
 
 
(Printed Name) 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 62 of 75 
Version Date 29 February 2016 
 
19.0 APPENDICES 
 
 
 
List of Appendices 
1. RESPONSE CRITERIA 
2. LABORATORY METHODS 
3. NCI CTC VERSION 4.0 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 63 of 75 
Version Date 29 February 2016 
 
APPENDIX 1 – RESPONSE CRITERIA 
 
Adapted from Journal of Clinical Oncology, Vol 25, No 5 (February 10), 2007: pp. 579-
586 
Revised Response Criteria for Malignant Lymphoma by Bruce D. Cheson,  
 
CR 
The designation of CR requires the following  
1. Complete disappearance of all detectable clinical evidence of disease and disease-
related symptoms if present before therapy.  
2a. Typically FDG-avid lymphoma: in patients with no pretreatment PET scan or when 
the PET scan was positive before therapy, a post-treatment residual mass of any size is 
permitted as long as it is PET negative.  
2b. Variably FDG-avid lymphomas/FDG avidity unknown: in patients without a 
pretreatment PET scan, or if a pretreatment PET scan was negative, all lymph nodes and 
nodal masses must have regressed on CT to normal size (≤ 1.5 cm in their greatest 
transverse diameter for nodes > 1.5 cm before therapy). Previously involved nodes that 
were 1.1 to 1.5 cm in their long axis and more than 1.0 cm in their short axis before 
treatment must have decreased to ≤ 1.0 cm in their short axis after treatment.  
3. The spleen and/or liver, if considered enlarged before therapy on the basis of a 
physical examination or CT scan, should not be palpable on physical examination and 
should be considered normal size by imaging studies, and nodules related to lymphoma 
should disappear. However, determination of splenic involvement is not always reliable 
because a spleen considered normal in size may still contain lymphoma, whereas an 
enlarged spleen may reflect variations in anatomy, blood volume, the use of 
hematopoietic growth factors, or causes other than lymphoma.  
4. If the bone marrow was involved by lymphoma before treatment, the infiltrate must 
have cleared on repeat bone marrow biopsy. The biopsy sample on which this 
determination is made must be adequate (with a goal of > 20 mm unilateral core). If the 
sample is indeterminate by morphology, it should be negative by immunohistochemistry. 
A sample that is negative by immunohistochemistry but that demonstrates a small 
population of clonal lymphocytes by flow cytometry will be considered a CR until data 
become available demonstrating a clear difference in patient outcome.  
CRu 
The use of the above definition for CR and that below for PR eliminates the category of 
CRu.  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 64 of 75 
Version Date 29 February 2016 
 
PR 
The designation of PR requires all of the following:  
1. At least a 50% decrease in sum of the product of the diameters (SPD) of up to six 
of the largest dominant nodes or nodal masses. These nodes or masses should be 
selected according to all of the following: they should be clearly measurable in at 
least 2 perpendicular dimensions; if possible they should be from disparate regions 
of the body; and they should include mediastinal and retroperitoneal areas of 
disease whenever these sites are involved.  
2. No increase should be observed in the size of other nodes, liver, or spleen.  
3. Splenic and hepatic nodules must regress by ≥ 50% in their SPD or, for single 
nodules, in the greatest transverse diameter.  
4. With the exception of splenic and hepatic nodules, involvement of other organs is 
usually assessable and no measurable disease should be present.  
5. Bone marrow assessment is irrelevant for determination of a PR if the sample was 
positive before treatment. However, if positive, the cell type should be specified 
(eg, large-cell lymphoma or small neoplastic B cells). Patients who achieve a CR 
by the above criteria, but who have persistent morphologic bone marrow 
involvement will be considered partial responders.  
When the bone marrow was involved before therapy and a clinical CR was 
achieved, but with no bone marrow assessment after treatment, patients should be 
considered partial responders.  
6. No new sites of disease should be observed.  
7. Typically FDG-avid lymphoma: for patients with no pretreatment PET scan or if 
the PET scan was positive before therapy, the post-treatment PET should be 
positive in at least one previously involved site.  
8. Variably FDG-avid lymphomas/FDG-avidity unknown: for patients without a 
pretreatment PET scan, or if a pretreatment PET scan was negative, CT criteria 
should be used.  
Stable Disease 
Stable disease (SD) is defined as the following:  
1. A patient is considered to have SD when he or she fails to attain the criteria needed 
for a CR or PR, but does not fulfill those for progressive disease (see Relapsed 
Disease [after CR]/Progressive Disease [after PR, SD]).  
2. Typically FGD-avid lymphomas: the PET should be positive at prior sites of 
disease with no new areas of involvement on the post-treatment CT or PET.  
3. Variably FDG-avid lymphomas/FDG-avidity unknown: for patients without a 
pretreatment PET scan or if the pretreatment PET was negative, there must be no 
change in the size of the previous lesions on the post-treatment CT scan.  
Relapsed Disease (after CR)/Progressive Disease (after PR, SD) 
Lymph nodes should be considered abnormal if the long axis is more than 1.5 cm 
regardless of the short axis. If a lymph node has a long axis of 1.1 to 1.5 cm, it should 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 65 of 75 
Version Date 29 February 2016 
 
