A Phase II Randomized, Open Label Study of Ad-RTS-hIL-12 Monotherapy or Combination With Palifosfamide in Subjects With Recurrent/Metastatic Breast Cancer and Accessible Lesions
Phase: PHASE2
Conditions: Breast Cancer Nos Metastatic Recurrent
Sponsor: Alaunos Therapeutics



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Ad-RTS-IL-12 
 
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6.1.2 
Inclusion and Exclusion Criteria .................................................................................................. 39 
6.1.3 
Registration/Randomization of Subjects ...................................................................................... 39 
6.2 
STUDY DRUGS ................................................................................................................................... 39 
6.2.1 
Accountability and Dispensation .................................................................................................. 39 
6.2.2 
Handling and Storage ................................................................................................................... 40 
6.2.3 
Treatment Regimen ...................................................................................................................... 40 
6.2.4 
Preparation and Administration of Study Drug ............................................................................ 41 
6.2.5 
Retreatment Criteria, Dose Delays and Modifications ................................................................. 44 
6.2.6 
Severity Grading and Management of Injection Site Reactions ................................................... 45 
6.2.7 
Prophylactic Antipyretic and/or Analgesic Administration .......................................................... 46 
6.2.8 
Disposition of Unused Study Drug ............................................................................................... 47 
6.3 
CONCOMITANT THERAPY .................................................................................................................. 47 
6.4 
EVALUATION AND ASSESSMENT PROCEDURES .................................................................................. 47 
6.4.1 
Schedule of Assessments .............................................................................................................. 47 
6.4.2 
Safety Evaluations ........................................................................................................................ 48 
6.4.3 
Efficacy Assessments ................................................................................................................... 49 
6.4.4 
For Participating Sites:  Assessments of Transgene Function, Immunological Activities and 
Biological Effects (please refer to Appendix 6) .......................................................................... 50 
7. 
ADVERSE EVENTS ............................................................................................................................. 51 
7.1 
ADVERSE EVENT (AE) DEFINITION ................................................................................................... 51 
7.2 
EVALUATION OF ADVERSE EVENTS (AES) ........................................................................................ 52 
7.2.1 
Determination of Seriousness ....................................................................................................... 52 
7.2.2 
Determination of Severity ............................................................................................................ 54 
7.2.3 
Causality Assessments .................................................................................................................. 54 
7.3 
DOCUMENTING ADVERSE EVENTS (AES) .......................................................................................... 55 
7.4 
REPORTING SERIOUS ADVERSE EVENTS (SAES) ............................................................................... 55 
7.5 
SPONSOR AND INVESTIGATOR RESPONSIBILITY FOR REPORTING ADVERSE EVENTS (AES)............... 56 
7.6 
FOLLOW-UP INFORMATION ................................................................................................................ 56 
7.7 
PREGNANCIES .................................................................................................................................... 56 
8. 
STATISTICAL PROCEDURES .......................................................................................................... 57 
8.1 
DETERMINATION OF SAMPLE SIZE ..................................................................................................... 57 
8.2 
SUBJECT RANDOMIZATION ................................................................................................................ 57 
8.3 
POPULATIONS FOR ANALYSIS ............................................................................................................ 57 
8.4 
STUDY ENDPOINTS ............................................................................................................................ 58 
8.4.1 
Primary Efficacy Endpoint ........................................................................................................... 58 
8.4.2 
Secondary Efficacy Endpoints ...................................................................................................... 58 
8.4.3 
Other Endpoints ............................................................................................................................ 58 
8.4.4 
Safety Endpoints ........................................................................................................................... 58 
8.5 
PROCEDURES FOR HANDLING MISSING, UNUSED, AND SPURIOUS DATA ........................................... 59 
8.6 
STATISTICAL ANALYSES.................................................................................................................... 59 
8.6.1 
Subject Status ............................................................................................................................... 59 

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8.6.2 
Baseline Characteristics ................................................................................................................ 59 
8.6.3 
Safety Analyses ............................................................................................................................ 60 
8.6.4 
Efficacy Analyses ......................................................................................................................... 60 
8.7 
IMMUNOLOGIC RESPONSES................................................................................................................ 60 
8.8 
PROCEDURES FOR REPORTING DEVIATIONS TO ORIGINAL STATISTICAL ANALYSIS PLAN ................. 61 
9. 
STUDY ADMINISTRATION ............................................................................................................... 61 
9.1 
ELECTRONIC CASE REPORT FORMS AND SOURCE DOCUMENTATION ................................................ 61 
9.2 
GOOD CLINICAL PRACTICE STATEMENT ........................................................................................... 62 
9.3 
SPONSOR MONITORING ..................................................................................................................... 62 
9.4 
DURATION OF THE STUDY ................................................................................................................. 62 
9.5 
RECORDS RETENTION ........................................................................................................................ 63 
9.6 
INSTITUTIONAL REVIEW BOARD........................................................................................................ 63 
9.7 
CONFIDENTIALITY AND HIPAA ........................................................................................................ 63 
10. 
INFORMED CONSENT ....................................................................................................................... 64 
10.1 
FDA INFORMED CONSENT REQUIREMENTS ....................................................................................... 64 
10.2 
SUBJECT INFORMED CONSENT FORM ................................................................................................ 64 
11. 
PROTOCOL APPROVAL PAGE ....................................................................................................... 65 
12. 
REFERENCES ...................................................................................................................................... 66 
13. 
APPENDICES ........................................................................................................................................ 69 
13.1 
APPENDIX 1:  EASTERN COOPERATIVE ONCOLOGY GROUP (ECOG) PERFORMANCE STATUS ........... 69 
13.2 
APPENDIX 2:  CYP450 3A4 INDUCERS, INHIBITORS AND SUBSTRATES ............................................. 70 
13.3 
APPENDIX 3:  REGIMEN FOR ANTIPYRETIC AND/OR ANALGESIC PROPHYLAXIS ................................ 71 
13.4 
APPENDIX 4:  MODIFIED RECIST CRITERIA ...................................................................................... 72 
13.5 
APPENDIX 5:  MODIFICATION OF DIET IN RENAL DISEASE (MDRD) EQUATION FOR ESTIMATING 
GLOMERULAR FILTRATION RATE (EGFR) ....................................................................................................... 75 
13.6 
APPENDIX 6:  SCHEDULE OF STUDY PROCEDURES AND ASSESSMENTS:  ADDITIONAL 
IMMUNOLOGIC ASSESSMENTS ......................................................................................................................... 76 
 

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2.  ABBREVIATIONS AND DEFINITIONS OF TERMS  
Ad 
Adenovirus 
 
 INR 
 International normalized ratio 
AE 
Adverse Event 
 
INXN-1001 
Small molecule Activator Ligand 
ALC 
Absolute lymphocyte Count 
 
INXN-2001 
Ad-RTS-hIL-12  
ALP 
Alkaline phosphatase 
 
IRB 
Institutional Review Board 
ALT 
Alanine Transaminase 
 
IP 
 Intraperitoneal(ly) 
ANC 
Absolute neutrophil count 
 
IT 
Intratumoral(ly) 
AST 
Aspartate Transaminase 
 
IV 
Intravenous(ly) 
BSA 
Body Surface Area 
 
IVIG 
 Intravenous immunoglobulin 
BUN 
Blood urea nitrogen 
 
LDH 
Lactate Dehydrogenase 
CBC 
Complete Blood Count 
 
 MDRD 
 Modified Diet in Renal Disease 
CBR 
Clinical Benefit Rate 
 
MDSC 
Myeloid Derived Suppressor Cell 
GCP 
Good Clinical Practice 
 
MedDRA 
 Medical Dictionary for Regulatory Activities 
CI 
Confidence interval 
 
mRECIST 
Modified Response Evaluation Criteria in Solid 
Tumors v1.1  
CR 
Complete response 
 
 
MRI 
Magnetic Resonance Imaging 
CRF 
Case Report Form 
 
MTD 
Maximum Tolerated Dose 
CT 
Computed Tomography 
 
NCI 
National Cancer Institute 
CTCAE 
Common Terminology Criteria for 
Adverse Events 
 
NK 
Natural Killer 
CTLs 
Cytotoxic T Lymphocytes 
 
NYHA 
New York Heart Association 
CYP450 
Cytochrome P450 
 
ORR 
Objective response rate 
DCs 
Dendritic Cells 
 
Palifosfamide 
 Isophosphoramide mustard, tris-salt 
DLT 
Dose-Limiting Toxicity 
 
PBMC 
Peripheral Blood Mononuclear Cells 
ECG 
electrocardiogram 
 
PBx 
Punch Biopsy 
ECOG 
Eastern Cooperative Oncology Group 
 
PD 
Progressive Disease 
EcR 
Ecdysone Receptor 
 
PFS 
Progression-free Survival 
EDC 
Electronic data capture 
 
PI 
Principal Investigator 
eGFR 
Estimated glomerular filtration rate 
 
PK 
Pharmacokinetic(s) 
ELISA 
Enzyme-linked immunosorbent assay 
 
PR 
Partial response 
FDA 
Food & Drug Administration 
 
PTT 
Partial Thromboplastin Time 
FNA 
Fine Needle Aspirate 
 
RBC 
Red blood cell 
G-CSF 
Granulocyte Colony Stimulating 
Factor 
 
 
 
GM-CSF 
Granulocyte Macrophage Colony 
Stimulating Factor 
 
SAE 
Serious Adverse Event 
HER2 
Human epidermal growth factor 
receptor 2 
 
SD 
Stable disease 
HIPAA 
Health Insurance Portability and 
Accountability Act of 1996 
 
SRC 
Safety Review Committee 
hIL-12 
Human Interleukin 12 
 
TEAE 
 Treatment-emergent adverse event 
IEC 
Independent Ethics Committee 
 
Tregs 
Regulatory T Cell 
IFOS 
ifosfamide 
 
ULN 
Upper Limit of Normal 
IHC 
immunohistochemistry 
 
vp 
Viral particles 
IL-2 
Interleukin 2 
 
WBC 
White blood cell 

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Ad-RTS-IL-12 
 
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2. PROTOCOL SYNOPSIS 
 
Title 
A Phase II, Randomized, Open-Label Study of Ad-RTS-hIL-12 
Monotherapy or Combination with Palifosfamide in Subjects with 
Recurrent/Metastatic Breast Cancer and Accessible Lesions 
Protocol Number 
ATI001-201   
Study Sponsor 
ZIOPHARM Oncology, Inc. 
Clinical Phase 
II 
Objectives 
Primary Objectives: 
 
Assess the safety and tolerability of INXN-1001 (activator 
ligand) + INXN-2001 (Ad-RTS-hIL-12]) as monotherapy and 
in combination with palifosfamide in subjects with recurrent 
and/or metastatic adenocarcinoma of the breast with accessible 
lesions  
 
Assess the efficacy of repeated cycles of intratumoral (IT) 
injections of INXN-2001 (Ad-RTS-hIL-12) with INXN-1001 
(oral activator ligand) as monotherapy or in combination with 
palifosfamide as measured by the 16-week progression-free 
survival (PFS) rate 
Secondary Objectives: 
 
Estimate PFS by modified Response Evaluation Criteria in 
Solid Tumors (mRECIST) v1.1 
 
Assess objective response rate (ORR) by mRECIST v1.1  
 
Assess duration of response  
 
Assess clinical benefit rate  
 
Evaluate pharmacodynamic tumor markers  (eg, breast cancer-
associated biomarkers such as MUC-1)  
 
Assess the pharmacokinetics (PK) of INXN-1001  
Study Drugs 
INXN-1001 (oral activator ligand) 
INXN-2001 (Ad-RTS-hIL-12) 
Palifosfamide  
No. Centers 
Multicenter (approximately 30 centers in the US) 
Anticipated No. of 
Subjects  
Approximately 9 subjects, up to 62 subjects  
 
Part 1 Safety Run-in: approximately 9 subjects 
 
Part 2 Randomization: up to 53 subjects 
Study Design 
This is a multicenter, open-label, randomized, Phase II study to 
evaluate the safety and efficacy of INXN-1001 + INXN-2001 (to be 

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Figure 1:  Study Design Schema 
 
Treatment Arm A:  Ad-RTS-hIL-12 Monotherapy 
During Part 1, Arm A will explore the safety of Ad-RTS-hIL-12 
monotherapy at 140 mg INXN-1001 daily for 7 days (n=6).  If 1 of the 
first 6 subjects survive progression-free at week 16, then enrollment in 
Arm A will be stopped.  If at least one of the 6 subjects survives 
progression-free at week 16, then Arm A will be expanded with 7 
additional subjects to be randomly assigned to Arm A.  These first 13 
subjects (6 + 7) on Arm A will undergo tumor assessment for 
progressive disease (PD) after 16 weeks of treatment.  If ≥3 of these 13 
subjects survive progression-free at week 16, this stage will be 
expanded to include 20 additional randomly assigned subjects. If ≥9 of 
these 33 (13 + 20) subjects survive progression-free at week 16, then 
this regimen would be considered worthy of further investigation (ie, a 
confirmatory trial).   
Treatment Arm C: Combination Therapy 
Once the monotherapy (Arm A) is determined to be safe and tolerable, 
Part 1 combination therapy (Arm C) begins.   
Part 1 of Arm C will evaluate the safety and tolerability of the 
combination of Ad-RTS-hIL-12 with palifosfamide in 3 subjects with a 
1-week interval between dosing of subjects.  If combination therapy is 
determined to be tolerable in 3 subjects following one cycle of 

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treatment, then this treatment arm will be included in Part 2 of the 
study. 
During Part 2, 9 additional subjects will be randomly assigned to Arm 
C. If <6 of the first 12 (3+9) subjects survive progression-free at week 
16, no additional subjects will be enrolled.  If ≥6 of the 12 subjects 
survive progression-free at week 16, an additional 14 subjects will be 
randomly assigned. If ≥15 of the 26 (3 + 9 +14) subjects in the 
expansion cohort survive progression-free at week 16, then this regimen 
would be considered worthy of further investigation (ie, a confirmatory 
trial). 
The primary efficacy endpoint is the 16-week PFS rate, defined as the 
proportion of subjects that remain progression-free at week 16 by 
mRECIST v1.1 for Arms A and C.  Futility decisions will be made 
using results at week 16 from both primary and secondary endpoints. 
The safety of study treatments will be assessed throughout the study by 
the frequency and severity of adverse events (AEs) as determined by 
the National Cancer Institute (NCI) Common Terminology Criteria for 
Adverse Events (CTCAE) v4.03.  
An SRC meeting can be convened if deemed necessary by the sponsor 
or the investigators at any point during the study. 
Study Population 
 
Inclusion criteria: 
1. Males or females of all races ≥ 18 years of age, who have provided 
written informed consent prior to completing any study-specific 
procedure.  
2. Histologically or cytologically confirmed adenocarcinoma of the 
breast, either locally recurrent or metastatic disease with injectable 
lesions, for which no proven curative therapy exists. Locally 
recurrent disease must not be amenable to surgical resection or 
radiation with curative intent. 
3. Subject has failed or progressed on at least 1 prior systemic 
chemotherapy regimen ± biologic/experimental therapy (if first-line 
therapy, failure or progression during the first 30 days).  
4. Resolution of all treatment-related toxicities to Grade 1 severity or 
lower, except for stable sensory neuropathy ≤ Grade 2 and alopecia. 
5. A minimum of 2 lesion(s) assessed by imaging using mRECIST 
v1.1.  1 or more lesions NOT to be injected AND at least 1 
injectable lesion(s) (may use radiographically-guided injection of 
lesions if available at site) 
6. Eastern Cooperative Oncology Group (ECOG) performance status 
0, 1, 2 
7. Male and female subjects must agree to use a highly reliable 
method of birth control (expected failure rate less than 5% per year) 
from the screening visit through 28 days after the last dose of study 
drug. Women of childbearing potential (perimenopausal women 
must be amenorrheic for at least 12 months to be considered of 

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non-childbearing potential) must have a negative pregnancy test at 
screening. 
8. Adequate bone marrow reserve as indicated by: 
a) Absolute neutrophil count (ANC) > 1500/μL (without use of 
growth factors within 7 days) 
b) Absolute lymphocyte count (ALC) > 700/μL (without use of 
growth factors within 7 days)  
c) Platelet count > 100,000/mm3 (without transfusion in prior 
7 days) 
d) Hemoglobin > 9.0 g/dL (without transfusion in prior 7 days) 
9. Adequate renal function as evidenced  by estimated glomerular 
filtration rate (eGFR) using the Modification of Diet in Renal 
Disease (MDRD) equation: eGFR ≥ 60 mL/min/1.73 m2 
10. Adequate liver function as evidenced by the following: 
a) Bilirubin ≤ 1.5 times the upper limits of normal (ULN) 
b) Alanine aminotransferase (ALT), and aspartate 
aminotransferase (AST) ≤ 2.5×ULN, in the case of liver 
metastases ≤ 5×ULN 
 
Exclusion Criteria: 
1. Subjects with human epidermal growth factor receptor 2 
(HER2)/neu-positive (immunohistochemistry [IHC]) 3+ or 
fluorescence in situ hybridization-amplified) breast tumors who are 
eligible for, but who have not received HER2-targeted therapy (eg, 
trastuzumab)  
2. Concomitant anticancer therapies (eg, endocrine therapy for breast 
cancer)   
3. Prior therapies discontinuation periods: 
a) Radiation within 3 weeks of enrollment  
b) Chemotherapy within 4 weeks of enrollment 
c) Nitrosoureas within 6 weeks of enrollment 
d) Biologic therapy and/or immunomodulatory therapy (eg, 
granulocyte colony stimulating factor [GCSF]/granulocyte 
macrophage colony stimulating factor [GM-CSF], interferons 
or interleukins, growth hormone, intravenous immunoglobulin 
[IVIG], retinoic acid), checkpoint inhibitors (eg, ipilimumab, 
anti-PD-1 or anti-PDL-1 antibodies) within 6 weeks of 
enrollment 
e) No washout period is required for endocrine therapy  
4. Radiation therapy encompassing >25% of bone marrow 
5. History of bone marrow or stem cell transplantation 
6. Any congenital or acquired condition leading to inability to 

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generate an immune response, including concomitant immune 
suppressive therapy  
7. Immunosuppressive therapy: 
a) Systemic immunosuppressive drugs including 
corticosteroids (prednisone equivalent >10 mg/day, 
http://www.medcalc.com/steroid.html) within 6 weeks 
b) Immune suppression/requiring immunosuppressive drugs, 
including subjects with organ allografts 
c) Active autoimmune disease requiring the equivalent of  
>10 mg/day of prednisone 
8. Major surgery within 4 weeks of study treatment, or major surgery 
planned for duration of study participation 
9. History of prior malignancy, unless the prior malignancy was 
diagnosed and definitively treated ≥5 years previously with no 
subsequent evidence of recurrence 
NOTE: This does not apply to previous breast cancer, carcinoma in 
situ of the cervix, inactive melanoma or non-melanoma skin cancer, 
or Grade 1 papillary bladder cancer 
10. Subjects with brain or subdural metastases, unless local therapy has 
completed and corticosteroids have been discontinued for this 
indication for ≥4 weeks before starting study treatment. Any signs 
(eg, radiologic) and/or symptoms of brain metastases must be stable 
for ≥4 weeks before starting study treatment; radiographic stability 
should be determined by comparing a contrast-enhanced computed 
tomography (CT) or magnetic resonance imaging (MRI) brain scan 
performed during screening to a prior scan performed at least 4 
weeks earlier.   
11. Any medications that induce, inhibit, or are substrates of 
cytochrome P450 (CYP450) 3A4 within 7 days prior to the first 
dose of study drug 
12. Subjects with meningeal carcinomatosis 
13. Known significant hypersensitivity to study drugs or excipients 
14. History of malabsorption syndrome or other condition that would 
interfere with enteral absorption 
15. International Normalized Ratio (INR) and activated partial 
thromboplastin time [PTT] <1.5 x ULN, if not therapeutically 
anticoagulated. Subjects who are being therapeutically 
anticoagulated with an agent such as Coumadin (warfarin sodium) 
or subcutaneous heparin may be included provided there is no prior 
evidence of underlying abnormality in coagulation parameters, 
screening test results are in appropriate therapeutic range, and 
anticoagulation regimen is stable and closely monitored. 
16. New York Heart Association (NYHA) Class II or greater 
congestive heart failure OR active ventricular arrhythmia requiring 
medication 

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17. Any other unstable or clinically significant concurrent medical 
condition (eg, infection requiring systemic anti-infective agents) 
that would, in the opinion of the investigator, jeopardize the safety 
of a subject and/or their compliance with the protocol  
18. Localized infection at site of injectable lesion(s) requiring anti-
infective therapy within 2 weeks of the first dose of study drug. 
NOTE:  Appropriate confirmatory testing (eg, punch biopsy [PBx] 
with bacterial counts) must be performed to rule out the presence of 
infection if ambiguous, or clinical signs of infection are evident 
Experimental 
Therapy 
INXN-1001 will be supplied by the Sponsor as a capsule for oral 
administration.  INXN-2001 will be supplied by the Sponsor as a sterile 
suspension for injection.  Palifosfamide will be supplied by the Sponsor 
as a powder in single-use glass vials. 
 
Dose & Schedule (21-day cycle):  
 
INXN-1001:  Subjects will be directed to take the INXN-1001 oral 
dose in a fed state (within approximately 30 minutes following a 
normal meal), once daily at the same time each day (±1 hour), 
beginning on Day 1 of each cycle.  Each subject will receive INXN-
1001 (140 mg daily for 7 days).  
 
INXN-2001:  INXN-2001 
 
 IT 
injection administered 3 hours (± 30 minutes) after INXN-1001 
dosing on Day 1 of each cycle.  If >1 injectable lesion is present, 
INXN-2001 will be injected into a different lesion at each cycle, 
and if the number of lesions is limited, the injections will be 
administered in sequential rotation or at investigator’s discretion. If 
only a single lesion is present, then repeat administrations into the 
same lesion are permitted, and radiologically-guided techniques 
may be used as available. 
 
Palifosfamide:  Palifosfamide (120 mg/m2/day) will be 
administered by intravenous (IV) infusion over approximately 
30 minutes on Days 1-3 of each cycle.   
Duration of 
Treatment 
In the absence of meeting treatment withdrawal criteria, subjects should 
receive 6 cycles of study treatment. 
Duration of Study 
The duration of this study from the time of initiating subject enrollment 
until the completion of survival follow-up is anticipated to be 
approximately 34 months. 
Safety Evaluations 
 
Safety parameters will include serious adverse events (SAEs), AEs, 
physical examinations, electrocardiograms (ECGs), vital signs, clinical 
laboratory evaluations, medical history, and prior/concomitant 
medications. A safety review for each arm of the study will occur 
following 1 cycle of therapy during Part 1. 

