Pilot Safety Trial of Preoperative Chemotherapy Combined With Dendritic Cell Vaccine in Patients With Locally Advanced, Triple-Negative Breast Cancer or ER-Positive, Her2-Negative Breast Cancer
Phase: PHASE1
Conditions: Breast Cancer
Sponsor: Baylor Research Institute

PILOT SAFETY TRIAL OF PREOPERATIVE CHEMOTHERAPY 
COMBINED WITH DENDRITIC CELL VACCINE IN PATIENTS WITH 
LOCALLY ADVANCED, TRIPLE-NEGATIVE BREAST CANCER OR ER-
POSITIVE, HER2-NEGATIVE BREAST CANCER 
 
Protocol Number: 
013-154 
 
 
Original Date: 
July 18, 2013 
Amendment 1 
March 06, 2014 
Amendment 2 
June 30, 2014  
Amendment 3 
November 20, 2014  
Amendment 4 
May 01, 2015  
Amendment 5 
March 21, 2016  
Amendment 6 
October 13, 2016  
 
 
IND Number: 
#15765 
 
 
Principal Investigator: 
Joyce O’Shaughnessy, MD 
 
Celebrating Women Chair in Breast Cancer 
Research, 
 
Baylor Sammons Cancer Center/ 
 
Texas Oncology 
 
Co-Chair, Breast Cancer Research 
Program, 
 
The US Oncology Network 
 
3410 Worth Street, Suite 400 
 
Dallas, TX 75246 
 
(214) 370-1795 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

2 
 
 
 
SITE INVESTIGATOR SIGNATURE PAGE 
 
The signature below constitutes the approval of this protocol entitled “Pilot Safety Trial of 
Preoperative Chemotherapy Combined with Dendritic Cell Vaccine in Patients with Locally 
Advanced, Triple-Negative Breast Cancer or ER-Positive, HER2-Negative Breast Cancer”, and 
provides the necessary assurances that this study will be conducted according to all stipulations 
of the protocol, including all statements regarding confidentiality, and according to local legal 
and regulatory requirements and applicable US federal regulations and ICH guidelines. 
 
 
Site Investigator: 
 
 
 
Signed: _____________________________________ Date: _________________ 
 
 
Name:______________________________________ 
 

3 
 
Table of Contents 
ABBREVIATIONS .................................................................................................................................... 7 
SYNOPSIS ................................................................................................................................................ 11 
1 
INTRODUCTION ............................................................................................................................. 16 
1.1 
BACKGROUND ON BREAST CANCER .................................................................................................... 16 
1.2 
BREAST CANCER AND IMMUNOTHERAPY ............................................................................................ 16 
1.3 
RATIONALE FOR TARGET ANTIGEN SELECTION ................................................................................... 17 
1.4 
RATIONALE FOR INTRATUMORAL DC INJECTION ................................................................................ 19 
1.5 
THERAPEUTIC DC VACCINES ............................................................................................................... 21 
1.6 
DOXORUBICIN, CYCLOPHOSPHAMIDE, AND PACLITAXEL .................................................................... 21 
1.7 
ADDITION OF CARBOPLATIN TO NEOADJUVANT CHEMOTHERAPY FOR BREAST CANCER...................... 22 
1.8 
ADDITION OF CAPECITABINE AS ADJUVANT CHEMOTHERAPY FOR TNBC ............................................. 23 
1.8.1 
Capecitabine ...................................................................................................................................... 23 
1.8.2 
Adjuvant Capecitabine Improves DFS in TNBC............................................................................... 23 
1.9 
RATIONALE ......................................................................................................................................... 24 
2 
TRIAL OBJECTIVES ...................................................................................................................... 24 
2.1 
PRIMARY OBJECTIVES ......................................................................................................................... 24 
2.2 
SECONDARY OBJECTIVES .................................................................................................................... 24 
3 
STUDY DESIGN ............................................................................................................................. 24 
4 
SELECTION AND WITHDRAWAL OF PATIENTS ........................................................................ 27 
4.1 
SAMPLE SIZE ....................................................................................................................................... 27 
4.2 
INCLUSION CRITERIA .......................................................................................................................... 27 
4.3 
EXCLUSION CRITERIA ......................................................................................................................... 28 
4.4 
PATIENT WITHDRAWAL FROM THE STUDY .......................................................................................... 28 
5 
PRIOR AND CONCOMITANT THERAPY ...................................................................................... 30 
5.1 
PROHIBITED TREATMENTS .................................................................................................................. 30 
6 
THERAPEUTIC AGENTS ............................................................................................................... 30 
6.1 
INVESTIGATIONAL PRODUCT .............................................................................................................. 30 
6.1.1 
Dendritic Cell (DC) vaccine .............................................................................................................. 30 
6.1.1.1 
Formulation and Supply .............................................................................................. 31 
6.1.1.2 
Packaging and labeling ............................................................................................... 31 
6.1.1.3 
Storage......................................................................................................................... 31 
6.1.1.4 
Preparation ................................................................................................................. 31 
6.1.1.5 
Vaccine Administration and Vaccine Schedule ............................................................ 33 
6.1.1.6 
Increase or Reduction in Dose of the Dendritic Cell (DC) Vaccine ............................ 36 
6.1.1.7 
Vaccine Manufacture ................................................................................................... 36 
6.1.1.8 
Vaccine Order Preparation and Shipment................................................................... 36 
6.2 
NON INVESTIGATIONAL PRODUCTS ..................................................................................................... 36 
6.3 
ACCOUNTABILITY PROCEDURES ......................................................................................................... 36 
6.4. 
POTENTIAL RISKS DURING STUDY ....................................................................................................... 36 
6.4.1 
Apheresis ........................................................................................................................................... 36 
6.4.2 
DC Vaccine administration ............................................................................................................... 37 
6.4.3 
Lipopolysaccharide (LPS) endotoxin ................................................................................................ 37 
6.5 
DRUG-DRUG INTERACTIONS ............................................................................................................... 38 
6.5.1 
Cyclophosphamide (Cytoxan®) ........................................................................................................ 38 
6.5.2 
Paclitaxel (Taxol®) ........................................................................................................................... 38 
6.5.3 
Carboplatin (Paraplatin®) ................................................................................................................. 38 
6.5.4 
Capecitabine (Xeloda®) .................................................................................................................... 39 
6.6 
PREMEDICATIONS ............................................................................................................................... 39 
6.6.1 
Doxorubicin and Cyclophosphamide ................................................................................................ 39 
6.6.2 
Paclitaxel and Carboplatin ................................................................................................................. 39 
7 
TREATMENT PLAN ....................................................................................................................... 40 
7.1 
CHEMOTHERAPY TREATMENT DELAY ................................................................................................. 42 
7.2 
CHEMOTHERAPY DOSE MODIFICATION FOR TOXICITY ......................................................................... 42 

4 
 
7.3 
HEMATOLOGIC TOXICITY .................................................................................................................... 43 
7.4 
RADIATION THERAPY .......................................................................................................................... 43 
8 
SCHEDULE OF PROCEDURES AND ASSESSMENTS ............................................................... 44 
8.1 
SCREENING ......................................................................................................................................... 44 
8.2 
REGISTRATION PROCEDURES .............................................................................................................. 45 
8.3 
APHERESIS PROCEDURES .................................................................................................................... 46 
8.4 
PERIPHERAL BLOOD MONONUCLEAR CELL ISOLATION ........................................................................ 46 
8.5 
PROCEDURES DURING STUDY DRUG TREATMENT ................................................................................ 46 
8.6 
PROCEDURES FOR VACCINE TREATMENT VISITS ................................................................................. 47 
8.7 
PROCEDURES FOR END OF TREATMENT VISIT (EOT) ........................................................................... 48 
8.8 
PROCEDURES FOR FOLLOW-UP VISITS ................................................................................................. 48 
8.9 
UNSCHEDULED VISITS ......................................................................................................................... 49 
8.10 
BLOOD SAMPLES FOR IMMUNOMONITORING ....................................................................................... 49 
8.11 
BIOPSIES ............................................................................................................................................. 49 
9 
SAFETY EVALUATIONS ............................................................................................................... 50 
9.1 
TOXICITY ASSESSMENT ....................................................................................................................... 50 
9.2 
LABORATORY DATA ........................................................................................................................... 50 
9.3 
PATIENT DIARIES ................................................................................................................................ 50 
9.4 
ADVERSE EVENTS ............................................................................................................................... 50 
9.4.1 
Definition of Adverse Event .............................................................................................................. 50 
9.4.2 
Definition of Serious Adverse Event ................................................................................................. 51 
9.4.3 
Definition of Unexpected Adverse Event .......................................................................................... 51 
9.4.4 
Relationship to Study Drug ............................................................................................................... 51 
9.4.5 
Assessment of Severity ..................................................................................................................... 52 
9.4.6 
Monitoring for Adverse Events During the Clinical Trial ................................................................. 52 
9.4.7 
Reporting of Adverse Events............................................................................................................. 52 
9.4.8 
Reporting of Serious Adverse Events ................................................................................................ 53 
9.4.9 
Removal Due to Adverse Events ....................................................................................................... 53 
9.4.10 
Removal of Patients with Disease Progression While on Study ........................................................ 54 
9.4.11 
Pregnancy .......................................................................................................................................... 54 
10 
EFFICACY ASSESSMENTS .......................................................................................................... 54 
10.1 
EVALUATION OF PATHOLOGIC RESPONSE............................................................................................ 54 
11 
STATISTICAL CONSIDERATIONS ............................................................................................... 56 
11.1 
POPULATIONS FOR ANALYSIS .............................................................................................................. 56 
11.1.1 
Analysis Populations ......................................................................................................................... 56 
11.1.2 
Patient Characteristics ....................................................................................................................... 56 
11.1.3 
Patient Disposition ............................................................................................................................ 56 
11.2 
HYPOTHESIS AND ENDPOINTS ............................................................................................................. 56 
11.3 
SAMPLE SIZE ....................................................................................................................................... 57 
11.4 
STATISTICAL METHODS ...................................................................................................................... 57 
12 
PROTOCOL AND DATA DEVELOPMENT .................................................................................... 59 
12.1 
ETHICS ................................................................................................................................................ 59 
12.1.1 
Institutional Review Board ................................................................................................................ 59 
12.1.2 
Modification of the Protocol ............................................................................................................. 59 
12.1.3 
Patient Informed Consent .................................................................................................................. 59 
12.1.4 
Confidentiality of Records ................................................................................................................ 60 
12.2 
STUDY RECORDS ................................................................................................................................. 60 
12.2.1 
Documentation .................................................................................................................................. 60 
12.2.2 
Case Report Form.............................................................................................................................. 60 
12.2.3 
Source Documents............................................................................................................................. 61 
12.2.4 
Electronic Databases ......................................................................................................................... 61 
12.2.5 
Databases Processing ........................................................................................................................ 61 
13 
QUALITY CONTROL AND QUALITY ASSURANCE PROCEDURES ......................................... 61 
13.1 
MULTIDISCIPLINARY TRIAL OVERSIGHT MEETINGS ............................................................................. 61 
13.2 
PROTOCOL INITIATION MEETING ......................................................................................................... 61 
13.3 
BIOSTATISTICAL SUPPORT .................................................................................................................. 62 

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14 
CLINICAL MONITORING PLAN .................................................................................................... 62 
14.1 
INTRODUCTION ................................................................................................................................... 62 
14.2 
PROCESSES ......................................................................................................................................... 62 
14.2.1 
General Guidelines ............................................................................................................................ 62 
14.2.2 
Study Monitoring Visits .................................................................................................................... 62 
14.2.2.1 
Investigational product accountability ........................................................................ 63 
14.2.2.2 
Protocol deviations and non-compliance .................................................................... 63 
14.2.2.3 
Informed consent review .............................................................................................. 63 
14.2.2.4 
CRF and source document verification ....................................................................... 63 
14.2.2.5 
Regulatory document/binder review ............................................................................ 64 
14.2.2.6 
Adverse event/serious adverse event reporting ............................................................ 64 
15 
REFERENCES ................................................................................................................................ 65 
APPENDIX I 
NCI COMMON TERMINOLOGY CRITERIA FOR ADVERSE EVENTS (CTCAE), 
VERSION 4.0 .......................................................................................................... 70 
APPENDIX II 
SCHEDULE OF ASSESSMENTS .......................................................................... 71 
APPENDIX III 
ECOG PERFORMANCE STATUS SCALE ........................................................... 75 
APPENDIX IV 
PATIENT DIARY .................................................................................................... 76 
APPENDIX V 
RESEARCH BIOPSIES – COLLECTION AND HANDLING ................................. 78 
APPENDIX VI 
013-154 AMENDMENT 1 LIST OF CHANGES ..................................................... 80 
APPENDIX VII 
013-154 AMENDMENT 2 LIST OF CHANGES ..................................................... 99 
APPENDIX VIII 
013-154 AMENDMENT 3 LIST OF CHANGES ..................................................... 110 
APPENDIX IX 
013-154 AMENDMENT 4 LIST OF CHANGES ..................................................... 128 
APPENDIX X 
013-154 AMENDMENT 5 LIST OF CHANGES ..................................................... 134 
APPENDIX XI 
013-154 AMENDMENT 6 LIST OF CHANGES ..................................................... 140 
 
 

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In-Text Tables 
Table 1. 
Treatment schema ......................................................................................................42 
Table 2. 
Dose Reduction Levels ..............................................................................................43 
  

7 
 
ABBREVIATIONS 
Abbreviation 
Term  
5FU 
5 fluorouracil 
AC 
doxorubicin/cyclophosphamide 
AE 
Adverse event 
ALL 
Acute lymphoid leukemia 
ALT 
Alanine aminotransferase 
AML 
Acute myeloid leukemia 
ANC 
Absolute neutrophil count 
APC 
Antigen-presenting cells 
AST 
Aspartate aminotransferase 
ATP 
Adenosine triphosphate 
BC 
Breast cancer 
BIIR 
Baylor Institute for Immunology Research 
BUN 
Blood urea nitrogen 
Bx 
Biopsy  
C 
Celsius 
Cb 
Carboplatin 
CBC 
Complete blood count 
CD 
Cluster of differentiation 
CEF 
Cytomegalovirus I, Epstein-Barr (E) Virus and Influenza (F) 
Virus 
CFR 
Code of federal regulations 
CHF 
Congestive heart failure 
CMF 
Cyclophosphamide, methotrexate, and fluorouracil 
CMP 
Complete metabolic profile 
CO2 
Carbon dioxide 
CPT 
Cell preparation tube 
CR 
Complete response 
CRF 
Case report form 
CT 
Computed tomography 
CTCAE 
Common terminology criteria for adverse events 
CTEP 
Cancer Therapy Evaluation Program 
CTMS 
Clinical Trials Management System 
CYP 
Cytochrome P450 
DCs 
Dendritic cells 
DFS 
Disease-free survival 
DLCO 
Diffusing capacity 
DMARDs 
Disease modifying antirheumatic drugs 

8 
 
DNA 
Deoxyribonucleic acid 
EBCTCG 
Early Breast Cancer Trialists’ Collaborative Group 
ECG 
Electrocardiogram  
ECOG 
Eastern Cooperative Oncology Group 
EOT 
End of treatment 
ER 
Estrogen receptor 
ESR 
Erythrocyte sedimentation rate 
FDA 
Food and Drug Administration 
FDG-PET 
Fluorodeoxyglucose positron emission tomography 
FFPE 
Formalin-fixed paraffin-embedded 
FISH 
Fluorescence in situ hybridization 
GGT 
Gamma-glutamyl transpeptidase 
Gm 
Gram  
GM-CSF 
Granulocyte-macrophage colony-stimulating factor 
GMP 
Good manufacturing practices 
HgB 
Hemoglobin  
HIPAA 
Health Insurance Portability and Accountability Act of 1996 
HIV 
Human immunodeficiency virus 
HMGB1 
High mobility group B1 
HTLV 
Human T-cell lymphotropic virus type 1 
HSC 
Hematopoietic stem cells 
HSR 
Hypersensitivity reactions 
IFN 
Interferon  
IND 
Investigational new drug 
IGFBP 
Insulin-like growth factor binding protein 
IHC 
Immunohistochemistry  
IL-x 
Interleukin-x 
IL-1R 
Interleukin-1 Receptor 
INR 
International normalized ratio 
IRB 
Institutional Review Board 
ISR 
Injection site reaction 
IT 
Intratumoral  
ITT 
Intent to treat 
IV 
Intravenous  
L 
Liter  
LA 
Locally advanced 
LD 
Longest diameter 
LFU 
Lost to follow-up 
LVEF 
Left ventricular ejection fraction 

9 
 
Mg 
Milligram 
Mm 
Millimeter 
M2 
Type 2 polarized macrophages 
MBC 
Metastatic breast cancer 
mDC 
Myeloid dendritic cells 
MDS 
Myelodysplastic syndromes 
Mg 
Milligram 
mL 
Milliliter 
MNC 
Mononuclear cells 
MRI 
Magnetic resonance imaging 
MUC 
Mucin 
NCI 
National Cancer Institute 
NE 
Not evaluable 
NYHA 
New York Heart Association 
OTC 
Over the counter 
PBMC 
Peripheral blood mononuclear cells 
pCR 
Pathologic complete response 
PI 
Principal Investigator 
PD 
Progressive disease 
PET 
Positron emission tomography 
PFS 
Progression-free survival 
PO 
Per os (oral administration) 
PR 
Partial response 
PS 
Performance scale 
RCB 
Residual cancer burden 
RECIST 
Response Evaluation Criteria in Solid Tumors 
RT 
Radiation therapy 
SAE 
Serious adverse event 
SC/SQ 
Subcutaneous  
SD 
Stable disease 
SOJIA 
Systemic Onset Juvenile Idiopathic Arthritis 
SOP 
Standard operating procedure 
T 
Paclitaxel  
TAC 
Docetaxel, doxorubicin, and cyclophosphamide 
TLR 
Toll-like receptor 
TNBC 
Triple-negative breast cancer 
TNF 
Tumor necrosis factor 
TSH 
Thyroid stimulating hormone 
TSLP 
thymic stromal lymphopoietin 

10 
 
ULN 
Upper limits of normal 
USP 
United States Pharmacopeial Convention 
WBC 
White blood cells 
WLN 
Within normal limits 
WOCBP 
Women of child bearing potential 
WT 
Wilms tumor (antigen) 
 

11 
 
 
SYNOPSIS 
Summary: Women with TNBC who do not achieve a pathologic complete response (pCR; 
residual disease after neoadjuvant chemotherapy) have an increased risk of recurrence, decreased 
overall survival, and post-recurrence survival as compared to women with non-TNBC who do not 
achieve a pCR. Women with ER+/HER2- breast cancer typically have a low likelihood of 
developing a pCR, and if these women have residual disease with high levels of Ki67 after 
preoperative therapy, this predicts for poor overall and progression-free survival with subsequent 
endocrine therapy. Immunotherapy could be an attractive strategy for these patients and some 
preliminary studies have been carried out. Recent studies have shown that human breast cancers 
can be immunogenic, and that enhancing the immune effector function already present may 
augment the cytotoxic effects of standard therapies.  
There are numerous strategies under investigation aimed at overcoming a patient’s immunologic 
resistance to cancer. Yet, vaccination remains the most attractive strategy because of its expected 
inducement of both therapeutic T cell immunity (effector T cells) and protective T cell immunity 
(tumor-specific memory T cells that can control tumor relapse). Several clinical studies have now 
demonstrated that immunity against tumor antigens can be enhanced in cancer patients by 
vaccination with ex vivo-generated tumor antigen-loaded dendritic cells (DCs). This strategy 
capitalizes on the unique capacity of DCs to prime lymphocytes and to regulate and maintain 
immune responses.  
Our goals are to boost T cell immunity targeted against breast cancer utilizing a tumor antigen-
loaded DC vaccine, to enhance chemotherapy effectiveness and decrease tumor metastagenicity, 
and to decrease the recurrence rates of LA TNBC and ER+/HER2– BC. Patients will be treated 
with a combination of antigen-loaded DC vaccinations along with standard preoperative 
chemotherapy, to improve immunogenicity and to increase the pCR rate achieved with standard 
therapy. The trial will consist of 2 patient cohorts: TNBC and ER+/HER2– BC. 
Objectives: The primary objective of this study is to determine the safety and feasibility of 
combining cyclin B1/WT1/CEF (antigen)-loaded DC vaccination with preoperative 
chemotherapy. 
The secondary objectives of this trial are to determine pathologic complete response rates; disease-
free survival; to assess immune biomarkers of immunity (antigen-specific CD8+ T cell immunity 
and TH2 T cells) in breast cancer biopsy specimens and blood samples in patients receiving DC 
vaccinations; and to assess the feasibility of immunizing LA TNBC and ER+/HER2– BC patients 
with patient-specific tumor antigens. 
Number of patients: 20 

12 
 
Inclusion Criteria: 
A patient will be considered for enrollment in this study if all of the following criteria are met:  
1. 
Female patients ≥18 years of age. 
2. 
Have either: 
a. locally advanced TNBC defined as invasive ductal cancer; ER- tumors with 
<10% of tumor nuclei immunoreactive; PR- tumors with <10% of tumor nuclei 
immunoreactive; T3 or T4 disease, regardless of nodal status (T2 disease is 
eligible if there are positive lymph nodes present by physical exam or imaging 
evaluation or histological evaluation, OR 
b. High-risk ER+ breast cancer defined as grade 3 invasive ductal or mixed 
ductal/lobular cancers, or grade 2 with Ki67 ≥20%; node positive as evidenced by 
physical exam or imaging evaluation or histological evaluation. 
3. 
HER2-negative breast cancer. If HER2-, it is defined as follows: 
a. FISH-negative (FISH ratio <2.0), or 
b. IHC 0-1+, or 
c. IHC 2+ AND FISH-negative (FISH ratio<2.0) 
4. 
Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1 
5. 
Adequate hematologic function, defined by: 
a. Absolute neutrophil count (ANC) >1500/mm3 
b. Platelet count ≥100,000/mm3 
c. Hemoglobin >9 g/dL (in the absence of red blood cell transfusion) 
6. 
Adequate liver function, defined by: 
a. AST and ALT ≤2.5 x the upper limit of normal (ULN)  
b. Total bilirubin ≤1.5 x ULN 
7. 
Adequate renal function, defined by: 
a. Serum creatinine ≤1.5 x ULN or calculated creatinine clearance of ≥60 ml/min 
8. 
Patients with previous history of invasive cancers (including breast cancer) are eligible if 
definitive treatment was completed more than 5 years prior to initiating current study 
treatment, and there is no evidence of recurrent disease. 
9. 
Eligible for treatment with paclitaxel, doxorubicin, cyclophosphamide, carboplatin, and 
capecitabine. 
10. Patient must be accessible for treatment and follow-up. 
11. All patients must be able to understand the investigational nature of the study and give 
written informed consent prior to study entry. 

13 
 
Exclusion Criteria: 
A patient will be ineligible for inclusion in this study any of the following criteria are met:  
1.  Evidence of metastatic disease on bone scan and CT scan of chest/abdomen (or PET CT 
scan). Patients with intrathoracic metastatic adenopathy are eligible. 
2. Active infection or unexplained fever >38.5°C during screening.  
3. Active infections including viral hepatitis and HIV. 
4. Active asthma or other condition requiring steroid therapy. 
5. Autoimmune disease including lupus erythematosus or rheumatoid arthritis. Topical or 
inhaled corticosteroids are allowed. 
6. Patients who are currently receiving or who have received previous systemic therapy for 
breast cancer (eg, chemotherapy, antibody therapy, targeted agents). The use of an LHRH 
agonist during chemotherapy in premenopausal women who wish to preserve ovarian 
function is allowed, but is not required. 
7. Women who are pregnant or lactating. All patients with reproductive potential must agree to 
use effective contraception from time of study entry until at least 3 months after the last 
administration of study drug. 
8. Have a NYHA Class III or IV CHF or LVEF <55%. Patients with significant cardiac disease 
history within 1 year or ventricular arrhythmias requiring medication are also excluded. 
9. Patients who have any severe and/or uncontrolled medical conditions or other conditions that 
could affect their participation such as: 
a. severe impaired lung functions as defined as spirometry and DLCO that is 50% of 
the normal predicted value and/or O2 saturation that is 88% or less at rest on room 
air 
b. liver disease such as cirrhosis or severe hepatic impairment (Child-Pugh class C). 
10. History of any other disease, physical examination finding, or clinical laboratory finding 
giving reasonable suspicion of a disease or condition that contraindicates use of an 
investigational drug, or that might affect interpretation of the results of this study, or render 
the patient at high risk for treatment complications. 
11. Any other investigational or anti-cancer treatments while participating in this study. 
12. Any other cancer 
Medication 
and Doses: 
This exploratory pilot safety, open label trial will evaluate the combination of 
preoperative chemotherapy and Dendritic Cell (DC) vaccinations in 2 cohorts of 
patients with LA TNBC or ER+/HER2– BC.  
• LA TNBC patients will be enrolled to receive DC vaccinations during the 
24 weeks of standard preoperative dose-dense 
doxorubicin/cyclophosphamide (AC) followed by paclitaxel and 
carboplatin (TCb) chemotherapy;  
• ER+/HER2– BC patients will receive DC vaccinations during the 
22 weeks of standard preoperative dose-dense AC followed by weekly 
paclitaxel (T) chemotherapy.  
• Study procedures will be similar in both groups. 
LA TNBC patients will receive standard preoperative dose-dense AC (4 cycles) 

14 
 
followed by TCb (4 cycles) chemotherapy, administered for 24 weeks. 
ER+/HER2– BC patients will receive standard preoperative dose-dense AC 
(4 cycles) followed by weekly T (12 cycles), administered for a total of 22 weeks. 
In both cohorts, chemotherapy will be combined with antigen-loaded DC 
vaccinations administered intratumoral (one injection of 0.2 mL at 3 x 106 
cells/mL) and subcutaneous (one injection of 1 mL at 15 x 106 cells/mL), for a 
total of 4 time points prior to definitive surgery.  
• 
During the AC cycles, both cohorts will receive vaccines administered on 
any one individual day between Days 9-12 of Cycles 1 and 3 of dose-
dense AC.  
• 
For TNBC patients, vaccines will be administered on any one individual 
day between Days 11-15 of Cycles 1 and 3 of TCb.  
• 
For ER+/HER2– patients, vaccines will be administered Day 1 during 
either Cycle 2 or Cycle 3 and on Day 1 during either Cycle 8 or Cycle 9 of 
T. Vaccine is to be administered after T infusion is completed in this 
cohort of patients.  
Standard pegfilgrastim support will be given for each AC treatment; however, no 
pegfilgrastim will be given during TCb or T cycles.  
Patients will undergo research biopsies of their breast cancer prior to the start of 
treatment and 1-2 days prior to or on Day 1 of Cycle 4 of AC to analyze the 
composition of the immune microenvironment. Patients who will have their 
definitive surgery outside a Baylor hospital will have a third research biopsy at 
least 1 week following the last chemotherapy dose and prior to surgery. Core 
biopsies will be obtained prior to treatment initiation for whole exome sequencing 
and expression analysis and for characterization of the tumor immune 
microenvironment.  
After preoperative treatment, patients will undergo definitive surgery, generally 
with mastectomy, and if available, fresh tissue (for patients who have their 
definitive surgery within a Baylor hospital) and residual FFPE breast cancer tissue 
will be collected for assessment of the immune microenvironment and for whole 
exome sequencing to identify cancer-associated mutations in the residual, 
chemotherapy-refractory cancer.  
After definitive surgery and during locoregional radiation therapy to the breast or 
chest wall and regional lymphatics per standard of care, patients will receive 
3 boost DC vaccinations subcutaneously of 1 mL (at 15 x 106 cells/mL), rotating 
injection sites in the dorsal or ventral surface of the upper arm, with antigen-loaded 
DCs. The timing of the boosters is the same for TNBC and ER+/HER2– cohorts. 
The first vaccination booster will occur once after the surgery and up to 3 days 
prior to radiation; the second booster will occur 30 days ± 3 days after radiation is 
completed; and the third booster will occur 90 days ± 3 days after the 2nd boost. 
TNBC patients who are non-pathologic complete responders and/or have positive 
lymph nodes following neoadjuvant treatment and surgery will receive 
capecitabine for 6-8 cycles (cycle length per physician discretion).  
 

15 
 
Duration of 
Study: 
Patients will be on study treatment for up to 1 year, and will be followed every 
3 months thereafter for 3 years. 
Efficacy Assessments: 
Pathologic complete response rate 
Disease-free survival 
Safety Assessments: 
Toxicity  

16 
 
 
1 INTRODUCTION 
1.1 
BACKGROUND ON BREAST CANCER 
Women with breast cancer who are treated with preoperative chemotherapy have the same 
survival as those who receive adjuvant therapy; however, pathologic complete response (pCR) 
after preoperative chemotherapy is a predictor of improved outcomes.1,2 Those treated with 
preoperative therapy who achieve a pCR or near pCR have significantly better distant relapse-
free survival than those with extensive residual disease independent of pathologic subtype. In 
addition, the degree of proliferation as indicated by expression levels of Ki67 is also a predictive 
factor for achieving a pCR. High Ki67 in pretreatment breast cancer tissue is associated with an 
increase in pCR, whereas high Ki67 in post-treatment residual disease is correlated with poorer 
disease-free and overall survival.3  
Women with triple-negative breast cancer (TNBC) have an increased pCR rate as compared to 
women with non-TNBC, and those with pCR have a 90% disease-free survival.4,5 However, 
women with TNBC who do not achieve a pCR (residual disease after neoadjuvant 
chemotherapy) have an increased risk of recurrence, decreased overall survival, and post-
recurrence survival as compared to women with non-TNBC who do not achieve a pCR. The risk 
of recurrence and death is time-dependent and significantly higher for women with TNBC in the 
first 3 years of follow-up, versus women with non-TNBC.4  
Women with ER+/HER2- breast cancer typically have a low likelihood of developing a pCR6, 
and if these women have residual disease with high levels of Ki67 after preoperative therapy, this 
predicts for poor overall and progression-free survival with subsequent endocrine therapy.3 ER+ 
patients whose cancers have high expression levels of Ki67 have a high rate of disease 
recurrence and new treatment options are necessary to improve their outcome.7 
These patients have a great unmet medical need as there is no known effective therapy which can 
improve outcome. Therefore, a high priority for clinical research in patients is to increase the 
pathologic complete response (pCR) rate in breast and axilla following preoperative therapy. 
Patients with T2, T3 and T4 cancers and with clinically N1/N2 axillary disease are at highest risk 
of not achieving a pCR with standard therapy, and of developing metastatic disease. 
1.2 
BREAST CANCER AND IMMUNOTHERAPY 
Immunotherapy could be an attractive strategy for overcoming chemotherapy resistance in 
TNBC or ER+/HER2– BC patients and some preliminary studies have been carried out.8-11 
Briefly, recent studies have shown that human breast cancers can be immunogenic, and that 
enhancing the immune effector function already present may augment the cytotoxic effects of 
standard therapies.10,11 In one preclinical study, IGFBP-2 was found at elevated levels in breast 
cancer patients’ sera, and an IGFBP-2–specific T-cell response inhibited tumor growth in a 
breast cancer mouse model.8 In a phase I clinical trial, 19 patients with HER2-overexpressing 
breast cancer were vaccinated with HER2 peptide-specific T-cells, resulting in the generation of 
both CD4 and CD8 T-cell immunity. The resulting peptide-specific T-cells recognized 

17 
 
endogenous HER2 protein and the immunity was maintained for a median of 12 months after the 
last vaccination.9 More recently, breast cancer tissues from a phase III clinical trial were 
analyzed for lymphocytic infiltrate, and the results demonstrated that increased infiltration of 
lymphocytes in tumor and stroma was associated with an overall good prognosis in ER-
negative/HER2-negative breast cancer patients. These findings were consistent regardless of the 
chemotherapy type administered, demonstrating that greater lymphocytic infiltration was a 
prognostic factor for ER-negative/HER2-negative breast cancer.12  
The presence of naturally occurring immunity against a broad range of tumor-associated antigens 
including HER-2/neu, MUC1, cyclin B1 and survivin has now been documented in patients with 
breast cancer.13 However, the natural immune response to the cancer co-exists with the cancer, 
and is therefore not protective, either because of tumor escape, for example, through clonal 
evolution, or because it might have been generated in and/or elicited an inappropriate 
immunosuppressive microenvironment.  
There are numerous strategies under investigation aimed at overcoming a patient’s immunologic 
resistance to cancer. Among these are 1) non-specific activation of the immune system with 
microbial components or cytokines; 2) antigen-specific adoptive immunotherapy with antibodies 
and/or T cells; and 3) antigen-specific active immunotherapy (vaccination). The major limitation 
of antibodies is that target proteins must be expressed on the cell surface whereas targets for T 
cells can be intracellular proteins whose peptides are presented on the cell surface in complexes 
with MHC molecules.14 The identification of defined tumor antigens in humans15, 16 prompted 
the development of adoptive T cell therapy. Yet, vaccination remains the most attractive strategy 
because of its expected inducement of both therapeutic T cell immunity (effector T cells) and 
protective T cell immunity (tumor-specific memory T cells that can control tumor relapse). 13,17,18 
Several clinical studies have now demonstrated that immunity against tumor antigens can be 
enhanced in cancer patients by vaccination with ex vivo-generated tumor antigen-loaded 
dendritic cells (DCs). This strategy capitalizes on the unique capacity of DCs to prime 
lymphocytes and to regulate and maintain immune responses. Whereas a number of antigen-
presenting cells can activate memory T cells, only DCs can prime naive T cells. This feature is 
essential to successful vaccination as it might allow generation of a “new” immune response, 
possibly not compromised by the cancer.19 
1.3 
RATIONALE FOR TARGET ANTIGEN SELECTION 
Transcriptional profiling of triple negative breast cancers demonstrates a very strong 
proliferation signature20,21 including enhanced transcription of cyclin B1. Cytoplasmic 
accumulation of cyclin B1 has been identified as an early event in breast cancer development.22 
Furthermore, cyclin B1 genes are among the transcripts analyzed in the 21-gene assay Oncotype 
Dx, the first clinically validated multigene assay that quantifies the likelihood of breast cancer 
recurrence.23  
Cyclin B1 is a regulatory protein that is an essential component of the mitotic cell cycle. The 
natural peak of cyclin B1 occurs between the G2-M phases of the cell cycle, and is reduced to 
near zero afterwards. However, in cancer cells, this protein is over-expressed during all phases of 
the cell cycle. Additionally, cyclin B1 is found in normal cells in the nucleus, whereas in cancer 

