A Pilot Study Of Changes In PD-L1 Expression During Preoperative Treatment With Nab-Paclitaxel And Pembrolizumab In Hormone Receptor-Positive Breast Cancer
Phase: PHASE1
Conditions: Breast Cancer
Sponsor: Adrienne G. Waks



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NCI-Supplied Agent(s):  N/A
Other Agent(s):  

Industry-Supplied: Pembrolizumab (MK-3475; Keytruda™), Merck

Commercial: Nab-Paclitaxel (Abraxane®), Abraxis
IND #:  131948
IND Sponsor:  
Protocol Type / Version Date: Amendment / Version 10 /  September 27, 2023

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SCHEMA
A: nab-paclitaxel; HR: hormone receptor; MK-3475: pembrolizumab

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TABLE OF CONTENTS
SCHEMA.........................................................................................................................................3
1.
OBJECTIVES......................................................................................................................7
1.1
Study Design............................................................................................................7
1.2
Primary Objectives...................................................................................................7
1.3
Secondary Objectives...............................................................................................7
1.4
Correlative Science Objectives................................................................................7
2.
BACKGROUND .................................................................................................................8
2.1
Neoadjuvant therapy for hormone receptor-positive breast cancer .........................8
2.2
Pembrolizumab ........................................................................................................9
2.3
Nab-Paclitaxel........................................................................................................12
2.4
Rationale for the combination of nab-paclitaxel and pembrolizumab...................13
2.5
Dosing of combination nab-paclitaxel and pembrolizumab..................................13
2.6
Rationale for the use of biomarker endpoints........................................................14
2.7
PD-L1 expression in ER+ breast tumors ...............................................................15
2.8
Correlative Studies Background ............................................................................16
3.
PARTICIPANT SELECTION...........................................................................................17
3.1
Eligibility Criteria..................................................................................................17
3.2
Exclusion Criteria ..................................................................................................19
3.3
Inclusion of Women and Minorities ......................................................................20
4.
REGISTRATION PROCEDURES ...................................................................................20
4.1
General Guidelines for DF/HCC Institutions ........................................................20
4.2
Registration Process for DF/HCC Institutions.......................................................20
4.3
General Guidelines for Other Investigative Sites ..................................................20
4.4
Registration Process for Other Investigative Sites.................................................21
5.
TREATMENT PLAN........................................................................................................21
5.1
Treatment Regimen................................................................................................21
5.2
Pre-Treatment Criteria ...........................................................................................22
5.3
Agent Administration.............................................................................................27
5.4
Definition of Dose-Limiting Toxicity (DLT) ........................................................28
5.5
General Concomitant Medication, Supportive Care Guidelines, and 
Contraception Guidelines.......................................................................................29
5.6
Additional Preoperative Chemotherapy.................................................................33
5.7
Criteria for Taking a Participant Off Protocol Therapy.........................................33
5.8
Duration of Follow Up...........................................................................................34
5.9
Criteria for Taking a Participant Off Study ...........................................................35
6.
DOSING DELAYS/DOSE MODIFICATIONS ...............................................................35
6.1
Management of toxicities attributable to pembrolizumab alone............................36
6.2
Management of toxicities attributable to nab-paclitaxel alone..............................42

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6.3
Management of hepatic toxicity attributable to both pembrolizumab and 
nab-paclitaxel.........................................................................................................45
7.
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS ............................46
7.1
Adverse Event Lists...............................................................................................47
7.2
Adverse Event Characteristics...............................................................................48
7.3
Expedited Adverse Event Reporting......................................................................48
7.4
Expedited Reporting to the Food and Drug Administration (FDA) ......................49
7.5
Expedited Reporting to Hospital Risk Management .............................................49
7.6
Routine Adverse Event Reporting .........................................................................49
7.7
Immediate Reporting of Adverse Events and Events of Clinical Interest 
(ECI) to Merck.......................................................................................................50
8.
PHARMACEUTICAL INFORMATION..........................................................................52
8.1
Pembrolizumab ......................................................................................................52
8.2
Nab-Paclitaxel........................................................................................................54
9.
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES ........................................56
9.1
Archival Tissue Requirements...............................................................................57
9.2
Procedures for obtaining breast tissue for study....................................................58
9.3
Tissue banking .......................................................................................................61
9.4
Procedures for obtaining blood specimens for study.............................................61
9.5
Procedures for obtaining stool for specimens for study.........................................63
9.6
Cell-free DNA (cfDNA) analysis ..........................................................................63
9.7
Blood banking........................................................................................................63
9.8
Hypotheses for secondary/correlative objectives...................................................64
9.9
Immunohistochemistry for primary endpoint (PD-L1 expression) and 
secondary/exploratory endpoints ...........................................................................64
9.10
Tumor infiltrating lymphocyte (TIL) percentage and determination of 
lymphocyte predominant breast cancer (LPBC)....................................................68
9.11
Exploratory correlative analyses of tumor tissue...................................................68
9.12
Exploratory correlative analyses of peripheral blood: flow cytometry to 
characterize immune markers in peripheral blood mononuclear cells 
(PBMCs) prior to, during, and after therapy with nab-paclitaxel and 
pembrolizumab ......................................................................................................69
9.13
Additional analysis.................................................................................................70
9.14
Analysis of DNA extraction from stool samples...................................................70
9.15
Analysis of RNA Extraction from stool samples...................................................70
9.16
Shotgun sequencing and metabolic pathway reconstruction of stool 
samples...................................................................................................................71
9.17
Site Performing Correlative Studies ......................................................................71
10.
STUDY CALENDAR .......................................................................................................71
11.
MEASUREMENT OF EFFECT .......................................................................................75
11.1
Antitumor Effect – Solid Tumors ..........................................................................75
11.2
Radiographic assessment .......................................................................................75

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11.3
Other radiographic response parameters:  Immune-Related Response 
Criteria (irRECIST) ...............................................................................................75
11.4
Clinical assessments...............................................................................................77
11.5
Pathologic Response..............................................................................................77
12.
DATA REPORTING / REGULATORY REQUIREMENTS...........................................78
12.1
Data Reporting.......................................................................................................78
12.2
Data Safety Monitoring..........................................................................................78
12.3
Multicenter Guidelines...........................................................................................79
12.4
Collaborative Research and Future Use of Data and Biospecimens......................79
13.
STATISTICAL CONSIDERATIONS...............................................................................79
13.1
Study Design/Endpoints ........................................................................................79
13.2
Sample Size, Accrual Rate and Study Duration ....................................................81
13.3
Stratification Factors..............................................................................................82
13.4
Interim Monitoring Plan ........................................................................................82
13.5
Analysis of Primary Endpoints..............................................................................82
13.6
Analysis of Secondary Endpoints..........................................................................82
13.7
Reporting and Exclusions ......................................................................................83
14.
PUBLICATION PLAN .....................................................................................................84
REFERENCES ..............................................................................................................................85
APPENDIX A
PERFORMANCE STATUS CRITERIA ..................................................90
APPENDIX B
New York Heart Association (NYHA) Classifications .............................91
APPENDIX C
Strong cyp3a inducers/inhibitors ...............................................................92

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1.
OBJECTIVES
1.1
Study Design
This is a randomized, open label study assessing changes in immune biomarkers during 
preoperative treatment with nab-paclitaxel in combination with pembrolizumab.  The population 
to be studied consists of participants with operable hormone receptor-positive, HER2-negative 
breast cancer who have not yet received treatment for their breast cancer.  Participants will receive 
an upfront randomized window of therapy with either nab-paclitaxel or pembrolizumab, with pre- 
and post-window biopsies (biopsy 1 and biopsy 2, respectively), followed by nab-paclitaxel in 
combination with pembrolizumab for an additional 12-13 weeks, with a third biopsy (biopsy 3) on 
combination treatment.  Participants will undergo surgery after completion of combination 
therapy, and tissue will also be collected at surgery.  Post-operatively, administration of further 
treatment is per the treating investigator’s discretion.
1.2
Primary Objectives
Objective: To characterize changes in tumor cell PD-L1 expression after treatment with either nab-
paclitaxel or pembrolizumab monotherapy.
Hypothesis: Nab-paclitaxel and pembrolizumab monotherapy will both increase tumor cell PD-L1 
expression.
1.3
Secondary Objectives
Secondary biomarker objectives:
-
To characterize changes in stromal tumor infiltrating lymphocytes; after treatment with 
either nab-paclitaxel or pembrolizumab monotherapy.
Safety objective:
-
To evaluate the safety and tolerability of combination nab-paclitaxel and pembrolizumab 
therapy in patients with hormone receptor-positive breast cancer treated in the neoadjuvant 
setting.
Efficacy objectives:
-
To determine the rate of pCR with combination nab-paclitaxel and pembrolizumab in the 
neoadjuvant setting
-
To determine the overall response rate, based on radiographic assessment, with 
combination nab-paclitaxel and pembrolizumab in the neoajuvant setting
-
To explore disease-free survival with combination nab-paclitaxel and pembrolizumab in 
the neoadjuvant setting
1.4
Correlative Science Objectives
-
To characterize changes in stromal tumor infiltrating lymphocytes after treatment with 
either 
nab-paclitaxel 
or 
pembrolizumab 
monotherapy 
followed 
by 
nab-
paclitaxel/pembrolizumab combination therapy (at the time of interval biopsy and 

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definitive breast surgery).
-
To explore whether levels of peri-tumoral immune biomarkers ((1) stromal tumor 
infiltrating lymphocytes; (2) PD-1 expression; (3) PD-L1 expression; (4) PD-L2 
expression; (5) CD8 expression) in pre-treatment biopsies correlate with response to 
treatment as assessed by residual cancer burden (RCB) and pathologic complete response 
(pCR) at surgery
-
To explore whether changes in peri-tumoral immune biomarkers ((1) stromal tumor 
infiltrating lymphocytes; (2) PD-1 expression; (3) PD-L1 expression; (4) PD-L2 
expression; (5) CD8 expression) on serial biopsies and at surgery correlate with response 
to treatment as assessed by RCB and pCR.
-
To characterize an expanded set of immune markers (based on histology, protein 
expression, and mRNA expression) in hormone receptor-positive breast tumors both pre-
treatment and on serial biopsies, and to explore whether any members of this expanded set 
correlate with response to treatment
-
To characterize the immune marker profile in peripheral blood mononuclear cells (PBMCs) 
both pre-treatment and on serial blood draws
-
To explore whether levels of immune markers in the peripheral blood correspond with 
levels of immune biomarkers in peri-tumoral tissue, both pre-treatment and on therapy
-
To explore cell-free DNA (cfDNA) in comparison to tumor specimens before and after 
immunotherapy
-
To characterize the structure and function of the gut microbiome in patients with breast 
cancer prior to starting this clinical trial.
-
To determine whether pre-treatment characteristics of the structure and function of the gut 
microbiome in patients with breast cancer is associated with response to treatment.
-
To characterize changes in the structure and function of the gut microbiome of patients 
with breast cancer after exposure to Nab-paclitaxel or Pembrolizumab alone (after W1 for 
both Arms)
-
To characterize changes in the structure and function of the gut microbiome of patients 
with breast cancer after exposure to Nab-paclitaxel and Pembrolizumab together (after W4)
-
To determine whether changes in the overall diversity of the gut microbiome, estimated by 
the Shannon Index, of patients with breast after exposure to Nab-paclitaxel or 
Pembrolizumab alone (after W1 for both Arms) is associated with response to treatment.
-
To determine whether changes in the overall diversity of the gut microbiome, estimated by 
the Shannon Index, of patients with breast after exposure after exposure to Nab-paclitaxel 
and Pembrolizumab together (after W4).
-
To determine if the abundance and functional profile of specific gut bacteria are associated 
with response to treatment.
-
To evaluate the functional pathways that may play a role as a predictive biomarker of 
response to treatment.
2.
BACKGROUND
2.1
Neoadjuvant therapy for hormone receptor-positive breast cancer
Hormone receptor positive breast cancer (defined as estrogen receptor and/or progesterone 
receptor expressing tumors) accounts for 60-70% of breast cancer and approximately 140,000 