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Efficacy Evaluations 
The primary efficacy endpoint is the 16-week PFS rate defined as the 
proportion of subjects that remain progression-free at week 16 by 
mRECIST v1.1.  
Pharmacodynamic 
Evaluations 
Biological markers of response will be assessed and will include 
examinations of cytokine and breast cancer-associated biomarker (eg, 
MUC-1) levels.  For certain participating sites, additional 
immunological analyses will be performed.  Please refer to Appendix 6.  
Pharmacokinetic 
Evaluations 
INXN-1001 PK will be assessed for subjects in in Part 1 Cycle 1 only. 
Statistical 
Considerations / 
Analyses 
This study is designed to evaluate the safety and efficacy of 
Ad-RTS-hIL-12 monotherapy or in combination with palifosfamide as 
determined by the 16-week PFS rate, defined as the proportion of 
subjects that survive progression-free at week 16.   
Statistical analysis will be performed separately for each study arm.  
Demographics and baseline characteristics will be summarized by 
treatment regimen. 
Primary Endpoints: 
 
Safety and tolerability of therapy 
 
16-week PFS rate  
Secondary Endpoints:  
 
Estimated PFS, duration of response, ORR, CBR  
Sample Size: 
The study will have 2 study arms and include a safety run-in as Part 1. 
Part 2 will have 2 study arms and utilize an adaptive Simon 2-stage 
design. Progressive disease will be assessed by mRECIST v1.1 at week 
12, week 16, and at the Follow-up Tumor Assessment (week 24). 
 
Treatment Arm A:  Ad-RTS-hIL-12 Monotherapy 
Part 1 will explore the safety Ad-RTS-hIL-12 monotherapy in 
6 subjects, after 1 Cycle of therapy. During Part 2 for efficacy 
assessments, assume a targeted proportion of subjects who survive 
progression-free at week 16 of 35% with a proportion of no interest of 
15%.    
a) Stage 1: if ≥1 subject of the first 6 subjects survives 
progression-free at week 16, add 7 subjects (n=13) to complete 
Stage 1 
b) Stage 2: if ≥3 of 13 subjects survive progression-free at week 
16 in Stage 1, add 20 subjects (n=33) to complete Stage 2 
c) Possible Confirmatory Trial: if ≥9 of the total of 33 subjects 
survive progression-free at week 16, consider confirmatory trial 
 

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Ad-RTS-IL-12 
 
Amendment 2 17 June 2013 
                             
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Treatment Arm C:  Combination Therapy 
Part 1 will explore the safety of combination therapy in 3 subjects after 
1 cycle of therapy. 
During Part 2 for efficacy assessments, assume a targeted proportion of 
subjects who survive progression-free at week 16 of 65% with a 
proportion of no interest of 40%.  
a) Stage 1: add 9 subjects (n=12) to complete Stage 1 
b) Stage 2: if ≥6 of 12 subjects survive progression-free at week 
16 in Stage 1, add 14 subjects (n=26) to complete Stage 2 
c) Possible Confirmatory Trial: if ≥15 of the total of 26 subjects 
survive progression-free at week 16, consider confirmatory trial 
The tumor responses will be assessed by mRECIST v1.1.   

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Ad-RTS-hIL-12 
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12. Urinalysis panel (dipstick) includes: appearance, pH, specific gravity, glucose, protein/albumin, blood, ketones, bilirubin, nitrates, and 
leukocyte esterase.  In addition, a microscopic exam for casts, crystals, and cells may be done if clinically indicated. 
13. Standard, single 12-lead ECG at screening, and prior to dosing of INXN-1001 and/or INXN-2001 injection and/or palifosfamide infusion 
on Day 1 of each cycle, and at the Post-Treatment Safety Assessment visit.  
14. Centralized registration of eligible subjects will be completed according to a process defined by the Sponsor. During Part 1 of the study, 
subjects will be registered by the Medical Monitor to one of the treatment arms; during Part 2, subjects will be randomly assigned to a 
treatment arm. 
15. Appropriate cancer staging procedures should be performed during screening.  For the purpose of this clinical trial, the following imaging 
is expected at screening: 
a. CT of the chest, and CT (or MRI) of the abdomen  
b. MRI (or CT) of the brain, if brain metastasis are known or suspected  
c. CT or MRI of other anatomical regions as clinically indicated 
All imaging should be of diagnostic quality and include IV contrast. PET imaging is an acceptable alternative modality provided the CT 
component is of diagnostic quality as per RECIST 1.1 guidelines.  
For subjects with measurable lesions, target lesions should be selected and measured as per mRECIST v1.1 guidelines. (Appendix 4)  
Lesions that will be/are injected with INXN-2001 and/or biopsied should not be selected as target lesions, but should be assessed 
qualitatively as non-target lesions.   
Disease sites are to be imaged throughout the study using the same method(s) used at screening.  Chest and abdomen imaging are required 
for all follow-up imaging time points; images of the brain and other anatomical regions should be acquired on follow-up if positive at 
screening and as clinically indicated.   
Tumor response assessments will occur at 12 weeks and 16 weeks (C5D1 and C6D7), and the Follow-up Tumor Assessment visit (24 
weeks) for all subjects, including those who may have experienced a dose delay. In the setting of this immunotherapy, a progression 
observed at week 12 requires confirmation at week 16.   Additional tumor response assessments may occur at the discretion of the 
investigator. 
16. A blood sample(s) for cytokine profiling, breast cancer-associated biomarker levels (eg, MUC-1), and also INXN-1001 levels. Please refer 
to the Laboratory Manual for details regarding sample processing and shipment.   
Screening (post-registration) 
Cycle 1 - Days 2, 3, 7, and 15 
Cycle 3 - Days 2, 3, 7, and 15 
Cycle 5 - Day 1 (to coincide with the tumor assessment) 
Cycle 6 - Days 2, 3, 7, and 15 
Post-treatment Safety Assessment 

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22. Post-Treatment Safety Assessment visit will be performed 28 ± 3 days after the last dose of study drug or prior to receiving another 
anticancer therapy. 
23. A Follow-Up Tumor Assessment visit will be performed 35 ± 7 days after the Post-Treatment Safety Assessment visit.  This assessment is 
required for all subjects, including those with prior objective evidence of disease progression to ensure that more slowly declining tumor 
burden in response to therapy is not missed.   
NOTE: Subjects without objective evidence of disease progression should continue to have tumor assessments performed at 8 to 10-week 
intervals until disease progression has been confirmed or an alternate anticancer therapy has been initiated, whichever occurs first. 
24. Interim cancer history information will include documentation of any new concomitant medications and any anticancer treatments 
received since the Post-Treatment Safety Assessment visit or the previous tumor assessment.

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3. INTRODUCTION 
3.1 
Disease Background (Recurrent/Metastatic Breast Cancer) 
It is estimated that there are nearly 3 million women living in the United States with a history 
of invasive breast cancer, and an additional 226,870 women will be diagnosed in 2012.1  
Approximately 50% of women diagnosed with primary breast cancer will eventually relapse 
and develop metastatic or advanced disease. In addition, around 10% of patients present with 
metastatic disease at first diagnosis.  The 5-year relative survival rate for women diagnosed 
with localized breast cancer is 98.6%; survival declines to 83.8% for regional stage and to 
23.3% for distant stage. In addition to stage, factors that influence survival include tumor 
grade, hormone receptor status, and human epidermal growth factor receptor 2 (HER2) 
status.   
Locoregional recurrence in breast cancer is an indicator of an aggressive tumor, and early 
recurrence carries a poor prognosis. Approximately 11 and 20 percent of patients treated with 
adjuvant therapies develop locoregional recurrence within 5 and 10 years, respectively.2 If 
disease is localized, surgical excision can be attempted.  Breast cancer recurrences after 
mastectomy pose a therapeutic challenge with few surgical options. Many patients have 
systemic disease either at the time of their cutaneous or other recurrence or soon after, some 
may manifest disease only at the dermal site of disease, and a few are cured with aggressive 
treatment. These lesions often are widespread throughout the chest wall or involve heavily 
irradiated tissue.  
Recent advancements in targeted therapy and improvements in treatment have heralded a 
significant improvement in survival, but metastatic breast cancer remains essentially 
incurable. Advanced metastatic breast cancer may be treated with systemic therapy 
(chemotherapy, biological therapy, targeted therapy, hormonal therapy), local therapy 
(surgery, radiation therapy), or a combination of these treatments.3  Guidelines from the 
National Comprehensive Cancer Network for treatment of women with a locoregional breast 
cancer recurrence suggest consideration of systemic therapy after locoregional management, 
but do not specify the type of therapy or the duration.4  In case instant response is required, 
such as rapidly progressive, threatening disease or massive symptoms, combination cytostatic 
therapy is usually administered. Monotherapy is a choice for patients in whom a long-term 
stabilization of metastatic disease is the objective.  
Almost all patients who have received first-line chemotherapy for their metastatic 
progression will relapse or progress and require subsequent treatment. For these patients 
requiring second- and subsequent-line therapy, the goals of treatment are to maintain a good 
quality of life and to prolong survival.5 Combination therapy is a mainstay of anticancer 
treatment, with optimal combinations producing synergistic antitumor responses, achieved by 
combining agents with non-overlapping mechanisms of action and safety profiles.   
The addition of systemic chemotherapy (palifosfamide) to immunotherapy (Ad-RTS-hIL-12) 
in patients who are treated for a recurrence or metastasis of breast cancer may decrease the 
risk of a subsequent local recurrence or distant metastasis.  This combination of therapeutic 

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Interleukin (IL)-12 is a potent immunostimulatory cytokine which activates and recruits 
dendritic cells (DC) that facilitate the cross-priming of tumor antigen-specific T cells.  IL-12 
functions as a key mediator for the generation of Th1 CD4+ effector T cells, activation of 
NK and CD8+ T cell cytotoxic activities, augmentation of antigen-specific antitumor 
responses, and the production of IFN- and TNF-.11-14  IL-12 also stimulates neutrophil and 
macrophage production of superoxides and nitric oxide, and induces the production of 
antiangiogenic factors by tumor cells.  IL-12 has been shown to have antitumor activity in 
several animal models. 
Clinical trials have been performed to assess the safety and efficacy of administering 
recombinant IL-12 protein to subjects with cancer, including, but not limited to, melanoma, 
renal cell carcinoma, colorectal, cervical, ovarian, and lung metastases.  IL-12 protein was 
delivered via intravenous (IV), intraperitoneal (IP), or subcutaneous administration. 15-24 
Systemic administration of IL-12 resulted in induction of systemic immune responses in 
some subjects, but there was limited clinical improvement and severe toxicity.  In a Phase II 
trial evaluating repeated IV administrations of recombinant IL-12 in subjects with renal cell 
carcinoma, 12 of 17 subjects were hospitalized and 2 died due to hypovolemic shock.  The 
study was halted, as most subjects experienced serious adverse events (SAEs) during the first 
cycle of treatment, and there was a high frequency of Grade 3 and 4 AEs, with 65% of 
subjects showing leukopenia and 47% showing hyperbilirubinemia and elevated aspartate 
transaminase (AST).24 Based on reports to date, strategies for the local delivery of IL-12 
through gene therapies may represent a safer and acceptable treatment approach in cancer 
patients.  
It is therefore important to achieve the immunological benefits that IL-12 provides while 
avoiding the toxicity elicited by systemic delivery. IT delivery of Ad-RTS-hIL-12 
accomplishes precisely this objective by allowing adjustment of IL-12 gene transcription by 
varying the dose of INXN-1001. The vector is localized in the tumor and the gene is 
produced locally in response to predetermined doses of the oral ligand. In this scenario the 
dose can be lowered if any toxicities are observed. 
3.3.2 Palifosfamide 
Palifosfamide is a potent, bi-functional, DNA alkylating agent that has activity in multiple 
tumors by evading typical resistance pathways.  Palifosfamide is in the same class as 
bendamustine, cyclophosphamide, and ifosfamide.  Palifosfamide is the functional active 
metabolite of ifosfamide (IFOS); however, palifosfamide has not been shown to cause 
toxicities observed with IFOS metabolites acrolein or chloracetaldehyde, such as 
hemorrhagic cystitis or neuropathy.  The initial clinical development of palifosfamide 
focused on assessing the safety and tolerability of palifosfamide when administered as a 
single agent to subjects with advanced solid tumors.  This approach was followed by Phase I 
through Phase III studies of palifosfamide in combination with doxorubicin as a potential 
treatment for advanced soft tissue sarcomas.  An additional combination chemotherapy 
regimen of palifosfamide with etoposide + carboplatin is also being evaluated as a potential 
therapy for subjects with small cell lung cancer.   

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3.4.2 Adenovirus Safety 
Adenoviral vectors have been used extensively to deliver a variety of gene products to human 
subjects, including cancer patients.  Although adenoviral vectors are immunogenic, and 
virtually all recipients have pre-existing humoral immunity to adenoviruses, they are 
generally considered to be a safe, well-tolerated method of gene delivery that results in 
minimal side effects in subjects.   
In a Phase I/II clinical trial in prostate cancer using direct intraprostatic injection of a 
replication-defective adenovirus vector encoding bacterial nitroreductase (dose levels 5 x 
1010-1 x 1012 virus particles), the vector was well tolerated, with minimal side effects, and 
had a short half-life in the circulation.26 Numerous studies have utilized adenoviral vectors to 
deliver the p53 gene via the IT route.  Oral leukoplakia subjects who were given multiple 
intraepithelial injections of recombinant adenovirus (rAd)-p53 (1 x 108 virus particles/cm2) 
did not demonstrate signs of dose-limiting toxicity (DLT), and administration of the (rAd)-
p53 was well tolerated.27  No DLT was observed in chemoradiation-resistant advanced 
esophageal carcinoma subjects receiving IT injections of adenovirus containing p53 (10 x 
1011 particles to 25 x 1011 particles).28 Adverse events attributed to Ad.5CMV-p53 treatment 
were generally mild to moderate, with the most common AEs being Grade 1 or 2 fever (100 
% of subjects) and local pain (30% of subjects.)  Three subjects displayed hyperglycemia that 
was attributed to nutrition, 2 subjects showed hypocalcemia, and 1 subject each experienced 
partial thromboplastin time (PTT) elongation or an increase in serum amylase or creatinine.  
No other signiﬁcant laboratory abnormalities were detected on follow-up evaluations.28   
An adenoviral vector encoding hIL-12 has been studied using IT injection in subjects with 
advanced digestive malignancies, at doses up to 3 x 1012 vp, and was well tolerated.  
Common AEs were similar to symptoms observed with gene delivery by other adenoviral 
vectors, including transient, mild to moderate fever, malaise, sweating, and lymphopenia.29   
3.4.3 Safety of Intratumoral Injection of IL-12 genes  
In comparison with administration of recombinant IL-12 protein, injection of plasmids or 
adenovirus containing hIL-12 genes to cancer subjects has proven to limit or abrogate the 
toxic effects of hIL-12, thus providing an effective way to provide this potent 
immunomodulatory cytokine.  In Phase I and II clinical trials where IL-12 was delivered 
locally, increased systemic IL-12 serum levels post-baseline were not observed.30-32 
Numerous studies have shown gene delivery of IL-12 to be well tolerated.  In a Phase I 
dose-escalation trial using electroporation to administer plasmid DNA-encoding hIL-12 into 
metastatic melanoma, minimal systemic toxicity and no IL-12-related AEs were observed in 
subjects treated at several dose levels.  Similarly, IT injection of a plasmid DNA-encoding 
human IL-12 (2 to 20 mg of total DNA) in subjects with melanoma was also well tolerated.34 
Limited elevations in serum cytokines were observed after treatment.  Intra-peritoneal (IP) 
injection of hIL-12 plasmid DNA formulated in polyethyleneglycol-polyethyleneimine-
cholesterol given to women with chemotherapy-resistant recurrent ovarian cancer also was 
found to be generally safe and well tolerated. Low-grade fever and abdominal pain were the 
most common side effects.38 Plasmid DNA was not detected in the subjects’ serum samples, 
and treatment-related increases in IFN-γ levels were observed only in pleural fluid but not in 

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During the conduct of this study, in addition to monitoring of safety and therapeutic efficacy, 
peripheral blood samples will be studied for indications of immunological and biological 
effects including analyses of breast cancer-associated cytokines/biomarkers. The combined 
clinical and laboratory data will be studied to assess for activity, and will be used in decision 
making for expansion of treatment arms.  
The population for this study was selected as those subjects with recurrent or metastatic 
breast cancer (which is rarely curable with standard therapy) and accessible lesions, who are 
therefore considered to be appropriate candidates for clinical trials exploring new forms of 
treatment. Because breast cancers may be responsive to immunotherapeutic approaches (see 
Section 4.1 Disease Background), this subject population may potentially benefit from 
investigational therapy with Ad-RTS-hIL-12 alone or in combination with palifosfamide.  
4. STUDY OBJECTIVES AND DESIGN 
4.1 
Objectives 
The primary objectives are to: 
 Assess the safety and tolerability of INXN-1001 + INXN-2001 (Ad-RTS-hIL-12) as 
monotherapy and in combination with palifosfamide in subjects with recurrent and/or 
metastatic adenocarcinoma of the breast and accessible lesions (ie, in the opinion of 
the investigator is/are palpable and/or injectable), which are not amenable to surgical 
resection or radiation with curative intent 
 Assess the efficacy of repeated cycles of IT injections of INXN-2001 (Ad-RTS-hIL-
12) with INXN-1001 (oral activator ligand) as monotherapy or in combination with 
palifosfamide as measured by the 16-week progression-free survival (PFS) rate, 
defined as the proportion of subjects who survive progression-free at week 16 in the 
study population 
The secondary objectives are to: 
 Estimate PFS by modified Response Evaluation Criteria in Solid Tumors (mRECIST) 
v1.1  
 Assess ORR by mRECIST v1.1 
 Assess duration of response 
 Assess clinical benefit rate (CBR = proportion of subjects with complete response 
[CR], partial response [PR], or stable disease [SD]) by mRECIST v1.1   
 Evaluate pharmacodynamic tumor markers  (eg, breast cancer-associated biomarkers 
such as MUC-1)  
 Assess the PK of INXN-1001 in subjects with recurrent and/or metastatic 
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4.1.1 Study Design and Treatment Arm Expansion Procedure 
4.1.1.1 Overall Study Design 
This is a randomized, open-label, Phase II study of Ad-RTS-hIL-12 monotherapy or Ad-
RTS-hIL-12 in combination with palifosfamide in subjects with recurrent/metastatic breast 
cancer with accessible lesions.   
Two treatment arms will be assessed for safety, followed by random assignment to Ad-RTS-
hIL-12 monotherapy or combination therapy.  Each subject will be treated for up to 
6 treatment cycles, with each cycle being 21 days in duration.   
Safety and tolerability will be assessed by the incidence and severity of AEs as determined 
by National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events 
(CTCAE) v4.03.  A SRC comprised of the Medical Monitor, enrolling Principal Investigators 
(PIs), and Sponsor representatives, will be convened to review safety information and to 
decide upon further subject enrollment.  
The antitumor activity of study treatment will be assessed according to mRECIST v1.1 
guidelines.31 (Appendix 4) 
4.1.2 Treatment Parameters and Duration 
Subjects will receive IT injections of INXN-2001 
 
 
 
on Day 1 of each cycle, will also receive oral doses of INXN-1001 (140 mg daily) for 7 days.  
Subjects enrolled in Arm C combination therapy will also receive palifosfamide (120 
mg/m2/day) by IV infusion over approximately 30 minutes on Days 1, 2, 3 of each cycle.   
All subjects may receive up to 6 cycles of study treatment. Subjects receiving 
Ad-RTS-hIL-12 with disease progression (per mRECIST v1.1 criteria) may still complete the 
6 treatment cycles, because tumor nodules may enlarge due to the anticipated induction of an 
inflammatory response, unless the progression is clinically significant in the opinion of the 
investigator (see Appendix 4).  Furthermore, in studies with a diversity of immunotherapies 
in different cancer types, objective responses have been shown to occur after an increase in 
tumor burden characterized as progressive disease (PD) by World Health Organization or 
RECIST criteria. 
4.1.3 Safety Review Committee (SRC) 
An SRC comprised of the Medical Monitor, enrolling PIs, and Sponsor representatives will 
hold periodic teleconferences to evaluate the safety and treatment status of all subjects 
available during the Safety Run-in (Part 1) at several stages: 
 after 6 subjects Arm A have completed the first cycle, 
 after 3 subjects in Arm C have completed the first cycle, 
 at any other time as needed following random assignment in Part 2.   

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The safety run-in of Arm C (n=3) will occur with a 1-week interval between dosing of 
subjects and an SRC will convene after all subjects have received 1 cycle of therapy.  The 
SRC has the authority to recommend dose or regimen modifications for safety concerns. 
A written summary documenting the results and recommendations of each review will be 
provided to the investigator(s) and maintained on file with the Sponsor.  Additional sub-
investigators and personnel may participate in reviews, as appropriate.   
Following a treatment arm review, the SRC may recommend proceeding with enrolling 
additional subjects in the current treatment arm or not enrolling any additional subjects.   
While the SRC is expected to reach a consensus opinion regarding any premature 
discontinuation or significant modification of the study, the Sponsor may independently stop 
the study at any time. 
4.1.4 Enrollment Procedure 
During Part 1, 6 eligible subjects will enroll into Arm A, followed by 3 subjects in Arm C. 
During Part 2, eligible subjects will be randomly assigned by the Sponsor or its 
representative:   
 Subjects will be adaptively randomized in a 1:1 ratio to receive Ad-RTS-hIL-12 
monotherapy (Arm A) or combination therapy (Arm C) according to the current 
status of the treatment arms and whether or not a subject has consented to the 
“Additional Immunologic Assessments” until the desired number of subjects is fully 
enrolled in each study arm.  
4.1.5 Treatment Arm Expansion Procedure 
Should a subject discontinue study treatment before receiving 6 cycles for reasons other than 
progression, another subject may be added to the treatment arm to allow for full analysis.  
Response evaluation and criteria for futility are described in Section 9 Statistical Methods.   
Subject enrollment and expansion of treatment Arms A and C will proceed according to a 
standard Simon 2-stage design (Table 1).  An alternate dose level of palifosfamide and/or 
INXN-1001 may be explored after review of all available safety and activity data, and will be 
communicated by an administrative letter and enacted upon issuance.   