18 
 
cells it is found in the cytoplasm.24 Several studies have shown that inactivation of the tumor 
suppressor gene p53, which occurs in all triple negative breast cancers, directly contributes to the 
aberrant regulation of cyclin B1 in tumor cells.25 Cyclin B1 has been found to be over-expressed 
in multiple forms of cancer, including breast cancer, and in most cancer cell lines.24 While 
studies involving the immunogenicity of cyclin B1 are limited, there are some indications that it 
is an important antigen to pursue.25 Cyclin B1-specific antibodies are found in the blood of 
patients with many cancer types, at both the premalignant and established phases.26 Cyclin B1-
specific T cells can be also found in healthy volunteers.27 Both antibodies and T cells against 
cyclin B1 protect from cancer in mouse models.27 Because cyclin B1 is necessary for cancer cell 
division, loss of the antigen is an unlikely means of tumor escape. Cyclin B1 is one of the 
cancer-related genes that comprises the Oncotype DX Recurrence Score assay.28 This assay, 
developed from the National Surgical Adjuvant Breast and Bowel Project (NSABP) trials, 
quantifies the likelihood of breast cancer recurrence, and also can predict for chemotherapy 
benefit (higher recurrence scores are indicative of greater therapy benefit).29 High Cyclin B1 
levels are associated with highly proliferative ER+ breast cancers and predict for a high risk of 
distant disease recurrence.  
In our lab at the Baylor Institute for Immunology Research (BIIR), we have shown that DCs 
loaded with killed breast cancer cells which express cyclin B1 induce differentiation of cyclin 
B1-specific T cells, and that these T cells are able to kill breast cancer tumors in vitro.27,30 In 
preliminary studies preparatory to the clinical trial proposed herein, we have also found that 
patients with various breast cancer subtypes can display a cyclin B1-specific memory T cell 
repertoire in their blood. These observations further support the targeting of this antigen for 
breast cancer immunotherapy. Herein, we propose to immunize breast cancer patients with cyclin 
B1 peptide-loaded DC vaccines, along with standard preoperative chemotherapy. 
Another important antigen that we will include in the DC vaccines is Wilm’s tumor antigen 
(WT1). The zinc finger transcription factor WT1 is expressed at 10–1000x fold higher levels in 
leukemic cells compared to normal CD34+ cells, and the magnitude of expression correlates with 
clinical aggressiveness of acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), 
and acute lymphoid leukemia (ALL).31 Although essential during embryogenesis, WT1 
expression after birth is limited to low levels predominantly in kidney podocytes and CD34+ 
hematopoietic stem cells (HSC). WT1-specific CD8+ T lymphocytes can distinguish over-
expressing targets from normal cells and have been demonstrated to inhibit the growth of and to 
lyse leukemic but not normal CD34+ cells.  
Recent whole genome and transcriptome sequencing analysis of metastatic tumor tissue obtained 
from 14 TNBC patients, has delineated the wide array of somatic genomic alterations in these 
advanced tumors. Genes mutated in multiple tumors included TP53, LRP1B, HERC1, CDH5, 
RB1, and NF1. WT1 was among the genes that contained focal structural mutations as were 
CTNNA1, PTEN, FBXW7, BRCA2, FGFR1, KRAS, HRAS, ARAF, BRAF, and PGCP. 
Furthermore, WT1 was found to be overexpressed on RNA sequencing in all 14 samples.32 
Furthermore, the analysis of public microarray datasets of 266 early breast cancer patients 
showed that WT1 mRNA expression was correlated with higher histological grades, ER-negative 
and basal-like and ERBB2 molecular breast cancer subtypes.33 Disease-free survival analysis 
showed worse prognosis the WT1 high expression group, and WT1 was found to be an 

19 
 
independent prognostic indicator in multivariate analysis. Finally, WT1 promotes proliferation 
and oncogenicity, and loss of expression is disadvantageous for the tumor, making outgrowth of 
antigen-loss variants less likely.  
In the ER+, HER2- breast cancer cell line, MCF-7, WT1 was correlated with high expression of 
ERα and HER2, which indicated that it may play a role in cancer progression and 
development.34 In addition, high levels of WT1 are associated with aggressive breast cancer 
biology, and in vitro, WT1 promoted estrogen-independent growth and anti-estrogen 
resistance.35 This finding indicates that WT1 is, in part, mechanistically responsible for the 
switch from estrogen-dependent to -independent breast cancer growth and survival. Thus, WT1 
is a very interesting candidate for therapeutic vaccination.  
1.4 
RATIONALE FOR INTRATUMORAL DC INJECTION 
Although it is generally believed that cytotoxic antineoplastic agents mediate their therapeutic 
effects in a cancer cell-autonomous fashion, recent results indicate that at least some 
chemotherapeutics inhibit tumor growth also indirectly, via the immune system. 
Indeed, our collaborators Drs Zitvogel and Kroemer demonstrated that a variety of transplantable 
or chemically induced, primary mouse cancers respond more efficiently to anthracyclines when 
they develop in hosts carrying an intact immune system.36 Tumors evolving in immunodeficient 
mice fail to show a reduction in growth after anthracycline treatment in conditions in which the 
same tumors growing in immunocompetent mice do exhibit a significant inflection in their 
progression. Accordingly, clinical studies indicate that anthracycline-killed tumor cells are 
particularly efficient in stimulating a therapeutic immune response in cancer patients. 
Anthracycline-based neoadjuvant therapy of breast cancer patients is more effective when the 
tumor is infiltrated by T cells before chemotherapy is initiated as well as if chemotherapy causes 
a significant influx of CD8+ T cells into the tumor bed and/or reduces the presence of 
immunosuppressive T regulatory (Treg) cells.36 The reason why anthracyclines provoke this 
complex anticancer immune response has only been partially elucidated. In contrast to many 
other cytotoxic chemotherapeutics, anthracyclines stimulate immunogenic cell death that is 
characterized by a compendium of subtle biochemical changes in the plasma membrane surface 
and in the microenvironment of dying cancer cells. These changes include the pre-apoptotic 
exposure of calreticulin on the plasma membrane surface (to facilitate the engulfment of portions 
of the dying cells by antigen-presenting cells, APC) and the post-apoptotic exodus of high 
mobility group B1 (HMGB1) from the nucleus (to engage with TLR4 receptors and to stimulate 
antigen presentation).36 Moreover, ATP release by autophagy-competent dying tumor cells 
(positive for LC3-II) is essential for the induction of an anticancer immune response, both by 
stimulating the recruitment of inflammatory cells (CD11b+LyC6high CD11clow CD86+) into the 
tumor bed and by ligating P2RX7 receptors on dendritic cells, hence facilitating the activation of 
the NLRP3 inflammasome and the consequent secretion of IL-1b by APC.36  
How chemotherapy-induced cell death leads to efficient antigen presentation to T cells has 
remained an open conundrum. Studies from Drs Zitvogel and Kroemer showed in the mice that 
intratumoral CD11c+CD11b+Ly6Chigh cells, which shared some characteristics of inflammatory 
dendritic cells (DC) and contained granulomonocytic precursors, were crucial for the induction 
of anticancer immunity post-chemotherapy.37 First, ATP released by dying tumor cells is 

20 
 
essential for the recruitment of myeloid cells into tumor beds and for the local differentiation of 
inflammatory DC. Second, manipulations aimed at avoiding the intratumoral accumulation of 
these CD11c+CD11b+Ly6Chigh cells, such as local overexpression of the ATP-degrading enzyme 
CD39, pharmacological blockade of purinergic receptors, or neutralization of CD11b, abolished 
the immune-dependent inhibition of tumor growth by anthracyclines. Third, 
CD11c+CD11b+Ly6Chigh were efficient in capturing and presenting tumor cell antigen to T cells 
and protected mice upon their adoptive transfer against challenge with cancer cells. Altogether, 
the results identify a population of tumor-infiltrating leukocytes as therapy-relevant antigen-
presenting cells. 
Drs. Zitvogel and Kroemer evaluated the 2 immunogenic cell death markers HMGB1 and LC3-
II, on paraffin-embedded BC specimen in a test (50 early BC treated with adjuvant 
anthracyclines that relapse at 3 years paired with 50 cases that were disease-free at 10 years) and 
a validation cohort on 150 HER2-negative early BC treated with adjuvant anthracyclines. 
Preliminary data suggest that LC-3-II staining was negative in the vast majority of cases of early 
breast cancers (>70%). These “autophagy deficient” cancers are also less infiltrated with CD8+ 
T cells but contained more CD68+ cells and had a greater chance of recurrence following 
adjuvant chemotherapy. A larger across Europe validation study is ongoing. 
Blocking ectoATPases (CD39) restored the recruitment of DC in tumors and the efficacy of 
chemotherapy in autophagy deficient murine cancers.38 However, anti-CD39 Ab are not 
available for the use in the human at this time. We propose to substitute the functional DCs via 
adoptive transfer of ex vivo generated autologous mature DCs injected locally into LA TNBCs 
and ER+/HER2– breast cancer patients post-systemic anthracycline therapy. Whereas we will 
not stratify in this early phase of DC vaccine assessment, all samples will be tested for LC3-II 
staining (and others such as CD68, CD8, Foxp3, phosphoSTAT6). Data will be used to properly 
power the follow up study. 
Another objective for intratumoral vaccination is the possibility to enhance the access of DCs to 
draining lymph nodes. Indeed, recent studies suggest that the rout of DC injection might 
determine the homing of elicited T cells. Indeed, for mucosal cancer vaccines, the homing to and 
retention of CD8+ T cells in the mucosa are critical for efficacy.39 In this context, the growth of 
orthotopic head and neck or lung cancers can be inhibited by a cancer vaccine provided that it is 
administered by the intranasal mucosal route, but not the intramuscular route. This is explained 
by the induction through intranasal vaccination of mucosal CD8+ T cells expressing the mucosal 
integrin CD49a, the expression of which is essential for the efficacy of cancer vaccines. Whereas 
in this pilot study we will not monitor DC migration, in the follow up study this parameter can be 
objectively assessed. 
 

21 
 
Overall survival
0
50
100
150
200
100
80
60
40
20
0
Time
Survival probability (%)
Number at risk
Group: 0
53
48
28
1
0
Group: 1
60
54
21
2
0
Group: 2
28
27
13
3
1
LC3 & HMGB1 combination
Negative HMGB1 and LC3
Positive HMGB1 OR LC3
Positive HMGB1 AND LC3
 
 
1.5 
THERAPEUTIC DC VACCINES  
Investigators within the Ralph M. Steinman Center for Cancer Vaccines at BIIR have carried out 
more than 7 phase I/II clinical trials testing ex vivo-generated DC vaccines in patients with stage 
IV melanoma, HIV, and more recently pancreatic cancer. We have found that a fraction of 
patients can experience durable tumor regressions as well as prolonged survival.40 We have also 
developed a DC vaccine optimized for CD8+T cell responses, ie, GM-CSF/IFN-α-generated DCs 
activated with TLR ligands and CD40L. We have developed a closed system for vaccine 
generation and a frozen vaccine that has been successfully administered in multicenter clinical 
trials in patients with melanoma and in patients with HIV. This vaccine was used, on 
compassionate basis, in a patient with a partially resected stage IV pancreatic cancer who was 
also treated with gemcitabine and 5FU. DC vaccine was loaded with patient-specific mutant 
peptides whose sequences were identified by the analysis of autologous tumor. Repeated 
vaccinations were delivered one day after the last day of each chemotherapy cycle. The analysis 
of immune responses revealed the expansion of CD8+ T cells specific to the pancreatic cancer 
antigens resulting from the vaccination. 
1.6 
DOXORUBICIN, CYCLOPHOSPHAMIDE, AND PACLITAXEL 
Adjuvant chemotherapy can substantially reduce the risk of breast cancer recurrence and death in 
high-risk patients,41 and there are many chemotherapy regimens with established efficacy and 
safety data. The value of chemotherapy is established from the data from individual randomized 

22 
 
trials and from the Early Breast Cancer Trialists’ Collaborative Group’s (EBCTCG) 15-year 
meta-analyses of randomized chemotherapy trials.42 The meta-analyses established that 
anthracycline-containing therapies, such as doxorubicin and cyclophosphamide (AC) and 
docetaxel, doxorubicin, and cyclophosphamide (TAC), offer superior efficacy, reducing the risk 
of recurrence by 11% and the risk of death by 16% compared with cyclophosphamide, 
methotrexate, and fluorouracil (CMF) combinations.42  
Significant improvements in disease-free survival (DFS) were reported with adjuvant dose-dense 
chemotherapy in women with node-positive breast cancer in the Phase III CALGB 9741 study of 
2005 women. Citron et al43 showed that when the taxane, paclitaxel (Taxol) (T), was given 
sequentially following standard chemotherapy, doxorubicin (A) and cyclophosphamide (C), in an 
every two-weekly dose-dense regimen, the rate of recurrence was significantly reduced by 26% 
(P=0.010) and the rate of death was reduced by 31% (P=0.014), compared to standard every 3-
week administration, with an acceptable toxicity profile. 
In a 2005 report of the findings of NSABP B-28, the addition of a taxane, adjuvant paclitaxel, to 
AC resulted in significant improvement in DFS. NSABP B-28 was conducted to determine 
whether 4 cycles of adjuvant T after 4 cycles of adjuvant AC (AC→T) would increase the DFS 
and OS compared with 4 cycles of AC alone in patients with resected operable, node-positive 
breast cancer.44 Patients (N=3060) were randomly assigned to the 2 groups. The addition of 
AC→T significantly reduced the hazard for developing a DFS event by 17% (relative risk [RR], 
0.83; 95% CI, 0.72 to 0.95; P=0.006). Five-year DFS was 76% ±2% for patients randomly 
assigned to AC→T compared with 72% ±2% for those randomly assigned to AC. Improvement 
in OS was small and not statistically significant (RR, 0.93; 95% CI, 0.78 to 1.12; P=0.46). Five-
year OS was 85% ±2% for both groups. Toxicity with the AC→T regimen was found to be 
acceptable in the adjuvant setting. 
Thus, the combination of AC, followed by a taxane such as paclitaxel (Taxol) is now widely 
accepted as an effective adjuvant treatment for early-stage breast cancer.  
Advances in adjuvant chemotherapy have resulted in improved outcomes in patients with ER- 
breast cancers to a greater extent than for those with ER+ breast cancers.45 Many of these have 
been implemented as neoadjuvant therapy. Standard AC→T given preoperatively to TNBC 
patients results in pathologic complete response rates of 30%-40%.5,46  
1.7 
ADDITION OF CARBOPLATIN TO NEOADJUVANT CHEMOTHERAPY FOR BREAST CANCER 
Carboplatin is approved for the treatment of ovarian cancer and small cell lung carcinoma, and is 
commonly used for the treatment of non-small cell lung cancer (NSCLC), head and neck cancer, 
and other tumors. In breast cancer, administration of carboplatin to previously untreated patients 
with metastatic disease results in response rates of 20% to 50%.47 Paclitaxel in combination with 
carboplatin is also highly active in breast cancer, with response rates of approximately 39% to 
62% for first-line treatment of metastatic disease.48 Notably, data suggest that the administration 
of carboplatin in combination with paclitaxel results in less thrombocytopenia than is expected 
from the use of carboplatin alone.47 
Emerging data suggests that TNBC tumors may be more sensitive to DNA damaging agents, 
including carboplatin. Two small single arm trials with cisplatin combination neoadjuvant 

23 
 
therapy or neoadjuvant monotherapy for patients with TNBC have reported complete tumor 
regressions or minimal residual disease at the time of surgery in 21% and 44% of patients.49,50 
The CALGB study 40603 evaluated the efficacy of neoadjuvant paclitaxel with or without 
carboplatin and/or bevacizumab followed by AC in patients with TNBC. The addition of 
carboplatin to the standard neoadjuvant chemotherapy regimen improved pathologic complete 
response in the breast in patients to 60% vs. 46% of patients who did not receive carboplatin, 
concluding that the addition of carboplatin was a reasonable addition to the standard neoadjuvant 
chemotherapy for TNBC.51   
1.8 
ADDITION OF CAPECITABINE AS ADJUVANT CHEMOTHERAPY FOR TNBC 
1.8.1 
Capecitabine  
Capecitabine is a prodrug that is enzymatically converted to 5-fluorouracil in the tumor where it 
inhibits DNA synthesis and slows growth of tumor tissue. Capecitabine is approved in both 
colorectal and breast cancer. Capecitabine demonstrated single-agent activity in subjects with 
MBC with an ORR of about 20% in subjects whose disease had progressed during or following 
anthracycline and taxane-based therapy.52 
Capecitabine is also indicated as a combination treatment with docetaxel in early-line treatment 
for MBC and in combination with ixabepilone or lapatinib as second-line treatment after failure 
of prior anthracycline and taxane-containing chemotherapy.52 
The recommended, approved dose of capecitabine is 1250 mg/m2 daily BID for 14 days, 
followed by 7 days without treatment. This dose/schedule necessitates dose interruptions or 
reductions in approximately 30% of patients, and in clinical trials, approximately 17% of patients 
discontinued the drug due to toxicities (primarily hand-foot syndrome, diarrhea and 
stomatitis).53,54 
1.8.2 
Adjuvant Capecitabine Improves DFS in TNBC 
Lee and colleagues recently published results from a 5 year follow up of a Phase III trial of 
adjuvant capecitabine in breast cancer patients with HER2-negative pathological residual 
invasive disease after neoadjuvant chemotherapy. Oral capecitabine was administered for 
8 cycles at 1250 mg/m2 PO BID after standard neoadjuvant chemotherapy that contained an 
anthracycline and/or a taxane, when patients did not have a complete pathologic response. 
Overall, disease-free survival (DFS) rate and overall survival increased with capecitabine as 
compared to standard therapy (DFS: 74.1% vs 67.6% and 89.2% vs 83.9%, respectively). 
Specifically in patients with triple-negative breast cancer that were non-pathologic complete 
responders following surgery and neoadjuvant treatment, there was a 42% reduction in the risk 
of recurrence with the addition of adjuvant capecitabine.Since women with TNBC who do not 
achieve a pCR have an increased risk of recurrence, decreased overall survival, and post-
recurrence survival, the addition of capecitabine provides an additional benefit and option for 
this population. 

24 
 
1.9 
RATIONALE 
Our goals are to boost T cell immunity targeted against breast cancer utilizing a tumor antigen-
loaded DC vaccine, to enhance chemotherapy effectiveness and decrease tumor metastagenicity, 
and to decrease the recurrence rates of LA TNBC and ER+/HER2– BCs. Patients with LA 
TNBC and ER+/HER2– BC will be treated with a combination of antigen-loaded DC 
vaccinations along with standard preoperative chemotherapy, to improve immunogenicity and to 
increase the pCR rate achieved with standard therapy. The trial will consist of 2 patient cohorts: 
TNBC and ER+/HER2– BC.  
2 TRIAL OBJECTIVES 
2.1 
PRIMARY OBJECTIVES 
The primary objective of this study is to determine the safety and feasibility of combining cyclin 
B1/WT1/CEF (antigen)-loaded DC vaccination with preoperative chemotherapy. 
2.2 
SECONDARY OBJECTIVES 
The secondary objectives of this trial are to determine pathologic complete response rates; 
disease-free survival; to assess immune biomarkers of immunity (antigen-specific CD8+ T cell 
immunity and TH2 T cells) in breast cancer biopsy specimens and blood samples in patients 
receiving DC vaccinations; and to assess the feasibility of immunizing LA TNBC and 
ER+/HER2– BC patients with patient-specific tumor antigens. 
3 STUDY DESIGN 
This exploratory pilot safety, open label trial will evaluate the combination of preoperative 
chemotherapy and Dendritic Cell (DC) vaccinations in 2 cohorts of patients with LA TNBC or 
ER+/HER2– BC.  
• LA TNBC patients will be enrolled to receive DC vaccinations during the 24 weeks of 
standard preoperative dose-dense doxorubicin/cyclophosphamide (AC) followed by 
paclitaxel and carboplatin (TCb) chemotherapy;  
• ER+/HER2– BC patients will receive DC vaccinations during the 22 weeks of standard 
preoperative dose-dense AC followed by weekly paclitaxel (T) chemotherapy.  
• Study procedures will be similar in both groups.  
The screening period is from signature of the informed consent form to final eligibility 
assessments. Eligible patients will undergo apheresis after registration and entry into the study. 
After collection of peripheral blood mononuclear cells, dendritic cell will be manufactured from 
the monocyte fraction, aliquoted and frozen. Patients will be given a total of 7 DC vaccinations. 
Patients will undergo research biopsies of their breast cancer prior to the start of treatment, and 
1-2 days prior to or on Day 1 of Cycle 4 of AC to analyze the composition of the immune 
microenvironment. Patients who will have their definitive surgery outside a Baylor hospital will 
have a third research biopsy at least 1 week following the last chemotherapy dose and prior to 

25 
 
surgery. Core biopsies will be obtained prior to treatment initiation for whole exome sequencing 
and expression analysis and for characterization of the tumor immune microenvironment.  
LA TNBC patients will receive standard preoperative dose-dense AC (4 cycles) followed by 
TCb (4 cycles) chemotherapy, administered for 24 weeks. ER+/HER2– BC patients will receive 
standard preoperative dose-dense AC (4 cycles) followed by weekly T (12 cycles), administered 
for a total of 22 weeks. In both cohorts, chemotherapy will be combined with antigen-loaded DC 
vaccinations administered intratumoral (one injection of 0.2 mL at 3 x 106 cells/mL) and 
subcutaneous (one injection of 1 mL at 15 x 106 cells/mL), for a total of 4 time points prior to 
definitive surgery.  
• During the AC cycles, both cohorts will receive vaccines administered on any one 
individual day between Days 9-12 of Cycles 1 and 3 of dose-dense AC.  
• For TNBC patients, vaccines will be administered on any one individual day between 
Days 11-15 of Cycles 1 and 3 of TCb.  
• For ER+/HER2– patients, vaccines will be administered Day 1 during either Cycle 2 or 
Cycle 3 and on Day 1 during either Cycle 8 or Cycle 9 of T. Vaccine is to be 
administered after T infusion is completed in this cohort of patients.  
Timing of the vaccinations is based on data that tumor cell death associated with doxorubicin 
treatment increases the generation and functional activation of CD8 T cells required for the 
antitumor activity of doxorubicin.56 Standard pegfilgrastim support may be given for each AC 
treatment; however, no pegfilgrastim will be given during TCb or T cycles.  
After preoperative treatment, patients will undergo definitive surgery, generally with 
mastectomy, and if available, fresh tissue (for patients who have their definitive surgery within a 
Baylor hospital) and residual FFPE breast cancer tissue will be collected for assessment of the 
immune microenvironment and for whole exome sequencing to identify cancer-associated 
mutations in the residual, chemotherapy-refractory cancer. Patients will be known to have 
axillary node positive disease at study entry based on biopsy or clinical criteria and will 
generally undergo level 1/2 axillary dissection at definitive surgery. However, patients may 
undergo SLN biopsy before or after chemotherapy at the physician’s discretion. 
After definitive surgery and during locoregional radiation therapy to the breast or chest wall and 
regional lymphatics per standard of care, patients will receive 3 boost DC vaccinations 
subcutaneously of 1 mL (at 15 x 106 cells/mL), rotating injection sites in the dorsal or ventral 
surface of the upper arm, with antigen-loaded DCs. The timing of the boosters is the same for 
TNBC and ER+/HER2– cohorts. The first vaccination booster will occur once after the surgery 
and up to 3 days prior to radiation; the second booster will occur 30 days ± 3 days after radiation 
is completed; and the third booster will occur 90 days ± 3 days after the 2nd boost.  
ER+/HER2– BC patients will also receive standard endocrine therapy during locoregional 
radiation therapy, at the physician’s discretion, and for at least 5 years thereafter. 
TNBC patients who are non-pathologic complete responders and/or have positive lymph nodes 
following neoadjuvant treatment and surgery will receive capecitabine for 6-8 cycles (number of 

26 
 
cycles per physician discretion). It will be the physician’s discretion to begin capecitabine 
treatment either during radiation or after radiation is complete. 
Blood samples for immunomonitoring studies will be obtained at baseline, prior to each DC 
vaccination, prior to surgery, prior to radiation, 2 weeks ± 3 days after the last DC vaccination, 
6 months and 1 year after the last DC vaccination. 
 
 
 

27 
 
4 SELECTION AND WITHDRAWAL OF PATIENTS 
4.1 
SAMPLE SIZE 
Twenty patients with newly diagnosed locally advanced TNBC or ER+/HER2– BC will be 
enrolled over 20 months. 
If a patient’s apheresis product or manufactured vaccine is suboptimal after a second apheresis 
procedure, the patient will be withdrawn from the study and replaced. See Section 8.3. 
4.2 
INCLUSION CRITERIA 
A patient will be considered for enrollment in this study if all of the following criteria are met:  
1. Female patients ≥18 years of age. 
2. Have either: 
a. locally advanced TNBC defined as invasive ductal cancers; ER- tumors with 
<10% of tumor nuclei immunoreactive57; PR- tumors with <10% of tumor nuclei 
immunoreactive; T3 or T4 disease, regardless of nodal status (T2 disease is 
eligible if there are positive lymph nodes present by physical exam or imaging 
evaluation or histological evaluation, OR 
b. High-risk ER+ breast cancer defined as grade 3 invasive ductal or mixed 
ductal/lobular cancers, or grade 2 with Ki67 ≥20%; node positive as evidenced by 
physical exam or imaging evaluation or histological evaluation. 
3. HER2-negative breast cancer. If HER2-, it is defined as follows: 
a. FISH-negative (FISH ratio <2.0), or 
b. IHC 0-1+, or 
c. IHC 2+ AND FISH-negative (FISH ratio<2.0) 
4. Eastern Cooperative Oncology Group (ECOG) Performance Status of 0-1 
5. Adequate hematologic function, defined by: 
a. Absolute neutrophil count (ANC) >1500/mm3 
b. Platelet count ≥100,000/mm3 
c. Hemoglobin >9 g/dL (in the absence of red blood cell transfusion) 
6. Adequate liver function, defined by: 
a. AST and ALT ≤2.5 x the upper limit of normal (ULN)  
b. Total bilirubin ≤1.5 x ULN 
7. Adequate renal function, defined by: 
a. Serum creatinine ≤1.5 x ULN or calculated creatinine clearance of ≥60 ml/min 
8. Patients with previous history of invasive cancers (including breast cancer) are eligible if 
definitive treatment was completed more than 5 years prior to initiating current study 
treatment, and there is no evidence of recurrent disease. 
9. Eligible for treatment with paclitaxel, doxorubicin, cyclophosphamide, carboplatin, and 
capecitabine. 
10. Patient must be accessible for treatment and follow-up. 

28 
 
11. All patients must be able to understand the investigational nature of the study and give 
written informed consent prior to study entry. 
4.3 
EXCLUSION CRITERIA 
A patient will be ineligible for inclusion in this study if any of the following criteria are met:  
1. Evidence of metastatic disease on bone scan and CT scan of chest/abdomen (or PET CT 
scan). Patients with intrathoracic metastatic adenopathy are eligible. 
2. Active infection or unexplained fever >38.5°C during screening.  
3. Active infections including viral hepatitis and HIV. 
4. Active asthma or other condition requiring steroid therapy. 
5. Autoimmune disease including lupus erythematosus or rheumatoid arthritis. Topical or 
inhaled corticosteroids are allowed. 
6. Patients who are currently receiving or who have received previous systemic therapy for 
breast cancer (eg, chemotherapy, antibody therapy, targeted agents). The use of an LHRH 
agonist during chemotherapy in premenopausal women who wish to preserve ovarian 
function is allowed, but is not required. 
7. Women who are pregnant or lactating. All patients with reproductive potential must agree to 
use effective contraception from time of study entry until at least 3 months after the last 
administration of study drug. 
8. Have a NYHA Class III or IV CHF or LVEF <55%. Patients with significant cardiac disease 
history within 1 year or ventricular arrhythmias requiring medication are also excluded. 
9. Patients who have any severe and/or uncontrolled medical conditions or other conditions 
that could affect their participation such as: 
a. severe impaired lung functions as defined as spirometry and DLCO that is 50% of 
the normal predicted value and/or O2 saturation that is 88% or less at rest on room 
air 
b. liver disease such as cirrhosis or severe hepatic impairment (Child-Pugh class C). 
10. History of any other disease, physical examination finding, or clinical laboratory finding 
giving reasonable suspicion of a disease or condition that contraindicates use of an 
investigational drug, or that might affect interpretation of the results of this study, or render 
the patient at high risk for treatment complications. 
11. Any other investigational or anti-cancer treatments while participating in this study. 
12. Any other cancer 
4.4 
PATIENT WITHDRAWAL FROM THE STUDY 
Patients will be withdrawn from the study (“off study”) if any of the following occur:  
1. Withdrawal of consent (patient will not be contacted and no further information will be 
collected). If the patient withdraws consent, then no additional data will be collected without 
his/her explicit consent; all data collected prior to withdrawal of consent may be used in the 
data analysis.  
2.  Termination of study by Baylor IRB or Principal Investigators  

29 
 
3.  Disease progression  
4. 
Intolerable toxicity 
5. 
An intercurrent illness, which would in the judgment of the Investigator, affect assessments 
of clinical status to a significant degree or require discontinuation of study treatment 
6. 
Apheresis product or manufactured vaccine is suboptimal after a second apheresis 
procedure. 
7. 
Non-protocol therapy (chemotherapy, radiotherapy, hormonal therapy, immunotherapy, or 
surgery) that is administered during study  
8. 
Noncompliance with protocol or treatment 
9. 
Pregnancy 
10. Lost to follow-up (3 attempts should be documented in the patient’s source document before 
the site considers the patient as LFU.) 
11. Patients who experience any of the following treatment- or vaccine-related symptoms or 
signs as outlined in NCI Common Terminology Criteria for Adverse Events (CTCAE) v4.03 
(Appendix I) will be removed from study treatment, but will be followed for outcomes and 
long-term toxicity, per protocol: 
• Grade 2 or higher allergic reactions including bronchospasm or generalized urticaria 
• Grade 3 or greater allergic toxicity 
• Grade 2 or greater autoimmune toxicity 
• Grade 2 allergic reactions related infusion 
• Grade 3 or greater hematologic or non-hematologic toxicity including site reactions 
NOTE: The treating physician may adjust chemotherapy doses based on individual patient 
histories to optimize dose delivery, per standard of care. However, if any patient requires more 
than one dose reduction of AC OR the need for more than one dose reduction of paclitaxel or 2 
dose reductions of carboplatin due to treatment delays for hematologic toxicity or for Grade 3 or 
4 non-hematologic toxicity, they will be removed from the study treatment. 
The date of and reason for discontinuation must be noted on the Case Report Form (CRF). Every 
effort should be made to complete the appropriate assessments. 
If the patient is withdrawn for any reason, the end of treatment assessments must be completed 
(see Section 8.7). Patients who withdraw from the study treatment due to intolerable toxicity will 
still be followed for outcome and toxicity, per protocol.  
Patients must still be followed for adverse events (AEs) for 30 calendar days after their last dose 
of study drug. All new AEs occurring during this period must be reported and followed until 
resolution, or after 30 days (whichever comes first), unless, in the opinion of the investigator, 
these values are not likely to improve because of the underlying disease. In this case, the 
investigators must record his or her reasoning for this decision in the patients’ medical records 
and as a comment on the CRF. 
All patients who have CTCAE grade 3 or 4 laboratory abnormalities at the time of withdrawal 
must be followed until the laboratory values have returned to grade 1 or 2, or until 30 days after 
the date of withdrawal (whichever comes first), unless it is, in the opinion of the investigator, not 

30 
 
likely that these values are to improve because of the underlying disease. In this case, the 
investigator must record his or her reasoning for making this decision in the patients’ medical 
records and as a comment on the CRF. 
5 PRIOR AND CONCOMITANT THERAPY 
All medications (prescribed or over the counter) and concomitant treatments including blood and 
blood products, taken at the time of signing the informed consent form or during the study must 
be reported on the source documentation and the Concomitant Medications page of the CRF.  
• Blood and blood products 
• Antifungals 
• Prophylactic antibiotics 
• Growth factors 
• Premedications (ranitidine, 
diphenhydramine) 
• LHRH agonist 
5.1 
PROHIBITED TREATMENTS 
Patients may not use any of the following therapies during the study: 
• Administration of other chemotherapy  
• Administration of other immunotherapy  
• Any other investigational agents  
• Herbal therapies or alternative therapies  
• Administration of pegfilgastrim during treatment with paclitaxel, and 
paclitaxel/carboplatin 
• Administration of coumarin-derived anticoagulants and phenytoin during treatment with 
capecitabine 
• Bisphosphonates or denosumab during the study, but may be used to treat osteoporosis 
after study therapy has been completed. 
Supportive care may be administered at the discretion of the investigator. 
6 THERAPEUTIC AGENTS 
6.1 
INVESTIGATIONAL PRODUCT 
In this protocol, the investigational product is the Dendritic Cell (DC) vaccine.  
6.1.1 
Dendritic Cell (DC) vaccine  
Immunity against tumor antigens can be boosted in cancer patients by vaccination with ex vivo-
generated tumor antigen-loaded dendritic cells (DCs). This strategy capitalizes on the unique 
capacity of DCs to prime lymphocytes and to regulate and maintain immune responses. Whereas 
a number of antigen-presenting cells can activate memory T cells, only DCs can prime naive T 
cells. This feature is essential to successful vaccination as it might allow generation of a “new” 
immune response, possibly not compromised by the cancer. 