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patients are diagnosed with this type of breast cancer in the United States each year, the majority 
of whom have operable disease.
Preoperative (neoadjuvant) chemotherapy is increasingly being used in the management of 
operable breast cancer (BC). Randomized trials comparing preoperative and postoperative 
chemotherapy show similar rates of disease-free and overall survival.1  However, the preoperative 
setting offers the advantage of disease downstaging and possibly reducing the extent of surgery. 
Furthermore, the response to the primary treatment may be used as a prognostic marker as better 
tumor response at surgery has been shown to be associated with longer disease-free survival.1  
Additionally, the preoperative treatment setting allows access to tissue, providing an optimal 
setting to identify potential mechanisms of action and biomarkers of response to therapy.
2.2
Pembrolizumab
The PD-1 pathway in cancer
The importance of intact immune surveillance in controlling outgrowth of neoplastic 
transformation has been known for decades.  Accumulating evidence shows a correlation between 
tumor-infiltrating lymphocytes (TILs) in cancer tissue and favorable prognosis in various 
malignancies.  In particular, the presence of CD8+ T-cells and the ratio of CD8+ effector T-cells / 
FoxP3+ regulatory T-cells seems to correlate with improved prognosis and long-term survival in 
many solid tumors.
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, T regs and Natural Killer 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-

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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 participants 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
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.  KeytrudaTM (MK-3475; pembrolizumab) has recently been 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. 
Please refer to the Full Prescribing Information for pembrolizumab for complete safety 
information: http://www.accessdata.fda.gov/scripts/cder/drugsatfda/.  
Clinical data are derived from an ongoing, first-in-human phase I study (PN001, NCT01295827) 
to evaluate the safety and clinical activity of pembrolizumab as a monotherapy, sponsored by 
Merck Sharp & Dohme.  There are five parts to this study (Parts A-D and F) (Investigator’s 
Brochure, 2014).
Part A was a 3+3 dose escalation study in participants with solid tumors to evaluate safety, 
tolerability, pharmacokinetics (PK), and pharmacodynamics, and to determine a maximum 
tolerated dose (MTD) or preliminary recommended phase 2 doses (RP2Ds).  Doses were 1, 3, and 
10 mg/kg every 2 weeks (Q2W); doses of either 2 mg/kg or 10 mg/kg were also administered every 
3 weeks (Q3W).  All 3 dose levels were well tolerated and no dose-limiting toxicities (DLTs) were 
observed; therefore, the MTD was not determined.  The RP2D was determined by the sponsor 
based on safety, PK, and pharmacodynamic measurements, along with the strength of antitumor 
activity signals observed.
Pharmacokinetics
The half-life (t1/2) of pembrolizumab is approximately 4 weeks and there is no indication of dose 
dependency or half-life in the three dose groups (1, 3, and 10 mg/kg) (Investigator’s Brochure, 
2014).  The long t1/2 supports a dosing interval of every 2 or 3 weeks.
There was a dose-related increase in exposure from 1 to 10 mg/kg.  Serum concentrations of 
pembrolizumab were lower by a factor of approximately 5 in participants receiving 2 mg/kg Q3W 
than in those receiving 10 mg/kg Q3W.  Steady-state trough concentrations were 20% greater in 
the participants receiving 10 mg/kg Q2W than in those receiving the same dose Q3W.
A population pharmacokinetic analysis has been performed using serum concentration time data 
from 476 participants. Within the resulting population PK model, clearance and volume 
parameters of pembrolizumab were found to be dependent on body weight. The relationship 

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between clearance and body weight, with an allometric exponent of 0.59, is within the range 
observed for other antibodies and would support both body weight normalized dosing or a fixed 
dose across all body weights.  Pembrolizumab has been found to have a wide therapeutic range 
based on the melanoma indication.  The population PK evaluation revealed that there was no 
significant impact of tumor burden on exposure. In addition, exposure was similar between the 
NSCLC and melanoma indications. Therefore, there are no anticipated changes in exposure 
between different indication settings.
The rationale for further exploration of 2 mg/kg and comparable doses of pembrolizumab in solid 
tumors is based on: 1) similar efficacy and safety of pembrolizumab when dosed at either 2 mg/kg 
or 10 mg/kg Q3W in melanoma participants, 2) the flat exposure-response relationships of 
pembrolizumab for both efficacy and safety in the dose ranges of 2 mg/kg Q3W to 10 mg/kg Q3W, 
3) the lack of effect of tumor burden or indication on distribution behavior of pembrolizumab (as 
assessed by the population PK model) and 4) the assumption that the dynamics of pembrolizumab 
target engagement will not vary meaningfully with tumor type.
The choice of the 200 mg Q3W as an appropriate dose for the switch to fixed dosing is based on 
simulations performed using the population PK model of pembrolizumab showing that the fixed 
dose of 200 mg every 3 weeks will provide exposures that 1) are optimally consistent with those 
obtained with the 2 mg/kg dose every 3 weeks, 2) will maintain individual patient exposures in the 
exposure range established in melanoma as associated with maximal efficacy response and 3) will 
maintain individual participants exposure in the exposure range established in melanoma that are 
well tolerated and safe. 
A fixed dose regimen will simplify the dosing regimen to be more convenient for physicians and 
to reduce potential for dosing errors.  A fixed dosing scheme will also reduce complexity in the 
logistical chain at treatment facilities and reduce wastage.
Anti-Drug Antibodies (ADA) Data
The occurrence of ADA has been observed in less than 1% of the participants screened, indicating 
a low potential of pembrolizumab to elicit the formation of ADA.  No impact of ADA on 
pembrolizumab exposure has been observed.
Efficacy
When treated with pembrolizumab monotherapy, the overall response rate (ORR) for ipilimumab 
(IPI)-treated Participants with melanoma was 25%/27% according to the Response Evaluation 
Criteria in Solid Tumors (RECIST)/investigator-assessed immune-related response criteria (irRC), 
respectively (Investigator’s Brochure, 2014).  The ORR for IPI-naïve participants with melanoma 
was 39%/43% by RECIST/investigator-assessed irRC, respectively.  The majority of responses 
were seen in participants with melanoma by 16 weeks of therapy; however, some responses have 
been reported after 24 weeks or more of therapy with pembrolizumab.  Responses can be delayed, 
and in some participants, a RECIST-defined progression followed by response has been observed.
The preliminary ORR for 38 participants with non-small cell lung cancer was 21% / 24% by 
RECIST/investigator-assessed irRC, respectively (Investigator’s Brochure, 2014).
Pharmacodynamics/Biomarkers

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Pharmacodynamic data (IL-2 release assay) has suggested that peripheral target engagement is 
durable (>21 days).  
PD-L1 is being investigated as a predictive biomarker for pembrolizumab treatment.  At the 15th 
World Conference on Lung Cancer, Garon et al presented preliminary data on a subset of 
participants suggesting that higher levels of tumor PD-L1 expression are associated with increased 
clinical activity.2  ORR by RECIST 1.1 occurred in 4 out of 7 participants with higher levels of 
PD-L1 expression (57%, 95% CI 18-90%) versus 2 out of 22 participants with lower levels of PD-
L1 expression (9%, 95% CI 1-29%).  These data are extremely preliminarily, and PD-L1 is not 
being used for patient selection.
Biomarkers to evaluate immune modulation and markers in the tumor microenvironment, such as 
T-cell infiltration, the baseline expression of markers of T-cell suppression FoxP3 or the 
immunoregulatory enzyme incoleamine 2,3-dioxygenase (IDO) in tumor biopsies, were associated 
with a high response rate in participants with advanced melanoma.3,4 
Safety data
The most frequent treatment-related adverse events (AEs) were fatigue, nausea, cough, pruritis, 
diarrhea, and rash (Investigator’s Brochure, 2014).  Most AEs were not considered serious.  The 
most commonly-reported immune-related AEs were rash, pruritis, vitiligo, hypothyroidism, 
arthralgia, diarrhea, and pneumonitis.
Important identified risks include: pneumonitis, thyroid disorders (hypothyroidism and 
hyperthyroidism), colitis, diarrhea, hepatitis, nephritis, uveitis, rash/pruritis, and neuropathy.
2.3
Nab-Paclitaxel
Nanoparticle albumin-bound (nab)-paclitaxel is an albumin-bound formulation of
paclitaxel that was developed to avoid the toxicities associated with the vehicles that are
necessary for parenteral administration of solvent-based (sb)-paclitaxel (polyethylated
castor oil and polysorbate 80). Nab-paclitaxel has a shorter infusion time (30 minutes)
than sb-paclitaxel and can be administered without steroid or antihistamine
premedication. In addition, it has an advantageous PK profile compared with
sb-paclitaxel and achieves a 33% higher tumor uptake in preclinical models.5
Nab-paclitaxel was approved for the treatment of metastatic breast cancer on the basis of a
randomized Phase III study in which participants received either nab-paclitaxel or sb-paclitaxel
(control) administered every 3 weeks (q3w) (n = 460).6  The primary efficacy endpoint of the study 
was response rate. Participants receiving nab-paclitaxel achieved a higher response rate (21.5% 
vs. 11.1% for those receiving sb-paclitaxel). The median time to disease progression was longer 
for participants who received nab-paclitaxel than for those randomized to the sb-paclitaxel arm 
(23.0 vs. 16.9 weeks, respectively). Although a higher paclitaxel dose was achieved in the nab-
paclitaxel arm, the incidence of Grade 4 neutropenia was significantly lower in the nab-paclitaxel 
arm than in the sb-paclitaxel (control) arm (9% vs. 22%, respectively). Grade 3 sensory neuropathy 
was more common with nab-paclitaxel than with sb-paclitaxel (10% vs. 2%, respectively) but was 
reported to be manageable and self-limiting with treatment interruption and dose reduction.