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Table 1 Study Design (see Protocol Synopsis)  
Part 
Treatment 
Arm 
Intervention (21-day cycle) 
1 
Safety Run-in 
A 
Ad-RTS-hIL-12 monotherapy (n=6)  
[INXN-1001 (140 mg daily)+ INXN-2001 
 
 
 
C 
Combination therapy; n=3  
[INXN-1001 (140 mg daily) + INXN-2001 
 
 
  
+ palifosfamide (120 mg/m2)]
2 
Randomization 
A 
Ad-RTS-hIL-12 monotherapy   
[INXN-1001 (140 mg daily) + INXN-2001 
 
 
 
C 
Combination therapy 
[INXN-1001 (140 mg daily) + INXN-2001
 
 
  
+ palifosfamide (120 mg/m2)]
5. SUBJECT SELECTION 
The target population for this study is adult subjects with recurrent and/or metastatic 
adenocarcinoma of the breast with accessible tumors (eg, in the opinion of the investigator 
is/are palpable and/or injectable) not amenable to surgical resection or radiation with curative 
intent. 
5.1 
Inclusion Criteria 
To be enrolled in the trial, each subject must satisfy all of the following inclusion criteria: 
1. Males or females of all races ≥ 18 years of age, who have provided written informed 
consent prior to completing any study-specific procedure.  
2. Histologically or cytologically confirmed adenocarcinoma of the breast, either locally 
recurrent or metastatic disease with injectable lesions, for which no proven curative 
therapy exists. Locally recurrent disease must not be amenable to surgical resection or 
radiation with curative intent. 
3. Subject has failed or progressed on at least 1 prior systemic chemotherapy regimen ± 
biologic/experimental therapy (if first-line therapy, failure or progression during or 
within the first 30 days).  
4. Resolution of all chemotherapy or radiation-related toxicities to Grade 1 severity or 
lower, except for stable sensory neuropathy ≤ Grade 2 and alopecia.  
5. A minimum of 2 lesion(s) assessed by imaging using mRECIST v1.1. 1 or more lesions 
NOT to be injected AND at least 1 injectable lesion(s) (eg, may use radiographically-
guided injection of lesions if available at site) 
6. Eastern Cooperative Oncology Group (ECOG) performance status 0, 1, 2 
7. Male and female subjects must agree to use a highly reliable method of birth control 
(expected failure rate less than 5% per year) from the screening visit through 28 days 
after the last dose of study drug. Women of childbearing potential (perimenopausal 

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women must be amenorrheic for at least 12 months to be considered of non-childbearing 
potential) must have a negative pregnancy test at screening. 
8. Adequate bone marrow reserve as indicated by: 
a) Absolute neutrophil count (ANC) > 1500/μL (without use of growth factors 
within 7 days) 
b) Absolute lymphocyte count (ALC) > 700/μL (without use of growth factors 
within 7 days)  
c) Platelet count > 100,000/mm3 (without transfusion in prior 7 days) 
d) Hemoglobin > 9.0 g/dL (without transfusion in prior 7 days) 
9. Adequate renal function as evidenced by eGFR using the Modification of Diet in Renal 
Disease (MDRD) equation: eGFR ≥ 60 mL/min/1.73 m2 
10. Adequate liver function as evidenced by the following: 
a) Bilirubin ≤ 1.5 times the upper limits of normal (ULN)  
b) ALT and AST ≤ 2.5×ULN, in the case of liver metastases ≤ 5×ULN 
5.2 
Exclusion Criteria 
Subjects will be excluded from enrolling in the trial if they meet any of the following 
exclusion criteria: 
1. Subjects with HER2/neu-positive immunohistochemistry 3+ or fluorescence in situ 
hybridization-amplified breast tumors who are eligible for, but who have not received 
HER2-targeted therapy (eg, trastuzumab)  
2. Concomitant anticancer therapies (eg, endocrine therapy for breast cancer)   
3. Prior therapies discontinuation periods: 
a) Radiation within 3 weeks of enrollment  
b) Chemotherapy within 4 weeks of enrollment 
c) Nitrosoureas within 6 weeks of enrollment 
d) Biologic therapy and/or immunomodulatory therapy (eg, granulocyte colony 
stimulating factor [G-CSF]/granulocyte macrophage colony stimulating factor 
[GM-CSF], interferons or interleukins, growth hormone, intravenous 
immunoglobulin [IVIG], retinoic acid), check point inhibitors (eg, ipilimumab, 
anti-PD-1 or anti-PDL-1 antibodies) within 6 weeks of enrollment 
e) No washout period is required for endocrine therapy  
4. Radiation therapy encompassing >25% of bone marrow 
5. History of bone marrow or stem cell transplantation 
6. Any congenital or acquired condition leading to an inability to generate an immune 
response, including concomitant immunosuppressive therapy  
7. Immunosuppressive therapy: 

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a) Systemic immunosuppressive drugs including corticosteroids (prednisone 
equivalent >10 mg/day, http://www.medcalc.com/steroid.html) within 6 weeks 
b) Immune suppression/requiring immunosuppressive drugs, including subjects with 
organ allografts  
c) Active autoimmune disease requiring the equivalent of  >10 mg/day of prednisone 
8. Major surgery within 4 weeks of study treatment, or major surgery planned for duration 
of study participation 
9. History of prior malignancy, unless the prior malignancy was diagnosed and definitively 
treated ≥5 years previously with no subsequent evidence of recurrence 
NOTE: This does not apply to previous breast cancer, carcinoma in situ of the cervix, 
inactive melanoma or non-melanoma skin cancer, or Grade 1 papillary bladder cancer 
10. Subjects with brain or subdural metastases are not eligible, unless local therapy 
completed and corticosteroids discontinued for this indication for ≥4 weeks before 
starting study treatment. Any signs (eg, radiologic) and/or symptoms of brain metastases 
must be stable for ≥4 weeks before starting study treatment; radiographic stability should 
be determined by comparing a contrast-enhanced computed tomography (CT) or 
magnetic resonance imaging (MRI) brain scan performed during screening to a prior scan 
performed at least 4 weeks earlier.   
NOTE: Screening for brain lesions by CT or MRI is not required for all potential 
subjects; however, if there are any neurological signs or symptoms consistent with brain 
metastases, then a brain CT or MRI should be performed as clinically indicated. 
11. Any medications that induce, inhibit or are substrates of cytochrome P450 (CYP450) 
3A4 within 7 days prior to the first dose of study drug 
12. Subjects with meningeal carcinomatosis 
13. Known significant hypersensitivity to study drugs or excipients 
14. History of malabsorption syndrome or other condition that would interfere with enteral 
absorption 
15. International Normalized Ratio (INR) and activated PTT <1.5 x ULN, if not 
therapeutically anticoagulated. Subjects who are being therapeutically anticoagulated 
with an agent such as Coumadin (warfarin sodium) or subcutaneous heparin may be 
included provided there is no prior evidence of underlying abnormality in coagulation 
parameters, screening test results are in appropriate therapeutic range, and 
anticoagulation regimen is stable and closely monitored 
16. New York Heart Association (NYHA) Class II or greater congestive heart failure OR 
active ventricular arrhythmia requiring medication 
17. Any other unstable or clinically significant concurrent medical condition (eg, infection 
requiring systemic anti-infective agents) that would, in the opinion of the investigator, 
jeopardize the safety of a subject and/or their compliance with the protocol 
18. Localized infection at site of injectable lesion(s) requiring anti-infective therapy within 
2 weeks of the first dose of study drug  

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NOTE:  Appropriate testing (eg, punch biopsy [PBx] with bacterial counts) must be 
performed to rule out infection in cases where the presence of infection is ambiguous or 
clinical signs of infection are evident. 
5.3 
Withdrawal of Subjects from Study Treatment and/or Study 
The investigator and/or the subject have the right to terminate the subject’s participation in 
the study at any time. Subjects who discontinue study drug should complete the 
Post-Treatment Safety Assessment visit.   
A subject may withdraw (or be withdrawn) from the study treatment prematurely for any of 
the following reasons: 
 PI determines further participation is not in subject’s best interest. 
 Clinically significant disease progression 
NOTE: In the absence of rapid clinical deterioration, disease progression should be 
confirmed by a repeat, consecutive assessment no less than 4 weeks from the date 
first documented to ensure that more slowly declining total tumor burden in response 
to therapy is not missed. 
 
A subject MUST be withdrawn in the event of any of the following: 
 Withdrawal of informed consent.   
Note: Any subject who wishes to withdraw from the study treatment may do so but 
will be counseled that follow-up for the effects of immunotherapy is strongly 
recommended. 
 Any treatment-related AE meeting withdrawal criteria. 
 Substantial noncompliance with the requirements of the study. 
 Subjects with a confirmed positive pregnancy test. 
 Any intercurrent illness that would, in the judgement of the investigator, affect 
assessments of clinical status to a significant degree and require discontinuation of 
protocol therapy. 
 
Every effort should be made to follow subjects who withdraw from study treatment with 
ongoing treatment-related AEs in order to determine the outcome of the event.  
5.4 
Replacement of Subjects 
Should a subject discontinue study treatment before receiving 6 cycles for reasons other than 
progression, another subject may be added to that study arm for full analysis. 
5.5 
Premature Termination of Study/Closure of Center 
The sponsor has the right to close the study at any time, although this should occur only after 
mutual consultation between the sponsor and the investigators. The institutional review board 
(IRB)/independent ethics committee (IEC) must be informed. Should the study/center be 

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closed prematurely, all study materials (completed, partially completed, and blank case report 
forms, study medication, etc.) must be stored or disposed of according to the sponsor’s 
instructions. Events that may trigger premature termination of the study or closure of a center 
include, but are not limited to, a new toxicity finding, results of any interim analysis, 
noncompliance with the protocol, change in development plans for the study drug, slow 
recruitment, or poor-quality data.   
6. TREATMENT PROCEDURES 
6.1 
Screening 
PIs at each site are responsible for maintaining a record of all subjects screened, including 
both those who enter the study and those who are excluded.  
6.1.1 Informed Consent 
Each potential subject must sign a written, informed consent form prior to performing any 
study specific screening procedure. 
6.1.2 Inclusion and Exclusion Criteria 
Inclusion and exclusion criteria will be reviewed for each potential subject and documented 
in the case report form (CRF).  
6.1.3 Registration/Randomization of Subjects 
Centralized registration/randomization of subjects will be completed according to a process 
defined by the sponsor (see Section 5.1.4).  Each subject will be assigned a unique 
identification number. Once assigned, a subject’s identification number will not be reused. 
6.2 
Study Drugs  
6.2.1 Accountability and Dispensation 
The PI must maintain accurate records accounting for the receipt and dispensation of the 
study drugs.   
The investigational materials are to be prescribed only by the PI or the sub-investigators 
named on the United States Food and Drug Administration (US FDA) Form 1572, and may 
only be dispensed by authorized personnel at the institution(s) listed therein.   
Under no circumstances will the PI allow the investigational drug(s) to be used other than as 
directed by the protocol.  

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Figure 4.  Study Arm Treatment Regimens 
 
 
6.2.4 Preparation and Administration of Study Drug 
Please refer to the Pharmacy Manual for additional information. 
6.2.4.1 Preparation and Administration of INXN-1001 
INXN-1001 will be provided by the Sponsor as capsules. 
INXN-1001 capsules will be dispensed for subject oral dosing by the site pharmacy. The site 
must instruct the subject to take each dose in a fed state (within approximately 30 minutes 
after the start of a normal meal).  
6.2.4.2 Monitoring of Subject Adherence and Managing Missed INXN-1001 Doses 
The first daily dose of INXN-1001 at each treatment cycle is expected to be administered to 
the subject at the clinical site, under careful medical supervision by the clinic staff to ensure 
that the subject does not have difficulty with the size or quantity of capsules to be 
administered. Thereafter, subjects may be allowed to self-administer the remaining 6 doses at 
approximately the same time and in the same relationship to meals as administered at the 
clinical site on Day 1 of the treatment cycle. Subjects are to be instructed to take all of the 
capsules in the same way for each of the remaining treatment period, and will be reminded to 
take their dose via a phone call when they will not have a clinic visit.  
Subjects should be instructed not to make up for missed doses.   
Subjects will also be instructed to bring the treatment container(s) back with all remaining 
capsules at the next visit, to provide an assessment of the degree of adherence. All subjects 
will be queried about dose schedule adherence and reasons for missed doses.  
6.2.4.3 Preparation and Administration of INXN-2001 
INXN-2001 will be supplied by the Sponsor as single-dose vials.  Information regarding the 
preparation of the INXN-2001 dose will be provided in the Pharmacy Manual.  

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INXN-2001 
 
 
 will be administered as an IT injection 3 hours (± 
30 minutes) after oral INXN-1001 dosing on Day 1 of each cycle.  INXN-2001 should be 
injected into a different lesion at each cycle.  If only 3 accessible lesions are present, the 
injections will be done in sequential rotation between 2 lesions.  If only 2 accessible lesions 
are present, then all injections will be into a single lesion.  If only 2 accessible lesions are 
present at screening, and the single injected lesion can no longer support the injection volume 
at subsequent cycles, then the Medical Monitor should be contacted for determination of a 
path forward.  Lesions displaying signs of localized infection should not be injected. 
Note:  In the absence of the availability of radiographically-guided injections, one accessible 
lesion will not be injected since that lesion will be used to evaluate the systemic effect of 
INXN-2001.  
The INXN-2001 IT administration should be delivered by multiple injections with a fine 
needle (no finer than 27 gauge) directly into each quadrant of the lesion or pathologic lymph 
node to reach all aspects of the entire lesion.  Attention must be paid to adequately infiltrate 
the circumference of the tumor margins.  
Should the tumor selected for injection not support the entire INXN-2001 injection volume 
(approximately 1 cc), another tumor should be injected with the remaining volume to ensure 
that all subjects receive approximately 
 
 
.  If another tumor is not available, then 
the remaining volume should be injected into a draining, pathologic lymph node of the 
injected tumor.  At any cycle, if no accessible lesion for INXN-2001 injection is present (eg, 
due to complete resolution), then INXN-2001 should be injected into a draining, pathologic 
lymph node of a previously accessible lesion.  A pathologic lymph node must be defined as a 
lesion per mRECIST (Appendix 4). 
NOTE:  
 All subjects receiving INXN-2001 must be adequately hydrated with approximately 
2000 mL per 24 hours of oral electrolyte solution for 72 hours during Cycles 1 and 2.  
Subjects must be instructed to maintain good oral hydration on and between dosing 
days.  
 
Each subject will be carefully monitored for possible local reactions at the injection site 
and/or hypersensitivity reactions, for at least 2 hours following the INXN-2001 injection. The 
subject should be instructed to call the clinical site if any such reactions develop or do not 
resolve within 24 to 48 hours. 
6.2.4.4 Preparation and Administration of Palifosfamide 
Palifosfamide should be administered IV at a dose of 120 mg/m2/day, as an approximate 30-
minute infusion on Days 1, 2, and 3 of a 28-day cycle, for up to 6 cycles. Palifosfamide is 
supplied in single-use glass vials each containing 350 mg of active product.  Each vial is to 
be reconstituted with sodium chloride injection, USP, to a final concentration of 50 mg/mL 
and appropriate dose transferred into a 250 mL 0.9% sodium chloride IV infusion bag.   

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Note: Total cumulative time from reconstitution in vial through completed dose 
administration should not exceed 2.5 hours (150 minutes). 
Information regarding the preparation of the palifosfamide dose will be provided in the 
Pharmacy Manual.  The dose (mg) of palifosfamide should be calculated based on the 
subject’s actual body weight as measured on Day 1 of each cycle.  Body surface area (BSA) 
may be calculated as per the standard practice at each investigative center; however, the same 
formula should be used throughout the study when calculating a subject’s BSA. The 
palifosfamide dose must be prepared as described in the Pharmacy Manual, and administered 
within permitted time window allowed for reconstitution in vial, dilution in the IV infusion 
bag, and through completion of the IV infusion.   
 
NOTE:  
 All subjects receiving palifosfamide must be adequately hydrated with at least 
500 mL of fluids (oral or IV as appropriate), in addition to the infusion administered, 
on each day of palifosfamide dosing.  Subjects should be instructed to maintain good 
oral hydration on and between dosing days.  
 Electrolytes and hematologic toxicity need to be carefully monitored during clinical 
studies with palifosfamide. 
 
Study treatment should be administered according to the planned 21-day treatment cycle, 
with treatment delays allowed for study-drug related toxicity as described in Section 7.2.5.  If 
the Day 1 visit for a re-treatment cycle is delayed for other reasons (eg, due to inclement 
weather), then the visit should be rescheduled to occur as soon as possible. If any non-
prolonged delay for other reasons is to occur, the Medical Monitor should be consulted.     
A missed Day 2 or Day 3 study drug administration may be rescheduled to Day 4 of the same 
treatment cycle.  If both Day 2 and Day 3 are missed, then only a single day may be 
rescheduled to Day 4 and the other will be skipped.  In either case, the total duration of the 
treatment cycle should remain 21 ± 1 day by shortening the rest interval by 1 day.  If the 
missed dose cannot be administered on Day 4, then it must be skipped and the subject should 
continue on protocol and take the next dose as originally planned. 

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6.2.5 Retreatment Criteria, Dose Delays and Modifications 
Subjects may receive up to 6 cycles of study drug treatment.  To receive each repeat 
treatment cycle, all treatment-related AEs must have resolved to Grade 1 or baseline and the 
following laboratory criteria must be met: 
Hemoglobin ≥ 9 g/L 
eGFR ≥ 60 mL/min/1.73 m2 
Lymphocytes > 700/ mm3 
AST and ALT ≤ 2.5 x ULN  
For subjects with documented liver 
metastases, ALT and AST ≤ 5×ULN 
Neutrophils ≥ 1,500/ mm3  
Total bilirubin < 1.5 x ULN 
Platelets ≥ 100,000/ mm3 
INR and PTT <1.5 x ULN 
 
Clinical laboratory tests drawn pre-treatment for analysis on Day 1 of each cycle may be 
used for determining if the re-treatment criteria have been met, and must be reviewed by the 
investigator or designee prior to the next cycle of study drug administration.  Two treatment 
delays for recovery to acceptable levels are allowed at weekly intervals up to a maximum 
of14 days. In the event that a treatment-related dose delay is necessary for palifosfamide, 
then the next cycle of study treatment will be administered at 80% of the dose (Table 3).  If 
an AE is clearly related to 1 study drug and not the other (in combination Treatment Arm C), 
then dose modification/delay is to occur for the relevant study drug (INXN-1001 and/or 
palifosfamide).  A maximum of two dose reductions, of either INXN-1001 or palifosfamide, 
will be allowed. 

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Table 3.  Dose Modifications for Palifosfamide-related Toxicitya 
ADVERSE EVENT 
PALIFOSFAMIDE 
Hematologic 
Platelet count <100 × 109/L  
Delay dose of palifosfamide up to 14 days until platelet count ≥ 100 X 
109/L, then reduce by 20%. 
ANC < 1500/mm3  
Delay dose of palifosfamide up to 14 days until ANC returns to ≥ 1500, 
then maintain dose when restarted.  
Neutropenic fever 
Delay dose of palifosfamide up to 14 days until resolved, then reduce by 
20%. 
Any Grade 4 hematologic 
toxicity 
Delay dose of palifosfamide up to 14 days until Grade ≤1 or baseline, then 
reduce by 20%. 
Estimated Glomerular Filtration Rate (eGFR) (Appendix 5) 
≥25% up to <50% decrease 
from baselineb 
Hold dose until repeat test is performed.  Reduce dose of palifosfamide by 
20% if confirmed on repeat test. 
≥50% decrease from baseline2 
Hold dose until repeat test is performed.  Discontinue palifosfamide if 
confirmed on repeat test. 
Non-hematologic (other than creatinine or urinary electrolyte wasting) 
Not treatment-related Grade 3 
if unresponsive to appropriate 
therapy. 
Delay dose of palifosfamide for up to 14 days until Grade 1 or baseline, 
then reduce by 20%. 
Not treatment-related Grade 4  Delay dose of palifosfamide up to 14 days until ≤ Grade 1 or baseline, then 
reduce by 20%. 
aWhen indicated, the maximum permitted delay of study drug administration due to toxicity and/or for confirmatory 
laboratory testing is 14 days.   
bBaseline eGFR determined based on the most recent serum creatinine measurement prior to study drug 
administration (ie, Cycle 1 Day 1 or Screening). 
 
Subjects who experience a treatment-related Grade 4 AE, other than nausea and/or vomiting 
in the absence of optimal treatment with antiemetics, will be discontinued from study 
treatment.  If, however, the subject has experienced a substantial benefit from treatment and 
the PI and Medical Monitor recommend continuation on the study, re-exposure to the 
experimental treatment may proceed on a case-by-case basis.   
6.2.6 Severity Grading and Management of Injection Site Reactions 
Injection of a biologic agent carries a potential risk of injection site reaction which is 
characterized as an intense reaction (usually immunologic) at or near the site of injection.  
Injection reactions will be graded according to the NCI CTCAE v4.03.  
Table 4 outlines the injection site reaction grading system, associated symptoms, and the 
recommended actions to be taken.  Reactions at the INXN-2001 injection site that occur 
within 24 hours after the injection and are attributed to INXN-2001 will be considered to be 
injection-related AEs.  
 

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6.2.8 Disposition of Unused Study Drug 
All unused study drug should be destroyed on-site in accordance with applicable site facility 
and US Occupational Safety and Health Administration procedures, after a full accountability 
has been documented. Any on-site destruction of unused study drug must be documented and 
the records maintained in the investigator’s study file.  
6.3 
Concomitant Therapy 
Concomitant medication information, including blood products, vitamins, and other 
supplements, will be collected for the time period beginning 28 days prior to the first dose of 
study drug through the Post-Treatment Safety Assessment visit.   
Permitted: 
 Subjects may receive standard treatments, including palliative and supportive care for 
any underlying illness, with the exception of palliative radiotherapy, which is NOT 
permitted. 
 Antidiarrheal therapy is permitted for study drug-induced diarrhea. 
 Antiemetics are permitted for study drug-induced nausea and vomiting. (except those 
listed Appendix 2) 
 Treatment with vitamin/mineral supplements is acceptable provided that they do not 
interfere with study endpoints, in the opinion of the investigator.  
Not Permitted: 
 Subjects may not receive medications, foods, or drinks that induce, inhibit, or are 
substrates of the CYP450 3A4 pathway within 7 days prior to the first dose of study 
drug through 96 hours after their last dose of INXN-1001.  See Appendix 2 for 
examples. 
 Subjects may not receive any other investigational agent or anticancer therapy 
(chemotherapy, radiotherapy, etc.) while receiving study treatment. 
6.4 
Evaluation and Assessment Procedures 
6.4.1 Schedule of Assessments 
A tabular schedule of evaluations and procedures is provided as Schedule of Study 
Procedures and Assessments following the Protocol Synopsis in Section 3.  