31 
 
6.1.1.1 
Formulation and Supply 
Final Formulation. The BIIR-BrcaVax-001 DC vaccine is prepared for injection into the patient 
by thawing the requisite number of frozen vials of DC vaccine and diluting the contents with 
USP injection grade sterile Lactated Ringer’s to wash the cells by centrifugation. The cells are 
washed 3 times with Lactated Ringer’s. Prior to the third wash, a sample is taken to determine 
the cell count and viability. After the third wash, the cells are resuspended in Lactated Ringer’s 
at 15 x 106 viable cells/mL. The cell suspensions are filled into a 2 mL sterile glass vaccine vial 
sealed with a serum stopper and metal cap, for delivery to the clinic. Therefore, the final 
formulation is comprised of DCs suspended in 100% Lactated Ringer’s. 
6.1.1.2 
Packaging and labeling 
The vaccine primary container, the glass vaccine vial, will be used to contain both the frozen DC 
vaccine product and the washed DC vaccine prepared for injection into the patient, and is labeled 
with the patient’s name, vaccine batch number, vaccine product name, manufacture date, name 
of the manufacturer, volume in the vaccine vial dose (concentration of cells in the vaccine vial or 
syringe), storage temperature, and the warning statements: “For Autologous Use Only” , and 
“Caution: New Drug – Limited by Federal (or United States) Law to  Investigational Use”. On 
the glass vaccine vial containing the DC vaccine that has been prepared for injection, a separate 
product expiration date and time label is attached. The expiration time is 2 hours after the 
washed, resuspended DC vaccine is been filled into the glass vaccine vial. 
The Vaccine Product container that is delivered to the bedside is a glass vaccine vial of 1.5 mL 
of prepared final Vaccine Product (15 x 106 viable cells/mL) to be drawn into a syringe for the 
intratumoral and/or subcutaneous injection. The vaccine-filled vial is placed in a clear biohazard 
plastic zip-lock bag and hard-foam shipping container for transport from the GMP facility to the 
clinic. Upon delivery to the clinic, the clinician inspects the vial to determine that it holds the 
correct Vaccine Product for the patient, dose and volume; and that no leak of the Vaccine 
Product has occurred. Before injection, the patient is asked to read aloud the name written on the 
glass vaccine vial label containing the vaccine preparation and to confirm that it is his/her name. 
6.1.1.3 
Storage 
Vaccines will be kept in a locked area with limited access at BIIR. Vaccines will be kept frozen 
in liquid nitrogen (vapor phase) until use (removal of vials to prepare the Vaccine Product for 
inoculation). 
6.1.1.4 
Preparation  
Vaccines will be prepared by the GMP Lab at BIIR. The BIIR-BrcaVax-001 DC vaccine product 
is prepared by culturing the breast cancer patient’s monocytes with granulocyte-macrophage 
colony stimulating factor (GM-CSF) and Interferon alpha (IFN-α) to generate the DC that are 
then loaded with tumor and control antigens. Tumor antigens include long peptides covering 
immunogenic spots of Cyclin B1 and WT1. Control antigens include a mix of CEF peptides 
covering the most common CD8+ T cell epitopes of CMV (C), EBV (E) and Flu (F) viruses.  
The antigen loaded DC are then activated with purified lipopolysaccharide (LPS), CD40 ligand 
(CD40L) and the toll-like receptor (TLR) 7/8 agonist CL075 prior to fill/freezing. 

32 
 
The BIIR-BrcaVax-001 DC vaccine product manufacturing process is conducted in a closed 
system, that is, the patient’s cells are processed in sterile cell collection and culture bags with 
media and cell transfers made using sterile tubing and connections. Addition of cytokines and 
antigens to the cell culture bags and collection of in-process samples for QC testing are 
performed with sterile needles and syringes. The cells are harvested into and washed in sterile 
plastic centrifuge tubes using sterile, disposable plastic pipettes to transfer cells and media. 
Manufacture of the BIIR-BrcaVax-001 DC vaccine product is conducted in the GMP vaccine 
manufacturing facility (Suite 105) located at BIIR (3434 Live Oak Street, Dallas, TX).  
The DC vaccine product is manufactured according to SOP VP142.01, titled “Procedure for 
manufacture of BIIR-BrcaVax-001, a dendritic cell vaccine product for the treatment of breast 
cancer”. To manufacture this frozen, autologous DC vaccine monocytes are enriched by 
elutriation from white blood cells that are obtained from the patient by apheresis. The patient’s 
monocytes, at a concentration of 1x106 viable cells/mL, are placed in cell culture in CellGro® 
DC culture media (CellGenix) supplemented with GM-CSF (LEUKINE®, Bayer) at 100 ng/mL 
and IFN-α (INTRON®A, Schering Corporation, now Merck) at 500 IU/mL. The cells are 
cultured in 100 mL cell culture bags (AFC) in a 37°C, 5% CO2 incubator. An odd number of cell 
culture bags will be set up to initiate the culture of each DC vaccine batch. Depending on the 
total number of monocytes obtained from the elutriation step the number of cell culture bags to 
be set up may vary.  
After 24 hours, GM-CSF and IFN-α are added to the cell culture bags to replenish the cell 
culture media at concentrations of 100 ng/mL and 500 IU/mL, respectively. After 48 hours of 
culture the antigen peptides are added to the cell culture bags in the following manner. CEF 
peptides are added to one of the cell culture bags (e.g., Bag #1 of 15) to give a final 
concentration of 2 µM. To half of the remaining cell culture bags (e.g., Bags #2-8 of 15) the 
Cyclin B1 peptides are added to give a final concentration of 2 µM. To the other half of the 
remaining cell culture bags (e.g., Bag #9-15 of 15) the WT1 peptides are added to give a final 
concentration of 3 µM. After adding the antigens the following DC activating agents are added 
to all of the cell culture bags; LPS at 5 EU/mL, CD40L at 100 ng/mL and CL075 at 1 µg/mL. 
The cells are then cultured for an additional 24 hours ± 1 hour. After completing the incubation 
the antigen-loaded and activated DC are harvested from the cell culture bags, combined, washed 
by centrifugation with Lactated Ringer’s, and then suspended in cell freezing solution (consisting 
of 10% dimethyl sulfoxide, 80% heat-inactivated autologous serum and 10% Plasma-Lyte A 
with dextrose) at 30x106 viable cells/mL for filling into glass vaccine vials. The vials containing 
1 mL of the DC vaccine suspension are then frozen for storage in a liquid nitrogen tank (at -
180°C in the liquid nitrogen vapor phase) prior to use. To prepare the inoculations for injection 
into the patient the required number of frozen DC vaccine vials are thawed, DMSO is washed 
out and the cell suspension is filled into a sterile glass vaccine vial for transport to the clinic. 
Each DC vaccine vial containing frozen cells is labeled with the following information: the 
patient’s name, DC vaccine product name, DC vaccine batch number, storage conditions, 
manufacture date (date frozen), volume in the vaccine vial or syringe, dose (concentration of 
cells in the vaccine vial or syringe), vial number (frozen vaccine vials), manufacturer’s name, 
and the warning statements: “For Autologous Use Only” , and “Caution: New Drug – Limited by 
Federal (or United States) Law to Investigational Use”. The same label information is attached to 

33 
 
the glass vaccine vial containing the Vaccine Product that is prepared for injection, along with a 
separate product expiration date and time label. All batches of frozen BIIR-BrcaVax-001 DC 
vaccine product and vaccine product prepared for injection remain in the custody of the Quality 
Assurance/Control Unit until they are released to the clinic or shipper. 
Extensive QC release testing of the frozen vaccine will include:  
a) Cell Count (Recovery) and Viability 
b) Evaluation of DC morphology by Giemsa staining of cytospun cells  
c) Evaluation of DC phenotype by multiparameter flow cytometry analysis 
d) Sterility testing (mycoplasma, gram stain, bacteria/fungus growth and endotoxin) 
e) Potency testing by phenotype and cytokine secretion. 
QC release testing of the washed DC vaccine for injection will include: 
a) Cell Count and Viability 
b) Sterility testing: gram stain and endotoxin (results available prior to injection) 
c) Sterility testing: bacterial and fungal growth (results available after injection) 
6.1.1.5 
Vaccine Administration and Vaccine Schedule 
LA TNBC patients will receive standard preoperative dose-dense dense AC (4 cycles) followed 
by TCb (4 cycles) chemotherapy, administered for 24 weeks. ER+/HER2– BC patients will 
receive standard preoperative dose-dense AC (4 cycles) followed by weekly T (12 cycles), 
administered for a total of 22 weeks. In both cohorts, chemotherapy will be combined with 
antigen-pulsed DC vaccinations administered for a total of 4 time points prior to definitive 
surgery. 
• During the AC cycles, both cohorts will receive vaccines administered on any one 
individual day between Days 9-12 of Cycle 1 and 3 of dose-dense AC. 
• For TNBC patients, vaccines will be administered on any one individual day between 
Days 11-15 of Cycle 1 and 3 of TCb. 
• For ER+/HER2– patients, vaccines will be administered Day 1 during either Cycle 2 or 
Cycle 3 and on Day 1 during either Cycle 8 or Cycle 9 of T. Vaccine is to be 
administered after T infusion is completed in patients. 
At each scheduled vaccination time point during the preoperative phase, the patient will receive a 
total of 2 injections. Each vaccination will consist of: 
• One intratumoral injection of 0.2 mL (3 x 106 cells/mL) 
• One subcutaneous injection of 1 mL (15 x 106 cells/mL), rotating injection sites in the 
dorsal or ventral surface of the upper arm (ipsilateral).  
NOTE: Needles used for drawing vaccine product into the syringe and for injection must be  
23-gauge or larger. Smaller sized needles (eg, 25- or 27-gauge) will either rupture the cells or 
cause them to clump. 
DC vaccines are timed with chemotherapy. All vaccine doses within a cycle are scheduled to be 
given approximately every 2 weeks apart. If necessary, a vaccine dose may be delayed for up to 

34 
 
2 weeks. In this case, subsequent doses should continue on a 2 week schedule, from the time of 
the delayed vaccine. If a vaccine dose is delayed more than 2 weeks, the PI and the BIIR Project 
Manager must be contacted for further instructions on continued dosing. Additional delays or 
modifications to the dosing schedule must be approved by the sponsor scientific chair.  
Timing of the vaccinations is based on data that tumor cell death associated with doxorubicin 
treatment increases the generation and functional activation of CD8 T cells required for the 
antitumor activity of doxorubicin.56 Standard pegfilgrastim support may be given for each AC 
treatment; however, no pegfilgrastim will be given during TCb or T cycles. DC vaccinations will 
be administered to the patient prior to administering chemotherapy on the given day, with the 
exception of weekly T for ER+/HER2– patients. Vaccine is to be administered after T infusion is 
completed in this cohort of patients. 
After definitive surgery and during locoregional radiation therapy to breast or chest wall and 
regional lymphatics per standard of care, patients will receive 3 boost DC vaccinations 
subcutaneously of 1 mL each (15 x 106 cells/mL), rotating injection sites in the dorsal or ventral 
surface of the upper arm (contralateral). The timing of the boosters is the same for TNBC and 
ER+/HER2– cohorts.  
• The first vaccination booster will occur once after the surgery and up to 3 days prior to 
radiation. 
• The second booster will occur 30 days ± 3 days after radiation is completed. 
• The third booster will occur 90 days ± 3 days after the 2nd boost.  
Patients will be monitored post DC infusion for any signs of infusion related reaction every 
15 minutes for 1 hour.  
ER+/HER2– BC patients will also receive standard endocrine therapy during locoregional 
radiation therapy, at the physician’s discretion, and for at least 5 years thereafter. TNBC patients 
who are non-pathologic complete responders and/or have positive lymph nodes following 
neoadjuvant treatment and surgery will receive capecitabine for 6-8 cycles (number of cycles per 
physician discretion). It will be the physician’s discretion to begin capecitabine treatment either 
during radiation or after radiation is complete. These adjuvant treatments will not alter the 
vaccine schedule delineated above. 
To reconcile the DC vaccine use and disposal, the procedure will be to ship the vial of 1.5 mL of 
prepared final Vaccine Product to the clinic and following vaccination of the patient, the unused 
portion of the Vaccine Product will be disposed of at the clinic by BIIR or Clinical Research 
Staff coordinating the study visit. 
 

35 
 
The DC vaccination schedule for LA TNBC is shown below.  
 
 
The DC vaccination schedule for ER+/HER2– BC is shown below.  
 

36 
 
6.1.1.6 
Increase or Reduction in Dose of the Dendritic Cell (DC) Vaccine 
An increase or reduction in the target dose of the dendritic cell (DC) vaccine is not permitted 
during the study. 
6.1.1.7 
Vaccine Manufacture 
The vaccine that is the subject of this IND will be manufactured in an equipped space in the BIIR 
at 3434 Live Oak Street, Dallas, Texas 75204, Room #105 GMP Facility, as described in the 
FDA IND application for this protocol.  
6.1.1.8 
Vaccine Order Preparation and Shipment 
Vaccine shipment will follow SOP VP132 “Formulated Liquid DC Vaccine Shipment at 
Ambient Temperature”. 
6.2 
NON INVESTIGATIONAL PRODUCTS 
In this protocol, the non-investigational products are: 
• Preoperative chemotherapy with preoperative dose-dense 
doxorubicin/cyclophosphamide (AC) and paclitaxel/carboplatin (TCb) or paclitaxel 
alone (T) 
• Radiation therapy to breast or chest wall and regional lymphatics  
• For ER+/HER2– BC patients only: standard endocrine therapy during and after 
radiation, per physician’s discretion 
• For TNBC non-pathologic complete responders: capecitabine treatment to begin either 
during radiation or after radiation is complete. 
• Supportive therapy (eg, pegfilgrastim, dexamethasone, cimetidine, and dyphenhydra) 
6.3 
ACCOUNTABILITY PROCEDURES 
The Investigator (or his/her designee) is responsible for maintaining accurate records of the 
receipt, dispensing, and use of all investigational materials, and may administer the study drug 
only to patients enrolled at the study. 
The study drug accountability record includes the study identification of the patient to whom the 
drug is administered, the quantity and the date of administration, and any returned, disposed of, 
or unused drug. This record is in addition to any drug accountability information recorded on the 
Case Report Form. 
6.4. 
POTENTIAL RISKS DURING STUDY 
6.4.1 
Apheresis 
The use of apheresis for the collection of human blood mononuclear cells is commonly done in 
the practice of hematology and oncology. For venous access, patients will either undergo 
venipuncture of the antecubital veins in both arms or a central venous catheter will be inserted in 
those patients whose venous access is insufficient to undergo apheresis by venipuncture. Short-
term side effects of apheresis include dysesthesias secondary to citrate anticoagulant, 

37 
 
ecchymoses at the site of venipunctures and nausea. The risk of infection related to venipuncture 
involving antecubital veins or insertion of central venous catheters is extremely low 
(approximately 1%). Other potential side effects of apheresis include hypotension, fever, catheter 
related infection and pneumothorax.  
6.4.2 
DC Vaccine administration  
It is anticipated that patients who receive DC vaccinations will experience no significant adverse 
events related to administration of the vaccine. DC vaccinations have been administered to 
approximately 2,000 cancer patients worldwide in medical trials and in some healthy volunteers 
without signs of significant toxicity other than mild injection site reactions (redness, induration 
and pain) and constitutional symptoms (chills, pyrexia, fatigue and myalgias) within 24 hours 
post-immunization that were managed on an outpatient basis and resolved within 48 hours. 
Patients may experience enlarged and tender lymph nodes contiguous with the subcutaneous 
and/or intradermal injection of DCs. Two out of approximately 30 patients vaccinated show 
exacerbation of pre-existing allergic reactions. DC vaccinations were not associated with any 
evidence of dose limiting toxicity. 
6.4.3 
Lipopolysaccharide (LPS) endotoxin 
No toxicity is anticipated from the use of LPS in the vaccine manufacturing process as the 
amount of residual endotoxin that could remain after extensive washing of the vaccine product 
will be quantitated prior to release. If the specifications for the vaccine are not met, the vaccine 
will not be administered. In process development studies using monocytes from normal donors to 
manufacture the DC vaccines, the total amount/concentration of endotoxin in sonicated vaccine 
cells has been measured and has been calculated that the amount to be injected would reach the 
concentration of 3.6 EU/10 mL, well below the 5 EU/10 mL as specified in FDA guidelines. The 
endotoxin preparation that will be used ex vivo to activate the DC vaccine has been certified by 
the FDA for in vivo use in healthy patients. 
Reference endotoxin administered as a 4 ng/kg IV bolus is associated with an acute 
inflammatory response that may consist of fever, chills, rigors, arthralgias, myalgias, malaise, 
fatigue, somnolence, mild anxiety, headache, nausea, vomiting, hypotension, hyperdynamic 
cardiac response, hyperglycemia and leukopenia/leukocytosis. Symptoms peak 2 to 3 hours after 
injection, lessen considerably by 6 to 8 hours post injection and resolve completely by 24 hours 
post administration. In the current study, however, endotoxin will be used for ex vivo activation 
of DCs and the maximum injected dose will not exceed a limit of <0.5 EU/mL. 
The endotoxin preparation used to activate the DC vaccine ex vivo is a reference endotoxin that 
has been certified by the FDA for in vivo use in healthy patients. The total amount/concentration 
of endotoxin in sonicated vaccine exposed to this concentration has been measured and it has 
been calculated that the total amount that would be injected subcutaneously will represent a 
maximum concentration of 3.6 EU/10 mL, well below the 5 EU/10 mL maximum specified in 
FDA guidelines. This amount of endotoxin is equivalent to a subcutaneous injection of 
0.025 ng/kg, well below the dose level that elicits an acute inflammatory response.   

38 
 
6.5 
DRUG-DRUG INTERACTIONS 
6.5.1 
Cyclophosphamide (Cytoxan®) 
The rate of metabolism and the leukopenic activity of cyclophosphamide reportedly are 
increased by chronic administration of phenobarbital.  
The Treating Physician should be alert for possible combined drug actions, desirable or 
undesirable, involving cyclophosphamide even though cyclophosphamide has been used 
successfully with other drugs, including other cytotoxic drugs. Cyclophosphamide treatment, 
which causes a marked and persistent inhibition of cholinesterase activity, potentiates the effect 
of succinylcholine chloride.  
If a patient has been treated with cyclophosphamide within 10 calendar days prior to general 
anesthesia, the anesthesiologist must be alerted.58 
6.5.2 
Paclitaxel (Taxol®) 
In a Phase 1 trial using escalating doses of paclitaxel (110–200 mg/m2) and cisplatin (50 or 
75 mg/m2) given as sequential infusions, myelosuppression was more profound when paclitaxel 
was given after cisplatin than with the alternate sequence (ie, paclitaxel before cisplatin). 
Pharmacokinetic data from these patients demonstrated a decrease in paclitaxel clearance of 
approximately 33% when paclitaxel was administered following cisplatin. 
The metabolism of paclitaxel is catalyzed by cytochrome P450 isoenzymes CYP2C8 and 
CYP3A4. Caution should be exercised when paclitaxel is concomitantly administered with 
known substrates (eg, midazolam, buspirone, felodipine, lovastatin, eletriptan, sildenafil, 
simvastatin, and triazolam), inhibitors (eg, atazanavir, clarithromycin, indinavir, itraconazole, 
ketoconazole, nefazodone, nelfinavir, ritonavir, saquinavir, and telithromycin), and inducers (eg, 
rifampin and carbamazepine) of CYP3A4.  
Caution should also be exercised when paclitaxel is concomitantly administered with known 
substrates (eg, repaglinide and rosiglitazone), inhibitors (eg, gemfibrozil), and inducers (eg, 
rifampin) of CYP2C8. 
Potential interactions between paclitaxel, a substrate of CYP3A4, and protease inhibitors 
(ritonavir, saquinavir, indinavir, and nelfinavir), which are substrates and/or inhibitors of 
CYP3A4, have not been evaluated in clinical trials. 
A sample list of drugs that have known interaction with cytochrome P450 can be found here: 
http://medicine.iupui.edu/flockhart/table.htm 
Reports in the literature suggest that plasma levels of doxorubicin (and its active metabolite 
doxorubicinol) may be increased when paclitaxel and doxorubicin are used in combination.59 
6.5.3 
Carboplatin (Paraplatin®) 
The renal effects of nephrotoxic compounds may be potentiated by carboplatin.60 

39 
 
6.5.4 
Capecitabine (Xeloda®) 
Anticoagulants  
Altered coagulation parameters and/or bleeding have been reported in patients taking 
capecitabine concomitantly with coumarin-derivative anticoagulants such as warfarin and 
phenprocoumon. These events occurred within several days and up to several months after 
initiating capecitabine therapy and, in a few cases, within 1 month after stopping capecitabine. 
These events occurred in patients with and without liver metastases. In a drug interaction study 
with single-dose warfarin administration, there was a significant increase in the mean AUC of S-
warfarin. The maximum observed INR value increased by 91%. This interaction is probably due 
to an inhibition of CYP2C9 by capecitabine and/or its metabolites.  
Phenytoin  
The level of phenytoin should be carefully monitored in patients taking capecitabine and 
phenytoin dose may need to be reduced. Postmarketing reports indicate that some patients 
receiving capecitabine and phenytoin had toxicity associated with elevated phenytoin levels. 
Formal drug-drug interaction studies with phenytoin have not been conducted, but the 
mechanism of interaction is presumed to be inhibition of the CYP2C9 isoenzyme by 
capecitabine and/or its metabolites.  
Leucovorin  
The concentration of 5-fluorouracil is increased and its toxicity may be enhanced by leucovorin. 
Deaths from severe enterocolitis, diarrhea, and dehydration have been reported in elderly patients 
receiving weekly leucovorin and fluorouracil.  
CYP2C9 substrates  
Other than warfarin, no formal drug-drug interaction studies between capecitabine and other 
CYP2C9 substrates have been conducted. Care should be exercised when capecitabine is 
coadministered with CYP2C9 substrates.52 
6.6 
PREMEDICATIONS 
6.6.1 
Doxorubicin and Cyclophosphamide 
There are no required/recommended premedications to prevent infusion reactions or life-
threatening events for the administration of doxorubicin and cyclophosphamide. However, all 
patients must be premedicated to prevent nausea and vomiting. The regimen selected is at 
the discretion of the Treating Physician. 
6.6.2 
Paclitaxel and Carboplatin 
Standard premedications for paclitaxel and carboplatin should be administered prior to each dose 
of paclitaxel and carboplatin: 
• Dexamethasone 8-20 mg PO (physicians may administer their standard HSR 
steroid prophylaxis regimen) 
• Diphenhydramine 25-50 mg IV (or equivalent)  

40 
 
• Cimetidine (300 mg) or ranitidine 50 mg IV (or equivalent)  
7 TREATMENT PLAN 
There are 2 patient cohorts in this study: LA TNBC patients and ER+/HER2– BC patients. 
LA TNBC: 
• DC vaccine plus preoperative chemotherapy for 24 weeks 
ER+/HER2– BC: 
• DC vaccine plus preoperative chemotherapy for 22 weeks; standard endocrine therapy 
during radiation, at the physician’s discretion, for at least 5 years thereafter. 
1. Once patients sign informed consent, they will be evaluated with a complete history, 
physical examination as well as initial studies as described in Section 8.1.  
a. LA TNBC patients will be enrolled to receive DC vaccinations during the 
24 weeks of standard preoperative dose-dense doxorubicin/cyclophosphamide 
(AC) followed by paclitaxel and carboplatin (TCb) chemotherapy;  
b. ER+/HER2– BC patients will receive DC vaccinations during the 22 weeks of 
standard preoperative dose-dense AC followed by weekly paclitaxel (T) 
chemotherapy. 
c. Study procedures will be similar in both groups.  
2. Eligible patients will then undergo apheresis to commence with vaccine manufacturing. 
After collection of peripheral blood mononuclear cells, dendritic cells will be 
manufactured from the monocyte fraction, aliquoted and frozen.  
3. Patients will also undergo research biopsies prior to the start of treatment and 1-2 days 
prior to or on Day 1 of Cycle 4 of AC to analyze the composition of the immune 
microenvironment. Patients who will have their definitive surgery outside a Baylor 
hospital will have a third research biopsy at least 1 week following the last chemotherapy 
dose and prior to surgery. Core biopsies will be obtained prior to treatment initiation for 
whole exome sequencing and expression analysis and for characterization of the tumor 
immune microenvironment.  
4. LA TNBC patients will receive standard preoperative dose-dense AC (4 cycles) followed 
by TCb (4 cycles) chemotherapy, administered for 24 weeks. ER+/HER2– BC patients 
will receive standard preoperative dose-dense AC (4 cycles) followed by weekly T 
(12 cycles), administered for a total of 22 weeks. In both cohorts, chemotherapy will be 
combined with antigen-loaded DC vaccinations administered intratumoral (one injection 
of 0.2 mL at 3 x 106 cells/mL) and subcutaneous (one injection of 1 mL at 15 x 106 
cells/mL), for a total of 4 time points prior to definitive surgery.  
a. During the AC cycles, both cohorts will receive vaccines administered on any one 
individual day between Days 9-12 of Cycles 1 and 3 of dose-dense AC. 

41 
 
b. For TNBC patients, vaccines will be administered on any one individual day 
between Days 11-15 of Cycles 1 and 3 of TCb.  
c. For ER+/HER2– patients, vaccines will be administered Day 1 during either 
Cycle 2 or Cycle 3 and on Day 1 during either Cycle 8 or Cycle 9 of T. Vaccine is 
to be administered after T infusion is completed in patients. 
d. Standard pegfilgrastim support will be given for each AC treatment; however, no 
pegfilgrastim will be given during TCb or T cycles.  
5. After preoperative treatment, patients will undergo definitive surgery, generally with 
mastectomy, and if available, fresh tissue (for patients who have their definitive surgery 
within a Baylor hospital) and residual FFPE breast cancer tissue will be collected for 
assessment of the immune microenvironment and for whole exome sequencing to identify 
cancer-associated mutations in the residual, chemotherapy-refractory cancer. Patients will 
be known to have axillary node positive disease at study entry based on biopsy or clinical 
criteria and will generally undergo level 1/2 axillary dissection at definitive surgery. 
However, patients may undergo SLN biopsy before or after chemotherapy at the 
physician’s discretion. 
6. After definitive surgery and during locoregional radiation therapy to the breast or chest 
wall and regional lymphatics per standard of care, patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL (at 15 x 106 cells/mL), rotating injection sites in the 
dorsal or ventral surface of the upper arm, with antigen-loaded DCs. The timing of the 
boosters is the same for TNBC and ER+/HER2– cohorts. The first vaccination booster 
will occur once after the surgery and up to 3 days prior to radiation; the second booster 
will occur 30 days ± 3 days after radiation is completed; and the third booster will occur 
90 days ± 3 days after the 2nd boost. 
7. ER+/HER2– BC patients will also receive standard endocrine therapy during locoregional 
radiation therapy, at the physician’s discretion, and for at least 5 years thereafter. 
8. TNBC patients who are non-pathologic complete responders and/or have positive lymph 
nodes following neoadjuvant treatment and surgery will receive capecitabine for 6-8 
cycles (number of cycles per physician discretion). It will be the physician’s discretion to 
either begin capecitabine treatment during radiation or after radiation is complete. 
 

42 
 
The treatment schema is shown in Table 1.   
Table 1. 
Treatment schema 
Agent 
Dose* 
Frequency of 
administration 
Route of 
administration 
Doxorubicin  
60 mg/m2 
Cycle 1-4, Day 1, 
q14 days 
IV 
Cyclophosphamide  
600 mg/m2 
Cycle 1-4, Day 1, 
q14 days 
IV 
Paclitaxel for  
LA TNBC 
80 mg/m2 
Cycle 5-8,  
Days 1, 8, 15, 
q28 days 
IV  
Paclitaxel for  
ER+/HER2– BC 
80 mg/m2 
Cycles 1-12, Day 1, 
q7 days 
IV  
Carboplatin  
AUC=6 
Cycle 5-8, Day 1, 
q28 days 
IV 
Capecitabine 
1000 mg/m2 
Cycles 6-8#, Days 1-
14, q21 days 
PO 
*Note: The treating physician may adjust chemotherapy doses based on individual patient 
histories to optimize dose delivery, per standard of care. 
# cycle number per physician discretion. 
 
7.1 
CHEMOTHERAPY TREATMENT DELAY 
If a treatment day variation is needed for reasons other than toxicity, an attempt should be made 
to keep the variation within the following parameters: ±4 calendar days. Any delay within this 
window is NOT a deviation. Note: This delay window does not apply to Cycle 1.  
Patients will continue with study therapy, at reduced chemotherapy doses at the physician’s 
discretion, when treatment is resumed after a delay in treatment. 
7.2 
CHEMOTHERAPY DOSE MODIFICATION FOR TOXICITY 
Standard of care dose reductions are to be made according to the system showing the greatest 
degree of toxicity. Toxicities will be graded according to the NCI Common Terminology Criteria 
for Adverse Events (CTCAE) Version 4.03 as linked in Appendix I. Each chemotherapy 
treatment cycle will begin only when:  
• ANC ≥1000 
• Platelets ≥100,000 
• Resolution of non-hematologic toxicities to ≤Grade 1 or baseline 
Dose reductions will be at the physician’s discretion. One dose reduction will be permitted for 
doxorubicin, cyclophosphamide, and paclitaxel. Two dose reductions are permitted for 
carboplatin. Capecitabine dose reductions are permitted per standard of care, drug package 
insert, or physician’s standard practice. No dose reductions for DC vaccines will be permitted. 
Patients will resume treatment with the next planned cycle (provided improvement/resolution in 
toxicities) as outlined below. Dose reductions are permanent. 

43 
 
If doxorubicin, cyclophosphamide, paclitaxel, carboplatin, and/or capecitabine treatment is 
interrupted, DC vaccinations may still be administered following consultation with the study PI, 
Dr. O'Shaughnessy. A patient will be deemed to be off study treatment if the patient stops DC 
vaccinations, but will continue to be followed for clinical outcome. 
The dose reduction levels doxorubicin, cyclophosphamide, paclitaxel, and carboplatin are shown 
in Table 2. 
Table 2. 
Dose Reduction Levels  
Level 
Doxorubicin 
Cyclophosphamide 
Paclitaxel 
Carboplatin 
Starting Dose 
(Level 0) 
60 mg/m2 
600 mg/m2 
80 mg/m2 
AUC=6 
Level -1a 
48 mg/m2 
480 mg/m2 
70 mg/m2 
AUC=5 
Level -2a 
N/A 
N/A 
N/A 
AUC=4 
a If patients cannot tolerate Level -1 (or Level -2 for carboplatin), there will be no further dose reduction; 
patients will be taken off chemotherapy but may continue with the vaccinations after the Treating Physician 
and study PI confer (per Section 9.4.9). 
7.3 
HEMATOLOGIC TOXICITY 
Treatment decisions and any potential dose reductions on standard of care drug should be 
made based on ANC and platelet counts on the day of treatment administration. 
• Patients must have ANC of ≥1000/mm3 on Day 1 of each cycle (if pegfilgrastim or 
filgrastim is being used) or of ≥1200/mm3 on Day 1 (if no pegfilgrastim is being used) 
to receive scheduled treatment. Treatment may be delayed to allow sufficient time for 
recovery. 
• Patients must have a platelet count of ≥100,000/mm2 on Day 1 of each cycle to 
receive scheduled chemotherapy treatment. Doxorubicin, cyclophosphamide, 
paclitaxel, and carboplatin should be delayed until platelet counts recover to 
≥100,000/mm2 and then treated with either full dose or reduced dose chemotherapy at 
the physician’s discretion. Treatment may be delayed to allow sufficient time for 
recovery. 
Use of hematopoietic growth factors to ameliorate hematologic toxicity is at the discretion of the 
physician investigator and should be in accordance with the American Society of Clinical 
Oncologists (ASCO) guidelines.  
7.4 
RADIATION THERAPY 
All patients who undergo lumpectomy or who undergo mastectomy and have 4 or more positive 
axillary nodes must be treated with radiation therapy (RT) according to the institutional or 
practice standards. All decisions regarding post mastectomy RT in patients with 1 to 3 positive 
nodes, as well as the specific radiation portals are at the discretion of the Treating Physician. The 
following data must be captured on the CRF: sites of radiation (breast, lymph node beds, boost 
site(s)); dates of radiation and doses administered; and list of regional lymphatic beds that were 
included in the field. 

44 
 
ER+/HER2– BC patients will also receive standard endocrine therapy during locoregional 
radiation therapy, at the physician’s discretion, for at least 5 years thereafter. The type of 
endocrine therapy, dosing, and duration must be captured on the CRF. 
TNBC patients who are non-pathologic complete responders and/or have positive lymph nodes 
following neoadjuvant treatment and surgery will receive capecitabine for 6-8 cycles (number of 
cycles per physician discretion). It will be the physician’s discretion to begin capecitabine 
treatment either during radiation or after radiation is complete. 
8 SCHEDULE OF PROCEDURES AND ASSESSMENTS 
The schedule of assessments for the trial is shown in Appendix II. If a required observation or 
procedure is missed, documentation is required in the source records, on the Protocol Deviation 
Form, and on the CRF, to explain the reason for this protocol deviation. 
For scheduling purposes, Day 1 is the first day of chemotherapy administration. Return 
appointments must always be scheduled from Day 1 of the study. It is imperative that all visits 
occur within the specified windows. 
8.1 
SCREENING 
Note: Assessments that are part of the standard of care of breast cancer patients and 
obtained within 4 weeks of the screening visit, are acceptable as part of the screening tests. 
Results of such tests will be acceptable even if obtained prior to the execution of the Inform 
Consent.  
Prior to entry into the study, the following assessments will be performed to determine if patient 
is eligible to continue in the study as per section 4.2 and 4.3 describing the inclusion and 
exclusion criteria for the study. 
1. A signed Patient Informed Consent Form and HIPAA Form must be obtained. 
2. It has been confirmed that the patient meets all inclusion criteria and none of the exclusion 
criteria. 
3. Assign patient screening number. 
4. Obtain demographic information (date of birth, ethnicity, race and sex). 
5. Within 4 weeks prior to enrollment obtain the following assessments: 
a) Complete medical history, including family history of breast and ovarian cancer, and 
collection of BRCA1/2 status, if applicable or known.  
b) Complete physical examination (including vital signs, height, and body weight)  
c) ECOG Performance Status Scale (Appendix III)    
d) Review and record of prior and concomitant medications  
e) Complete blood count (CBC) with differential and platelet count   
f) Complete metabolic profile (CMP) including: serum chemistries (creatinine, glucose, 
total protein, blood urea nitrogen [BUN], total carbon dioxide [CO2], albumin, total 
bilirubin, alkaline phosphatase, and aspartate transaminase [AST] and alanine 
transaminase [ALT]) and electrolytes (total calcium, chloride, potassium, sodium) 

45 
 
g) Clinical assessment of the patient’s locoregional disease (ie, by physical 
examination) 
h) Radiological assessment of tumor stage (eg, chest and abdomen CT, radionuclide 
bone scan). A PET/CT scan is acceptable for the initial staging evaluation.  
6. Females of childbearing potential must have a serum or urine pregnancy test performed 
within 7 calendar days prior to enrollment. 
7. Baseline LVEF (left ventricular ejection fraction) determination must be obtained by 
echocardiogram within 6 weeks before the first dose of study drugs and must be ≥55%  
8. Apheresis Processing Profile Test (Hepatitis B Core AB, Hepatitis B surface AG, Hepatitis 
C Virus AB, HIV Virus 1/2 AB, HTLV and syphilis). 
9. Schedule appointment for apheresis procedure. 
10. A toxicity assessment/assessment of adverse events, since the day the informed consent was 
signed. 
11. Whole blood collection (40 mL) for immunomonitoring studies. 
8.2 
REGISTRATION PROCEDURES 
The enrollment process begins when the Coordinator has obtained a signed informed consent.  
Patients who continue to meet eligibility criteria at the screening visit, the study coordinator will 
complete a Patient Registration Form which will be e-mailed to the Project Manager at BIIR 
(contact details and forms will be provided at the study initiation visit) for sponsor representative 
review to approve registration into the study. The Project Manager will respond back to the site 
by email with the form advising approval from Sponsor Representative. The Sponsor 
Representative may also require additional information or clarifications prior to advising of 
his/her opinion.    
Patients who fail to meet the entrance criteria as detailed in Section 4.2 and 4.3 are defined as 
“screen failures”. For patients defined as “screen failure”, the screening log will include the 
following information: protocol number, investigator, patient number (screening number), date 
of birth, gender, screen failure date and reason for failure. 
A screening log will be maintained by research staff during the entire time of the study. The 
screening log will be kept in a binder for review for any reason (ie, monitoring/audit). 
The PI may be allowed the opportunity to review and grant exceptions for minor deviations in 
eligibility, in order to maximize patient accrual without jeopardizing patient safety or scientific 
integrity of these studies. Examples might include minor deviations of baseline labs, timing of 
prior treatment or tests, etc. It is recognized that these questions arise frequently. The procedure 
to be followed is for the Investigator or his/her representative (ie, study coordinator) to e-mail the 
request to the PI and Project Manager at BIIR for an exception. The PI would then make a 
determination, which is binding. In no instance should this exception constitute a safety issue for 
the patient or a significant deviation from the scientific purpose of the study.  
Treatment must begin within 20±7 working days (not counting the day of dosing) after the 
patient’s registration on study. 