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Regimens containing anthracycline and taxanes are standard of care of localized breast cancer. 
Recent preoperative data from the GeparSepto study suggests that nab-paclitaxel may be more 
effective than conventional paclitaxel as part of neoadjuvant therapy for breast cancer.  In this 
randomized phase III neoadjuvant study, nab-paclitaxel given as 125 mg/m2 weekly for 12 weeks, 
followed by 4 cycles of epirubicin/cyclophosphamide, was associated with a pCR rate of 38%, 
significantly higher than the rate seen with standard paclitaxel (29%, p<0.01).7
2.4
Rationale for the combination of nab-paclitaxel and pembrolizumab
While chemotherapy has a role in the treatment of hormone receptor positive (HR+) breast cancer, 
there is compelling evidence that it is less effective in HR+ tumors than in HR- tumors.8  
Accordingly, HR+ participants have low (2-10%) rates of pathologic complete response (pCR) at 
surgery following neoadjuvant chemotherapy.9  Therefore, there is a great need to understand how 
and when to leverage other therapeutic modalities, i.e. immunotherapy, alone or in combination 
with chemotherapy to improve treatment efficacy in the HR+ breast cancer subset.
Nab-paclitaxel is an attractive chemotherapeutic agent for combining with immunotherapy given 
the lack of need for steroid premedication.  To our knowledge there are no current data 
documenting the pCR rate from single-agent nab-paclitaxel therapy in HR+ breast cancer.  In a 
study of a different taxane, docetaxel, given as a single agent in the preoperative setting, 8% of 
estrogen receptor-positive (ER+) participants (N=52) and 13% of progesterone receptor-positive 
(PR+) participants (N=47) achieved “good” pathologic response, defined as pCR or minimal 
residual disease based on residual cancer burden (RCB) scores of 0-1.10,11  This is on par with the 
low pCR rates seen for HR+ disease in other treatment settings, as detailed above.
There is increasing evidence that in addition to causing tumor cell death, certain
conventional chemotherapies may have immunogenic effects.12  Clinical evidence exists to suggest 
that T-cell and NK-cell functions are enhanced in participants with breast cancer (stage II/III) 
treated with taxanes compared with participants who did not receive taxanes.13  A recent study in 
the 4 T1 breast cancer mouse model demonstrated remarkable synergy between therapy with PD-
1 specific antibody and paclitaxel. As opposed to paclitaxel monotherapy, the combination 
significantly suppressed tumor growth and 80% of the mice (4 of 5) survived tumor-free until day 
90.14  A small study (N=25) in breast cancer participants undergoing neoadjuvant therapy with 
paclitaxel showed that in increase in the number of tumor infiltrating lymphocytes (TILs) from 
baseline to surgery correlated with an increased apoptotic tumor response, and better clinical 
responses.15
In addition, tumor cell killing by cytotoxic chemotherapy can be expected to expose the immune 
system to high levels of tumor antigens, and this process itself may stimulate antigen presentation 
and immune activation against tumors.16  There is therefore strong reason to believe that 
chemotherapy can work synergistically with immune modulation.
2.5
Dosing of combination nab-paclitaxel and pembrolizumab
A phase I/II study of carboplatin, nab-palictaxel, and pembrolizumab is currently ongoing in 

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advanced non-small cell lung cancer.  The phase I/cohort 1 portion of this study involved 
enrollment of 12 patients to treatment with carboplatin (AUC 6 q3weeks), nab-paclitaxel (100 
mg/m2 weekly), and pembrolizumab (2 mg/kg q3weeks).  Cohort 1 completed enrollment (12/12 
planned patients) with a total of two dose-limiting toxicities (one grade 4 hyperglycemia; one 
febrile neutropenia).  There was no significant immune-related toxicity observed beyond what 
would be expected from prior experiences with PD-1 inhibitors given as a single agent; the only 
instance of high-grade potentially immune-related toxicity was the single episode of grade 4 
hyperglycemia, as mentioned.  This trial has now moved into phase II enrollment using the phase 
I/cohort 1 doses, with the exception of changing pembrolizumab to flat dosing of 200 mg 
q3weeks per industry sponsor preference (Jyoti Patel MD and Ryan Getzler MD, personal 
communication).  Of note, this phase I/II trial differs from our proposed phase II trial in that we 
plan to treat with nab-paclitaxel/pembrolizumab alone, with omission of carboplatin.  As nab-
paclitaxel and carboplatin have many overlapping toxicities (most notably cytopenias, 
neuropathy, and fatigue), if anything the toxicities of nab-paclitaxel/pembrolizumab are expected 
to be less than the toxicities of carboplatin/nab-paclitaxel/pembrolizumab.
Based on the acceptable toxicity profile to date of triplet therapy in non-small cell lung cancer, 
the present study will be a phase II study using doublet nab-paclitaxel (dosed at 125 mg/m2 
weekly, in accordance with prior efficacy data from the neoadjuvant GeparSepto study in breast 
cancer; see Section 2.3) plus pembrolizumab at 200 mg q3weeks.  The rationale for switching to 
a fixed dose regimen for pembrolizumab is described in Section 2.2.
2.6
Rationale for the use of biomarker endpoints
There is growing evidence that signatures of tumor-associated immunologic activity are seen in 
breast cancer and are significant prognostic predictors.  Many different groups have demonstrated 
that the amount of tumor-infiltrating lymphocytes (TILs) in a breast tumor specimen, commonly 
assessed simply by histological evaluation of a standard hematoxylin and eosin-stained slide by a 
trained pathologist, is a significant predictor of both response to therapy and overall disease 
outcomes in the neoadjuvant and adjuvant settings.17-22  However, the majority of this work has 
been done on triple negative and HER2-positive (HER2+) breast cancers.
Compared to hormone receptor-negative tumors, ER+ breast cancers tend to have a significantly 
lower percentage of TILs in untreated specimens (median 10% versus median 12.5%, p=0.02, in 
the HER2-positive NeoALTTO cohort),17 and a lower prevalence of lymphocyte predominant 
breast cancer (LPBC, commonly defined as breast cancer with >60% stromal TILs) (12.0% versus 
36.5% LPBC in the GeparQuinto cohort).19  By mRNA analysis, PD-1 expression is inversely 
correlated with ESR1 expression, and PD-1 expression is significantly higher in HER2+, triple 
negative, and grade 2/3 breast tumors.  (Of note, PD-1 expression correlates significantly with PD-
L1 expression across multiple datasets.)23  In sum, therefore, ER+ breast tumors appear to have a 
generally less “immune active” profile at baseline, compared to the HER2+ and triple negative 
subsets.
While the value of TILs for predicting response to neoadjuvant and adjuvant chemotherapy is well 
established in triple negative and HER2+ breast cancer, the predictive value of tumor-associated 
immune signatures in ER+ tumors treated with chemotherapy is not yet clear.  Analysis of some 

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datasets has failed to show an association between TIL percentage in baseline tumor tissue and 
disease outcome.22  Conversely, other datasets (i.e. GeparQuinto) do demonstrate an association 
between more immune activity in ER+ tumors and improved clinical responses to therapy.19  Our 
group’s data suggest that gene expression signatures associated with “immune activation” identify 
a subset of ER+ breast cancers with higher rates of pCR to neoadjuvant chemotherapy.  Moreover, 
these “immune activation” signatures appear to be proliferation-independent (Stover DG et al, data 
not yet published).
Overall, many unanswered questions remain about the significance of immunologic profile in ER+ 
breast cancers and, by proxy, the role of checkpoint inhibitor therapy in this disease subset.  
Though these tumors appear to start out less immune-activated than triple negative or HER2+ 
counterparts, it is not known how these characteristics change over the course of treatment.  As 
outlined in the prior section, there is reason to believe that treatment with chemotherapy is 
immune-activating.  It is also not known how use of chemotherapy in conjunction with 
immunotherapy affects the immune characteristics of ER+ tumors.  The neoadjuvant setting is an 
ideal platform for serial tissue sampling to provide a high volume of information about dynamic 
changes in peri-tumoral immune markers.  Therefore, the current trial proposes to examine changes 
in immune-related biomarkers over the course of neoadjuvant treatment for ER+ breast cancer.  
We have selected PD-L1 protein expression as the core immune marker to evaluate based on prior 
evidence across multiple malignancies that it is significantly associated with a tumor’s clinical 
characteristics.
Regarding the requirement for 3 breast core biopsies on this protocol: Plentiful data from other 
malignancies, such as melanoma, indicate the utility of immune-related biomarkers for predicting 
response to single agent checkpoint inhibitor therapy.24  However, early clinical data from 2 trials 
presented at San Antonio Breast Cancer Symposium 2015 suggest that PD-1/PD-L1 inhibition 
alone will not be effective therapy for the majority of ER+ breast cancers.25,26 At the same time, 
our group’s data demonstrate that RNA signatures of immune activation are predictive of response 
to neoadjuvant chemotherapy, as described above.  Many chemotherapy agents are 
immunogenic,27 therefore may synergize with checkpoint inhibitor partners, but an understanding 
of the distinct immunologic effects of chemo- versus checkpoint-inhibitor therapy will be an 
important precursor to ultimately evaluating the promise of such combination regimens.  Taken 
together, these data indicate that in ER+ breast cancer in particular, it is important to separately 
evaluate potential immune-related biomarkers of response to (a) chemotherapy, (b) checkpoint 
inhibitor therapy, and (c) combined chemo-/checkpoint inhibitor therapy.  The 3 biopsies proposed 
here are all low-risk core biopsies of breast tissue, have been deemed acceptable by the patient 
advocate advisor to this protocol, and will facilitate biomarker assessment in each of these separate 
categories.  
2.7
PD-L1 expression in ER+ breast tumors
Prior data from 650 evaluable cases indicate that 20.1% of treatment-naïve ER+ primary breast 
tumors express PD-L1 with an H-score >100, while 22.1% of ER+ primary breast tumors 
express PD-L1 with H-score >0.28  Further, PD-L1 expression on ER+ primary tumors does not 
follow a normal distribution (Muenst S, personal communication).  There is no standard accepted 
definition of a threshold for PD-L1 positivity in ER+ breast cancers, or for breast cancers in 
general; a variety of different definitions are used in the literature.28-30

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2.8
Correlative Studies Background
2.8.1
Blood and Tissue Analysis
The development of immune signatures in breast cancer that go beyond simple histology is at a 
very early stage.  Given the promise of immune-based therapies in other solid malignancies such 
as melanoma and non-small cell lung cancer, with preliminary data demonstrating activity of 
immune checkpoint inhibition in advanced breast cancer participants,31,32 there is a great need to 
better characterize the immune profile of breast tumors across multiple disease subtypes, and at 
different points in the course of therapy.  Recently, more in-depth methods of immunologic 
profiling are being explored in breast cancer, for example mRNA expression of immune-activating 
and immunosuppressive factors, and these additional immune profiles also appear to have 
prognostic significance.18  The bulk of our correlative science in this trial focuses on characterizing 
a broad array of immune markers in early ER+ breast cancer before, during, and after therapy, 
exploring baseline levels and dynamic changes over time.
In melanoma, the solid malignancy currently at the forefront of understanding the anti-tumor 
immune response, investigation into expression of immune mediators in the peripheral blood is at 
an early phase.33  As a correlative study to this trial, we will characterize the immune marker 
profile of peripheral blood mononuclear cells (PBMCs) in enrolled breast cancer Participants, both 
at baseline and while on therapy.  Peripheral blood will be monitored for T cell, B cell, NK, and 
NK T cells markers by flow cytometry.  These include CD45RA (naïve T cells), CD45RO 
(memory), CD16 and CD56 (NK), CD19 (B cell), CD25 and CD69 activation, CD44 and Inducible 
costimulator (ICOS).  We will determine if "global" CD3/4/8 T cell activation occurs by flow 
cytometry. CD83 and CD86 subpopulations of cells will be assessed for markers of T cell 
activation.
Given the demonstrated clinical significance of TILs in breast cancer specimens, we will 
investigate whether there is a peripheral marker whose level corresponds to TIL percentage, or to 
a different immune marker in the tumor microenvironment.  These correlative projects are made 
possible by collaboration with Drs. Scott Rodig and Evisa Gjinin, and Mariano Severgnini, all of 
whom are lab scientists with extensive experience with immune profiling in melanoma.  Further 
details can be found in Section 9.
2.8.2
Microbiome Analysis
Breast Cancer (BC) is the most frequently diagnosed cancer and the second cause of cancer 
death in American women42.  In the advanced setting, despite multiple available systemic 
therapies, virtually all patients will die from their disease.  Thus, the exploration of new 
treatments, such as immune checkpoint inhibitors (ICI), including pembrolizumab, is imperative.
An increasing body of preclinical and clinical evidence suggests that breast cancer is an 
immunogenic malignancy43.  It is now recognized that a fraction of breast tumors, mainly triple-
negative breast cancer (TNBC), have substantial lymphocyte infiltration, and that this pathologic 
feature has prognostic implications44.  Early clinical trials assessing the efficacy of PD-1/PD-L1 
inhibitors given as monotherapy showed that only a small fraction of patients derive benefit from 