only be considered abnormal if its short axis is more than 1.0. Lymph nodes ≤ 1.0 x ≤ 1.0 
cm will not be considered as abnormal for relapse or progressive disease.  
1. Appearance of any new lesion more than 1.5 cm in any axis during or at the end of 
therapy, even if other lesions are decreasing in size. Increased FDG uptake in a 
previously unaffected site should only be considered relapsed or progressive 
disease after confirmation with other modalities. In patients with no prior history of 
pulmonary lymphoma, new lung nodules identified by CT are mostly benign. Thus, 
a therapeutic decision should not be made solely on the basis of the PET without 
histologic confirmation.  
2. At least a 50% increase from nadir in the SPD of any previously involved nodes, or 
in a single involved node, or the size of other lesions (eg, splenic or hepatic 
nodules). To be considered progressive disease, a lymph node with a diameter of 
the short axis of less than 1.0 cm must increase by ≥ 50% and to a size of 1.5 x 1.5 
cm or more than 1.5 cm in the long axis.  
3. At least a 50% increase in the longest diameter of any single previously identified 
node more than 1 cm in its short axis.  
4. Lesions should be PET positive if observed in a typical FDG-avid lymphoma or 
the lesion was PET positive before therapy unless the lesion is too small to be 
detected with current PET systems (< 1.5 cm in its long axis by CT).  
Measurable extranodal disease should be assessed in a manner similar to that for nodal 
disease. For these recommendations, the spleen is considered nodal disease. Disease that 
is only assessable (eg, pleural effusions, bone lesions) will be recorded as present or 
absent only, unless, while an abnormality is still noted by imaging studies or physical 
examination, it is found to be histologically negative. 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 66 of 75 
Version Date 29 February 2016 
 
Appendix 2 – Laboratory methods 
SCHEDULE OF LABORATORY ASSESSMENTS 
 
Pre-
treatment 
Cycle 1 
Day 1 
Cycle 1 
Day 8 
Cycle 1 
Day 15 
Cycle 1 
Day 22 
Cycle 2 
Day 1 
 
Post 
Cycle 2 
Disease 
Progress
ion 
Archived Tumor 
slides (required) 
X 
 
 
 
 
 
 
 
Fresh  or Archived 
Tumor Biopsy 
(required) 
X 
 
 
 
 
 
 
 
Fresh Tumor Biopsy 
(optional) 
 
 
 
 
 
 
X 
X 
Blood for cytokine 
profiling a 
X 
X 
X 
X 
X 
X 
 
 
Blood for C-
Reactive Protein 
(CRP) b 
X 
 
 
 
 
X 
 
X 
a: Collect blood for cytokine profiling within 7 days prior to first dose of ruxolitinib and at 3 hours 
post first dose on Cycle 1 Day 1. Weekly samples will be collected prior to the morning dose of 
ruxolitinib on Cycle 1, days 8, 15, 22, and on Cycle 2, day 1.  Analysis of C-Reactive Protein 
(CRP) will be done on samples collected for cytokine profiling at the pre-treatment and Cycle 2 
Day 1 timepoints. . 
b: C-Reactive Protein (CRP)  will be tested from cytokine blood collection at Pre-treatment and at 
Cycle 2, day 1 and no additional blood is required for these two timepoints.  An additional 
separate sample for CRP will be collected at time of relapse or progression.   
 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 67 of 75 
Version Date 29 February 2016 
 