46 
 
8.3 
APHERESIS PROCEDURES 
The procedure used to collect monocytes during apheresis was developed by Gambro, Inc. Refer 
to the BIIR SOP Number VP 113.05 for the Gambro system of collection. The use of apheresis 
in the collection of human blood mononuclear cells (MNC) is commonplace. The procedure 
involves a standard venipuncture of an antecubital vein with return venipuncture in the opposite 
extremity and lasts approximately 3-4 hours (corresponding to 6-10L). Patients will have 
apheresis performed at Baylor University Medical Center (BUMC) Apheresis Collection Center 
and the apheresis bag will be transported to Baylor Institute for Immunology Research (BIIR) 
cGMP Facility for processing. If necessary, a central venous line will be placed for venous 
access in patients who have inaccessible antecubital veins.  
The goal of the MNC collection is to collect a product that meets the following specifications: 
• White blood cell (WBC) content - ≥5 x 109 to 30 x 109 
• Monocyte content - ≥1 x 109 
• Granulocyte content - <3% 
• Red blood cell (RBC) content - <7.5 Ml 
 
One blood draw will be performed at the time of apheresis: 
1. Peripheral blood will be collected in Red Top (non-anticoagulated) tubes (60 mL) for serum 
to be used in vaccine manufacturing. 
Failure of peripheral venous access during apheresis will not be considered a collection of cells, 
as, with the subject’s consent, a central venous line can be placed and an apheresis completed. In 
the event that the apheresis is suboptimal, ie, that an inadequate monocyte collection is achieved 
or that the vaccine cannot be manufactured from the product collected, one additional apheresis 
will be allowed no less than 7-10 days after the first apheresis. Apheresis product must meet 
required specifications for vaccine to be manufactured. Manufactured vaccine must meet 
required specification to be released for injection.  
Refer to the “Guidelines for the Collection of Mononuclear Cell (MNC) Products for the Elutra® 
Cell Separation System Monocyte Enrichment Protocol”, SOP Number: VP 122.04. 
 
8.4 
PERIPHERAL BLOOD MONONUCLEAR CELL ISOLATION 
After the mononuclear cells are collected from the patients, and received by the cGMP Facility at 
BIIR they will undergo, for further processing for generation of the DC vaccine. Specifically the 
monocytes will be separated from other mononuclear cells using a closed elutriation system 
ELUTRA (Gambro). 
Refer to the “Apheresis Product Processing by Elutriation Using the Gambro Elutra™”, SOP 
Number: VP 113.05. 
8.5 
PROCEDURES DURING STUDY DRUG TREATMENT 
The following evaluations will be performed at the beginning of each cycle, unless otherwise 
specified: 

47 
 
NOTE: For ER+/HER2– patients during the T cycles, the following evaluations will be 
performed on Day 1 every 3 weeks (Day 1, Cycles 1, 4, 7, and 10). 
There is a window (up to 4 calendar days prior to the scheduled time point) for assessments 
during the study. Assessments that are to be done on days when study drug is administered must 
be done prior to dosing as these assessments (CBC, CMP, assessment of response, PS, etc) may 
determine whether or not standard of care drug is administered, or if a dose reduction is 
necessary.  
1. An abbreviated medical history on Day 1 of each cycle (unless otherwise indicated), to 
capture events that have occurred since the last cycle. Events that were not captured in the 
baseline complete medical history should be recorded on the AE page of the CRF. 
2. A physical examination, including vital signs and body weight. 
3. Assessment of PS on the ECOG scale (Appendix III).  
4. Assessment of concomitant medications Day 1 of each cycle. 
5. CBC with differential and platelet count 
6. CMP  
7. Assessment of LVEF by ECHO, as clinically indicated 
8. Tumor response by clinical assessment of the patient’s breast and axillary disease (ie, by 
physical examination) must be performed every 2 weeks during therapy. The largest diameter 
of the breast mass and axillary LN(s) will be assessed and recorded every 2 weeks during 
preoperative chemotherapy. 
9. Research biopsies of the patient’s breast tissue must be obtained prior to the first day of 
treatment and also 1-2 days prior or on Day 1 of Cycle 4 of AC for assessment of modulation 
of the immune microenvironment. Patients who will have their definitive surgery outside of 
a Baylor hospital will have a third research biopsy at least 1 week following the last 
chemotherapy dose and prior to surgery. 
10. Immunomonitoring studies: Obtain approximately 30 mL of whole blood prior to all 
vaccinations; prior to surgery; and prior to radiation (see Section 8.10). 
11. Breast cancer tissue will be collected for assessment of the immune microenvironment and 
for tumor whole exome sequencing at time of definitive surgery for patients who have their 
definitive surgery within a Baylor hospital. 
12. A toxicity assessment/assessment of adverse events must be performed Day 1 of each cycle 
of chemotherapy and Day 1 of each vaccination. 
13. Patient diary assessment 
8.6 
PROCEDURES FOR VACCINE TREATMENT VISITS 
The following evaluations will be performed at the time of vaccine administration, unless 
otherwise specified: 
1. Assessment of PS on the ECOG scale (Appendix III), only during visits prior to definitive 
surgery. No assessment of ECOG is required at vaccine visits post-surgery. 
2. Assessment of concomitant medications 

48 
 
3. Assessment of LVEF by ECHO, as clinically indicated 
4. A toxicity assessment/assessment of adverse events 
5. Patient diary assessment 
6. Immunomonitoring studies: Obtain approximately 30 mL of whole blood prior to all 
vaccinations. 
8.7 
PROCEDURES FOR END OF TREATMENT VISIT (EOT) 
A final study visit (End of Treatment or Off Treatment Visit) will be completed for all patients 
after their last dose of the DC vaccine. The End of Treatment Visit will occur within 14 days ± 2 
days after the patient has either: 
• Completed all the treatment specified under this Study  
• When patient is withdrawn from the study for whatever reason excepting those 
withdrawing consent. Patients who withdraw consent may not want any further 
assessment; however, they should be encouraged to have these final assessments done. 
NOTE: End of treatment, or off treatment, is NOT considered off study or withdrawn from the 
study. 
The following evaluations will be performed at this visit:  
1. A medical history  
2. A physical examination, including vital signs and body weight 
3. Assessment of concomitant medications 
4. CBC with differential and platelet count 
5. CMP   
6. Immunomonitoring studies: obtain approximately 40 mL of whole blood 2 weeks ± 3 days 
after the last DC vaccination (see Section 8.10). 
7. Tumor clinical assessment of the patient’s disease (ie, by physical examination) 
8. Toxicity assessment/assessment of adverse events 
9. Patient diary assessment 
8.8 
PROCEDURES FOR FOLLOW-UP VISITS 
Patients will be followed every 3 months thereafter for 3 years following the last DC vaccination. 
The following evaluations will be performed at these visits: 
1. An abbreviated medical history  
2. A physical examination, including vital signs and body weight. 
3. CBC with differential and platelet count. 
4. CMP 
5. A toxicity assessment/assessment of adverse events 
6. Obtain approximately 30 mL of whole blood for immune response to vaccine at 6 months 
and 1 year after the last DC vaccination. 

49 
 
8.9 
UNSCHEDULED VISITS 
In special cases (ie, follow up on adverse events) as judged by the Investigator, an additional 
visit to those scheduled can be performed. This visit will be recorded in the patient’s records and 
on the “Unscheduled visit” CRF pages.  
If the patient is discontinued prematurely, refer to Section 8.7 for required assessments. The 
resulting data should be documented on the appropriate CRF pages. If, at an unscheduled visit, 
the investigator determines the patient may remain on study drug, the visit assessments should be 
documented on the Unscheduled Visit CRF pages. 
NOTE: Assessments for an Unscheduled Visit are identical to Section 8.5. 
8.10 
BLOOD SAMPLES FOR IMMUNOMONITORING  
Whole blood collection for immunomonitoring studies will be obtained as follows: 
• 40 mL (4 CPT tubes and 2 tempus tubes) at baseline 
• 30 mL prior to each treatment-vaccination cycle; prior to surgery and prior to radiation 
(3 CPT tubes and 2 tempus tubes). 
• 40 mL (4 CPT tubes and 2 tempus tubes) 2 weeks ± 3 days after the last DC vaccination  
• 30 mL at 6 months and 1 year after the last DC vaccination. 
Some of the investigational procedures that could be conducted in the future on the blood and 
blood cell samples taken from patients who participate in this study will be done in laboratories 
that work closely with BIIR. Patients will be asked to give their permission for these blood 
samples to be used for future research projects. If the patient agrees that their blood samples can 
be shared, no information that identifies the patient will be given to any of the laboratories. Any 
material shared with any investigator within BIIR or other investigators outside of BIIR will be 
supplied with code number identifiers only, without the patient’s name or other identifying 
information. Access to this database is limited to study investigators and project managers only 
and is safeguarded by a password protection system. Passwords are not shared. If research 
findings are published from this study the research patient will not be identified by name. 
8.11 
BIOPSIES  
Research biopsies will be obtained at the following time points (See Appendix V for tissue 
collection and handling): 
• A minimum of four*14-gauge needle biopsy cores will be collected at baseline, prior to 
the initiation of preoperative chemotherapy (2 cores frozen, and 2 cores in RNAlater®). 
• A minimum of four* 14-gauge needle biopsy cores will be collected 1-2 days prior to or 
on Day 1 of Cycle 4 of AC (2 cores frozen, and 2 cores in RNAlater®). 
• A minimum of four*14-gauge needle biopsy cores will be collected at least 1 week 
following the last chemotherapy dose and prior to surgery (2 cores frozen, and 2 cores in 
RNAlater®), for those patients who will have their definitive surgery outside a Baylor 
hospital. 

50 
 
• Fresh tissue (for patients who have their definitive surgery within a Baylor hospital) and 
FFPE breast tissue from definitive surgery will be collected at the time of surgery and 
through the pathology department, respectively. 
*Note: if 4 research biopsy cores cannot be obtained due to limited tumor tissue, only 2 cores are 
essential for RNAlater®. 
9 SAFETY EVALUATIONS 
9.1 
TOXICITY ASSESSMENT 
Toxicities will be graded according to the NCI Common Terminology Criteria for Adverse 
Events (CTCAE) Version 4.03 as linked in Appendix I. This document can also be downloaded 
from the Cancer Therapy Evaluation Program (CTEP) home page <http://ctep.cancer.gov>. 
Events must be documented on the AE page of the CRF. 
Follow up for toxicity will be recorded the first 30 days following the last DC vaccination and 
any long-term toxicity will be followed for 3 years after completing study therapy. 
Note: Patients who die or withdraw consent are considered withdrawn from the study and no 
further information will be collected. 
9.2 
LABORATORY DATA 
For the treatment of the patient, laboratory data will be obtained according to the schedule of 
assessments. Only the laboratory data requested on the CRF need to be recorded on the 
appropriate laboratory CRF page. In addition, abnormal results that are associated with an AE 
will be documented on the Adverse Event page of the CRF if the laboratory abnormality fits the 
definition of an AE or can potentially result in an AE. 
9.3 
PATIENT DIARIES 
All enrolled patients will be requested to complete patient diaries (see Appendix IV, Patient 
Diary) for review and collection of any adverse events during administration of vaccine.   
All patients will be instructed to begin completing the diary the evening following administration 
of the DC vaccine and continue to record any new symptoms, whether or not they may be related 
to the vaccine, every evening for 1 week. 
Patients will be instructed to return the completed diary to the clinic and give to the study 
coordinator at the next scheduled clinical visit. The study coordinator will record any adverse 
events documented in the diary in the Case Report Form. 
9.4 
ADVERSE EVENTS 
9.4.1 
Definition of Adverse Event 
An adverse event (AE) is any untoward medical occurrence in a patient or clinical investigation 
patient administered a pharmaceutical product during the course of a study and which does not 
necessarily have to have a causal relationship with this treatment. Adverse events may include 

51 
 
changes in laboratory parameters during the course of the study. Disease progression will not be 
considered an adverse event. 
9.4.2 
Definition of Serious Adverse Event 
A serious adverse event (experience) or reaction is any untoward medical occurrence that at any 
dose: 
• Results in death,  
(NOTE: Any death from any cause while a patient is receiving treatment on this protocol, 
or ≤ 30 days following the last dose of protocol treatment must be reported.) 
• Is life-threatening, 
(NOTE: The term “life-threatening” in the definition of “serious” refers to an event in which 
the patient was at risk of death at the time of the event; it does not refer to an event which 
hypothetically might have caused death if it were more severe.) 
• Requires inpatient hospitalization or prolongation of existing hospitalization,  
(NOTE: Hospitalization is considered an overnight stay, therefore visits to hospital, without 
admission, are not considered serious unless they meet another criterion, (eg, medically 
significant). Planned surgery, or planned admission for study drug, is not considered an SAE 
unless, the hospitalization is prolonged or if another criterion is met.) 
• Results in persistent or significant disability/incapacity, or 
• Is a congenital anomaly/birth defect 
• Additionally, important medical events that may not be immediately life threatening or 
result in death or hospitalization, but that may jeopardize the patient or may require 
intervention to prevent one of the other outcomes listed in the definition above.  
Examples of such events are intensive treatment in an emergency room or at home for 
allergic bronchospasm; blood dyscrasias or convulsions that do not result in 
hospitalization; or development of drug dependency or drug abuse. 
9.4.3 
Definition of Unexpected Adverse Event 
An adverse reaction is considered unexpected if it is not consistent with the risk information 
described in the general investigational plan or elsewhere in the current application. 
9.4.4 
Relationship to Study Drug 
The following classifications should be used to assess the relationship between an adverse event 
and the study drugs: 
• Not related: There is not a temporal relationship to investigational product administration 
(too early, or late, or investigational product not taken), or there is a reasonable causal 
relationship between non-investigational product, concurrent disease, or circumstance 
and the AE. 
 

52 
 
• Probably related: There is a reasonable causal relationship between the investigational 
product and the AE. The event responds to dechallenge. Rechallenge is not required. 
 
• Possibly related: There is reasonable causal relationship between the investigational 
product and the AE. Dechallenge information is lacking or unclear. 
 
• Definitely related: There is a reasonable causal relationship between the investigational 
product and the AE. The event responds to withdrawal of investigational product 
(dechallenge), and recurs with rechallenge when clinically feasible 
9.4.5 
Assessment of Severity 
Adverse events are to be recorded on the AE page of the CRF. The severity (intensity) of AEs 
will be graded according to the following definitions: 
• Mild: The patient experiences awareness of symptoms but these are easily tolerated or 
managed without specific treatment. 
 
• Moderate: The patient experiences discomfort enough to cause interference with usual 
activity, and/or the condition requires specific treatment. 
 
• Severe: The patient is incapacitated with inability to work or do usual activity, and/or the 
event requires significant treatment measures. 
Changes in the severity of an AE should be documented to allow an assessment to be made of 
the duration of the event at each level of intensity. Adverse events characterized as intermittent 
require documentation of onset and duration of each episode. 
9.4.6 
Monitoring for Adverse Events During the Clinical Trial 
Patients will have baseline vital signs including temperature, pulse, respiration rate and blood 
pressure prior to each DC vaccination. Patients will receive 7 DC vaccinations intratumorally 
and/or subcutaneously. Patients will have vital signs taken approximately every 15 minutes for 
1 hour post injection prior to patient’s release. These patients will be followed at frequent 
intervals during the vaccination period and instructed prior to discharge to contact the study 
coordinator if unusual symptoms should develop at any time before the next scheduled office 
visit. 
All AEs, regardless of severity, will be followed up by the Investigator until resolution is 
satisfactory. All AEs will be recorded for up to 30 days following the last study treatment. 
All serious adverse events that occur while a patient is still enrolled in this study will be followed 
by study personnel until resolution or stabilization of the event regardless of the patient’s study 
status. 
9.4.7 
Reporting of Adverse Events 
Adverse events will be recorded for the duration of a patient’s study treatment, and for up to 
30 days following the last study treatment. All AEs, regardless of causal relationship are to be 

53 
 
recorded in the source documentation. The Investigator will attempt to establish a diagnosis of 
the event based on signs, symptoms, and/or other clinical information. The diagnosis should be 
documented as the AE/SAE and not the individual signs /symptoms. The events, and the 
relationship of each event to treatment, will be assessed by the Treating Physician and recorded 
on the CRF. Additional information about each event, such as treatment required, eventual 
outcome, and whether or not therapy had to be interrupted or dosages reduced, will also be 
recorded on the CRF. 
All Grade 2, 3 and 4 adverse events (AEs), Grades 1 and 2 alopecia, and all grades of 
neutropenia will be recorded in the CRF throughout the trial.  
Toxicities will be graded according to the NCI Common Terminology Criteria for Adverse 
Events (CTCAE) Version 4.03 as linked in Appendix I. The event, and the relationship of each 
event to treatment, will be assessed by the Investigator and recorded on the CRF. Additional 
information about each event, such as treatment required, whether or not therapy had to be 
interrupted or dosages reduced, and eventual outcome will also be recorded on the CRF. 
Pre-existing conditions will be recorded at baseline on the Medical History Form. If a pre-
existing condition does not change, it does not have to be reported as an AE on subsequent 
cycles. 
9.4.8 
Reporting of Serious Adverse Events  
All SAEs and unexpected adverse events will be reported per Baylor standard operating 
procedure (SOP) within 24 hours of becoming aware of the event. All SAEs will be reported by 
completing a SAE Report Form and emailing the form to the PI and BIIR Project Manager. 
Baylor IRB will be notified via iRIS.  
All SAEs and unexpected adverse events must be documented on the Serious Adverse Event 
Report Form and on the adverse event CRF page. The event term used on the SAE report should 
match the term in the CRF. Follow-up information for SAEs, unexpected adverse events and 
information on non-serious AEs that become serious should also be reported to the as soon as it 
is available; follow up of a patient should be conducted until resolution of the adverse event.  
The Sponsor (or delegate) is required to report all serious and unexpected adverse events associated 
with the use of Study Drug to FDA, in compliance with CFR 312.32. All SAEs that are unexpected 
and associated with use of the study cellular therapy are to be reported to MedWatch at 
http://www.fda.gov/medwatch/index.html. Form FDA 3500A will be completed, printed and 
submitted online at this URL. (Form FDA 3500 includes biologics (including human cells, 
tissues, and cellular and tissue-based products). 
The Sponsor (or delegate) will notify the FDA by telephone or by facsimile transmission of any 
unexpected fatal or life-threatening events associated with the use of the cellular therapy as soon 
as possible but no later than 7 calendar days after the event. 
9.4.9 
Removal Due to Adverse Events  
Patients who experience any of the following vaccine-related symptoms or signs as outlined in 
NCI Common Terminology Criteria for Adverse Events (CTCAE) v4.03 (Appendix I) will be 

54 
 
removed from study treatment, but will be followed for outcomes and long-term toxicity, per 
protocol: 
• Grade 2 or higher allergic reactions including bronchospasm or generalized urticaria 
• Grade 3 or greater allergic toxicity 
• Grade 2 or greater autoimmune toxicity 
• Grade 2 allergic reactions related infusion 
• Grade 3 or greater non-hematologic toxicity including site reactions. 
NOTE: The treating physician may adjust chemotherapy doses based on individual patient 
histories to optimize dose delivery, per standard of care. However, if any patient requires more 
than one dose reduction of doxorubicin/cyclophosphamide (AC) OR the need for more than one 
dose reduction of paclitaxel or 2 dose reductions of carboplatin due to treatment delays for 
hematologic toxicity or for Grade 3 or 4 non-hematologic toxicity, they will be removed from the 
study treatment. 
9.4.10 
Removal of Patients with Disease Progression While on Study 
Disease progression is not a criterion for removal from study. A patient may be withdrawn if in 
the opinion of their physician, continuation of DC infusion is not in their best interest, or if they 
require salvage treatment that may interfere with the response to DC infusion.  
9.4.11 
Pregnancy  
Women of childbearing potential (WOCBP) must be using an adequate method of contraception 
to avoid pregnancy throughout the study in such a manner that the risk of pregnancy is 
minimized. 
Before study enrollment, WOCBP must be advised of the importance of avoiding pregnancy 
during study participation and the potential risk factors for an unintentional pregnancy. The 
patient must sign an informed consent form documenting this discussion. 
If pregnancy is confirmed in a patient during the course of the study, the patient must be 
withdrawn from the study. The pregnancy must immediately be recorded on the source 
documents and CRF and will be reported by completing the Pregnancy Notification Form and 
emailing the form to the PI and BIIR Project Manager. In addition, the Investigator must report 
to the Baylor IRB any follow-up information regarding the course of the pregnancy, including 
perinatal and neonatal outcome. Infants will be followed for a minimum of 8 weeks. 
10 EFFICACY ASSESSMENTS 
10.1 
EVALUATION OF PATHOLOGIC RESPONSE 
Pathologic response to therapy is a secondary endpoint of the study protocol. Patients will 
undergo surgical resection of residual breast and axillary malignant tissue after protocol-directed 
treatment. The pathologic specimen will be graded according to the tumor regression grading 
schema called the Residual Cancer Burden (RCB).61 The following parameters are required from 
pathologic examination in order to calculate RCB after neoadjuvant treatment: 

55 
 
http://www3.mdanderson.org/app/medcalc/index.cfm?pagename=jsconvert3  
1. The largest two dimensions (mms) of the residual tumor bed in the breast (largest tumor 
bed if multicentric disease) 
2. Submission of the entire largest cross-sectional area of the residual tumor bed for 
histologic mapping, with specific identification of those slides in the pathology report 
(eg, "the largest cross-sectional area of primary tumor bed was submitted in cassettes A5 
- A9") 
• 
If the residual tumor is large (i.e. largest diameter > 5 cm), then at least 
5 representative cassettes from the largest cross-sectional area are sufficient, but 
should be identified in the original pathology report (e.g. "representative sections 
from the largest cross-sectional area of primary tumor bed were submitted in 
cassettes A5 - A9") 
3. Histologic assessment of the percentage of the tumor bed area that contains carcinoma 
(all carcinoma, i.e. invasive and in situ), select one of the following: 
o 0%, 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% 
• 
To assess cellularity it is helpful to scan across the sections of tumor bed and then 
estimate the average cellularity from the different microscopic fields. 
• 
When estimating percentage cancer cellularity in any microscopic field, compare 
the involved area with obvious standards, e.g. more or less than half, one quarter, 
one fifth, one tenth, one twentieth, etc. 
• 
Expect there to be variable cellularity within the cross section of any tumor bed, 
but estimate the overall cellularity from the average of the estimates in different 
microscopic fields of the tumor bed. 
• 
e.g. if cellularity in different fields of the tumor bed were estimated as 20%, 10%, 
20%, 0%, 20%, 30%, then an average estimate of overall cellularity would be 
20%. 
4. Histologic estimate of the percentage of the carcinoma in the tumor bed that is in situ, 
select one of the following: 
o 0%, 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% 
5. The number of positive (metastatic) lymph nodes 
6. The largest diameter (mm) of the largest nodal metastasis 
A pathologic complete response (pCR) is defined as NO pathologic evidence of invasive disease 
in the breast or axillary lymph nodes. 
The presence or absence of a pCR will be assessed separately for the tumor and the lymph nodes. 
For patients who do not achieve a pCR, the size of the residual cancer in the tumor, on 
pathologic exam, will be documented in the as well as the number of positive lymph nodes. 
Patients will have their pathologic response scored using the RCB scale. 

56 
 
 
11 STATISTICAL CONSIDERATIONS 
11.1 
POPULATIONS FOR ANALYSIS 
11.1.1 
Analysis Populations 
Intent-To-Treat (ITT) Population: Includes all patients registered on the study (eligible and 
ineligible). This population will be included in overall patient listings, in summary tables of 
patient demographics and baseline disease characteristics, and also in the list of treatment 
discontinuations after enrollment. 
Evaluable Population: Includes all eligible patients who meet the protocol-specified efficacy 
analyses requirements and who have received at least 1 inoculation of DC vaccine therapy. This 
population will comprise those patients who will be assessed for pathologic response. Early 
discontinuation of treatment (in Cycles 1-2), secondary to toxicity, will be considered a treatment 
failure. If death occurs before the completion of 1 cycle, the patient will be reported as evaluable, 
early death, but deemed not evaluable for response. 
Safety Population: Includes all patients (eligible and ineligible) who receive at least 
1 inoculation of DC vaccine therapy. This safety population will also be used for the summaries 
and analysis of all safety parameters (drug exposure, tables of adverse events information, 
including serious adverse events, etc.). Adverse events that are unrelated to treatment and that 
occur >30 days after the administration of treatment will not be reported or analyzed. 
11.1.2 
Patient Characteristics 
Patient characteristics including demographics and pretreatment characteristics, breast mass and 
axillary lymph node size, staging evaluation at baseline, medical history, and family history will 
be summarized. Descriptive statistics including sample size, mean, standard deviation, median, 
and minimum and maximum values will be presented for continuous variables. Frequency 
distributions will be presented for categorical variables. 
11.1.3 
Patient Disposition 
Patient disposition including the number of patients enrolled, completed, and discontinued from 
the study will be summarized overall and by study site. The reasons for discontinuation will also 
be summarized, and patients who discontinued will be listed. 
11.2 
HYPOTHESIS AND ENDPOINTS 
This is an exploratory and descriptive clinical trial in which the primary objective is to 
demonstrate the safety and feasibility of combining DC vaccines with preoperative 
chemotherapy.  
The secondary objectives of this trial are to determine pathologic complete response rates; 
disease-free survival; to assess immune biomarkers of immunity (antigen-specific CD8+ T cell 
immunity and TH2 T cells) in breast cancer biopsy specimens and blood samples in patients 
receiving DC vaccinations; and to assess the feasibility of immunizing LA TNBC or 

57 
 
ER+/HER2– BC patients with patient-specific tumor antigens.  
11.3 
SAMPLE SIZE 
Twenty patients will be enrolled over 20 months. 
Twenty patients provides 80% power to reject the null hypothesis that more than 20% of patients 
will develop toxicity with the combination that leads to treatment cessation, or delay in treatment 
of more than 4 weeks.  
If a patient’s apheresis product or manufactured vaccine is suboptimal after a second attempt at 
apheresis, those patients will be withdrawn from the study, and replaced. 
11.4 
STATISTICAL METHODS 
Statistical analysis will be performed by Institute for Health Care Research and Improvement 
(IHCRI), an affiliate of Baylor Health Care System. 
The administration of DC vaccine with preoperative chemotherapy will be considered safe if 
fewer than 5 of the 20 patients experience a toxicity that leads to a delay in their receiving 
chemotherapy on schedule of more than 4 weeks, or to cessation of therapy. 
Patients’ toxicity will be monitored real-time, cycle by cycle, and all grade 3-4 toxicities and any 
delays in treatment will be reviewed by the PI. The trial accrual will be put on hold for any 
incident of congestive heart failure (as none is expected) and if more than 5 patients experience a 
delay in receiving the planned chemotherapy on schedule due to toxicity, at any time in the 
accrual of the 20 patients. The conduct of the trial will be monitored by the Baylor Research 
Institute (BRI) quality assurance personnel.  
Immunologic studies will explore immune responses in the peripheral blood and the primary 
breast cancer tissues. Peripheral blood lymphocytes at each pre- and post-vaccination time points 
will be analyzed by flow cytometry for immune phenotyping and T cell subtype quantification 
according to standardized protocols. Breast cancer tissue analyses from the baseline biopsy and 
from the residual tissue obtained at definitive surgery will include: qualitative assessment of 
immune cell subsets such as T effectors, Tregs, NK cells, dendritic cells, macrophage subsets, B 
cells and expression of immune checkpoint targets such as PD-1 and PD-L1, and iTH2 cells. 
Blood and breast cancer tissue samples will be analyzed by transcriptional profiling for changes 
over time including in the BIIR-described transcriptional IL-1 signature. Findings will be 
correlated with clinical endpoints.   
Statistical analysis of immunologic studies: Continuous variables will be summarized with 
means or medians and standard deviations. Dichotomous and categorical variables will be 
summarized using counts and proportions with exact 95% confidence intervals. These summaries 
will be computed for each patient both pre- and post- administration of each DC vaccination. 
Plots will be used to show the changes in immune response over time both for each individual. 
For each vaccination, comparisons in the pre- and 14-day post-vaccine responses will be 
compared using paired t-tests (or Wilcoxon signed rank tests, if appropriate) for continuous 
variables. McNemar’s test will be used to identify significant changes in the percentage of 
individuals with a dichotomous characteristic pre- and post-vaccine. Associations between 

58 
 
immune parameters will be explored graphically (eg, scatter plots, box plots) and numerically 
(eg, correlations, χ2 tests). The relationships between the immune parameters and clinical 
outcomes (pCR rates and DFS) will be assessed using a variety of statistical techniques. 
Univariate and multivariate modeling will be used to quantify the associations between immune 
correlates and clinical outcomes. In the case of a time-to-event clinical outcome (ie, DFS), the 
Cox proportional hazards model will be used. For binary and continuous outcomes, logistic and 
linear regression will be used. Kaplan-Meier techniques will be used to quantify time-to- event 
outcomes (DFS) and Cox proportional hazards models will be used to assess risk factors and 
compare subgroups of interest. 
Interim analysis - Safety: An interim safety analysis will be performed after 10 patients have 
been enrolled, and accrual will be held at that time. If 2 of 4 or >4 of 9 patients experience the 
following, then accrual will be put on hold:  
• Any vaccine-related toxicity as outlined in Section 9.4.9 
• More than one dose reduction in AC or paclitaxel, or 2 dose reductions for carboplatin for 
hematologic or nonhematologic toxicity, as per Section 9.4.9. 
 
Constitutional symptoms that are expected to occur with vaccine therapies are not included in 
this interim safety analysis. 
The team of specialists (“DC vaccine team”) involved in this study comprises physicians, 
scientists, medical writers, trial coordinators, data specialists, regulatory experts, and laboratory 
staff. All safety and efficacy data as well as the biomarker data (when available) will be 
reviewed monthly at multidisciplinary trial oversight meetings, where all experts will be in 
attendance. 
In the event the safety conditions above occur and accrual is put on hold, a discussion will be 
held with the DC vaccine team and the FDA to discuss the safety issues, strategies to reduce 
toxicity, and whether to lift the accrual hold. If major delayed toxicity is observed later during 
the trial, the study may also be suspended or terminated for safety concerns. 
 

59 
 
12 PROTOCOL AND DATA DEVELOPMENT 
12.1 
ETHICS 
12.1.1 
Institutional Review Board 
This protocol will be implemented only after review and full approval of the protocol and the 
Patient Informed Consent Form has been obtained from a properly constituted IRB. This written 
approval must be dated and it must clearly identify the protocol, any amendments, the Patient 
Informed Consent Form, and any applicable recruiting materials and patient compensation 
programs approved. 
During implementation of this protocol, the PI is required to send various documents to the IRB 
for review: 
1. Changes to the current protocol. 
2. All protocol amendments and Patient Informed Consent Form revisions. 
3. Required progress reports. 
Particular attention is drawn to the Food and Drug Administration (FDA) regulations regarding 
the IRB. The PI is responsible for the initial and continuing review and approval of the proposed 
clinical study in accordance with these regulations. At least once a year, the IRB will be asked to 
review and re-approve the tissue collection protocol; the request must be documented in writing. 
At the end of the trial, the PI will notify the IRB that the trial has been completed. 
12.1.2 
Modification of the Protocol 
Any changes to this protocol that affect study objectives, study design, study procedures, patient 
population, or significant administrative procedures will require a formal amendment to the 
protocol. Any proposed protocol amendments must be sent in writing to the Baylor IRB. Prior to 
implementation, an amendment must be agreed upon by the Sponsor and PI and approved by the 
IRB. 
General administrative changes to the protocol are minor corrections and/or clarifications that do 
not affect the manner in which the study is to be conducted. Such administrative changes will be 
agreed upon by the Sponsor and PI and will be documented in a memorandum. The applicable 
IRB will be notified of administrative changes according to applicable IRB guidelines.  
12.1.3 
Patient Informed Consent 
The informed consent should meet the requirements of the latest version of the Declaration of 
Helsinki and any applicable regulations and guidelines. It must be approved by an institutional 
ethics committee/IRB. 
Prior to entry into the trial and before any protocol-required procedures are performed, the 
Investigator must explain the nature of the trial, its intended purpose, and the implications of 
participation to potential patients or to their legal representatives. They will be told about the 
possible risks and benefits, and the possible adverse experiences. They will be informed that 
patients’ participation is voluntary, and that they may withdraw consent to participate at any 

60 
 
time. They will also be informed that if patients choose not to participate in the trial, alternative 
treatments are available; such refusal will not prejudice further treatment of their disease. 
Potential patients or their legal representatives must be given the opportunity to ask questions 
about the trial protocol and the procedures involved. 
Finally, each patient will be told that his or her records may be accessed by authorized personnel 
and other authorized individuals without violating the patient’s confidentiality, to the extent 
permitted by the applicable laws and/or regulations. By signing the written Patient Informed 
Consent Form, the patient or his or her legal representative is authorizing such access. Following 
this explanation and prior to entry into the trial, the written, dated, and signed Patient Informed 
Consent Form must be obtained from each patient or his or her legal representative; a copy will 
be given to the person signing the form. 
12.1.4 
Confidentiality of Records 
Case report forms, study reports and all other communications relating to this study will identify 
patients by initials and assigned patient numbers by Baylor Institute for Immunology Research. 
Access to all pertinent medical records to verify data recorded on the case report forms and to 
audit the data collection process will be allowed only to personnel who are directly involved with 
this aspects of the conduct of the study. All records will be kept in a secured location in the 
offices of the Investigator. The US Food and Drug Administration (FDA) may also request 
access to study records and source documents. 
12.2 
STUDY RECORDS 
12.2.1 
Documentation 
A log of all patients evaluated for this protocol must be maintained. Patients excluded from 
admission will be provided with a clear explanation of the specific reasons why they have been 
excluded from the study. Patients who are included will be assigned a patient identification 
number. 
For each patient treated with the study drug(s), the Research Coordinator is required to prepare 
and maintain case histories that include all observations and other data pertinent to the 
investigation. This will include all source documents needed to verify the accuracy of all 
observations and other data contained in the CRFs on each study patient. 
The Investigator or his/her designee is required to retain the records related to the trial for a 
period of 2 years following the date a marketing application is approved for the indication being 
investigated. If no application is to be filed or if the application is not approved for such 
indication, the records must be retained until 2 years after the investigation is discontinued and 
the regulatory agencies are notified. 
12.2.2 
Case Report Form  
Data will be entered at the site using the protocol CRF. The Investigator or his/her designee is 
responsible for recording all data relating to the trial on the CRFs. Data reported on the CRF that 
are derived from source documents must be consistent with the source documents or the 
discrepancies must be explained. 