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6.4.2.8 Hematology 
Hematology tests include: complete blood count (CBC) and white blood cell (WBC) count, 
differential WBC count, red blood cell (RBC) count, hematocrit, hemoglobin, RBC indices, 
reticulocyte count, MCV (mean corpuscular volume) and platelet count. PTT and INR will 
also be evaluated.   
6.4.2.9 Serum Chemistry 
Serum chemistry tests include: AST, ALT, LDH, ALP, creatinine, total bilirubin, total 
protein, albumin, blood urea nitrogen (BUN), glucose, sodium, potassium, chloride, calcium, 
phosphorus and bicarbonate.  The eGFR will be calculated from the serum creatinine at each 
chemistry time point using the MDRD equation (Appendix 5); in cases where the MDRD 
equation may not be suitable, a 24-hour urine creatinine clearance test may be substituted 
with prior approval of the Medical Monitor. 
6.4.2.10 Urinalysis 
Urinalysis panel (dipstick) includes: appearance, pH, specific gravity, glucose, 
protein/albumin, blood, ketones, bilirubin, nitrates, and leukocyte esterase.  In addition, a 
microscopic exam for casts, crystals, and cells may be done if clinically indicated.   
6.4.2.11 Electrocardiogram (ECGs) 
A standard, single, 12-lead ECG for local safety assessment will be performed at screening, 
2.5 to 3 hours after INXN-1001 dosing (and prior to palifosfamide infusion and INXN-2001 
injection) on Day 1 of each cycle, and at the Post-Treatment Safety Assessment visit. The 
ECGs will be used to evaluate the QT/QTc interval. 
6.4.2.12 Immune Response Analyses 
Plasma and/or serum cytokine levels will be assayed using enzyme-linked immunosorbant 
assay (ELISA) methodology.  One or more serum biomarkers (eg, MUC-1) or cytokines will 
be assessed. 
6.4.2.13 INXN-1001 Pharmacokinetic Assessment 
INXN-1001 PK assessment will occur for subjects enrolled in Part 1 during Cycle 1 of study 
treatment. Whole blood samples will be collected on Day 1, Day 2, Day 7, and Day 8; as 
defined in Table 2A, Schedule of Assessments.  INXN-1001 levels will also be assessed 
using the samples drawn for cytokine analysis. 
6.4.3 Efficacy Assessments 
Appropriate cancer staging procedures should be performed during screening.  For the 
purpose of this clinical trial, the following imaging is expected at screening: 
a. CT of the chest, and CT (or MRI) of the abdomen  
b. MRI (or CT) of the brain if brain metastasis are known or suspected  

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c. CT or MRI of other anatomical regions as clinically indicated 
For each subject, disease sites are to be assessed throughout the study using the same 
method(s) of assessment used at screening. Chest and abdomen imaging are required for all 
follow-up imaging time points; images of the brain and other anatomical regions should be 
acquired on follow-up if positive at screening and as clinically indicated. 
Target and non-target lesions should be selected and measured as per mRECIST v1.1 
guidelines39 (see Appendix 4). Lesions that will be/are injected with INXN-2001 and/or 
biopsied should not be selected as target lesions, but should be assessed as non-target lesions.    
For each subject, disease sites are to be assessed throughout the study using the same 
method(s) of assessment used at screening. Tumor response assessments will occur at 
12 weeks, 16 weeks, and the Follow-up Tumor Assessment visit (24 weeks) for all subjects, 
including those who may have experienced a dose delay.  Additional tumor response 
assessments may occur at the discretion of the investigator.   
The investigator will evaluate each subject for response to therapy according to mRECIST 
v1.1 guidelines.  
 
In the setting of this immunotherapy, a progression observed ≤ week 12 requires 
confirmation at week 16 (see Appendix 4 for further details). Subjects without objective 
evidence of disease progression at the Follow-Up Tumor Assessment visit should continue to 
have tumor assessments performed at 8-10 week intervals until disease progression has been 
documented, or an alternate anticancer therapy has been initiated, or up to 1 year, whichever 
occurs first.   
 
In addition to radiological imaging techniques, photographs of visible cutaneous lesions 
should also be obtained.  Digital photograph(s) with included measuring tape should be taken 
of all visible injected and non-injected tumors, and of any remaining visible local reactions in 
or around the injected lesion(s).  Important guidelines regarding photographic methodology 
will be provided in a separate manual.  
6.4.4 For Participating Sites:  Assessments of Transgene Function, Immunological 
Activities and Biological Effects (please refer to Appendix 6) 
6.4.4.1 Transgene Function 
For subjects receiving Ad-RTS-hIL-12, punch biopsies (PBx) or fine-needle aspirates (FNA) 
of the tumor(s) and/or associated tumor-involved draining lymph nodes will be collected for 
in vivo assessment of the presence of the adenoviral vector, possible ongoing transgene 
expression of IL-12, and expression of IL-12-induced downstream genes.  Expression of IL-
12 and IL-12-induced genes will be evaluated via qRT-PCR, using a panel of primers to 
known IL-12 regulated genes in breast cancer as well as signaling pathways downstream 
from IL-12.   
For all subjects, FNAs of the tumor(s) and/or associated tumor-involved draining lymph 
nodes will be collected for immunohistochemistry (IHC).   

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 Anticipated day-to-day fluctuations of pre-existing conditions, including the disease 
under study, that do not represent a clinically significant exacerbation or worsening 
need not be considered AEs.  
 In the event that a constellation of symptoms results in a confirmed diagnosis, the 
diagnosis (not the symptoms) should be recorded as the AE term. 
 If a diagnosis cannot be established, the symptoms should be recorded as the AE(s).  
 If an ongoing symptom has been included in the medical history, an associated 
severity grade and frequency should also be documented so that a worsening in 
severity or frequency of a symptom can be readily identified as an AE. 
 Progression of disease is not itself an AE; however, the presenting sign or symptom 
of the disease progression should be documented as an AE (eg, increase in pain).  
Exception:  If a subject experiences progression of disease that results in death, 
‘progression of disease’ may be reported as an SAE if, by medical opinion, the term 
best describes the cause of death. 
7.2 
Evaluation of Adverse Events (AEs) 
7.2.1 Determination of Seriousness 
The investigator will determine the seriousness of an AE based on the following: 
7.2.1.1 Serious Adverse Event (SAE) 
 An AE is considered an SAE if at least 1 of the following conditions applies: 
 
 Death: An AE that results in death during the active study period or within 30 days 
following study drug administration.  In addition, a reported death at any time post-
study that is thought to be related to study drug administration; 
 Life-threatening adverse event: An AE that places the subject, in the view of the 
investigator, at immediate risk of death from the event as it occurred (ie, this does not 
include a reaction that, had it occurred in a more severe form, might have caused 
death); 
 Permanent, persistent, or significant disability: A disability is defined as any 
substantial disruption of a person’s ability to conduct normal life functions; 
 Inpatient hospitalization or prolongation of existing hospitalization: In general, 
hospitalization refers to admission of a subject into a hospital for at least a 24-hour 
stay. Hospitalizations for routine blood transfusions, hospitalization for an elective or 
diagnostic procedure, or surgery for a pre-existing condition that has not worsened, 
are not considered SAEs.  (Emergency room visits that do not result with admission 
are not considered as SAEs); 
 A congenital anomaly/birth defect: A fixed, permanent impairment established at or 
before birth; 

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 Important medical event: Events that may not result in death, be life-threatening, or 
require hospitalization may be considered SAEs when, based upon appropriate 
medical judgment, they jeopardize the subject and require medical or surgical 
intervention to prevent a life-threatening situation, hospitalization or death; 
 New cancer: Occurrence or diagnosis of a new cancer during the trial is considered an 
SAE. (This does not pertain to metastasis of current disease); 
 Any AE associated with an overdose of the study drug: An overdose of study drug is 
defined as an occurrence of administered dose exceeding that which is prescribed by 
the investigator per protocol. 
 
7.2.1.2 Non-Serious Adverse Event 
Adverse events that do not fulfill the previous criteria are classified as non-serious AEs. 

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7.2.2 Determination of Severity 
The severity of AEs will be assessed according to the NCI CTCAE, v. 4.03. If the AE is not 
defined in the NCI CTCAE, v. 4.03, the investigator will determine the severity of an AE 
based on the following definitions: 
 Mild (Grade 1): The AE is noticeable to the subject, but does not interfere with 
routine activity. The AE does not require discontinuing administration or reducing the 
dose of the study drug. 
 Moderate (Grade 2): The AE interferes with routine activity, but responds to 
symptomatic therapy or rest. The AE may require reducing the dose, but not 
discontinuing administration of the study drug. 
 Severe (Grade 3): The AE significantly limits the subject’s ability to perform routine 
activities despite symptomatic therapy. In addition, the AE leads to discontinuing 
administration or reducing the dose of the study drug. 
 Life Threatening (Grade 4): The AE requires discontinuing administration of the 
study drug. The subject is at immediate risk of death. 
 Death (Grade 5): The subject dies as a direct result of the complication or condition  
 
Adverse events should be reported using the maximum intensity of the event (eg, if a subject 
reported nausea lasting 3 days, 1 start date and stop date should be recorded along with the 
maximum intensity experienced for that event over that 3-day timeframe). 
7.2.3 Causality Assessments 
The investigator will use medical consideration to determine the potential relationship of the 
AE to the study drugs based on his/her clinical judgment.  Assessment of causality will be 
based upon the following: 
 Alternative possible causes of the AE, including the subject’s underlying disease or 
co-morbid conditions, other drugs, other host and environmental factors; 
 The temporal sequence between the exposure to study drug and the AE; 
 Whether the clinical or laboratory manifestations of the AE are consistent with known 
actions or previously reported toxicity of the study drug (or similar drugs); 
 Whether the AE resolved or improved with decreasing the dose or stopping the study 
drug (ie, dechallenge); or recurred or worsened with re-exposure to the drug (ie, 
rechallenge). 
 
The relationship between the study drug and the AE will be described using one of the 
following categories: 
 Unrelated: Another factor is clearly the cause of the AE. 
 Possibly Related: There is a reasonable possibility that the study drug is the cause of 
the AE, including that the study drug and another factor(s) are equally likely as 
causes of the AE. 
 Related: The AE can be fully explained by the administration of study drug. 

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7.3 
Documenting Adverse Events (AEs) 
All AEs (including SAEs) are to be accurately recorded on the Adverse Event page of the 
subject’s electronic CRF from the time the subject signs the informed consent until the 
Post-Treatment Safety visit. Each event will be assessed for serious criteria, severity, and 
causality (see “Causality Assessments”). The date of onset, as well as the duration of the 
event will be recorded. In addition, treatments provided to the subject, actions taken with the 
study drugs, and the outcome of the AE will also be noted. 
7.4 
Reporting Serious Adverse Events (SAEs) 
Time Frame for Reporting 
 
SAEs must be reported to the Sponsor or Sponsor’s designee (within 24 hours) of becoming 
aware of the event (regardless of the initiation of any new anticancer therapy) including the 
following: 
 Any death or SAE experienced by the subject from the signing of informed consent to 
30 days after the last dose of study drug, regardless of relationship to study drug. 
 Any death or SAE that the Investigator becomes aware of, and believes to be study 
drug related, that occurs more than 30 days after the subject last received study drug. 
 
Study drug-related AEs/SAEs that are ongoing at the time of the Post-Treatment Safety 
Assessment visit should continue to be followed until resolution, return to baseline, or until 
they have stabilized or become chronic (and following consultation and agreement by the 
ZIOPHARM Medical Monitor). 
 
Information to be provided by the Investigator   
 
Within 24 hours of becoming aware of the SAE or subject death, the investigator must notify 
the Sponsor or designee and transmit information to the Sponsor or designee. Information 
(initial and follow-up) should be provided on an electronic and/or paper SAE Report form 
signed and dated by the investigator.  The SAE Report form and copies of source documents 
(with subject identifiers redacted) will be transmitted by fax.  A hospital discharge summary 
should be provided if the subject was hospitalized.  An SAE report will be considered final 
once all relevant information has been received and reviewed by the Sponsor. 
The SAE Report form is provided in the investigator study files.  Please refer to the 
investigator study files for instructions on how to complete the form. The investigator will 
provide all of the following information related to the event: 
 
 Investigator identification 
 Subject identification  (e.g., subject number, initials, sex, age or date of birth) 
 Information regarding study drug administration (e.g., start/stop date, dose, and 
frequency ) 
 Description of event 
 Action taken with the study drugs in relation to the SAE 
 Outcome of the SAE 

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In addition to the above information, the investigator must provide, for each event term, an 
assessment of: 
 Severity/intensity 
 Relationship to the study drug (causality assessment) 
7.5 
Sponsor and Investigator Responsibility for Reporting Adverse Events (AEs) 
All AEs and SAEs will be reported to regulatory authorities, IRBs/IECs, and investigators in 
accordance with all applicable global laws and regulations.  The investigator must submit all 
Safety Letters from the Sponsor to his/her IRB/IEC per agreements and local requirements. 
The investigator must keep copies of all safety reports, including correspondence with 
ZIOPHARM and the IRB/IEC, in the study file.  
7.6 
Follow-up Information 
Appropriate diagnostic tests should be performed and therapeutic measures, as medically 
indicated, should be instituted. Appropriate consultation and follow-up evaluations should be 
carried out until the event has resolved, stabilized, returned to baseline, or is otherwise 
explained by the investigator. 
 
Follow-up data concerning the SAE (eg, diagnostic test reports, hospital summaries, etc.) 
must be promptly reported (within 24 hours of receipt) to the Sponsor or Sponsor’s designee, 
until resolution of the SAE. Should the FDA or National Regulatory Authorities require that 
the Sponsor submit additional data on the event, the investigator will be asked to provide 
those data to the Sponsor in a timely fashion. 
 
Required Follow-up for Serious Adverse Events (SAEs) 
All treatment-related AEs/SAEs that are ongoing at the time of the Post-Treatment Safety 
visit will be followed until: 
 The event resolves, or 
 The event returns to baseline if a baseline value is available, or 
 The event stabilizes (and following consultation and agreement by the ZIOPHARM 
Medical Monitor), or 
 The event can be attributed to factors other than the study drug or other than study 
procedure. 
7.7 
Pregnancies 
Subjects who become pregnant during the study should immediately discontinue 
participation in the study. The Sponsor should be immediately notified. 
An initial Pregnancy Report form and a Pregnancy Outcome Form are to be completed by the 
investigator or designee. The Pregnancy Report form and the completion guidelines will be 
provided in the investigator study files.  Please refer to the investigator study files for details 
on how to complete these forms. 

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8. STATISTICAL PROCEDURES  
Data from this study will be analyzed and included in a clinical study report that will be 
prepared after the last subject has completed the Post-Treatment Safety Assessment visit.  
Additional data collected from subjects who have not progressed by the Follow-Up Tumor 
Assessment visit and are continuing to be followed for tumor response at the time of the final 
data cut-off date will be presented in an addendum to the study report. 
8.1 
Determination of Sample Size 
In view of up to 3 novel investigational drugs being tested in this study, the sponsor has 
incorporated a Safety Run-in (Part 1) to evaluate safety for each study arm before fully 
enrolling all subjects required in Stage 1 of Part 2 for each study arm (for details please see 
Section 5.1.1).   
The sample size of Part 2 is determined based on a Simon 2-stage design for each study arm.  
For Ad-RTS-hIL-12 monotherapy (Arm A) with 13 subjects evaluated in Stage 1 and an 
additional 20 subjects in Stage 2 if applicable, it will provide 80% power at 1-sided 5% 
significance level to differentiate 35% targeted proportion of subjects who survive 
progression-free at week 16 from a proportion of no interest of 15%. If ≥3 of 13 subjects 
survived progression-free at week 16 in Stage 1, 20 additional subjects will be evaluated in 
Stage 2.   
For the Ad-RTS-hIL-12 + palifosfamide combination (Arm C), with 12 subjects evaluated in 
Stage 1 and an additional 14 subjects evaluated in Stage 2, it will provide 80% power at 1-
sided 5% significance level to differentiate 65% targeted proportion of subjects who survive 
progression-free at week 16 from a proportion of no interest of 40%. If ≥6 of 12 subjects 
survived progression-free at week 16 in Stage 1, 14 additional subjects will be evaluated in 
Stage 2.   
8.2 
Subject Randomization 
Following the safety run-in period in Part 1, subjects will be randomly assigned to Treatment 
Arms A or C in Part 2 with a 1:1 ratio, adaptively, until reaching the desired number of 
subjects assigned in each arm.  For details please refer to Section 5.1.4. 
8.3 
Populations for Analysis 
The following subject populations will be evaluated and used for presentation and analysis of 
the data: 
 Safety Population: All subjects who received at least 1 dose of study drug (INXN-
1001, INXN-2001, and/or palifosfamide).  

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 Efficacy Evaluable Population: All subjects who received at least 1 dose of study 
drug (INXN-1001, INXN-2001, with or without palifosfamide) and have at least 1 
post-screening response evaluation. 
8.4 
Study Endpoints 
8.4.1 Primary Efficacy Endpoint 
The primary efficacy endpoint is the 16-week PFS rate, calculated as the number of subjects 
who had not progressed or died prior to 16 weeks from the date of their first dose, divided by 
the number of subjects in the study arm. Subjects who neither progressed nor died, but had 
their last tumor assessment prior to 16 weeks, will not be categorized as progression-free and 
will not be included in the numerator. Progressive disease (PD) will be determined by 
mRECIST v1.1 (please refer to Appendix 4). 
8.4.2 Secondary Efficacy Endpoints 
Tumor-related secondary efficacy endpoints are defined as the following: 
 PFS: time from the date of first dose to the date of PD or death (if prior to 
progression). Subjects without PD or death occurring as of the time of analysis will 
be censored as of the last date of disease evaluation. PD will be evaluated by 
mRECIST v1.1 
 ORR by mRECIST v1.1: Proportion of subjects achieving a confirmed PR or CR 
according to mRECIST v1.1 during study.  All objective responses (CR or PR) 
require confirmation by a repeat tumor assessment at least 4 weeks (28 days) after the 
response is first observed in order for the response to be considered confirmed.   
 Duration of response:  time from the date of first objective response (PR or CR) by 
mRECIST v1.1, until the date of PD or 1 year. Duration of response in subjects who 
have not progressed or died at the time of analysis will be censored as of the date of 
their last tumor assessment.  
 Clinical benefit rate (CBR = proportion of subjects with CR, PR or SD) by mRECIST 
v1.1  
8.4.3 Other Endpoints 
Cytokine and breast cancer biomarker (eg, MUC-1) levelswill be explored in serum samples.  
For study sites participating in additional immunologic assessments, please refer to Appendix 
6.  INXN-1001 PK analysis will be performed in Cycle 1 for all subjects enrolled the Safety 
Run-in (Part 1).   
8.4.4 Safety Endpoints 
The safety endpoints will include AEs, vital signs, ECG, physical examinations, laboratory 
data, and concomitant medications. All AEs will be coded according to Medical Dictionary 

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for Regulatory Activities (MedDRA®, version 13.0 or later).  Concomitant medications will 
be coded using the World Health Organization Drug Dictionary, September 2006 or later.   
The incidence, onset timing, duration, severity, relationship, and outcome will be listed for 
each AE. All treatment-emergent AEs (TEAEs) occurring on-study will be analyzed by 
treatment group and listed in by-subject data listings.  Events that are considered related to 
treatment (possibly related or related) will also be tabulated.     
Treatment-emergent AEs will be tabulated overall and by subject. ‘Treatment-emergent’ is 
defined as any AE that occurs during or after administration of the first dose of study drug 
through the Post-Treatment Safety Assessment visit (28 days after last dose of study drug); 
any event after the first dose of study drug that is considered study drug-related regardless of 
the start date of the event; or any event that is present at baseline that worsens in intensity or 
is subsequently considered to be drug related by the investigator.  Serious TEAEs and related 
TEAEs will be summarized in a similar fashion.  AEs to be presented will include TEAEs, 
treatment-emergent SAEs, and treatment-emergent related AEs, as well as the severity of the 
events.  Timing relative to study treatment administration will also be presented.  Treatment-
related SAEs will also be summarized by treatment group and presented on a case-by-case 
basis in listings and narratives.  
Dosing and study drug tolerability will also be assessed.   
8.5 
Procedures for Handling Missing, Unused, and Spurious Data 
No imputation of values for missing data will be performed.  Standard clinical monitoring 
and data management practices will be used to ensure the integrity of data. 
8.6 
Statistical Analyses 
8.6.1 Subject Status 
Subject status will be summarized for all randomized subjects by Study Arm.  The numbers 
of subjects in the Efficacy population and Safety population will be summarized, as well as 
those receiving a non-randomized treatment.   
In addition, major protocol violations will be summarized by Study Arm and presented in 
listings.   
8.6.2 Baseline Characteristics 
Demographic and baseline disease characteristic data will be summarized.  Data to be 
tabulated will include at least demographic features such as sex, age, and race, as well as 
disease-specific status and medical history. 

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8.6.3 Safety Analyses 
Safety tables will be presented for all safety parameters including TEAEs, dosing, vital signs, 
ECGs, and clinical laboratory tests.  The Safety Population will be used for these analyses. 
AEs will be coded using MedDRA® for the purpose of summarization.  All AEs occurring 
during the study will be included in by-subject data listings.  Treatment-emergent events will 
be tabulated.  Deaths, SAEs, and AEs resulting in study discontinuation will be listed.   
Safety variables will be tabulated and presented by study arm.  Exposure to study drug and 
reasons for discontinuation of study treatment will be tabulated. 
8.6.4 Efficacy Analyses 
The Efficacy Evaluable Population will be used for the analyses of efficacy data by study 
arm. 
8.6.4.1 Primary Efficacy Analyses 
The primary analysis of the primary endpoint (16-week PFS rate) will be summarized using 
both a point estimate and its exact binomial 2-sided 95% confidence interval (CI). The 16-
week PFS rate will be also estimated using the Kaplan-Meier method. The 95% CI of the 
PFS rate at 16 weeks will be calculated using the Greenwood formula.  
8.6.4.2 Secondary and Other Analyses 
PFS is defined per subject as the time (in months) from first dosing date to the date of 
progression. Subjects who died without a reported prior progression will be considered to 
have progressed on their date of death. Subjects who did not progress or die will be censored 
on the date of their last tumor assessment. Duration of response will be computed from the 
time measurement criteria were met for PR or CR until the date of documented PD or 1 year. 
Subjects who neither progressed nor died will be censored on the date of last tumor 
assessment. 
INXN-1001 PK parameters to be determined will include, but are not limited to, the 
maximum concentration (Cmax), time to maximum concentration (Tmax), half-life (t1/2), area-
under-the-concentration time curve (AUC), volume of distribution (Vd), and clearance (CL).  
Where possible, descriptive statistics of the PK parameters will be provided; individual 
subject INXN-1001concentrations, actual sampling times, and PK parameters will be listed. 
8.7 
Immunologic Responses  
The trial will assess the cytokine profiles and breast cancer-associated biomarkers (eg, MUC-
1) for all subjects.   
In addition, participating sites will include additional immunologic assessments as described 
in Appendix 6.  The immunological effects of each treatment cycle on the cellular and 
humoral immune responses in the peripheral circulation and in tumor biopsy specimens.  