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immunotherapy with an approximate 20% objective response rate (ORR) among patients with 
PDL1+ TNBC45,46, and a 12% ORR among those with PDL1+ hormone receptor (HR)-positive 
BC47.  Therefore, new research approaches combining therapeutic agents aiming to boost 
antitumor immunity, as well as developing predictive biomarkers of response, are needed to 
increase the rates of clinical success of immunotherapy in BC.
In this context, the gut microbiota has been recognized as a modulator of immune system 
development48. Healthy individuals have microbial populations in their intestinal tract that vary 
markedly in composition49,50.  The diversity of intestinal microbiota represents a significant 
challenge to the host’s immune defenses, which must balance immune tolerance of beneficial 
microbes with inflammatory responses against pathogens.  Alterations in the gut microbiota and 
their resulting interactions with intestinal epithelium and the host immune system are associated 
with many disease, including cancer51.  Recently, two preclinical studies provided to ICI, raising 
the possibility that stool microbiota could be used as biomarker predictors of efficacy to 
immunotherapy52,53.  Interestingly, postmenopausal women with breast cancer have altered 
composition and low diversity of their gut microbiota compared to healthy controls54.
Identification of biomarkers that predict response to ICI-based therapies can spare de novo 
resistant patients from the unnecessary risks of immune-related adverse events.  In addition, the 
identification of bacterial species associated with response could open new strategies to 
maximize the clinical benefit of cancer immunotherapy through the modulation of gut 
microbiota.
This correlative project is made possible by collaboration with the BWH/Harvard Cohorts 
Biorepository and 
. Further details can be found in Section 9.  
3.
PARTICIPANT SELECTION
Participants must meet the following criteria on screening examination to be eligible to
participate in this study.
3.1
Eligibility Criteria 
3.1.1
Participants must have histologically or cytologically confirmed invasive breast cancer.
3.1.2
Participants must have operable breast cancer, with tumors greater than or equal to 2 cm in 
size; Participants must not have any evidence of distant metastatic disease. Inflammatory 
breast cancer is permitted. 
3.1.3
All confirmed invasive disease must have been tested for ER, PR, and HER2 and 
participants must have hormone receptor-positive, HER2-negative breast cancer (ER>1% 
or PR>1%, AND HER2-negative per ASCO CAP guidelines, 2013).
3.1.4
Participants with multicentric, multifocal, and/or contralateral cancers are allowed as long 
as one lesion meets eligibility and no biopsied tumor is HER2+.

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3.1.5
Prior systemic therapy: No prior chemotherapy, biologic therapy, hormonal therapy or 
investigational therapy for this operable breast cancer.
3.1.6
Prior radiation therapy: No prior radiation to the ipsilateral breast.
3.1.7
The participant is 18 years old
3.1.8
The participant has an Eastern Cooperative Oncology Group (ECOG) performance status 
≤1 (see Appendix A)
3.1.9
Participants must have normal organ and marrow function as defined below:

Absolute neutrophil count 1500/mm3

Platelets 100,000/mm3

Hemoglobin 9 g/dL

Total Bilirubin 1.5 mg/dL (< 2.0 in participants with known Gilbert’s 
syndrome)

Serum creatinine 1.5 mg/dL OR calculated GFR 60mL/min

Alanine aminotransferase (ALT) and aspartate aminotransferase (AST)  2.5 
times the upper limit of normal.

International normalized ratio (INR) or Prothrombin Time (PT) <1.5 times the 
upper limit of normal unless subject is receiving anticoagulant therapy, as long 
as PT or PTT is within therapeutic range of intended use of anticoagulants.

Activated Partial Thromboplastin Time (aPTT) <1.5 times the upper limit of 
normal unless subject is receiving anticoagulant therapy, as long as PT or PTT 
is within therapeutic range of intended use of anticoagulants.
3.1.10 The participant is capable of understanding and complying with the protocol and has signed 
the informed consent document.
3.1.11 The participant must be willing to undergo the three required research biopsies over the 
course of protocol therapy.  Participants who undergo an attempted research biopsy 
procedure for the purpose of this protocol, and in whom inadequate tissue is obtained, are 
not required to undergo a repeat biopsy in order to continue on protocol.  
3.1.12 The effects of pembrolizumab on the developing human fetus are unknown. For this reason, 
both women and men of child-bearing potential must agree to use adequate contraception 
(Section 5.5.2) starting with the first dose of study therapy and for the duration of study 
participation, through 120 days after the last dose of study medication.  
Note: Abstinence is acceptable if this is the usual lifestyle and preferred contraception for 
the subject.  Should a woman become pregnant or suspect she is pregnant while she or her 
partner is participating in this study, she should inform her treating physician immediately.  
While on the study, women may not breast-feed.  Women of childbearing potential are 
defined as those who have not been surgically sterilized or have not been free from menses 
for > 1 year.
3.1.13 Female subject of childbearing potential should have a negative urine or serum pregnancy 
test within 7 days prior to receiving the first dose of study medication.  If the urine test is 
positive or cannot be confirmed as negative, a serum pregnancy test will be required.
3.1.14 Participants on bisphosphonates may continue receiving bisphosphonate therapy during 
study treatment.

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3.2
Exclusion Criteria
3.2.1
The participant has received prior pembrolizumab or any other anti-PD-1, anti-PD-L1, or 
anti-PD-L2 therapy, or has participated in any prior studies involving pembrolizumab
3.2.2
Hypersensitivity to pembrolizumab or any of its excipients.
3.2.3
The participant has any history or evidence of active, non-infectious pneumonitis or 
interstitial lung disease.
3.2.4
The participant has an uncontrolled intercurrent illness including, but not limited to, 
uncontrolled hypertension, unstable angina pectoris, uncontrolled cardiac arrhythmia, 
congestive heart failure (New York Heart Association Class III or IV; see Appendix B), 
active ischemic heart disease, myocardial infarction within the previous six months, 
uncontrolled diabetes mellitus, chronic liver or renal disease, or severe malnutrition.
3.2.5
Concurrent use of potent CYP3A4 inhibitors (see Appendix C), such as ketoconazole and 
erythromycin, should be avoided during the study treatment with nab-paclitaxel.
3.2.6
Pregnant women are excluded from this study because pembrolizumab has the potential 
for teratogenic or abortifacient effects.  Because there is an unknown but potential risk for 
adverse events in nursing infants secondary to treatment of the mother with 
pembrolizumab, breastfeeding should be discontinued if the mother is treated with 
pembrolizumab.
3.2.7
Active infection requiring intravenous antibiotics at week 1 day 1.
3.2.8
Individuals with a history of a second malignancy are ineligible except for the following 
circumstances.  Individuals with a history of other malignancies are eligible if they have 
been disease-free for at least 5 years and are deemed by the investigator to be at low risk 
for recurrence of that malignancy. Individuals with the following cancers are eligible if 
diagnosed and treated within the past 5 years: cervical cancer in situ, and non-melanoma 
cancer of the skin.  Participants with other cancers diagnosed within the past 5 years and 
felt to be at low risk of recurrence should be discussed with the study sponsor to determine 
eligibility.
3.2.9
The participant has a medical condition that requires chronic systemic steroid therapy or 
any other form of immunosuppressive medication including disease modifying agents.  
Replacement therapy (eg., thyroxine, insulin, or physiologic corticosteroid replacement 
therapy for adrenal or pituitary insufficiency, etc.) is not considered a form of systemic 
treatment.
3.2.10 The participant has an active autoimmune disease or a documented history of autoimmune 
disease or syndrome that requires systemic steroids or immunosuppressive agents.
3.2.11 The participant is known to be positive for Hepatitis B surface antigen, or Hepatitis C RNA. 
Testing for screening is not required.   
3.2.12 Known HIV-positive participants.  HIV-positive patients on combination antiretroviral 
therapy are ineligible because of the potential for pharmacokinetic interactions with 
pembrolizumab.  In addition, these participants are at increased risk of lethal infections 
with bone marrow suppressive therapy, i.e. nab-paclitaxel.  Appropriate studies will be 
undertaken in participants receiving combination antiretroviral therapy when indicated. 
Testing for screening is not required. 
3.2.13 The participant has received a live vaccine within 28 days of planned start of study therapy.  
Note: seasonal influenza vaccines for infection are generally inactivated flu vaccines and 
are allowed; however intranasal influenza vaccines (i.e. Flu-Mist ®) are live attenuated 
vaccines, and are not allowed.

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3.3
Inclusion of Women and Minorities
Both men and women of all races and ethnic groups are eligible for this trial.
4.
REGISTRATION PROCEDURES
4.1
General Guidelines for DF/HCC Institutions
Institutions will register eligible participants in the Clinical Trials Management System (CTMS) 
OnCore.  Registrations must occur prior to the initiation of protocol therapy. Any participant not 
registered to the protocol before protocol therapy begins will be considered ineligible and 
registration will be denied.
The following registration/randomization procedures should be followed:

An investigator will confirm eligibility criteria and a member of the study team will 
complete the protocol-specific eligibility checklist.

The eligibility checklist(s) and all pages of the consent form(s) will be faxed to the ODQ 
at 
.

The ODQ Registrar will (a) review the eligibility checklist, (b) register the participant on 
the protocol, and (c) randomize the participant.

