T-Cell Immune Checkpoint Inhibition Plus Hypomethylation for Locally Advanced HER2-Negative Breast Cancer - A Phase 2 Neoadjuvant Window Trial of Pembrolizumab and Decitabine Followed by Standard Neoadjuvant Chemotherapy
Phase: PHASE2
Conditions: Breast Adenocarcinoma, Estrogen Receptor- Negative Breast Cancer, Estrogen Receptor-positive Breast Cancer, HER2/Neu Negative, Invasive Breast Carcinoma, Progesterone Receptor Negative, Progesterone Receptor Positive Tumor, Stage II Breast Cancer, Stage IIA Breast Cancer, Stage IIB Breast Cancer, Stage IIIA Breast Cancer, Stage IIIB Breast Cancer, Triple-negative Breast Carcinoma
Sponsor: Virginia Commonwealth University

MCC-15-11083
T-Cell Immune Checkpoint Inhibition Plus Hypomethylation for Locally Advanced HER2-Negative
Breast Cancer - A Phase 2 Neoadjuvant Window Trial of Pembrolizumab and Decitabine Followed by
Standard Neoadjuvant Chemotherapy
NCT02957968
11/22/2020

 Virginia Commonwealth University Massey Cancer Center 
 
MCC Protocol #: MCC-15-11083                                                
FDA IND#: 132112 
T-Cell Immune Checkpoint Inhibition Plus Hypomethylation for Locally Advanced  
HER2-Negative Breast Cancer – A Phase 2 Neoadjuvant Window Trial of 
Pembrolizumab and Decitabine Followed by Standard Neoadjuvant Chemotherapy 
Sponsor-Investigator 
Harry D. Bear, MD, PhD 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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TABLE OF CONTENTS 
REVISION HISTORY .................................................................................................................... 2 
LIST OF FIGURES ..................................................................................................................... 12 
LIST OF TABLES ....................................................................................................................... 12 
LIST OF ABBREVIATIONS ....................................................................................................... 13 
STUDY SCHEMA ....................................................................................................................... 14 
1 
BACKGROUND ........................................................................................................... 15 
 
IMMUNOTHERAPY OF CANCER – PROMISE AND LIMITATIONS ............................................ 15 
 
OBSTACLES/ESCAPE FROM IMMUNOTHERAPY ................................................................. 15 
 
EVIDENCE FOR ROLE OF HOST IMMUNE RESPONSE IN BREAST CANCER .......................... 16 
 
IMMUNOTHERAPEUTIC APPROACHES TO BREAST CANCER ............................................... 18 
 
DNAMTI CAN OVERCOME RESISTANCE TO/ESCAPE FROM IMMUNOTHERAPY ................... 18 
 
IMMUNE CHECKPOINT INHIBITION .................................................................................... 21 
 
PROPOSED IMMUNOTHERAPY REGIMEN .......................................................................... 22 
 
RATIONALE FOR THE NEOADJUVANT CHEMOTHERAPY REGIMENS .................................... 24 
 
RATIONALE FOR ADDITION OF EXTENDED PEMBROLIZUMAB IN COHORT A (ADDED WITH 
VERSION 10) .................................................................................................................. 25 
 
RATIONALE FOR REVISED DEFINITION OF HORMONE RECEPTOR STATUS ......................... 25 
 
CORRELATIVE STUDIES .................................................................................................. 26 
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OBJECTIVES .............................................................................................................. 28 
 
PRIMARY OBJECTIVE ...................................................................................................... 28 
 
SECONDARY OBJECTIVES ............................................................................................... 28 
 
EXPLORATORY OBJECTIVES ........................................................................................... 29 
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STUDY DESIGN .......................................................................................................... 29 
 
GENERAL DESCRIPTION .................................................................................................. 29 
 
SAFETY LEAD-IN PHASE ................................................................................................. 30 
 
SITE PARTICIPATION ....................................................................................................... 31 
 
REQUIREMENTS FOR COLLECTION OF SAMPLES FOR CORRELATIVE STUDIES ................... 31 
 
STUDY ACCRUAL ............................................................................................................ 31 
 
PRIMARY ENDPOINT ....................................................................................................... 31 
 
SECONDARY ENDPOINTS ................................................................................................ 32 
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PATIENT SELECTION ................................................................................................ 33 
 
INCLUSION CRITERIA ...................................................................................................... 33 
 
EXCLUSION CRITERIA ..................................................................................................... 36 
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STUDY ENTRY AND WITHDRAWAL PROCEDURES ............................................... 39 
 
STUDY ENTRY PROCEDURES .......................................................................................... 39 
 
STUDY WITHDRAWAL ...................................................................................................... 39 
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STUDY TREATMENT .................................................................................................. 40 
 
BASELINE TESTS AND PROCEDURES ............................................................................... 40 
 
BASELINE AND POST-IMMUNOTHERAPY CORE NEEDLE RESEARCH BIOPSIES .................... 40 
 
MARKING THE PRIMARY TUMOR SITE PRIOR TO INITIATION OF THERAPY .......................... 40 
 
SUMMARY OF STUDY TREATMENT AND NEOADJUVANT CHEMOTHERAPY REGIMENS ......... 40 

 
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ADMINISTRATION OF DECITABINE .................................................................................... 42 
 
ADMINISTRATION OF PEMBROLIZUMAB ............................................................................ 43 
 
STANDARD NEOADJUVANT CHEMOTHERAPY .................................................................... 46 
 
RECOMMENDED EVALUATION OF POTENTIAL IMMUNE-RELATED ADVERSE EVENTS ........... 48 
 
BREAST SURGERY .......................................................................................................... 50 
 
AXILLARY STAGING ......................................................................................................... 50 
 
PROHIBITED MEDICATIONS AND TREATMENTS ................................................................. 51 
 
DURATION OF THERAPY .................................................................................................. 51 
 
POST-TREATMENT VISITS ............................................................................................... 51 
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DOSING DELAYS/DOSING MODIFICATIONS ........................................................... 53 
 
RECORDING DOSE DELAYS AND OMISSIONS .................................................................... 53 
 
TOXICITY GRADING ......................................................................................................... 53 
 
DECITABINE TREATMENT MODIFICATION .......................................................................... 53 
 
PEMBROLIZUMAB TREATMENT MODIFICATION .................................................................. 53 
 
NEOADJUVANT CHEMOTHERAPY DOSE MODIFICATIONS ................................................... 54 
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ADVERSE EVENTS: DEFINITIONS AND REPORTING REQUIREMENTS .............. 55 
 
DEFINITIONS................................................................................................................... 55 
 
KNOWN AES .................................................................................................................. 57 
 
PREGNANCY AND LACTATION .......................................................................................... 57 
 
SECONDARY MALIGNANCY .............................................................................................. 57 
 
EVENT OF CLINICAL INTEREST ........................................................................................ 58 
 
IMMUNE-RELATED ADVERSE EVENTS .............................................................................. 58 
 
CLINICALLY SIGNIFICANT IMMUNE-RELATED ADVERSE EVENTS ........................................ 58 
 
TIME PERIOD AND GRADE OF AE CAPTURE ..................................................................... 59 
 
PROCEDURES FOR RECORDING EVENTS ......................................................................... 60 
 
EXPEDITED REPORTING PROCEDURES ............................................................................ 60 
 
REQUIREMENTS FOR EXPEDITED REPORTING TO MERCK AND COMPANY, INC ................... 63 
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PHARMACEUTICAL INFORMATION ......................................................................... 63 
 
DECITABINE ................................................................................................................... 63 
 
PEMBROLIZUMAB (KEYTRUDA) ........................................................................................ 66 
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MEASUREMENT OF EFFECT .................................................................................... 73 
 
ASSESSMENT OF LPBC .................................................................................................. 73 
 
PATHOLOGIC ASSESSMENT OF EFFECT ........................................................................... 73 
 
CLINICAL EXAM ASSESSMENT OF EFFECT ....................................................................... 74 
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CORRELATIVE STUDIES ........................................................................................... 74 
 
PARTICIPATION IN CORRELATIVE STUDIES ....................................................................... 74 
 
COLLECTION, PROCESSING, AND DISTRIBUTION OF SAMPLES .......................................... 74 
 
TUMOR SAMPLES FROM CORE NEEDLE BIOPSY ............................................................... 75 
 
TUMOR SAMPLES FROM SURGICAL SPECIMENS ............................................................... 76 
 
CORRELATIVE BLOOD SAMPLES ...................................................................................... 76 
 
TRACKING TUMOR AND BLOOD SAMPLES ........................................................................ 76 
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STUDY CALENDAR .................................................................................................... 77 
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STATISTICAL CONSIDERATIONS ............................................................................ 85 
 
STUDY DESIGN ............................................................................................................... 85 
 
SAMPLE SIZE AND ACCRUAL RATE .................................................................................. 85 

 
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ANALYSIS POPULATIONS ................................................................................................. 86 
 
STATISTICAL ANALYSIS PLAN .......................................................................................... 86 
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DATA AND SAFETY MONITORING ........................................................................... 87 
 
COORDINATING CENTER ................................................................................................. 87 
 
MONITORING AND AUDITING ............................................................................................ 87 
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REGULATORY COMPLIANCE AND ETHICS ............................................................ 88 
 
ETHICAL STANDARD ....................................................................................................... 88 
 
REGULATORY COMPLIANCE ............................................................................................ 88 
 
INSTITUTIONAL REVIEW BOARD ....................................................................................... 88 
 
INFORMED CONSENT PROCESS ...................................................................................... 88 
 
PATIENT CONFIDENTIALITY ............................................................................................. 88 
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DATA COLLECTION AND MANAGEMENT ............................................................... 89 
 
DATA MANAGEMENT RESPONSIBILITIES ........................................................................... 89 
 
CRFS AND DATA COLLECTION ........................................................................................ 89 
 
ONCORE DATA ENTRY ................................................................................................... 90 
 
STUDY RECORD RETENTION ........................................................................................... 90 
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REFERENCES ............................................................................................................. 91 
APPENDIX 1. PERFORMANCE STATUS CRITERIA ............................................................... 98 
APPENDIX 2. COCKCROFT-GAULT FORMULA ..................................................................... 99 
APPENDIX 3. SUPPORTIVE CARE FOR MANAGEMENT OF ADVERSE EVENTS WITH 
POTENTIAL IMMUNOLOGIC ETIOLOGY ............................................................................... 100 
APPENDIX 4. RECOMMENDED PROCEDURES FOR EVALUATION OF SURGICAL 
BREAST SPECIMENS ............................................................................................................. 103 
 

 
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LIST OF FIGURES 
Figure 1. Expression Patterns of Immune-Related Genes Correlate with Lymphocyte Infiltration
 .................................................................................................................................................... 17 
Figure 2. Lymphocyte-Predominant Breast Cancers have Higher pCR Rates ........................... 17 
Figure 3. Decitabine Resulted in Increased MHC Class I Expression in 4T1 Cells .................... 19 
Figure 4. Decitabine Increased 4T1 Expression of Cancer Testis Antigens ............................... 19 
Figure 5. Decitabine Increased Interferon-Gamma Release Compared to Untreated 4T1 Cells 20 
Figure 6. Decitabine Decreased Total Spleen MDSCs in 4T1 Tumor-Bearing Mice .................. 20 
Figure 7. Decitabine Enhances Effects of AIT in Slowing Tumor Growth ................................... 21 
 
LIST OF TABLES 
Table 1. Summary of Study Treatment Regimen and Neoadjuvant Chemotherapy Regimens .. 41 
Table 2. Management of Pembrolizumab Infusion-related Reaction .......................................... 45 
Table 3. Recommended Evaluation of Potential Immune-Related Adverse Events ................... 49 
Table 4. Expedited Reporting Requirements for Participating Sites ........................................... 61 
Table 5. Expedited Reporting Requirements for Sponsor-Investigator/Coordinating Center...... 62 
Table 6. AEOSI Adverse Reactions Considered Expected for Pembrolizumab Listed by 
Maximum Toxicity Grade ............................................................................................................ 70 
Table 7. Other Adverse Reactions Considered Expected for Pembrolizumab ........................... 71 
Table 8. Most Frequently Reported (≥ 10%) Adverse Events in Patients Treated with 
Pembrolizumab ........................................................................................................................... 72 
Table 9. Study Requirements During Screening and Prior to Initiating Study Treatment (All 
Cohorts) ...................................................................................................................................... 78 
Table 10. Study Requirements During Neoadjuvant Decitabine and Pembrolizumab Treatment 
Through Initiation of Standard Neoadjuvant Chemotherapy (All Cohorts) .................................. 79 
Table 11. Study Requirements From Standard Neoadjuvant Chemotherapy through End of 
Study (Cohorts A and B) ............................................................................................................. 81 
Table 12. Study Requirements From Standard Neoadjuvant Chemotherapy through End of 
Study (Cohort A2) ....................................................................................................................... 83 

 
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LIST OF ABBREVIATIONS 
AC 
doxorubicin and cyclophosphamide 
AE 
adverse event 
AEOSI 
adverse events of special interest 
ALT 
alanine aminotransferase 
ANC 
absolute neutrophil count 
AST 
aspartate aminotransferase 
BCT 
breast-conserving therapy 
CBC 
complete blood count 
CR 
complete response 
CrCL 
creatinine clearance 
CRF 
case report form 
CTA 
cancer testis antigens 
CTCAE 
Common Terminology Criteria for Adverse Events 
CTLA-4 
cytotoxic T lymphocyte-associated protein 4 
CTRL 
Clinical and Translational Research Laboratory 
DNAMTi 
DNA methyltransferase inhibitors  
DSMC 
Data and Safety Monitoring Committee 
ECI 
EDV 
event of clinical interest 
early discontinuation visit 
ER 
estrogen receptor 
FDA 
Food and Drug Administration 
H&E 
hematoxylin and eosin 
HER2 
human epidermal growth factor receptor 2 
HR 
hormone receptor 
IHC 
immunohistochemistry 
INR 
international normalized ratio 
irAE 
immune-related adverse event 
IRB 
Institutional Review Board 
LPBC 
lymphocyte-predominant breast cancer 
MCC 
Massey Cancer Center 
MDS 
myelodysplastic syndrome 
MDSC 
myeloid-derived suppressor cell 
MISP 
Merck Investigator Studies Program 
NCI 
National Cancer Institute 
NSAID 
non-steroidal anti-inflammatory drug 
pCR 
pathologic complete response 
PD-1 
programmed cell death-1 
PgR 
progesterone receptor 
PRMC 
Protocol Review and Monitoring Committee 
RCB 
Residual Cancer Burden 
SAE 
serious adverse event 
SAR 
suspected adverse reaction 
SJS 
Stevens-Johnson Syndrome 
SSAR 
serious suspected adverse reaction 
TEN 
toxic epidermal necrolysis 
TIL 
tumor-infiltrating lymphocyte 
TNBC 
triple-negative breast cancer 
TRegs 
regulatory T cells 
UP 
unanticipated problem 
VAD 
vascular access device 
VCU 
Virginia Commonwealth University 
WCBP 
woman of child-bearing potential 

 
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STUDY SCHEMA 
 
 
 
Eligibility Screening & Study Registration 
Core Needle Biopsy at Time of 
VAD Placement; Blood Sample  
Unresected Locally Advanced HER2-Negative Breast Cancer  
(TNBC or Hormone Receptor-Positive) 
Decitabine 15 mg/m2 IV daily on 4 days during Days 1-5 
12 Month Survival Follow-Up / Off Study 
At about 12 months after surgery or early discontinuation of protocol treatment 
(Includes resolution of irAE F/U for Cohort A2 patients) 
Core Needle Biopsy 3-7 Days after Day 22 
Pembrolizumab; Blood Sample  
Clinical Response Assessment 
Adjuvant Pembrolizumab  
(Cohort A2 Only) 
200 mg IV Q3W up to 8 cycles post-surgery 
Standard Neoadjuvant Chemotherapy 
Cohort B  
(ER-positive and/or PgR-positive; 
HER2-negative) 
AC q 2 weeks or q 3 weeks x 4 → 
Weekly Paclitaxel or Nab-Paclitaxel x 
12 weeks   
or 
Weekly Paclitaxel or Nab-Paclitaxel x 
12 weeks → AC q 2 weeks or q 3 
weeks x 4 
 
Surgery 
Breast-conserving surgery or mastectomy; 
axillary staging 
Cohort A  
(TNBC) 
AC q 2 or 3 weeks x 4 →  
Weekly Paclitaxel or Nab-Paclitaxel + 
Carboplatin (weekly x 12 or q 3 weeks x 
4) 
or 
Weekly Paclitaxel or Nab-Paclitaxel + 
Carboplatin (weekly x 12 or 
q 3 weeks x 4) → AC q 2 or 
3 weeks x 4 
Pembrolizumab 200 mg IV on Days 8 and 22 
Blood Sample  
Cohort A2  
(TNBC with Extended Pembrolizumab) 
Q3W neoadjuvant Pembrolizumab (200mg IV), in 
addition to: 
AC q 2 weeks or q 3 weeks x 4 →  
Weekly Paclitaxel or Nab-Paclitaxel + Carboplatin 
(weekly x 12 weeks or q 3 weeks x 4) 
or 
Weekly Paclitaxel or Nab-Paclitaxel + Carboplatin 
(weekly x 12 weeks or q 3 weeks x 4) →  
AC q 2 weeks or q 3 weeks x 4 
30 Day Post-Surgery Safety Follow-up  
Submission of 
Residual 
Tumor or 
Tumor Bed 
Samples 
Surgery 
Breast-conserving surgery or mastectomy; 
axillary staging 
30 Day Post-Surgery Safety Follow-Up 
6-Month irAE Follow-Up 
6 months after surgery or nonsurgical 
decision 
Clinical Response Assessment 
30-Day Safety Follow-Up  
30 days after last dose of adjuvant 
pembrolizumab 

 
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1 BACKGROUND 
 Immunotherapy of Cancer – Promise and Limitations 
Over the past 4 decades, the promise of immunotherapy for treating cancer has waxed 
and waned, but has recently enjoyed a dramatic renaissance of enthusiasm. For many 
years, the successes of manipulating the immune response to induce regression of 
cancers were largely limited to murine models, human melanoma, and renal cell 
carcinoma, with little cause for optimism in the treatment of epithelial malignancies, which 
are the most common causes of cancer death (4-6). 
Immunotherapeutic approaches can be roughly divided into 2 main categories – active and 
passive. Active immune therapies are aimed at stimulating and activating the host’s own 
immune system to recognize and destroy cancer cells. This category includes vaccines, 
infusion of immunologically active cytokines, and altering the tumor itself to make it more 
immunogenic. Passive immunotherapy refers to treatments that involve infusing antigen-
targeted molecules or cells into the host, which then attack the tumor directly, either 
causing tumor cell destruction or inhibition of tumor growth. These passive approaches 
include adoptive cellular therapy, such as infusion of T lymphocytes which have been 
removed from the patient, manipulated and expanded in vitro, and then reinfused into the 
host, sometimes in combination with recombinant cytokines that encourage expansion of 
the cells and increase their activity (7). For example, tumor-infiltrating lymphocytes grown 
from biopsy samples of melanoma tumors have induced dramatic regression in patients 
with metastatic disease. More recently, T cells genetically modified to express chimeric 
antigen receptors (CAR T cells) created from antibody-antigen combining regions and T-
cell signaling molecules have been used successfully to treat hematologic malignancies (8-
10). Monoclonal antibodies, either alone or linked to cytotoxic molecules, are another 
example of passive immunotherapy that has had considerable success (11). To a varying 
degree, monoclonal antibodies that recognize cancer cell surface targets may be both 
passive and active, in the sense that antibodies bound to cancer cells can directly inhibit 
signaling by the target molecule and can also trigger host immune cells (eg, natural killer 
[NK] cells) to attack and kill the cancer cells (12) (13). 
The most recent wave of excitement about immunotherapy has been generated by what 
may be considered a “hybrid” form of therapy that is both passive and active. This 
approach, termed “immune checkpoint inhibition”, uses monoclonal antibodies to inhibit 
mechanisms that suppress T-cell activation and function, and will be discussed in more 
detail below (14) (15). 
 Obstacles/Escape from Immunotherapy 
The success of immunotherapy for cancer has been hampered by a variety of highly 
effective escape mechanisms that allow cancers to avoid immune destruction. These 
obstacles, in fact, have been added to the so-called “hallmarks” that characterize many 
cancers (16). The escape mechanisms include: lack of non-self antigens, immunoediting or 
loss of immunogenic tumor antigens, low expression of major histocompatibility complex 
(MHC) molecules required for antigenic peptide epitope presentation, secretion of 
immunosuppressive cytokines (eg, TGF-β, interleukin 10 (IL-10), vascular endothelial 
growth factor [VEGF]), induction/infiltration of suppressor cells (myeloid-derived 
suppressor cells [MDSCs]), T regulatory cells [Tregs]), and stimulation of immune 

 
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checkpoint molecules on T cells (PD-1, CTLA-4) (14, 15, 17-26). Overcoming these 
obstacles will likely be necessary for host immunity to have a significant impact on cancer. 
 Evidence for Role of Host Immune Response in Breast Cancer 
Although immune therapies for breast cancer have had limited success, with the prominent 
exception of monoclonal antibodies targeting HER2 (11), evidence of the importance of 
host immune responses to breast cancer has been available for at least 4 decades. For 
example, Di Paola et al reported more than 40 years ago that lymphocyte infiltration in 
breast cancers and signs of immune activation in the regional lymph nodes were highly 
predictive of better patient outcomes (27). More recently, immunohistochemical (IHC) 
assessment of breast cancers has shown that CD8+ T cells infiltrating the tumor or stroma 
of breast cancers was predictive of a better prognosis (28-31). We have also identified a 5 
immune-related gene signature based on RNA microarrays that identifies patients with a 
high likelihood of not experiencing a recurrence (32). 
Moreover, lymphocytic infiltration of breast cancers and associated gene expression 
profiles, assessed using core biopsy tumor samples, have been shown to correlate 
strongly with responses to neoadjuvant chemotherapy, as well as the benefit of adding a 
platinum compound to the regimen of neoadjuvant chemotherapy for  
triple-negative breast cancer (TNBC) (33-36) (Figure 1 and Figure 2). 