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Cytokine profiling will be performed by ELISA.  Whole blood will be collected for flow 
cytometry analysis, immune response assay, and/or ELISPOT assays for measurement of the 
response to breast cancer-associated antigens.  Samples will also be screened for the relative 
percentages of mononuclear immune cell subpopulations.  At each time point, the change in 
immunologic response (CTL and Treg frequency in blood) from baseline and from the 
preceding time point will be correlated with the INXN-1001 dosage level, as well as with 
serum cytokine levels.  In addition, tumor PBx or FNAs will be examined for cytokine 
expression, presence of injected adenovirus and CTL frequency, Treg and myeloid-derived 
suppressor cell frequency, and other immunological markers.  The change in each measure 
from baseline and from the preceding biopsy will be correlated with the treatment arm. 
8.8 
 Procedures for Reporting Deviations to Original Statistical Analysis Plan 
A formal statistical plan for the analysis and presentation of data from this study will be 
prepared prior to database lock. Deviations from the statistical analyses outlined in this 
protocol will be indicated in this plan; any further modifications will be noted in the final 
clinical study report. 
9. STUDY ADMINISTRATION 
9.1 
Electronic Case Report Forms and Source Documentation 
For each subject, eCRFs and corresponding source records will be maintained at each clinical 
site.  The Sponsor or designee will provide the study sites with secure access to and sufficient 
training on the electronic data capture (EDC) application, to permit site personnel to enter or 
correct information in the eCRFs for the subjects for whom they are responsible.   
 eCRFs should be completed in a timely manner, and every effort should be made to have 
forms completed and up-to-date in anticipation of a visit by the Sponsor’s monitor. Specific 
instructions will be provided to the site.  All requested information must be entered on the 
eCRF in the spaces provided. If an item is not available or is not applicable, it should be 
documented as such; do not leave a space blank. 
It is the investigator’s responsibility to ensure the accuracy, completeness, clarity, and 
timeliness of the data reported in the subject’s eCRF.  Through the EDC application, the 
investigator must provide formal approval of all subject information in the eCRFs and 
changes to the eCRFs to endorse the final submitted data for the subjects for whom he/she is 
responsible.  The audit trail entry will show the user’s identification information and the date 
and time of any corrections.   
eCRF completion may be delegated to other study personnel; however, such delegation must 
be documented in writing.  If, for any reason, certain data are lacking to complete an 
individual report form, the investigator will provide a written statement explaining the 
reasons for the lack of data. 

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Sponsor or designee will retain the eCRF data and corresponding audit trails.  A copy of the 
final archival eCRF in the form of a compact disk or other electronic media will be placed in 
the investigator’s study file. 
9.2 
Good Clinical Practice Statement 
The study will be conducted in accordance with ethical principles that have their origin in the 
Declaration of Helsinki and are consistent with International Conference on Harmonisation 
(ICH) Good Clinical Practice (GCP) guidelines, applicable regulatory requirements, and 
ZIOPHARM policies. 
9.3 
Sponsor Monitoring 
After satisfactory receipt of all necessary regulatory paperwork, the sponsor’s monitor will 
arrange that all study material be delivered to the study site at a mutually convenient time. 
An initiation visit by ZIOPHARM and its monitoring personnel will be made. At this 
meeting, all personnel expected to be involved in the conduct of the study will undergo an 
orientation to include review of study protocol, instruction for CRF completion and overall 
responsibilities, including those for drug accountability and study file maintenance. 
Throughout the course of the study, the sponsor’s monitor will make frequent contact with 
the investigator, and this will include telephone and/or on-site visits. During these visits, 
CRFs will be reviewed for completeness and adherence to protocol. As part of the data audit, 
it is expected that source documents (eg, hospital records, office records) will be made 
available for review by the monitor. The monitor also will perform drug accountability 
checks, and may periodically request review of the investigator’s study file to assure 
completeness of documentation in all respects of study conduct. 
Upon study completion, the monitor will arrange for a final review of the study files, after 
which the file should be secured by storage for the appropriate period as specified in Section 
10.5. The investigator or appointed delegate will receive the sponsor’s representative during 
these on-site visits and will cooperate in providing the documents for inspection and 
responding to inquiries that may arise as part of this review. The investigator will also permit 
inspection of the study files by authorized representatives of the FDA. 
9.4 
Duration of the Study 
The duration of this study from the time of initiating subject enrollment until the completion 
of survival follow-up is anticipated to be approximately 34 months, including 24 months for 
enrollment and the later of 1 year of further follow-up. 
Each subject’s participation in this study will last approximately 6.5 months, including: 
 28-day screening period. 
 6 cycles (18 weeks) of study treatment. 

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 Post-Treatment Safety Assessment visit performed 28 days after the last dose of study 
drug.   
 Follow-Up Tumor Assessment visit performed 35 ± 7 days after the Post-Treatment 
Safety Assessment visit. 
In addition, subjects who discontinue or complete study treatment without objective evidence 
of disease progression should continue to be followed until disease progression has been 
documented or an alternate anticancer therapy has been initiated, whichever occurs first.  The 
active study period refers to the study period from informed consent through the 
Post-Treatment Safety Assessment visit.   
9.5 
Records Retention 
Records of drug disposition, CRFs, and reports of the clinical trial must be maintained by the 
investigator for a period of at least 2 years following the date on which the test article is 
approved by FDA for marketing for the purposes that were investigated in the study. If no 
application is to be filed or if the application is not approved for such indication, the records 
must be stored for 2 additional years and then returned to ZIOPHARM. No records will be 
destroyed, but will be indefinitely stored. 
9.6 
Institutional Review Board 
This protocol and the study informed consent form must be reviewed and approved by the 
Institutional Biosafety Committee (where applicable) and IRB/IEC prior to the start of the 
study, and a copy of the approval letter supplied to ZIOPHARM. During the course of the 
study, the investigator shall make timely and accurate reports to the IRB/IEC on study 
progress at intervals not exceeding 1 year, as well as satisfying any other local IRB/IEC 
reporting regulations. Copies of all reports to, and correspondence with, the IRB/IEC must be 
provided to ZIOPHARM. Further, within 3 months of the completion or early termination of 
the study, a final report should be made to the IRB/IEC and ZIOPHARM by the investigator. 
All protocol revisions must originate with and be documented by ZIOPHARM. If the 
requested revision is an amendment, the investigator must sign it. The FDA will be notified 
of all revisions by ZIOPHARM. The investigator must submit the amendment to his/her 
IRB/IEC for review and approval prior to implementation. Documentation of approval signed 
by the chairperson or designee of the IRB/IEC must be sent to ZIOPHARM.  
It is the investigator’s obligation to maintain an IRB/IEC correspondence file and to make 
this available for review to ZIOPHARM representatives as part of the routine study 
monitoring process. 
9.7 
Confidentiality and HIPAA 
The written Informed Consent will explain that study data will be stored in a database, 
maintaining confidentiality in accordance with national data legislation. All data processed 
by ZIOPHARM, or its representative, will be identified by subject number and study code. 

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The written Informed Consent will also explain that, for data verification purposes, 
authorized representatives of ZIOPHARM, a regulatory authority (FDA), and/or the IRB/IEC 
may require direct access to parts of the hospital or clinic records relevant to the study that 
include the subject’s medical history.  
The Informed Consent Form will be accompanied by or include a separate document 
incorporating US Health Insurance Portability and Accountability Act (HIPAA)-compliant 
wording by which the subjects authorize the use and disclosure of their Protected Health 
Information. 
10. INFORMED CONSENT 
10.1 FDA Informed Consent Requirements 
The investigator or his/her staff will explain the nature of the study, its purpose and 
associated procedures, the expected duration, and the potential risks involved to the 
prospective subject prior to enrollment. The Informed Consent should also indicate that, by 
signature, the subject or, where appropriate, a legal guardian, permits access to relevant 
medical records by the Sponsor and by representatives of the US FDA. If a prospective 
subject does not understand English, an appropriate translation into his or her primary 
language must be made available. The investigator or designee will obtain written, informed, 
and witnessed consent. The individual will have ample time and opportunity to ask questions. 
He/she will be informed about the right to withdraw from the study at any time without any 
disadvantage and without having to provide a reason for this decision. Following the 
discussion regarding the study, the prospective subject will be asked if he/she is willing to 
sign and personally date a statement of informed consent. Only if the individual voluntarily 
agrees to sign the informed consent statement and has done so, may he/she enroll into the 
study. A copy of his/her signed and dated informed consent will be provided to each subject. 
The signed Informed Consent Form is to remain in the investigator’s file.  
The Informed Consent Form and any other written information provided to the subjects will 
be revised whenever important new information becomes available that may be relevant to 
the subject’s consent, or if there is an amendment to the protocol that necessitates a change to 
the content of the subject’s informed consent. The investigator will inform the subject of 
changes in a timely manner and will ask the subject to confirm continuation of his/her 
participation in the study by his/her signature on the revised Informed Consent Form (if 
applicable). Any written Informed Consent Form and written information must receive 
IRB/IEC approval/favorable opinion in advance of use. 
10.2 Subject Informed Consent Form 
ZIOPHARM will provide a sample subject Informed Consent Form for modification, as 
appropriate, by the investigator. 

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11. PROTOCOL APPROVAL PAGE 
A Phase II Randomized, Open-Label Study of Ad-RTS-hIL-12 Monotherapy or 
Combination with Palifosfamide-tris in Subjects with Recurrent/Metastatic Breast 
Cancer and Accessible Lesions  
With the exception of a change intended to eliminate an immediate hazard to subjects, the 
study shall be conducted as described in the approved protocol. All deviations from the 
protocol will be documented in the CRF.  Any significant deviation or deviation related to 
dosing or safety evaluation will be reported to ZIOPHARM and documented in the CRF. 
I agree to the terms of this study protocol.  I will conduct the study according to the 
procedures specified herein, and according to principles of Good Clinical Practice and local 
regulations and requirements. 
 
 
Center Name:   ______________________________ 
 
 
Principal Investigator 
 
Print Name:  ______________________________ 
 
Signature: 
______________________________ 
 
Date:   
______________________________ 
 

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13. APPENDICES  
13.1 Appendix 1:  Eastern Cooperative Oncology Group (ECOG) Performance Status 
ECOG PERFORMANCE STATUS37 
Grade 
Performance Status 
0 
Fully active, able to carry on all pre-disease performance without restriction. 
1 
Restricted in physically strenuous activity but ambulatory and able to carry 
out work of a light or sedentary nature, eg, light house work, office work. 
2 
Ambulatory and capable of all selfcare but unable to carry out any work 
activities. Up and about more than 50% of waking hours. 
3 
Capable of only limited selfcare, confined to bed or chair more than 50% of 
waking hours. 
4 
Completely disabled. Cannot carry on any selfcare. Totally confined to bed 
or chair. 
5 
Dead. 
37 Oken MM, Creech RH, Tormey DC, Horton J, Davis TE, McFadden ET, Carbone PP. Toxicity and Response 
Criteria of the Eastern Cooperative Oncology Group. Am J Clin Oncol 5:649-55, 1982. 
 
  

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13.2 Appendix 2:  CYP450 3A4 Inducers, Inhibitors and Substrates 
Medications, foods and drinks which induce, inhibit or are substrates of the CYP450 3A4 
pathway include but are not limited to the following: 
Alfentanil 
Disopyramide (Norpace) 
Lopinavir (Kaletra) 
Ranolazine (Ranexa) 
Alfuzosin (Uroxatral) 
Donepezil (Aricept) 
Loratadine 
Repaglinide (Prandin) 
Almotriptan (Axert) 
Droperidol 
Lovastatin 
Rifabutin (Rimactane) 
Alprazolam 
Dutasteride (Avodart) 
Maraviroc (Selzentry) 
Rifampin 
Aminoglutethimide 
Ebastine (Kestine) 
Mefloquine (Lariam) 
Rifapentine 
Amlodipine (Norvasc) 
Efavirenz (Sustiva) 
Miconazole 
Ritonavir 
Amprenavir 
Eletriptan (Relpax) 
Midazolam 
Saquinavir 
Aprepitant (Emend) 
Eplerenone (Inspra) 
Mifepristone (Mifeprex) 
Sibutramine (Meridia) 
Astemizole 
Erythromycin 
Modafinil (Provigil) 
Simvastatin 
Atazanavir (Reyataz) 
Estazolam (ProSom) 
Nafcillin  
Sirolimus (Rapamune) 
Atorvastatin (Lipitor) 
Eszopiclone (Lunesta) 
Nefazodone 
Sildenafil 
Bepridil (Vascor) 
Ethosuximide (Zarontin) 
Nelfinavir 
Solifenacin (Vesicare) 
Bexarotene (Targretin) 
Felodipine 
Nevirapine 
St. John's wort 
Bosentan (Tracleer) 
Fentanyl (Sublimaze) 
Nevirapine (Viramune) 
Sufentanil (Sufenta) 
Bromocriptine (Parlodel) 
Finasteride (Proscar) 
Nicardipine (Cardene) 
Tacrolimus 
Budesonide (Entocort) 
Fluconazole 
Nifedipine (Adalat) 
Tadalafil (Cialis) 
Buprenorphine (Subutex) 
Fluoxetine 
Nimodipine (Nimotop) 
Tamsulosin (Flomax) 
Bupropion /(Buspar) 
Flurazepam (Dalmane) 
Nisoldipine (Sular) 
Telithromycin 
Carbamazepine (eg, Tegretol) 
Fluvoxamine 
Nitrendipine (Baypress) 
Teniposide (Vumon) 
Cerivastatin 
Fosamprenavir 
Oxcarbazepine 
Terfenadine 
Cevimeline (Evoxac) 
Fosamprenavir (Lexiva) 
Oxybutynin (Ditropan) 
Testosterone 
Chloramphenicol 
Fosphenytoin 
Oxycodone (Percodan) 
Tiagabine (Gabitril) 
Cilostazol (Pletal) 
Galantamine (Reminyl) 
Paricalcitol (Zemplar) 
Tinidazole (Tindamax) 
Cisapride 
Granisetron (Kytril) 
Phenobarbital 
Tipranavir (Aptivus) 
Clarithromycin 
Grapefruit juice 
Phenytoin 
Topiramate (Topamax) 
Clonazepam (Klonopin) 
Griseofulvin 
Pimozide (Orap) 
Triazolam 
Clopidogrel (Plavix) 
Halofantrine (Halfan) 
Pioglitazone 
Troleandomycin 
Colchicine 
Ifosfamide (Ifex) 
Posaconazole 
Vardenafil (Levitra) 
Conivaptan 
Indinavir 
Praziquantel (Biltricide) 
Verapamil 
Danazol 
Isoniazid 
Primidone 
Voriconazole 
Dapsone (Avlosulfon) 
Isradipine (DynaCirc) 
Propoxyphene 
Zafirlukast 
Darunavir (Prezista) 
Itraconazole 
Quazepam (Doral) 
Ziprasidone (Geodon) 
Dasatinib 
Ixabepilone (Ixempra) 
Quetiapine (Seroquel) 
Zolpidem (Ambien) 
Dasatinib (Sprycel) 
Ketoconazole (Nizoral) 
Quinacrine 
Zonisamide (Zonegran) 
Delavirdine 
Lapatinib (Tykerb) 
Quinidine 
Zopiclone (Imovane) 
Dihydroergotamine 
Levomethadyl (Orlaam) 
Quinine  
Diltiazem 
Loperamide (Imodium) 
Quinupristin 

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13.3 Appendix 3:  Regimen for Antipyretic and/or Analgesic Prophylaxis 
Recombinant adenoviral vectors have the potential to elicit potent cellular and humoral immune 
responses in recipients. While the mechanism responsible for these effects is poorly understood, 
transient low-grade fevers are common after systemic recombinant adenovirus vector administration 
and temperatures up to 104o F with chills and generalized malaise have been observed in first and/or 
subsequent treatment cycles.  
Because low grade fever is very likely to occur prophylaxis with a non-steroidal anti-inflammatory 
agent (ibuprofen) or acetaminophen (if a subject cannot tolerate ibuprofen) is strongly recommended 
starting with Cycle 1.   
 
Ibuprofen is available without a prescription in 200 mg tablets. Usually 800 mg every 6-8 hours 
will prevent and/or decrease fever.  
 
Side effects of ibuprofen include nausea and vomiting, which may be prevented if the 
medication is taken with food. Rare side effects include diarrhea, constipation, heartburn, 
and stomach pain. People with stomach ulcers or kidney disease, and those with an aspirin 
allergy should avoid ibuprofen.  
 
Common brand names of ibuprofen include Advil®, Motrin®, and Nuprin®.  
 
Aspirin should be avoided as it may be toxic in large doses in adults. 
 
While meta-analyses suggest that ibuprofen is a better antipyretic medication than 
acetaminophen, acetaminophen also prevents and or reduces a fever. It is available without a 
prescription in 325 mg or 500 mg tablets. Again, 1000 mg tablets every 6-8 hours should be used 
to eliminate fever. The maximum dose of acetaminophen in adults should not exceed 4 grams in a 
24 hour period. 
 Side effects are rare, but some people are allergic to the medication. Over doses may cause 
liver failure. Therefore, people with liver disease and chronic alcohol users should avoid this 
medication.  
 Common brand names of acetaminophen are Aspirin Free Anacin®, Feverall®, Genapap®, 
Panadol®, Tempra®, and Tylenol®.  
In general, a fever can be treated with the same non-steroidal anti-inflammatory agents (eg, 
ibuprofen) or with acetaminophen. Alternating doses of ibuprofen with acetaminophen will also 
effectively control fever and prevent accidental overdose. If a fever occurs in spite of prophylactic 
medication or does not respond to usual doses of ibuprofen or acetaminophen then a combination of 
both acetaminophen and ibuprofen may be needed to stop the fever.  If a fever does occur after 
administration of the adenoviral vector in any cycle then antipyretic prophylaxis should be used in all 
subsequent dose cycles. 

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13.4 Appendix 4:  Modified RECIST Criteria 
Progression-free survival (PFS) rate and response to treatment will be determined on the 
basis of RECIST v.1.135 as applied to this trial, taking into account response patterns that 
have been observed with immunotherapies.  In studies with a diversity of immunotherapies in 
different cancer types, objective responses have been shown to occur after an initial increase 
in tumor burden characterized as PD by World Health Organization or RECIST criteria.36  
 
The 4 observed patterns of response to immunotherapy in subjects with advanced cancer 
have been: 
1. Immediate response - response in baseline lesions-evident by week 12, with no new 
lesions  
2. Durable stable disease - which in some subjects was followed by a slow, steady 
decline in total tumor burden  
3. Response after initial increase in tumor burden  
4. Response in the presence of new lesions - a reduction in total tumor burden during or 
after the appearance of new lesion(s) at time points later than week 12 
 
To capture these response patterns observed with some immunotherapeutic agents, a 
modification of RECIST v1.1 (mRECIST) will be utilized.  
At Baseline: 
The disease burden at baseline will be categorized into target and non-target lesions.  
A maximum of 5 target lesions (no more than 2 target lesions per organ), representative of all 
involved organs, may be selected.  
Target lesions are lesions that can be accurately measured in at least one dimension and 
whose minimum lesion size is as follows: 
 Non-nodal lesions  ≥ 10 mm or ≥ 2 times the slice thickness/reconstruction interval 
 Nodal target lesions (lymph nodes): the short axis must measure ≥ 15 mm irrespective 
of modality/scanner type and slice thickness/interval 
Lesions that are/will be injected with INXN-2001 and/or biopsied should not be selected as 
target lesions. 
 
At Each Subsequent Assessment: 
Target lesions are measured at every time point and an overall Sum of Diameters (SOD) will 
be determined by adding the longest diameters of all non-nodal lesions and short axes (ie, 
widest dimensions perpendicular to the long axes) of nodal lesions.  

Protocol ATI001-201 
CONFIDENTIAL  
ZIOPHARM Oncology, Inc. 
Ad-RTS-hIL-12 
Amendment 2 17 June 2013 
 
Page 73 of 78 
Target lesions are assessed as Complete Response (CR), Partial Response (PR), Stable 
Disease (SD), Progressive Disease (PD), or Not Evaluable (NE) at every time point based on 
the SOD. 
 
Target Lesion Assessment 
Definition 
Complete Response (CR) 
CR is declared if all of the following are true for target 
lesions: 
 The disappearance of all non-nodal target lesions 
 Any pathological lymph nodes must have a reduction 
in short axis to <10 mm. 
Partial Response (PR) 
PR is declared if there is a decrease of at least 30% in the 
sum of diameters of target lesions taking as reference the 
baseline sum of diameters of target lesions.   
Progressive Disease (PD) 
PD is only declared if all of the following are true for target 
lesions: 
 SOD of all target lesions increases at least 20% taking 
as reference the smallest SOD recorded at or after 
baseline 
 Actual SOD increase is ≥5 mm from the smallest 
SOD recorded at or after baseline 
Stable Disease (SD) 
SD is declared  if target lesion assessment does not meet  
criteria for PR, PD or CR 
 
Selection and Assessment of Non-Target Lesions: 
Non-target lesions are all other lesions, including additional potentially measurable lesions 
and truly non-measurable lesions, such as lesions that are/will be injected with INXN-2001 
and/or biopsied, all bone lesions, ascites, pleural and pericardial effusion, inflammatory 
breast disease, lymphangitic involvement of skin or lung, and brain lesions. Non-target 
lesions will be assessed qualitatively, and the possible assessments are CR, Non-CR/Non-PD 
(NN), and PD.  
If pleural effusions or ascites (selected as non-target lesions at baseline) are stable in size or 
minimally enlarging, they will be assessed as NN. New fluid collections or any effusion that 
significantly worsens will be considered a sign of PD unless cytopathology results are 
available that support a non-malignant nature. 
Non-target lesions should only be assessed as PD if the progression is unequivocal. In the 
setting of a subject who also has measurable disease, there must be an overall level of 
substantial worsening in the context of the overall disease burden. A modest increase in size 
of one or more non-target lesions is not considered sufficient to qualify for unequivocal 
progression status. In the absence of measurable disease, the change in the overall non-
measurable disease burden should be comparable to at least a 20% increase in overall 
diameter or 73% in approximate overall volume. 