61 
 
Paper CRFs must be completed legibly in ink. Individual case report forms will be reviewed, 
signed and dated by the Investigator when patients complete the study, withdraw from treatment 
or are withdrawn from the study by the Investigator. Corrections to entries will be crossed out 
with a single line and the correct value written above. The corrected entry will then be initialed 
and dated by the person authorized to make corrections in the case report forms.  
The Investigator must verify that all data entries on the CRFs are accurate and correct. CRFs 
must be completed within 15 calendar days of the end of each cycle and within 15 calendar 
days following completion of study therapy. 
12.2.3 
Source Documents 
Source documents consist of, but not limited to, in-patient hospital charts, clinic notes, original 
test results, laboratory data, worksheets, drug accountability records, consent forms, etc. Source 
documents must be available for review and inspection during on-site monitoring of the study by 
the Sponsor agent and their designee(s), IRB, and/or appropriate regulatory authorities.  
12.2.4 
Electronic Databases  
Databases containing patient demographics and other data pertinent to the main objectives of the 
study will be maintained by the study Sponsor and the data management team at Baylor 
University Medical Center.  The databases will be password protected and will be available for 
authorized personnel only to view the data.   
12.2.5 
Databases Processing 
Case report form data will be entered into a quality controlled database. Data will be reviewed 
and validated. Data clarifications will be requested of investigators or their designees, and the 
database will be edited appropriately. The database will be authorized for release when all data 
management quality control procedures are completed. Data entered in these databases will be 
the main source of clinical data to be reviewed by the Data Safety Monitoring Board. 
13 QUALITY CONTROL AND QUALITY ASSURANCE PROCEDURES 
13.1 
MULTIDISCIPLINARY TRIAL OVERSIGHT MEETINGS 
The team of specialists (“DC vaccine team”) involved in this study is comprised of physicians, 
scientists, medical writers, trial coordinators, data specialists, regulatory experts, and laboratory 
staff. All safety and efficacy data as well as the biomarker data (when available) will be 
reviewed monthly at multidisciplinary trial oversight meetings, where all experts will be in 
attendance.  
13.2 
PROTOCOL INITIATION MEETING  
All personnel involved in the implementation of this study protocol will attend a protocol 
initiation meeting prior to opening the study to enrollment. During this protocol initiation 
meeting, each person will be informed of his/her responsibilities for the duration of the study. 
The procedures for assuring that adequate and correct documentation of all study activity is 
maintained throughout the study will be reviewed. Case report forms and other pertinent study 

62 
 
materials will be examined as well as procedures for reporting serious adverse events and 
variations from protocol. 
13.3 
BIOSTATISTICAL SUPPORT  
Consulting and monitoring of the study design and data analysis will be provided by statistical 
staff at the Institute for Health Care Research and Improvement (IHCRI), an affiliate of Baylor 
Health Care System.  IHCRI has extensive experience in clinical trial design and conduction. 
14 CLINICAL MONITORING PLAN  
14.1 
INTRODUCTION 
Clinical monitoring for the site will be conducted an interdepartmental group entitled Baylor 
Research Institute (BRI) Research Quality Improvement hereinafter referred to as the sponsor’s 
agent. A monitoring plan has been designed to ensure consistent and constant oversight of the 
clinical trial in accordance with the principles of the International Conference on Harmonization 
(ICH) Guidelines (E6), FDA “Guidelines for the Monitoring of Clinical Investigations”,  
applicable SOPs at Baylor University Medical Center, applicable SOPs at each individual 
clinical site and applicable 21CFR regulatory requirements. 
14.2 
PROCESSES 
14.2.1 
General Guidelines 
• Prior to implementation, the study must have the approval of the FDA and of a 
properly constituted Institutional Review Board (IRB) or Independent Ethics 
Committee (IEC). 
• 100% of all patients entered in the study will be monitored. 
• Each patient enrolled will be monitored for 100% of the elements. 
• The first monitoring visit will be scheduled to comply with the monitoring plan upon 
the registration of the first patient and will continue as described in the monitoring 
plan until all data has been monitored for every patient. 
14.2.2 
Study Monitoring Visits 
A representative from the sponsor’s agent will contact the study site a minimum of 2 weeks in 
advance to schedule a monitoring visit. After a monitoring visit has been scheduled the date will 
be confirmed in writing by the sponsor’s agent. It is anticipated that each monitoring visit will 
require approximately 2 days. A Monitoring Visit Report will be submitted to the Sponsor of the 
IND and a follow-up letter outlining observations and outstanding issues noted during the visit 
will be submitted to the investigator at each clinical site following the monitoring visit. 
Components reviewed during study monitoring consist of, but are not limited to: 
• Investigational product accountability 
• Protocol deviations and non-compliance 
• Informed Consent review 

63 
 
• Case Report Form (CRF) and source document verification 
• Regulatory document/binder review 
• Adverse Event/Serious Adverse Event reporting 
14.2.2.1 Investigational product accountability 
The principal investigator, co-investigator or designated staff member will maintain accurate 
records of the receipt, dispensing and use of all investigational products for this study using 
forms provided by BIIR. The log will be monitored against source documentation for the 
accuracy of investigational products receipt, use and dispensation. 
14.2.2.2 Protocol deviations and non-compliance 
The representative from the sponsor’s agent will use Data Clarification forms to notify the site of 
all protocol deviations. All concerns observed during routine monitoring visits that relate to 
significant occurrences of non-compliance to protocol or other regulatory requirements will be 
addressed through a Clinical Trial Escalation procedure initiated by the sponsor’s agent. All such 
concerns will be reported to the BIIR Project Manager overseeing monitoring of the project who 
will in turn notify the Sponsor Representative or a delegated representative at BIIR. 
14.2.2.3 Informed consent review 
Proper informed consent will be obtained from all participating patients in the clinical trial. 
During monitoring visits, each informed consent will be reviewed by the sponsor’s agent to 
ensure that all consent forms have been properly signed and dated by each participating patient 
or their authorized representative, the person obtaining the informed consent and the principal 
investigator. A copy of the signed document will be given to the patient, an additional copy will 
be filed with the regulatory documents at each site and another copy will be maintained in the 
patient’s medical record if this procedure is in conformance with the institution’s policy.   
14.2.2.4 CRF and source document verification 
Records related to the clinical trial will be maintained in accordance with FDA CFR 312.62. 
Corrections will be made on the original document so as not to obscure an audit trail and will 
include the date of correction, initials of the individual making the correction, and the reason for 
the change. 
Source documents to be reviewed at each clinical site include, but are not limited to: 
• medical charts 
• nursing notes 
• medical consultation notes 
• discharge summaries 
• laboratory reports 
• diagnostic reports 
• clinical notes 

64 
 
14.2.2.5 Regulatory document/binder review  
100% review of all essential regulatory documents will be performed at each site visit. Such 
documents include, but are not limited to: 
• Study protocol 
• Protocol clarifications/amendments 
• Investigator annual reports 
• Site signature/delegation of authority logs 
• Informed consent forms 
• IRB review and approval documentation 
• IRB correspondence 
• IRB membership list 
• Laboratory certificate(s) of accreditation 
• Laboratory Director(s) curriculum vitae 
• Laboratory(s) reference ranges 
• Safety reports 
• Investigator(s) curriculum vitae and medical license 
• Form FDA 1572 
• Financial disclosure forms 
• Patient screening/enrollment log(s) 
Copies of all essential documents will be maintained in the offices of the regulatory specialist 
and updated on an ongoing basis. 
14.2.2.6 Adverse event/serious adverse event reporting 
The sponsor’s agent will ensure that all requirements of the overseeing IRB and of the protocol 
have been met and documented appropriately by the clinical site. All serious adverse events will 
be monitored for appropriate reporting to the Sponsor Representative so that all serious adverse 
events may be reported to the FDA by the Sponsor Representative according to timelines 
outlined in 21CFR 312 subpart D. 

65 
 
15 REFERENCES 
1. Fisher B, Brown A, Mamounas E, et al. Effect of preoperative chemotherapy on local-
regional disease in women and operable breast cancer: findings from National Surgical 
Adjuvant Breast and Bowel Project B-18. J Clin Oncol. 15:2483-2493, 1997. 
2. Rastogi P, Anderson SJ, Bear HD, et al. Preoperative chemotherapy: updates of National 
Surgical Adjuvant Breast and Bowel Project Protocols B-18 and B-27. J Clin Oncol. 
26:778-785, 2008. 
3. Yoshioka T, Hosoda M, Yamamoto M, et al. Prognostic significance of pathologic 
complete response and Ki67 expression after neoadjuvant chemotherapy in breast cancer. 
Breast Cancer Epub ahead of print, 2013. 
4. Liedtke C, Mazouni C, Hess KR, et al. Response to neoadjuvant therapy and long-term 
survival in patients with triple-negative breast cancer. J Clin Oncol 26:1275-1281, 2008. 
5. Von Minckwitz G, Blohmer JU, Costa S, et al. Neoadjuvant chemotherapy adapted by 
interim response improves overall survival of primary breast cancer patients – results of 
the GeparTrio trial. SABCS. S3-2 abstract, 2011. 
6. Houssami N, Macaskill P, von Minckwitz G, et al. Meta-analysis of the association of 
breast cancer subtype and pathologic complete response to neoadjuvant chemotherapy. 
Eur J Cancer 48(18):3342-3354, 2012. 
7. von Minckwitz G, Untch M, Blohmer J-U, et al. Definition and impact of pathologic 
complete response on prognosis after neoadjuvant chemotherapy in various intrinsic 
breast cancer subtypes. J Clin Oncol 30(15):1796-804, 2012. 
8. Park KH, Gad E, Goodell V, et al. Insulin-like growth factor-binding protein-2 is a target 
for the immunomodulation of breast cancer. Cancer Res 68, 8400-8409, 2008. 
9. Knutson KL, Schiffman K, Disis ML. Immunization with a HER-2/neu helper peptide 
vaccine generates HER-2/neu CD8 T-cell immunity in cancer patients. J Clin Invest 107, 
477-484 2001. 
10. Anderson KS. Tumor vaccines for breast cancer. Cancer Invest 27, 361-368, 2009. 
11. Disis ML, Schiffman K. Cancer vaccines targeting the HER2/neu oncogenic protein. 
Semin Oncol 28, 12-20, 2001. 
12. Loi S, Sirtaine N, Piette F, et al. Prognostic and predictive value of tumor-infiltrating 
lymphocytes in a phase III randomized adjuvant breast cancer trial in node-positive breast 
cancer comparing the addition of docetaxel to doxorubicin with doxorubicin-based 
chemotherapy: BIG 02-98. J Clin Oncol 31:860-867, 2013. 
13. Finn OJ. Cancer vaccines: between the idea and the reality. Nat Rev Immunol 3, 630-641, 
2003. 
14. Townsend AR, Gotch FM, Davey J. Cytotoxic T cells recognize fragments of the 
influenza nucleoprotein. Cell 42, 457-467, 1985. 

66 
 
15. Boon T, Cerottini JC, Van den Eynde B, et al. Tumor antigens recognized by T 
lymphocytes. Annu Rev Immunol 12, 337-365, 1994. 
16. Rosenberg SA. Cancer vaccines based on the identification of genes encoding cancer 
regression antigens. Immunol Today 18, 175-182, 1997. 
17. Pardoll DM. Cancer vaccines. Nat Med 4, 525-531, 1998. 
18. Gilboa E. The makings of a tumor rejection antigen. Immunity 11, 263-270, 1999. 
19. Palucka K, Banchereau J. Cancer immunotherapy via dendritic cells. Nat Rev Cancer 12, 
265-277, 2012. 
20. Schneider BP, Winer EP, Foulkes WD, et al. Triple-negative breast cancer: risk factors to 
potential targets. Clin Cancer Res 14, 8010-8018, 2008. 
21. Sorlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas 
distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98, 
10869-10874, 2001. 
22. Kao H, Marto JA, Hoffmann TK, et al. Identification of cyclin B1 as a shared human 
epithelial tumor-associated antigen recognized by T cells. J Exp Med 194, 1313-1323, 
2001. 
23. Straver ME, Glas AM, Hannemann J, et al. The 70-gene signature as a response predictor 
for neoadjuvant chemotherapy in breast cancer. Breast Cancer Res Treat 119:551-558, 
2010. 
24. Egloff AM, Vella LA, Finn OJ. Cyclin B1 and other cyclins as tumor antigens in 
immunosurveillance and immunotherapy of cancer. Cancer Res 66, 6-9, 2006. 
25. Yu M, Zhan Q, Finn OJ. Immune recognition of cyclin B1 as a tumor antigen is a result 
of its overexpression in human tumors that is caused by non-functional p53. Mol 
Immunol 38, 981-987, 2002. 
26. Suzuki H, Graziano DF, McKolanis J. et al. T cell-dependent antibody responses against 
aberrantly expressed cyclin B1 protein in patients with cancer and premalignant disease. 
Clin Cancer Res 11, 1521-1526, 2005. 
27. Neidhardt-Berard EM, Berard F, Banchereau J, et al. Dendritic cells loaded with killed 
breast cancer cells induce differentiation of tumor-specific cytotoxic T lymphocytes. 
Breast Cancer Res 6, R322-328, 2004. 
28. Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-
treated, node-negative breast cancer. New Engl J Med 351:2817-2826, 2004. 
29. Paik S, Tang G, Shak S, et al. Gene expression and benefit of chemotherapy in women 
with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 24(23):3726-
3734, 2006. 
30. Saito H, Dubsky P, Dantin C, et al. Cross-priming of cyclin B1, MUC-1 and survivin 
specific CD8+T cells by dendritic cells loaded with killed allogeneic breast cancer cells. 
Breast Cancer Res 8, R65, 2006. 

67 
 
31. Chapuis AG, Ragnarsson GB, Nguyen HN, et al. Transferred WT1-reactive CD8+ T cells 
can mediate antileukemic activity and persist in post-transplant patients. Sci Transl Med 
5(174):174ra27, 2013. 
32. Craig DW, O'Shaughnessy JA, Kiefer JA, et al. Genome and transcriptome sequencing in 
prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. 
Mol Cancer Ther 12(1):104-16, 2013. 
33. Qi XW, Zhang F, Yang XH, et al. High Wilms' tumor 1 mRNA expression correlates 
with basal-like and ERBB2 molecular subtypes and poor prognosis of breast cancer. 
Oncol Rep 28(4):1231-6, 2012. 
34. Nasomyon T, Samphao S, Sangkhathat S, et al. Correlation of Wilms' tumor 1 isoforms 
with HER2 and ER-α and its oncogenic role in breast cancer. Anticancer Res 34(3):1333-
1342, 2014.  
35. Wang L and Wang Z-Y. The Wilms' tumor suppressor WT1 induces estrogen-
independent growth and anti-estrogen insensitivity in ER-positive breast cancer MCF7 
cells. Oncol Rep 23:1109-1117, 2010.  
36. Kroemer G, Galluzzi L, Kepp O, et al. Immunogenic cell death in cancer therapy. Annu 
Rev Immunol. 31:51-72, 2013. 
37. Ma Y, Adjemian S, Mattarollo SR, et al. Anticancer chemotherapy-induced intratumoral 
recruitment and differentiation of antigen-presenting cells. Immunity 38(4):729-41, 2013. 
38. Michaud M, Martins I, Sukkurwala AQ, et al. Autophagy-dependent anticancer immune 
responses induced by chemotherapeutic agents in mice. Science 334(6062):1573-7, 2011. 
39. Sandoval F, Terme M, Nizard M, et al. Mucosal imprinting of vaccine-induced CD8+ T 
cells is crucial to inhibit the growth of mucosal tumors. Sci Transl Med 5:72ra20, 2013. 
40. Banchereau J, Palucka AK. Dendritic cells as therapeutic vaccines against cancer. Nat 
Rev Immunol 5, 296-306, 2005. 
41. Early Breast Cancer Trialists’ Collaborative Group. Effects of adjuvant tamoxifen and of 
cytotoxic therapy on mortality in early breast cancer. An overview of 61 randomized 
trials among 28,896 women. N Engl J Med. 319:1681-1692, 1988. 
42. Early Breast Cancer Trialists’ Collaborative Group. Effects of chemotherapy and 
hormonal therapy for early breast cancer on recurrence and 15-year survival: An 
overview of the randomised trials. Lancet 365:1687-1717, 2005. 
43. Citron ML, Berry DA, Cirrincione C, et al. Randomized trial of dose-dense versus 
conventionally scheduled and sequential versus concurrent combination chemotherapy as 
postoperative adjuvant treatment of node-positive primary breast cancer: first report of 
Intergroup Trial C9741/Cancer and Leukemia Group B Trial 9741. J Clin Oncol 21:1431-
1439, 2003. 
44. Mamounas EP, Bryant J, Lembersky B, et al. Paclitaxel after doxorubicin plus 
cyclophosphamide as adjuvant chemotherapy for node-positive breast cancer: results from 
NSABP B-28. J Clin Oncol 23:3686-3696, 2005. 

68 
 
45. Berry DA, Cirrincione C, Henderson IC, et al. Estrogen-receptor status and outcomes of 
modern chemotherapy for patients with node-positive breast cancer. JAMA 295:1658-
1667, 2006. 
46. Carey LA, Dees EC, Sawyer L, et al. The triple-negative paradox: primary tumor 
chemosensitivity of breast cancer subtypes. Clin Cancer Res 13:2329, 2007. 
47. Decatris MP, Sundar S, O'Byrne KJ. Platinum-based chemotherapy in metastatic breast 
cancer: current status. Cancer Treat Rev 30(1):53-81, 2004. 
48. Belani CP, Kearns CM, Zuhowski EG, et al. Phase 1 trial, including pharmacokinetic and 
pharmacodynamic correlations, of combination paclitaxel and carboplatin in patients with 
metastatic non-small-cell lung cancer. J Clin Oncol 17(2):676-84, 1999. 
49. Telli ML, Jensen KC, Kurian AW, et al. PrECOG 0105: Final efficacy results from a 
phase II study of gemcitabine (G) and carboplatin (C) plus iniparib (BSI-201) as 
neoadjuvant therapy for triple-negative (TN) and BRCA1/2 mutation-associated breast 
cancer. J Clin Oncol 31 Suppl. Abstract 1003, 2013. 
50. Silver DP, Richardson AL, Eklund AC, et al. Efficacy of neoadjuvant Cisplatin in triple-
negative breast cancer. J Clin Oncol 28(7):1145-53, 2010. 
51. Sikov WM, Berry DA, Perou CM, et al. Impact of the addition of carboplatin and/or 
bevacizumab to neoadjuvant weekly paclitaxel followed by dose-dense AC on pathologic 
complete response rates in triple-negative breast cancer. San Antonio Breast Cancer 
Symposium. Abstract S5-01, 2013. 
52. Xeloda package insert, 2015 
53. Mackean M, Planting A, Twelves C, et al. Phase I and pharmacologic study of 
intermittent twice-daily oral therapy with capecitabine in patients with advanced and/or 
metastatic cancer. J Clin Oncol 16(9):2977-85, 1998. 
54. O'Shaughnessy JA, Blum J, Moiseyenko V, et al. Rnadomized, open-label, phase II trial 
of oral capecitabine (Xeloda) vs. a reference arm of intravenous CMF 
(cyclophosphamide, methotrexate and 5-fluorouracil) as first-line therapy for 
advanced/metastatic breast cancer. Ann Oncol 12(9):1247-54, 2001. 
55. Lee S-J, Toi M, Ohtani S, et al. A phase III trial of adjuvant capecitabine in breast cancer 
patients with HER2-negative pathological residual invasive disease after neoadjuvant 
chemotherapy (CREATE-X/JBCRG-04). SABCS 2015, Abstract S1-07. 
56. Mattarollo SR, Loi S, Duret H, et al. Pivotal role of innate and adaptive immunity in 
anthracycline chemotherapy of established tumors. Cancer Res 71:4809-4820, 2011. 
57. Yi M, Huo L, Koenig KB, et al. Estrogen receptor positivity: 10% or 1%? Cancer 
Research 72(24): Suppl 3, 2012. 
58. Cytoxan package insert, 2005 
59. Taxol package insert, 2011 
60. Paraplatin package insert, 2010 

69 
 
61. Symmans WF, Peintinger F, Hatzis C, et al. Measurement of residual breast cancer 
burden to predict survival after neoadjuvant chemotherapy. J Clin Oncol 25:4414-4422, 
2007. 

70 
 
Appendix I 
NCI Common Terminology Criteria for Adverse Events (CTCAE), 
Version 4.0 
Publish Date: May 28, 2009 
 
COMMON TERMINOLOGY CRITERIA FOR ADVERSE EVENTS (CTCAE)  
Version 4.0 
 
As of May 28, 2009 (v4.03: June 14, 2010), NCI has edited version 4.0 of the Common 
Terminology Criteria for Adverse Events. These may be obtained at the following web link 
http://evs.nci.nih.gov/ftp1/CTCAE/CTCAE_4.03_2010-06-14_QuickReference_8.5x11.pdf. 
 
DO NOT USE CTC VERSION 3.0 TO GRADE TOXICITIES IN THIS STUDY! 
 
 

Appendix II 
Schedule of Assessments  
LA TNBC Patients: 
 
Category 
Screening 
Apheresis 
Pre-Operative Chemotherapy Week 1 to Week 
24a 
Surgery 
Week  
28 ± 1 
Week 
RT 
Week 32 ± 2 Weeks 
EOT 
14 days 
± 2 days 
after last 
DC 
vaccine 
2 weeks 
± 3 days 
after last 
DC 
Vaccine 
 
Follow 
Up 
(every 3 
months 
for 3 
years) 
Vaccine Booster 
Up to 
3 days 
prior 
to 1st 
RT 
30 days ± 
3 days 
after RT is 
completed 
90 
days 
 ± 3 
days 
after 
2nd 
boost 
AC 
Cycle 1 
AC 
Cycle 3 
TCb 
Cycle 1 
TCb  
Cycle 
3 
Each Cycle  
(AC 1-4 and 
TCb 1-4) 
Day of Cycle 
-28 
to -
1 
 
9-12b 
9-12b 
11-15b 
11-15b 
1 
PER   PROTOCOL 
Informed Consent and HIPAA 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/ Exclusion criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical Historyc, d 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
X 
 
X 
Vital Signs, Weight and Heighte 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
X 
 
X 
Physical Examf 
X 
 
X 
X 
X 
X 
Xg 
 
 
 
 
X 
 
X 
ECOG 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
 
 
 
Pregnancy Test for WCBPh  
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Concomitant Medications 
X 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
 
CBC 
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
X 
CMP 
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
X 
Clinical Assessment  
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
 
Radiological Assessment 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Apheresis Profile Test 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Blood for Vaccine Manufacturing 
 
60 
mL 
 
 
 
 
 
 
 
 
 
 
 
 
LVEFi,j 
X 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
 
 
 
Blood Draw for Immunomonitoringk 
40 
mL 
 
30 mL 
30 mL 
30 mL 
30 mL 
 
 
30 mL 
30 mL 
30 mL 
 
40 mL 
30 mLk 
Research Biopsies 
Xl 
 
 
Xl 
 
 
 
Xm 
 
 
 
 
 
 
DC Vaccine 
 
 
X 
X 
X 
X 
 
 
X 
X 
X 
 
 
 
Capecitabine for TNBC no pCR pts 
 
 
 
 
 
 
 
 
Xn 
Xn 
Xn 
 
 
 

72 
 
 
                                                 
a TNBC patients will receive preoperative dose-dense doxorubicin/cyclophosphamide followed by paclitaxel and carboplatin (AC/TCb) chemotherapy for 24 weeks combined.  
b During the AC cycles, both cohorts will receive vaccinations on any one individual day between Days 9-12 of Cycles 1 and 3 of dose-dense AC. For TNBC patients, vaccinations 
will be administered on any one individual day between Days 11-15 of Cycles 1 and 3 of TCb. 
c Medical history should include family history of breast and ovarian cancer, and collection of BRCA1/2 status, if applicable or known. 
d Only an abbreviated medical history will be obtained to capture events that have occurred since the last cycle. Events that were not captured in the baseline complete medical history 
should be recorded on the AE page of the CRF. 
e Height will only be obtained at the screening visit. 
f Only a limited physical assessment focusing on the affected breast, including vital signs and body weight, will be performed at vaccine treatment visits. 
g Only an abbreviated physical exam will be performed 
h Serum or urine pregnancy test will be performed for all women of childbearing potential within 7 days prior to enrollment. Negative result must be available prior to first dose of the 
study drugs. 
i Left ventricular ejection fraction determination must be obtained by echocardiogram within 6 weeks before the first dose of study drugs and must be >55%. 
j Assessment of LVEF as clinically indicated. 
k For 40 mL blood draws, 4 CPT tubes and 2 tempus tubes will be used for collection. For 30 mL blood draws, 3 CPT tubes and 2 tempus tubes will be used for collection. For blood 
draws occurring during follow-up, 30 mL will only be collected at 6 months and 1 year after the last DC vaccination. 
l Patients will undergo research biopsies of their breast cancer prior to the start of treatment and 1-2 days prior or on Day 1 of Cycle 4 of AC to analyze the composition of the 
immune microenvironment. Core biopsies will be obtained to collect tissue for future whole exome sequencing and expression analysis.  
m Patients who will have their definitive surgery outside a Baylor hospital will have a third research biopsy at least 1 week following the last chemotherapy dose and prior to surgery. 
If available, fresh tissue (for patients who have their definitive surgery within a Baylor hospital) and residual FFPE breast cancer tissue will be collected for assessment of the 
immune microenvironment and for whole exome sequencing to identify cancer-associated mutations in the residual, chemotherapy-refractory cancer. 
n TNBC patients who are non-pathologic complete responders and/or have positive lymph nodes following neoadjuvant treatment and surgery will receive capecitabine for 6-8 cycles 
(number of cycles per physician discretion). It will be the physician’s discretion to begin capecitabine treatment either during radiation or after radiation is complete. 
o Follow up for toxicity will be recorded the first 30 days after last DC vaccine and any long-term toxicity will be followed for 3 years after completing study therapy. 
 
Instruct Diary 
Completion/Assessment 
 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
 
Adverse Events  
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Toxicity Assessment 
 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
Xo 

Schedule of Assessments  
ER+/HER2- Patients: 
 
Category 
Screening 
Apheresis 
Pre-Operative Chemotherapy Week 1 to Week 
22p 
Surgery 
Week 
25 ± 1 
Week 
RT 
Week 29 ± 2 Weeks 
EOT 
14 days 
± 2 days 
after last 
DC 
vaccine 
2 weeks 
± 3 days 
after last 
DC 
Vaccine 
 
Follow 
Up 
(every 3 
months 
for 3 
years) 
Vaccine Booster 
Up to 
3 
days 
prior 
to 1st 
RT 
30 days ± 3 
days after 
RT is 
completed 
90 
days 
 ± 3 
days 
after 
2nd 
boost 
AC 
Cycle 1 
AC 
Cycle 
3 
T 
Cycle  
2 or 3 
T 
Cycle  
8 or 9 
Each Cycle 
(AC 1-4 and  
T 1, 4, 7, 10) 
Day of Cycle 
-28 
to -
1 
 
9-12q 
9-12q 
1q 
1q 
1 
PER   PROTOCOL 
Informed Consent and HIPAA 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Inclusion/ Exclusion criteria 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical Historyr, s 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
X 
 
X 
Vital Signs, Weight and Heightt 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
X 
 
X 
Physical Examu 
X 
 
X 
X 
X 
X 
Xv 
 
 
 
 
X 
 
X 
ECOG 
X 
 
X 
X 
X 
X 
X 
 
 
 
 
 
 
 
Pregnancy Test for WCBPw  
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Concomitant Medications 
X 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
 
CBC 
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
X 
CMP 
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
X 
Clinical Assessment  
X 
 
 
 
 
 
X 
 
 
 
 
X 
 
 
Radiological Assessment 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Apheresis Profile Test 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
Blood for Vaccine Manufacturing 
 
60 
mL 
 
 
 
 
 
 
 
 
 
 
 
 
LVEFx,y 
X 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
 
 
 
Blood Draw for Immunomonitoringz 
40 
mL 
 
30 mL 
30 mL 
30 mL 
30 mL 
 
 
30 mL 
30 mL 
30 mL 
 
40 mL 
30 mLz 
Research Biopsies 
Xaa 
 
 
Xaa 
 
 
 
Xbb 
 
 
 
 
 
 
DC Vaccine 
 
 
X 
X 
X 
X 
 
 
X 
X 
X 
 
 
 
Endocrine Therapycc 
 
 
 
 
 
 
 
 
X 
X 
X 
X 
X 
X 
Instruct Diary 
 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
 

74 
 
 
                                                 
p Patients will receive preoperative dose-dense doxorubicin/cyclophosphamide followed by paclitaxel (AC/T) chemotherapy for 22 weeks combined. 
q During the AC cycles, both cohorts will receive vaccinations on any one individual day between Days 9-12 of Cycles 1 and 3 of dose-dense AC. For ER+/HER2– patients, 
vaccines will be administered Day 1 during either Cycle 2 or Cycle 3 and on Day 1 during either Cycle 8 or Cycle 9 of T. Vaccine is to be administered after T infusion is completed 
in this cohort of patients. 
r Medical history should include family history of breast and ovarian cancer, and collection of BRCA1/2 status, if applicable or known. 
s Only an abbreviated medical history will be obtained to capture events that have occurred since the last cycle. Events that were not captured in the baseline complete medical history 
should be recorded on the AE page of the CRF. 
t Height will only be obtained at the screening visit. 
u Only a limited physical assessment focusing on the affected breast, including vital signs and body weight, will be performed at vaccine treatment visits. 
v Only an abbreviated physical exam will be performed 
w Serum or urine pregnancy test will be performed for all women of childbearing potential within 7 days prior to enrollment. Negative result must be available prior to first dose of 
the study drugs. 
x Left Ventricular Ejection fraction determination must be obtained by echocardiogram within 6 weeks before the first dose of study drugs and must be >55%. 
y Assessment of LVEF as clinically indicated. 
z For 40 mL blood draws, 4 CPT tubes and 2 tempus tubes will be used for collection. For 30 mL blood draws, 3 CPT tubes and 2 tempus tubes will be used for collection. For blood 
draws occurring during follow-up, 30 mL will only be collected at 6 months and 1 year after the last DC vaccination. 
aa Patients will undergo research biopsies of their breast cancer prior to the start of treatment and 1-2 days prior or on Day 1 of Cycle 4 of AC to analyze the composition of the 
immune microenvironment. Core biopsies will be obtained to collect tissue for future whole exome sequencing and expression analysis. 
bb Patients who will have their definitive surgery outside a Baylor hospital will have a third research biopsy at least 1 week following the last chemotherapy dose and prior to surgery. 
If available, fresh tissue (for patients who have their definitive surgery within a Baylor hospital) and residual FFPE breast cancer tissue will be collected for assessment of the 
immune microenvironment and for whole exome sequencing to identify cancer-associated mutations in the residual, chemotherapy-refractory cancer. 
cc ER+/HER2– BC patients will also receive standard endocrine therapy during locoregional radiation therapy, at the physician’s discretion, and for at least 5 years thereafter. 
dd Follow up for toxicity will be recorded the first 30 days after last DC vaccine and any long-term toxicity will be followed for 3 years after completing study therapy. 
 
Completion/Assessment 
Adverse Events  
X 
 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Toxicity Assessmentdd 
 
 
X 
X 
X 
X 
X 
 
X 
X 
X 
X 
 
X 

Appendix III 
ECOG Performance Status Scale 
Grade  
Description 
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 light or sedentary nature—(eg, light 
housework or office work) 
2 
Ambulatory and capable of all self care, but unable to carry out 
any work activities; up and about > 50% of waking hours 
3 
Capable only of limited self-care, confined to bed or chair 
>50% of waking hours 
4 
Completely disabled; cannot carry out any self care; totally 
confined to bed chair 
5 
Dead 
 
Source: Oken MM, Creech RH, Tormey DC, et al. Toxicity and Response Criteria of The Eastern Cooperative 
Oncology Group. Am J Clin Oncol. 1982; 5:649-655. 