 
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Figure 1. Expression Patterns of Immune-Related Genes Correlate with Lymphocyte Infiltration 
In 481 tumors from GeparSixto: A. Hierarchic clustering of 12 immunologically relevant genes showed 
3 different immune groups of tumors with different expression of immunologic genes and different 
amounts of tumor-infiltrating lymphocytes (TILs). Immune Group A - low expression of all immune 
genes; immune group B - intermediate expression levels; immune group C - high expression of 
immunologic genes. Corresponding levels of stromal TILs for each tumor as well as lymphocyte-
predominant breast cancer (LPBC) status is shown in lower section of panel B. Evaluation of CXCL9 
and PD-1 mRNA levels showed positive correlation (corr) between both markers (Pearson correlation 
coefficient, 0.813). C. Three immune clusters were significantly different for percentage of LPBC 
tumors and pathologic complete response (pCR) rate. 
 
 
 
Figure 2. Lymphocyte-Predominant Breast Cancers have Higher pCR Rates 
Pathologic complete response (pCR) rates increased in tumors with LPBC phenotype, compared 
with tumors with non-LPBC phenotype in the GeparSixto cohort. (LPBC: lymphocyte-predominant 
breast cancer; PM: nonpegylated liposomal doxorubicin; PMCb: PM with carboplatin) 

 
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 Immunotherapeutic Approaches to Breast Cancer 
Until recently, immunological approaches to breast cancer therapy have focused on 
vaccines targeting HER2, mammaglobin, telomerase reverse transcriptase,  
MUC-1, and other potential breast cancer-specific antigens. There have certainly been 
“successes” in the sense of inducing immune responses, but the clinical gains have been 
modest, at best (37). Recently, evidence of clinical activity against breast cancer using 
immune checkpoint inhibiting agents has been reported (38-42). While response rates 
have been in the mid- to low teens, these studies, along with the immunological correlates 
with prognosis and response to chemotherapy, suggest the potential of these agents to 
have a positive impact, especially when combined with other immunologic manipulations. 
 DNAMTi Can Overcome Resistance to/Escape from Immunotherapy 
A large number of studies, including research from our laboratories, have demonstrated 
that DNA methyltransferase inhibitors (DNAMTi) exert an array of effects that may increase 
the likelihood of responses to immune therapies (29, 43-49). Immunoediting, or the 
elimination through genetic or epigenetic changes of tumor antigen expression with a 
reduction in immunogenicity, is a normal process that cancer cells undergo in order to 
evade and escape the immune system (18). Epigenetic alterations include excessive 
deacetylation of histones as well as excessive methylation of the genome, thereby 
silencing or inactivating numerous genes that are involved in tumor suppression, 
apoptosis, antigen presentation, and those that serve as tumor antigens in dedifferentiated 
cells (50) (51). Indeed, loss of HER2/neu has been shown to be related to genome 
methylation (52). In previous studies, MHC Class I molecules have also been shown to be 
silenced through this mechanism, diminishing the immune response (51, 53, 54). The DNA 
methyltransferase inhibitors 5-aza-2’-deoxycytidine (decitabine) and azacitidine are global 
hypomethylation agents, and it has been suggested that, through liberation of silenced 
tumor antigens, these agents may increase responses to immunotherapy, including 
vaccines (43, 54-56). 
Strategies utilizing DNA methyltransferase inhibition in combination with immunotherapy 
have been tested in clinical trials. Odunsi et al recently published their findings that an NY-
ESO-1 CTA-targeting cancer vaccine combined with decitabine treatment resulted in 
enhanced immune responses in advanced platinum-resistant ovarian cancer (44). We 
have also used this strategy to increase host immune responses to multiple myeloma in 
patients (57). Also, in our center, it has been shown in a HER2 transgenic murine breast 
cancer model that antigen-negative variants (ANV) that have lost expression of HER2 
emerge as recurrences after immune rejection of HER2-expressing tumors. Moreover, 
treatment of tumor cells from these ANV tumors with decitabine in vitro restored HER2 
expression (52). 
Tumors can also escape from immune attack by inducing immunosuppressive responses 
in the form of an increase in splenic and circulating MDSCs and regulatory T cells (58-60). 
Recruitment of MDSCs by tumors has also been shown to be altered by demethylating 
agents and to be highly dependent on methylation (43). In our own laboratory we have 
demonstrated that decitabine treatment of 4T1 mammary carcinoma cells increased 
expression of tumor antigens (HER2 and cancer testis antigens) and antigen-presenting 
molecules (MHC Class I) and increased immunogenicity, assessed by interferon-gamma 
secretion from tumor-sensitized T lymphocytes co-cultured with 4T1 tumor cells (Figure 3, 
Figure 4, and Figure 5). 

 
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Figure 3. Decitabine Resulted in Increased MHC Class I Expression in 4T1 Cells 
MHC: major histocompatibility complex 
 
 
 
Figure 4. Decitabine Increased 4T1 Expression of Cancer Testis Antigens 
Dec: decitabine 
 

 
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Figure 5. Decitabine Increased Interferon-Gamma Release Compared to Untreated 4T1 Cells 
 
 
In vivo treatment of 4T1 tumor-bearing syngeneic mice dramatically decreased the  
tumor-induced MDSC burden in spleen, liver, and peripheral blood, and increased the 
efficacy of adoptive immunotherapy with T cells (61) (Figure 6 and Figure 7). 
 
 
Figure 6. Decitabine Decreased Total Spleen MDSCs in 4T1 Tumor-Bearing Mice 
MDSC: myeloid-derived suppressor cell 
 
 

 
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Figure 7. Decitabine Enhances Effects of AIT in Slowing Tumor Growth 
Decitabine (DEC) in combination with adoptive immunotherapy (AIT) with T lymphocytes expanded 
in IL-7 + IL-15 resulted in a significant decrease in 4T1 tumor size compared to AIT alone (CYP: 
cyclophosphamide). 
A group at Johns Hopkins has recently demonstrated that treatment with a combination of 
azacitidine, entinostat (an HDAC inhibitor), anti-CTLA-4 antibody and anti-PD-1 antibody 
could cure advanced 4T1 mammary carcinomas in syngeneic mice (62). They attributed an 
effect on MDSCs as the major mechanism accounting for this therapeutic effect. 
Interestingly, in contrast to our results with decitabine, they did not observe a significant 
effect on MDSCs with azacitidine alone in this murine model. 
Luo et al showed that treatment of breast cancer cell lines with the next-generation 
hypomethylating agent, guadecitabine, upregulated MHC-I expression in response to 
interferon-γ (63).  
Altered epigenetic regulation including DNA hypermethylation by DNAMT1 has been 
implicated as one of the causes of TNBC tumorigenesis (64). DNAMT1 expression is 
associated with poor breast cancer survival, and it is overexpressed in TNBC subtype. 
DNAMT1 inhibitors exert anti-tumorigenic effects against TNBC cells. This includes the 
hypomethylating agents azacitidine, decitabine, and guadecitabine that might sensitize 
TNBC patients to immune checkpoint blockade therapy (64).  
 Immune Checkpoint Inhibition 
As mentioned above, immune checkpoint pathways, which function to limit autoimmunity 
under normal circumstances, have been shown to be a significant obstacle to immunologic 
destruction of cancers. Binding of B-7 on an antigen-presenting cell to CTLA-4 on a T cell 
recognizing an antigen on the same cell causes inhibition of T-cell activation, rather than 
stimulation. At the effector phase of T-cell response to a tumor cell, binding of PD-L1 to the 
programmed death receptor (PD-1) leads to negative regulation of the T-cell response to 
the tumor antigen. Monoclonal antibodies to these receptors have now been shown to 
induce tumor regressions in a high proportion of patients, dramatically increasing 
progression-free survival (PFS) compared to standard therapies. This has been 
demonstrated not only in melanoma, but also in bladder cancer, lung cancer, and, as noted 

 
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above, in breast cancer. Indeed, for patients with advanced lung cancer, anti-PD-1 
antibody has been shown to be superior to taxane chemotherapy (14, 15, 22-26, 65-68). 
Toxicities are largely attributable to autoimmune or inflammatory responses, which is not 
surprising (69). However, the frequency of severe toxicities with anti-PD-1 antibodies has 
generally been lower than with the anti-CTLA-4 compounds, which were available earlier. 
For example, in patients with advanced melanoma, the anti-PD-1 nivolumab was superior 
to ipilimumab (anti-CTLA-4) in terms of PFS as well as toxicity (70). Although some trials of 
anti-PD-1 agents selected patients whose tumors were positive for PD-L1 for inclusion, it is 
not clear that baseline expression of PD-L1 is an obligate predictor of benefit from anti-PD-
1 therapy (67) (66). This may be because, as has been shown for 4T1 murine mammary 
carcinoma, immune attack actually induces PD-L1 expression by the tumor cells, which do 
not express this cell surface marker in vitro (71). 
Based on the information reviewed here, we hypothesize that combined treatment of 
breast cancer patients with a DNAMT inhibitor and anti-PD-1 antibody will:  
1) increase the lymphocytic infiltration into primary breast cancers; 2) alter the gene 
expression pattern in primary breast cancers to a pattern more indicative of CD8+  
T-cell responses; 3) increase tumor antigen expression in the tumor; 4) decrease 
infiltration of breast cancer with immunosuppressive cells, such as MDSCs and Tregs; and 
5) increase the likelihood of pCR after the administration of standard neoadjuvant 
chemotherapy. 
 Proposed Immunotherapy Regimen 
1.7.1 Decitabine 
1.7.1.1 Initial Overview 
Decitabine, a nucleoside metabolic inhibitor, was approved by the Food 
and Drug Administration (FDA) in 2006 for treatment of patients with 
myelodysplastic syndromes (MDS). Decitabine hypomethylates DNA by 
inhibiting DNA methyltransferase. 
The most commonly occurring adverse reactions observed following 
administration of decitabine in MDS clinical trials include neutropenia, 
thrombocytopenia, anemia, fatigue, pyrexia, nausea, cough, petechiae, 
constipation, diarrhea, and hyperglycemia. However, in this study, patients 
do not have impaired bone marrow function prior to therapy and they will 
receive a short course of decitabine (only one cycle of decitabine 
administered once daily for a total of 5 doses). Therefore, we anticipate 
that decitabine will be tolerated well with very few AEs. 
1.7.1.2 Rationale for Revised Decitabine Dosing 
The initial MCC-15-11083 study design specified that decitabine  
20 mg/m2/day would be administered on 5 consecutive days  
(100 mg/m2 total) during the first week of neoadjuvant study therapy. Grade 
3 or 4 neutropenia was observed in 3 of the first 5 patients during the 
weeks following administration of decitabine. No infectious complications 
occurred during the neutropenia in these patients, but to minimize the risk 
of infection, maintain the study-specified treatment schedule, and avoid 

 
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potential delays in initiating chemotherapy, the decision was made in 
Protocol Version 6 to decrease the decitabine dosing to 15 mg/m2 and the 
number of decitabine doses from 5 to 4 for a total dose of 60 mg/m2. 
1.7.2 Pembrolizumab 
The PD-1 receptor-ligand interaction is a major pathway hijacked by tumors to 
suppress immune control. The normal function of PD-1, expressed on the cell 
surface of activated T cells under healthy conditions, is to down-modulate unwanted 
or excessive immune responses, including autoimmune reactions. PD-1 (encoded 
by the gene Pdcd1) is an Ig superfamily member related to CD28 and CTLA-4, 
which has been shown to negatively regulate antigen receptor signaling upon 
engagement of its ligands (PD-L1 and/or PD-L2). The structure of murine PD-1 has 
been resolved. PD-1 and family members are type I transmembrane glycoproteins 
containing an Ig Variable-type (V-type) domain responsible for ligand binding and a 
cytoplasmic tail, which is responsible for the binding of signaling molecules. The 
cytoplasmic tail of PD-1 contains 2 tyrosine-based signaling motifs, an 
immunoreceptor tyrosine-based inhibition motif (ITIM) and an immunoreceptor 
tyrosine-based switch motif (ITSM). Following T-cell stimulation, PD-1 recruits the 
tyrosine phosphatases SHP-1 and SHP-2 to the ITSM motif within its cytoplasmic 
tail, leading to the dephosphorylation of effector molecules such as CD3ζ, PKCθ, 
and ZAP70, which are involved in the CD3 T-cell signaling cascade. The 
mechanism by which PD-1 down modulates T-cell responses is similar to, but 
distinct from that of CTLA-4 as both molecules regulate an overlapping set of 
signaling proteins. PD-1 was shown to be expressed on activated lymphocytes 
including peripheral CD4+ and CD8+ T cells, B cells, Tregs, and NK cells. 
Expression has also been shown during thymic development on CD4-CD8- (double 
negative) T cells as well as subsets of macrophages and dendritic cells. The ligands 
for PD-1 (PD-L1 and PD-L2) are constitutively expressed or can be induced in a 
variety of cell types, including non-hematopoietic tissues as well as in various 
tumors. Both ligands are type I transmembrane receptors containing both IgV- and 
IgC-like domains in the extracellular region and contain short cytoplasmic regions 
with no known signaling motifs. Binding of either PD-1 ligand to PD-1 inhibits T-cell 
activation triggered through the T-cell receptor. PD-L1 is expressed at low levels on 
various non-hematopoietic tissues, most notably on vascular endothelium, whereas 
PD-L2 protein is only detectably expressed on antigen-presenting cells found in 
lymphoid tissue or chronic inflammatory environments. PD-L2 is thought to control 
immune T-cell activation in lymphoid organs, whereas PD-L1 serves to dampen 
unwarranted T-cell function in peripheral tissues. Although healthy organs express 
little (if any) PD-L1, a variety of cancers were demonstrated to express abundant 
levels of this T-cell inhibitor. PD-1 has been suggested to regulate tumor-specific  
T-cell expansion in patients with melanoma. This suggests that the  
PD-1/PD-L1 pathway plays a critical role in tumor immune evasion and should be 
considered as an attractive target for therapeutic intervention. 
Pembrolizumab is a potent and highly selective humanized monoclonal antibody 
(mAb) of the IgG4/kappa isotype designed to directly block the interaction between 
PD-1 and its ligands, PD-L1 and PD-L2. Keytruda (pembrolizumab) is approved in 
the United Stated for the treatment of patients with unresectable or metastatic 
melanoma and disease progression following ipilumumab and, if BRAF V600 
mutation positive, a BRAF inhibitor. Examples of additional indications include non-

 
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small cell lung cancer (NSCLC), head and neck squamous cell carcinoma, classical 
Hodgkin lymphoma, primary mediastinal large B-cell lymphoma, urothelial 
carcinoma, microsatellite instability-high cancer, and gastric/gastroesophageal 
junction cancer. 
Adverse reactions that have been reported in at least 20% of patients with 
melanoma receiving pembrolizumab include fatigue, cough, nausea, pruritus, rash, 
decreased appetite, constipation, arthralgia, and diarrhea. As described in Section 
9.2.13 immune-mediated reactions (eg, immune-mediated pneumonitis, colitis, 
hepatitis, hypophysitis, nephritis, hyperthyroidism, and hypothyroidism) can occur. 
1.7.3 Safety Lead-in Phase 
1.7.3.1 Original Safety Lead-in Plan 
In this study, a fixed dose of 200 mg of pembrolizumab will be administered 
on 2 treatment days following a short course of decitabine (a total of 5 
doses administered on 5 consecutive days). We anticipate that there will be 
very few AEs associated with the planned immunotherapy in this 
neoadjuvant window trial. However, a safety lead-in phase will be 
conducted in the initial 6 patients enrolled in the study for identification of 
any clinically significant immune-related adverse events (irAEs) that occur 
during immunotherapy and the dose-dense AC portion of neoadjuvant 
chemotherapy (see Section 3.2). 
1.7.3.2 Extended Safety Lead-in Plan 
One of the first 5 patients treated during the safety lead-in phase 
developed immune-related Guillain-Barré syndrome. Also, in the first 5 
patients, 2 developed grade 3 neutropenia and 1 developed grade 4 
neutropenia. Based on the observed neutropenia, a decision was made to 
reduce the total dose of decitabine from 100 mg/m2 delivered on 5 days to 
60 mg/m2 delivered on 4 days.  
In view of these toxicities, the decision was made to extend the safety lead-
in by 5 additional patients to a total of 11 patients. The number of additional 
patients required was solved so that the 5 additional patients to the 6 
already planned would yield an 80% likelihood that the posterior probability 
that the irAE rate was less than 30%. The posterior probability of the irAE 
rate was modeled as a beta distribution with parameters (1+Xnew) and (9- 
Xnew), where Xnew corresponds to the number of irAEs in the remaining 6 
patients to be enrolled. The prior distribution for the irAE rate was defined 
as a beta distribution with parameters 1 and 4, corresponding to the 
information obtained from the first 5 patients. 
 Rationale for the Neoadjuvant Chemotherapy Regimens 
In HER2-negative breast cancer, it is standard practice to administer an anthracycline, an 
alkylating agent, and a taxane during neoadjuvant treatment (72). One of the most 
commonly used regimens is doxorubicin/cyclophosphamide (AC), followed by paclitaxel 