Protocol ATI001-201 
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ZIOPHARM Oncology, Inc. 
Ad-RTS-hIL-12 
Amendment 2 17 June 2013 
 
Page 75 of 78 
 
13.5 Appendix 5:  Modification of Diet in Renal Disease (MDRD) Equation for 
Estimating Glomerular Filtration Rate (eGFR) 
The eGFR adjusted for body surface area will be calculated using serum creatinine (SCr) and 
the 4-variable MDRD equation.38 
When using isotope dilution mass spectrometry (IDMS)-traceable serum creatinine: 
 For creatinine in mg/dL: 
 eGFR (mL/min/1.73 m2) = 175 x (SCr)-1.154 x (Age)-0.203 x 0.742 (if female) x 1.212 (if Black)  
 For creatinine in µmol/L: 
 eGFR (mL/min/1.73 m2) = 30,849 x (SCr)-1.154 x (Age)-0.203 x 0.742 (if female) x 1.212 (if Black)  
When using non-IDMS-traceable serum creatinine: 
 For creatinine in mg/dL: 
 eGFR (mL/min/1.73 m2) = 186 x (SCr)-1.154 x (Age)-0.203 x 0.742 (if female) x 1.212 (if Black)  
 For creatinine in µmol/L: 
 eGFR (mL/min/1.73 m2) = 32,788 x (SCr)-1.154 x (Age) -0.203 x 0.742 (if female) x 1.212 (if Black) 
CAUTION REGARDING GFR CALCULATORS 
When using GFR calculators, care must be taken to ensure that the correct 4-variable MDRD 
equation is being applied; some older calculators only use the equation for 
non-IDMS-traceable creatinine values.  The study Medical Monitor MUST be consulted in 
cases where a local serum creatinine and repeat eGFR determination are performed to 
determine study eligibility. 
Example of an acceptable calculator: The National Kidney Foundation (New York, NY) 
provides an internet accessible GFR calculator that accommodates IDMS and 
non-IDMS-traceable creatinine values in either mg/dL or µmol/L.  If using this calculator, 
please select “African American” for all subjects who are Black, regardless of country of 
origin.  The calculator is available on-line at: 
http://www.kidney.org/professionals/kdoqi/gfr_calculator.cfm 

 
 
PROTOCOL AMENDMENT SUMMARY 
 
 
Protocol Title: 
A Phase II Randomized, Open-Label Study of Ad-RTS-
hIL-12 Monotherapy or Combination with 
Palifosfamide-tris in Subjects with Recurrent/Metastatic 
Breast Cancer and Accessible Lesions 
Protocol Number: 
ATI001-201 
Study Drugs: 
INXN-2001 (Ad-RTS-hIL-12) 
INXN-1001 (oral activator ligand)  
Palifosfamide-tris 
Date of Protocol: 
Original protocol:  17 Aug 2012   
Amendment 1:       04 Jan 2013 
 
 
 
NOTE TO INVESTIGATORS 
Amendment 1 dated 04 Jan 2013 will be used to conduct the study in place of any 
preceding version of this protocol.   
 
 
 
 
 
CONFIDENTIAL 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
Confidential 
Page 2 of 22 
 
1. Tabular Summary of Revisions Implemented in the Amended Protocol 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Global changes: 
Editorial 
Numerous editorial changes throughout the protocol; additions/revisions made to the list of 
abbreviations and abbreviations throughout 
Clarity and readability 
Global change: 
Primary efficacy 
endpoint 
Throughout the protocol, the primary efficacy endpoint was changed from progression-free rate at 
week 12 to progression-free rate at week 16.  Tumor response assessments will occur at week 
12, 16 and the Follow-up Tumor Assessment week 24. 
 
Original protocol: 
Primary Objectives: 
Assess the efficacy of repeated cycles of intratumoral injections of INXN-2001 (Ad-RTS-hIL-12) 
with INXN-1001 (oral activator ligand) as monotherapy or in combination with palifosfamide-tris 
as measured by the 12-week progression-free survival (PFS) rate, defined as the proportion of 
subjects who survive progression-free at week 12 in the study population. 
 
Revised text: 
Primary Objectives: 
Assess the efficacy of repeated cycles of intratumoral injections of INXN-2001 (Ad-RTS-hIL-12) 
with INXN-1001 (oral activator ligand) as monotherapy or in combination with palifosfamide-tris 
as measured by the 16-week progression-free survival (PFS) rate, defined as the proportion of 
subjects who survive progression-free at week 16 in the study population. 
Response patterns that 
have been observed with 
immunotherapies in 
different cancer types 
include objective 
responses have been 
shown to occur after an 
initial increase in tumor 
burden characterized by 
RECIST criteria.  Week 16 
will better capture these 
responses. 
Global change: 
Secondary efficacy 
endpoint  
Remove overall survival as a secondary endpoint of the study 
Added:  Assess the PK of INXN-1001 in subjects with recurrent and/or metastatic 
adenocarcinoma of the breast 
Revise the secondary 
objectives of the study. 
Global change: 
Response criteria for 
tumor assessments 
Revised text: 
Throughout the protocol, immune-related response criteria (irRC) has been changed to modified 
RECIST (mRECIST) criteria.  All treatment arms will utilize mRECIST criteria for tumor 
response assessments.  A new Appendix 4 has been included to provide details for the mRECIST 
criteria.  
Deleted text: 
All mentions of immune-related response criteria (irRC) have been deleted. (irRC) 
Modified RECIST 
(mRECIST) criteria are 
appropriate for assessment 
of tumor responses in this 
study. 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 3 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Global change: 
Pharmacokinetic 
assessment added Part 
1 Arm A   
PK assessments were added at the following time points for Arm A Cycles 1 and 2: 
Blood samples for PK analysis of INXN-1001 for Part 1 treatment Arm A CYCLE 1 
ONLY should be obtained on the following days and time points: 
Day 1: [6 samples] Pre-dose (≤30 minutes prior to INXN-1001 dosing), 0.5, 1, 2, 4, 6 
hours post-INXN-1001 dosing 
Day 2: [1 sample] Pre-dose (≤ 30 minutes prior to INXN-1001 dosing) 
Day 7: [3 samples] Pre-dose (≤ 30 minutes prior to INXN-1001 dosing), 1-2 hours, 4-6 
hours post-INXN-1001 dosing 
Day 8: [1 sample] 24 ± 3 hours post-Day 7 INXN-1001 dose 
PK assessment will 
facilitate and 
understanding of drug 
levels and the safety 
profile for the treatment 
with study drug 
Global change: 
Study Design 
 
Arm A Ad-RTS-hIL-
12 Monotherapy has 
2 cohorts 
Added text: 
A dose escalation of INXN-1001 will be evaluated with 3 subjects in each cohort of Arm A 
with safety assessment: 
During Part 1, Arm A will explore the safety of Ad-RTS-hIL-12 monotherapy in 2 cohorts, 
3 subjects each. Arm A will enroll cohort 1 at 140 mg INXN-1001 (n=3), and cohort 2 at 
160 mg INXN-1001 (n=3).  If Ad-RTS-hIL-12 monotherapy is tolerable in 6 subjects 
(cohorts 1 and 2), then 3 additional subjects will be enrolled during Part 2 for efficacy 
analysis. All additional subjects enrolled in Part 2 will be at the 160-mg dose of INXN-1001. 
Futility decisions will be made based on activity observed in subjects receiving INXN-1001 
at the 160-mg dose only.  If at least one of the 6 subjects (3 + 3) survives progression-free at 
week 16, then Arm A will be expanded with 7 additional subjects to be randomly assigned 
to Arm A.  These first 13 subjects (6 + 7) on Arm A will undergo tumor assessment for 
progressive disease (PD) after 16 weeks of treatment.  If ≥3 of these 13 subjects survive 
progression-free at week 16, this stage will be expanded to include 20 additional randomly 
assigned subjects. If ≥9 of these 33 (13 + 20) subjects survive progression-free at week 16, 
then this regimen would be considered worthy of further investigation (ie, a confirmatory 
trial).   
A stepped approach with 
INXN-1001 dosing will 
allow for a run-in safety 
analysis for the study 
treatment  
Global change: 
Safety assessments of 
study treatments 
Added and clarified text: 
The safety of study treatments will be assessed by the frequency and severity of adverse events 
(AEs) as determined by the National Cancer Institute (NCI) Common Terminology Criteria for 
Adverse Events (CTCAE) v4.03 during the Safety Run-in (Part 1) at several stages: 
• After 3 subjects in the 140 mg cohort of Arm A have completed the first cycle 
• After 3 subjects in the 160 mg cohort of Arm A have completed the first cycle 
• After 6 subjects in Arm B have completed the first cycle 
• After 3 subjects in Arm C have completed the first cycle 
Revised timing of safety 
assessment by stage 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 5 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
up information will be collected for all subjects until 1 year following the completion of 
enrollment, whichever is later.   
capture tumor responses 
with immunotherapies 
Section 3 
Protocol Synopsis 
Experimental 
Therapy: INXN-1001 
+ INXN-2001; 
palifosfamide-tris 
Added text: 
• 
INXN-1001:  …Each subject will receive INXN-1001 (cohort 1, 140 mg, n=3; cohort 2 
and all other subjects, 160 mg).  
• 
INXN-2001:  If only a single lesion is present, then repeat administrations into the same 
lesion are permitted, and radiologically-guided techniques may be used as available. 
 
Indicate that Arm A in Part 
1 has 2 cohorts with dose 
escalation 
 
If available, sites may use 
radiologically-guided 
techniques to obtain 
biopsies 
Section 3 
Table 2A, B 
Schedule of 
Assessments 
Added separate Schedule of Assessments for subjects in Arm A cohorts 1 & 2 [contains PK 
sampling schedule] 
Blood samples for PK analysis of INXN-1001 for Part 1 treatment Arm A CYCLE 1 
ONLY should be obtained on the following days and time points: 
Day 1: [6 samples] Pre-dose (≤30 minutes prior to INXN-1001 dosing), 0.5, 1, 2, 4, 6 
hours post-INXN-1001 dosing 
Day 2: [1 sample] Pre-dose (≤ 30 minutes prior to INXN-1001 dosing) 
Day 7: [3 samples] Pre-dose (≤ 30 minutes prior to INXN-1001 dosing), 1-2 hours, 4-6 
hours post-INXN-1001 dosing 
Day 8: [1 sample] 24 ± 3 hours post-Day 7 INXN-1001 dose 
 
Added assessments:   
- Vital Signs (blood pressure assessment): Cycle 1 and Cycle 2, Days 3 and 4 
- Imaging Studies/Tumor Assessment: Cycle 6 Day 7 (week 16) 
- Immune cell evaluation by flow cytometry: screening, Cycle 1 and Cycle 3 Day 7, Post-
Treatment Safety Assessment visit, Follow-Up Tumor Assessment 
- Breast cancer biomarkers: screening, Cycles 1, 3, 6 Days 2, 3, 7, 15, Post-Treatment safety 
Assessment visit 
 
Revised Assessments: 
- PBMC  Cycle 1 and Cycle 3 Day 7 only 
-  ECG at screening, prior to dosing on Day 1 of each cycle, Post-Treatment Safety 
Assessment visit  
- Digital photography Cycle 2 and Cycle 6 Day 7 (Day 21) 
 
Added details for collection 
of PK samples for subjects 
in cohorts 1 & 2, Cycle 1 
only 
 
 
 
 
 
 
 
Additional 
pharmacodynamic marker 
sampling added to further 
explore effects of treatment 
 
 
 
 
 
Modify timing of 
assessments 
 
 
 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 6 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Edited Table Heading: 
Post-Treatment Safety Assessment Visit 28 ± 3 days post-last dose INXN 1001 study drug 
 
 
Clarified language in table 
heading 
Section 3  
Table 2A,B 
Schedule of 
Assessments 
Footnotes 
 
Added text: 
6. Vital signs include blood pressure, pulse, temperature, and respirations.  On Day 1 of each 
cycle, vital signs will be recorded prior to INXN-1001 dosing and hourly for the first two 
hours after INXN-2001 dosing.  Subject’s blood pressure should be monitored closely 
with hydration as needed to prevent hypotension for up to 72 hours after 
administration of INXN-1001.  Blood pressure assessment is required on Day 4 for 
Cycle 1 and Cycle 2. 
13. Standard, single 12-lead ECG at screening, and prior to dosing of INXN-1001 and/or 
INXN-2001 injection and/or palifosfamide infusion on Day 1 of each cycle, and at the 
Post-Treatment Safety Assessment visit.  
16. Appropriate cancer staging procedures should be performed during screening,  For the 
purpose of this clinical trial, the following imaging is expected at screening: 
a. 
CT of the chest, and CT (or MRI) of the abdomen and pelvis 
b. MRI (or CT) of the brain, if brain metastasis are known or suspected  
c. 
CT or MRI of other anatomical regions as clinically indicated 
All imaging should be of diagnostic quality and include IV contrast.  For subjects with 
measurable lesions, target lesions should be selected and measured as per modified 
RECIST 1.1 guidelines.  (see Appendix 4)  Lesions that will be/are injected with INXN-
2001 and/or biopsied should not be selected as target lesions, but should be measured (if 
measureable) assessed qualitatively as non-target lesions.   
Disease sites are to be imaged throughout the study using the same method(s) used at 
screening.  Specific image acquisition guidelines will be provided.  Chest and abdomen 
pelvis imaging is required for all follow-up imaging timepoints; images of the brain and 
other anatomical regions should be acquired on follow-up if positive at screening and as 
clinically indicated.   
Tumor response assessments will occur at 12 and 16 weeks (C4D21 and C6D7) and the 
Follow-up Tumor Assessment visit (24 weeks) for all subjects, including those who may 
have experienced a dose delay.  In the setting of this immunotherapy, a progression 
observed ≥ week 12 requires confirmation at week 16.  Additional tumor response 
 
Include instruction to 
monitor blood pressure 
following INXN-1001 
administration  
 
 
Modify timing of ECG to 
be prior to any study drug 
administration 
 
Remove imaging of pelvis, 
revised response criteria 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 7 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
assessments may occur at the discretion of the Investigator. 
NOTE: In addition to the standard RECIST v1.1 guidelines established to evaluate 
antitumor responses to chemotherapeutic agents, antitumor response will be assessed 
using total tumor burden (TTB), where the sum of the products of the two longest 
diameters (SLD) is used to calculate Total Tumor Burden = SLDindex lesions + 
SLDnew, for measurable lesions. (Appendix 4) 
17. Biopsies (PBx, FNA) will be collected for all subjects according to the table below, and 
were removed for Cycle 6 Day 7 and Follow-up Tumor Assessment. 
 
Activity 
Screening 
Day -28 to -1 
Cycles 1 and 3 ONLY 
Post- 
Treatment 
Safety 
Assessment 
Visit 
Pre- 
Registration 
Post- 
Registration 
Cycle 1 
Day 7±1 
Cycle 3 
Day 7±1 
28±3 days 
post-INXN-
1001 dose 
Biopsy / FNAa 
 
Xa 
Xb 
Xb 
X 
Tumor injected 
with INXN-
2001 
 
 
PBxb 
FNAb 
PBx 
Non-Injected 
Tumor and/or 
Draining 
Lymph Node  
 
PBxa 
PBxb 
FNAb 
PBx 
PBx:  Punch biopsy (≥4 mm in diameter); FNA: fine needle aspiration biopsy 
a At screening, the PBx and FNAs should be obtained only AFTER subject 
registration/randomization has been completed (ie, after approval by sponsor for 
study participation) and before start of treatment.   
b PBx’s and FNAs on Day 7 should be obtained after  the Day 7 administration of INXN-1001 
for subjects in Arms A and C.  Note: NO PBx will be collected on Cycle 1 
 
 
 
 
 
 
 
 
Revise biopsy schedule and 
remove Cycle 6 Day 7and 
Follow-Up Tumor 
Assessment visit biopsy 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Day 7 for subjects in Cohorts 1&2 of Arm A in Part 1 of the study. 
c 
PBx is not required at Follow Up Tumor Assessment visit if ≤30 days since last 
biopsy.  A pathologic, draining lymph node must be defined as a lesion per mRECIST 
(Appendix 4).  If a non-injected distal lesion responds to treatment, then a FNA will be 
obtained to assess the mechanism of the response. 
 
19.  Blood sample for analysis of immune cell levels by flow cytometry should be obtained 
at screening, Cycle 1 Day 7, Cycle 3 Day 7, the Post-Treatment Safety Assessment 
visit, and Follow-up Tumor Assessment visit.  Please refer to the laboratory manual 
for details regarding sample processing and shipment. 
 
20. Blood samples for cytokine profile and breast cancer-associated biomarker levels should 
be obtained at screening, Day 2 [24 hours (± 4 hours) post-INXN-2001], Day 3, Day 7 and 
Day 15 of Cycles 1, 3 and 6 and the Post-Treatment Safety Assessment. Please refer to 
the Laboratory Manual for details regarding sample processing and shipment.   
 
21.  Digital photograph(s) of all visible injected and non-injected tumor(s), and of any visible 
local reactions in or around the injected lesion(s).  Photographs are required at 
screening, Cycle 2 Day 7 or 15, Cycle 4 Day 21, Cycle 6 Day 7, Post-Treatment Safety 
Assessment and Follow-Up Treatment Assessment visits and ad hoc as the investigator 
deems necessary.  Details regarding photographic methodology will be provided in a 
separate manual. 
22. Intratumoral INXN-2001 
 
  
 injection should be given 3 hours ± 30 minutes 
after the INXN-1001 dose.  Lesions displaying signs of localized infection should not be 
injected.  Subjects must be adequately hydrated on each day of study drug 
administration.  Subjects should be instructed to maintain good oral hydration on and 
between dosing days.  Each subject will be carefully monitored for possible local reactions 
at the injection site and/or hypersensitivity reactions, for at least 2 hours following the 
INXN-2001 injection. A detailed description of physical location(s) of the injected tumor(s) 
and surrounding tissue, and any visible local reactions will be documented.  The subject 
should be instructed to call the clinical site if any such reactions develop or don’t resolve 
within 24 to 48 hours.  Please refer to Section 8.2.5 for additional information.  
23. The subject will be dispensed INXN-1001 for self-administration on Days 2 through 7.  
Subjects must be adequately hydrated on each day of study drug administration.  
 
 
 
 
 
 
 
 
 
 
 
 
Add blood sample for flow 
cytometry assay for 
immune cell levels 
 
 
Add breast cancer-
associated biomarker 
assessment 
 
 
Revise scheduling for 
digital photography 
 
 
 
 
Clarify lesions displaying 
signs of localized infection 
are not to be injected. 
 
 
 
 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 9 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Subjects should be instructed to maintain good oral hydration on dosing days.  The 
first INXN-1001 dose will be given at the clinical site in a fed state (30 minutes after the 
start of a normal meal) and at least 4 hours before another meal and then the remaining 6 
doses will be self-administered at the same time every day (±1 hour) in the fed state.  
Subjects should return bottles of INXN-1001 for reconciliations to determine extent of 
subject adherence to self-administration preferably on the Day 7 visit of each cycle.  Please 
refer to Section 8.2.5 for additional information. 
26. Day 1 clinical laboratory assessments may be performed within 2 15 days of the previous 
cycle through Day 1 (prior to dosing) the clinic visit.   
 
 
 
Indicate that adequate 
hydration is required during 
study drug administration. 
Section 4.1  
Disease Background 
Added text: 
The addition of systemic chemotherapy (palifosfamide) to immunotherapy (Ad-RTS-hIL-12) in 
patients who are treated for a recurrence or metastasis of breast cancer may decrease the risk of a 
subsequent local recurrence or distant metastasis.  This combination of therapeutic agents has 
not yet been studied in human subjects, particularly in this disease; therefore, the safety 
profile is not yet clearly defined.  The Phase II study proposed in this protocol (ATI001-201) 
will therefore examine the safety, anti-tumor activity, and immunological effects of intratumoral 
injections of INXN-2001 + orally administered INXN-1001 (Ad-RTS-hIL-12 monotherapy) alone 
and in combination with palifosfamide in subjects with advanced breast cancer. 
Clarify that a primary 
objective of this study is to 
determine the safety of 
these two agents which 
have not previously been 
tested in metastatic breast 
cancer 
Section 4.2.3 
INXN-1001 
(Activator Ligand) 
INXN-1001 is an orally active small molecule diacylhydrazine and is fully active at the RTS
 
receptor. INXN-1001 drug product is formulated (referred to as F 22 formulation) as a semi-
solid containing INXN-1001 as a dry powder and excipients. 
Revise language around 
formulation to simplify 
Section 4.3.1  
IL-12 Immunotherapy 
Added text: 
Interleukin (IL)-12 is a potent immunostimulatory cytokine which activates and recruits dendritic 
cells (DC) that facilitate the cross-priming of tumor antigen-specific T cells.  IL-12 functions as a 
key mediator for the generation of Th1 CD4+ effector T cells, activation of natural killer (NK) 
and CD8+ T cell cytotoxic activities, augmentation of antigen-specific anti-tumor responses, 
and the production of IFN-γ and TNF-α.11-14 IL-12 also has anti angiogenic activity stimulates 
neutrophil and macrophage production of superoxides and nitric oxide, and induces the 
production of anti-angiogenic factors by tumor cells.  IL-12 has been shown to have anti-
tumor activity in several animal models. 
 
It is therefore important to achieve the immunological benefits that IL-12 provides while 
avoiding the toxicity elicited by systemic delivery. IT delivery of Ad-RTS-hIL-12 
Clarify the rationale for IL-
12 immunotherapy 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Page 12 of 22 
 
Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Section 5.1.3 Safety 
Review Committee 
Added text: 
A SRC comprised of the Medical Monitor, Principal Investigators and sponsor representatives 
will hold periodic teleconferences to evaluate the safety and treatment status of all subjects.  The 
SRC will review and assess the safety data after 1 cycle during the initial Ad RTS IL 12 and 
palifosfamide monotherapy arms, and the Ad RTS hIL 12 + palifosfamide combination 
therapy arm as described below and in Section 5.1.5, during the Safety Run-in (Part 1) at 
several stages: 
• 
After 3 subjects in the 140 mg cohort of Arm A have completed the first cycle 
• 
After 3 subjects in the 160 mg cohort of Arm A have completed the first cycle 
• 
After 6 subjects in Arm B have completed the first cycle 
• 
After 3 subjects in Arm C have completed the first cycle 
and at any other time as needed following random assignment in Part 2.  The safety run-in of 
Arm C (n=3) will occur with a 1-week interval between dosing of subjects and an SRC will 
convene after all subjects have received 1 cycle of therapy. 
 
Deleted text: 
Following a treatment arm review, the SRC may recommend proceeding with enrolling additional 
subjects in the current treatment arm or not enrolling any additional subjects.  If a subject has 
experienced a substantial benefit from treatment and the SRC recommends continuation on 
the study, re-exposure to the experimental treatment may proceed at a lower dose of INXN-
1001 or palifosfamide on a case by case basis.  Any subject who experiences a Grade 4 
toxicity related to study treatment will be withdrawn from study. 
 