I.  TUMOR TISSUE REQUIREMENTS 
 
A.  ARCHIVED TUMOR TISSUE 
Archived tumor tissue obtained at the time of initial diagnosis of DLBC or PTCL is 
required for all subjects for RNA sequencing and comparison of gene expression between 
initial and current tumor tissue.  A minimum of 5 unstained 10 µm slides will be 
submitted to the central lab. 
 
Complete and fax the completed Tumor Tissue Requisition and Shipment Notification 
Form on the day of shipment and include a copy of the form in each shipment. 
 
Include a copy of the site tumor pathology report in the shipment.   The report must have 
subject identifiers removed and the patient study ID and study protocol number must be 
written at the top of the report. 
 
Ship to: 
 
 
Dr. Kai Fu 
 
 
University of Nebraska Medical Center 
 
 
601 South Saddle Creek Rd. 
 
 
Omaha, NE  68105- 31356 
 
 
402-559-3135 
 
 
Phone:  402-559-7526 
 
 
Fax:  402-559-6018 
 
 
Pager:  402-888-2528 
 
 
 
 
B. PRE-TREATMENT BIOPSY 
A pre-treatment biopsy of tumor tissue collected since the most recent prior therapy is 
required for all subjects.  Either excisional tumor biopsy or two 14 gauge (or larger) cores 
will be collected and submitted to the Central lab.  The central lab will perform 
morphologic review and gene expression profiling.  No reports from the central lab will 
be provided back to the investigator and site but the tumor content and degree of necrosis 
and degeneration will be recorded in the database. If a formal pathology review is 
required for clinical use, please collect additional tissue for review by your local 
pathologist. 
 
Preparing tissue for transport to the Central Labs: 
 
1.  Collect either an excisional biopsy or two 14 gauge or larger cores of tumor tissue.  
If cores are collected, each core must be at least 2 cm in length to ensure enough tissue 
for evaluation. If long cores cannot be obtained, additional cores should be collected to 
provide an equivalent amount of tissues. Transport tissue in saline soaked non-stick 
pads to the hematopathologist immediately (within 15 minutes).   


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 68 of 75 
Version Date 29 February 2016 
 
 
2.  The tissue will be examined by a hematopathologist within 60 minutes of tissue 
collection, and each of the core biopsies or the excisional biopsy is divided into two 
halves.  Label the halves of each biopsy “A” and “B”.   Label according to the 
illustration: 
 
 
If two cores are collected, label as follows: 
 
 
 
 
If excisional tissue is collected, label as follows: 
 
“Portion A”                                  “Portion B” 
 
 
 
*If the excisional tissue is large it can be divided 
into “Biopsy 1” and “Biopsy 2” before separation 
to portion “A” and “B”. 
“Biopsy 1, portion A” 
“Biopsy 1, portion B” 
 
 
 
 
 
 
 
 
 
 
“Biopsy 2, portion A” 
“Biopsy 2, portion B” 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
3.  All portion “A” halves are to be processed individually and fixed in neutral 
buffered formalin (If two core biopsies are collected, two separate portion  A samples 
will be processed and shipped). Tissue must be processed into a paraffin block for 
submission to the Central Pathologist. Whole block(s) must be submitted, and partially 
cut blocks will not be acceptable as insufficient tissues may be left for subsequent 
studies.  Label each block as illustrated above and include the study number, subject 
number, and date of biopsy.   Ship to the Central Lab at ambient temperature.   
 
4.  All portion “B” halves are to be snap-frozen individually in separate plastic 
containers and stored at -80oC until shipment to the Central Lab.  Label each specimen 
as illustrated above and include the study number, subject number, and date of biopsy.  
Ship to the Central Lab frozen in sufficient dry ice to ensure that the tissue will remain 
frozen for over 24 hours ( See SOP for shipment).   
 