 
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(73). AC will be administered every 2 or 3 weeks with weekly paclitaxel or Nab-paclitaxel 
following completion of AC.  
Bines et al reviewed 15 ongoing or retrospective clinical trials in which nearly 5000 patients 
with breast cancer were treated with a taxane followed by AC in at least 2 of the study 
arms in either the neoadjuvant or adjuvant therapy setting. No disadvantages in efficacy or 
toxicity of administering the taxane prior to AC were identified (74). Therefore, at the 
treating medical oncologist’s discretion, the chemotherapy sequence may be reversed by 
administering AC after completion of the weekly paclitaxel or Nab-paclitaxel regimen (75). 
The TNBC cohort will include the addition of carboplatin to paclitaxel or Nab-paclitaxel. In 
TNBC, there is emerging evidence that the administration of carboplatin may increase the 
pCR rate following neoadjuvant chemotherapy, which is generally associated with 
improved survival outcomes (76-78). Additionally, it has been shown by Denkert et al that 
the addition of carboplatin to neoadjuvant anthracycline/taxane-based chemotherapy 
significantly improved pCR rates in tumors with a positive immune score and TILs (34). 
 Rationale for Addition of Extended Pembrolizumab in Cohort A (Added with Version 
10) 
The results of the Keynote-522 trial (Funded by Merck Sharp & Dohme [a subsidiary of 
Merck]; ClinicalTrials.gov NCT03036488) showed that among patients with early TNBC, 
the percentage with a pCR was significantly higher among those who received 
pembrolizumab plus neoadjuvant chemotherapy than among those who received placebo 
plus neoadjuvant chemotherapy (1). Recently, the addition of pembrolizumab was also 
reported to increase event-free survival compared to placebo (79). Based on these results, 
the inclusion of pembrolizumab with neoadjuvant chemotherapy and continuation of 
pembrolizumab as postoperative adjuvant therapy was added with Protocol Version 10 as 
a treatment option for Cohort A. This extended pembrolizumab regimen has recently been 
approved by the US FDA (Pembrolizumab [Keytruda] prescribing information, dated 
August 2021). 
Beginning with Protocol Version 11, patients receiving this extended pembrolizumab 
regimen will be designated as Cohort A2. This cohort was created to facilitate increased 
clarity in assessment schedules, analysis populations, and overall study schema. At sites 
active on Protocol Version 10 or later, TNBC patients initially registered to Cohort A may 
be reassigned to Cohort A2 per investigator discretion. Reassignment to Cohort A2 must 
be documented before initiating standard neoadjuvant chemotherapy on study. 
 Rationale for Revised Definition of Hormone Receptor Status 
MD Anderson Cancer Center investigators reported clinical outcomes of primary breast 
carcinomas with complete information on ER status in a retrospective study of 9639 
patients treated between January 1990 and December 2011. Patients were separated into 
3 groups based on the percentage of tumor cell nuclei with positive staining for ER. The 
largest group of 7764 patients (80.5%) had ≥ 10% positive staining, while 250 (2.6%) had 
1-9% positive staining and 1625 (16.9%) had < 1% staining. At a median follow-up of 5.1 
years, the patient cohorts with tumors with 1-9% ER staining or < 1% ER staining had 
worse distant recurrence-free survival (P < 0.0001), recurrence-free survival (P < 0.0001) 
and overall survival (P < 0.0001) rates compared with patients with ≥ 10% ER staining. 
Patients with 1-9% ER staining had similar distant recurrence-free, recurrence-free, and 

 
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overall survival rates (P = 0.8), (P = 0.96) and (P = 0.1), respectively, as patients with < 1% 
ER staining (80). 
A more recent study using the PAM50 gene signature to determine intrinsic subtypes in 60 
ER weakly positive (Allred scores 3-5) breast cancers and 88  
ER-negative (Allred scores 0-2) breast cancers were evaluated in a recently reported 
retrospective study. Among the breast cancers with lower proportion and intensity of 
staining for ER, only 6 (10%) were of luminal subtype, 24 (40%) were HER2 enriched, and 
30 (50%) were basal like. The distribution of subtypes in the ER-negative patients were 
very similar with luminal subtypes in 5 (6%), HER2 enriched in 34 (39%), and basal like in 
49 (56%). With a median follow-up of 54 months, no statistical differences in recurrence (p 
= 0.53) or death (p = 0.41) were identified between the Allred 3-5 and Allred 0-2 groups 
(81). 
In summary, the underlying biology and clinical outcomes of HER2-negative tumors with 
lower proportion and intensity of staining for ER on IHC (1-9% or Allred scores 3-5) are 
very similar to those considered negative for ER staining (IHC < 1%, Allred 0-2). Therefore, 
patients with < 10% staining for ER and PgR by IHC will define the TNBC cohort.  

 
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1.11.2.1 Studies Using Tumor Samples 
Multiplex fluorescent staining of multiple biomarkers on the same formalin-
fixed, paraffin-embedded (FFPE) tumor slide will be performed with the 
Opal staining system and the Vectra microscope (PerkinElmer). This 
multiplex approach allows for 6 markers, in addition to DAPI nuclear 
staining, for each slide. Markers of immune cell subsets including helper T 
cells (CD4), cytotoxic T cells (CD8), B cells (CD20), and regulatory T cells 
(FOXP3) can be analyzed along with additional markers of tumoral immune 
evasion (PD-L1) and cytokeratin (CK) as a marker of epithelial cells to 
delineate stroma versus tumor. Multiple markers will be analyzed in 2-slide 
sets as a discovery component of this clinical trial. Biomarkers of interest at 
this time include the following: 
• 
Subtypes of immune cells, including helper T cells (CD4), cytotoxic T 
cells (CD8), B cells (CD20), regulatory T cells (FOXP3), and MDSCs 
(CD33+/HLA-DR low/neg) (84) 
• 
Immune checkpoints PD-L1, PD-1, and LAG3 
Analysis of CK will be performed on all slides in order to delineate between 
tumor and stroma for characterization of spatial distribution of immune 
cells. 
Additionally, tissue will be evaluated for analysis of RNA expression, which 
may predict for a positive immune response. Work by Drs. Ascierto and 
Bear identified gene expression signatures that correlated with improved 
outcomes in breast cancer patients in retrospective analysis (32, 85). 
Immunologic gene expression profiles associated with high pCR rates were 
also described by Denkert et al (34). Evaluation of gene expression 
signatures, which may be associated with improved outcomes will be 
analyzed, as well as the evaluation of how epigenetic modulation with 
decitabine affects these expression signatures. 
Unstained FFPE slides from both core needle biopsies and the surgical 
resection specimen will be sent to QualTek Molecular Laboratories, the 
laboratory contracted by Merck for their proprietary PD-L1 staining. 

 
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A portion of the resected tumor obtained in this study will be sent to a third 
party laboratory for gene expression analysis to elucidate genes associated 
with function and modulation of the PD-1/PD-L1 axis. Tumor biopsy FFPE 
samples will be checked for quality, presence of tumor, and overall 
size/condition by H&E staining. Sufficient material, about 5 slides on 
average, will be sent to Almac for RNA isolation. 
A set of more than 680 genes focused largely on genes known to be 
involved in T-cell biology, immune regulation, cellular markers of TILs, and 
tumor-associated macrophages will be evaluated on collected samples. 
Nanostring analysis is particularly well suited to gene expression studies 
from FFPE material where RNA degradation due to cross-linking results in 
less than optimal results from conventional gene expression platforms (eg, 
RTqPCR, microarrays), which require enzymatic steps to create cDNA or 
cRNA. The Nanostring Counter System, in contrast, provides direct binding 
and quantitation of mRNA species, and can be used to obtain high quality 
data from partially degraded (FFPE) samples, which can in turn be 
correlated with findings by IHC and routine histopathologic analysis. 
1.11.2.2 Studies Using Blood Samples 
Blood samples will be collected at 3 time points: baseline, post-decitabine, 
and post-pembrolizumab. These samples will be used for the evaluation of 
circulating MDSCs by flow cytometry CD33+, CD11b+, HLA-DRlow/neg, 
CD15, and CD14. 
2 OBJECTIVES 
 Primary Objective 
To determine and quantify if treatment with neoadjuvant decitabine followed by 
pembrolizumab increases lymphocyte infiltration into tumor and/or stroma in patients with 
locally advanced, HER2-negative breast cancer 
 Secondary Objectives 
2.2.1 To evaluate the safety and toxicity of sequential decitabine plus pembrolizumab 
followed by AC, weekly paclitaxel (or paclitaxel plus carboplatin) or Nab-paclitaxel 
(or Nab-paclitaxel plus carboplatin) administered as neoadjuvant therapy 
In patients with locally advanced, HER2-negative breast cancer who have received 
neoadjuvant decitabine and pembrolizumab: 
2.2.2 To determine if the study treatment increases the proportion of tumors with  
≥ 60% tumor or stromal area infiltrated with lymphocytes (ie, LPBC) 
In patients with locally advanced, HER2-negative breast cancer who have received 
neoadjuvant decitabine and pembrolizumab followed by a standard neoadjuvant 
chemotherapy regimen: 

 
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2.2.3 To determine the rate of pCR in the breast and lymph nodes (pCR breast and 
nodes) 
2.2.4 To determine the rate of Residual Cancer Burden (RCB) Index value of 0-1 
(Section 10.2.3) following all neoadjuvant therapy 
2.2.5 To determine the rate of clinical complete response in the breast and lymph 
nodes (cCR breast and nodes) following all neoadjuvant therapy 
2.2.6 To characterize the alteration of T lymphocyte and other host cell infiltration and 
immune response gene signatures in breast cancers resulting from treatment with 
decitabine and pembrolizumab 
2.2.7 To evaluate the correlation of pre-existing and post-immunotherapy immune 
response signatures with response to neoadjuvant chemotherapy 
2.2.8 To correlate the Merck proprietary PD-L1 assay results with response to therapy 
2.2.9 To evaluate the level of circulating MDSCs at baseline, following treatment with 
decitabine alone, and following treatment with pembrolizumab administered after 
decitabine 
2.2.10 To examine the PFS rate at 12 months (±30 days) following surgery or the 
decision not to undergo surgery 
3 STUDY DESIGN 
 General Description 
This study is a 2-cohort, open-label, multicenter, phase 2 study of a short course of 
immunotherapy consisting of sequential decitabine followed by pembrolizumab 
administered prior to a standard neoadjuvant chemotherapy regimen for patients with 
locally advanced HER2-negative breast cancer. (Refer to Section Error! Reference 
source not found. for the definition of HER2-negative breast cancer.) The primary efficacy 
objective is to determine if the immunotherapy increases the presence and percentage of 
tumor and/or stromal area of infiltrating lymphocytes prior to initiation of standard 

 
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neoadjuvant chemotherapy. At enrollment, patients will be assigned to one of 2 cohorts 
based on hormone receptor status. 
• 
Cohort A - patients with HER2-negative, hormone receptor-negative breast cancer 
(defined as both ER and PgR with < 10% positive staining on IHC)  
Note: before beginning standard neoadjuvant chemotherapy, patients in Cohort A 
may be reassigned to Cohort A2 to receive extended pembrolizumab as part of new 
standard neoadjuvant and postoperative adjuvant therapy. See Section 5.1.3. 
• 
Cohort B - patients with HER2-negative, hormone receptor-positive breast cancer 
(defined as either ER or PgR with ≥ 10% positive staining on IHC) 
Both cohorts will receive the identical doses and treatment schedules of decitabine and 
pembrolizumab followed by a standard neoadjuvant chemotherapy regimen. Both cohorts 
will receive 4 cycles of AC and 12 doses of weekly paclitaxel or Nab-paclitaxel. Paclitaxel 
or Nab-paclitaxel will be combined with carboplatin for Cohorts A and A2 (TNBC). The 
sequence of the 2 regimens will be at the discretion of the treating medical oncologist 
following the safety lead-in phase (refer to Table 1). 
For the primary endpoint, Cohorts A and A2 will be evaluated together, separate from 
Cohort B. Secondary endpoints will be evaluated as described in Sections 3.7 and 13.4.2. 
Note regarding cohort assignment: when patients have multifocal disease with 
heterogeneous hormone receptor (ER/PgR) status, enrollment cohort assignment may be 
determined by treating investigator based on his/her assessment of the most clinically 
relevant hormone receptor phenotype; rationale for this assignment will be documented. 
Note regarding option of adjusting standard neoadjuvant regimen: when a treating 
investigator determines after enrollment that it is in the patient’s best interest to omit or add 
carboplatin to the weekly paclitaxel or Nab-paclitaxel regimen, and that plan differs from 
the cohort-assigned treatment plan, the treating investigator will confer with the Sponsor-
Investigator about the reason for variance from cohort-assigned standard neoadjuvant 
treatment, and the outcome of the discussion will be documented. 
The safety objective will be to evaluate the safety and toxicity of sequential decitabine plus 
pembrolizumab followed by standard neoadjuvant therapy. If the breast tumor is resectable 
following completion of all protocol therapy, breast-conserving surgery or mastectomy and 
axillary surgical staging (either sentinel node biopsy and/or axillary dissection) will be 
performed. Patients in Cohort A2 will continue to standard adjuvant pembrolizumab 
treatment. 
 Safety Lead-In Phase 
A safety lead-in phase will be conducted during immunotherapy and dose-dense AC in the 
first 11 patients enrolled irrespective of cohort. Clinically significant irAEs (listed in Section 
8.6) will be reported in an expedited manner (Section 8.10), and accrual will be halted until 
the safety lead-in phase has been completed. Recommendations for clinical evaluation to 
confirm that an AE is immune related (ie, an irAE) are provided in Section 6.8. 
Determination of adequate safety will be based on assessment of irAEs through dose-
dense AC. The safety evaluation plan is summarized below: 

 
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• 
The initial 11 patients will be followed through dose-dense AC. Accrual will be held 
until the last patient enrolled during the safety lead-in phase has completed dose-
dense AC. 
• 
If ≤2 of the first 11 patients experience a clinically significant irAE (Section 8.6) before 
completion of dose-dense AC, study accrual may continue and the safety lead-in 
phase will be completed. 
• 
If 3 or more of the initial 11 patients experience a clinically significant irAE (Section 
8.6) before completion of dose-dense AC, accrual to the study will be suspended until 
the Massey Cancer Center (MCC) Data Safety and Monitoring Committee (DSMC) 
reviews the reported irAEs and determines whether study revision or study closure is 
required. 
 Site Participation 
3.3.1 MCC Affiliate Network Participation 
Eligibility assessment, patient informed consent, administration of the investigational 
components of the treatment regimen (ie, decitabine and pembrolizumab), 
performance of the research biopsies, collection of blood samples for correlative 
studies, and administration of all neoadjuvant chemotherapy to patients enrolled 
during the safety lead-in phase will be performed at MCC at the VCU Medical 
College of Virginia location. Patients referred by collaborating MCC affiliate member 
physicians and enrolled in the study after the safety lead-in phase has been 
completed will return to the referring physician for administration of the standard 
chemotherapy regimen and for breast surgery by their initial breast surgeon unless 
the patient requests transfer of care to MCC. 
3.3.2 Multicenter Site Participation 
MCC-15-11083 will be conducted at multicenter sites.
 
  
 Requirements for Collection of Samples for Correlative Studies 
Correlative studies will be conducted using tumor samples procured by core needle biopsy 
performed at MCC at baseline and 3-7 days following administration of the last 
administered dose of pre-chemotherapy pembrolizumab. For patients who have surgery, 
samples from the surgical resection specimen will also be collected for the correlative 
studies. Correlative blood samples will be collected at 3 time points. 
 Study Accrual 
The projected sample size for the MCC-15-11083 study is 32-50 patients. Accrual is 
expected to be completed in about 72 months from the time of the first patient enrollment. 
 Primary Endpoint 
The increase in percent of tumor and stroma with infiltrating lymphocytes from baseline 
pre-treatment biopsy to post-immunotherapy biopsy following administration of decitabine 
followed by pembrolizumab 

 
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 Secondary Endpoints 
3.7.1 Using criteria in the National Cancer Institute Common Terminology Criteria for 
Adverse Events Version 5.0 (CTCAE v5.0), all AEs captured as described in 
Section 8.9 
3.7.2 The percentage of patients meeting criteria for LPBC following treatment with 
decitabine and pembrolizumab compared to the percentage before treatment 
(LPBC is defined as breast cancer with ≥ 60% intratumoral or stromal area with 
infiltrating lymphocytes.) 
3.7.3 The proportion of patients with pCR in the breast and post-therapy lymph nodes 
defined as the absence of any invasive cancer in the resected breast specimen 
and absence of cancer on H&E evaluation of all resected lymph nodes following 
completion of neoadjuvant therapy (ypT0/is; ypN0). Note: patients in Cohort A2, 
who receive prolonged pembrolizumab treatment, will be evaluated separately 
from those who receive only pre-chemotherapy pembrolizumab 
3.7.4 The proportion of patients with no or minimal residual disease in the resected 
breast and axillary specimen defined as RCB Index value 0 or 1 (Section 10.2.3). 
Note: patients in Cohort A2, who receive prolonged pembrolizumab treatment, will 
be evaluated separately from those who receive only pre-chemotherapy 
pembrolizumab 
3.7.5 The proportion of patients with cCR defined as the absence of tumor based on 
physical examination of the breast and nodes following completion of all 
neoadjuvant therapy. Note: patients in Cohort A2, who receive prolonged 
pembrolizumab treatment, will be evaluated separately from those who receive 
only pre-chemotherapy pembrolizumab 
3.7.6 Enumeration of T cells and immune cell subsets, including CD8+ cytotoxic T cells, 
CD4+ helper T cells, FOXP3+ regulatory T cells, CD20+ B cells, and MDSCs in 
the tumor sample procured by core needle biopsy following completion of 
sequential decitabine followed by pembrolizumab compared to the number of 
these cells in tumor samples procured at baseline 
3.7.7 Evaluation of expression of PD-L1 within tumor, stroma, and infiltrating immune 
cells at baseline and following immunotherapy 
3.7.8 Correlation of intensity of PD-L1 expression by Merck assay as it relates to pCR 
rates from chemotherapy 
3.7.9 Evaluation of MDSCs identified in blood samples post-decitabine and  
post-pembrolizumab compared to MDSCs found in blood samples collected at 
baseline 
3.7.10 Proportion of patients who are alive and have not had disease progression or 
relapse at 12 months following surgery (or the decision not to undergo surgery). 
Note: patients in Cohort A2, who receive prolonged pembrolizumab treatment, will 
be evaluated separately from those who receive only pre-chemotherapy 
pembrolizumab 

 
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4 PATIENT SELECTION 
 Inclusion Criteria 
A patient must meet all of the following inclusion criteria to be eligible for this study. 
Inclusion Criteria 
Yes 
No 
N/A 
4.1.1 
Invasive adenocarcinoma of the breast diagnosed by core 
needle biopsy 
 
 
 
4.1.2 
Breast cancer determined to be HER2-negative per current 
American Society of Clinical Oncology/College of American 
Pathologists (ASCO/CAP) HER2 Guidelines (If IHC was 
performed, IHC 0 or 1+; if fluorescence in situ hybridization 
[FISH] or other in situ hybridization test, dual probe 
HER2/CEP17 ratio < 2.0 with an average HER2 copy number 
< 4.0 signals/cell) 
 
 
 
4.1.3 
Breast cancer determined to be hormone receptor-positive or 
hormone receptor-negative defined as follows: 
• 
Hormone receptor-positive: ≥ 10% staining by IHC for either 
estrogen receptor (ER) or progesterone receptor (PgR) 
• 
Hormone receptor-negative: < 10% staining by IHC for both ER and 
PgR 
Note: Refer to Section 1.10 for the rationale of the definitions provided above, to 
Section 3.1 for cohort assignments, and Section 13.2 regarding accrual limitations 
based on hormone receptor status. 
 
 
 
4.1.4 
Locally advanced breast cancer defined as any of the 
following per American Joint Committee on Cancer (AJCC) 
Staging Criteria: 
Note: Imaging methods that may be used for tumor measurement to 
determine eligibility include breast ultrasound and breast MRI. 
Mammography may not be used. 
• 
T2 based on tumor measurements by physical examination or 
imaging and with clinically positive regional lymph nodes (cN1 
or cN2), irrespective of hormone receptor status 
• 
Hormone receptor-negative patients with tumor size of 3-5 cm 
measured by physical examination or imaging with clinically 
negative regional lymph nodes (cN0)  
• 
Any T3 based on tumor measurements by physical examination 
or imaging, irrespective of hormone receptor status 
• 
Any T4 (including inflammatory breast cancer), irrespective of 
hormone receptor status 
 
 
 
 
 

 
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Inclusion Criteria 
Yes 
No 
N/A 
4.1.5 
Ipsilateral axillary lymph nodes must be evaluated by MRI or 
ultrasound within 12 weeks prior to study registration to 
determine clinical nodal status. If imaging is suspicious or 
abnormal, an FNA or core biopsy of the questionable 
node(s) on imaging is required. Nodal status should be 
classified according to the following criteria: 
• 
Nodal status – negative 
− 
Imaging of the axilla is negative; OR 
− 
Imaging of the axilla is suspicious or abnormal AND FNA or 
core biopsy is negative. 
• 
Nodal status – positive 
− 
FNA or core biopsy of node(s) is cytologically or histologically 
suspicious or positive 
 
 
 
4.1.6 
Breast imaging performed prior to study registration as 
follows: 
• 
Ipsilateral breast – within 12 weeks 
• 
Contralateral breast – within 24 weeks 
 
 
 
4.1.7 
Age ≥ 18 years 
 
 
 
4.1.8 
Eastern Cooperative Oncology Group (ECOG) performance 
status of 0 or 1 (see Appendix 1) 
 
 
 
4.1.9 
Adequate bone marrow function as defined below: 
• 
Absolute neutrophil count (ANC) ≥ 1,500/mm3 
• 
Platelet count ≥ 100,000/mm3 
• 
Hemoglobin ≥ 10.0 g/dL 
 
 
 
4.1.10 Adequate renal function as defined below: 
Serum creatinine ≤ upper limit of normal (ULN) for the lab or a 
calculated creatinine clearance ≥ 60 mL/min (see Appendix 2 for the 
Cockcroft-Gault formula for calculating creatinine clearance) 
 
 
 

 
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Inclusion Criteria 
Yes 
No 
N/A 
4.1.11 Adequate hepatic function as defined below: 
• 
Total bilirubin ≤ ULN for the laboratory 
• 
Aspartate aminotransferase (AST) ≤ 1.5 x ULN for the laboratory 
• 
Alanine aminotransferase (ALT) ≤ 1.5 x ULN for the laboratory 
• 
Alkaline phosphatase (ALP) ≤ 2.5 x ULN for the laboratory 
Note: If ALP is > 1.5 x ULN, imaging to rule out bone and liver metastasis is 
required. 
 