During Part 1 for Arm C, 
staggered dosing of subjects 
for safety observations 
Section 5.1.4   
Randomization 
Enrollment 
Procedure 
Revised text: 
During Part 1, 3 eligible subjects will enroll initially into Arm A cohort 1, followed by 3 
subjects in Arm B, followed by enrollment of the next 6 subjects in parallel under alternating 
assignment, followed by enrollment 3 subjects in Arm C, as per the following pattern: AAA, 
BBB, ABABAB, CCC 
This pattern may be subject to change based on Sponsor discretion. 
During Part 2, eligible subjects will be centrally randomly assigned using an interactive 
response system established by the Sponsor or its representative: 
Clarify enrollment process 
into treatment arms during 
Part 1 of the study 

Protocol ATI001-201 Amendment 1 
 
04 JANUARY 2013 
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Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
Section 5.1.5 
Treatment Arm 
Expansion Procedure 
Deleted text: 
Three treatment arms are planned for the safety run in part of the study as described in 
Table 2.  Palifosfamide monotherapy Arm B will complete enrollment with 6 subjects in 
Part 1 of the study and will not proceed to Part 2.  
Added text: 
Based on a review of available safety and clinical response data, the SRC may identify a 
single treatment arm (Arm A and/or Arm C) to be expanded to better define the safety, 
tolerability and activity of the study treatment.  Expansion decisions will be made after 
evaluation of tumor response at week 16.  Should a subject discontinue study treatment 
before receiving 6 cycles for reasons other than progression, another subject may be added 
to the treatment arm to provide a total of 3 or 6 subjects for full analysis.  Response 
evaluation and criteria for treatment arm expansion or futility are described in Section 9 
Statistical Methods.   
Deleted text: 
Two separate analyses will be performed: a safety analysis after cycle 1 (all 3 arms) and an 
efficacy analysis after week 12 (any open treatment arms).  Initially, 6 subjects will be 
enrolled into the Ad RTS hIL 12 monotherapy arm.  After the last subject has completed 
the first cycle of treatment, a meeting of the SRC will be convened to review the overall 
occurrence of adverse events and relevant laboratory data in the treatment arm.  Following 
this review, the SRC will advise on subject enrollment.  The same process will be followed 
concurrently for the palifosfamide monotherapy (n=6) followed by Ad RTS hIL 12 + 
palifosfamide combination therapy (n=3) safety run in arms. 
Based on a review of available safety and clinical response data, the SRC may identify a 
single treatment arm (Arm A and/or Arm C) to be expanded to better define the safety, 
tolerabilitcycles for reasons other than toxicity, another subject may be added to the 
treatment arm to provide a total of 3 or 6 subjects for full analysis.  Response evaluation 
and criteria for treatment arm expansion or futility are described in Section 10 Statistical 
Methods. 
 
Clarify treatment arm 
expansion and replacement 
of subjects 

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Section in Amended 
Protocol 
Revised Text/Section 
Rationale for Change 
2001.  
 
Section 7.2.5 
Retreatment Criteria, 
Dose Delays and 
Modifications 
Added text: 
Treatment delays for recovery to acceptable levels are allowed at weekly intervals up to a 
maximum of 3 weeks 14 days. In the event that a treatment-related dose delay is necessary, then 
the next cycle of study treatment will be administered at 80% of the dose (Table 3).  If an AE is 
related to one study drug and not the other (in combination Treatment Arm C) then dose 
modification/delay occurs for both study drugs (palifosfamide and INXN-1001). 
Clarify time for treatment 
delays, and with which 
drugs 
Section 7.2.7 
Prophylactic 
Antipyretic and/or 
Analgesic 
Administration 
Added text: 
Since fever and flu-like symptoms are commonly experienced following adenoviral vector 
administration, it is strongly recommended that subjects be treated with prophylactic antipyretic 
and/or analgesic medications prior to study drug administration and up to Day 4 of each cycle. 
 
Allow for administration of 
antipyretics and/or 
analgesics at appropriate 
times 
Section 7.4.2.5 
Vital Signs 
Added text: 
Vital signs will include blood pressure, pulse, temperature, and respiration.  Subject’s blood 
pressure is to be monitored closely with hydration as needed to prevent hypotension for up 
to 72 hours after administration of INXN-1001.  Blood pressure assessment is required on 
Day 3 and Day 4 for Cycle 1 and Cycle 2. 
Include instruction to 
monitor blood pressure 
following INXN-1001 
administration.  
Section 7.4.2.11 
Electrocardiograms 
(ECGs) 
Revised text: 
A standard, single, 12-lead ECG for local safety assessment will be done performed at screening, 
2½ to 3 hours after INXN 1001 dosing (and prior to palifosfamide infusion and INXN 2001 
injection) prior study drug administration on Day 1 of each cycle, and at the Post-Treatment 
Safety Assessment visit. The ECGs will be used to evaluate the QT/QTc interval. 
 
Clarify that ECGs are to be 
performed prior to study 
drug administration on Day 
1 of each cycle. 
Section 7.4.2.13  
Immune Response 
Analyses 
Deleted text: 
Plasma and/or serum cytokine levels (eg, IL 12, IFN γ, etc.) will be assayed using multiplex 
and/or ELISA methodology.  One or more serum biomarkers (eg,  CEA, CA15 3, CA27.29 or 
other breast cancer specific biomarkers) or cytokines may be assessed in as close to real time 
as possible for one or more time points in a dosing cycle at the request of  the Medical Monitor or 
other sponsor representative(s). 
Delete specific markers to 
be analyzed 
Section 7.4.2.14 
INXN-1001 
Pharmacokinetic 
Assessment 
Added text: 
INXN-1001 PK assessment will occur for subjects enrolled in Part 1 Arm A (Ad-RTS-hIL-
12 monotherapy) during Cycle 1 of study treatment. Whole blood samples will be collected 
on Day 1, Day 2, Day 7, and Day 8 as defined in Table 2A, Schedule of Assessments. 
Specify the sampling for 
PK during Cycle 1 

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Section 7.4.3 
Efficacy Assessments 
Revised and added text: 
Appropriate cancer staging procedures should be performed during screening.  , including chest 
and abdominal CT or MRI scans.  PET scans may be accepted in place of CT or MRI 
scans following consultation and agreement by the ZIOPHARM Medical Monitor  
For the purpose of this clinical trial, the following imaging is expected at screening: 
a. CT of the chest, and CT (or MRI) of the abdomen  
b. MRI (or CT) of the brain if brain metastasis are known or suspected  
c. 
CT or MRI of other anatomical regions as clinically indicated 
For each subject, disease sites are to be assessed throughout the study using the same 
method(s) of assessment used at screening. Chest and abdomen imaging are required for 
all follow-up imaging time points; images of the brain and other anatomical regions should 
be acquired on follow-up if positive at screening and as clinically indicated. 
 
In addition to the standard RECIST v1.1 guidelines established to evaluate anti tumor 
responses to chemotherapeutic agents, the sponsor will be analyzing anti tumor response by 
assessing total tumor burden over time.38 Total tumor burden is allowed to progress up to 
25% from baseline, and new lesions arising do not define progression unless the total 
burden of target and new lesions summed is increased by more than 25%.  Please refer to 
Appendix 4 for a further description of irRC. 
 
All subjects will have tumor assessments performed within 2 weeks prior to the Post
Treatment Safety Assessment visit and again at the Follow up Tumor Assessment visit.  The 
Investigator will evaluate each subject for response to therapy according to mRECIST v1.1 
guidelines.  For this trial, disease progression will require at least one of the following: 
 
• 
a 20% increase,  in addition to an absolute minimum increase of  5 mm in the Sum 
of Diameter of the target lesions,  
• 
an unequivocal progression of the non-target lesions,  
• 
a clinically significant new lesion. 
 
In the setting of this immunotherapy, a progression observed ≤ week 12 requires 
confirmation at week 16. (see Appendix 4 for further details) Subjects without objective 
evidence of disease progression at the Follow-Up Tumor Assessment visit should continue to 
Clarify imaging guidance 
and align with Schedule of 
Assessments 
 
 
 
 
 
 
 
 
 
 
 
 
Redundant with other 
language in this section 

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description of irRC.  
Section 9.4.3  
Other Efficacy 
Endpoints 
Deleted and added text: 
Pharmacodynamic tumor markers may be explored (eg, circulating tumor cells, cytotoxic T 
lymphocytes, other breast cancer-associated biomarkers such as CA15 3, CA27.29, 
carcinoembryonic antigen) in serum or tumor tissue samples.  INXN-1001 PK analysis will be 
performed in Cycle 1 for subjects enrolled in Arm A. during the Safety Run-in (Part 1). 
Delete specific markers to 
be analyzed 
Section 9.6.4.2 
Secondary and Other 
Efficacy Analyses 
Deleted text: 
PFS is defined per subject as the time (in months) from first dosing date to the date of 
progression. Subjects who died without a reported prior progression will be considered to have 
progressed on their date of death. Subjects who did not progress or die will be censored on the 
date of their last tumor assessment. The overall survival is defined as the time (in months) 
from first dosing date until the date of death. For those subjects who did not die, survival 
duration will be censored at the last date the subject was known to be alive. Duration of 
response will be computed from the time measurement criteria were met for PR or CR until the 
date of documented PD or death 1 year. Subjects who neither progressed nor died will be 
censored on the date of last tumor assessment. 
Added text: 
INXN-1001 PK parameters to be determined will include, but are not limited to, the 
maximum concentration (Cmax), time to maximum concentration (Tmax), half-life (t1/2), area-
under-the-concentration time curve (AUC), volume of distribution (Vd), and clearance (CL).  
Where possible, descriptive statistics of the PK parameters will be provided; individual 
subject INXN-1001concentrations, actual sampling times, and PK parameters will be listed. 
Delete overall survival as an 
endpoint 
Section 9.7 
Immunological 
Responses 
Revised text: 
The trial will assess the immunological effects of each treatment cycle on the cellular and 
humoral immune responses in the peripheral circulation and in tumor biopsy specimens.  
Cytokine profiling will be performed by multiplex analysis.  Whole blood will be collected for 
flow cytometry analysis, immune response assay and/or ELISPOT assays to test anti tumor T 
lymphocyte responses against adenovirus and/or the RTS™ components as well as against 
breast cancer-associated antigens.  Samples will also be screened for the relative percentages of 
mononuclear immune cell subpopulations.  At each time point, the change in immunologic 
response (CTL and Treg frequency in blood) from baseline and from the preceding time point 
will be correlated with the INXN-1001 dosage level. 
In addition, tumor punch biopsies or FNAs will be examined for IL 12 cytokine expression, 
Delete specific markers to 
be analyzed, add assay 
methodology 

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presence of injected adenovirus and CTL frequency, Treg and myeloid-derived suppressor cell 
frequency, and other immunological markers.  The change in each measure from baseline and 
from the preceding biopsy will be correlated with the treatment arm. 
 
Section 14.4 
Appendix 4 
Deleted: Appendix 4 Immune Related Response Criteria 
 
Added: Appendix 4 Modified RECIST Criteria: 
  
Progression free survival (PFS) rate and response to treatment will be determined on the 
basis of RECIST 1.139 as applied to this trial, taking into account response patterns that 
have been observed with immunotherapies.  In studies with a diversity of immunotherapies 
in different cancer types, objective responses have been shown to occur after an initial 
increase in tumor burden characterized as progressive disease by World Health 
Organization or RECIST criteria.40  
 
The 4 observed patterns of response to immunotherapy in patients with advanced cancer 
have been: 
1. Immediate response - response in baseline lesions-evident by week 12, with no new 
lesions  
2. Durable stable disease - which in some patients was followed by a slow, steady 
decline in total tumor burden  
3. Response after initial increase in tumor burden  
4. Response in the presence of new lesions - a reduction in total tumor burden during 
or after the appearance of new lesion(s) at time points later than week 12 
 
To capture these response patterns observed with some immunotherapeutic agents, a 
modification of RECIST v1.1 will be utilized.  
At Baseline: 
The disease burden at baseline will be categorized into target and non-target lesions.  
A maximum of 2 target lesions per organ and 5 target lesions in total, representative of all 
involved organs, may be selected.  
Target lesions are lesions that can be accurately measured in at least one dimension and 
whose minimum lesion size is as follows: 
 
Response patterns that 
have been observed with 
immunotherapies in 
different cancer types 
include objective 
responses have been 
shown to occur after an 
initial increase in tumor 
burden. This study will 
capture these responses 
using modified RECIST 
criteria, which are 
described in detail in this 
new Appendix. 

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• 
Non-nodal lesions  ≥ 10 mm or ≥ 2 times the slice thickness/reconstruction interval 
• 
Nodal target lesions (lymph nodes): the short axis must measure ≥ 15 mm 
irrespective of modality/scanner type and slice thickness/interval 
 
Lesions that are/will be injected with INXN-2001 and/or biopsied should not be selected as 
target lesions. 
 
At each subsequent Assessment: 
Target lesions are measured at every timepoint and a single Sum of Diameters (SOD) will be 
determined by adding the longest diameters of all non-nodal lesions and short axes (ie, 
widest dimensions perpendicular to the long axes) of nodal lesions. Target lesions are 
assessed as Complete Response (CR), Partial Response (PR), Stable Disease (SD), 
Progressive Disease (PD) or Not Evaluable (NE) at every time point based on the SOD. 
 
Target Lesion Assessment 
Definition 
Complete Response (CR) 
CR is declared if all of the following are true for target 
lesions: 
• 
The disappearance of all non-nodal target lesions 
• 
Any pathological lymph nodes must have a 
reduction in short axis to < 10 mm. 
Partial Response (PR) 
PR is declared if there is a decrease of at least 30% in the 
sum of diameters of target lesions taking as reference the 
baseline sum of diameters of target lesions.   
Progressive Disease (PD) 
PD is only declared if all of the following are true for 
target lesions: 
• 
SOD of all target lesions increases at least 20% taking 
as reference the smallest SOD recorded at or after 
baseline 
• 
Actual SOD increase is ≥ 5 mm from the smallest 
SOD recorded at or after baseline 
Stable Disease (SD) 
SD is declared  if target lesion assessment does not meet  
criteria for PR, PD or CR 

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Selection and Assessment of Non-Target Lesions 
 
Non-target lesions are all other lesions, including additional potentially measurable lesions 
and truly non-measurable lesions such as lesions that are/will be injected with INXN-2001 
and/or biopsied, all bone lesions, ascites, pleural and pericardial effusion, inflammatory 
breast disease, lymphangitic involvement of skin or lung, and brain lesions. Non-target 
lesions will be assessed qualitatively, and the possible assessments are CR, Non-CR/Non-PD 
(NN), and PD.  
 
Non-target lesions should only be assessed PD if the progression is unequivocal. In the 
setting of a patient who also has measurable disease, there must be an overall level of 
substantial worsening in the context of the overall disease burden. A modest increase in size 
of one or more non-target lesions is not considered sufficient to qualify for unequivocal 
progression status. In the absence of measurable disease the change in the overall non-
measurable disease burden should be comparable to at least a 20% increase in overall 
diameter or 73% in approximate overall volume. 
 
New Lesions 
The determination of new lesions should be unequivocal and not be attributable to 
differences in the scanning technique, change in modality or findings thought to represent 
something other than tumor. This is particularly important when the patient’s baseline 
lesions show partial or complete response.  
New lesions should be reported as equivocal or unequivocal when first noted. New lesions 
observed at week 12 should not be considered unequivocally progression; however, they 
should be re-assessed at subsequent time points. Lesions that were noted as equivocal 
should be re-assessed as Equivocal, Unequivocal, NN, PD, or Benign on subsequent 
timepoints; Lesions that were unequivocal should be re-assessed as Unequivocal, Absent or 
NE. 
  
As initial flare ups have been reported in the context of immunotherapy, new lesions should 
only be taken as a sign of progression if they are: 
 
• 
Unequivocally present, and  

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• 
Defined as clinically significant. 
 
Clinical significance should relate to the size and location of the new lesion, such as new 
brain involvement, significant vascular invasion or compression. 
 
Any lesion that does not meet the above criteria should be considered an equivocal new 
lesion that does not justify in isolation an overall assessment of progression at that time 
point. Such equivocal new lesions should be re-evaluated at the next time point. 
 

 
PROTOCOL AMENDMENT SUMMARY 
 
 
Protocol Title: 
A Phase II Randomized, Open-Label Study of Ad-RTS-
hIL-12 Monotherapy or Combination with Palifosfamide 
in Subjects with Recurrent/Metastatic Breast Cancer and 
Accessible Lesions 
Protocol Number: 
ATI001-201 
Study Drugs: 
INXN-2001 (Ad-RTS-hIL-12) 
INXN-1001 (oral activator ligand)  
Palifosfamide 
Date of Protocol: 
Amendment 2:       17 June 2013 
Amendment 1:       04 Jan 2013 
Original protocol:  17 Aug 2012   
 
 
 
NOTE TO INVESTIGATORS 
Amendment 2 dated 17 June 2013 will be used to conduct the study in place of any 
preceding version of this protocol.   
 
 
 
 
 
 
 
CONFIDENTIAL 

Protocol ATI001-201 Amendment 2 
 
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Page 2 of 20 
Tabular Summary of Revisions Implemented in the Amended Protocol 
Section in Amended 
Protocol 
Revised or Deleted Text/Section 
Rationale for Change 
Title Page, Page 
Headings and Footers 
Amendment 2:  17 June 2013 
Updated Protocol 
Amendment 
Abbreviations and 
Definitions of Terms 
Several new abbreviations were included: eg, MCV, RXR.   
Clarify abbreviations 
Global 
• Study Design changes include: 
o 
Arm A Cohorts 1 and 2 have been removed in Part 1; design for this 
Amendment is a single Arm A  Ad-RTS-hIL-12 monotherapy in  6 
subjects in Part 1 at 140 mg oral INXN-1001 administered daily x 7 days 
+ a single intratumoral injection of INXN-2001 
 with a 21-
day cycle. 
o 
Arm B (Palifosfamide monotherapy) has been removed from the study: 
Arm B of this study, palifosfamide as a monotherapy, was initially 
included to enhance the safety run in portion of the study and first time 
use in this therapeutic indication.  In early 2013, ZIOPHARM completed 
(under IND 61792) a study entitled, “A Phase I Multicenter, Open-label 
Study to Assess the Drug Metabolism and Pharmacokinetics (DMPK) of 
Palifosfamide-tris and Bioequivalence of Aseptically-processed and 
Terminally-sterilized Drug Product in Subjects with Advanced 
Malignancies”.  As part of this study, 3 subjects with advanced breast 
cancer were enrolled and received 150 mg/m2 palifosfamide.  There were 
no serious adverse events experienced by these subjects which 
demonstrate that palifosfamide as a monotherapy in breast cancer subjects 
appears to be safe. It should also be noted that the dose of palifosfamide 
to be used in this combination study is lower (120 mg/m2).  As a result, 
Arm B of this study has been removed. 
Clarity and accuracy, 
correct redundancy 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Inclusion Criteria 
Section 3  
Protocol Synopsis 
Exclusion Criteria 
 
Section 6.2  
Exclusion Criteria 
3. Prior therapies discontinuation periods: 
a) Radiation within 3 weeks of enrollment  
b) Chemotherapy within 4 weeks of enrollment 
c) Nitrosoureas within 6 weeks of enrollment 
d) Biologic therapy and/or immunomodulatory therapy (eg, granulocyte 
colony stimulating factor [GCSF]/granulocyte macrophage colony 
stimulating factor [GM-CSF], interferons or interleukins, growth 
hormone, intravenous immunoglobulin [IVIG], retinoic acid), checkpoint 
inhibitors (eg, ipilimumab, anti-PD-1 or anti-PDL-1 antibodies) within 6 
weeks of enrollment  
e)  
4. No washout period is required for endocrine therapy  
7. Immunosuppressive therapy: 
a) Systemic immunosuppressive drugs including corticosteroids 
(prednisone equivalent >10 mg/day, 
http://www.medcalc.com/steroid.html) within 6 weeks 
b) Immune suppression/requiring immunosuppressive drugs, including 
subjects with organ allografts 
10.     
 
Updated criteria to reflect 
currently available 
checkpoint inhibitors, prior 
therapy washout periods 
Section 3 
Protocol Synopsis 
Experimental Therapy 
Dose and Schedule 
Revised text: 
INXN-1001 will be supplied by the Sponsor as a capsule for oral administration.  
INXN-2001 will be supplied by the Sponsor as a sterile suspension for injection.  
Palifosfamide will be supplied by the Sponsor as a powder in single-use glass 
vials. 
 
 
Update language to reflect 
study design and  simplify 
the language regarding the 
fed state for study subjects 
 

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Section in Amended 
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Rationale for Change 
Dose & Schedule (21-day cycle):  
• 
INXN-1001:  Subjects will be directed to take the INXN-1001 oral dose in a 
fed state (within approximately 30 minutes following a normal meal), once 
daily at the same time each day (±1 hour), beginning on Day 1 of each cycle.  
Each subject will receive INXN-1001 (140 mg daily for 7 days).  
• 
INXN-2001:  INXN-2001 
 
 
 IT injection 
administered 3 hours (± 30 minutes) after INXN-1001 dosing on Day 1 of 
each cycle.  If >1 injectable lesion is present, INXN-2001 will be injected into 
a different lesion at each cycle, and if the number of lesions is limited, the 
injections will be administered in sequential rotation or at investigator’s 
discretion. If only a single lesion is present, then repeat administrations into 
the same lesion are permitted, and radiologically-guided techniques may be 
used as available. 
Palifosfamide:  Palifosfamide (120 mg/m2/day) will be administered by 
intravenous (IV) infusion over approximately 30 minutes on Days 1-3 of each 
cycle. 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Revise dose of 
palifosfamide 
Section 3 
Protocol Synopsis 
Pharmacodynamic 
Evaluations 
Revised  text: 
Biological markers of response will be assessed and will include examinations of 
cytokine and breast cancer-associated biomarker (eg, MUC-1) levels.  For certain 
participating sites, additional immunological analyses will be performed.  Please 
refer to Appendix 6. 
 
Modified to simplify the 
protocol to reflect all 
subjects will have biologic 
markers of response 
(cytokines, breast ca 
biomarker) assessed   
 
Additional immunological 
analyses will be performed 
at participating sites and are 
described in a new 
Appendix 6 
Section 3 
Protocol Synopsis 
Pharmacokinetics 
Revised text: 
INXN-1001 PK will be assessed for subjects in in Part 1 Cycle 1 only. 
Clarify PK assessments will 
be in Part 1 Cycle 1 only  
Section 3  
Table 2A, B 
Updates were made to both of the Schedule of Assessments Tables: 
 
 
 

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Section in Amended 
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Rationale for Change 
thromboplastin time) and INR (international normalized ratio) will also 
be evaluated. 
14.  
15. Appropriate cancer staging procedures should be performed during 
screening.  For the purpose of this clinical trial, the following imaging is 
expected at screening: 
a. 
CT of the chest, and CT (or MRI) of the abdomen  
b. MRI (or CT) of the brain, if brain metastasis are known or suspected  
c. 
CT or MRI of other anatomical regions as clinically indicated 
All imaging should be of diagnostic quality and include IV contrast. PET 
imaging is an acceptable alternative modality provided the CT component is 
of diagnostic quality as per RECIST 1.1 guidelines.  
For subjects with measurable lesions, target lesions should be selected and 
measured as per mRECIST v1.1 guidelines. (Appendix 4)  Lesions that will 
be/are injected with INXN-2001 and/or biopsied should not be selected as 
target lesions, but should be assessed qualitatively as non-target lesions.   
Disease sites are to be imaged throughout the study using the same method(s) 
used at screening.  Chest and abdomen imaging are required for all follow-up 
imaging time points; images of the brain and other anatomical regions should 
be acquired on follow-up if positive at screening and as clinically indicated.   
Tumor response assessments will occur at 12 weeks and 16 weeks (C5D1 
and C6D7), and the Follow-up Tumor Assessment visit (24 weeks) for all 
subjects, including those who may have experienced a dose delay. In the 
setting of this immunotherapy, a progression observed at week 12 requires 
confirmation at week 16.   Additional tumor response assessments may occur 
at the discretion of the investigator. 
16. A sample(s) for cytokine profiling, breast cancer-associated biomarker levels 
(eg, MUC-1), and also INXN-1001 levels. Please refer to the Laboratory 
Manual for details regarding sample processing and shipment.   