An email confirmation of the registration and/or randomization will be sent to the Overall 
PI, study coordinator(s) from the Lead Site
Following registration, participants may begin protocol therapy. Issues that would cause treatment 
delays should be discussed with the Overall Principal Investigator (PI). If a participant does not 
receive protocol therapy following registration, the participant’s registration on the study must be 
canceled. Registration cancellations must be made in OnCore as soon as possible.
4.2
Registration Process for DF/HCC Institutions
DF/HCC Standard Operating Procedure for Human Subject Research Titled Subject Protocol 
Registration (SOP #: REGIST-101) must be followed.  
4.3
General Guidelines for Other Investigative Sites
N/A

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4.4
Registration Process for Other Investigative Sites
N/A
5.
TREATMENT PLAN
5.1
Treatment Regimen
This is a pilot study examining biomarker changes over the course of treatment with nab-paclitaxel, 
pembrolizumab, or both in hormone receptor-positive (HR+) breast cancer.  A baseline research 
biopsy (biopsy 1) is required.  After registration, participants will be randomized to receive a run-in 
of either two weeks of nab-paclitaxel (cohort A) or one dose of pembrolizumab (cohort B) 
monotherapy.  A post-monotherapy biopsy (biopsy 2) will then be performed.  Participants will 
then receive combination nab-paclitaxel (administered weekly) and pembrolizumab (administered 
every 3 weeks) for a total of 15 weeks (cohort A) or 14 weeks (cohort B).  At completion, each 
patient will have received 12 doses of weekly nab-paclitaxel, and 5 doses of every-3-week 
pembrolizumab.
Treatment will be administered on an outpatient basis.  Reported adverse events and potential risks 
are described in Section 7.1.  Appropriate dose modifications are described in Section 6.  Details 
of the regimen are described in Table 1.  No investigational or commercial agents of therapies 
other than those described below may be administered with the intent to treat the participant’s 
malignancy.
Table 1: Regimen description
Regimen Description
Agent
Premedications; 
Precautions
Dose
Route
Schedule
Pembrolizumab
Not routinely 
necessary unless 
prior infusion 
reaction.
200 mg, at 
a final 
concentrati
on of 1 
mg/mL to 
10 mg/mL 
in NS or 
D5
IV over 
approximately 
30 minutes 
(range: 25-40 
minutes).  
Please refer to 
Section 8.1.4 
for compatible 
infusion set 
materials 
including in-
line filter.  
Infuse prior to 
starting nab-
paclitaxel 
infusion.
Day 1, 
every 3 
weeks

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Nab-paclitaxel
Not routinely 
necessary unless 
prior infusion 
reaction
125 mg/m2 
in NS*
IV over 30 
minutes.**  
Start nab-
paclitaxel 
infusion after 
pembrolizumab 
infusion is 
complete.
Day 1, 
weekly
*Dose reductions may be made as per Table 4.  Further details about dose reductions 
can be found in Sections 6.2 and 6.3.
**Limiting the infusion of nab-paclitaxel to 30 minutes, as directed, decreases the 
likelihood of infusion-related reactions
5.1.1
Treatment Schedule – Cohort A
Participants randomized to cohort A will undergo a baseline biopsy (biopsy 1), then start treatment 
with a 2-week run in of weekly nab-paclitaxel monotherapy, followed by a second biopsy post-
monotherapy (biopsy 2).  On week 3, nab-paclitaxel will be continued, and pembrolizumab will 
begin its every-3-week dosing.  Weekly nab-paclitaxel will continue for a total of 12 weeks.  
Every-3-week pembrolizumab will be administered for 5 doses total (weeks 3, 6, 9, 12, 15).  A 
biopsy on doublet therapy (biopsy 3) will be obtained between weeks 6 and 7.  Neoadjuvant 
therapy will complete at week 15, with the fifth and final dose of pembrolizumab.
5.1.2
Treatment Schedule – Cohort B
Participants randomized to cohort B will undergo a baseline biopsy (biopsy 1), then start treatment 
with a 2-week run in of pembrolizumab monotherapy, followed by a second biopsy post-
monotherapy (biopsy 2).  On week 3, weekly nab-paclitaxel will start, and continue for a total of 
12 weeks.  Every-3-week pembrolizumab will be administered for 5 doses total (weeks 1, 4, 7, 10, 
13).  A biopsy on doublet therapy (biopsy 3) will be obtained between weeks 6 and 7.  Neoadjuvant 
therapy will complete at week 14, with the twelfth and final dose of nab-paclitaxel.
5.2
Pre-Treatment Criteria
5.2.1
Screening for trial eligibility
Day -28 to Day 1:  Screening Visit
Eligibility and exclusion criteria are provided in Section 3.  These criteria will be assessed within 
28 days of registration to establish eligibility and baseline values.
Informed consent will be obtained after the study has been fully explained to the participant and 
before the conduct of any research screening procedures.  If screening assessments occur within 3 
days before start of study treatment, then they may serve as the Week 1 Day 1 visit labs.
Demographic information and baseline characteristics will be collected at the Screening Visit.  
Standard demographic parameters include age, sex, and race/ethnicity (recorded in accordance 
with prevailing regulations).  Hormone receptor and HER2 status will also be collected.

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Additional testing required, as per Section 3, is:  CBC with differential, basic metabolic panel 
which includes liver function tests (LFTs), coagulation panel, urine or serum HCG (in women of 
childbearing potential), testing for Hepatitis B/C and HIV, and EKG.  A urine or serum pregnancy 
test must be completed within 7 days prior to receiving the first dose of study medication.
A baseline tumor biopsy, obtained within 14 days before starting protocol therapy, is also required.  
Further details about collection and handling of tumor biopsy specimen can be found in Section 
9.1.1.
All participants will also be asked to provide archival tumor tissue (either paraffin blocks or 15-
20 unstained slides) from their diagnostic biopsy.  However, if archival tissue is not available or 
not evaluable, that will not be a basis to exclude the participant from any portion of the trial or the 
planned analysis. This tissue can be obtained at any point during the study and does not need to be 
collected during the screening window. 
5.2.2
On-Treatment Visits– Cohort A
Reasonable effort should be made to conduct study visits on the day scheduled (+/- 3 days).
Any changes from screening clinical evaluation findings that meet the definition of an AE will be 
recorded on the AE page of the eCRF.
Weekly assessments, weeks 1-12 day 1
If screening assessments occur within 3 days before start of study treatment, then they may serve 
as the Week 1 Day 1 visit.  Body weight should be documented on each treatment day such that 
drug dosing can be calculated accordingly.
Draw blood sample for:
Criteria to treat at week 1 day 1:

Absolute neutrophil count >1500/mm3

Platelets >100,000/mm3

ALT and AST <2.5 x ULN

Total bilirubin <1.5 x ULN (2.0 x ULN in a patient with well documented Gilbert 
syndrome)
Criteria to treat at day 1 of subsequent weeks:

Absolute neutrophil count >1000/mm3

Platelets >75,000/mm3

ALT and AST <3.0 x ULN

Total bilirubin <1.5 x ULN (2.0 x ULN in a patient with well documented Gilbert 
syndrome)

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-
CBC with differential
-
Basic metabolic panel
-
LFTs (ALT, AST, alkaline phosphatase, total bilirubin)
Record:
-
Height/weight (height at week 1 day 1 only)
-
Vital signs
Review all laboratory results before administering study treatment.
Every-3-week assessments, weeks 3-15 day 1 (prior to pembrolizumab dosing; weeks 3, 6, 9, 12, 
15)
The following assessments should be performed on the indicated weeks, in addition to the standard 
weekly assessments listed above. If a pembrolizumab dose(s) is held, the assessments below 
should move to coincide with the pembrolizumab infusions. 
Draw blood sample for:
-
TSH and free T4
Record:
-
Weight
-
Vital signs
-
Physical exam
-
Concomitant medications
-
AEs or SAEs
Review all laboratory results (except TSH and T4) before administering study treatment.
The total dose of each drug will be calculated according to institutional standards.
5.2.3
On-Treatment Visits – Cohort B
Criteria to treat at week 1 day 1:

Absolute neutrophil count >1500/ mm3

Platelets >100,000/ mm3

ALT and AST <2.5 x ULN

Total bilirubin <1.5 x ULN (2.0 x ULN in a patient with well documented Gilbert 
syndrome)
Criteria to treat at day 1 of subsequent weeks:

Absolute neutrophil count >1000/mm3

Platelets >75,000/mm3

ALT and AST <3.0 x ULN

Total bilirubin <1.5 x ULN (2.0 x ULN in a patient with well documented Gilbert 
syndrome)

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Reasonable effort should be made to conduct study visits on the day scheduled (+/- 3 days).
Any changes from screening clinical evaluation findings that meet the definition of an AE will be 
recorded on the AE page of the eCRF.
Every-3-week assessments, weeks 1-13 day 1 (prior to pembrolizumab dosing; weeks 1, 4, 7, 10, 
13)
The following assessments should be performed on the indicated weeks, in addition to the standard 
weekly assessments listed below. If a pembrolizumab dose(s) is held, the assessments below 
should move to coincide with the pembrolizumab infusions.
If screening assessments occur within 3 days before start of study treatment, then they may serve 
as the baseline Week 1 Day 1 visit and screening tests do not need to be repeated.  Body weight 
should be recorded on each treatment day such that drug dosing can be calculated accordingly.
Draw blood sample for:
-
TSH and free T4
Record:
-
Height/weight (height on week 1 day 1 only)
-
Vital signs
-
Physical exam
-
Concomitant medications
-
AEs or SAEs
Review all laboratory results (except TSH and T4) before administering study treatment.
Weekly assessments, weeks 3-14 day 1
Draw blood sample for:
-
CBC with differential
-
Basic metabolic panel
-
LFTs (ALT, AST, alkaline phosphatase, total bilirubin)
Record:
-
Weight
-
Vital signs
Review all laboratory results before administering study treatment.
The total dose of each drug will be calculated according to institutional standards.
5.2.4
Additional On-Treatment Assessments – Both Cohorts
Biopsies
Three breast tumor biopsies should be collected at the following time points:
1. Biopsy 1: at baseline, within 14 days prior to week 1 day 1 of protocol therapy

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2. Biopsy 2: after monotherapy, within 3 days prior to week 3 day 1 (while the allowed biopsy 
window is 3 days prior to week 3 day 1, it is preferred that the biopsy be performed as close 
to week 3 day 1 as possible—i.e. 0-1 days prior to week 3-day 1 treatment is most 
preferred)
3. Biopsy 3: after doublet therapy, within 3 days prior to week 7 day 1
A biopsy should also be obtained in participants who go off study for progressive disease, and in 
participants in whom treating physicians choose to give additional chemotherapy after protocol 
therapy, instead of proceeding to surgery. Additional instructions for obtaining a fourth tissue 
sample at the time of breast surgery are below.
Specific instructions for tumor biopsy handling are described in Section 9.1.1.
Physical Examinations
A physical examination, including breast examination, should be performed and documented at all 
specified protocol visits (see Section 10, Study Calendar). 
Patients who go off study for progressive disease, and/or undergo additional non-trial 
chemotherapy before surgery
As above, tumor biopsies should be obtained in patients who go off study for progressive disease, 
and in patients in whom treating physicians choose to give additional chemotherapy after protocol 
therapy, instead of proceeding to surgery.
Tumor Staging - Breast MRI, mammogram, or breast ultrasound 
All participants are required to have a MRI, mammogram, or ultrasound performed at screening 
(within 28 days prior to start of study treatment) and at pre-surgery (2-3 weeks after study treatment 
ends). Breast imaging must include imaging of the ipsilateral axilla. MRI is strongly 
recommended, although other imaging modalities (mammogram, ultrasound) are permitted if 
practical or financial considerations preclude MRI, as long as the target lesion can be adequately 
measured.   This same imaging modality must be used at screening and prior to surgery to assess 
radiographic tumor response.
Whole-Body Staging - CT scans/bone scan
It is recommended, but not required that all participants with anatomic Stage IIa disease and above 
(by AJCC 8th edition) will have CT scans of chest, abdomen and pelvis and bone scans, or PET-
CT scans, performed during screening to rule out metastatic disease.
Surgical Assessment
All participants will be seen and examined by the treating surgeon at Screening and at the Pre-
Operative Visit.  Each visit will include a clinical breast and lymph node examination and review 
of the imaging studies (mammogram, MRI, and any other radiographic method) of the breast and 
axilla.  After examining the subject and reviewing the pertinent radiographic studies at the 
Screening visit, the surgeon will determine whether the subject is a candidate for potentially 
curative surgery. At both the Screening and Pre-Operative visits, the surgeon will also determine 
whether subject is eligible for breast conservation surgery.  If the subject is not a breast 