76 
 
Appendix IV 
Patient Diary 
 
BAYLOR INSTITUTE FOR  IMMUNOLOGY RESEARCH              
 
 
 
 
SUBJECT DIARY 
Baylor IRB Project #013-154 “Pilot Safety Trial of Preoperative 
Chemotherapy Combined with Dendritic Cell Vaccine in Patients 
With Locally Advanced, Triple-Negative Breast Cancer or ER-
Positive, HER2-Negative Breast Cancer” 
 
Subject ID #XXX-XXX-XX-___-___ 
 
 
 
 
 
 
 
 
 
 
 

77 
 
 

78 
 
Appendix V 
Research Biopsies – Collection and Handling 
RNAlater ® example: 
 
 

79 
 
MATERIALS REQUIRED (SPECIMEN KIT PROVIDED BY BIIR BPM CORE): 
1. 
Specimen containers 
2. 
Requisition Form  
3. 
Labels 
4. 
Specimen poly bag 
LABELING AND REQUISITION: 
All specimens should be clearly labeled BEFORE being sent to the BIIR BPM Core, to ensure correct 
identification of the patient and sample. Each specimen/container must be labeled with the labels from the KIT. 
Specimen container(s) must be tightly sealed to ensure safe handling and quality patient results. Leaking 
specimen container(s) may result in poor fixation, illegible labeling and lost tissue samples.  
All specimens must be submitted with a completed Biopsy Tissue Collection Form. Indicate the date, the time 
the specimen was removed from the patient and the time the specimen was placed in containers on the BPM 
Biopsy Tissue Collection Form where indicated. 
SPECIMEN COLLECTION: 
Obtain 4 to 5 core biopsies. Place 2-3 core biopsies into a non-breakable, leak proof, sterile container and the 
remaining 2 core biopsies into the containers containing RNAlater®. 
FRESH BIOPSY PREPARATION INSTRUCTIONS: 
1. Place the biopsies on a piece of slightly moistened saline gauze. Care should be taken to keep the 
tissue from drying out. The tissue should NOT be immersed in saline. 
2. Place the tissue on the gauze into the container tightening the screw cap (please use one container per 
specimen). 
3. Label containers appropriately. 
4. Specimens must be placed into a specimen polybag.  
5. The completed Biopsy Tissue Collection Form must be placed in the separate pocket of the poly bag 
for this purpose (separated from the specimen container).  
RNAlater® BIOPSY PREPARATION INSTRUCTIONS: 
1. Place the 2 -3 dissected tissue specimens (less than 0.5 cm in any one dimension) in a vial containing 
RNAlater®. 
2. Cap the vial and ensure tissue is fully submerged in the solution. 
3. Label containers appropriately. 
4. Specimens must be placed into a specimen polybag.  
5. The completed Biopsy Tissue Collection Form must be placed in the separate pocket of the poly bag 
for this purpose (separated from the specimen container).  
DELIVERY INSTRUCTIONS: 
1. Transport specimens at room temperature in a small Styrofoam container to BIIR BPM Core located at 
the Sammons Cancer Center, suite 600, within one hour of the procedure.  
 
2. For inquiries contact: 
• 
BIIR BPM Core at 214-820-7834 or bpmcore@bswhealth.org 
• 
Luz Stella Muniz (Project Manager) at 214-820-7310 or luz.muniz@bswhealth.org  
 

 
IRB File # 013-154 Amendment 1 
Version Date: March 06, 2014 
80 
 
Appendix VI 
013-154 Amendment 1 List of Changes 
Protocol Section 
Original Text 
Revised Text 
Rationale 
Title Page 
---------------- 
Amendment 1, Date: January 31, 
2014; 
IND 15765; 
Protocol 013-154; 
3410 Worth Street, Suite 6224 
Dallas, TX 75246 
Updated protocol 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 1. 
Updated protocol 
Study Synopsis – Summary  
In the second group, IL-1 blockade 
with anakinra will be added to the 
treatment regimen. 
In the second group, IL-1 blockade 
with anakinra will be added to the 
preoperative chemotherapy and DC 
vaccine. 
Updated to match text in protocol. 
Study Synopsis – Inclusion Criteria 
Section 4.2 – Inclusion Criteria 
5. 
Adequate hematologic function, 
defined by: 
a. Absolute neutrophil count 
(ANC) >1500/mm3 
b. Platelet count 
≥100,000/mm3 
c. Hemoglobin >9 g/dL 
5. 
Adequate hematologic function, 
defined by: 
a. Absolute neutrophil count 
(ANC) >1500/mm3 
b. Platelet count 
≥100,000/mm3 
c. Hemoglobin >9 g/dL (in the 
absence of red blood cell 
transfusion) 
Clarification of inclusion criterion #5”. 
Study Synopsis – Exclusion Criteria; 
Section 4.3 – Exclusion Criteria 
1. Evidence of metastatic disease 
on bone scan and CT scan of 
chest/abdomen (or PET CT scan). 
1. Evidence of metastatic disease 
on bone scan and CT scan of 
chest/abdomen (or PET CT scan). 
Patients with intrathoracic 
metastatic adenopathy are 
Clarification of exclusion criterion #1. 

 
IRB File # 013-154 Amendment 1 
Version Date: March 06, 2014 
81 
 
Protocol Section 
Original Text 
Revised Text 
Rationale 
eligible. 
Study Synopsis – Medication and 
Doses  
Section 3 – Study Design (4th, 5th, and 
6th paragraphs) 
Section 7 – Treatment Plan, #4 
; the following 10 patients will receive 
DC vaccinations and anakinra 100 mg 
SC for 7 days, followed by 7 days off, 
then repeating during the 16 weeks of 
preoperative chemotherapy. 
… 
Patients will receive standard 
preoperative dose-dense 
doxorubicin/cyclophosphamide (4 
cycles) followed by paclitaxel (4 
cycles; AC/T) chemotherapy, 
administered every 2 weeks for 16 
weeks combined with antigen-loaded 
DC vaccinations administered 
intratumoral (one injection of 0.5 mL 
at 2 x 106 cells/mL) and subcutaneous 
(one injection of 1 mL at 14 x 106 DCs) 
on Day 2 of Cycles 1 and 3 of dose-
dense AC and on Day 3 of Cycles 1 and 
3 of T (4 timepoints). Standard 
pegfilgrastim support will be given on 
Day 2 of each AC treatment. 
After preoperative treatment, patients 
will undergo definitive surgery, 
generally with mastectomy, and if 
available, the residual FFPE breast 
cancer tissue will be collected for 
; the following 10 patients will be a 
staggered enrollment, and will receive 
DC vaccinations and anakinra 100 mg 
SC for 7 days, followed by 7 days off, 
then repeating during the 16 weeks of 
preoperative chemotherapy. 
… 
Patients will receive standard 
preoperative dose-dense 
doxorubicin/cyclophosphamide (4 
cycles) followed by paclitaxel (4 
cycles; AC/T) chemotherapy, 
administered every 2 weeks for 16 
weeks combined with antigen-loaded 
DC vaccinations administered 
intratumoral (one injection of 0.2 mL 
at 3 x 106 cells/mL) and subcutaneous 
(one injection of 1 mL at 15 x 106 DCs) 
on any one individual day between 
Days 9-12 of Cycles 1 and 3 of dose-
dense AC and on any one individual 
day between Days 9-12 of Cycles 1 
and 3 of T (4 timepoints). Standard 
pegfilgrastim support will be given for 
each AC treatment. 
After preoperative treatment, patients 
will undergo definitive surgery, 
Modification of enrollment of 
patients, introducing a staggered 
enrollment in order to monitor the 
safety of the novel combination; brief 
description of enrollment. 
 
Modification to the vaccine 
specifications and timing of vaccine 
administration. 
 
Removal of pegfilgrastim 
administration specificity.  
 
Addition of fresh tissue collection at 
the time of definitive surgery, in 
addition to FFPE. 

 
IRB File # 013-154 Amendment 1 
Version Date: March 06, 2014 
82 
 
Protocol Section 
Original Text 
Revised Text 
Rationale 
assessment of the immune 
microenvironment and for whole 
exome sequencing to identify cancer-
associated mutations in the residual, 
chemotherapy-refractory cancer. 
 
After definitive surgery and during 
locoregional radiation therapy to the 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
(at 14 x 106 cells/mL) in the ventral 
surface of the upper arm, with 
antigen-loaded DCs. The first 
vaccination booster will occur once 
after the surgery and prior to 
radiation; the second booster will 
occur one month after radiation is 
completed; and the third booster will 
occur 3 months after the 2nd boost. 
generally with mastectomy, and if 
available, fresh tissue and residual 
FFPE breast cancer tissue will be 
collected for assessment of the 
immune microenvironment and for 
whole exome sequencing to identify 
cancer-associated mutations in the 
residual, chemotherapy-refractory 
cancer. 
After definitive surgery and during 
locoregional radiation therapy to the 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
(at 15 x 106 cells/mL) in the ventral 
surface of the upper arm, with 
antigen-loaded DCs. The first 
vaccination booster will occur once 
after the surgery and up to 3 days 
prior to radiation; the second booster 
will occur 30 days ± 3 days after 
radiation is completed; and the third 
booster will occur 90 days ± 3 days 
after the 2nd boost. 
Section 3 – Study Design (1st 
paragraph) 
Section 6.1.2.3 – Dosing and 
Administration 
Section 7 – Treatment Plan, #1 
Enrollment in Group 1 will complete 
before enrollment can begin in Group 
2. Study procedures will be similar in 
both groups.  
Enrollment in Group 1 will complete 
before enrollment can begin in Group 
2. For Group 2, there will be a 
staggered enrollment, in order to 
observe the safety of AC/T 
Modification of enrollment of 
patients, introducing a staggered 
enrollment in order to monitor the 
safety of the novel combination; 
extensive description of enrollment. 

 
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chemotherapy, DC vaccinations, and 
anakinra. After the first 3 patients 
have been enrolled in Group 2, 
enrollment will be held for 
observation of these patients for the 
4 months of AC/T chemotherapy plus 
anakinra plus DC vaccine for adverse 
events, prior to enrolling a second set 
of 3 patients. Observation of these 
next 3 patients will occur over the 
4 months of AC/T, anakinra, and DC 
vaccine for toxicity prior to completing 
enrollment of the last 4 patients in 
Group 2. Study procedures will be 
similar in both groups.  
 
Section 3 – Study Design Schema 
(Figure) 
(Figure) 
Figure of study design schema was 
updated to reflect the changes in the 
protocol. 
Section 4.1 – Sample Size 
Section 11.3 – Sample Size 
Twenty patients with newly diagnosed 
locally advanced TNBC will be enrolled 
over 14 months (10 patients per 
group). 
Twenty patients with newly diagnosed 
locally advanced TNBC will be enrolled 
over 20 months (10 patients per 
group). 
Updated the time to accrual 
Section 4.4 – Patient Withdrawal from 
the Study 
12. Patients who experience any of 
the following vaccine-related 
symptoms or signs as outlined in 
NCI Common Terminology 
Criteria for Adverse Events 
(CTCAE) v4.03 (Appendix I) will 
be removed from study: 
• 
Grade II or higher allergic 
12. Patients who experience any of 
the following treatment- or 
vaccine-related symptoms or 
signs as outlined in NCI Common 
Terminology Criteria for Adverse 
Events (CTCAE) v4.03 (Appendix 
I) will be removed from study 
treatment, but will be followed 
Updated and clarified the criteria for 
withdrawing patients from study, to 
include study treatment in addition to 
vaccine therapy. In particular, 
decreased the autoimmune toxicity 
from ≥Grade 3 to ≥Grade 2, to 
increase safety. 

 
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reactions including 
bronchospasm or 
generalized urticaria 
• 
Grade III or greater 
allergic toxicity 
• 
Grade III or greater 
autoimmune toxicity 
• 
Grade II allergic reactions 
related infusion 
• 
Grade III or greater 
hematologic or non-
hematologic toxicity 
including site reactions 
 
The date of and reason for 
discontinuation must be noted on the 
Case Report Form (CRF). Every effort 
should be made to complete the 
appropriate assessments. 
If the patient is withdrawn for any 
reason, the end of study assessments 
must be completed. After withdrawal 
from protocol, patients must be 
followed for adverse events (AEs) for 
30 calendar days after their last dose 
of study drug. 
for outcomes and long-term 
toxicity, per protocol: 
• 
Grade 2 or higher allergic 
reactions including 
bronchospasm or 
generalized urticaria 
• 
Grade 3 or greater 
allergic toxicity 
• 
Grade 2 or greater 
autoimmune toxicity 
• 
Grade 2 allergic reactions 
related infusion 
• 
Grade 3 or greater 
hematologic or non-
hematologic toxicity 
including site reactions 
 
NOTE: If any patient requires more 
than one dose reduction of 
doxorubicin/cyclophosphamide (AC) 
OR the need for more than one dose 
reduction of paclitaxel due to 
treatment delays for hematologic 
toxicity or for Grade 3 or 4 non-
hematologic toxicity, they will be 
removed from the study treatment. 
The date of and reason for 
discontinuation must be noted on the 
Case Report Form (CRF). Every effort 
should be made to complete the 

 
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appropriate assessments. 
If the patient is withdrawn for any 
reason, the end of study assessments 
must be completed. Patients who 
withdraw from the study treatment 
due to intolerable toxicity will still be 
followed for outcome and toxicity, per 
protocol.  
Patients must still be followed for 
adverse events (AEs) for 30 calendar 
days after their last dose of study 
drug. 
Section 6.1.1.1 – Formulation and 
Supply 
Final Formulation. The BIIR-BrcaVax-
001 DC vaccine is prepared for 
injection into the patient by thawing 
the requisite number of frozen vials of 
DC vaccine and diluting the contents 
with USP injection grade sterile 
normal saline to wash the cells by 
centrifugation. The cells are washed 3 
times with normal saline. Prior to the 
third wash a sample is taken to 
determine the cell count and viability. 
After the third wash the cells are 
divided and resuspended in normal 
saline at either 14x106 viable cells/mL 
or 2x106 viable cells/mL. The cell 
suspensions are drawn into separate 
syringes, that is, 1 mL at 14x106 
cells/mL for subcutaneous injection 
Final Formulation. The BIIR-BrcaVax-
001 DC vaccine is prepared for 
injection into the patient by thawing 
the requisite number of frozen vials of 
DC vaccine and diluting the contents 
with USP injection grade sterile 
Lactated Ringer’s to wash the cells by 
centrifugation. The cells are washed 3 
times with Lactated Ringer’s. Prior to 
the third wash, a sample is taken to 
determine the cell count and viability. 
After the third wash, the cells are 
resuspended in Lactated Ringer’s at 
15 x 106 viable cells/mL. The cell 
suspensions are filled into a 2 mL 
sterile glass vaccine vial sealed with a 
serum stopper and metal cap, for 
delivery to the clinic. Therefore, the 
Updated vaccine manufacturing 
procedure, for increased cell viability. 

 
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and 0.5 mL at 2x106 cells/mL for 
intratumoral injection, for delivery to 
the clinic. Therefore, the final 
formulation is comprised of 100% 
normal saline. 
DC vaccines are supplied in single-use, 
preservative-free 1 mL syringes. Each 
subcutaneous injection will consist of 
1 mL at 14x106 cells/mL and each 
intratumoral injection will consist of 
0.5 mL at 2x106 cells/mL. 
final formulation is comprised of DCs 
suspended in 100% Lactated Ringer’s. 
Section 6.1.1.2 – Packaging and 
Labeling 
The vaccine primary container, ie, the 
frozen glass vaccine vial and syringe 
containing the DC vaccine product for 
infusion into the patient, is labeled 
with the patient’s name, vaccine batch 
number, vaccine product name, 
manufacture date, information on cell 
fill concentration, and the “For 
Investigational Use Only” warning 
statement. 
Before infusion the patient is asked to 
read aloud the name written on the 
syringe label containing the vaccine 
preparation and to confirm that it is 
his/her name. 
The Vaccine Product container that is 
delivered to the bedside is a BD 1 mL 
syringe for the intratumoral injection 
and/or a 3 mL syringe for the 
The vaccine primary container, the 
glass vaccine vial, will be used to 
contain both the frozen DC vaccine 
product and the washed DC vaccine 
prepared for injection into the 
patient, and is labeled with the 
patient’s name, vaccine batch 
number, vaccine product name, 
manufacture date, name of the 
manufacturer, volume in the vaccine 
vial dose (concentration of cells in the 
vaccine vial or syringe), storage 
temperature, and the warning 
statements: “For Autologous Use 
Only” , and “Caution: New Drug – 
Limited by Federal (or United States) 
Law to  Investigational Use”. On the 
glass vaccine vial containing the DC 
vaccine that has been prepared for 
Updated vaccine manufacturing 
procedure, for increased cell viability. 

 
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subcutaneous injection affixed with a 
syringe cap. The vaccine filled 
syringe(s) is/are placed in a clear 
biohazard plastic zip-lock bag. Upon 
delivery to the clinic, the clinician 
inspects the syringe(s) to determine 
that it holds the correct volume and 
that no leak of the Vaccine Product 
has occurred. 
 
injection, a separate product 
expiration date and time label is 
attached. The expiration time is 2 
hours after the washed, resuspended 
DC vaccine is been filled into the glass 
vaccine vial. 
The Vaccine Product container that is 
delivered to the bedside is a glass 
vaccine vial of 1.5 mL of prepared final 
Vaccine Product (15 x 106 viable 
cells/mL) to be drawn into a syringe 
for the intratumoral and/or 
subcutaneous injection. The vaccine-
filled vial is placed in a clear biohazard 
plastic zip-lock bag and hard-foam 
shipping container for transport from 
the GMP facility to the clinic. Upon 
delivery to the clinic, the clinician 
inspects the vial to determine that it 
holds the correct Vaccine Product for 
the patient, dose and volume; and 
that no leak of the Vaccine Product 
has occurred. Before injection, the 
patient is asked to read aloud the 
name written on the glass vaccine vial 
label containing the vaccine 
preparation and to confirm that it is 
his/her name. 

 
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Section 6.1.1.3 – Storage 
Vaccines will be kept in a locked area 
with limited access at BIIR. Vaccines 
will be kept frozen in liquid nitrogen 
(vapor phase) until use. 
Vaccines will be kept in a locked area 
with limited access at BIIR. Vaccines 
will be kept frozen in liquid nitrogen 
(vapor phase) until use (removal of 
vials to prepare the Vaccine Product 
for inoculation). 
Updated vaccine manufacturing 
procedure, for increased cell viability. 
Section 6.1.1.4 – Preparation 
The following table gives an example 
of the number of bags to be initiated 
for DC culture based on a different 
number of monocytes available for 
culture. 
... 
After completing the incubation the 
antigen-loaded and activated DC are 
harvested from the cell culture bags, 
combined, washed by centrifugation 
with normal saline, and then 
suspended in cell freezing solution 
(consisting of 10% dimethyl sulfoxide, 
80% heat-inactivated autologous 
serum and 10% Plasma-Lyte A with 
dextrose) at 30x106 viable cells/mL for 
filling into glass vaccine vials. The vials 
containing 1 mL of the DC vaccine 
suspension are then frozen for storage 
in a liquid nitrogen tank (at -180°C in 
the liquid nitrogen vapor phase) prior 
to use. To prepare the inoculations for 
injection into the patient the required 
frozen DC vaccine vials are thawed, 
An odd number of cell culture bags 
will be set up to initiate the culture of 
each DC vaccine batch. 
... 
After completing the incubation the 
antigen-loaded and activated DC are 
harvested from the cell culture bags, 
combined, washed by centrifugation 
with Lactated Ringer’s, and then 
suspended in cell freezing solution 
(consisting of 10% dimethyl sulfoxide, 
80% heat-inactivated autologous 
serum and 10% Plasma-Lyte A with 
dextrose) at 30x106 viable cells/mL for 
filling into glass vaccine vials. The vials 
containing 1 mL of the DC vaccine 
suspension are then frozen for storage 
in a liquid nitrogen tank (at -180°C in 
the liquid nitrogen vapor phase) prior 
to use. To prepare the inoculations for 
injection into the patient the required 
number of frozen DC vaccine vials are 
thawed, DMSO is washed out and the 
cell suspension is filled into a sterile 
Corrected a misstatement of inclusion 
of a table. 
 
Updated vaccine manufacturing 
procedure, for increased cell viability. 

 
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DMSO is washed out and the cell 
suspension is drawn into syringes for 
transport to the clinic. Each DC 
vaccine vial and filled syringe is 
labeled with the following 
information: the patient’s name, DC 
vaccine product name, DC vaccine 
batch number, storage conditions, 
manufacture date (date frozen), 
target fill volume and concentration, 
vial number, manufacturer’s name, 
and the statement “Caution: New 
Drug – Limited by Federal (or United 
States) Law to Investigational Use”. All 
batches of frozen BIIR-BrcaVax-001 DC 
vaccine product remain in the custody 
of the Quality Assurance/Control Unit 
until they are released to the clinic or 
shipper. 
Extensive release testing of the frozen 
vaccine will include:  
a) Cell Count (Recovery) and 
Viability 
b) Evaluation of DC morphology by 
Giemsa staining of cytospun 
cells  
c) Evaluation of DC phenotype by 
multiparameter flow 
cytometry analysis 
d) Sterility testing 
glass vaccine vial for transport to the 
clinic. Each DC vaccine vial containing 
frozen cells is labeled with the 
following information: the patient’s 
name, DC vaccine product name, DC 
vaccine batch number, storage 
conditions, manufacture date (date 
frozen), volume in the vaccine vial or 
syringe, dose (concentration of cells in 
the vaccine vial or syringe), vial 
number (frozen vaccine vials), 
manufacturer’s name, and the 
warning statements: “For Autologous 
Use Only” , and “Caution: New Drug – 
Limited by Federal (or United States) 
Law to Investigational Use”. The same 
label information is attached to the 
glass vaccine vial containing the 
Vaccine Product that is prepared for 
injection, along with a separate 
product expiration date and time 
label. All batches of frozen BIIR-
BrcaVax-001 DC vaccine product and 
vaccine product prepared for injection 
remain in the custody of the Quality 
Assurance/Control Unit until they are 
released to the clinic or shipper. 
Extensive QC release testing of the 
frozen vaccine will include:  
a) Cell Count (Recovery) and 

 
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e) Potency testing by phenotype. 
Viability 
b) Evaluation of DC morphology by 
Giemsa staining of cytospun 
cells  
c) Evaluation of DC phenotype by 
multiparameter flow 
cytometry analysis 
d) Sterility testing (mycoplasma, 
gram stain, bacteria/fungus 
growth and endotoxin) 
e) Potency testing by phenotype 
and cytokine secretion. 
QC release testing of the washed DC 
vaccine for injection will include: 
a) Cell Count and Viability 
b) Sterility testing: gram stain and 
endotoxin (results available 
prior to injection) 
c) Sterility testing: bacterial and 
fungal growth (results 
available after injection) 
Section 6.1.1.5 – Vaccine 
Administration and Vaccine Schedule 
At each scheduled vaccination during 
the preoperative phase, the patient 
will receive a total of 2 injections. 
Each vaccination will consist of: 
• One intratumoral injection 
of 0.5 mL (2x106 cells/mL) 
• One subcutaneous injection 
of 1 mL (14 x 106 cells/mL) 
in the ventral surface of the 
At each scheduled vaccination during 
the preoperative phase, the patient 
will receive a total of 2 injections. 
Each vaccination will consist of: 
• One intratumoral injection 
of 0.2 mL (3 x 106 cells/mL) 
• One subcutaneous injection 
of 1 mL (15 x 106 cells/mL) 
in the ventral surface of the 
Updated vaccine manufacturing 
procedure, for increased cell viability. 
 
Updated DC vaccination schedule 
figure to reflect changes in the 
protocol. 

 
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upper arm (ipsilateral). The 
cells are delivered along the 
length of the inoculation 
path as the cells are 
continuously injected as the 
needle is slowly withdrawn. 
... 
After definitive surgery and during 
locoregional radiation therapy to 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
each (14 x 106 cells/mL) in the ventral 
surface of the upper arm 
(contralateral). 
... 
(Figure) 
upper arm (ipsilateral). 
... 
After definitive surgery and during 
locoregional radiation therapy to 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
each (15 x 106 cells/mL) in the ventral 
surface of the upper arm 
(contralateral). 
... 
To reconcile the DC vaccine use and 
disposal, the procedure will be to ship 
the vial of 1.5 mL of prepared final 
Vaccine Product to the clinic and 
following vaccination of the patient, 
the unused portion of the Vaccine 
Product will be returned to the GMP 
QC laboratory for reconciliation and 
testing. 
(Figure) 
Section 6.1.1.6 – Increase or 
Reduction in Dose of the Dendritic Cell 
(DC) Vaccine 
An increase or reduction in the dose 
of the dendritic cell (DC) vaccine is not 
permitted during the study. 
An increase or reduction in the target 
dose of the dendritic cell (DC) vaccine 
is not permitted during the study. 
Clarification of the statement 
regarding the dose of vaccine. 
Section 6.1.1.8 – Vaccine Order 
Preparation and Shipment 
Vaccine order preparation and 
shipment will follow SOP VP115.04. 
Vaccine shipment will follow SOP 
VP132 “Formulated Liquid DC Vaccine 
Shipment at Ambient Temperature”. 
Updated vaccine manufacturing 
procedure, for increased cell viability. 

 
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Section 6.3 – Accountability 
procedures 
---------------- 
For the purpose of accountability, all 
unused Anakinra and package inserts 
from used Anakinra, which was 
dispensed to the patient, should be 
returned to the clinic at each visit. 
Added an accountability procedure for 
anakinra.  
Section 7.2 – Chemotherapy Dose 
Modification for Toxicity 
If doxorubicin, cyclophosphamide, and 
paclitaxel are withheld for any reason, 
anakinra and DC vaccinations may still 
be administered at the discretion of 
the Treating Physician and in 
consultation with the study PI, Dr. 
O'Shaughnessy. Patients may remain 
on-treatment regardless of which 
study drug is discontinued. A patient 
will be deemed to be off study 
treatment if the patient stops DC 
vaccinations, but will continue to be 
followed for clinical outcome. 
If doxorubicin, cyclophosphamide, and 
paclitaxel treatment is interrupted, 
anakinra and DC vaccinations may still 
be administered following 
consultation with the study PI, Dr. 
O'Shaughnessy. A patient will be 
deemed to be off study treatment if 
the patient stops DC vaccinations, but 
will continue to be followed for 
clinical outcome. 
Clarification on treatment interruption 
with regard to vaccine administration. 
Section 8.3 – Apheresis Procedures 
Section 11.3 – Sample Size 
The procedure involves a standard 
venipuncture of an antecubital vein 
with return venipuncture in the 
opposite extremity and lasts 
approximately 2-3 hours. 
... 
In the event that the apheresis is sub-
optimal, ie, that an inadequate 
monocyte collection is achieved or 
that the vaccine cannot be 
manufactured from the product 
collected, one additional apheresis 
The procedure involves a standard 
venipuncture of an antecubital vein 
with return venipuncture in the 
opposite extremity and lasts 
approximately 3-4 hours 
(corresponding to 6-10L). 
... 
One blood draw will be performed at 
the time of apheresis: 
2. Peripheral blood will be collected 
in Red Top (non-anticoagulated) 
tubes (60 mL) for serum to be 
Updated heading to include 
“Procedures”. 
Addition of an assessment to be 
performed at the time of apheresis, 
and clarified the procedure for a 
suboptimal apheresis, and addressed 
whether a patient will be replaced or 
not. 

 
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will be allowed. 
used in vaccine manufacturing. 
In the event that the apheresis is 
suboptimal, ie, that an inadequate 
monocyte collection is achieved or 
that the vaccine cannot be 
manufactured from the product 
collected, one additional apheresis 
will be allowed at least 1 week later. 
Apheresis product must meet 
required specifications for vaccine to 
be manufactured. Manufactured 
vaccine must meet required 
specification to be released for 
injection. NOTE: If a patient’s 
apheresis product or manufactured 
vaccine is suboptimal after a second 
attempt at apheresis, those patients 
will be withdrawn from the study, and 
replaced. 
Section 8.5 – Procedures During Study 
Drug Treatment 
Any delay within this window is NOT a 
deviation. 
 
10. Breast cancer tissue for formalin 
embedding will be collected for 
assessment of the immune 
microenvironment and for tumor 
whole exome sequencing at time 
of definitive surgery. 
 
 
10. Breast cancer tissue will be 
collected for assessment of the 
immune microenvironment and 
for tumor whole exome 
sequencing at time of definitive 
surgery. 
 
Deleted sentence for clarity. 
 
Deleted formalin embedding from 
tissue collection to allow for flexible 
preservation methods. 

 
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Section 8.6 – Procedures for Vaccine 
Treatment Visits 
7. CBC with differential and platelet 
count 
8. CMP 
---------------- 
Deleted unnecessary assessments. 
Section 8.9 – Unscheduled Visits 
In special cases (ie, suspicion of 
disease progression or follow up on 
adverse events) as judged by the 
Investigator, an additional visit to 
those scheduled can be performed. 
If a patient experiences a worsening in 
disease activity and it is the 
investigator’s assessment that the 
patient’s condition has worsened from 
baseline, then the patient may be 
terminated from the study. If the 
patient is discontinued prematurely, 
refer to Section 8.4 for required 
assessments. 
In special cases (ie, follow up on 
adverse events) as judged by the 
Investigator, an additional visit to 
those scheduled can be performed. 
If the patient is discontinued 
prematurely, refer to Section 8.7 for 
required assessments. 
NOTE: Assessments for an 
Unscheduled Visit are identical to 
Section 8.5. 
Clarification of assessments for an 
unscheduled visit. 
Section 8.10 – Blood Samples for 
Immunomonitoring 
Whole blood collection for 
immunomonitoring studies will be 
obtained as follows: 
• 
100 mL at baseline 
• Approximately 30 mL prior each 
treatment-vaccination cycle; 
prior to surgery and prior to 
radiation. 
• 100 mL 2 weeks after the last 
DC vaccination 
Whole blood collection for 
immunomonitoring studies will be 
obtained as follows: 
• 100 mL (11 ACD tubes and 2 
tempus tubes) at baseline 
• Approximately 30 mL prior each 
treatment-vaccination cycle; 
prior to surgery and prior to 
radiation (3 ACD tubes and 2 
tempus tubes). 
• 100 mL (11 ACD tubes and 2 
tempus tubes) 2 weeks after 
the last DC vaccination 
Added a description of the blood 
collection tubes to be used. 

 
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Section 8.11 – Biopsies 
• FFPE breast tissue from 
definitive surgery will be 
collected through the 
pathology department. 
• Fresh tissue and FFPE breast 
tissue from definitive surgery 
will be collected at the time of 
surgery and through the 
pathology department. 
Addition of fresh tissue collection at 
the time of definitive surgery, in 
addition to FFPE. 
Section 9.4.9 – Removal Due to 
Adverse Events 
Patients who experience any of the 
following vaccine-related symptoms 
or signs as outlined in NCI Common 
Terminology Criteria for Adverse 
Events (CTCAE) v4.03 (Appendix I) will 
be removed from study: 
• Grade II or higher allergic 
reactions including 
bronchospasm or generalized 
urticaria 
• Grade III or greater allergic 
toxicity 
• Grade III or greater 
autoimmune toxicity 
• Grade II allergic reactions 
related infusion 
• Grade III or greater hematologic 
or non-hematologic toxicity 
including site reactions. 
Patients who experience any of the 
following vaccine-related symptoms 
or signs as outlined in NCI Common 
Terminology Criteria for Adverse 
Events (CTCAE) v4.03 (Appendix I) will 
be removed from study treatment, 
but will be followed for outcomes and 
long-term toxicity, per protocol: 
• Grade 2 or higher allergic 
reactions including 
bronchospasm or generalized 
urticaria 
• Grade 3 or greater allergic 
toxicity 
• Grade 2 or greater autoimmune 
toxicity 
• Grade 2 allergic reactions 
related infusion 
• Grade 3 or greater non-
hematologic toxicity including 
site reactions. 
NOTE: If any patient requires more 
than one dose reduction of 
doxorubicin/cyclophosphamide (AC) 
OR the need for more than one dose 
Updated and clarified the criteria for 
withdrawing patients from study, to 
include study treatment in addition to 
vaccine therapy. In particular, 
decreased the autoimmune toxicity 
grade from ≥Grade 3 to ≥Grade 2, to 
increase safety. 

 
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reduction of paclitaxel due to 
treatment delays for hematologic 
toxicity or for Grade 3 or 4 non-
hematologic toxicity, they will be 
removed from the study treatment. 
Section 11.4 – Statistical Methods 
(Interim Safety Analysis) 
An interim safety analysis will be 
performed after 4 and 9 patients have 
completed 4 vaccines. Accrual will be 
put on hold if 2 of 4 or >4 of 9 patients 
experience the following:  
• any vaccine related Grade 4 
organ or injection site toxicity 
• a Grade 3 toxicity (other than 
autoimmune toxicity)  that 
does not resolve to Grade 1 or 
less within 2 weeks 
Constitutional symptoms that are 
expected to occur with vaccine 
therapies are not included in this 
interim safety analysis. 
In the event safety conditions above 
occur, a discussion will be held with 
the DSMB and the FDA to map out 
further vaccine development 
strategies. Otherwise, enrollment will 
continue. If major delayed toxicity are 
observed later during the trial, the 
study may also be suspended or 
terminated for safety concerns. 
An interim safety analysis will be 
performed after 4 and 9 patients have 
completed 4 vaccines in both Groups 
1 and 2. Accrual will be put on hold if 
2 of 4 or >4 of 9 patients experience 
the following:  
• 
Any vaccine-related toxicity as 
outlined in Section 9.4.9 
• 
More than one dose reduction 
in AC or paclitaxel for 
hematologic or 
nonhematologic toxicity, as 
per Section 9.4.9. 
Constitutional symptoms that are 
expected to occur with vaccine 
therapies are not included in this 
interim safety analysis. 
A separate interim safety analysis will 
be performed for Group 1 and Group 
2 separately, and the incidence of AEs 
in both groups will be compared.  
In the event the safety conditions 
above occur and accrual is put on 
hold, a discussion will be held with the 
DSMB and the FDA to discuss the 
Modifications to perform an interim 
safety analysis per group rather than 
overall. Included additional safety 
measures to include treatment 
toxicity, and procedures for accrual 
hold. 