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the last dose of study drug or prior to receiving another anticancer therapy. 
23. A Follow-Up Tumor Assessment visit will be performed 35 ± 7 days after 
the Post-Treatment Safety Assessment visit.   
24. Interim cancer history information will include documentation of any new 
concomitant medications and any anti-cancer treatments received since the 
Post-Treatment Safety Assessment visit or previous tumor assessment 
Section 4.3.2 
Palifosfamide 
Revised text: 
Palifosfamide is currently being investigated in a Phase III clinical trial.  The 
MATISSE trial is evaluating palifosfamide (130 mg/m2 × 3 q21 days) in 
combination with carboplatin and etoposide as a treatment for subjects with 
extensive-stage small cell lung cancer. 
Updated with recent trial 
experience for 
palifosfamide 
Section 4.3.3  
Nonclinical Efficacy 
Studies 
Nonclinical studies are described in the Investigator’s Brochure and were deleted. 
Simplify the protocol 
Section 4.4 Summary 
of Prior Clinical 
Experience and 
Safety 
Section 4.4.1  This section was updated per the most recent Investigator’s 
Brochure with clinical safety experience in 15 subjects in the ATI001-101 trial in 
subjects with metastatic melanoma. 
Section 4.4.4  In addition, the palifosfamide safety experience was updated 
following the blinding safety data cut for the Phase III trial in soft-tissue sarcoma 
with n=437 subjects. 
Updated with recent trial 
experience/results for 
palifosfamide 
Section 4.5 Rationale 
for Study Design and 
Dose Selection 
The objectives of this Phase II clinical trial are to assess the safety and tolerability, 
PFS rate at 16 weeks, ORR, and immunological and biological effects of IT 
injections of INXN-2001 + INXN-1001 as monotherapy or in combination with 
palifosfamide.  To provide an opportunity to monitor the safety of Ad-RTS-hIL-12 
monotherapy and Ad-RTS-hIL-12 + palifosfamide (combination therapy) in 
subjects with breast cancer, a safety run-in will occur, with evaluation following 
one cycle of study drug.  
The study will commence with Ad-RTS-hIL-12 monotherapy using a 140-mg dose 
of INXN-1001 administered daily Days 1-7 in 6 subjects (21-day cycle).  
Following a safety assessment, combination therapy of Ad-RTS-hIL-12 + 
palifosfamide (120 mg/m2, Days 1, 2, 3 of a 21-day cycle, n=3) will commence.  
Safety in Part 1 of the study will determine commencement of randomization for 
Clarify Study Design as 2 
Arms, 2 Parts 
 
Reduce redundant text 

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Revised or Deleted Text/Section 
Rationale for Change 
Part 2.   
Section 6.1 
Study Objectives 
Revised text: 
• 
Evaluate pharmacodynamic tumor markers  (eg, breast cancer-associated 
biomarkers such as MUC-1)  
Align with current study 
objectives, cytokines and 
breast cancer biomarkers 
will be assessed for all 
subjects 
Section 5.1.1.1 
Overall Study Design 
Deleted text: 
 
Deleted to improve clarity 
Section 5.1.2 
Treatment Parameters 
and Duration 
Revised text: 
 
Subjects will receive IT injections of INXN-2001 
 per 
injection) on Day 1 of each cycle, will also receive oral doses of INXN-1001 (140 
mg daily) for 7 days.  Subjects enrolled in Arm C combination therapy will also 
receive palifosfamide (120 mg/m2/day) by IV infusion over approximately 
30 minutes on Days 1, 2, 3 of each cycle.   
Update study design and 
revise descriptions of the 
study Phases; revise dosing 
regimen 
Section 5.1.3 Safety 
Review Committee 
(SRC) 
Revised text: 
 
An SRC comprised of the Medical Monitor, enrolling PIs, and Sponsor 
representatives will hold periodic teleconferences to evaluate the safety and 
treatment status of all subjects available during the Safety Run-in (Part 1) at 
several stages: 
• 
after 6 subjects Arm A have completed the first cycle, 
• 
after 3 subjects in Arm C have completed the first cycle, 
• 
at any other time as needed following random assignment in Part 2.   
The safety run-in of Arm C (n=3) will occur with a 1-week interval between 
dosing of subjects and an SRC will convene after all subjects have received 1 cycle 
of therapy.  The SRC has the authority to recommend dose or regimen 
modifications for safety concerns. 
A written summary documenting the results and recommendations of each review 
will be provided to the investigator(s) and maintained on file with the Sponsor.  
Simplify language and 
clarify the role of the SRC  

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Protocol 
Revised or Deleted Text/Section 
Rationale for Change 
Additional sub-investigators and personnel may participate in reviews, as 
appropriate.   
Following a treatment arm review, the SRC may recommend proceeding with 
enrolling additional subjects in the current treatment arm or not enrolling any 
additional subjects.   
While the SRC is expected to reach a consensus opinion regarding any premature 
discontinuation or significant modification of the study, the Sponsor may 
independently stop the study at any time. 
Section 5.1.4 
Enrollment 
Procedure 
Revised Text: 
During Part 1, 6 eligible subjects will enroll into Arm A, followed by 3 subjects in 
Arm C. 
During Part 2, eligible subjects will be randomly assigned by the Sponsor or its 
representative:   
Subjects will be adaptively randomized in a 1:1 ratio to receive Ad-RTS-hIL-12 
monotherapy (Arm A) or combination therapy (Arm C) according to the current 
status of the treatment arms and whether or not a subject has consented to the 
“Additional Immunologic Assessments” until the desired number of subjects is 
fully enrolled in each study arm. 
Clarify enrollment 
procedure for updated study 
design 
Section 5.1.5  
Treatment Arm 
Expansion Procedure 
Revised text: 
Should a subject discontinue study treatment before receiving 6 cycles for reasons 
other than progression, another subject may be added to the treatment arm to allow 
for full analysis.  Response evaluation and criteria for futility are described in 
Section 9 Statistical Methods.   
Subject enrollment and expansion of treatment Arms A and C will proceed 
according to a standard Simon 2-stage design (Table 1).  An alternate dose level of 
palifosfamide and/or INXN-1001 may be explored after review of all available 
safety and activity data, and will be communicated by an administrative letter and 
enacted upon issuance.   
Clarify treatment arm 
expansion procedure for 
updated study design 
Section 7.2.3 
Treatment Regimen 
Revised text: 
A combination of up to 3 investigational medications will be evaluated for safety, 
tolerability, efficacy, and biological effects in this trial. The small molecule INXN-
1001 will be administered as oral capsules (once daily doses on Days 1-7) in 
Update treatment regimen  
 
Clarify importance of  and 
recommendation for 

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combination with an IT injection of INXN-2001 (on Day 1 of each cycle). For 
each 21-day treatment cycle, INXN-2001 dosing will occur 3 hours ± 30 minutes 
after the first dose of INXN-1001.  INXN-2001 will be given as IT injections 
 
 
 
 in 1 mL per treatment.  Following Cycle 1, if no 
accessible lesion for INXN-2001 injection is present (eg, due to complete 
resolution), then INXN-2001 should be injected into an alternate lesion or a 
draining, pathologic lymph node of a previously accessible lesion.  A pathologic 
lymph node must be defined as a lesion per mRECIST (Appendix 4).  The 
injections will be administered on the first day of each cycle throughout the study. 
Subjects must be adequately hydrated on each day of study drug administration.  
Subjects must be instructed to maintain good oral hydration on and between dosing 
days.  Oral hydration (approximately 2000 mL oral electrolyte solution per 24 
hours) and administration of prophylactic antipyretics is highly recommended for 
72 hours following injection of INXN-2001 because most toxicity (including 
intense fevers, chills, fatigue and dehydration) has been observed during this time 
period.  Blood pressure should be monitored regularly. For treatment Arm C 
Combination Therapy (Ad-RTS-hIL-12 + palifosfamide), palifosfamide will be 
administered following administration of INXN-1001 as a 30-minute IV infusion, 
and on Day 1 of each cycle the infusion should complete before injection with 
INXN-2001.   
Palifosfamide will be administered intravenously at a dose of 120 mg/m2/day as a 
30-minute infusion on Days 1, 2, and 3 of a 21-day cycle for up to 6 cycles.  
The temporal sequence of the treatment regimens for study Arms A and C are 
shown in Figure 4.  For subjects enrolled in Arm C Ad-RTS-hIL-12 + 
Palifosfamide Combination Therapy, the sequence of regimens A + palifosfamide 
will be followed concurrently as shown below. 
 
Figure 4 was revised to display Arms A and C instead of Arms A and B.  Arm B 
has been deleted from the study. 
hydration 
Section 7.2.4.1 
Preparation and 
Administration of 
INXN-1001 
Revised text: 
INXN-1001 capsules will be dispensed for subject oral dosing by the site 
pharmacy. The site must instruct the subject to take each dose in a fed state (within 
approximately 30 minutes after the start of a normal meal).  
Clarify definition of  the fed 
state 

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Section 7.2.4.2 
Monitoring of Subject 
Adherence 
Added text: 
Subjects are to be instructed to take all of the capsules in the same way for each of 
the remaining treatment period, and will be reminded to take their dose via a phone 
call when they will not have a clinic visit.  
Emphasize the importance 
of adherence 
Section 7.2.4.3 
Preparation and 
Administration of 
INXN-2001 
Added text: 
NOTE:  
• 
All subjects receiving INXN-2001 must be adequately hydrated with 
approximately 2000 mL per 24 hours of oral electrolyte solution for 72 
hours during Cycles 1 and 2.  Subjects must be instructed to maintain 
good oral hydration on and between dosing days.  
Clarify/revise inclusion 
criteria 
Section 7.2.4.4 
Preparation and 
Administration of 
Palifosfamide 
Added text: 
Note: Total cumulative time from reconstitution in vial through completed 
dose administration should not exceed 2.5 hours (150 minutes). 
Add clarity and detail 
regarding reconstitution of 
palifosfamide 
Section 7.2.5  
Retreatment Criteria, 
Dose Delays and 
Modifications 
Added text: 
Clinical laboratory tests drawn pre-treatment for analysis on Day 1 of each cycle 
may be used for determining if the re-treatment criteria have been met, and must 
be reviewed by the investigator or designee prior to the next cycle of study drug 
administration.  Two treatment delays for recovery to acceptable levels are allowed 
at weekly intervals up to a maximum of 14 days. In the event that a treatment-
related dose delay is necessary for palifosfamide, then the next cycle of study 
treatment will be administered at 80% of the dose (Table 3).  If an AE is clearly 
related to 1 study drug and not the other (in combination Treatment Arm C), then 
dose modification/delay is to occur for the relevant study drug (INXN-1001 and/or 
palifosfamide).  A maximum of two dose reductions, of either INXN-1001 or 
palifosfamide, will be allowed. 
 
Deleted text: 
 
Clarify dose delays and 
modifications which may 
occur for either INXN-1001 
or palifosfamide 
Section 7.2.6  
Severity Grading and 
Management of 
Injection Site 
Added text: 
Table 3. Injection Site Reaction Severity Grading and Management 
Update language for 
clarification 

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Reactions 
CTCA
E 
Grade 
Symptoms 
Course of Action 
1 
Tenderness with or 
without associated 
symptoms (eg, warmth, 
erythema, itching) 
No intervention required. 
2 
Pain; lipodystrophy; 
edema; phlebitis 
Proceed with further dosing cycles.   
 
3 
Ulceration or necrosis; 
severe tissue damage; 
operative intervention 
indicated 
Discontinue further study treatment and 
notify Medical Monitor.  
If  toxicity meets seriousness criteria, 
immediately report as per SAE reporting 
procedures; see Section 8.4. 
4 
Life-threatening 
consequences; urgent 
intervention indicated 
Permanently discontinue study treatment 
and notify Medical Monitor.   
Defaults to “serious”.  Immediately 
report as per SAE reporting procedures; 
see Section 8.4.  
5 
Death 
Immediately notify Medical Monitor and 
report as per SAE reporting procedures; 
see Section 8.4. 
Discontinue further subject enrollment. 
Section 7.2.7 
Prophylactic, 
Antipyretic and/or 
Analgesic 
Administration 
NOTE:  Since fever and flu-like symptoms (eg, fever, headache, chills, 
dehydration, etc.) are commonly experienced following adenoviral vector 
administration, it is highly recommended that subjects be treated with 
prophylactic, antipyretic and/or analgesic medications prior to study drug 
administration for the first 72hr of each cycle. 
 
Clarify symptoms that may 
necessitate prophylactic 
antipyretics and/or 
analgesics and the timing of 
these 
 

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Analysis 
Plasma and/or serum cytokine levels will be assayed using enzyme-linked 
immunosorbant assay (ELISA) methodology.  One or more serum biomarkers (eg, 
MUC-1) or cytokines will be assessed. 
Section 7.4.2.13 
INXN-1001 
Pharmacokinetic 
Assessment 
Revised text: 
INXN-1001 PK assessment will occur for subjects enrolled in Part 1 during Cycle 
1 of study treatment. Whole blood samples will be collected on Day 1, Day 2, Day 
7, and Day 8; as defined in Table 2A, Schedule of Assessments.  INXN-1001 
levels will also be assessed using the samples drawn for cytokine analysis. 
Align PK with new dosing 
regimen 
Section 8.4.4 
Efficacy Assessments 
Deleted text: 
The investigator will evaluate each subject for response to therapy according to 
mRECIST v1.1 guidelines (see Appendix 4). 
• 
 
Added text: 
Subjects without objective evidence of disease progression at the Follow-Up 
Tumor Assessment visit should continue to have tumor assessments performed at 
8-10 week intervals until disease progression has been documented, or an alternate 
anticancer therapy has been initiated, or up to 1 year, whichever occurs first.   
 
Align efficacy assessments 
with revised study design 
Section 8.2.3 
Causality Assessments 
Deleted text: 
The Investigator will use medical consideration to determine the potential 
relationship of the AE to the study drugs based on his/her clinical judgment.  For 
SAEs, the Sponsor will provide a separate assessment of causality.  The 
Investigator’s assessment and/or the Sponsor’s assessment will be considered for 
expedited reporting of SAEs per relevant regulatory requirements.   
Revise safety language for 
clarity 
Section 8.4  
Reporting Serious 
Adverse Events 
Revised text: 
 
SAEs must be reported to the Sponsor or Sponsor’s designee immediately within 
Revise safety language for 
clarity 

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24 hours of becoming aware of the event (regardless of the initiation of any new 
anti-cancer therapy) including the following: 
• 
Any death or SAE experienced by the patient from the signing of 
informed consent to 30 days after the last dose of study drug, regardless 
of relationship to study drug. 
• 
Any death or SAE that the Investigator becomes aware of, and believes to 
be study drug related, that occurs more than 30 days after the patient last 
received study drug. 
 
Study drug-related AEs/SAEs that are ongoing at the time of the Post-Treatment 
Safety Assessment visit should continue to be followed until resolution, return to 
baseline, or until they have stabilized or become chronic (and following 
consultation and agreement by the ZIOPHARM Medical Monitor). 
 
In addition to the above information, the Investigator must provide, for each event 
term, an assessment of the following: 
• 
Severity of the SAE/intensity 
• 
Relationship to the study drug (causality assessment) 
Section 9.1 
Determination of 
Sample Size 
Added text: 
In view of up to 3 novel investigational drugs being tested in this study, the 
sponsor has incorporated a Safety Run-in (Part 1) to evaluate safety for each study 
arm before fully enrolling all subjects required in Stage 1 of Part 2 for each study 
arm (for details please see Section 5.1.1).   
Update text 
Section 9.4.2   
Secondary Efficacy 
Endpoints 
Revised text: 
Duration of response:  time from the date of first objective response (PR or CR) by 
mRECIST v1.1, until the date of PD or 1 year. 
Clarify the duration of 
response timeframe 
Section 9.4.3 
Other Efficacy 
Endpoints 
Revised text: 
Cytokine and breast cancer biomarker (eg, MUC-1) levels will be explored in 
serum samples.  For study sites participating in additional immunologic 
assessments, please refer to Appendix 6.  INXN-1001 PK analysis will be 
Simplify and clarify 
immunologic analyses 

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performed in Cycle 1 for all subjects enrolled the Safety Run-in (Part 1).   
Section 9.6.4.2 
Secondary and Other 
Efficacy Analyses 
Deleted text: 
 
Simplify and clarify 
immunologic analyses 
Section 9.7  
Immunologic 
Responses 
Added text: 
The trial will assess the cytokine profiles and breast cancer-associated biomarkers 
(eg, MUC-1) for all subjects.   
In addition, participating sites will include additional immunologic assessments as 
described in Appendix 6.  The immunological effects of each treatment cycle on 
the cellular and humoral immune responses in the peripheral circulation and in 
tumor biopsy specimens.  Cytokine profiling will be performed by ELISA.  Whole 
blood will be collected for flow cytometry analysis, immune response assay, 
and/or ELISPOT assays for measurement of the response to breast cancer-
associated antigens.   
Simplify and clarify 
immunologic analyses 
Section 10.4 
Duration of the Study 
Deleted text: 
The duration of this study from the time of initiating subject enrollment until the 
completion of survival follow-up is anticipated to be approximately 34 months, 
including 24 months for enrollment and the later of 1 year of further follow-up. 
Revised text: 
f) 
Follow-Up Tumor Assessment visit performed 35 ± 7 days after the Post-
Treatment Safety Assessment visit. 
Clarify duration and update 
to align with dosing 
regimen and cycle length 
Section 13  
References 
Deleted references: 
25.  26.  27.  28.   
References deleted from 
deleted Nonclinical studies 
which are contained in the 
Investigator’s Brochure 

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Section 14.3 
Appendix 3 
Added/revised text: 
 
Because low grade fever is very likely to occur, prophylaxis with a non-steroidal 
anti-inflammatory agent (ibuprofen) or acetaminophen (if a subject cannot tolerate 
ibuprofen) is strongly recommended starting with Cycle 1.   
• 
Ibuprofen is available without a prescription in 200 mg tablets. Usually 1 2 
tablets 800 mg every 4-6-8 hours will prevent and/or decrease fever. The 
lowest expected efficacious dose should be used.  
• 
Side effects of ibuprofen include nausea and vomiting, which may be 
prevented if the medication is taken with food. Rare side effects include 
diarrhea, constipation, heartburn, and stomach pain. People with 
stomach ulcers or kidney disease, and those with an aspirin allergy 
should avoid ibuprofen.  
• 
Common brand names of ibuprofen include Advil®, Motrin®, and 
Nuprin®.  
• 
Aspirin should be avoided as it may be toxic in large doses in adults. 
• 
While meta-analyses suggest that ibuprofen is a better anti-pyretic medication 
than acetaminophen, acetaminophen also prevents and or reduces a fever. It is 
available without a prescription in 325 mg or 500 mg tablets. Again, 1 2 
tablets 1000 mg every 4 6-8 hours should be used to eliminate fever. The 
maximum dose of acetaminophen in adults should not exceed 4 grams in a 24 
hour period. 
Deleted Text: 
If you choose not to institute prophylactic anti pyretic therapy on Cycle1, Day 1 
then a subject should be instructed in how to treat fever if it occurs following viral 
vector injection. 
Update dosing of 
antipyretics 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Section 14.6  
Appendix 6 
Added Appendix 6: 
A new Appendix ONLY for study sires participating in additional immunologic 
Add a new Appendix to 
describe additional 
immunologic analyses that 

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assessments: 
Schedule of Study Procedures and Assessments - Additional Immunologic 
Assessments 
• 
Biopsy / FNA  
• 
PBMC  (ie, cellular immune response) 
• 
Immune cell evaluation (ie, flow cytometry) 
will occur in consented 
subjects at participating 
sites 
 

 Appendix 1 
Palifosfamide dose justification in combination with Ad-RTS-IL-12 
The combination of intratumoral (IT) delivery of Ad-RTS-mIL-12 + INXN-1001 generates a 
localized immune response which requires the careful coordination of a number of signals.  An 
intricate system of checks and balances has evolved to ensure the appropriate response to the 
localized cytokine stimuli.  The activation of naïve T cells in response to a specific antigen or 
cytokine requires multiple signals including tumor cells own expression of tumor associated 
antigens. The localized production of IL-12 which results in systemic stimulation of the host 
immune system, causing an influx of cytotoxic CD8+ T cells coupled with a reduction in CD4 + 
regulatory T cells.  The end result is targeted tumor cytotoxicity as well as the induction of T cell 
memory resulting in systemic immune modulation.  
It is well recognized that responses to many chemotherapeutic drugs are paradoxical since at low 
doses they actively suppress tumor cell-mediated immunity while at higher doses reduce tumor 
volume while inducing myelosuppression.  Palifosfamide an alkylating agent used in 
chemotherapy is paradoxical in this regard.  The administration of metronomic doses of 
alkylating agents such as palifosfamide should avoid the potential of immunosuppression while 
preferentially reducing regulatory T cells and myeloid dependant suppressor cells resulting in 
priming the immune system..  The balance between palifosfamide-induced cytotoxicity and 
induction of effective immunity is critical to the success of combination immunotherapy.  
 
To test this hypothesis, the effect of Ad-RTS-mIL12 + INXN-1001 in combination with 
palifosfamide was evaluated in a subcutaneous 4T1 syngeneic BALB/c mouse model.  The 
results of this study demonstrated that combinations of Ad-RTS-mIL-12 + INXN-1001 + 
palifosfamide 120 mg/m2 resulted in greater tumor mIL-12 levels concomitant with a reduction 
in myeloid dependant suppressor cells when compared to corresponding AD-RTS-mIL-12 + 
INXN1001 or palifosfamide alone. The combination elicited a supra-additive decrease in tumor 
growth rate over each treatment alone, without inducing toxicity.  The increase in tumor IL-12 
levels from the combination resulted in a prolonged time for tumor to quadruple (an index of 
efficacy) greater than the sum of each agent alone resulting in an increased survival greater than 
the sum of each agent alone (AACR 2012). 
 
In summary, combinations of Ad-RTS-mIL12 + INXN-1001 + palifosfamide 120 mg/m2 support 
the hypothesis that metronomic dosing of chemotherapeutic agents augments specific T cell  
immune response to enhance immunotherapy, which could potentially be translated into a safe 
clinical regimen for the treatment of metastatic breast cancer.