 
 
4.1.12 LVEF assessment (ie, 2-D echocardiogram or MUGA scan) 
performed within 12 weeks prior to study registration 
indicates an LVEF ≥ 50% regardless of the cardiac imaging 
facility’s lower limit of normal 
 
 
 
4.1.13 Women who are not postmenopausal or have not 
undergone hysterectomy must have a documented negative 
serum pregnancy test within 72 hours prior to initiating study 
treatment. 
Note: Postmenopausal is defined as any of the following: 
• 
Age ≥ 60 years 
• 
Age < 60 years and amenorrheic for at least 1 year with follicle-
stimulating hormone (FSH) and plasma estradiol levels in the 
postmenopausal range 
• 
Bilateral oophorectomy 
 
 
 
4.1.14 A female patient who is a woman of child-bearing potential 
(WCBP) and a male patient with a partner who is a WCBP 
must agree to use a medically accepted method for 
preventing pregnancy for the duration of immunotherapy 
and neoadjuvant chemotherapy and until after completion of 
breast surgery or, for patients who do not receive 
neoadjuvant chemotherapy, for a minimum of 6 months 
following the last dose of pembrolizumab or decitabine 
(refer to Section 9.2.12 for information regarding methods of 
preventing pregnancy) 
 
 
 
4.1.15 Ability to understand and willingness to sign the consent 
form 
 
 
 
 
 
 

 
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 Exclusion Criteria 
Exclusion Criteria 
Yes 
No 
N/A 
4.2.1 
Breast cancer treatment for the currently diagnosed breast 
cancer including radiation therapy, chemotherapy, targeted 
therapy, or endocrine therapy prior to study registration 
 
 
 
4.2.2 
Administration of a live vaccine within 30 days prior to 
initiating study treatment 
Note: Seasonal influenza vaccines for injection are generally inactivated flu 
vaccines and are permitted; however, intranasal influenza vaccines 
(eg, Flu-Mist) are live attenuated vaccines, and are not allowed. 
 
 
 
4.2.3 
Administration of a monoclonal antibody within 4 weeks 
prior to initiating study treatment or has not recovered (ie, ≤ 
grade 1 or at baseline) from AEs due to a monoclonal 
antibody administered more than 4 weeks earlier 
 
 
 
4.2.4 
Administration of any investigational agent within 4 weeks 
prior to initiating study treatment 
 
 
 
4.2.5 
Evidence of metastatic disease that is extensive enough to 
preclude consideration of subsequent definitive surgery for 
the primary tumor 
 
 
 
4.2.6 
History of ipsilateral invasive breast cancer or ipsilateral 
ductal carcinoma in situ (DCIS) 
Note: Patients with history of ipsilateral lobular carcinoma in situ (LCIS) are 
eligible. 
 
 
 
4.2.7 
History of solid organ or allogeneic stem cell transplant 
 
 
 
4.2.8 
Previous therapy for any malignancy with an anthracycline 
or taxane for Cohorts A and B and carboplatin for Cohort A 
 
 
 

 
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Exclusion Criteria 
Yes 
No 
N/A 
4.2.9 
Cardiac disease that would preclude administration of the 
drugs included in the study treatment regimen including, 
but not limited to: 
• 
Angina pectoris that requires the current use of anti-anginal 
medication 
• 
Ventricular arrhythmias except for benign premature ventricular 
contractions 
• 
Supraventricular and nodal arrhythmias requiring a pacemaker 
or not controlled with medication 
• 
Conduction abnormality requiring a pacemaker 
• 
Valvular disease with documented compromise in cardiac 
function; and symptomatic pericarditis 
 
 
 
4.2.10 
Nervous system disorder (ie, paresthesia, peripheral motor 
neuropathy, or peripheral sensory neuropathy) ≥ grade 2, 
per CTCAE v5.0 
 
 
 
4.2.11 
Administration of or condition requiring administration of 
systemic steroid therapy or any other form of 
immunosuppressive therapy within 7 days prior to initiating 
study treatment 
Exception: Patients with conditions that can be managed with 
steroids equivalent to or less than an oral prednisone dose of 10 
mg daily would not be excluded from the study. 
 
 
 
4.2.12 
Previous therapy for this cancer with an anti-PD-1, anti-PD-
L1, anti-PD-L2 agent, or any other immunomodulatory 
agent 
 
 
 
4.2.13 
Known or presumed hypersensitivity to decitabine or 
pembrolizumab (or any of their excipients) 
 
 
 
4.2.14 
Diagnosed immunodeficiency, eg, human 
immunodeficiency virus (HIV) 
 
 
 

 
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Exclusion Criteria 
Yes 
No 
N/A 
4.2.15 
Active autoimmune disease requiring systemic treatment 
within the past 2 years (ie, with use of disease-modifying 
agents, corticosteroids, or immunosuppressive drugs) or a 
documented history of clinically severe autoimmune disease 
or a syndrome that requires systemic steroids or 
immunosuppressive agents 
Note: Patients with the conditions or medical history listed below are 
NOT excluded from this study. 
• 
Vitiligo 
• 
Resolved childhood asthma/atopy 
• 
Requirement for intermittent use of bronchodilators or local 
steroid injections or topical steroids 
• Hypothyroidism stable on hormone replacement 
• Sjogren's Syndrome 
 
 
 
4.2.16 
Known history or evidence of interstitial lung disease or 
active, non-infectious pneumonitis 
 
 
 
4.2.17 
Known history of active bacillus tuberculosis (TB) 
 
 
 
4.2.18 
Active infection requiring systemic therapy 
 
 
 
4.2.19 
Known active Hepatitis B or C 
 
 
 
4.2.20 
Pregnancy or breastfeeding 
 
 
 
4.2.21 
Diagnosis or treatment for another malignancy within 5 
years prior to study registration, with the following 
exceptions: complete resection of basal cell carcinoma or 
squamous cell carcinoma of the skin, any in situ malignancy, 
and low-risk prostate cancer after curative therapy 
 
 
 
4.2.22 
Medical, psychological, or social condition that, in the 
opinion of the investigator, may increase the patient’s risk or 
limit the patient’s adherence with study requirements 
 
 
 
 
 

 
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5 STUDY ENTRY AND WITHDRAWAL PROCEDURES 
 Study Entry Procedures 
5.1.1 Required Pre-Registration Screening Tests and Procedures 
Refer to the study calendars in Section 12 for the screening tests and procedures 
that are required prior to registration and for the timing of these events relative to the 
start of treatment. 
5.1.2 Registration Process 
 
 
• 
Completed registration cover sheet or request form as provided by the 
coordinating center 
• 
Attestation of patient eligibility (either included in the request form above, or a 
completed, signed, and dated eligibility checklist) 
• 
Signed and dated consent form 
The Coordinating Center will complete the registration process by assigning a study 
identification (ID) number and returning a Confirmation of Registration to the 
registering study team. Study treatment may not begin until the Confirmation of 
Registration assigning a study ID number has been received from the registrar. 
The registering site will enter the patient’s initial enrollment data  
(eg, demographics, consent, eligibility, on-study) into the OnCore database within 
24 hours following study registration (before the baseline core needle biopsy for 
sample procurement is performed). 
5.1.3 Reassignment to Cohort A2 with Extended Pembrolizumab 
Before beginning standard neoadjuvant chemotherapy, patients initially enrolled to 
Cohort A may be reassigned to Cohort A2 to receive extended pembrolizumab as 
part of standard neoadjuvant and postoperative adjuvant therapy as described in 
Sections 6.7 and 6.13, at the investigator’s discretion. Patients may not initiate 
neoadjuvant chemotherapy with extended pembrolizumab (ie, Cohort A2 treatment) 
until the decision to do so has been documented in source documents and the 
OnCore database and been confirmed by the Coordinating Center. 
 Study Withdrawal 
A patient may decide to withdraw from study participation at any time. Patients must be 
withdrawn from the study when any of the following occurs: 
• 
The patient has withdrawn consent for study treatment and study procedures. 
• 
If, in the investigator's opinion, continuation of the study requirements would be 
harmful to the patient's well-being. 
• 
The patient is lost to follow-up. 

 
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The reason for and date associated with study withdrawal or removal from the study must 
be documented in the source documents and OnCore database. 
6 STUDY TREATMENT 
 Baseline Tests and Procedures 
Refer to the study calendar in Section 12 for requirements prior to initiation of therapy. The 
baseline core needle biopsy and initiation of study treatment should begin as soon as 
possible following study registration. 
 Baseline and Post-Immunotherapy Core Needle Research Biopsies 
Both of the required core needle biopsy procedures for tumor sample procurement will be 
performed at participating sites. Patients from MCC Affiliate Network sites will have these 
biopsy procedures performed at the VCU MCC downtown location. For instructions, refer 
to Section 3.3.1. 
• 
Prior to initiation of decitabine, tumor samples must be procured by core needle 
biopsy. When possible, this procedure should be performed concurrently with 
placement of a vascular access device (VAD) required for administration of standard 
chemotherapy. 
• 
A second core needle biopsy must be performed 3-7 days after the last dose of pre-
chemotherapy pembrolizumab (ie, after the second dose of pembrolizumab). The 
biopsy must be performed before initiation of standard neoadjuvant chemotherapy. 
Note: If a decision is made that the second pembrolizumab dose will not be 
administered, the biopsy should still be performed, within 7 days of the decision (prior 
to standard neoadjuvant chemotherapy). 
• 
Ultrasound guidance may be used for either the pre-or post-immunotherapy biopsies if 
the tumor is not easily palpable. 
• 
Four (4) 10-14 gauge cores should be obtained at each of the 2 biopsy time points. 
 Marking the Primary Tumor Site Prior to Initiation of Therapy 
Patients who are considered potential candidates for breast-conserving therapy (BCT) 
should have the primary tumor site marked in some way prior to initiating chemotherapy or, 
at least, prior to disappearance of the tumor clinically. This can be achieved with such 
methods as insertion of a radiopaque marker or clip, tattoos of the tumor boundary on the 
skin (especially for smaller breasts), or by making a transparent template with the tumor 
site marked on it. Other techniques are acceptable as long as they provide assurance that 
the primary tumor site can be located and excised. If a clip is used, a specimen radiograph 
should be performed to confirm its removal. 
 Summary of Study Treatment and Neoadjuvant Chemotherapy Regimens 
The study treatment regimen and neoadjuvant chemotherapy regimens are outlined on 
Table 1. 

 
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Table 1. Summary of Study Treatment Regimen and Neoadjuvant Chemotherapy Regimens 
Patients 
Drug 
Dose 
Route of 
Administration 
Dosing Interval 
Cycles/Doses 
Immunotherapy 
All Patients 
DecitabineA 
15 mg/m2  
IV infusion  
over 60 minutes 
Days 1 through 4B  
(total of 4 doses) 
PembrolizumabC 
200 mg  
IV infusion  
over 30 minutes 
Day 8 and Day 22 
(total of 2 doses) 
Neoadjuvant Chemotherapy Regimen Initiated Up to 27 Days  
After the Last Dose of Pre-Chemotherapy Pembrolizumab (After the Post-Pembrolizumab 
Biopsy)D 
Cohort A 
Doxorubicin 
60 mg/m2 
IV push  
over 15 minutes 
Every 2 or 3 weeks for 
a total of 4 cyclesE 
Cyclophosphamide 
600 mg/m2 
IV infusion  
over 30-60 minutes 
Followed By F 
Paclitaxel 
 
Or  
 
Nab-Paclitaxel 
80 mg/m2  
 
 
 
125 mg/m2 
IV infusion  
over 60 minutes 
 
 
IV infusion  
over 30 minutes 
Weekly for a total of 12 
doses 
CarboplatinG 
AUC 1.5 
 
Or 
  
AUC 5 
IV infusion  
over 30-60 minutes 
Weekly x 12 (AUC 1.5)  
 
Or 
  
q3w x 4 (AUC 5) 
Cohort A2 
Doxorubicin 
60 mg/m2 
IV push  
over 15 minutes 
Every 3 weeks for a 
total of 4 cyclesE 
Cyclophosphamide 
600 mg/m2 
IV infusion  
over 30-60 minutes 
Followed By F 
Paclitaxel 
 
Or  
 
Nab-Paclitaxel 
80 mg/m2  
 
 
 
125 mg/m2 
IV infusion  
over 60 minutes 
 
 
IV infusion  
over 30 minutes 
Weekly for a total of 12 
doses 
CarboplatinG 
AUC 1.5 
 
Or 
  
AUC 5 
IV infusion  
over 30-60 minutes 
Weekly x 12 (AUC 1.5)  
 
Or 
  
q3w x 4 (AUC 5) 
Throughout Neoadjuvant Chemotherapy 
PembrolizumabC 
200 mg 
IV infusion  
over 30 minutes 
Every 3 weeks 
throughout neoadjuvant 
chemotherapy 

 
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Table 1. Summary of Study Treatment Regimen and Neoadjuvant Chemotherapy Regimens 
Patients 
Drug 
Dose 
Route of 
Administration 
Dosing Interval 
Cycles/Doses 
Cohort B 
Doxorubicin 
60 mg/m2 
IV push  
over 15 minutes 
Every 2 or 3 weeks for 
a total of 4 cyclesE 
Cyclophosphamide 
600 mg/m2 
IV infusion  
over 30-60 minutes 
Followed By F 
Paclitaxel 
 
Or  
 
Nab-Paclitaxel  
80 mg/m2  
 
 
 
125 mg/m2 
IV infusion  
over 60 minutes 
 
 
IV infusion  
over 30 minutes  
Weekly for a total of 12 
doses 
Breast Surgery  
Patients Who 
Are Surgical 
Candidates 
Breast-conserving surgery or mastectomy (with or without reconstruction) and axillary 
staging following recovery from the last cycle of neoadjuvant chemotherapy 
Adjuvant pembrolizumab for Cohort A2 only  
PembrolizumabC 
200 mg 
IV infusion  
over 30 minutes 
Every 3 weeks for up to 
8 additional cycles post 
surgery 
A. Refer to Section 6.5 and 9.1 for dose preparation and additional instructions. 
B. If a dose is missed during Days 1-4, decitabine may be administered on Day 5. 
C. Refer to Section 6.6 and 9.2 for dose preparation and additional instructions. For Cohort A2, omit 
pembrolizumab with the first dose of neoadjuvant chemotherapy if less than 3 weeks have passed 
since the previous dose of pembrolizumab 
D. Begin standard neoadjuvant chemotherapy as soon as possible after the second core 
needle research biopsy (which should be performed 3-7 days after the last dose of pre-
chemotherapy pembrolizumab) and should start by day 49. Refer to Section 6.7 for additional 
instructions. 
E. Primary prophylaxis with G-CSF is required during dose-dense AC (see Section 6.7.4 for 
instructions). 
F. At the treating medical oncologist’s discretion following the safety lead-in, the paclitaxel regimen 
may be administered first followed by AC. 
G. Carboplatin may be administered at AUC 5 every 3 weeks at investigator discretion (Section 6.7.2). 
 Administration of Decitabine 
6.5.1 Decitabine Regimen for All Patients 
Beginning within 2 weeks following study registration and after the core needle 
biopsy to procure tumor samples and placement of a VAD, administer 
decitabine 15 mg/m2 IV once daily for a total of 4 doses.  
Note: When possible, doses should be given consecutively on days 1 through 4. 
However, if dosing on 4 consecutive days is not possible for any reason, the 

 
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schedule may be adjusted for dosing on 4 non-consecutive days, or a dose may be 
omitted. However, patients must receive at least 3 doses of decitabine to continue 
with study treatment, and decitabine dosing must be completed on or before day 5. 
6.5.2 Premedications for Decitabine 
Patients should be premedicated for nausea and vomiting, but should NOT receive 
dexamethasone or other steroids. Otherwise, the choice of antiemetic is at the 
investigator’s discretion. 
6.5.3 Administration of Decitabine 
Refer to Section 9.1.5 for instructions regarding reconstitution and preparation. 
• 
Administer reconstituted decitabine in 0.9% Sodium Chloride Injection,  
5% Dextrose Injection, or Lactated Ringer’s Injection. 
• 
Administer the total dose over a period of 60 minutes (+/- 10 minutes). 
6.5.4 Supportive Care 
Supportive care to manage AEs related to decitabine is at the investigator’s 
discretion with the exception that administration of steroids is NOT permitted unless 
required to manage a severe allergic reaction. In that case, the patient’s 
participation in the study would be discontinued following the 30-day period for 
evaluation of AEs. 
 Administration of Pembrolizumab 
6.6.1 Pembrolizumab Regimen for All Patients 
• 
Pembrolizumab 200 mg IV will be administered on day 8 and day 22  
(total of 2 doses). 
• 
The first dose of pembrolizumab should be administered 1 week following the 
first dose of decitabine. 
• 
Decitabine toxicities must be as follows: 
− 
Anemia, neutropenia, and thrombocytopenia ≤ grade 2 
− 
Other clinically significant toxicities (in the opinion of the investigator) ≤ 
grade 1 
• 
If the patient cannot receive pembrolizumab on day 8 due to decitabine-related 
toxicity or for any other reason, the first dose of pembrolizumab may be delayed 
up to 1 week. If pembrolizumab cannot be administered by day 15, 
pembrolizumab will not be administered, the second research biopsy will not be 
performed, and standard neoadjuvant chemotherapy should begin as soon as 
possible. 
• 
The second dose of pembrolizumab should be administered 2 weeks following 
the first dose. If the second dose of pembrolizumab cannot be given on day 22, 
the second dose may be delayed for up to 1 week. If the second dose cannot be 

 
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given by day 29, the second dose of pembrolizumab will be omitted and the 
patient should undergo breast biopsy as soon as possible followed by initiation 
of the standard neoadjuvant chemotherapy regimen. 
• 
If fewer than 3 doses of decitabine have been administered, pembrolizumab will 
not be given, and the second research biopsy will not be performed. 
6.6.2 Extended Pembrolizumab Administration in Cohort A2 
See Section 6.7.2 for administration of pembrolizumab during standard neoadjuvant 
chemotherapy. 
Patients in Cohort A2 who complete breast surgery may receive adjuvant 
pembrolizumab 200mg IV infusion over 30 minutes every 3 weeks for up to 8 cycles 
as outlined in Table 1 beginning 30 to 60 days post-surgery.  
Administration of the extended pembrolizumab regimen should be according to the 
current prescribing information and standard practices followed by the treating 
medical oncologist. This includes use of premedications and supportive care before, 
during, and after each pembrolizumab treatment. 
 