5.   Complete and fax the completed Tumor Tissue Requisition and Shipment 
Notification Form on the day of shipment and include a copy of the form in each 
shipment. 
 
6.  Include a copy of the site tumor pathology report in the shipment.  If the 
confirmation of relapse biopsy is obtained concurrent with this research biopsy, please 
provide the report by fax to Dr. Fu at 402-559-6018 when it becomes available.  The 
report must have subject identifiers removed and the patient study ID and study 
protocol number must be written at the top of the report. 
 
6.  Ship to the Central Lab on day of collection or as soon as possible. If a delayed 
shipment is necessary please contact the Sponsor for approval.   Please ensure that 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 69 of 75 
Version Date 29 February 2016 
 
shipments can be delivered within 24 hours after shipment (do not ship on Thursday 
and Fridays, or within 2 days before holidays). 
 
Ship to: 
 
 
Dr. Kai Fu 
 
 
University of Nebraska Medical Center 
 
 
601 South Saddle Creek Rd. 
 
 
Omaha, NE  68106 
 
 
402-559-3135 
 
 
Phone:  402-559-7526 
 
 
Fax:  402-559-6018 
 
 
Pager:  402-888-2528 
 
 
7. Should there not be sufficient fresh tissue the Central lab to complete the gene 
profiling requirements, then archive tissue from a previous relapse biopsy will be 
requested.  If both the fresh and relapse tissue are not available, then analysis will be 
perform using an archived block from the initial diagnostic biopsy specimen.  Submission 
of this tissue would be handled as indicated above for the Archived tissue submissions. 
 
 
 
C.  OPTIONAL ON-STUDY TUMOR BIOPSIES 
Two additional tumor biopsies will be collected for those subjects who provide consent. 
A biopsy will be collected On-therapy sometime after the completion of  2 cycles of 
therapy, and/or a biopsy will be collected at 6 weeks post-treatment in patients with 
disease progression..  Samples will be collected and shipped according to the instructions 
provided for the Pretreatment Tumor Tissue Biopsy.    
 
 
 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 70 of 75 
Version Date 29 February 2016 
 
II.   BLOOD SAMPLES  
A. CYTOKINE Plasma Sample Blood Collection and preparation (includes C-
reactive protein analysis at pretreatment and at cycle 2, day 1) 
  
1.  Collect 7cc to 10cc whole blood into EDTA tubes (Purple top).  * At Cycle 1, 
day 1 predose timepoint only: Make two to three blood smear slides and air dry, 
and save them at room temperature until shipment to the central lab. 
 
2.  Process within 2 hours of collection.  Cells are removed from plasma by 
centrifugation for 10 minutes at 1,000-2,000 rpm using a refrigerated centrifuge. 
Centrifugation for 15 minutes at 2,000 rpm depletes platelets in the plasma sample. 
The resulting supernatant is designated plasma. 
 
3.  Following centrifugation, immediately transfer the plasma apportioned into two 
clean polypropylene aliquot tubes using a pipette. The samples should be 
maintained at 2-8°C while handling. Store and at –20°C, or lower until shipment to 
the central lab. It is important to avoid freeze/thaw cycles. Samples which are 
hemolyzed, icteric, or lipemic can invalidate certain tests.  
 
4.  Transfer the cell pellet to a 50 ml Falcon tube which contains 40 ml ice cold 
ddH2O. Mix it gently by inverting tube for several times to lyse the red cells (about 
10 sec). Then divide the mixture into two 50mL Falcon tubes in equal volume, add 
25 ml 2 X PBS in each tube and mix it gently by inverting the tube several times. 
Centrifuge the tubes at 1000 rpm (250g) for 10 min, remove supernatant and re-
suspended the cell pellets in 500µL 1XPBS of each. Transfer both into a clean 
polypropylene aliquot tube, centrifuge at 2000g for 5 min. Discard the supernatant, 
and save the cell pellet in -80°C until shipment to the central lab. Label it with 
whole cell pellet. 
 