 
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safety issues, strategies to reduce 
toxicity, and whether to lift the 
accrual hold. If major delayed toxicity 
is observed later during the trial, the 
study may also be suspended or 
terminated for safety concerns. 
References 
---------------- 
Yi M, et al. 
Addition of reference to support 
inclusion criteria #2 in the protocol. 
Appendix II – Schedule of Assessments ---------------- 
Addition of Apheresis blood collection 
assessment, 60 mL 
Addition to footnote C and O: Events 
that were not captured in the baseline 
complete medical history should be 
recorded on the AE page of the CRF. 
New footnote I and U, for Blood Draw 
for Immunomonitoring:  For 100 mL 
blood draws, 11 ACD tubes and 2 
tempus tubes will be used for 
collection. For 30 mL blood draws, 3 
ACD tubes and 2 tempus tubes will be 
used for collection.  
Addition to footnote K and W: Fresh 
tissue and.... 
Language updated to match protocol. 
Appendices IV – Mononuclear Cell 
Collection, and V – Gambro Elutra 
Apheresis 
All of appendices IV and V and 
references therein 
---------------- 
Deleted 2 SOPs that were originally 
included in the protocol, as policies 
and procedures are not usually 
included in protocols, since 
manufacturing policies and 
procedures are held confidential and 

 
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proprietary by the research 
organization. 
Appendix VI 
---------------- 
All of Appendix VI 
Added the Amendment 1 list of 
changes as an appendix to the 
protocol, in order to identify changes 
from version to version of the 
protocol quickly. 
 
Minor grammatical errors or misspellings were corrected as needed. 
 
 

 
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Appendix VII 
013-154 Amendment 2 List of Changes 
Protocol Section 
Original Text 
Revised Text 
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Title Page 
---------------- 
Amendment 2, Date: June 30, 2014 
Updated protocol 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 2. 
Updated protocol 
Study Synopsis – Inclusion Criteria 
Section 4.2 – Inclusion Criteria 
2. 
Have locally advanced TNBC with 
T3-T4 disease, and positive 
lymph nodes (radiologically or 
histologically positive), defined as 
invasive ductal cancers, ER- 
tumors with <10% of tumor 
nuclei immunoreactive 
9. 
Eligible for treatment with 
paclitaxel, doxorubicin, and 
cyclophosphamide. 
2. 
Have: 
a. locally advanced TNBC 
defined as invasive ductal 
cancer 
b. ER- tumors with <10% of 
tumor nuclei 
immunoreactive 
c. PR- tumors with <10% of 
tumor nuclei 
immunoreactive 
d. T3 or T4 disease, regardless 
of nodal status; T2 disease is 
eligible if there are positive 
lymph nodes present by 
physical exam or imagine 
evaluation or histological 
evaluation. 
9. 
Eligible for treatment with 
paclitaxel, doxorubicin, 
cyclophosphamide, and 
carboplatin. 
Expanded inclusion criteria to include 
patients with T2 disease, in order to 
increase accrual to the study. Also 
amended inclusion criteria to include 
the addition of carboplatin to the 
treatment regimen. 

 
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Study Synopsis – Medication and 
Doses  
 
Section 3 – Study Design  
 
Section 6.1.1.5 – Vaccine 
Administration and Vaccine Schedule 
 
Section 7 – Treatment Plan 
 
Appendix II – Schedule of Assessments 
 
Throughout protocol 
... 16 weeks of standard preoperative 
dose-dense 
doxorubicin/cyclophosphamide 
followed by paclitaxel chemotherapy; 
the following 10 patients will be a 
staggered enrollment, and will receive 
DC vaccinations and anakinra 100 mg 
SC for 7 days, followed by 7 days off, 
then repeating during the 16 weeks of 
preoperative chemotherapy. Four to 5 
core biopsies will be obtained prior to 
treatment initiation for whole exome 
sequencing and expression analysis 
and for characterization of the tumor 
immune microenvironment. 
Patients will receive standard 
preoperative dose-dense 
doxorubicin/cyclophosphamide (4 
cycles) followed by paclitaxel (4 
cycles; AC/T) chemotherapy, 
administered every 2 weeks for 16 
weeks combined with antigen-loaded 
DC vaccinations administered 
intratumoral (one injection of 0.2 mL 
at 3 x 106 cells/mL) and subcutaneous 
(one injection of 1 mL at 15 x 106 DCs) 
on any one individual day between 
Days 9-12 of Cycles 1 and 3 of dose-
dense AC and on any one individual 
...24 weeks of standard preoperative 
dose-dense 
doxorubicin/cyclophosphamide (AC) 
followed by paclitaxel and carboplatin 
(TCb) chemotherapy; the following 
10 patients will be a staggered 
enrollment, and will receive DC 
vaccinations and anakinra 100 mg SC 
for 7 days, followed by 7 days off, 
then repeating during the 24 weeks of 
preoperative chemotherapy. Core 
biopsies will be obtained prior to 
treatment initiation for whole exome 
sequencing and expression analysis 
and for characterization of the tumor 
immune microenvironment. 
Patients will receive standard 
preoperative dose-dense 
doxorubicin/cyclophosphamide (4 
cycles; AC) followed by paclitaxel and 
carboplatin (4 cycles; TCb) 
chemotherapy, administered for 24 
weeks combined with antigen-loaded 
DC vaccinations administered 
intratumoral (one injection of 0.2 mL 
at 3 x 106 cells/mL) and subcutaneous 
(one injection of 1 mL at 15 x 106 DCs) 
on any one individual day between 
Days 9-12 of Cycles 1 and 3 of dose-
Addition of carboplatin to the 
treatment regimen. Changes are 
throughout the protocol. 
Modifications to the treatment plan 
are summarized: 
• Carboplatin added during Taxol 
(“TCb”) 
• 24 weeks of preoperative 
chemotherapy 
• Vaccine during one individual 
day, Days 11-15 of TCb 
• No pegfilgrastim will be given 
during TCb cycles. 
• Research biopsy prior to or on 
Day 1 of Cycle 4 of AC. 

 
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day between Days 9-12 of Cycles 1 
and 3 of T (4 timepoints). Standard 
pegfilgrastim support will be given for 
each AC treatment.  
dense AC and on any one individual 
day between Days 11-15 of Cycles 1 
and 3 of TCb (4 timepoints). Standard 
pegfilgrastim support will be given for 
each AC treatment; however, no 
pegfilgrastim will be given during TCb 
cycles. 
Patients will undergo research 
biopsies of their breast cancer prior to 
the start of treatment and 1-2 days 
prior to or on Day 1 of Cycle 4 of AC to 
analyze the composition of the 
immune microenvironment. Core 
biopsies will be obtained prior to 
treatment initiation for whole exome 
sequencing and expression analysis 
and for characterization of the tumor 
immune microenvironment.  
Section 1.8 – Addition of Carboplatin 
to Neoadjuvant Chemotherapy for 
Breast Cancer 
---------------- 
Carboplatin is approved for the 
treatment of ovarian cancer and small 
cell lung carcinoma, and is commonly 
used for the treatment of non-small 
cell lung cancer (NSCLC), head and 
neck cancer, and other tumors. In 
breast cancer, administration of 
carboplatin to previously untreated 
patients with metastatic disease 
results in response rates of 20% to 
50%.48 Paclitaxel in combination with 
Addition of background on 
carboplatin, due to the addition of 
carboplatin to the treatment regimen. 

 
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carboplatin is also highly active in 
breast cancer, with response rates of 
approximately 39% to 62% for first-
line treatment of metastatic disease.49 
Notably, data suggest that the 
administration of carboplatin in 
combination with paclitaxel results in 
less thrombocytopenia than is 
expected from the use of carboplatin 
alone.48 
Emerging data suggests that TNBC 
tumors may be more sensitive to DNA 
damaging agents, including 
carboplatin. Two small single arm 
trials with cisplatin combination 
neoadjuvant therapy or neoadjuvant 
monotherapy for patients with TNBC 
have reported complete tumor 
regressions or minimal residual 
disease at the time of surgery in 21% 
and 44% of patients.50,51 The CALGB 
study 40603 evaluated the efficacy of 
neoadjuvant paclitaxel with or 
without carboplatin and/or 
bevacizumab followed by AC in 
patients with TNBC. The addition of 
carboplatin to the standard 
neoadjuvant chemotherapy regimen 
improved pathologic complete 

 
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response in the breast in patients to 
60% vs. 46% of patients who did not 
receive carboplatin, concluding that 
the addition of carboplatin was a 
reasonable addition to the standard 
neoadjuvant chemotherapy for 
TNBC.52   
Section 3 – Study Design  
 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, and 2 
weeks after the last DC vaccination. 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, 2 weeks 
after the last DC vaccination, and at 
each follow up appointment. 
Added research blood draws during 
the follow up portion of the study 
(was previously written into the 
protocol, but missing in this 
paragraph). 
Section 3 – Study Design Schema 
(Figure) 
(Figure) 
Figure of study design schema was 
updated to reflect the changes in the 
protocol. 
Section 4.4 – Patient Withdrawal from 
Study 
 
Section 9.4.9 – Removal Due to 
Adverse Events  
NOTE: If any patient requires more 
than one dose reduction of 
doxorubicin/cyclophosphamide (AC) 
OR the need for more than one dose 
reduction of paclitaxel due to 
treatment delays for hematologic 
toxicity or for Grade 3 or 4 non-
hematologic toxicity, they will be 
removed from the study treatment. 
NOTE: If any patient requires more 
than one dose reduction of 
doxorubicin/cyclophosphamide (AC) 
OR the need for more than one dose 
reduction of paclitaxel or 2 dose 
reductions of carboplatin due to 
treatment delays for hematologic 
toxicity or for Grade 3 or 4 non-
hematologic toxicity, they will be 
removed from the study treatment. 
Modification due to the addition of 
carboplatin to the treatment regimen. 
Section 5.1 – Prohibited Treatments 
Administration of pegfilgastrim during 
treatment with paclitaxel 
Administration of pegfilgastrim during 
treatment with paclitaxel and 
carboplatin 
Modification due to the addition of 
carboplatin to the treatment regimen. 

 
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Sectoin 6.1.1.5 – Vaccine 
Administration and Vaccine Schedule 
---------------- 
 
(Figure) 
DC vaccines are timed with 
chemotherapy. All vaccine doses 
within a cycle are scheduled to be 
given approximately every 2 weeks 
apart. If necessary, a vaccine dose 
may be delayed for up to 2 weeks. In 
this case, subsequent doses should 
continue on a 2 week schedule, from 
the time of the delayed vaccine. If a 
vaccine dose is delayed more than 2 
weeks, the PI and the BIIR Project 
Manager must be contacted for 
further instructions on continued 
dosing. Additional delays or 
modifications to the dosing schedule 
must be approved by the sponsor 
scientific chair. 
 
(Figure) 
Clarification of vaccine delay. 
Modification of DC vaccine schedule 
figure due to the changes in timing 
caused by the addition of carboplatin 
to the treatment regimen. 
Section 6.5.4 – Carboplatin 
(Paraplatin®) 
---------------- 
 
The renal effects of nephrotoxic 
compounds may be potentiated by 
carboplatin.58 
Addition of section due to the 
addition of carboplatin to the 
treatment regimen. 
Section 6.6.3 – Paclitaxel and 
Carboplatin 
Section 6.6.3 – Paclitaxel 
Standard premedications for paclitaxel 
and carboplatin should be 
administered prior to each dose of 
paclitaxel and carboplatin: 
Section 6.6.3 – Paclitaxel 
Standard premedications for paclitaxel 
and carboplatin should be 
administered prior to each dose of 
paclitaxel and carboplatin: 
Modification due to the addition of 
carboplatin to the treatment regimen. 

 
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Section 7 – Treatment Plan, Table 1 
Paclitaxel   175 mg/m2   Cycle 5-8, Day 
1, q14 days 
Paclitaxel   80 mg/m2   Cycle 5-8, Days 
1, 8, 15; q28 days 
 
Carboplatin   AUC=6   Cycle 5-8, Day 1; 
q28 days  
Modification of the treatment schema 
due to the addition of carboplatin to 
the treatment regimen. 
Section 7.2 – Chemotherapy Dose 
Modification for Toxicity 
Dose reductions will be at the 
physician’s discretion. One dose 
reductions will be permitted for 
doxorubicin, cyclophosphamide, and 
paclitaxel. No dose reductions for 
anakinra and DC vaccines will be 
permitted. Patients will resume 
treatment with the next planned cycle 
(provided improvement/resolution in 
toxicities) as outlined below. Dose 
reductions are permanent. 
If doxorubicin, cyclophosphamide, and 
paclitaxel treatment is interrupted, 
anakinra and DC vaccinations may still 
be administered following 
consultation with the study PI, Dr. 
O'Shaughnessy. A patient will be 
deemed to be off study treatment if 
the patient stops DC vaccinations, but 
will continue to be followed for 
clinical outcome. 
The dose levels doxorubicin, 
cyclophosphamide, and paclitaxel are 
shown in Table 2. 
Dose reductions will be at the 
physician’s discretion. One dose 
reduction will be permitted for 
doxorubicin, cyclophosphamide, and 
paclitaxel. Two dose reductions are 
permitted for carboplatin. No dose 
reductions for anakinra and DC 
vaccines will be permitted. Patients 
will resume treatment with the next 
planned cycle (provided 
improvement/resolution in toxicities) 
as outlined below. Dose reductions 
are permanent. 
If doxorubicin, cyclophosphamide, 
paclitaxel, and carboplatin treatment 
is interrupted, anakinra and DC 
vaccinations may still be administered 
following consultation with the study 
PI, Dr. O'Shaughnessy. A patient will 
be deemed to be off study treatment 
if the patient stops DC vaccinations, 
but will continue to be followed for 
clinical outcome. 
The dose levels doxorubicin, 
Modification of the dose reductions 
and dose levels (including table) due 
to the addition of carboplatin to the 
treatment regimen. 

 
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(Table 2) 
cyclophosphamide, paclitaxel, and 
carboplatin are shown in Table 2. 
 
(Table 2) 
Section 8.5 – Procedures during Study 
Drug Treatment 
9. Research biopsies of the patient’s 
breast tissue must be obtained 
prior to the first day of treatment 
and also 1-2 days prior or on Day 1 
of Cycle 3 of AC for assessment of 
modulation of the immune 
microenvironment.  
9. Research biopsies of the patient’s 
breast tissue must be obtained 
prior to the first day of treatment 
and also 1-2 days prior or on Day 1 
of Cycle 4 of AC for assessment of 
modulation of the immune 
microenvironment.  
Change in research biopsy timing. 
Section 8.10 – Blood Samples for 
Immunomonitoring 
ACD tubes 
CPT tubes 
30 mL at the time of each follow-up 
appointment 
Change from ACD tubes to CPT tubes. 
 
Added research blood draws during 
the follow up portion of the study 
(was previously written into the 
protocol, but missing in this 
paragraph). 
Section 8.11 – Research biopsies 
Four... 
A minimum of four... 1-2 days prior to 
or on Day 1 of Cycle 4 of AC.... 
Allowed for a minimum amount of 
biopsies, in the occasion the tumor is 
large enough to provide additional 
cores. 
 
Changed the timing of the research 
biopsy. 
Section 9.4.6 – Monitoring for Adverse 
Events during the Clinical Trial 
Patients will receive seven DC 
vaccinations intravenously. 
Patients will receive 7 DC vaccinations 
intratumorally and/or subcutaneously. 
Corrected the typo/method of 
vaccinating. 

 
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Section 11.4 – Statistical Methods 
Interim analysis - Safety: An interim 
safety analysis will be performed after 
4 and 9 patients have completed 4 
vaccines in both Groups 1 and 2. 
Accrual will be put on hold if 2 of 4 or 
>4 of 9 patients experience the 
following:  
• 
Any vaccine-related toxicity as 
outlined in Section 9.4.9 
• 
More than one dose reduction 
in AC or paclitaxel for 
hematologic or 
nonhematologic toxicity, as 
per Section 9.4.9. 
Constitutional symptoms that are 
expected to occur with vaccine 
therapies are not included in this 
interim safety analysis. 
A separate interim safety analysis will 
be performed for Group 1 and Group 
2 separately, and the incidence of AEs 
in both groups will be compared.  
In the event the safety conditions 
above occur and accrual is put on 
hold, a discussion will be held with the 
DSMB and the FDA to discuss the 
safety issues, strategies to reduce 
toxicity, and whether to lift the 
Interim analysis - Safety: An interim 
safety analysis will be performed after 
4 and 9 patients have completed 4 
vaccines in both Groups 1 and 2. 
Accrual will be put on hold if 2 of 4 or 
>4 of 9 patients experience the 
following:  
• 
Any vaccine-related toxicity as 
outlined in Section 9.4.9 
• 
More than one dose reduction 
in AC or paclitaxel, or 2 dose 
reductions for carboplatin for 
hematologic or 
nonhematologic toxicity, as 
per Section 9.4.9. 
Constitutional symptoms that are 
expected to occur with vaccine 
therapies are not included in this 
interim safety analysis. 
A separate interim safety analysis will 
be performed for Group 1 and Group 
2 separately, and the incidence of AEs 
in both groups will be compared.  
The team of specialists (“DC vaccine 
team”) involved in this study 
comprises physicians, scientists, 
medical writers, trial coordinators, 
data specialists, regulatory experts, 
Modified dose reduction statement 
due to the addition of carboplatin to 
the treatment regimen. 
 
Addressed the team of specialist 
named “DC vaccine team”, which 
replaces the need for a DSMB. 

 
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accrual hold. 
and laboratory staff. All safety and 
efficacy data as well as the biomarker 
data (when available) will be reviewed 
monthly at multidisciplinary trial 
oversight meetings, where all experts 
will be in attendance. 
In the event the safety conditions 
above occur and accrual is put on 
hold, a discussion will be held with the 
DC vaccine team and the FDA to 
discuss the safety issues, strategies to 
reduce toxicity, and whether to lift the 
accrual hold. 
Section 13.1 – Multidisciplinary Trial 
Oversight Meetings 
Section 13.1 – Data Safety Monitoring 
Board – entire section 
The team of specialists (“DC vaccine 
team”) involved in this study is 
comprised of physicians, scientists, 
medical writers, trial coordinators, 
data specialists, regulatory experts, 
and laboratory staff. All safety and 
efficacy data as well as the biomarker 
data (when available) will be reviewed 
monthly at multidisciplinary trial 
oversight meetings, where all experts 
will be in attendance. 
Removal of the DSMB and replaced 
with an internal multidisciplinary 
team. 
References 
---------------- 
Decatris MP et al 
Belani CP, et al 
Telli ML, et al 
Silver DP, et al 
Additional references to support the 
addition of carboplatin to the 
treatment regimen in the protocol. 

 
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Sikov WM, et al 
Paraplatin package insert 
Appendix V – Research Biopsies – 
Collection and Handling 
---------------- 
Instructions for collection fresh tissue 
samples. 
Added instructions for the collection 
of fresh tissue that were previously 
missing from the appendix. 
 
Minor grammatical errors or misspellings were corrected as needed. 
 
 
 

 
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Appendix VIII 
013-154 Amendment 3 List of Changes 
Protocol Section 
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Title Page; 
 
Appendix IV - Patient Diaries 
Title: Pilot safety trial of anakinra 
combined with chemotherapy and 
dendritic cell vaccine in patients with 
and locally advanced, triple-negative 
breast cancer. 
New title: Pilot safety trial of 
preoperative chemotherapy combined 
with dendritic cell vaccine in patients 
with locally advanced, triple-negative 
breast cancer or ER-positive, HER2-
negative breast cancer. 
 
Amendment 3, Date: November 17, 
2014 
Updated title of the protocol, 
amendment version and date to 
reflect the changes in the protocol. 
 
Updated title on the title page of the 
patient diary. 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 3. 
Updated protocol 
Thoughout the protocol 
---------------- 
 
With and without anakinra 
…and ER+/HER2- breast cancer (BC). 
 
---------------- 
Changes reflect the addition of 
patients with ER+/HER2- breast cancer 
and the removal of anakinra 
treatment from the trial. Changes are 
throughout the protocol. 
Study Synopsis – Summary 
---------------- 
 
Immunotherapy could be an attractive 
strategy for overcoming 
chemotherapy resistance in TNBC 
patients and some preliminary studies 
have been carried out. 
 
In addition, blockade of IL-1β 
represents a novel approach to breast 
Women with ER+/HER2- breast cancer 
typically have a low likelihood of 
developing a pCR, and if these women 
have residual disease with high levels 
of Ki67 after preoperative therapy, 
this predicts for poor overall and 
progression-free survival with 
subsequent endocrine therapy. 
 
Immunotherapy could be an attractive 
Updated to reflect changes in the 
protocol. 

 
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cancer immunotherapy. TSLP 
secretion from breast cancer cells is 
regulated by IL-1β. Results showed 
high levels of IL-1β in the breast 
cancer microenvironment. IL-1β 
induces TSLP production from breast 
cancer cells lines in a dose and contact 
dependent manner. Cancer cells 
induce IL-1β secretion from DCs and 
monocytes in a contact-dependent 
fashion. This is mediated by cancer 
cell-derived TGF- β. Administration of 
the IL-1R antagonist, anakinra, 
prevents tumor growth in vivo, blocks 
OX40L+ expression on DCs, and blocks 
iTH2 generation in vivo. 
 
Our goals are to boost T cell immunity 
targeted against breast cancer 
utilizing a tumor antigen-loaded DC 
vaccine, to reverse the immune 
suppressive tumor microenvironment 
by IL-1 blockade, to enhance 
chemotherapy effectiveness and 
decrease tumor metastagenicity, and 
to decrease the recurrence rates of LA 
TNBC. Patients with LA TNBC will be 
treated with a combination of 
antigen-loaded DC vaccinations along 
with standard preoperative 
strategy for these patients and some 
preliminary studies have been carried 
out. 
 
---------------- 
 
Our goals are to boost T cell immunity 
targeted against breast cancer 
utilizing a tumor antigen-loaded DC 
vaccine, to enhance chemotherapy 
effectiveness and decrease tumor 
metastagenicity, and to decrease the 
recurrence rates of LA TNBC and 
ER+/HER2– BC. Patients will be 
treated with a combination of 
antigen-loaded DC vaccinations along 
with standard preoperative 
chemotherapy, to improve 
immunogenicity and to increase the 
pCR rate achieved with standard 
therapy. The trial will consist of 2 
patient cohorts: TNBC and ER+/HER2– 
BC. 

 
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chemotherapy, to improve TNBC 
immunogenicity and to increase the 
pCR rate achieved with standard 
therapy. The trial will consist of 2 
patient cohorts. In the first group, 
patients will receive DC vaccinations in 
combination with preoperative 
chemotherapy. In the second group, 
IL-1 blockade with anakinra will be 
added to the preoperative 
chemotherapy and DC vaccine. 
Study Synopsis – Objectives; 
 
Section 2.1 – Primary Objective; 
 
Section 2.2 – Secondary Objectives 
The primary objective of this study is 
to determine the safety and feasibility 
of combining cyclin B1/WT-1/CEF 
(antigen)-loaded DC vaccination with 
preoperative chemotherapy, and to 
combine DC vaccination with 
preoperative chemotherapy in 
addition to IL-1 blockade with 
anakinra in patients with LA TNBC. 
 
The secondary objectives of this trial 
are to determine pathologic complete 
response rates, with and without 
anakinra; disease-free survival; to 
assess immune biomarkers of 
immunity (antigen-specific CD8+ T cell 
immunity and TH2 T cells) in breast 
cancer biopsy specimens and blood 
samples in patients receiving DC 
The primary objective of this study is 
to determine the safety and feasibility 
of combining cyclin B1/WT1/CEF 
(antigen)-loaded DC vaccination with 
preoperative chemotherapy. 
 
The secondary objectives of this trial 
are to determine pathologic complete 
response rates; disease-free survival; 
to assess immune biomarkers of 
immunity (antigen-specific CD8+ T cell 
immunity and TH2 T cells) in breast 
cancer biopsy specimens and blood 
samples in patients receiving DC 
vaccinations; and to assess the 
feasibility of immunizing LA TNBC and 
ER+/HER2– BC patients with patient-
specific tumor antigens. 
Changes in the objectives reflect the 
addition of patients with ER+/HER2- 
breast cancer and the removal of 
anakinra treatment from the trial. 

 
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vaccinations, with and without IL-1 
blockade with anakinra; and to assess 
the feasibility of immunizing LA TNBC 
patients with patient-specific tumor 
antigens. 
Study Synopsis – Inclusion Criteria; 
 
Section 4.2 – Inclusion Criteria 
2. Have: 
a. locally advanced TNBC 
defined as invasive ductal 
cancer 
b. ER- tumors with <10% of 
tumor nuclei immunoreactive 
c. PR- tumors with <10% of 
tumor nuclei immunoreactive 
d. T3 or T4 disease, regardless 
of nodal status; T2 disease is 
eligible if there are positive 
lymph nodes present by 
physical exam or imaging 
evaluation or histological 
evaluation. 
2. Have either: 
a. locally advanced TNBC 
defined as invasive ductal 
cancer; ER- tumors with 
<10% of tumor nuclei 
immunoreactive; PR- tumors 
with <10% of tumor nuclei 
immunoreactive; T3 or T4 
disease, regardless of nodal 
status (T2 disease is eligible 
if there are positive lymph 
nodes present by physical 
exam or imaging evaluation 
or histological evaluation, 
OR 
b. High-risk ER+ breast cancer 
defined as grade 3 invasive 
ductal or mixed 
ductal/lobular cancers, or 
grade 2 with Ki67 ≥20%; 
node positive as evidenced 
by physical exam or imaging 
evaluation or histological 
evaluation. 
Inclusion criteria have been modified 
to include patients with ER+/HER2- 
breast cancer. 

 
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Study Synopsis – Exclusion Criteria; 
 
Section 4.3 – Exclusion Criteria 
---------------- 
 
6. ….The use of an LHRH agonist 
during chemotherapy in 
premenopausal women who 
wish to preserve ovarian function 
is allowed, but is not required. 
Clarification of exclusion criterion #6, 
which would allow for the use of an 
LHRH agonist. 
Study Synopsis – Medication and 
Doses;  
 
Section 3 – Study Design;  
 
Section 6.1.1.5 – Vaccine 
administration and vaccine schedule; 
 
Section 7 – Treatment Plan 
This exploratory pilot safety, open 
label trial will evaluate the 
combination of preoperative 
chemotherapy and Dendritic Cell (DC) 
vaccinations in 2 groups of patients 
with LA TNBC. The first 10 patients will 
be enrolled to receive DC vaccinations 
during the 24 weeks of standard 
preoperative dose-dense 
doxorubicin/cyclophosphamide (AC) 
followed by paclitaxel and carboplatin 
(TCb) chemotherapy; the following 
10 patients will be a staggered 
enrollment, and will receive DC 
vaccinations and anakinra 100 mg SC 
for 7 days, followed by 7 days off, 
then repeating during the 24 weeks of 
preoperative chemotherapy. Core 
biopsies will be obtained prior to 
treatment initiation for whole exome 
sequencing and expression analysis 
and for characterization of the tumor 
immune microenvironment. 
Patients will receive standard 
preoperative dose-dense 
This exploratory pilot safety, open 
label trial will evaluate the 
combination of preoperative 
chemotherapy and Dendritic Cell (DC) 
vaccinations in 2 cohorts of patients 
with LA TNBC or ER+/HER2– BC.  
• LA TNBC patients will be 
enrolled to receive DC 
vaccinations during the 24 
weeks of standard 
preoperative dose-dense 
doxorubicin/cyclophosphamid
e (AC) followed by paclitaxel 
and carboplatin (TCb) 
chemotherapy;  
• ER+/HER2– BC patients will 
receive DC vaccinations during 
the 22 weeks of standard 
preoperative dose-dense AC 
followed by weekly paclitaxel 
(T) chemotherapy.  
• Study procedures will be 
similar in both groups. 
LA TNBC patients will receive standard 
preoperative dose-dense AC (4 cycles) 
Modification of the study design to 
reflect the addition of patients with 
ER+/HER2- breast cancer and the 
removal of anakinra treatment from 
the trial. 

 
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doxorubicin/cyclophosphamide (4 
cycles; AC) followed by paclitaxel and 
carboplatin (4 cycles; TCb) 
chemotherapy, administered for 24 
weeks combined with antigen-loaded 
DC vaccinations administered 
intratumoral (one injection of 0.2 mL 
at 3 x 106 cells/mL) and subcutaneous 
(one injection of 1 mL at 15 x 106 DCs) 
on any one individual day between 
Days 9-12 of Cycles 1 and 3 of dose-
dense AC and on any one individual 
day between Days 11-15 of Cycles 1 
and 3 of TCb (4 timepoints)…. 
 
After definitive surgery and during 
locoregional radiation therapy to the 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
(at 15 x 106 cells/mL) in the ventral 
surface of the upper arm, with 
antigen-loaded DCs. The first 
vaccination booster will occur once 
after the surgery and up to 3 days 
prior to radiation; the second booster 
will occur 30 days ± 3 days after 
radiation is completed; and the third 
booster will occur 90 days ± 3 days 
followed by TCb (4 cycles) 
chemotherapy, administered for 24 
weeks. ER+/HER2– BC patients will 
receive standard preoperative dose-
dense AC (4 cycles) followed by 
weekly T (12 cycles), administered for 
a total of 22 weeks. In both cohorts, 
chemotherapy will be combined with 
antigen-loaded DC vaccinations 
administered intratumoral (one 
injection of 0.2 mL at 3 x 106 cells/mL) 
and subcutaneous (one injection of 1 
mL at 15 x 106 cells/mL), for a total of 
4 time points prior to definitive 
surgery.  
• 
During the AC cycles, both 
cohorts will receive vaccines 
administered on any one 
individual day between Days 
9-12 of Cycles 1 and 3 of dose-
dense AC.  
• 
For TNBC patients, vaccines 
will be administered on any 
one individual day between 
Days 11-15 of Cycles 1 and 3 
of TCb.  
For ER+/HER2– patients, vaccines will 
be administered Day 1 during either 
Cycle 2 or Cycle 3 and on Day 1 during 
either Cycle 8 or Cycle 9 of T. Vaccine 

 
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after the 2nd boost. 
is to be administered after T infusion 
is completed in this cohort of 
patients…. 
 
After definitive surgery and during 
locoregional radiation therapy to the 
breast or chest wall and regional 
lymphatics per standard of care, 
patients will receive 3 boost DC 
vaccinations subcutaneously of 1 mL 
(at 15 x 106 cells/mL), rotating 
injection sites in the dorsal or ventral 
surface of the upper arm, with 
antigen-loaded DCs. The timing of the 
boosters is the same for TNBC and 
ER+/HER2– cohorts. The first 
vaccination booster will occur once 
after the surgery and up to 3 days 
prior to radiation; the second booster 
will occur 30 days ± 3 days after 
radiation is completed; and the third 
booster will occur 90 days ± 3 days 
after the 2nd boost. 
Section 1.1 – Background on breast 
cancer 
---------------- 
 
Therefore, a high priority for clinical 
research in patients with locally 
advanced TNBC is to increase the 
pathologic complete response (pCR) 
rate in breast and axilla following 
…In addition, the degree of 
proliferation as indicated by 
expression levels of Ki67 is also a 
predictive factor for achieving a pCR. 
High Ki67 in pretreatment breast 
cancer tissue is associated with an 
increase in pCR, whereas high Ki67 in 
Addition of scientific literature in 
support of the addition of patients 
with ER+/HER2- breast cancer. 

 
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preoperative therapy. Patients with T3 
and T4 cancers and with clinically 
N1/N2 axillary disease are at highest 
risk of not achieving a pCR with 
standard therapy, and of developing 
metastatic disease. 
post-treatment residual disease is 
correlated with poorer disease-free 
and overall survival.3 
… Women with ER+/HER2- breast 
cancer typically have a low likelihood 
of developing a pCR6, and if these 
women have residual disease with 
high levels of Ki67 after preoperative 
therapy, this predicts for poor overall 
and progression-free survival with 
subsequent endocrine therapy.3 ER+ 
patients whose cancers have high 
expression levels of Ki67 have a high 
rate of disease recurrence and new 
treatment options are necessary to 
improve their outcome.7 
 
Therefore, a high priority for clinical 
research in patients is to increase the 
pathologic complete response (pCR) 
rate in breast and axilla following 
preoperative therapy. Patients with 
T2, T3 and T4 cancers and with 
clinically N1/N2 axillary disease are at 
highest risk of not achieving a pCR 
with standard therapy, and of 
developing metastatic disease. 
Section 1.3 – Rationale for target 
antigen selection 
---------------- 
 
… Cyclin B1 is one of the cancer-
related genes that comprises the 
Oncotype DX Recurrence Score 
Addition of scientific literature in 
support of the target antigens for 
addition of patients with ER+/HER2- 

 
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assay.28 This assay, developed from 
the National Surgical Adjuvant Breast 
and Bowel Project (NSABP) trials, 
quantifies the likelihood of breast 
cancer recurrence, and also can 
predict for chemotherapy benefit 
(higher recurrence scores are 
indicative of greater therapy 
benefit).29 High Cyclin B1 levels are 
associated with highly proliferative 
ER+ breast cancers and predict for a 
high risk of distant disease 
recurrence…. 
 
In the ER+, HER2- breast cancer cell 
line, MCF-7, WT1 was correlated with 
high expression of ERα and HER2, 
which indicated that it may play a role 
in cancer progression and 
development.34 In addition, high levels 
of WT1 are associated with aggressive 
breast cancer biology, and in vitro, 
WT1 promoted estrogen-independent 
growth and anti-estrogen resistance.35 
This finding indicates that WT1 is, in 
part, mechanistically responsible for 
the switch from estrogen-dependent 
to -independent breast cancer growth 
and survival. 
breast cancer. 

 
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Section 1.4 – Rationale for 
intratumoral DC injection 
We propose to substitute the 
functional DCs via adoptive transfer of 
ex vivo generated autologous mature 
DCs injected locally into LA TNBCs at 
48 hours post-systemic anthracyclines. 
We propose to substitute the 
functional DCs via adoptive transfer of 
ex vivo generated autologous mature 
DCs injected locally into LA TNBCs and 
ER+/HER2– breast cancer patients 
post-systemic anthracycline therapy. 
Updated the timing on DC vaccine due 
to changes to the treatments and 
patient cohorts. 
(Previous) Section 1.5 – Rationale for 
targeting IL-1 
All of Section 1.5 
---------------- 
 
Removed background on anakinra due 
to the removal of anakinra as a 
treatment in this trial. 
Section 1.8 – Rationale 
Our goals are to boost T cell immunity 
targeted against breast cancer 
utilizing a tumor antigen-loaded DC 
vaccine, to reverse the immune 
suppressive tumor microenvironment 
by IL-1 blockade, to enhance 
chemotherapy effectiveness and 
decrease tumor metastagenicity, and 
to decrease the recurrence rates of LA 
TNBC. Patients with LA TNBC will be 
treated with a combination of 
antigen-loaded DC vaccinations along 
with standard preoperative 
chemotherapy, to improve TNBC 
immunogenicity and to increase the 
pCR rate achieved with standard 
therapy. The trial will consist of 2 
patient cohorts. In the first group, 
patients will receive DC vaccinations in 
combination with preoperative 
chemotherapy. In the second group, 
Our goals are to boost T cell immunity 
targeted against breast cancer 
utilizing a tumor antigen-loaded DC 
vaccine, to enhance chemotherapy 
effectiveness and decrease tumor 
metastagenicity, and to decrease the 
recurrence rates of LA TNBC and 
ER+/HER2– BCs. Patients with LA 
TNBC and ER+/HER2– BC will be 
treated with a combination of 
antigen-loaded DC vaccinations along 
with standard preoperative 
chemotherapy, to improve 
immunogenicity and to increase the 
pCR rate achieved with standard 
therapy. The trial will consist of 2 
patient cohorts: TNBC and ER+/HER2– 
BC. 
Modification of the overall rationale 
of the study, to reflect the addition of 
patients with ER+/HER2- breast cancer 
and the removal of anakinra 
treatment from the trial. 