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conservation candidate, the reason(s) will be documented in the CRF (multicentric tumor, tumor 
location, tumor size, other).
Axillary Assessment
An axillary assessment will be performed at screening.  Ipsilateral axillary lymph nodes will be 
assessed as clinically normal or clinically suspicious by physical examination and will be assessed 
as clinically normal or clinically suspicious independently by imaging. Axillary imaging and/or 
biopsy do not need to be repeated if performed prior to the screening period. Participants with 
suspicious nodes documented by physical exam OR by imaging will have a biopsy of the nodes 
(fine needle aspirate or core needle biopsy). If clinical evaluation and biopsy results are discordant, 
the biopsy may be repeated at the discretion of the Investigator.  
Immediate Post-Surgical Tumor Sampling
Formalin-fixed paraffin embedded tumor blocks as well as fresh tissue from the surgical specimen 
should be obtained.  Details of this process are described in Section 9.1.2.
5.3
Agent Administration
5.3.1
Pembrolizumab
Pembrolizumab administration
Merck will provide the investigator with an adequate supply of pembrolizumab.  Pembrolizumab 
will be administered by trained medical personnel at the investigational site.  Treatment 
compliance will be monitored through documentation of study treatment administration in the 
participant’s medical record.
Pembrolizumab will be administered in clinic on day 1 (+/- 3 days) of weeks 3, 6, 9, 12, and 15 
(cohort A) or day 1 (+/- 3 days) of weeks 1, 4, 7, 10, and 13 (cohort B).  It will be administered as 
a 30-minute IV infusion.  Sites should make every effort to target infusion timing to be as close to 
30 minutes as possible.  However, given the variability of infusion pumps from site to site, a 
window of -5 and + 10 minutes is permitted (i.e. infusion time is 30 minutes:  -5 min/ +10 min).
Pembrolizumab should be administered prior to nab-paclitaxel administration.  There should be 
no overlap in timing of the two administrations.
5.3.2
Nab-paclitaxel
Nab-paclitaxel administration
Please refer to the FDA-approved package insert for nab-paclitaxel for product information, 
extensive preparation instructions, and comprehensive list of adverse events.
Nab-paclitaxel will be administered as an intravenous infusion over 30 minutes.  Filters are not 
required for preparation or administration of nab-paclitaxel.  If filters are used as part of 
institutional procedure, the pore size must be ≥ 15 microns.

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5.3.3
Other Modality(ies) or Procedures
N/A
5.3.4
Investigational Imaging Agent Administration
N/A
5.4
Definition of Dose-Limiting Toxicity (DLT) 
Dose-limiting toxicity is defined as any of the following events occurring within 21 days 
(3 weeks_ after the first dose of therapy, if judged by the investigator to be possibly, 
probably, or definitely related to study drug administration:

Death

Asymptomatic grade 4 hematologic toxicity lasting ≥14 days unless deemed by 
the investigator to be clinically insignificant

Grade 4 thrombocytopenia of any duration

≥ Grade 3 Febrile neutropenia 

≥ Grade 3 Thrombocytopenia if associated with bleeding

≥ Grade 3 elevation in AST or ALT associated with a grade 2 elevation in 
bilirubin that is at least possibly related to study drug (Hy’s Law) 

≥ Grade 3 non-hematologic laboratory value if:
o
Medical intervention is required to treat the patient, or
o
The abnormality leads to hospitalization, or
o
The abnormality persists >7 days
Excluding:

Alkaline phosphatase <10.0x ULN in a patient with grade 2 
alkaline phosphatase elevation at baseline as a result of bone 
metastasis 

Any laboratory values deemed by the investigator to be clinically 
insignificant

≥ Grade 3 pneumonitis of any duration

≥ Grade 3 Fatigue lasting >5 days

> Grade 3 other non-laboratory toxicity lasting >3 days despite optimal supportive 
care, excluding the following:
o
Alopecia of any grade
DLTs will be assessed during the DLT assessment window (lasting for 21 days or 3 
weeks after initiation of study therapy).  
Management and dose modifications associated with the above adverse events are 
outlined in Section 6.

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Number of Participants with DLT 
in a Given Arm (Cohort A or B)
Enrollment Decision
0 -1 out of 6
Continue trial enrollment
>2 out of 6 
Halt trial enrollment
5.5
General Concomitant Medication, Supportive Care Guidelines, and Contraception Guidelines
Medications or vaccinations specifically prohibited in the exclusion criteria are not allowed during 
the ongoing trial.  If there is a clinical indication for one of these or other medications or 
vaccinations specifically prohibited during the trial, discontinuation from trial therapy or 
vaccination may be required.  The Principal Investigator should discuss any questions regarding 
this with the Merck Clinical team.  The final decision on any supportive therapy or vaccination 
rests with the Principal Investigator and/or the participants treating physician. 
Acceptable Concomitant Medications
All treatments that the investigator considers necessary for a participant’s welfare may be 
administered at the discretion of the investigator in keeping with the community standards of 
medical care.
Prohibited Concomitant Medications
Participants are prohibited from receiving the following therapies during the Screening and 
Treatment Phase of this trial:

Antineoplastic systemic chemotherapy or biological therapy 

Immunotherapy not specified in this protocol

Chemotherapy not specified in this protocol

Biologic or targeted agents not specified in this protocol

Investigational agents other than pembrolizumab

Radiation therapy

Any systemically active oral, injected, or implanted hormonal method of contraception 
except for progesterone coated intrauterine devices (IUDs) that had been previously 
implanted.

Estrogen replacement therapy.

Live vaccines within 28 days prior to the first dose of trial treatment and while 
participating in the trial.  Examples of live vaccines include, but are not limited to, the 
following: measles, mumps, rubella, varicella/zoster, yellow fever, rabies, BCG, and 
typhoid vaccine. 

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
Systemic glucocorticoids for any purpose other than to modulate symptoms from an 
event of suspected immunologic etiology.  The use of physiologic doses of 
corticosteroids may be approved after consultation with the Sponsor.
Participants that, in the assessment by the investigator, require the use of any of the 
aforementioned treatments for clinical management should be removed from the trial.  
Participants may receive other medications that the investigator deems to be medically 
necessary.
Care should be taken with concomitant use of strong CYP3A4 inhibitors/inducers (e.g., 
ketoconazole and itraconazole; see Appendix C) and nab-paclitaxel. An alternate medication with 
no or minimal potential to inhibit CYP3A4 should be considered. If a strong CYP3A4 inhibitor is 
co-administered with nab-paclitaxel, Participants should be closely monitored for adverse 
reactions.
The exclusion criteria section describes other medications which are prohibited in this trial.
There are no prohibited therapies during the Post-Treatment Follow-up Phase.
5.5.1
Supportive Care Guidelines – general medications
The following treatments are permitted throughout the duration of the study treatment phase and 
during follow-up:

Standard therapies for pre-existing medical conditions unless listed as prohibited therapy 
below. Any medication intended solely for supportive care (e.g., analgesics, anti-diarrheal, 
anti-depressants) may be used at the investigator’s discretion.  Antiemetics and 
anti-diarrheal medications should not be administered prophylactically before initial 
treatment with study drugs.  At the discretion of the investigator, prophylactic antiemetic 
and anti-diarrheal medication(s) may be used as per standard clinical practice before 
subsequent doses of study drugs.

Hematopoietic growth factors (e.g., G-CSF, granulocyte macrophage colony stimulating 
factor) may be used at investigator’s discretion for the primary prophylaxis and/or 
management of treatment-emergent neutropenia and/or for secondary prophylaxis as per 
NCCN/European Society for Medical Oncology guidelines 34,35 or local standard practice. 
However, treatment with granulocyte-colony stimulating factors will not permitted during 
the first two weeks of protocol therapy unless the patient has febrile neutropenia and the 
physician considers its use as clinically indicated. It will be left to the treating physician 
choice from week 3 onwards. 

Bisphosphonate or denosumab therapy for osteoporosis or osteopenia to be used in 
accordance with the approved labeled indication and/or nationally recognized treatment 
guidelines.  Participants already receiving bisphosphonate/denosumab at the time of study 
entry can continue the treatment.

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
Anticoagulants - Anticoagulation with heparin, heparin derivatives, and/or warfarin may 
be given at the discretion of the treating physician. Coagulation parameters should be 
checked at least once monthly, or more frequently at discretion of treating physician. 

Pain medications administered per standard clinical practice are acceptable while the 
patient is enrolled in the study.
Participants who experience toxicities should be treated symptomatically as clinically indicated.  
Medications that are considered necessary for the subject’s welfare and that are not expected to 
interfere with the evaluation of study treatment or be restricted may be given at the discretion of 
the investigator.  Ancillary treatments will be given as medically indicated.
5.5.2
Contraception Guidelines
Pembrolizumab may have adverse effects on a fetus in utero.  Furthermore, it is not known if 
pembrolizumab has transient adverse effects on the composition of sperm.  
For this trial, male participants will be considered to be of non-reproductive potential if they have 
azoospermia (whether due to having had a vasectomy or due to an underlying medical condition).  
Female participants will be considered of non-reproductive potential if they are either: 
(1) postmenopausal (defined as at least 12 months with no menses without an 
alternative medical cause; in women < 45 years of age a high follicle stimulating 
hormone (FSH) level in the postmenopausal range may be used to confirm a post-
menopausal state in women not using hormonal contraception or hormonal 
replacement therapy. In the absence of 12 months of amenorrhea, a single FSH 
measurement is insufficient.); 
OR 
(2) have had a hysterectomy and/or bilateral oophorectomy, bilateral salpingectomy or 
bilateral tubal ligation/occlusion, at least 6 weeks prior to screening; 
OR 
(3) has a congenital or acquired condition that prevents childbearing.
Female and male participants of reproductive potential must agree to avoid becoming pregnant or 
impregnating a partner, respectively, while receiving study drug and for 120 days after the last 
dose of study drug by complying with one of the following:  
(1) practice abstinence† from heterosexual activity; 
OR 
(2) use (or have their partner use) acceptable contraception during heterosexual 

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activity.  
Acceptable methods of contraception are‡:
Single method (one of the following is acceptable):

intrauterine device (IUD)

vasectomy of a female subject’s male partner 

contraceptive rod implanted into the skin
 
Combination method (requires use of two of the following):

diaphragm with spermicide (cannot be used in conjunction with cervical 
cap/spermicide)

cervical cap with spermicide (nulliparous women only)  

contraceptive sponge (nulliparous women only) 

male condom or female condom (cannot be used together)

hormonal contraceptive: oral contraceptive pill (estrogen/progestin pill or 
progestin-only pill), contraceptive skin patch, vaginal contraceptive ring, or 
subcutaneous contraceptive injection
†Abstinence (relative to heterosexual activity) can be used as the sole method of 
contraception if it is consistently employed as the subject’s preferred and usual lifestyle 
and if considered acceptable by local regulatory agencies and ERCs/IRBs.  Periodic 
abstinence (e.g., calendar, ovulation, sympto-thermal, post-ovulation methods, etc.) 
and withdrawal are not acceptable methods of contraception. 
‡If a contraceptive method listed above is restricted by local regulations/guidelines, 
then it does not qualify as an acceptable method of contraception for participants 
participating at sites in this country/region.
Participants should be informed that taking the study medication may involve unknown risks to 
the fetus (unborn baby) if pregnancy were to occur during the study.  In order to participate in the 
study participants of childbearing potential must adhere to the contraception requirement 
(described above) from the day of study medication initiation (or 14 days prior to the initiation of 
study medication for oral contraception) throughout the study period up to 120 days after the last 
dose of trial therapy.  If there is any question that a subject of childbearing potential will not 
reliably comply with the requirements for contraception, that subject should not be entered into 
the study.
5.6
Additional Preoperative Chemotherapy
If there is clinical or radiographic evidence of significant residual disease after completion of 
protocol treatment, after a mandatory biopsy the participant may receive additional preoperative 
chemotherapy. It is strongly encouraged that if additional preoperative chemotherapy is being 
considered, that the case is discussed with the overall study primary investigator prior to biopsy. 
The fourth mandatory biopsy collection marks the end of protocol mandated chemotherapy; 

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however additional data will be collected to document additional chemotherapy and response to 
the additional chemotherapy.
5.7
Criteria for Taking a Participant Off Protocol Therapy
Treatment will continue for 15 weeks (cohort A) or 14 weeks (cohort B), or until one of the 
following criteria applies:

Disease progression (except as described above, in Section 5.2.4)

Intercurrent illness that prevents further administration of treatment

Unacceptable adverse event(s)

Participant demonstrates an inability or unwillingness to comply with the medication 
regimen and/or documentation requirements

Participant decides to withdraw from the protocol therapy

General or specific changes in the participant's condition render the participant 
unacceptable for further treatment in the judgment of the treating investigator
Participants will be removed from the protocol therapy when any of these criteria apply.  The 
reason for removal from protocol therapy, and the date the participant was removed, must be 
documented in the case report form (CRF) and taken off treatment in OnCore. Alternative care 
options will be discussed with the participant.
In the event of unusual or life-threatening complications, treating investigators must immediately 
notify 
the 
Core 
Site 
PI, 
 
 
 
 
 
 
.
 