5. Send blood smear, plasma sample and whole cell pellet to the central lab according 
to the shipment instruction below.   B.  CYTOKINE Peripheral Blood 
Mononuclear Cell (PBMC) Sample Collection and preparation  
1.  Collect 10cc whole blood into EDTA tubes (purple top). Process within 2 hours 
of collection according to Ficoll-Hypaque method:  
 
2.  Place fresh heparinized blood into 15- or 50-ml conical centrifuge tubes. Using a 
sterile pipet, add an equal volume of room-temperature 1 × PBS. Mix well. 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 71 of 75 
Version Date 29 February 2016 
 
3.  Pellet the leukocyte/RBC fraction by centrifuging the cells 15 min at 200 × g, 
room temperature. The platelet cell fraction will remain in the upper suspension. 
Using a sterile pipet, remove the supernatant suspension containing this platelet cell 
fraction. The blood should immediately be gently mixed, and should be examined 
when it reaches the laboratory for small blood clots. As the clotting reaction 
releases proteins that can affect lymphocyte phenotype and function, samples 
containing clots should be discarded. 
  
4.  Using a sterile pipet, add an equal volume of room-temperature 1× PBS 
suspension (if utilizing a 15-ml conical tube) or bring the leukocyte/RBC cell 
suspension to a final volume of 40 ml with 1× PBS (if utilizing a 50-ml conical 
tube). 
 
5.  Slowly layer the Ficoll-Hypaque solution underneath the leukocyte/RBC/PBS 
mixture by placing the tip of the pipet containing the Ficoll-Hypaque at the bottom 
of the sample tube. Use 3ml Ficoll-Hypaque per 10ml blood/PBS mixture. Use a 
maximum of 10 ml Ficoll-Hypaque per 40 ml leukocyte/RBC/PBS mixture. 
 
To maintain the Ficoll-Hypaque/blood interface, it is helpful to hold the centrifuge 
tube at a 45◦ angle. Alternatively, the leukocyte/RBC/PBS mixture may be slowly 
layered over the Ficoll-Hypaque solution. See Figure below. 
 
6.  Centrifuge 20 to 30 min at 2000 rpm (900 × g), 18◦ to 20◦C, with no brake. 
After a centrifugation with Ficoll-Hypaque, platelets (specific gravity, 1.040) and 
plasma (specific gravity, 1.025 to 1.029) are located above the Ficoll-Hypaque, 
lymphocytes (specific gravity, 1.070), and some platelets are found at the plasma-


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 72 of 75 
Version Date 29 February 2016 
 
Ficoll-Hypaque interface. Granulocytes (specific gravity, 1.087 to 1.092) and RBCs 
(specific gravity, 1.093 to 1.096) form a cell pellet at the bottom of the tube (see 
Fig. below) 
 
7. Using a sterile pipet, remove the upper layer that contains the plasma and most of 
the remaining cell platelet fraction. Using another pipet, transfer the mononuclear 
lymphocyte cell layer to another centrifuge tube. This will appear as a white, cloudy 
band between the plasma and the Ficoll-Hypaque layers. Wash cells by adding 
HBSS (∼3 times the volume of the mononuclear cell layer) and centrifuging 10 min 
at 450 to 600×g, 18◦ to 20◦C. Remove supernatant, re-suspend cells in HBSS, and 
repeat the wash once to remove any remaining platelets. 
 
The washing steps described above usually remove most of the platelets from the 
mononuclear cell suspension. There are certain disease states associated with 
increased platelet concentrations (mononuclear cell to platelet cell ratio >10:1) in 
the peripheral blood, and additional steps are needed to remove the extra platelets in 
these cases. Add 3 ml FBS to a centrifuge tube for each milliliter of mononuclear 
cells. Layer the cell suspension (1-2 × 107 cells/ml) over the FBS (alternatively, 
carefully layer the FBS under the cell suspension, which will rise as FBS is added). 
Centrifuge 15 min at 150 × g, 18◦ to 20◦C. Discard the supernatant containing the 
platelets. Re-suspend cell pellet in complete RPMI-1640 and proceed as in step 8. 
8.  Re-suspend mononuclear lymphocyte cells in complete RPMI-1640. Count cells 
and determine viability by trypan blue exclusion. If desired, purity of PBMC 
population can be determined by flow cytometry. 
9. Centrifuge 5 min at 2000 × g, 18◦ to 20◦C. Discard the supernatant and save the 
PBMC in -80°C until shipment to the central lab. Label it clearly with “PBMC” and 
estimate cell number.  