Note: Patients in Cohort A2 will receive a total of 18 pembrolizumab doses (2 doses 
in the window segment prior to new-adjuvant chemotherapy, 8 doses during neo-
adjuvant chemotherapy treatment, and up to 8 doses post-surgery) 
6.6.3 Premedications for Pembrolizumab 
• 
Patients may be premedicated for nausea and vomiting. Choice of antiemetic is 
at the investigator’s discretion with the exception that steroids are NOT 
permitted. 
• 
Refer to Table 2 for management of infusion reactions. 
6.6.4 Administration of Pembrolizumab 
Refer to Section 9.2.6 for preparation instructions. 
• 
Administer reconstituted pembrolizumab in intravenous infusion bag of either 
0.9% Sodium Chloride Injection or 5% Dextrose Injection. 
• 
Administer infusion solution over 30 minutes through an IV line containing a 
sterile, non-pyrogenic, low-protein binding 0.2 micron to 5 micron in-line or add-
on filter. (Do not co-administer other drugs through the same infusion line.) 
• 
Every effort should be made to plan for administration as close to 30 minutes as 
possible. However, a window of -5 minutes and +10 minutes is permitted. 
6.6.5 Pembrolizumab Infusion Reaction Treatment Guidelines 
Severe infusion reactions have been reported in 2 (0.1%) of 1562 patients receiving 
pembrolizumab in clinical trials. Management of a pembrolizumab infusion reaction 
is outlined on Table 2. 

 
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Table 2. Management of Pembrolizumab Infusion-related Reaction 
Grade 
(NCI CTCAE v5.0) 
Treatment 
Premedication at  
Subsequent Dosing 
Grade 1 
Mild transient reaction; 
infusion interruption not 
indicated; intervention not 
indicated 
Increase monitoring of vital signs as medically 
indicated until the patient is deemed medically 
stable in the opinion of the investigator. 
None 
Grade 2 
Therapy or infusion 
interruption indicated but 
responds promptly to 
symptomatic treatment  
(eg, antihistamines, 
NSAIDS, narcotics, IV 
fluids); prophylactic 
medications indicated for  
≤ 24 hours 
Stop infusion and monitor symptoms. 
Additional appropriate medical therapy may 
include but is not limited to: 
• 
IV fluids 
• 
Antihistamines 
• 
NSAIDS 
• 
Acetaminophen 
• 
Narcotics 
Increase monitoring of vital signs as medically 
indicated until the patient is deemed medically 
stable in the opinion of the investigator. 
If symptoms resolve within one hour of stopping 
drug infusion, the infusion may be restarted at 
50% of the original infusion rate (eg, from 100 
mL/hour to 50 mL/hour). Otherwise dosing will 
be held until symptoms resolve; the patient 
should be premedicated for the next scheduled 
dose. Pembrolizumab should be permanently 
discontinued for patients who develop grade 2 
toxicity despite adequate premedication. 
Patient may be 
premedicated 1.5 hour  
(± 30 minutes) prior to 
infusion of 
pembrolizumab with: 
• Diphenhydramine  
50 mg po  
(or equivalent dose 
of antihistamine). 
• Acetaminophen  
500-1000 mg po  
(or equivalent dose 
of antipyretic). 
Grade 3 
Prolonged (ie, not rapidly 
responsive to symptomatic 
medication and/or brief 
interruption of infusion); 
recurrence of symptoms 
following initial 
improvement; 
hospitalization indicated 
for other clinical sequelae  
(eg, renal impairment, 
pulmonary infiltrates) 
Grade 4 
Life-threatening 
consequences; urgent 
intervention indicated; 
pressor or ventilatory 
support indicated 
Stop infusion. 
Additional appropriate medical therapy may 
include but is not limited to: 
• 
IV fluids 
• 
Antihistamines 
• 
NSAIDS 
• 
Acetaminophen 
• 
Narcotics 
• 
Oxygen 
• 
Pressors 
• 
Corticosteroids 
• 
Epinephrine 
Increase monitoring of vital signs as medically 
indicated until the patient is deemed medically 
stable in the opinion of the investigator. 
Hospitalization may be indicated. 
Permanently discontinue pembrolizumab. 
No subsequent dosing 
Note: Appropriate resuscitation equipment should be available in the room and a physician readily 
available during the period of drug administration. 
6.6.6 Supportive Care 
• 
Patients should receive appropriate supportive care measures as deemed 
necessary by the treating investigator. Supportive care measures for the 

 
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management of AEs with potential immunologic etiology, ie, irAEs, are outlined 
in Appendix 3. 
• 
Supportive care for management of symptoms that are not thought to have 
potential immunologic etiology may be managed at the investigator’s discretion 
with the exception that corticosteroids should not be administered until after the 
last research biopsy is performed. Any toxicity that is at least possibly related to 
pembrolizumab and has been determined to be an irAE will have corticosteroids 
administered as part of the routine management of irAEs (see Appendix 3). 
• 
Use of G-CSF 
− G-CSF should be avoided prior to the second research biopsy, but may be 
administered per investigator discretion to manage neutropenia-related AEs 
should they occur following decitabine. 
− G-CSF subsequent to the second research biopsy is at the treating medical 
oncologist’s discretion, as are the G-CSF dose and schedule. 
− Use of G-CSF will be captured in the database. 
 Standard Neoadjuvant Chemotherapy 
During the safety lead-in phase of the study, all neoadjuvant chemotherapy will be 
administered at MCC. After completion of the safety lead-in phase, standard neoadjuvant 
chemotherapy may be administered at MCC Affiliate Network sites or participating sites. 
6.7.1 Timing 
• 
Standard neoadjuvant chemotherapy should begin 26-49 days after initiation of 
decitabine and as soon as possible following the second research biopsy. 
• 
The second core needle biopsy for procurement of tumor samples must be 
performed before initiation of chemotherapy. 
Cohort A2 Treatment Assignment: TNBC patients initially registered to Cohort A 
may be assigned to Cohort A2 in order to receive extended pembrolizumab 
concurrent with standard neoadjuvant chemotherapy.  
Note: decision to extend pembrolizumab and Cohort A assignment must be 
documented prior to initiation of any neoadjuvant chemotherapy on trial as 
described in Section 5.1.3. 
6.7.2 Chemotherapy Regimens 
As outlined on Table 1, the neoadjuvant chemotherapy regimen to be administered 
is cohort-specific. 
Note: Following the safety lead-in phase, the paclitaxel regimen may be 
administered prior to administration of the AC regimen at the treating medical 
oncologist’s discretion. 

 
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• 
Cohort A 
Doxorubicin 60 mg/m2 + cyclophosphamide 600 mg/m2 (AC) once every  
2 weeks or 3 weeks for 4 cycles 
Followed by 
Paclitaxel 80 mg/m2 IV or Nab-Paclitaxel 125 mg/m2 IV once weekly for 
12 weeks + carboplatin AUC 1.5 once weekly or AUC 5 every 3 weeks for 12 
weeks 
• 
Cohort A2 
Doxorubicin 60 mg/m2 + cyclophosphamide 600 mg/m2 (AC) once every  
2 weeks or 3 weeks for 4 cycles 
Followed by 
Paclitaxel 80 mg/m2 IV or Nab-Paclitaxel 125 mg/m2 IV once weekly for 
12 weeks + carboplatin AUC 1.5 once weekly or AUC 5 every 3 weeks for 12 
weeks 
Throughout Neoadjuvant Chemotherapy 
Pembrolizumab 200mg IV infusion over 30 minutes every 3 weeks throughout 
neoadjuvant chemotherapy 
Note: omit pembrolizumab with the first dose of neoadjuvant chemotherapy if 
less than 3 weeks have passed since the previous dose of pembrolizumab 
• 
Cohort B 
Doxorubicin 60 mg/m2 + cyclophosphamide 600 mg/m2 (AC) once every  
2 weeks or 3 weeks for 4 cycles 
Followed by 
Paclitaxel 80 mg/m2 IV or Nab-Paclitaxel 125 mg/m2 IV once weekly for 
12 weeks 
6.7.3 Preparation, Administration, and Supportive Care Instructions 
Preparation and administration of chemotherapy should be according to the current 
prescribing information for each agent and standard practices followed by the 
treating medical oncologist. This includes use of premedications and supportive 
care before, during, and after each chemotherapy treatment. 
6.7.4 Use of G-CSF During Standard Neoadjuvant Chemotherapy 
• 
Primary prophylaxis with pegfilgrastim or filgrastim is required during dose-
dense AC. Follow current prescribing information for the agent used. 
• 
If G-CSF support is required during weekly paclitaxel or Nab-paclitaxel therapy, 
filgrastim must be used. 

 
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• 
Do not administer G-CSF within 24 hours of chemotherapy administration. 
6.7.5 Alternative Chemotherapy Regimens 
For patients who experience toxicity related to the chemotherapy regimen described 
in Section 6.7.2 and are not able to complete the chemotherapy as specified or who 
have disease progression, the treating medical oncologist may choose to: 
• 
Discontinue chemotherapy before completion of all cycles and proceed to 
surgery, or 
• 
Discontinue protocol-specified chemotherapy and administer an alternative 
neoadjuvant chemotherapy regimen 
 Recommended Evaluation of Potential Immune-related Adverse Events 
When the patient experiences signs and symptoms of potential irAEs, the patient should 
be evaluated to determine if the AE is an irAE. Recommendations for evaluation of 
symptoms are provided on Table 3. 
Refer to Appendix 3 for clinical management of irAEs. 

 
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Table 3. Recommended Evaluation of Potential Immune-Related Adverse Events 
Sign/Symptom 
Recommended Evaluations/Referrals 
Potential irAE 
Constitutional (not attributable to cytotoxic chemotherapy) 
Malaise 
• Consider following lab tests: 
BMP 
TSH and Free T4 
Cortisol (7-9 am) 
ACTH 
Prolactin 
Also for females: 
LH and FSH 
Also for males: 
Testosterone 
• Consider endocrinology referral 
Endocrinopathy/ 
Hypophysitis 
Dizziness 
Headache 
Persistent headaches or 
headaches with vision changes 
Consider pituitary MRI (in addition to lab tests above) 
Hypophysitis 
New onset ≥ grade 3 
hyperglycemia in absence of  
pre-existing diabetes 
Consider endocrinology consult 
New onset  
Type 1 diabetes 
Gastrointestinal (not attributable to cytotoxic chemotherapy) 
Abdominal pain 
• Consider testing for Clostridium difficile (infectious 
diarrhea) 
• Consider evaluation for ileus or perforation 
• Consider colonoscopy or flexible sigmoidoscopy for 
lower GI symptoms. If lower endoscopy is performed, 
include random biopsies of colonic mucosa, even if 
tissue appears grossly normal during examination. 
Lymphocytic infiltrate in biopsy specimens are 
diagnostic of immune enterocolitis. 
• Consider upper endoscopy with random biopsies for 
refractory vomiting undergoing evaluation for immune 
enterocolitis 
• Consider GI consult 
Enterocolitis 
Hepatitis 
Blood or mucous in the stool 
Fever 
Vomiting (≥ grade 2) 
Diarrhea 
• ≥ grade 2 lasting more than 48 
hours (before AC); 
• ≥ grade 3 (after AC) 
Peritoneal signs 
≥ Grade 2 AST, ALT or bilirubin 
Cardiopulmonary (not attributable to cytotoxic chemotherapy) 
Cough 
Consider following: 
• Chest x-ray or chest CT (contrast is not required to 
evaluate parenchyma) or bronchoscopy 
• If during chemotherapy or fever is present, check 
CBC and treat empirically for infectious pneumonia 
as indicated while evaluating for pneumonitis. 
• Cardiac evaluation 
Pneumonitis 
Myocarditis 
Dyspnea 
Hypoxemia 
Chest pain 
Neurologic (not attributable to cytotoxic chemotherapy) 
Weakness, numbness, or tingling 
unrelated to paclitaxel; paresis 
Consider following depending on presentation:  
• Brain MRI 
• Neurology consultation 
• CSF evaluation 
 
Immune-mediated 
Neurologic Event (eg, 
Guillain-Barre syndrome; 
myasthenic syndrome; 
encephalitis) 

 
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 Breast Surgery 
As soon as possible following recovery from neoadjuvant chemotherapy and after the 
clinical tumor assessment, the patient should undergo a lumpectomy or mastectomy. BCT 
should be selected according to the patient’s preference and the surgeon’s evaluation. The 
surgery may be performed by the patient’s breast surgeon. 
• 
Patients who are not considered candidates for BCT or who do not desire BCT will 
undergo a total mastectomy; breast reconstruction is permitted. 
• 
Patients who are deemed to be good candidates for BCT will undergo segmental 
excision of the primary tumor bed. If the residual tumor is non-palpable, methods to 
ensure adequate excision of the primary tumor site should be used to guide the 
excision (Section 6.3). If the tumor location was marked with clips, a specimen 
radiograph should be obtained intraoperatively to document that the lesion has been 
removed including the clips. 
• 
The margins of the resected specimen of patients who had BCT should be 
histologically free of invasive tumor and DCIS. In patients for whom pathologic 
examination demonstrates tumor at the margin, additional operative procedures should 
be performed to obtain clear margins. 
If breast surgery is not performed, the reason for that decision will be documented. An 
EDV will be conducted within 10 days of the decision, and a safety follow-up visit will be 
conducted 30 days (±10 days) from the time of the decision not to undergo surgery. 
Documentation of irAEs will continue as described in Section 8.8. 
 Axillary Staging 
• 
Staging procedures performed prior to initiation of study treatment: 
− 
Sentinel node (SN) biopsy prior to initiation of study treatment is discouraged. 
− 
Even if FNA or core biopsy of an axillary node(s) was performed before initiation 
of neoadjuvant therapy, surgical evaluation of the axilla (either SN biopsy and/or 
axillary dissection as described below) must be performed following completion 
of all neoadjuvant therapy, regardless of whether the pre-treatment FNA or 
core biopsy was positive or negative. 
• 
Post-neoadjuvant therapy axillary staging is required. Use of a SN biopsy procedure 
following completion of neoadjuvant therapy is at the discretion of the patient’s 
surgeon. If SN biopsy is not performed, surgical evaluation of the axilla is required. 
− 
If the post-neoadjuvant therapy SN biopsy is positive, additional surgical 
evaluation of the axilla is required. 
− 
If the post-neoadjuvant therapy SN biopsy is negative, further surgical nodal 
staging procedure is not required. If, however, the only SN identified by isotope 
scan is in the internal mammary nodal chain, the axilla should be explored for 
blue or suspicious nodes. 

 
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 Prohibited Medications and Treatments 
6.11.1 Cancer Treatment 
Cancer treatment (eg, chemotherapy, biological therapy, immunotherapy, radiation 
therapy) other than the treatment specified in the protocol for this study is not 
permitted during neoadjuvant therapy. Adjuvant therapy is at the discretion of the 
primary oncologist. 
6.11.2 Other Medications 
• 
Live vaccines (examples of live vaccines include, but are not limited to, the 
following: measles, mumps, rubella, varicella/zoster, yellow fever, rabies, BCG, 
and typhoid vaccine) are prohibited. 
• 
Systemic glucocorticoids for any purpose other than to modulate symptoms from 
an event of suspected immunologic etiology are prohibited. Exception: Steroids 
equivalent to or less than an oral prednisone dose of 10 mg daily are permitted 
and steroids are allowed without limitation (eg, to manage standard neoadjuvant 
chemotherapy-induced side effects) AFTER the last research biopsy has been 
completed. 
• 
Any investigational agent not specified in the protocol for this study is not 
permitted. 
 Duration of Therapy 
Study treatment will be administered as outlined on Table 1 unless one of the following 
occurs (also see study withdrawal criteria in Section 5.2): 
• 
AE that requires discontinuation of study treatment (see Section 7) 
• 
Pregnancy 
• 
Determination by the investigator that discontinuation is in the patient’s best medical 
interest 
• 
Patient decision to discontinue study treatment 
• 
Withdrawal of study sponsor support 
The reason for discontinuation of study treatment must be documented in the source 
documents and in the OnCore database.  
 Post-Treatment Visits 
Patients who do not initiate pembrolizumab are off-study after the 30-day safety follow-up 
period as outlined in Section 8.8. Patients who do initiate pembrolizumab are off-study 
after the last PFS assessment as outlined in Section 6.13.4. 
6.13.1 Early Discontinuation Visit 
Patients who discontinue (ie, do not complete) study treatment at any point after 
initiating standard neoadjuvant chemotherapy will undergo an Early Discontinuation 
Visit (EDV) within 10 days of the decision to discontinue study treatment. The 

 
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reason for discontinuation of study treatment will be documented in the source 
documents and in the OnCore database.  
6.13.2 Safety Follow-up 
Safety follow-up visits will be conducted 30 days (±10 days) following surgery or 
the decision not to undergo surgery (all cohorts) and completion of adjuvant 
pembrolizumab (Cohort A2). If a patient discontinues study treatment, then every 
attempt should be made to perform a safety follow-up visit 30 days (±10 days) after 
the EDV. 
6.13.3 Evaluation of AEs 
The plan for evaluating and reporting AEs during treatment and follow-up is outlined 
in Section 8.8. 
6.13.4 Immune-related AEs 
The follow-up assessments noted below are required for patients who have received 
one or more pembrolizumab doses. 
• 
At the safety follow-up visit conducted 30 days (±10 days) following surgery or 
the decision not to undergo surgery, patients will be evaluated for occurrence of 
irAEs. An ongoing requirement for steroid management of any irAE will be 
noted.  
• 
For Cohorts A and B, a follow-up visit will be conducted 6 months (± 30 days) 
following surgery or the decision not to undergo surgery. The following will be 
assessed:  
− 
the status of irAEs noted at the 30-day safety follow-up visit as having a 
steroid management requirement. An ongoing requirement for steroid 
management of previously known irAEs will be noted.  
− 
the occurrence, in the interim since the 30-day safety follow-up visit , of any 
new (late-occurring) irAE(s) requiring steroid management. An ongoing 
requirement for steroid management of new (late-occurring) irAEs will be 
noted. 
• 
For Cohort A2, irAEs will be assessed at 12 months (± 30 days) after the end of 
neoadjuvant treatment or surgery. 
6.13.5 Postoperative Evaluation of Treatment Response 
• 
All patients who have breast surgery will have a 30-day (±10 day) follow-up 
evaluation of surgical outcome (see Section 10.2) following surgery. 
• 
Patients in Cohort A2 who receive adjuvant therapy will have a 30-day (±10 
days) safety follow-up visit after completion of adjuvant therapy. 
• 
Patients who discontinue or complete treatment with ongoing SD, PR, pCR, or 
cCR (see Section 10) remain in follow-up status for PFS by reported clinical 
status for up to 12 months (± 30 days) after surgery (or discontinuation of 

 
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treatment if surgery is not performed) until one of the following occurs: disease 
progression, relapse, or death. 
7 DOSING DELAYS/DOSING MODIFICATIONS 
 Recording Dose Delays and Omissions 
All dosing delays and omissions will be recorded in the source documents and captured in 
the OnCore database. 
 Toxicity Grading 
AEs will be characterized and graded according to NCI CTCAE v5.0. 
 Decitabine Treatment Modification 
• 
Because the decitabine treatment plan is to only administer a total of 4 doses on 4 out 
of 5 consecutive days, there are no planned dose reductions for decitabine. 
• 
If 2 or more decitabine doses must be omitted, study treatment will be discontinued. 
• 
The only AE requiring discontinuation of decitabine is ≥ grade 3 allergic reaction. 
 Pembrolizumab Treatment Modification 
7.4.1 First Pembrolizumab Dose 
See Section 6.6.1 for instructions regarding the timing of pembrolizumab if 
completion of decitabine was delayed. 
7.4.2 Second Pembrolizumab Dose 
There are no planned reductions in the pembrolizumab dose. AEs requiring 
omission of the second pembrolizumab dose are the following: 
• 
≥ grade 3 infusion reaction (see Table 2) 
• 
grade 3 maculopapular rash 
• 
≥ grade 2 bullous dermatitis 
• 
≥ grade 3 Stevens-Johnson Syndrome 
• 
≥ grade 4 toxic epidermal necrolysis 
• 
≥ grade 2 myocarditis 
• 
≥ grade 2 pneumonitis 
• 
≥ grade 2 diarrhea persisting for at least 2 days despite medical intervention 
• 
≥ grade 3 diarrhea 
• 
≥ grade 2 enterocolitis 
• 
≥ grade 2 pancreatitis 

 
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• 
≥ grade 2 creatinine increase 
• 
≥ grade 2 increase in AST and/or ALT 
• 
≥ grade 2 increase in total bilirubin 
• 
≥ grade 3 hyperthyroidism 
• 
≥ grade 2 hypophysitis  
• 
new onset of type 1 diabetes mellitus 
• 
≥ grade 2 Guillain-Barre syndrome 
• 
≥ grade 3 hyperglycemia 
• 
≥ grade 2 vasculitis  
• 
sclerosing cholangitis 
• 
other severe or ≥ grade 3 irAEs 
• 
persistent grade 2 irAEs that do not recover to ≤ grade 1 by 3 weeks following 
administration of the first dose of pembrolizumab 
7.4.3 Extended Pembrolizumab Doses (Cohort A2) 
Dose modifications for extended pembrolizumab doses (Cohort A2) will be at the 
investigator’s discretion based on current prescribing information. 
 Neoadjuvant Chemotherapy Dose Modifications 
Dose modifications during neoadjuvant chemotherapy will be at the treating medical 
oncologist’s discretion based on current prescribing information for each agent and 
standard practices followed by the treating medical oncologist. 
If toxicity occurs during AC that requires discontinuation of AC prior to completion of 4 
cycles, weekly paclitaxel with carboplatin (Cohorts A and A2) or weekly paclitaxel  
(Cohort B) may be initiated when the patient has recovered from the AC-related toxicity.  
If the paclitaxel regimen is given first and toxicity occurs requiring discontinuation prior to 
completion of the regimen, AC may be initiated when the patient has recovered from the 
paclitaxel-related and/or carboplatin-related toxicity. Refer to Section 6.7.5 for additional 
information. 
Note: AEs occurring during standard neoadjuvant chemotherapy may be related to 
immunotherapy (ie, irAEs). Refer to Section 6.8 for recommended evaluation of potential 
irAEs, Section 8.6 for a list of clinically significant irAEs, and Appendix 3 for recommended 
supportive care for irAEs. 