 
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IL-1 blockade with anakinra will be 
added to the preoperative 
chemotherapy and DC vaccine. 
Section 3 – Study Design Schema 
(Figure) 
(Figure) 
Figure of study design schema was 
updated to reflect the changes in the 
protocol. 
Section 4.1 – Sample Size 
Twenty patients with newly diagnosed 
locally advanced TNBC will be enrolled 
over 20 months (10 patients per 
group). 
Twenty patients with newly diagnosed 
locally advanced TNBC or ER+/HER2– 
BC will be enrolled over 20 months. 
 
If a patient’s apheresis product or 
manufactured vaccine is suboptimal 
after a second apheresis procedure, 
the patient will be withdrawn from 
the study and replaced. See Section 
8.3. 
Removed the wording for groups, to 
reflect the addition of patients with 
ER+/HER2- breast cancer and the 
removal of anakinra treatment from 
the trial. Clarified replacement patient 
population. 
Section 4.4 – Patient Withdrawal from 
the Study 
---------------- 
 
7. Apheresis product or 
manufactured vaccine is 
suboptimal after a second 
apheresis procedure. 
Addition of a reason to withdraw a 
patient due to apheresis procedure 
failures. 
Section 5 – Prior and concomitant 
therapy 
---------------- 
 
• LHRH agonist 
Modified the list of reported conmeds 
to allow for the use of an LHRH 
agonist for women who wish to 
preserve ovarian function. 
Section 5.1 – Prohibited treatments 
• Administration of hormonal 
therapy (with the exception of 
replacement steroids) 
• Administration of TNF blocking 
agents 
---------------- 
Deletion of prohibited treatments to 
allow for the use of an LHRH agonist 
and the removal of anakinra from the 
trial. 

 
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Section 6.1 – Investigational product 
In this protocol, the investigational 
products are the Dendritic Cell (DC) 
vaccines and anakinra (Kineret). 
In this protocol, the investigational 
product is the Dendritic Cell (DC) 
vaccine. 
Modification of the investigational 
product to address the removal of 
anakinra from the trial. 
Section 6.1.1.5 – Vaccine 
administration and vaccine schedule 
---------------- 
 
(Figure) 
NOTE: Needles used for drawing 
vaccine product into the syringe and 
for injection must be  
23-gauge or larger. Smaller sized 
needles (eg, 25- or 27-gauge) will 
either rupture the cells or cause them 
to clump. 
 
(2 Figures) 
Clarified the needle size required for 
vaccine administration. 
 
Modification and addition of DC 
vaccination schedules to reflect the 
addition of patients with ER+/HER2- 
breast cancer. 
Previous Section 6.1.2 – Anakinra 
All of Section 6.1.2 
---------------- 
 
Removed anakinra as an 
investigational product due to its 
removal as a treatment in this trial. 
Section 6.2 – Non investigational 
products 
---------------- 
In this protocol, the non-
investigational products are: 
• Preoperative chemotherapy with 
preoperative dose-dense 
doxorubicin/cyclophosphamide 
(AC) and 
paclitaxel/carboplatin (TCb) or 
paclitaxel alone (T) 
• Radiation therapy to breast or 
chest wall and regional 
lymphatics  
Modification of the non-
investigational products to address 
the new treatment regimens that will 
be used for the addition of patients 
with ER+/HER2- breast cancer. 

 
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• For ER+/HER2– BC patients only: 
standard endocrine therapy 
during and after radiation 
 
Section 6.3 – Accountability 
procedures 
For the purpose of accountability, all 
unused Anakinra and package inserts 
from used Anakinra, which was 
dispensed to the patient, should be 
returned to the clinic at each visit. 
---------------- 
Removed anakinra information in 
accountability procedures due to its 
removal as a treatment in this trial. 
Previous Section 6.4.1 - Anakinra 
All of Section 6.4.1 
---------------- 
 
Removed anakinra as a potential risk 
due to its removal as a treatment in 
this trial. 
Previous Section 6.5.1 - Anakinra 
All of Section 6.5.1 
---------------- 
 
Removed drug-drug interaction 
information for anakinra due to its 
removal as a treatment in this trial. 
Previous Section 6.6.1 - Anakinra 
All of Section 6.6.1 
---------------- 
 
Removed premedication information 
for anakinra due to its removal as a 
treatment in this trial. 
Section 7 – Treatment schema, 
Table 1 
Anakinra 
 
Paclitaxel 
---------------- 
 
Paclitaxel for LA TNBC 
Paclitaxel for ER+/HER2– BC 
Modification of the treatment schema 
due to the addition of patients with 
ER+/HER2– breast cancer, and the 
removal of anakinra from treatment in 
this trial. 
Section 7.1 – Chemotherapy 
Treatment Delay 
Patients who miss a dose of anakinra 
by more than a few hours should be 
instructed to take the missed dose as 
soon as possible and contact the 
Investigator. The next day dose should 
not be doubled if a daily dose is 
---------------- 
 
Deleted, due to the removal of 
anakinra in this trial. 

 
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missed.  
Section 7.4 – Radiation therapy 
---------------- 
 
ER+/HER2– BC patients will also 
receive standard endocrine therapy 
during locoregional radiation therapy, 
at the physician’s discretion, for at 
least 5 years thereafter. The type of 
endocrine therapy, dosing, and 
duration must be captured on the 
CRF. 
Addition of endocrine therapy to 
begin during radiation therapy, to 
reflect the addition of patients with 
ER+/HER2- breast cancer. 
Section 8.1 – Screening  
11. Whole blood collection (100 mL) 
for immunomonitoring studies. 
11. Whole blood collection (40 mL) 
for immunomonitoring studies. 
Reduced the amount of blood 
required for whole blood collection. 
Section 8.3 – Apheresis Procedures 
In the event that the apheresis is 
suboptimal, ie, that an inadequate 
monocyte collection is achieved or 
that the vaccine cannot be 
manufactured from the product 
collected, one additional apheresis 
will be allowed at least 1 week later. 
Apheresis product must meet 
required specifications for vaccine to 
be manufactured. Manufactured 
vaccine must meet required 
specification to be released for 
injection. NOTE: If a patient’s 
apheresis product or manufactured 
vaccine is suboptimal after a second 
attempt at apheresis, those patients 
Failure of peripheral venous access 
during apheresis will not be 
considered a collection of cells, as, 
with the subject’s consent, a central 
venous line can be placed and an 
apheresis completed. In the event 
that the apheresis is suboptimal, ie, 
that an inadequate monocyte 
collection is achieved or that the 
vaccine cannot be manufactured from 
the product collected, one additional 
apheresis will be allowed no less than 
7-10 days after the first apheresis. 
Apheresis product must meet 
required specifications for vaccine to 
be manufactured. Manufactured 
Modified the time that a second 
apheresis can occur, and clarified that 
the apheresis second attempt is for an 
apheresis procedure, and not an 
attempt at only accessing a patient’s 
veins. 

 
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will be withdrawn from the study, and 
replaced.  
vaccine must meet required 
specification to be released for 
injection.  
Section 8.5 – Procedures during study 
drug treatment 
---------------- 
 
1. A medical history on Day 1 of each 
cycle…. 
NOTE: For ER+/HER2– patients during 
the T cycles, the following evaluations 
will be performed on Day 1 every 3 
weeks (Day 1, Cycles 1, 4, 7, and 10). 
 
1. An abbreviated medical history…. 
Clarification of the assessments to be 
performed during study, to reflect the 
addition of patients with ER+/HER2- 
breast cancer. 
 
Clarified that an abbreviated medical 
history is sufficient during study drug 
treatment.  
Section 8.6 – Procedures for Vaccine 
Treatment Visits 
1. A medical history (note changes 
from baseline) 
2. A physical examination, including 
vital signs and body weight. 
1. An abbreviated medical history 
(note changes from baseline) 
2. A limited physical assessment 
focusing on the affected breast, 
including vital signs and body 
weight. 
Clarified that an abbreviated medical 
history and a limited physical 
assessment is sufficient during vaccine 
treatment visits. 
Section 8.8 – Procedures for Follow-
Up Visits 
1. A medical history 
1. An abbreviated medical history 
Clarified that an abbreviated medical 
history is sufficient during follow-up 
visits. 
Section 8.10 – Blood Samples for 
Immunomonitoring 
Whole blood collection for 
immunomonitoring studies will be 
obtained as follows: 
• 
100 mL (11 CPT tubes and 2 
tempus tubes) at baseline 
• 
30 mL prior to each 
treatment-vaccination cycle; 
prior to surgery and prior to 
radiation (3 CPT tubes and 2 
Whole blood collection for 
immunomonitoring studies will be 
obtained as follows: 
• 
40 mL (4 CPT tubes and 2 
tempus tubes) at baseline 
• 
30 mL prior to each 
treatment-vaccination cycle; 
prior to surgery and prior to 
radiation (3 CPT tubes and 2 
Reduced the amount of blood 
required for whole blood collection. 

 
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tempus tubes). 
• 
100 mL (11 CPT tubes and 2 
tempus tubes) 2 weeks after 
the last DC vaccination  
• 
30 mL at the time of each 
follow-up appointment 
tempus tubes). 
• 
40 mL (4 CPT tubes and 2 
tempus tubes) 2 weeks after 
the last DC vaccination  
• 30 mL at the time of each 
follow-up appointment 
Section 9.3 – Patient diaries 
Patients enrolled in Group 2, in 
addition to collection of new 
symptoms after vaccine 
administration, will be instructed to 
record any new symptoms that may 
have developed during administration 
of anakinra.  
---------------- 
Removal of patient diaries for 
anakinra, due to its removal as a 
treatment in this trial. 
Section 9.4.6 – Monitoring for Adverse 
Events During the Clinical Trial 
Patients will have vital signs taken 
approximately 15 minutes and 30 
minutes following the DC vaccinations 
and again at approximately 1 hour 
post injection prior to patient’s 
release. 
Patients will have vital signs taken 
approximately every 15 minutes for 1 
hour post injection prior to patient’s 
release. 
Modified to include a vital sign time 
point at 45 minutes. 
Section 11.4 – Statistical Methods 
…in Group 1 patients… 
 
The administration of DC vaccine plus 
anakinra plus preoperative 
chemotherapy in Group 2 patients will 
be considered safe if no more than 3 
of the 10 patients experience a 
toxicity that leads to chemotherapy 
dosing delay of more than 4 weeks. 
 
Quantitative and avidity evaluation of 
---------------- 
 
 
Removed statistical analyses that 
were associated with administration 
of anakinra, due to its removal as a 
treatment in this trial. 

 
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tumor-infiltrating and peripheral 
blood cyclin B1 and patient-specific 
mutation, antigen-specific T cells will 
be carried out for patients who 
received anakinra versus patients who 
did not receive anakinra. 
 
…and for patients who received 
anakinra versus patients who did not 
receive anakinra.  
 
…administration of anakinra versus no 
administration of anakinra, …. 
 
…in both Groups 1 and 2…. 
 
A separate interim safety analysis will 
be performed for Group 1 and Group 
2 separately, and the incidence of AEs 
in both groups will be compared. 
References 
(Deleted:) 
Coussens 2013 
Teschendorff 2010 
Kristensen 2012 
Terabe 2004 
Zhang 2008 
DeNardo 2011 
Galon 2006 
Pascual 2005 
Kineret package insert 2009 
New references:  
Yoshioka 2013 
Houssami 2012 
Von Minckwitz 2012 
Paik 2004 
Paik 2006 
Nasomyon 2014 
Wang 2010 
 
---------------- 
Removal of anakinra references, and 
addition of scientific literature to 
support the addition of patients with 
ER+/HER2- breast cancer. 

 
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Appendix II - Schedule of Assessments 
Group 1 
 
Group 2 
LA TNBC 
 
ER+/HER2- 
Language updated to match protocol. 
Appendix V – Research Biopsies – 
Collection and Handling 
Specimens must not be subjected to 
freezing or extreme temperatures 
---------------- 
 
Removed this statement, due to a 
change in processes. 
 
 
Minor grammatical errors or misspellings were corrected as needed. 
 
 

 
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Appendix IX 
013-154 Amendment 4 List of Changes 
Protocol Section 
Original Text 
Revised Text 
Rationale 
Title Page 
---------------- 
Amendment 4, Date: May 01, 2015 
Updated amendment version and 
date to reflect the changes in the 
protocol. 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 4. 
Updated protocol 
Study Synopsis – Inclusion Criteria 
 
Section 4.2 – Inclusion Criteria 
11. 
Patients must be willing to 
undergo research biopsies to obtain 
breast cancer tissue for whole exome 
sequencing and evaluation of tumor 
immune microenvironment. 
---------------- 
Patients will be encouraged to donate 
a portion of their tissue, but they can 
refuse without being off study. 
Study Synopsis – Exclusion Criteria 
 
Section 4.3 – Exclusion Criteria 
9. Patients who have any severe 
and/or uncontrolled medical 
conditions or other conditions 
that could affect their 
participation such as: 
a. severe impaired lung 
functions as defined as 
spirometry and DLCO that 
is 50% of the normal 
predicted value and/or O2 
saturation that is 88% or 
less at rest on room air 
b. uncontrolled diabetes as 
defined by fasting serum 
glucose >1.5 x ULN 
c. liver disease such as 
9. Patients who have any severe 
and/or uncontrolled medical 
conditions or other conditions 
that could affect their 
participation such as: 
a. severe impaired lung 
functions as defined as 
spirometry and DLCO that 
is 50% of the normal 
predicted value and/or O2 
saturation that is 88% or 
less at rest on room air 
b. liver disease such as 
cirrhosis or severe hepatic 
impairment (Child-Pugh 
class C). 
Removal of fasting serum glucose 
>1.5 x ULN as an exclusion criterion. 

 
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cirrhosis or severe hepatic 
impairment (Child-Pugh 
class C). 
Synopsis - Medication and Doses; 
 
Section 3 - Study Design 
 
Section 7 - Treatment Plan 
 
Section 8.5 - Procedures During Study 
Drug Treatment 
 
Patients will undergo research 
biopsies of their breast cancer prior to 
the start of treatment and 1-2 days 
prior to or on Day 1 of Cycle 4 of AC to 
analyze the composition of the 
immune microenvironment. Core 
biopsies will be obtained prior to 
treatment initiation for whole exome 
sequencing and expression analysis 
and for characterization of the tumor 
immune microenvironment.  
After preoperative treatment, patients 
will undergo definitive surgery, 
generally with mastectomy, and if 
available, fresh tissue and residual 
FFPE breast cancer tissue will be 
collected for assessment of the 
immune microenvironment and for 
whole exome sequencing to identify 
cancer-associated mutations in the 
residual, chemotherapy-refractory 
cancer. 
Patients will undergo research 
biopsies of their breast cancer prior to 
the start of treatment and 1-2 days 
prior to or on Day 1 of Cycle 4 of AC to 
analyze the composition of the 
immune microenvironment. Patients 
who will have their definitive surgery 
outside a Baylor hospital will have a 
third research biopsy at least 1 week 
following the last chemotherapy dose 
and prior to surgery. Core biopsies will 
be obtained prior to treatment 
initiation for whole exome sequencing 
and expression analysis and for 
characterization of the tumor immune 
microenvironment.  
After preoperative treatment, patients 
will undergo definitive surgery, 
generally with mastectomy, and if 
available, fresh tissue (for patients 
who have their definitive surgery 
within a Baylor hospital) and residual 
FFPE breast cancer tissue will be 
collected for assessment of the 
immune microenvironment and for 
whole exome sequencing to identify 
Addition of one biopsy time point, for 
patients who will have their definitive 
surgery outside a Baylor hospital.  

 
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cancer-associated mutations in the 
residual, chemotherapy-refractory 
cancer. 
Section 3 – Study Design Schema 
(Figure) 
(Figure) 
Figure of study design schema was 
updated to reflect the changes in the 
protocol. 
Section 4.4 – Patient Withdrawal from 
the study 
 
Section 7 – Table 1 
 
Section 9.4.9 – Removal due to 
Adverse Events 
5. Treatment is interrupted for more 
than 4 weeks for any reason 
(Note: Delays do not count 
scheduled weeks of rest) 
 
NOTE: If any patient requires more 
than one dose reduction of AC…. 
---------------- 
 
 
 
 
NOTE: The treating physician may 
adjust doses based on individual 
patient histories to optimize dose 
delivery, per standard of care. If any 
patient requires…. 
Modifications to the protocol to have 
patients remain on study even if their 
treatment is interrupted for more 
than 4 weeks. 
 
Clarification that the treating 
physician may modify dosing of 
chemotherapy per standard of care, 
dependent on an individual’s patient 
history (also added as a footnote in 
Table 1). 
Section 6.1.1.5 – Vaccine 
administration and vaccine schedule 
To reconcile the DC vaccine use and 
disposal, the procedure will be to ship 
the vial of 1.5 mL of prepared final 
Vaccine Product to the clinic and 
following vaccination of the patient, 
the unused portion of the Vaccine 
Product will be returned to the GMP 
QC laboratory for reconciliation and 
testing. 
(2 Figures) 
To reconcile the DC vaccine use and 
disposal, the procedure will be to ship 
the vial of 1.5 mL of prepared final 
Vaccine Product to the clinic and 
following vaccination of the patient, 
the unused portion of the Vaccine 
Product will be disposed of at the 
clinic by BIIR or Clinical Research Staff 
coordinating the study visit. 
(2 Figures) 
Modified the reconciliation procedure 
of the DC vaccines disposal. 
 
Modification of DC vaccination 
schedules to reflect the addition of a 
3rd biopsy for those patients who will 
have their definitive surgery outside a 
Baylor hospital. 

 
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Section 7.1 – Chemotherapy 
treatment delay 
1. Treatment may be delayed no more 
than 4 weeks for any reason (Note: 
Delays do not count scheduled weeks 
of rest). 
2. Patients who are off study 
treatment for more than 4 weeks for 
any reason will be considered 
withdrawn from the study. 
---------------- 
 
Modifications to the protocol to have 
patients remain on study even if their 
treatment is interrupted for more 
than 4 weeks. 
 
Section 7.2 – Chemotherapy dose 
modification for toxicity 
There are no chemotherapy dose 
escalations on this study. 
---------------- 
 
Clarification that the treating 
physician may modify dosing of 
chemotherapy per standard of care, 
dependent on an individual’s patient 
history. 
Section 7.3 – Hematologic toxicity 
Treatment may be delayed for up to 4 
weeks beyond a scheduled treatment 
to allow sufficient time for recovery. 
Treatment may be delayed to allow 
sufficient time for recovery. 
Modifications to the protocol to have 
patients remain on study even if their 
treatment is interrupted for more 
than 4 weeks. 
Section 8.6 - Procedures for Vaccine 
Treatment Visits 
1. An abbreviated medical history 
(note changed from baseline) 
2. A limited physical assessment 
focusing on the affected breast, 
including vital signs and body weight. 
---------------- 
Modification to the procedures that 
are performed during vaccine 
treatment visits. Medical history and 
physical assessment are not necessary 
at these visits.  
Section 8.11 - Biopsies 
• Fresh tissue and FFPE breast tissue 
from definitive surgery will be 
collected at the time of surgery and 
through the pathology department, 
respectively. 
• A minimum of four*14-gauge 
needle biopsy cores will be 
collected at least 1 week following 
the last chemotherapy dose and 
prior to surgery (2 cores frozen, and 
2 cores in RNAlater®), for those 
patients who will have their 
definitive surgery outside a Baylor 
Addition of one biopsy time point, for 
patients who will have their definitive 
surgery outside a Baylor hospital. 

 
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hospital. 
• Fresh tissue (for patients who have 
their definitive surgery within a 
Baylor hospital) and FFPE breast 
tissue from definitive surgery will 
be collected at the time of surgery 
and through the pathology 
department, respectively. 
Section 11.4 – Statistical Methods 
An interim safety analysis will be 
performed after 4 and 9 patients have 
completed 4 vaccines. Accrual will be 
put on hold if 2 of 4 or >4 of 9 patients 
experience the following: 
An interim safety analysis will be 
performed after 10 patients have 
been enrolled, and accrual will be held 
at that time. If 2 of 4 or >4 of 9 
patients experience the following, 
then accrual will be put on hold: 
Modification of the safety interim 
analysis, which changed the number 
of patients included, and also will hold 
accrual to the trial when the number 
is reached.  
Section 14.2.1 – General guidelines 
• Prior to study initiation, the 
protocol must have the approval 
of the FDA and of a properly 
constituted Institutional Review 
Board (IRB) or Independent Ethics 
Committee (IEC). 
• 100% of all patients entered in the 
study will be monitored. 
• Each patient enrolled will be 
monitored 100%. 
• The first monitoring visit will be 
scheduled to occur within a month 
upon the registration of the first 
patient and continue every 4 to 6 
weeks until all data has been 
monitored for every patient. 
• Prior to implementation, the study 
must have the approval of the FDA 
and of a properly constituted 
Institutional Review Board (IRB) or 
Independent Ethics Committee 
(IEC). 
• 100% of all patients entered in the 
study will be monitored. 
• Each patient enrolled will be 
monitored for 100% of the 
elements. 
• The first monitoring visit will be 
scheduled to comply with the 
monitoring plan upon the 
registration of the first patient and 
will continue as described in the 
Removed redundant statements and 
clarified that monitoring should follow 
the established monitoring plan. 

 
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• Prior to implementation, the study 
must have the approval of the FDA 
and of a properly constituted 
Institutional Review Board (IRB) or 
Independent Ethics Committee 
(IEC). 
monitoring plan until all data has 
been monitored for every patient. 
Section 14.2.2 – Study Monitoring 
Visits 
A Monitoring Visit Report will be 
submitted to the Sponsor of the IND 
and a follow-up letter outlining 
observations and outstanding issues 
noted during the visit will be 
submitted to the investigator at each 
clinical site within 15 days following 
the monitoring visit. 
A Monitoring Visit Report will be 
submitted to the Sponsor of the IND 
and a follow-up letter outlining 
observations and outstanding issues 
noted during the visit will be 
submitted to the investigator at each 
clinical site following the monitoring 
visit. 
Removal of 15 day time limit, to 
comply with the established 
monitoring plan. 
Appendix II - Schedule of Assessments 
Group 1 
 
Group 2 
LA TNBC 
 
ER+/HER2- 
Language updated to match protocol. 
 
Minor grammatical errors or misspellings were corrected as needed. 
 

 
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Appendix X 
013-154 Amendment 5 List of Changes 
Protocol Section 
Original Text 
Revised Text 
Rationale 
Title Page 
---------------- 
Amendment 5, Date: March 21, 2016 
Updated amendment version and 
date to reflect the changes in the 
protocol. 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 5. 
Updated protocol 
Synopsis – Inclusion criteria 
 
Section 4.2 – Inclusion criteria 
 
9. Eligible for treatment with 
paclitaxel, doxorubicin, 
cyclophosphamide, and 
carboplatin. 
9. Eligible for treatment with 
paclitaxel, doxorubicin, 
cyclophosphamide, carboplatin, 
and capecitabine. 
Updated inclusion criterion due to the 
addition of capecitabine for patients 
who do not achieve a pCR. 
Synopsis – Medication and Doses 
 
Section 3 – Study Design 
 
Section 7 – Treatment Plan 
 
Section 7.4 – Radiation therapy 
 
Appendix II – Schedule of Assessments 
---------------- 
TNBC patients who are non-pathologic 
complete responders and/or have 
positive lymph nodes following 
neoadjuvant treatment and surgery 
will receive capecitabine for 6-8 cycles 
(cycle length per physician discretion). 
It will be the physician’s discretion to 
begin capecitabine treatment either 
during radiation or after radiation is 
complete. 
Modified treatment plan/study design 
due to the addition of capecitabine for 
TNBC patients who do not achieve a 
pCR. 
Section 1.8 – Addition of capecitabine 
as adjuvant chemotherapy for TNBC 
---------------- 
1.8.1 Capecitabine  
Capecitabine is a prodrug that is 
enzymatically converted to 5-
fluorouracil in the tumor where it 
inhibits DNA synthesis and slows 
growth of tumor tissue. Capecitabine 
Modified background information due 
to the addition of capecitabine for 
TNBC patients who do not achieve a 
pCR. 

 
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is approved in both colorectal and 
breast cancer. Capecitabine 
demonstrated single-agent activity in 
subjects with MBC with an ORR of 
about 20% in subjects whose disease 
had progressed during or following 
anthracycline and taxane-based 
therapy.52 
Capecitabine is also indicated as a 
combination treatment with docetaxel 
in early-line treatment for MBC and in 
combination with ixabepilone or 
lapatinib as second-line treatment 
after failure of prior anthracycline and 
taxane-containing chemotherapy.52 
The recommended, approved dose of 
capecitabine is 1250 mg/m2 daily BID 
for 14 days, followed by 7 days 
without treatment. This 
dose/schedule necessitates dose 
interruptions or reductions in 
approximately 30% of patients, and in 
clinical trials, approximately 17% of 
patients discontinued the drug due to 
toxicities (primarily hand-foot 
syndrome, diarrhea and 
stomatitis).53,54 
1.8.2 Adjuvant Capecitabine 

 
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Improves DFS in TNBC 
Lee and colleagues recently published 
results from a 5 year follow up of a 
Phase III trial of adjuvant capecitabine 
in breast cancer patients with HER2-
negative pathological residual invasive 
disease after neoadjuvant 
chemotherapy. Oral capecitabine was 
administered for 8 cycles at 1250 
mg/m2 PO BID after standard 
neoadjuvant chemotherapy that 
contained an anthracycline and/or a 
taxane, when patients did not have a 
complete pathologic response. 
Overall, disease-free survival (DFS) 
rate and overall survival increased 
with capecitabine as compared to 
standard therapy (DFS: 74.1% vs 
67.6% and 89.2% vs 83.9%, 
respectively). Specifically in patients 
with triple-negative breast cancer that 
were non-pathologic complete 
responders following surgery and 
neoadjuvant treatment, there was a 
42% reduction in the risk of 
recurrence with the addition of 
adjuvant capecitabine.Since women 
with TNBC who do not achieve a pCR 
have an increased risk of recurrence, 

 
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decreased overall survival, and post-
recurrence survival, the addition of 
capecitabine provides an additional 
benefit and option for this population. 
Section 3 – Study Design 
 
Section 8.10 – Blood samples for 
immunomonitoring 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, 2 weeks 
after the last DC vaccination, and at 
each follow up appointment. 
 
(Old study design flow chart) 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, 2 weeks ± 3 
days after the last DC vaccination, and 
at each follow up appointment. 
 
(New study design flow chart) 
Addition of a 3 day window to the 
timing of the blood collection 2 weeks 
after the last vaccination. 
 
Updated figure to match Amendment 
5 changes. 
Section 5.1 – Prohibited treatments 
---------------- 
• Administration of coumarin-
derived anticoagulants and 
phenytoin during treatment with 
capecitabine 
Addition of prohibited treatments, 
due to the addition of capecitabine in 
Amendment 5. 
Section 6.1.1.5 – Vaccine 
administration and vaccine schedule 
---------------- 
 
TNBC patients who are non-pathologic 
complete responders and/or have 
positive lymph nodes following 
neoadjuvant treatment and surgery 
will receive capecitabine for 6-8 cycles 
(number of cycles per physician 
discretion). It will be the physician’s 
discretion to begin capecitabine 
treatment either during radiation or 
after radiation is complete. These 
adjuvant treatments will not alter the 
Modified treatment plan due to the 
addition of capecitabine for TNBC 
patients who do not achieve a pCR. 

 
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vaccine schedule delineated above. 
Section 6.2 – Non investigational 
products 
---------------- 
 
• 
For TNBC non-pathologic complete 
responders: capecitabine 
treatment to begin either during 
radiation or after radiation is 
complete. 
Modified treatment plan due to the 
addition of capecitabine for TNBC 
patients who do not achieve a pCR. 
Section 6.5.4 – Capecitabine 
---------------- 
 
Entire section 
Included the drug-drug interactions 
for capecitabine, due to 
Amendment 5. 
Section 7 – Treatment plan 
Table 1: 
---------------- 
 
Table 1: 
Capecitabine/1000 mg/m2/Cycles 6-8, 
Days 1-14, q21 days/PO 
Included the treatment schema for 
capecitabine, due to Amendment 5. 
Section 7.2 – Chemotherapy dose 
modification for toxicity 
---------------- 
 
Capecitabine dose reductions are 
permitted per standard of care, drug 
package insert, or physician’s standard 
practice. 
Included the dose reduction 
information for capecitabine, due to 
Amendment 5. 
Section 8.6 – Procedures for vaccine 
treatment visits 
1. Assessment of PS on the ECOG scale 
(Appendix III) 
1. Assessment of PS on the ECOG scale 
(Appendix III), only during visits prior 
to definitive surgery. No assessment 
of ECOG is required at vaccine visits 
post-surgery. 
Modification of assessing ECOG status 
for vaccine visits. 
Section 8.7 – Procedures for end of 
treatment visit (EOT) 
…within 24-48 hours… 
 
ECOG performance status scale 
(Appendix III) 
…within 14 days ± 2 days… 
 
---------------- 
Modification of EOT assessment 
window to allow for more flexibility to 
the patient. 
 
Removal of ECOG assessment for EOT 

 
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visit. 
Section 8.8 – Procedures for follow up 
visits 
ECOG performance status scale 
(Appendix III) 
---------------- 
Removal of ECOG assessment for 
follow up visits. 
References 
---------------- 
New references: 
Xeloda PI, 2015 
Mackean et al, 1998 
O'Shaughnessy et al, 2001 
Lee et al, 2015 
Additional references to support the 
addition of capecitabine to the 
treatment regimen in the protocol. 
 
Minor grammatical errors or misspellings were corrected as needed. 
 

 
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Appendix XI 
013-154 Amendment 6 List of Changes 
Protocol Section 
Original Text 
Revised Text 
Rationale 
Title Page 
---------------- 
Amendment 6, Date: October 13, 
2016 
Updated amendment version and 
date to reflect the changes in the 
protocol. 
Table of Contents, In-Text Tables, and 
Abbreviations 
---------------- 
 
Corresponding headings and pages 
have been changed to reflect 
modifications as a result of 
Amendment # 6. 
Updated protocol 
Section 3 – Study Design 
 
 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, 2 weeks ± 3 
days after the last DC vaccination, and 
at each follow up appointment. 
Blood samples for immunomonitoring 
studies will be obtained at baseline, 
prior to each DC vaccination, prior to 
surgery, prior to radiation, 2 weeks ± 3 
days after the last DC vaccination, 
6 months and 1 year after the last DC 
vaccination. 
Updating the amount of blood 
collected for patients during the 
follow up visits; reduction from every 
3 months for 3 years to once at 6 
months and 1 year after the last 
vaccination. 
Section 4.4 – Patient Withdrawal from 
the study 
---------------- 
 
If the patient is withdrawn for any 
reason, the end of study assessments 
must be completed. 
…(“off study”)… 
 
If the patient is withdrawn for any 
reason, the end of treatment 
assessments must be completed (see 
Section 8.7). 
Clarification for withdrawn from the 
study, which can also be labeled “off 
study”. 
 
Clarification that assessments are end 
of treatment assessments, referencing 
the appropriate section in the 
protocol. 
Section 8.5 – Procedures during study 
drug treatment 
---------------- 
10. Immunomonitoring studies: 
Obtain approximately 30 mL of 
whole blood prior to all 
vaccinations; prior to surgery; 
and prior to radiation (see 
Section 8.10). 
Addition of an assessment to the 
proper section (it is not an additional 
or new assessment). 

 
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Section 8.7 – Procedures for end of 
treatment visit (EOT) 
… (End of Treatment Visit)… 
 
---------------- 
… (End of Treatment or Off Treatment 
Visit)… 
 
NOTE: End of treatment, or off 
treatment, is NOT considered off 
study or withdrawn from the study. 
 
6. Immunomonitoring studies: 
obtain approximately 40 mL of 
whole blood 2 weeks ± 3 days 
after the last DC vaccination (see 
Section 8.10). 
 
Clarification for “end of treatment”, 
which can also be labeled “off 
treatment”. 
 
Clarifying that end of treatment does 
not equal off study/withdrawal from 
the study. 
 
Addition of an assessment to the 
proper section (it is not an additional 
or new assessment). 
Section 8.8 – Procedures for follow up 
visits 
6. Obtain approximately 30 mL of 
whole blood for immune 
response to vaccine. 
6. Obtain approximately 30 mL of 
whole blood for immune response 
to vaccine at 6 months and 1 year 
after the last DC vaccination. 
Modification of the blood collection. 
Blood was previously collected at 
every 3 months for 3 years during the 
follow up phase of the protocol, but is 
modified to only 2 blood collections 
total during follow up. 
Section 8.10 – Blood samples for 
immunomonitoring 
• 30 mL at the time of each follow-
up appointment 
• 30 mL at 6 months and 1 year after 
the last DC vaccination. 
Modification of the blood collection. 
Blood was previously collected at 
every 3 months for 3 years during the 
follow up phase of the protocol, but is 
modified to only 2 blood collections 
total during follow up. 
Appendix II - Schedule of Assessments 
For 40 mL blood draws, 4 CPT tubes 
and 2 tempus tubes will be used for 
collection. For 30 mL blood draws, 3 
CPT tubes and 2 tempus tubes will be 
used for collection.  
For 40 mL blood draws, 4 CPT tubes 
and 2 tempus tubes will be used for 
collection. For 30 mL blood draws, 3 
CPT tubes and 2 tempus tubes will be 
used for collection. For blood draws 
Language updated to match the 
protocol amendment. 

 
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occurring during follow-up, 30 mL will 
only be collected at 6 months and 1 
year after the last DC vaccination. 
 
Minor grammatical errors or misspellings were corrected as needed.