5.8
Duration of Follow Up
The first post-surgery follow-up visit will be considered the participant's final in-clinic study visit.  
If breast surgery is not performed the participant’s final visit will be within 28 days after the last 
dose of protocol-specified therapy (i.e., nab-paclitaxel or pembrolizumab, whichever occurred 
later). 
Simplified post-surgery follow-up information will be subsequently collected. Decisions regarding 
choice of post-surgical treatment and disease assessments will be at the discretion of the treating 
team and not mandated by the protocol.  The investigator is not required to actively monitor 
participants for adverse events after the final visit.  However, the Overall PI should be notified if 
the investigator becomes aware of any death or other serious adverse event that is considered 
related to the study medication.

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Post-surgery follow-up information will be collected at assessments every 6 months until 5 years 
after surgery, or until a disease-free survival event.
Disease-free survival (DFS) will be defined from the time of randomization until the occurrence 
of the first of the following events:

Local/regional recurrence: a recurrent or new invasive ipsilateral breast cancer, invasive 
breast cancer in the axilla, regional lymph nodes, chest wall, or skin of the ipsilateral breast.

Contralateral invasive breast cancer,

Distant recurrence: metastatic disease that has either been biopsy confirmed or clinically 
diagnosed as recurrent invasive breast cancer. A single new lesion on a bone scan without 
evidence of lytic disease on x-ray and without symptoms does not in and of itself constitute 
distant recurrence, but multiple new bone lesions, or increased isotope uptake associated 
with new bone symptoms are more likely due to metastases. Bone metastases must be 
documented with x-rays and clinical description.

Death from any cause
In situ cancer is not included as DFS event. If a participant has in situ breast cancer (on the 
ipsilateral or contralateral side) diagnosed during follow-up before any of the DFS events above, 
then the participant should continue to be followed for DFS on study (even if she is given hormonal 
therapy after the in-situ diagnosis). These participants will be followed for survival.  
If a participant is diagnosed with a non-melanoma skin cancer or a cervical carcinoma in situ, 
he/she will continue on this study and continue to be followed for DFS. 
It is recommended that any disease-free survival event should be biopsied to confirm recurrent 
disease. Information on breast cancer status, new anti-cancer therapy, and new onset malignancy 
diagnoses will be collected via simplified CRFs.  Following an IDFS event, survival information 
(i.e., date and cause of death or last known alive date if not deceased and new onset malignancy 
information) will be collected.
5.9
Criteria for Taking a Participant Off Study
Participants will be removed from study when any of the following criteria apply:

Patient completed required follow-up

Lost to follow-up

Withdrawal of consent for data submission

Death
The reason for taking a participant off study, and the date the participant was removed, must be 
documented in the case report form (CRF).

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For Centralized Subject Registrations, the research team submits a completed Off Treatment/Off 
Study form to ODQ when a participant comes off study.  This form can be found on the ODQ 
website or obtained from the ODQ registration staff.
For Decentralized Subject Registrations, the research team updates the relevant Off Treatment/Off 
Study information in OnCore.
6.
DOSING DELAYS/DOSE MODIFICATIONS
Dose delays and modifications will be made as indicated in the following table(s). The descriptions 
and grading scales found in the revised NCI Common Terminology Criteria for Adverse Events 
(CTCAE) version 4.0 will be utilized for dose delays and dose modifications. A copy of the 
CTCAE version 4.0 can be downloaded from the CTEP website
 
 
Dosing interruptions are permitted in the case of medical / surgical events or logistical reasons not 
related to study therapy (e.g., elective surgery, unrelated medical events, patient vacation, and/or 
holidays). Participants should be placed back on study therapy within 3 weeks of the scheduled 
interruption, unless otherwise discussed with the Overall PI. The reason for interruption should be 
documented in the participant's study record.
Once doses are reduced, they may not be re-escalated.
General guidelines regarding dose modification:

If, in the opinion of the investigator, a toxicity is considered to be due solely to one 
component of the study treatment (i.e. pembrolizumab or nab-paclitaxel) and the dose 
of that component is delayed or modified in accordance with the guidelines below, the 
other component may be administered if there is no contraindication

If it is anticipated that nab-paclitaxel will be delayed by >3 weeks, then pembrolizumab 
should be given without the chemotherapy if there is no contraindication.

Nab-paclitaxel doses may be delayed and/or reduced and pembrolizumab may be 
delayed as a result of toxicities.  No dose reductions are allowed for pembrolizumab.

It is recommended that participants receive all planned doses of pembrolizumab and 
nab-paclitaxel. 
o
Nab-paclitaxel doses that are held should be made up at the completion of planned 
therapy, so as to not disturb the treatment schedule. 
o
Pembrolizumab doses may be delayed or made up at the completion of planned 
therapy. This is at the investigator’s discretion. If pembrolizumab doses are 
delayed, all other assessments assigned to specific Week numbers on the Required 
Data Table should remain the same.  
6.1
Management of toxicities attributable to pembrolizumab alone
 
Hepatotoxicity has been previously described in participants on both single agent pembrolizumab 

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and single agent nab-paclitaxel; therefore, management of this toxicity is addressed separately, in 
Section 6.3. 
For toxicities in this Section, which are attributable to pembrolizumab alone, only pembrolizumab 
should be held as directed.  It is permissible to continue nab-paclitaxel despite discontinuation of 
pembrolizumab in these cases.
Treating physicians may discontinue or hold Pembrolizumab for intolerable AEs regardless of 
grade and duration if it is in the best interest of the patient.
Adverse events (both non-serious and serious) associated with pembrolizumab exposure may 
represent an immunologic etiology.  These adverse events may occur shortly after the first dose or 
several months after the last dose of treatment.  Pembrolizumab must be withheld for drug-related 
toxicities and severe or life-threatening AEs as per Table 2 below.  As noted below the table, for 
recurrence of any grade 3 or higher event (exception: grade 2 or higher for pneumonitis), 
pembrolizumab must be permanently discontinued.
Table 2: Dose modification guidelines for pembrolizumab for drug-related adverse events
General instructions:
1. Corticosteroid taper should be initiated upon AE improving to less than or equal to Grade 1 baseline 
and continue to taper over at least 4 weeks.
2. For situations where pembrolizumab has been withheld, pembrolizumab can be resumed after AE 
has been reduced to less than or equal to Grade 1 or baseline and corticosteroid has been tapered. 
Pembrolizumab should be permanently discontinued if AE does not resolve within 12 weeks of last 
dose or corticosteroids cannot be reduced to ≤10 mg prednisone or equivalent per day within 12 
weeks. 
3. 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.
Immune-
related AEs
Toxicity 
grade or 
conditions 
(CTCAEv4.
0)
Action taken 
to 
pembrolizum
ab
irAE management with 
corticosteroid and/or 
other therapies 
Monitor and follow-up 
Grade 2
Withhold 
Pneumonitis 
Grade 3 or 
4, or 
recurrent 
Grade 2
Permanently 
discontinue
Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed 
by taper

Monitor participants for 
signs and symptoms of 
pneumonitis

Evaluate participants with 
suspected pneumonitis 
with radiographic imaging 
and initiate corticosteroid 
treatment

Add prophylactic 
antibiotics for 
opportunistic infections

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Grade 2 or 3
Withhold
Diarrhea / 
Colitis 
Grade 4
Permanently 
discontinue
Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed 
by taper

Monitor participants for 
signs and symptoms of 
enterocolitis (ie, diarrhea, 
abdominal pain, blood or 
mucus in stool with or 
without fever) and of 
bowel perforation 
(ie, peritoneal signs and 
ileus).

Participants with ≥ Grade 2 
diarrhea suspecting colitis 
should consider GI 
consultation and 
performing endoscopy to 
rule out colitis. 

Participants with 
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.
Grade 2
Continue
Consider 
administering 
corticosteroids (initial 
dose of 0.5 - 1 mg/kg 
prednisone or 
equivalent) followed 
by taper
AST / ALT 
elevation or 
Increased 
bilirubin
Grade 3 or 4 Withhold
Administer 
corticosteroids (initial 
dose of 1-2 mg/kg 
prednisone or 
equivalent) followed 
by taper

Monitor with liver function 
tests (consider weekly or 
more frequently until liver 
enzyme value returned to 
baseline or is stable

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Type 1 
diabetes 
mellitus 
(T1DM) or 
Hyperglycemi
a
Newly onset 
T1DM or 
Grade 3 or 4 
hyperglyce
mia 
associated 
with 
evidence of 
-cell 
failure
Withhold
Initiate insulin 
replacement therapy 
for participants with 
T1DM 
Administer anti-
hyperglycemic in 
participants with 
hyperglycemia 

Monitor participants for 
hyperglycemia or other 
signs and symptoms of 
diabetes.
Grade 2
Withhold
Hypophysitis
Grade 3 or 4 Withhold or 
permanently 
discontinue1 
Administer 
corticosteroids and 
initiate hormonal 
replacements as 
clinically indicated.  

Monitor for signs and 
symptoms of hypophysitis 
(including hypopituitarism 
and adrenal insufficiency) 
Grade 2
Continue 
Hyperthyroidi
sm 
Grade 3 or 4 Withhold or 
permanently 
discontinue1
Treat with non-
selective beta-blockers 
(eg, propranolol) or 
thionamides as 
appropriate 

Monitor for signs and 
symptoms of thyroid 
disorders. 
Hypothyroidis
m
Grade 2-4
Continue 
Initiate thyroid 
replacement hormones 
(eg, levothyroxine or 
liothyroinine) per 
standard of care

Monitor for signs and 
symptoms of thyroid 
disorders. 
Grade 2
Withhold 
Nephritis and 
Renal 
dysfunction
Grade 3 or 4 Permanently 
discontinue
Administer 
corticosteroids 
(prednisone 1-2 mg/kg 
or equivalent) 
followed by taper.