 
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8 ADVERSE EVENTS: DEFINITIONS AND REPORTING 
REQUIREMENTS 
 Definitions 
8.1.1 Adverse Event (AE) 
AE means any untoward medical occurrence associated with the use of a drug in 
humans, whether or not considered drug related. 
8.1.2 Suspected Adverse Reaction (SAR) 
Any AE for which there is a reasonable possibility that the drug caused the AE. 
“Reasonable possibility” means that there is evidence to suggest a causal 
relationship between the drug and the AE. 
An AE with an attribution of possible, probable, or definite (see Section 8.1.8) is a 
SAR. 
8.1.3 Serious AE (SAE) or Serious SAR (SSAR) 
An AE or SAR is considered “serious” if, in the view of either the investigator or 
sponsor, it results in any of the following outcomes: 
• 
death, 
• 
a life-threatening AE, 
An AE or SAR is considered to be “life-threatening” if, in the view of either the 
investigator or sponsor, its occurrence places the patient at immediate risk of 
death. It does not include an AE or SAR that, had it occurred in a more severe 
form, might have caused death. 
• 
inpatient hospitalization or prolongation of existing hospitalization, 
Planned inpatient hospitalizations, eg, for planned surgery, or those that occur 
for logistical reasons, eg, to complete a therapy that cannot be completed due to 
outpatient clinic business hours, are exempt from SAE reporting. Events that 
prolong such hospitalizations and otherwise meet reporting criteria are, 
however, still subject to SAE reporting requirements. 
• 
a persistent or significant incapacity or substantial disruption of the ability to 
conduct normal life functions, or 
• 
a congenital anomaly/birth defect. 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered serious when, based upon appropriate medical 
judgement, they may jeopardize the patient and may require medical or surgical 
intervention to prevent one of the outcomes listed in this definition. 
8.1.4 Unexpected SAR 
A SAR is considered “unexpected” if: 

 
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• 
it is not listed in the investigator brochure or is not listed at the specificity or 
severity that has been observed; 
• 
or, if an investigator brochure is not required, is not consistent with the risk 
information described in the prescribing information. 
“Unexpected” as used in this definition, also refers to SARs that are mentioned in 
the investigator brochure as occurring with a class of drugs or as anticipated from 
the pharmacological properties of the drug, but are not specifically mentioned as 
occurring with the drug under investigation. 
8.1.5 Unanticipated Problem 
UPs include any incident, experience, or outcome that meets all of the following 
criteria: 
• 
unexpected (in terms of nature, severity, frequency) given (a) the research 
procedures that are described in the protocol-related documents, such as the 
research protocol and informed consent document approved by the institutional 
review board (IRB); and (b) the characteristics of the patient population being 
studied; 
• 
related or possibly related to participation in the research (possibly related 
means there is a reasonable possibility that the incident, experience, or outcome 
may have been caused by the procedures involved in the research); and 
• 
suggests that the research places patients or others at a greater risk of harm 
(including physical, psychological, economic, or social harm) than was 
previously known or recognized. 
8.1.6 AE Description and Grade 
The descriptions and grading scales found in CTCAE v5.0 will be utilized for AE 
reporting. 
8.1.7 AE Expectedness 
AEs can be ‘Unexpected’ or ‘Expected’. 
• 
Expected AEs are those AEs, the specificity and severity of which, that are 
consistent with the listings for decitabine found in Section 9.1 and the FDA-
approved prescribing information for Dacogen, and for pembrolizumab found in 
protocol Section 9.2 or in the most current version of the Keytruda Investigator’s 
Brochure. Refer to the prescribing information for each of the drugs included in 
the standard neoadjuvant chemotherapy regimen. 
• 
Unexpected AEs are those AEs occurring in one or more patients participating in 
the study, the nature, severity, or frequency of which is not consistent with 
either: 
− 
The known or foreseeable risk of AEs associated with the procedures 
involved in the research that are described in (a) the protocol-related 
document, such as the IRB-approved research protocol, any applicable 
investigator brochure, and the current IRB-approved informed consent 

 
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document, and (b) other relevant sources of information, such as product 
labeling and package inserts; or 
− 
The expected natural progression of any underlying disease, disorder, or 
condition of the patient(s) experiencing the AE and the patient’s 
predisposing risk factor profile for the AE. 
8.1.8 AE Attribution 
• 
Definite – The AE is clearly related to the study treatment. 
• 
Probable – The AE is likely related to the study treatment. 
• 
Possible – The AE may be related to the study treatment. 
• 
Unlikely – The AE is doubtfully related to the study treatment. 
• 
Unrelated – The AE is clearly NOT related to the study treatment. 
 Known AEs 
The known AEs for decitabine can be found in protocol Section 9.1 and in the decitabine 
(Dacogen) prescribing information. The expected AEs for pembrolizumab can be found in 
protocol Section 9.2 and in the pembrolizumab (Keytruda) Investigator’s Brochure. Refer to 
the prescribing information for the known AEs for each of the drugs included in the 
neoadjuvant chemotherapy regimen. 
 Pregnancy and Lactation 
If a patient inadvertently becomes pregnant while on treatment with either decitabine or 
pembrolizumab, study treatment will immediately be discontinued. The patient will be 
contacted at least monthly to determine the patient’s status until the pregnancy has been 
completed or terminated. The outcome of the pregnancy will be reported to the Sponsor-
Investigator within 24 hours if the outcome is a serious adverse experience (eg, death, 
abortion, congenital anomaly, or other disabling or life-threatening complication to the 
mother or newborn). 
The study investigator will make every effort to obtain permission to follow the outcome of 
the pregnancy and report the condition of the fetus or newborn to the Coordinating Center. 
If a male patient impregnates his female partner, the Sponsor-Investigator must be 
informed immediately; the same reporting requirements will apply. 
Pregnancy or lactation occurring through the 30-day follow-up period will be reported as a 
UP. Also, refer to Section 8.9 for instructions regarding reporting pregnancy and lactation. 
 Secondary Malignancy 
A secondary malignancy is a new cancer caused by previous treatment for a malignancy, 
eg, chemotherapy or radiation therapy. Metastatic disease is not a secondary malignancy. 
Any secondary malignancy should be reported via expedited reporting mechanisms. (Refer 
to Section 8.9 regarding reporting of secondary malignancy.) 

 
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 Event of Clinical Interest 
Events of clinical interest (ECIs) for this trial include: 
• 
An overdose of pembrolizumab, defined as any pembrolizumab dose of  
1,000 mg or greater (≥ 5 times the study-specified dose), that is not associated with 
clinical symptoms or abnormal laboratory results will be reported as  
non-serious ECI using the terminology “accidental or intentional overdose without 
adverse effect” 
An AE that is associated with (“results from”) the overdose of pembrolizumab, the AE is 
reported as a SAE, even if no other seriousness criteria are met. Such an event will 
also be noted as an ECI in the study database. 
• 
From initiation of study treatment through the 30 day follow-up period, occurrence of all 
of the following at the same time will be reported as an ECI: 
− 
An elevated AST or ALT lab value that is ≥ 3 x ULN; and  
− 
an elevated total bilirubin lab value that is ≥ 2 x ULN and, at the same time,  
− 
an alkaline phosphatase lab value that is < 2 x ULN, as determined by way of 
protocol-specified laboratory testing or unscheduled laboratory testing. 
Note: These criteria are based upon available regulatory guidance documents. The 
purpose of the criteria is to specify a threshold of abnormal hepatic tests that may 
require an additional evaluation for an underlying etiology. 
 Immune-related Adverse Events  
For this trial, an irAE is an immune-mediated AE that is possibly, probably, or definitely 
related to pembrolizumab. 
Clinically significant irAEs will be reported in an expedited manner (See Section 8.10 and 
Table 4 and Table 5). Refer to Section 8.7 for a list of clinically significant irAEs. 
Serious irAEs will be reported as SAEs regardless of whether clinically significant or not. 
Recommendations for evaluation of AEs to determine if the AE is an irAE are provided in 
Section 6.8, requirements for expedited reporting of irAEs are specified in Section 8.10, 
and supportive care recommendations for irAEs are outlined in Appendix 3. 
 Clinically Significant Immune-related Adverse Events 
Clinically significant irAEs identified for consideration are listed below. When a severity 
grade is specified, the grading is based on CTCAE v5.0 terminology and criteria. When a 
severity grade is not specified, the development of that toxicity at any grade warrants 
review to determine whether it qualifies as a clinically significant irAE. 
• 
Pneumonitis (≥ grade 2) 
• 
Myocarditis (≥ grade 2) 
• 
Diarrhea (≥ grade 3 persisting for a minimum of 2 days despite usual medical 
intervention, responded to steroids, and has no other apparent cause) 

 
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• 
Enterocolitis (≥ grade 2) 
• 
Pancreatitis (≥ grade 2) 
• 
Severe skin reactions 
− Bullous dermatitis (≥ grade 2) 
− Stevens-Johnson Syndrome (≥ grade 3) 
− Toxic epidermal necrolysis (≥ grade 4) 
• 
Creatinine increased (≥ grade 2) 
• 
Hepatic toxicity 
− 
Elevation in AST or ALT (≥ grade 3) 
− 
Total bilirubin ≥ 2 x ULN 
• 
Hypophysitis (≥ grade 2)  
• 
Adrenal insufficiency (≥ grade 2)  
• 
Hyperthyroidism (≥ grade 3) 
• 
Hyperglycemia (≥ grade 3) 
• 
Guillain-Barre syndrome (≥ grade 2) 
• 
Myasthenia gravis (≥ grade 2) 
• 
Other severe or ≥ grade 3 treatment-related AEs determined to be irAEs 
 Time Period and Grade of AE Capture 
All AEs, regardless of grade or attribution, will be captured from the time of study 
registration until initiation of standard neoadjuvant chemotherapy. This includes any AEs 
occurring during biopsy (eg, hemorrhage). 
For patients who do not initiate pembrolizumab, all AEs will be captured until 30 days 
following the last dose of decitabine or until another cancer treatment is initiated, 
whichever occurs first. 
For patients who initiate pembrolizumab, irAEs (clinically significant and non-clinically 
significant) will be captured as described in Section 6.13.4. 
Clinically significant irAEs will be reported in an expedited manner through the end 30-day 
follow-up period (Section 8.6). 
SAEs will be captured from the start of study treatment until 30 days (± 10 days) following 
surgery or until a decision is made to forego surgery. All ECIs and other reportable events 
(eg, pregnancy, pregnancy outcomes, lactation, second or secondary malignancies) will be 
captured from the start of study treatment through end of the 30-day follow-up period. 
All UPs will be captured from the start of study treatment through the end of the 30-day 
follow-up period. 

 
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 Procedures for Recording Events 
• 
AEs, irAEs, SAEs, UPs, ECIs, and other reportable events will be recorded in MCC’s 
OnCore Clinical Trials Management System.  
• 
In most cases, it is acceptable to record in OnCore only the highest grade of a toxicity 
occurring during a particular study segment when an event has serial fluctuations in 
grade over time. 
• 
SAEs will be entered into the OnCore SAE domain. UPs will be entered into the 
OnCore Deviations domain. An SAE that is both an SAE and a UP will be entered in 
both domains. 
• 
AEs requiring expedited reporting must also be recorded by routine AE capture (ie, in 
AE eCRFs). 
 Expedited Reporting Procedures 
Participating sites will refer to Table 4 for expedited reporting requirements and 
instructions. The Sponsor-Investigator/Coordinating Center will refer to Table 5 for 
expedited reporting requirements and instructions. Also, see Section 8.6 for irAEs requiring 
expedited reporting. 

 
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Table 4. Expedited Reporting Requirements for Participating Sites 
SAEsA 
UPsA 
irAEs  
(clinically significant)A, B 
ECIs and other reportable 
eventsA, C, D, E 
Sponsor-Investigator 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
 
 
  
 
 
 
  
 
 
Merck and Company, IncF 
IRBG 
 
 
IRB (if applicable)G 
 
 
 
A. Report event within 1 business day of becoming aware of the occurrence, with the exception of pregnancy and lactation, which 
must be reported within 24 hours. A PDF of a de-identified OnCore SAE or Deviation record may be used for expedited event 
reporting purposes. 
B. Refer to Section 6.8 for recommended evaluation of potential irAEs, and Section 8.6 for a list of clinically significant irAEs. 
C. Refer to Sections 8.3, 8.4, and 8.11 for requirements and instructions for expedited reporting of pregnancy, lactation, and new 
primary malignancy. 
D. Serious irAEs should be reported as SAEs regardless of whether clinically significant or not clinically significant. 
E. Refer to Section 8.5 for a list of ECIs. 
F. Refer to Section 8.11.1 for instructions for expedited reporting of SAEs to Merck Global Safety 
G. Report SAEs and UPs to the IRB of record according to local institutional guidelines. 

 
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Table 5. Expedited Reporting Requirements for Sponsor-Investigator/Coordinating Center  
SSARs 
UPs 
ECIs and other Merck-reportable eventsA 
FDAB 
DSMCC 
Email:
 
Merck and Company, IncD 
Merck and Company, IncB, D 
IRBE 
 
A. Refer to Section 8.5 for a list of ECIs. Refer to Sections 8.3, 8.4, and 8.11 for requirements and instructions for expedited reporting of 
pregnancy, pregnancy outcome, lactation, and new primary malignancy. 
B. Using a MedWatch Form 3500A, the Sponsor-Investigator will report to the FDA and Merck (within the timeframes shown below): 
• 
Any AE that meets all of the following criteria: 
i. possibly, probably, or definitely related to study drug (ie, the event is a SAR); and 
ii. serious (ie, a SSAR); and  
iii. unexpected.  
Events meeting these criteria will be reported to the FDA within 15 days of determining that the event is reportable. 
• 
A clinically important increase in the rate of SSARs within 15 days of determining that the event is reportable. 
• 
Any unexpected fatal or life-threatening SSARs within 7 days of receipt of the information regarding the event. Refer to Section 
8.11 for requirements and instructions for expedited reporting to Merck Global Safety. 
C. Report to DSMC within 1 business day of becoming aware of UP. A PDF of a de-identified Oncore Deviation record may be used for 
expedited event reporting purposes. 
D. Refer to Section 8.11 for requirements and instructions for expedited reporting to Merck Global Safety. 
E. Report each UP to the VCU IRB within 5 business days of becoming aware of the occurrence. 

 
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 Requirements for Expedited Reporting to Merck and Company, Inc 
8.11.1 Reports from Participating Sites and/or the Coordinating Center to Merck Global 
Safety 
All expedited reports to Merck Global Safety (as outlined in Table 4 and/or Table 5) 
are to be faxed with related supporting information to the fax number listed below. 
 Attn:
 
8.11.2 Reports from the Coordinating Center to Merck Global Safety 
All expedited reports to Merck Global Safety (as outlined in Table 5) must be 
reported by the Coordinating Center to Merck Global Safety within 2 business days. 
• 
AEs that are both an SAE and an ECI should be reported one time as an SAE 
only; however, the event must be appropriately identified as an ECI in the 
database. 
• 
Although pregnancy and lactation are not considered AEs, it is the responsibility 
of investigators or their designees to report any pregnancy or lactation in a 
patient (spontaneously reported to them) that occurs during the trial. 
Pregnancies and lactations that occur from the time of treatment through 120 
days following the last administered dose of pembrolizumab, or 30 days 
following the last administered dose of pembrolizumab if the patient initiates new 
anticancer therapy, whichever is earlier, must be reported by the Sponsor-
Investigator. All reported pregnancies must be followed to the 
completion/termination of the pregnancy. 
Pregnancy outcomes of spontaneous abortion, missed abortion, benign 
hydatidiform mole, blighted ovum, fetal death, intrauterine death, miscarriage, 
and stillbirth must be reported as serious events (Important Medical Events). If 
the pregnancy continues to term, the outcome (ie, health of infant) must also be 
reported. 
 
 
 
 
 
 
  
 
 
 

 
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10 MEASUREMENT OF EFFECT 
 Assessment of LPBC 
Tumor samples will be obtained by core needle biopsy at baseline (prior to initiation of any 
treatment) and after completion of pembrolizumab (prior to initiation of neoadjuvant 
chemotherapy). Lymphocyte infiltration in the tumor and stroma will be assessed as 
described in Section 11.3. 
 Pathologic Assessment of Effect 
10.2.1 Timing of Evaluation 
The determination of pCR will be performed by the local pathologist following 
examination of tissue (breast and nodes) removed at the time of surgery. See 
Appendix 4 for suggested procedures to evaluate the surgical specimens for 
determination of pCR. 
10.2.2 Criteria for Evaluation of Pathologic Response 
pCR in breast and axillary lymph nodes as well as non-axillary SN (pCR breast and 
nodes) will be determined based on the following definition: 
No histologic evidence of invasive tumor cells in the surgical breast specimen, 
axillary nodes, or SNs identified after neoadjuvant therapy 
10.2.3 Residual Cancer Burden 
The RCB Index will be calculated locally and entered into the OnCore database for 
all patients who have residual disease. This can be done by the site pathologist or 
by entering data at 
http://www3.mdanderson.org/app/medcalc/index.cfm?pagename=jsconvert3  
Data collected is based on instructions provided by Symmans et al (86): 
• 
Size of the tumor bed 
• 
Cellularity of residual primary tumor 
• 
Percentage of DCIS component 
• 
Number of positive nodes 
• 
Size of macrometastasis 

 
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 Clinical Exam Assessment of Effect 
To document the presence or absence of cCR, protocol-required tumor assessment by 
physical exam must be performed following the last cycle of neoadjuvant chemotherapy 
(prior to surgery). 
Note: It is recommended that patients also have a breast examination for tumor 
assessment before each cycle of preoperative therapy to ensure that there is no disease 
progression. 
10.3.1 Determination of cCR (Breast and Nodes) 
The following criteria will be employed to determine if there has been a cCR (breast 
and nodes) following the last cycle of neoadjuvant chemotherapy (before surgery): 
• 
Resolution of all palpable disease identified at baseline, and 
• 
No new lesions or other signs of disease progression. 
Resolution of all imaging abnormalities is not required for this endpoint. 
10.3.2 Progressive Disease 
Criteria to be used for determination of progressive disease are at the investigator's 
discretion. In the event of progressive disease, see Section 6.7.5 for further 
treatment instructions. 
11 CORRELATIVE STUDIES 
 Participation in Correlative Studies 
Section 1.11 outlines the plans and rationale for the correlative studies. Core needle 
biopsies to procure tumor samples and submission of residual tumor or, in the case of 
pCR, submission of tissue from the tumor bed, and collection of blood samples are study 
requirements. 
 Collection, Processing, and Distribution of Samples 
• 
Refer to the MCC-15-11083 Biospecimen Manual 
• 
The study team at the participating site will coordinate collection and  
de-identification of all correlative samples. 
• 
MCC Clinical and Translational Research Lab (CTRL) will receive, process, store, 
and/or distribute the correlative blood and tumor samples as described in Sections 
11.3, 11.4, and 11.5. 
• 
The pathology department where the patient has surgery will perform the 
postoperative pathologic evaluation. 
• 
Questions regarding study requirements should be directed to the Coordinating 
Center.  