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 73 of 75 
Version Date 29 February 2016 
 
10. Freeze sample in one aliquot tube at -80C until shipment to the central lab.  See 
shipping instructions. 
 
Shipment of Cytokine Plasma and PBMC samples (includes C-reactive protein at Pre-
treatment and at Cycle 2, day 1): 
1.  Samples may be batched and shipped on a monthly basis. 
2.  Package samples according to IATA regulations. 
2.   Label specimens appropriately with subject study ID, date and time of collection, and 
type of collection (plasma or PBMC). Complete and fax the completed Blood Sample 
Requisition and Shipment Notification Form on the day of shipment and include a copy 
of the form in the shipment. 
3.  Slides made from the C1, D1 predose timepoint will be transported at ambient 
temperature using overnight express service. 
4.  The plasma, pellet, PBMC tubes will be shipped frozen and on dry ice to Dr. Fu.  
Transportation will be through overnight express service in sufficient dry ice to ensure 
that the samples will remain frozen for over 24 hours. Please ensure that shipments can 
be delivered within 24 hours after shipment (do not ship on Fridays, or days before 
holidays). 
 
 
Ship to: 
 
 
Dr. Kai Fu 
 
 
University of Nebraska Medical Center 
 
 
601 South Saddle Creek Rd. 
 
 
Omaha, NE  68106 
 
 
402-559-3135 
 
 
Phone:  402-559-7526 
 
 
Fax:  402-559-6018 
 
 
Pager:  402-888-2528 
 
5.  Dr. Fu’s laboratory will be informed of the shipment and tracking number 
immediately and the status of the shipment will be tracked. A detailed log of the 
specimen will be kept. 
 
 
C.  C-REACTIVE PROTEIN Blood Collection (use these instructions when 
collecting blood only for CRP and not for cytokine profiling) at time of 
progression or relapse 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 74 of 75 
Version Date 29 February 2016 
 
1.  Collect 7cc to 10cc whole blood and centrifuge within 2 hours of collection. 
Stability: For serum and plasma: 
   Ambient: 15 days 
   Refrigerated: 2 months 
   Frozen: 3 years 
 
Plasma  
Collect 7cc to 10cc blood in a light green-top (lithium heparin) gel tube(s). Spin 
down and send 1 mL of lithium heparin plasma. Store at -80. 
Note:  Indicate plasma on request form. 
 
Serum 
Collect 7cc to 10cc blood in a gold-top serum gel tube(s) or a plain, red-top tube(s). 
Spin down and send 1 mL of serum. 
Note:  Indicate serum on request form. 
 
2. Label specimen appropriately with subject study ID, date and time of collection, 
and type of collection (plasma or serum). Complete and fax the completed Blood 
Sample Requisition and Shipment Notification Form on the day of shipment and 
include a copy of the form in the shipment. 
 
3.  Ship either ambient, refrigerated, or frozen according to the stability chart above.  
Package samples according to IATA regulations. Transportation will be through 
overnight express service to ensure that shipments can be delivered within 24 hours 
after shipment (do not ship on Fridays, or days before holidays). 
  
 
Ship to: 
  
Dr. Kai Fu 
  
University of Nebraska Medical Center 
  
601 South Saddle Creek Rd. 
  
Omaha, NE  68106 
  
402-559-3135 
  
Phone:  402-559-7526 
  
Fax:  402-559-6018 
  
Pager:  402-888-2528 
 
4.  Dr. Fu’s laboratory will be informed of the shipment and tracking number 
immediately and the status of the shipment will be tracked. A detailed log of the 
specimen will be kept. 
 
 


 
Protocol # 283-11, Amendment 7  
CONFIDENTIAL 
 
 
Page 75 of 75 
Version Date 29 February 2016 
 
 
APPENDIX 3 – GRADING OF ADVERSE EVENTS 
 
Adverse Events will be graded according to the National Cancer Institute Common 
Toxicity Criteria for Adverse Events (CTCAE), Version 4, which may be found at the 
following website: 
 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm#ctc_
40