 
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 Tumor Samples from Core Needle Biopsy 
11.3.1 Collection Time Points 
Core needle biopsies to procure research tumor samples from the primary tumor in 
the breast will be performed at 2 time points: 
• 
After study registration (before initiation of study treatment); preferably at the 
time of VAD placement 
• 
Within 3-7 days after administration of the last dose of pembrolizumab (before 
initiation of neoadjuvant chemotherapy) 
Note: If, for any reason, no pembrolizumab is given (eg, if fewer than 3 doses of 
decitabine are administered or decitabine-related toxicity prevents 
pembrolizumab administration), the second research biopsy will not be 
performed. 
11.3.2 Sample Requirements 
Refer to the MCC-15-11083 Biospecimen Manual 
At the time of each core needle biopsy procedure using a 10-14 gauge needle, 4 
cores of tumor will be obtained and placed in formalin. Samples procured at the time 
of the 2 core needle biopsy procedures will be used for all of the following: 
• 
Evaluation of TILs 
A tumor sample (1 slide with 4 micron thick specimen) will be used for 
evaluating TILs, which is the primary objective of the MCC-15-11083 study. 
Assessment and evaluation of TILs will be performed by VCU Anatomic 
Pathology and will be based on the procedures described by Salgado et al (83). 
• 
Multiplex immunofluorescence assays 
Tumor samples (2 unstained slides, each with 4 micron thick specimen) will be 
analyzed using the Vectra microscope with validated antibodies according to 
standard operating procedures for the Opal staining system and Vectra 
microscope. 
• 
Evaluation of PD-L1  
Tumor tissue from the 2 research core biopsies and, if available, from the 
surgical resection specimen (see Section 11.4), should be submitted on 5 
unstained slides, per the QualTek Sample Handling Manual. 
Tumor samples will be shipped from the Coordinating Center to QualTek 
Molecular Laboratories for proprietary PD-L1 staining. (Refer to the QualTek 
MISP Sample Handling Manual for instructions regarding slide preparation and 
shipping.) 

 
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• 
Nanostring gene analysis 
FFPE tumor samples, about 5 slides on average, will be sent to Merck for 
provision to Almac for genomic analysis by next-generation sequencing panel (≥ 
680 genes) to determine if there are gene expression patterns associated with 
response to decitabine and pembrolizumab and/or that predict response to 
neoadjuvant chemotherapy. 
 Tumor Samples from Surgical Specimens 
Refer to the MCC-15-11083 Biospecimen Manual 
11.4.1 Sample Requirements 
An FFPE block of tumor or, if there was no remaining tumor (ie, pCR) an FFPE 
block from the tumor bed will be requested following surgical resection. 
11.4.2 Testing and Analysis 
Unstained slides will be cut from the block and provided to the following 
laboratories: 
• 
Evaluation of PD-L1  
• 
QualTek Molecular Laboratories – 5 unstained slides, each with 5 micron thick 
specimen (Refer to the QualTek MISP Sample Handling Manual for instructions 
regarding the preparation and shipping of tumor samples.) 
• 
Multiplex immunofluorescence assays – 2 unstained slides 
• 
Samples (2 unstained slides for each patient) will be analyzed using the Vectra 
microscope with validated antibodies according to standard operating 
procedures. 
 Correlative Blood Samples 
11.5.1 Blood Sample Collection Time Points 
Blood samples will be collected at the following time points: 
• 
Prior to initiation of study treatment (after study registration) 
• 
After the last dose of decitabine (before the first pembrolizumab dose) 
• 
After the second dose of pembrolizumab (before initiation of standard 
neoadjuvant chemotherapy) 
11.5.2 Blood Sample Collection, Labeling, and Analysis 
Refer to MCC-15-11083 Biospecimen Manual 
 Tracking Tumor and Blood Samples 
Collection and distribution of all samples will be logged by the study team at the 
participating site in OnCore. 

 
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12 STUDY CALENDAR 
The schedule of tests, exams, assessments, collection of samples for correlative studies, and 
administration of study drugs are listed on 2 tables: requirements during screening and after 
registration (before treatment begins) on Table 9; requirements during neoadjuvant decitabine 
and pembrolizumab on Table 10; and cohort-specific requirements during standard neoadjuvant 
chemotherapy through end of study on Table 11 and Table 12. 
 

 
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Table 9. Study Requirements During Screening and Prior to Initiating Study Treatment (All Cohorts) 
Assessments and 
Other Requirements 
Screening 
(Prior to Study Registration) 
After Study 
Registration 
Within  
24 Weeks 
Within  
12 Weeks 
Within  
4 Weeks 
Within  
72 Hours  
(Prior to Initiation of 
Treatment)  
Before 
Treatment 
Begins 
Informed Consent 
XError! 
Reference 
source not 
found. 
 
Demographics 
X 
 
Height 
X 
 
Weight 
X 
 
Vital Signs 
X 
 
Performance StatusError! Reference source 
not found. 
X 
 
Medical/Surgical HistoryC  
X 
 
Baseline Conditions 
X 
 
Concurrent MedicationsD  
X 
 
Physical Examination 
X 
 
Tumor Assessment and 
MeasurementE 
 
 
X 
 
 
CBC, Differential, Platelet Ct  
X 
 
Serum ChemistryF 
X 
 
TSH, Cortisol 
X 
 
 
Serum Pregnancy TestG 
 
X 
Ipsilateral Breast ImagingH 
 
X 
 
 
Contralateral Breast Imaging 
X 
 
 
 
ECG 
 
X 
 
 
2-D echocardiogram  
(or MUGA) 
 
X 
 
 
Correlative Blood Sample 
 
 
 
 
XI 
Core Needle Biopsy for Correlative 
Tumor Samples 
 
 
 
 
XJ 
Table 9 Footnotes: 
A. If a patient has been consented but not registered within 4 weeks, reconsenting is not required unless 
a new IRB-approved version of the consent form is available. 
B. Refer to Appendix 1 for ECOG criteria. 
C. Assessment of Medical History will include, if known, tumor genomic profile (ie, MammaPrint, 
Oncotype, other). 
D. Include over-the-counter medications. 
E. Physical exam will be used to assess and measure the primary breast tumor and regional lymph 
nodes to determine clinical response after all neoadjuvant therapy as described in Section 10.3. 
Refer to Section Error! Reference source not found. regarding eligibility. 
F. Chemistry includes the following: basic metabolic panel (sodium, potassium, carbonate, chloride, 
glucose, calcium, BUN, creatinine) and hepatic panel (ALT, AST, ALP, total bilirubin, direct bilirubin, 
albumin, total protein). 
G. Only required for WCBP (see Section Error! Reference source not found. for definitions and related 
requirements). 

 
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H. Mammogram required at baseline but may not be used for tumor measurements. MRI (or ultrasound) 
also required at baseline and may be used for tumor measurements for eligibility purposes 
I. Baseline blood sample can be collected on treatment day 1 but must be prior to administration of 
decitabine (see Section 11.5). 
J. For convenience, the first research biopsy could be performed at the time of VAD placement; refer to 
Section 11.3 and provided MCC-15-11083 Biospecimen Manual for additional instructions. 
Table 10 Footnotes 
A. Except for the pregnancy test, which must be performed within 72 hours prior to initiation of treatment, Day 
1 assessments do not need to be repeated if done within 14 days prior to initiation of study treatment. 
B. Prior to administration of the first pembrolizumab dose. 
C. Assessments, exams, and lab tests may be performed within 3 days prior to day 22 or on day 22 (prior to 
administration of pembrolizumab). Dose may be delayed up to day 29 (Section 6.6.1). If the 2nd dose of 
pembrolizumab must be delayed, day 22 requirements may be performed within 3 days before or on the 
day the 2nd dose of pembrolizumab is to be administered. 
D. Procedures timed relative to the last dose of pre-chemotherapy pembrolizumab may shift accordingly. 
E. See Appendix 1 for ECOG criteria. 
F. 
During the follow-up visits, only capture medication required for managing (late-occurring) irAEs. 
G. Assessment and reporting based on the NCI CTCAE v5.0. Refer to Sections 8.5, 8.6, 8.8, 8.10, and 8.11 
regarding expedited reporting. 
H. Chemistry includes the following panels: basic metabolic panel (sodium, potassium, carbonate, chloride, 
glucose, calcium, BUN, and creatinine) and the hepatic panel (ALT, AST, ALP, total bilirubin, direct bilirubin, 
albumin, and total protein). 
I. 
Refer to Table 1 in Section 6.4 for a summary of the treatment regimen; for decitabine instructions refer to 
Sections 6.5 and 9.1; for pembrolizumab instructions refer to Sections 6.6 and 9.2. 
J. 
Decitabine will be given daily for a total of 4 doses (see Section 6.5 for additional instructions). 
K. See Section 11.5. 
L. 
The first dose of pembrolizumab should be administered on day 8 but may be delayed until day 15; the 
second dose of pembrolizumab should be administered 2 weeks after the first dose (see Section 6.6 for 
additional instructions). 
Table 10. Study Requirements During Neoadjuvant Decitabine and Pembrolizumab Treatment Through Initiation of 
Standard Neoadjuvant Chemotherapy (All Cohorts) 
Assessments and 
Other Requirements 
Neoadjuvant Window Treatment  
Study Day (± 3 days) 
Early 
Discontinuation 
(within 10 days) 
(Section 6.13.1) 
1A 
2, 3, 4 
8B 
22C 
25-29D 
26-49D 
Weight 
X 
 
X 
X 
 
 
X 
Vital Signs  
X 
 
X 
X 
 
 
X 
Performance StatusE 
X 
 
X 
X 
 
 
X 
Physical Examination 
 
 
X 
X 
 
 
X 
Concurrent MedicationsF 
 
 
X 
X 
X 
(performed prior to 
initiation of standard 
chemotherapy) 
X 
AE AssessmentG 
 
 
X 
X 
X 
CBC, Differential, Platelet Count 
X 
 
X 
X 
X 
Blood ChemistryH 
X 
 
X 
X 
X 
Decitabine AdministrationI 
XJ 
XJ 
 
 
 
 
 
Correlative Blood SampleK 
 
 
X 
 
X 
 
 
Pembrolizumab AdministrationI 
 
 
XL 
XL 
 
 
 
Core Needle Biopsy for Correlative Tumor 
Samples 
 
 
 
 
XM 
 
 
TSH, Cortisol 
 
 
 
 
 
XN 
X 
Initiation of Standard Neoadjuvant Chemotherapy 
 
 
 
 
 
XO 
 

 
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M. Performed 3-7 days after administration of the 2nd dose of pembrolizumab (before neoadjuvant 
chemotherapy begins); refer to Section 11.3 for instructions regarding the collection and initial processing of 
correlative tumor sample. 
N. Performed prior to initiation of standard neoadjuvant chemotherapy 
O. As soon as possible after the biopsy (if blood counts and chemistries are acceptable for administration of 
chemotherapy). 

 
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Table 11. Study Requirements From Standard Neoadjuvant Chemotherapy through End of Study (Cohorts A and B) 
Assessments and 
Other Requirements 
During Standard 
Neoadjuvant 
ChemotherapyA 
(Section 6.7) 
Prior to 
Surgery (if 
applicable) 
Breast-Conserving Surgery or Mastectomy with Axillary Staging 
(if applicable) 
30-Day 
Follow-UpB 
(± 10 days) 
6-Month irAE 
Follow-UpB,C 
(±30 days) 
12-Month 
Follow-upB 
(± 30 days) 
Early 
Discontinuation 
(within 10 days) 
(Section 6.13.1) 
TSH, Cortisol 
XD 
 
X 
X 
 
X 
Initiation of Standard Neoadjuvant Chemotherapy 
XE 
 
 
 
 
 
AE AssessmentF 
X 
X 
XG 
X 
 
X 
Weight 
 
 
 
 
 
X 
Vital Signs  
 
 
 
 
 
X 
Performance StatusH 
 
 
 
 
 
X 
Physical Examination 
 
X 
X 
 
 
X 
Ipsilateral Breast Imaging 
 
X 
XI 
 
 
 
Tumor Measurement 
 
XJ 
XI,J 
 
 
 
Concurrent MedicationsK 
 
 
 
X 
 
X 
CBC, Differential, Platelet Count 
 
 
 
 
 
X 
Blood ChemistryL 
 
 
 
 
 
X 
Submission of Samples from Surgical ResectionM 
 
 
X 
 
 
 
Determination of pCR and RCBN 
 
 
X 
 
 
 
Survival Status 
 
 
 
XO 
XO 
 

 
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Table 11 Footnotes 
A. Except for TSH and cortisol, tests and exams during neoadjuvant chemotherapy are at the discretion of the treating medical oncologist. 
B. Refer to Section Error! Reference source not found.. 
C. For all patients who received one or both pembrolizumab doses, assess at 6 months (± 30 days) after surgery or the decision not to undergo 
surgery by in-person visit and/or medical record review: (1) the status of irAEs noted at the 30-day time point as having a steroid management 
requirement (an ongoing requirement for steroid management of previously known irAEs will be noted), (2) the occurrence, in the interim since 
the 30-day time point, of any new (late-occurring) irAE(s) requiring steroid management (an ongoing requirement for steroid management of 
new [late-occurring] irAEs will be noted). Note: 6-month irAE assessment is NOT required for patients who received postoperative 
chemotherapy and/or immunotherapy.  
D. TSH and cortisol tests are to be done prior to initiation of standard neoadjuvant chemotherapy and between the standard neoadjuvant 
chemotherapy regimens. 
E. As soon as possible after the second research biopsy (if blood counts and chemistries are acceptable for administration of chemotherapy). 
F. Assessment and reporting based on the NCI CTCAE v5.0. Refer to Sections 8.5, 8.6, 8.8, 8.10, and 8.11 regarding expedited reporting. 
G. Refer to Sections 8.4 and 8.11 for reporting requirements that may extend beyond 30 days. 
H. See Appendix 1 for ECOG criteria. 
I. 
For those patients who did not proceed to surgery. 
J. Physical exam will be used to assess and measure the primary breast tumor and regional lymph nodes following completion of all 
neoadjuvant therapy (prior to surgery). 
K. During the follow-up visits, only capture medication required for managing (late-occurring) irAEs. 
L. Chemistry includes the following panels: basic metabolic panel (sodium, potassium, carbonate, chloride, glucose, calcium, BUN, and 
creatinine) and the hepatic panel (ALT, AST, ALP, total bilirubin, direct bilirubin, albumin, and total protein). 
M. If there was no residual tumor (ie, pCR), submission of samples of the tumor bed is required (see Section 11.4). 
N. In addition to determining pCR (breast and nodes), the RCB Index will be calculated locally and entered into the OnCore database for 
all patients who have residual disease (see Section 10.2.3). 
O. Capture disease status per Section 6.13.5. 
 
 
 
 
 
 

 
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Table 12. Study Requirements From Standard Neoadjuvant Chemotherapy through End of Study (Cohort A2) 
Assessments and 
Other Requirements 
During Standard 
Neoadjuvant 
Chemotherapy with 
PembrolizumabA 
(Section 6.7) 
Prior to 
Surgery (if 
applicable) 
Breast-Conserving Surgery or Mastectomy with Axillary Staging (if applicable) 
30-Day 
Follow-UpB 
(± 10 days) 
 
Adjuvant 
Treatment 
PhaseC 
(± 3 days) 
C1-≤C8 
D1 
30 Day 
Safety 
Follow-UpB 
(± 10 days) 
12-Month 
Follow-upB,D 
(± 60 days) 
Early 
Discontinuation 
(within 10 days) 
(Section 6.13.1) 
TSH, Cortisol 
XE 
 
X 
 
X 
 
X 
Initiation of Standard 
Neoadjuvant Chemotherapy 
XF 
 
 
 
 
 
 
Pembrolizumab 
Administration 
X 
 
 
X 
 
 
 
AE AssessmentG 
X 
X 
XH 
X 
XH 
X 
X 
Weight 
 
 
 
X 
 
 
X 
Vital Signs  
 
 
 
X 
 
 
X 
Performance StatusI 
 
 
 
X 
 
 
X 
Physical Examination 
 
X 
X 
 
X 
 
X 
Ipsilateral Breast Imaging 
 
X 
XJ 
 
XJ 
 
 
Tumor Measurement 
 
XK 
XJ,K 
 
XJ,K 
 
 
Concurrent MedicationsL 
 
 
X 
X 
X 
X 
X 
CBC, Differential, Platelet 
Count 
 
 
 
X 
X 
 
X 
Blood ChemistryM 
 
 
 
X 
X 
 
X 
Submission of Samples 
from Surgical ResectionN 
 
 
X 
 
 
 
 
Determination of pCR and 
RCBO 
 
 
X 
 
 
 
 
Survival Status 
 
 
 
 
 
XP 
 

 
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Table 12 Footnotes 
A. Except for TSH and cortisol, tests and exams during neoadjuvant chemotherapy are at the discretion of the treating medical oncologist. 
B. Refer to Section Error! Reference source not found.. 
C. In general, assessments/procedures are performed on Day 1 of each cycle prior to dosing of any study treatment unless otherwise specified. 
Each treatment cycle is 3 weeks (21 days) for up to 8 cycles. Initiation of adjuvant therapy should begin 30-60 days post-surgery. 
D. Assess at 12 months (± 30 days) after surgery or the decision not to undergo surgery by in-person visit and/or medical record review: (1) the 
status of irAEs noted at the 30-day time point as having a steroid management requirement (an ongoing requirement for steroid management 
of previously known irAEs will be noted), (2) the occurrence, in the interim since the 30-day time point, of any new (late-occurring) irAE(s) 
requiring steroid management (an ongoing requirement for steroid management of new [late-occurring] irAEs will be noted). Note: 12-month 
irAE assessment is NOT required for patients who received postoperative chemotherapy and/or immunotherapy off study.  
E. TSH and cortisol tests are to be done prior to initiation of standard neoadjuvant chemotherapy and between the standard neoadjuvant 
chemotherapy regimens. 
F. As soon as possible after the biopsy (if blood counts and chemistries are acceptable for administration of chemotherapy). 
G. Assessment and reporting based on the NCI CTCAE v5.0. Refer to Sections 8.5, 8.6, 8.10, and 8.11 regarding expedited reporting. 
H. Refer to Sections 8.4 and 8.11 for reporting requirements that may extend beyond 30 days. 
I. 
See Appendix 1 for ECOG criteria. 
J. For those patients who did not proceed to surgery. 
K. Physical exam will be used to assess and measure the primary breast tumor and regional lymph nodes following completion of all 
neoadjuvant therapy (prior to surgery). 
L. Include over-the-counter medications. During the follow-up visits, only capture medication required for managing (late-occurring) 
irAEs. 
M. Chemistry includes the following panels: basic metabolic panel (sodium, potassium, carbonate, chloride, glucose, calcium, BUN, and 
creatinine) and the hepatic panel (ALT, AST, ALP, total bilirubin, direct bilirubin, albumin, and total protein). 
N. If there was no residual tumor (ie, pCR), submission of samples of the tumor bed is required, except for those who do not proceed to 
surgery (see Section 11.4). 
O. In addition to determining pCR (breast and nodes), the RCB Index will be calculated and reported by the pathology department. If 
RCB has not been calculated by the pathology department, information required for calculation of RCB is to be submitted to the 
Coordinating Center for calculation of RCB (see Section 10.2.3). 
P. Capture disease status per Section 6.13.5. 

 
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13 STATISTICAL CONSIDERATIONS 
 Study Design 
This is a single-arm phase 2 study of decitabine followed by pembrolizumab in the 
treatment of patients with locally advanced TNBC or ER-positive and/or PgR-positive,  
HER2-negative breast cancer. The primary objective is to determine if treatment with 
neoadjuvant decitabine followed by pembrolizumab increases lymphocyte infiltration into 
tumor and/or stroma in patients with locally advanced, HER2-negative breast cancer in 
each of the cohorts. 
 Sample Size and Accrual Rate 
According to Loi et al, each 10% increase in TILs was associated with a 13% reduction in 
distant recurrence in TNBC (29), and according to Denkert et al and Issa-Nummer et al, 
each 10% increase in tumor or stromal TIL infiltration was associated with a significant 
increase (hazard ratio of 1.2) in pCR to neoadjuvant chemotherapy (34, 36).Therefore, this 
study is powered to detect a 10% increase in TILs from baseline to the post-treatment 
period. Among the TNBC patients (Cohort A), the range of the percentage of stromal 
lymphocyte infiltration was 3 to 85 (29), and using the range rule that SD=(min-max)/4, the 
approximate standard deviation (SD) is 20.5%. A sample size of 28 achieves 80% power 
to detect a mean of paired differences of 0.10 with an estimated SD of difference of 0.205 
with a significance level of 0.05 using a one-sided paired t-test. To allow for the possibility 
that 10% of patients enrolled may be inevaluable, we anticipate enrolling 32 patients in 
order to ensure that 28 in Cohort A will be evaluable. 
Among the hormone receptor-positive patients (Cohort B), the range of stromal lymphocyte 
infiltration was 0.5 to 72.5 (29), and using the range rule that SD=(min-max)/4, the 
approximate SD is 18%. A sample size of 18 achieves 80% power to detect a mean of 
paired differences of 0.11 with an estimated SD of difference of 0.18 with a significance 
level of 0.05 using a one-sided paired t-test. As Cohort A is the primary target group in this 
trial given that TILs are significantly more likely to be observed in TNBC, Cohort B will not 
over-enroll past N=18 patients to account for inevaluability.  
Based on previous recruiting history, we anticipate that 2-3 patients will be enrolled per 
month over a period of about 24 months. With the addition of 3 months during which 
accrual will be held while the last patient enrolled in the safety lead-in phase completes 
dose-dense AC, the enrollment period was expected to be about 27 months. However, 
based on the initial recruitment experience and the addition of the extended 
pembrolizumab option, the expected enrollment period has been extended to 72 months 
from the time of the first patient enrollment. 

 
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 Analysis Populations 
13.3.1 Safety Lead-In Population 
The first 11 patients who have received at least 3 doses of decitabine and at least 1 
dose of pembrolizumab will be evaluable for safety during the safety lead-in phase. 
13.3.2 Safety-Evaluable Population 
Patients who have received at least 3 doses of decitabine and at least 1 dose of 
pembrolizumab will be evaluable for safety and toxicity analyses. 
13.3.3 Efficacy-Evaluable Population 
• 
For tumor immune infiltrate analysis: 
Patients who have received at least 3 doses of decitabine and at least 1 
pembrolizumab dose and have had procurement of a tumor sample following 
the second core needle biopsy, ie, the biopsy performed after the last 
administered dose of pre-chemotherapy pembrolizumab 
• 
For clinical response: 
Patients who have received at least 3 doses of decitabine, at least 1 dose of 
pembrolizumab, and any chemotherapy, and have had a physical examination 
to measure the tumor following completion of all neoadjuvant therapy 
• 
For pathologic assessment: 
Patients who have received at least 3 doses of decitabine, at least 1 dose of 
pembrolizumab, and any chemotherapy, and have had breast surgery 
 Statistical Analysis Plan 
13.4.1 Analysis of the Primary Endpoint 
A one-sided paired t-test will be used to compare baseline and post-treatment 
percentage of tumor and stromal areas with infiltrating lymphocytes. The paired  
t-test will be applied separately to Cohorts A and B. Cohort A analysis of the primary 
endpoint will include patients in Cohort A2. 
13.4.2 Analysis of Secondary Endpoints 
SAEs and UPs will be reported using frequencies and percentages separately for 
Cohorts A and B. The total number and percentage of patients with a SAE or UP will 
be provided as well as the average number of SAEs and UPs for each patient. 
McNemar’s test will be used to compare patients with LPBC before and after 
treatment with decitabine and pembrolizumab. The frequency and percent of 
patients that achieve pCR will be tabulated and a one-sample binomial test will be 
used to compare the observed proportion to 0.28, the expected pCR rate in the 
population. All inferential tests will be considered significant at the 0.05 level. 

 
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Frequencies and proportions/percents will be reported for pCR in breast and  
post-therapy lymph nodes, and cCR rate. Descriptive statistics such as the mean, 
median, SD, and range will be reported for the number of T cells, T-cell subsets, B 
cells, and MDSCs in tumor samples. The distribution of cell counts and IHC positive 
cells will be examined to determine whether they can be modeled using a Gaussian, 
Poisson, or negative binomial model, for which the latter 2 are recommended for 
count or rate data, particularly when the distribution is skewed. Exploratory 
regression analyses will be performed to determine whether any baseline 
demographic or clinical characteristics are significantly associated with cell counts. 
13.4.3 Subset Analyses 
Subset analyses will be conducted to account for any variability in actual therapy 
given during the standard neoadjuvant phase. 
14 DATA AND SAFETY MONITORING 
 Coordinating Center 
While patients are on treatment, the Sponsor-Investigator, study team members (eg, site 
investigators, research nurses, clinical research associates) and Coordinating Center staff 
will meet at least monthly to review study status. The biostatistician will review data with 
the Sponsor-Investigator and Coordinating Center staff at least quarterly. This review will 
include, but not be limited to, reportable events and an update of the ongoing study 
summary that describes study progress in terms of the study schema. All meetings, 
including attendance, are documented. 
 Monitoring and Auditing 
14.2.1 MCC Compliance Office 
Compliance specialists in the MCC Compliance Office will provide monitoring and 
auditing for this study. 
14.2.2 Data Safety and Monitoring Committee 
The study will be reviewed by the MCC DSMC initially according to the risk level 
specified by the MCC Protocol Review and Monitoring Committee (PRMC) and then 
according to a schedule based on study status and quality indicators. The DSMC 
will review reports provided by the Sponsor-Investigator/study team and the MCC 
Compliance Office focusing on data integrity and patient safety. 

 
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15  REGULATORY COMPLIANCE AND ETHICS 
 Ethical Standard 
This study will be conducted in conformance with the principles set forth in The Belmont 
Report: Ethical Principles and Guidelines for the Protection of Human Patients of Research 
(US National Commission for the Protection of Human Patients of Biomedical and 
Behavioral Research, April 18, 1979). 
 Regulatory Compliance 
This study will be conducted in compliance with the clinical trial protocol and with federal 
regulations, as applicable, including: 21 CFR 50 (Protection of Human Patients/Informed 
Consent); 21 CFR 56 (Institutional Review Boards); 21 CFR 312 (IND Application); and 45 
CFR 46 Subparts A (Common Rule), B (Pregnant Women, Human Fetuses and 
Neonates), C (Prisoners), and D (Children). 
 Institutional Review Board 
Each participating site must provide for the review and approval of this protocol and the 
associated informed consent documents and recruitment material by an appropriate IRB 
registered with the Office for Human Research Protections (OHRP). Any amendments to 
the protocol or consent materials must also be approved. Only institutions holding a current 
US Federalwide Assurance issued by OHRP may participate. 
 Informed Consent Process 
Informed consent is a process that is initiated prior to the individual’s agreeing to 
participate in the study and continues throughout the individual’s study participation. 
Discussion of risks and possible benefits of this therapy will be provided to patients and 
their families. Consent forms describing the study interventions/study procedures, and 
risks are given to the patient and written documentation of informed consent is required 
prior to starting intervention/administering study product. 
Consent forms will be IRB-approved and the patient will be asked to read and review the 
document. Upon reviewing the document, the investigator will explain the research study to 
the patient and answer any questions that may arise. The patient will sign the informed 
consent document prior to any procedures being done specifically for the study. Patients 
should have the opportunity to discuss the study with their surrogates or think about it prior 
to agreeing to participate. Patients may withdraw consent at any time throughout the 
course of the trial. A copy of the informed consent document will be given to patients for 
their records; the original consent form will be maintained in the research records.  
 Patient Confidentiality 
Patient confidentiality is strictly held in trust by the Sponsor-Investigator, participating 
investigators, staff, and the sponsor and its agents. This confidentiality includes the clinical 
information relating to participating patients, as well as any genetic or biological testing. 

 
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The study protocol, documentation, data, and all other information generated will be held in 
strict confidence. No information concerning the study or the data will be released to any 
unauthorized third party without prior written approval of the sponsor- investigator. 
The participating site will allow access to all source data and documents for the purposes 
of monitoring, audits, IRB review, and regulatory inspections. Source documents provided 
to the Coordinating Center for the purpose of auditing or monitoring will be  
de-identified and labeled with the study number, patient ID number, and patient initials. 
The study monitor or other authorized representatives of the Sponsor-Investigator may 
inspect all documents and records required to be maintained by the investigator, including 
but not limited to, medical records (office, clinic, or hospital) and pharmacy records for the 
patients in this study. The clinical study site will permit access to such records. 
16 DATA COLLECTION AND MANAGEMENT 
 Data Management Responsibilities 
The Sponsor-Investigator is responsible for: (i) reviewing SAE reports; (ii) determining if 
SARs need to be reported to the FDA, and if so, filing the report; (iii) filing annual IND 
reports; and (iv) filing IND amendments. 
The Sponsor-Investigator is responsible for: (i) the overall conduct of the investigation; (ii) 
ongoing review of trial data including all safety reports; and (iii) apprising participating sites 
of any UPs. 
The responsible investigator at each site is responsible for: (i) the data management at his 
or her site; and (ii) reporting SAEs, UPs, and other events requiring expedited reporting as 
described in Sections 8.10 and 8.11. 
Any laboratory conducting correlative studies must maintain the laboratory records and 
documentation (laboratory notebooks, laboratory protocols, print-outs, recordings, 
photographs, etc.) 
 CRFs and Data Collection 
MCC will provide standard electronic CRFs (eCRFs) and create study-specific eCRFs to 
be able to capture all information required by the protocol. The eCRFs will be approved by 
the Coordinating Center to ensure the most effective data acquisition. 
The investigator(s) and study coordinator(s) must maintain source documents for each 
patient in the study. All information on eCRFs will be traceable to these source documents, 
which are generally maintained in the patient’s file. 
All eCRFs should be completed and available for collection within a timely manner, 
preferably no more than 5-7 days after the patient’s visit. 

 
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 OnCore Data Entry 
Data will be entered into MCC’s OnCore database on an ongoing basis by all participating 
centers via remote access. Sites are responsible for updating data to allow for data 
compilation and review. Electronic data submissions will be reviewed periodically for data 
timeliness and accuracy. Sites will be queried periodically and significant problems with 
delinquency or accuracy may result in suspension of enrollment at a site. 
 Study Record Retention 
As applicable, study records will be maintained a minimum of 5 years beyond the 
publication of any abstract or manuscript reporting the results of the protocol or submission 
of a final report to clinicaltrials.gov. 

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

 
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APPENDIX 2. COCKCROFT-GAULT FORMULA 
 
 
Calculated Creatinine Clearance (Cockcroft-Gault) 
 
Creatinine clearance (mL/min) = [(140 - Age) × Weight in kg ×G] / (Creatinine × 72) 
 G=1 (males); G=0.85 (females) 

 
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APPENDIX 3. SUPPORTIVE CARE FOR MANAGEMENT OF ADVERSE 
EVENTS WITH POTENTIAL IMMUNOLOGIC ETIOLOGY 
Appendix 3 provides suggested supportive care measures for the management of AEs with 
potential immunologic etiology. Where appropriate, these guidelines include the use of oral or 
intravenous treatment with corticosteroids as well as additional anti-inflammatory agents if 
symptoms do not improve with administration of corticosteroids. Note that several courses of 
steroid tapering may be necessary as symptoms may worsen when the steroid dose is 
decreased. While the steroid dosing/tapering regimen will be at the discretion of the treating 
physician, the following recommendations may be considered: 
• 
Corticosteroids are given at a dose of 1-2 mg/kg prednisone or equivalent followed by taper.  
• 
Corticosteroid taper should be initiated upon AE improving to Grade 1 or less and continue 
to taper over at least 4 weeks.  
• 
For severe and life-threatening irAEs, IV corticosteroid should be initiated first followed by 
oral steroid.  
• 
Other immunosuppressive treatment should be initiated if irAEs cannot be controlled by 
corticosteroids. 
For each disorder, attempts should be made to rule out other causes such as bacterial or viral 
infection, which might require additional supportive care. It may be necessary to perform 
conditional procedures such as bronchoscopy, endoscopy, or skin photography as part of 
evaluation of the event. 
The treatment guidelines are intended to be applied when the investigator determines the 
events to be related to pembrolizumab. If after the evaluation the event is determined not to be 
related, the investigator does not need to follow the treatment guidance (as outlined below). 
Pneumonitis 
• 
For Grade 2 events, treat with systemic corticosteroids. When symptoms improve to 
Grade 1 or less, steroid taper should be started and continued over no less than 4 
weeks. 
• 
For Grade 3-4 events, immediately treat with intravenous steroids. Administer additional 
anti-inflammatory measures, as needed. 
• 
Add prophylactic antibiotics for opportunistic infections in the case of prolonged steroid 
administration. 
When symptoms improve to Grade 1 or less, a steroid taper should be started and 
continued over no less than 4 weeks. 
Diarrhea/Colitis 
Patients should be carefully monitored for signs and symptoms of enterocolitis (such as 
diarrhea, abdominal pain, blood or mucus in stool, with or without fever) and of bowel 
perforation (such as peritoneal signs and ileus). 
All patients who experience diarrhea/colitis should be advised to drink liberal quantities of clear 
fluids. If sufficient oral fluid intake is not feasible, fluid and electrolytes should be substituted via 
IV infusion. For Grade 2 or higher diarrhea, consider GI consultation and endoscopy to confirm 
or rule out colitis. 

 
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• 
For Grade 2 diarrhea/colitis, administer oral corticosteroids. 
• 
For Grade 3 or 4 diarrhea/colitis, treat with intravenous steroids followed by high-dose 
oral steroids. 
When symptoms improve to Grade 1 or less, steroid taper should be started and continued over 
no less than 4 weeks. 
Type 1 diabetes mellitus (if new onset, including diabetic ketoacidosis [DKA]) or ≥ Grade 
3 Hyperglycemia, if associated with ketosis (ketonuria) or metabolic acidosis (DKA) 
• 
Administer anti-hyperglycemic in patients with hyperglycemia 
• 
Insulin replacement therapy is recommended for Type I diabetes mellitus and for Grade 
3-4 hyperglycemia associated with metabolic acidosis or ketonuria. 
• 
Evaluate patients with serum glucose and a metabolic panel, urine ketones, glycosylated 
hemoglobin, and C-peptide. 
Hypophysitis 
• 
For Grade 2 events, treat with corticosteroids. When symptoms improve to Grade 1 or 
less, steroid taper should be started and continued over no less than 4 weeks. Initiate 
hormonal replacements as clinically indicated. 
• 
For Grade 3-4 events, treat with an initial dose of IV corticosteroids followed by oral 
corticosteroids. When symptoms improve to Grade 1 or less, steroid taper should be 
started and continued over no less than 4 weeks. Initiate hormonal replacements as 
clinically indicated. 
When symptoms improve to Grade 1 or less, a steroid taper should be started and 
continued over no less than 4 weeks 
Hyperthyroidism or Hypothyroidism 
Thyroid disorders can occur at any time during treatment. Monitor patients for changes in 
thyroid function (at the start of treatment, periodically during treatment, and as indicated based 
on clinical evaluation) and for clinical signs and symptoms of thyroid disorders. 
• 
Grade 2 hyperthyroidism events (and Grade 2-4 hypothyroidism) 
• 
In hyperthyroidism, treat with non-selective beta-blockers (eg, propranolol) or 
thionamides as appropriate. 
• 
In hypothyroidism, thyroid hormone replacement therapy, with levothyroxine or 
liothyroinine, is indicated per standard of care. 
• 
Grade 3-4 hyperthyroidism 
• 
Treat with an initial dose of IV corticosteroid followed by oral corticosteroids. When 
symptoms improve to Grade 1 or less, steroid taper should be started and continued 
over no less than 4 weeks. Treat with non-selective beta-blockers (eg, propranolol) 
or thionamides as appropriate. 
When symptoms improve to Grade 1 or less, a steroid taper should be started and 
continued over no less than 4 weeks. 

 
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Hepatic 
• 
For Grade 2 events, monitor liver function tests more frequently until returned to 
baseline values or stabilized (consider weekly); treat with IV or oral corticosteroids. 
• 
For Grade 3-4 events, treat with intravenous corticosteroids for 24 to 48 hours; monitor 
liver function tests more frequently until returned to baseline values or stabilized 
(consider weekly). 
When symptoms improve to Grade 1 or less, a steroid taper should be started and 
continued over no less than 4 weeks. 
Renal Failure or Nephritis 
• 
For Grade 2 events, treat with corticosteroids. 
• 
For Grade 3-4 events, treat with systemic corticosteroids. 
When symptoms improve to Grade 1 or less, steroid taper should be started and continued 
over no less than 4 weeks. 
Myocarditis 
• 
Based on severity of event, treat with systemic corticosteroids. 
• 
For Grade 3-4 events, initiate IV corticosteroids followed by oral corticosteroids. 
When symptoms improve ≤ Grade 2, steroid taper should be started and continued over no 
less than 4 weeks 
 
All other immune-related AEs 
• 
For Grade 2 events that are intolerable or persistent, based on type and severity of 
event, treat with systemic corticosteroids 
• 
For Grade 3-4 events, based on type and severity of event, initiate IV corticosteroids 
followed by oral corticosteroids. 
When symptoms improve to Grade 1 or less, steroid taper should be started and continued 
over no less than 4 weeks 
 
 

 
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APPENDIX 4. RECOMMENDED PROCEDURES FOR EVALUATION OF 
SURGICAL BREAST SPECIMENS 
The following procedures used for processing breast specimens following neoadjuvant 
chemotherapy at MD Anderson Cancer Center are provided as guidelines for participating 
investigators. 
 
Specimens should be oriented with sutures by the surgeon following removal. The surgeon and 
breast pathologist should confer to ensure optimal evaluation of the primary tumor site for 
possible pCR. 
 
• 
In cases showing significant clinical response in the breast 
• 
The breast resection specimen is radiographed to identify metallic markers which were 
placed during or prior to chemotherapy. 
• 
Each specimen is inked using multiple colors to identify each face of the specimen, and 
then sectioned into 3-5 mm slices. 
• 
The sliced specimen is radiographed and a radiologist reviews the films to determine the 
presence and extent of residual tumor. 
• 
The pathologist examines the sliced specimen grossly to identify suspicious areas and 
notes their proximity to margins. 
• 
The radiographic and pathologic evaluation is discussed with the surgeon who decides 
whether additional margins should be obtained. 
• 
Permanent paraffin sections of the suspicious areas and margins are obtained. The 
number of sections taken is based on the gross inspection, radiologic features, and size 
of the resection specimen. 
• 
The entire radiographic abnormality as well as firm and suspicious appearing breast 
tissue is submitted for histologic evaluation. 
• 
In general, for non-palpable (clinical complete response) cases at least 10-15 blocks are 
examined to assess the presence of residual microscopic disease. 
• 
In cases with residual palpable mass (partial clinical response or no response in the 
breast) 
• 
The resection specimen is inked and sectioned into 3-5 mm slices. 
• 
The pathologist examines the slices and determines the tumor size on gross evaluation 
and confirms the tumor size by microscopic evaluation. 
• 
Evaluation of axillary lymph nodes regardless of response 
All axillary lymph nodes are also carefully evaluated by serial gross sectioning. 
• 
One or 2 representative histologic sections are evaluated for lymph nodes that contain 
grossly identifiable metastatic carcinoma. 
• 
The lymph nodes that do not show grossly identifiable tumor are submitted for histologic 
evaluation in their entirety. One representative histologic section is evaluated per 
paraffin block. Immunohistochemical staining for cytokeratin is not routinely performed 
on negative nodes.