Monitor changes of renal 
function
Grade 1 or 2
Withhold
Myocarditis
Grade 3 or 4
Permanently 
discontinue
Based on severity of 
AE administer 
corticosteroids

Ensure adequate evaluation 
to confirm etiology and/or 
exclude other cause
Infusion 
Reaction2
Grade 3 or 4
Permanently 
discontinue
See Table 5

See Table 5
Intolerable/ 
persistent 
Grade 2
Withhold
All other 
immune-
related AEs
Grade 3
Withhold or 
discontinue 
based on the 
type of event.  
Events that 
Based on type and 
severity of AE 
administer 
corticosteroids 

Ensure adequate evaluation 
to confirm etiology and/or 
exclude other causes

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require 
discontinuatio
n include and 
not limited to:  
Gullain-Barre 
Syndrome, 
encephalitis
Grade 4 or 
recurrent 
Grade 3 
Permanently 
discontinue
1. Withhold or permanently discontinue pembrolizumab is at the discretion of the investigator or treating 
physician.  
2. See Table 5 for further guidance on all grades of pembrolizumab infusion reactions. 
NOTE: 
For participants with Grade 3 or 4 immune-related endocrinopathy where withhold of pembrolizumab is 
required, pembrolizumab may be resumed when AE resolves to ≤ Grade 2 and is controlled with 
hormonal replacement therapy or achieved metabolic control (in case of T1DM).  
Supportive care for pembrolizumab toxicity, particularly suspected immune-mediated toxicity
Participants should receive appropriate supportive care measures as deemed necessary by the 
treating investigator.  Suggested supportive care measures for the management of adverse events 
with potential immunologic etiology are outlined in Section 6. 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. For each disorder, attempts should be made to rule out other causes such 
as metastatic disease or bacterial or viral infection, which might require additional supportive care. 
The treatment guidelines are intended to be applied when the investigator determines the events to 
be related to pembrolizumab.
Note: if after the evaluation the event is determined not to be related, the investigator is instructed 
to follow the ECI reporting guidance (see Section 7.7.2).
It may be necessary to perform conditional procedures such as bronchoscopy, endoscopy, or skin 
photography as part of evaluation of the event.

Pneumonitis: 
o
Pembrolizumab should be permanently discontinued following any event of 
pneumonitis grade 2 or higher.
o
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.
o
For Grade 3-4 events, immediately treat with intravenous steroids.  Administer 
additional anti-inflammatory measures, as needed.

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o
Add prophylactic antibiotics for opportunistic infections in the case of prolonged 
steroid administration.

Diarrhea/Colitis: 
Participants 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).  
o
All participants 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.
o
For Grade 2 diarrhea/colitis that persists greater than 3 days, administer oral 
corticosteroids. 
o
For Grade 3 or 4 diarrhea/colitis that persists > 1 week, treat with intravenous 
steroids followed by high dose oral steroids.  
o
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)
o
For T1DM or Grade 3-4 Hyperglycemia

Insulin replacement therapy is recommended for Type I diabetes mellitus 
and for Grade 3-4 hyperglycemia associated with metabolic acidosis or 
ketonuria. 

Evaluate Participants with serum glucose and a metabolic panel, urine 
ketones, glycosylated hemoglobin, and C-peptide. 

Hypophysitis:
o
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. 
Replacement of appropriate hormones may be required as the steroid dose is 
tapered.
o
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. Replacement of 
appropriate hormones may be required as the steroid dose is tapered.

Hyperthyroidism or Hypothyroidism: 
Thyroid disorders can occur at any time during treatment. Monitor Participants 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.
o
Grade 2 hyperthyroidism events (and Grade 2-4 hypothyroidism):

In hyperthyroidism, non-selective beta-blockers (e.g. propranolol) are 
suggested as initial therapy.

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
In hypothyroidism, thyroid hormone replacement therapy, with 
levothyroxine or liothyronine, is indicated per standard of care.
o
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. Replacement of 
appropriate hormones may be required as the steroid dose is tapered.

Hepatic: (see associated dose modification guidelines for nab-paclitaxel in Section 6.3)
o
For Grade 2 events, monitor liver function tests more frequently until returned to 
baseline values (consider weekly).

Treat with IV or oral corticosteroids
o
For Grade 3-4 events, treat with intravenous corticosteroids for 24 to 48 hours. 
o
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:
o
For Grade 2 events, treat with corticosteroids.
o
For Grade 3-4 events, treat with systemic corticosteroids.
o
When symptoms improve to Grade 1 or less, steroid taper should be started and 
continued over no less than 4 weeks. 

Management of Infusion Reactions: Signs and symptoms usually develop during or 
shortly after drug infusion and generally resolve completely within 24 hours of completion 
of infusion. Table 3 below shows treatment guidelines for participants who experience an 
infusion reaction associated with administration of pembrolizumab.
Table 3: Infusion Reaction Treatment Guidelines for Pembrolizumab
NCI CTCAE Grade
Treatment
Premedication 
at 
subsequent 
dosing
Grade 1
Mild reaction; infusion interruption 
not indicated; intervention not 
indicated
Increase monitoring of vital signs as medically 
indicated until the subject is deemed medically 
stable in the opinion of the investigator.
None
Grade 2
Requires infusion interruption but 
responds promptly to symptomatic 
treatment (e.g., antihistamines, 
NSAIDS, narcotics, IV fluids); 
prophylactic medications indicated for 
< =24 hrs
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 subject 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 (e.g., from 100 
mL/hr to 50 mL/hr).  Otherwise dosing will be 
held until symptoms resolve and the subject 
should be premedicated for the next scheduled 
dose.
Participants who develop Grade 2 toxicity 
despite adequate premedication should be 
permanently discontinued from further trial 
treatment administration.
Subject may be premedicated 1.5h 
(± 30 minutes) prior to infusion of 
pembrolizumab (pembrolizumab) 
with:
Diphenhydramine 50 mg po (or 
equivalent dose of antihistamine).
Acetaminophen 500-1000 mg po 
(or equivalent dose of antipyretic).

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NCI CTCAE Grade
Treatment
Premedication 
at 
subsequent 
dosing
Grades 3 or 4
Grade 3:
Prolonged (i.e., not rapidly responsive 
to symptomatic medication and/or 
brief interruption of infusion); 
recurrence of symptoms following 
initial improvement; hospitalization 
indicated for other clinical sequelae 
(e.g., renal impairment, pulmonary 
infiltrates)
Grade 4:
Life-threatening; 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 subject is deemed medically 
stable in the opinion of the investigator.
Hospitalization may be indicated.
Subject is permanently discontinued from 
further trial treatment administration.
No subsequent dosing
Appropriate resuscitation equipment should be available in the room and a physician readily available during the period of drug 
administration.
6.2
Management of toxicities attributable to nab-paclitaxel alone
Hepatotoxicity has been previously described in participants on both single agent pembrolizumab 
and single agent nab-paclitaxel; therefore, management of this toxicity is addressed separately, in 
Section 6.3. 
For toxicities in this Section, which are attributable to nab-paclitaxel alone, concurrent holding of 
pembrolizumab is at the discretion of the treating physician, as described in the general guidelines 
at the start of this Section.  
Dose reduction guidelines for nab-paclitaxel are shown in Table 4, below. In instances where the 
direction is to immediately dose reduce nab-paclitaxel, it is at the investigator’s discretion if they 
would like to first hold nab-paclitaxel, followed by a dose reduction.  
Table 4: Nab-paclitaxel dose reduction levels
Dose Level
Nab-paclitaxel Dose
0
125 mg/m2 weekly
-1
100 mg/m2 weekly
-2
75 mg/m2 weekly
Further dose reductions warranted
Discontinue nab-paclitaxel. Continuation with 
pembrolizumab is at investigator discretion
Hematologic Toxicity
Absolute neutrophil count (ANC) must be >1000/μl and platelet count must be >75,000/ μl on day 
1 of each week (after week 1) in order to treat.  If these parameters are not met, treatment should 
be managed as listed below in Table 5.
At any time, if treatment is delayed or skipped for >3 weeks for hematologic toxicity (possibly, 
probably, or definitely related to nab-paclitaxel), discontinue nab-paclitaxel. Patients may continue 

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on study with pembrolizumab at the discretion of the treating investigator.
Table 5: Nab-paclitaxel dose reductions for hematologic toxicity
Event
Occurrence
Action to Be Taken
First
Decrease nab-paclitaxel by 
one dose level
OR
Add growth factor support to 
stay at current dose level.
This decision is at the 
investigator’s discretion. 
Second
Decrease nab paclitaxel by 
one dose level
Grade 3 or 4 febrile 
neutropenia
or
Delay of next week by >7 
days for nadir ANC <1000/μl
or
Nadir ANC<500/μl for >7 
days
Third
Discontinue nab-paclitaxel. 
Continuation with 
pembrolizumab is at 
investigator discretion
First
Decrease nab-paclitaxel by 
one dose level
Second
Decrease nab paclitaxel by 
one dose level
Nadir platelet count <75,000/ 
μl
Third
Discontinue nab-paclitaxel. 
Continuation with 
pembrolizumab is at 
investigator discretion
Neurotoxicity
Neurologic toxicity should be managed as instructed below, in Table 6.
At any time, if treatment is delayed or skipped for >3 weeks for neurologic toxicity (possibly, 
probably, or definitely related to nab-paclitaxel), discontinue nab-paclitaxel. Patients may continue 
on study with pembrolizumab at the discretion of the treating investigator.
Table 6: Nab-paclitaxel dose reductions for neurologic toxicity
Event
Occurrence
Action to Be Taken
Peripheral neuropathy grade 
2
First
Decrease nab-paclitaxel by 
one dose level
Second
Hold treatment until 
decreases to grade <1, then 
restart nab-paclitaxel at a 
reduction of one dose level
Third
Discontinue nab-paclitaxel. 

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Continuation with 
pembrolizumab is at 
investigator discretion
Peripheral neuropathy grade 
3
First
Hold treatment until 
decreases to grade <1, then 
restart nab-paclitaxel at a 
reduction of one dose level.
Second
Hold treatment until 
decreases to grade <1, then 
restart nab-paclitaxel at a 
reduction of one dose level
Third
Discontinue nab-paclitaxel. 
Continuation with 
pembrolizumab is at 
investigator discretion
Peripheral neuropathy grade 
4
Any
Discontinue nab-paclitaxel. 
Continuation with 
pembrolizumab is at 
investigator discretion
Other non-hematologic toxicity
Other toxicities not specifically outlined above should be managed as instructed below, in Table 
7.  Use of maximum supportive medical care is encouraged, within the parameters outlined in 
Section 5.5, concomitant medications and supportive care guidelines.
At any time, if treatment is delayed or skipped for >3 weeks for the same type of toxicity (possibly, 
probably, or definitely related to nab-paclitaxel), discontinue nab-paclitaxel. Patients may continue 
on study with pembrolizumab at the discretion of the treating investigator.
Table 7: Dose reductions for nab-paclitaxel for other toxicities
Grade
Occurrence
Action to Be Taken
3 or 4
First
Hold treatment until 
decreases to grade <2, then 
restart nab-paclitaxel at a 
reduction of one dose level.
Second
Hold treatment until 
decreases to grade <2, then 
restart nab-paclitaxel at a 
reduction of one dose level
Third
Discontinue nab-paclitaxel. 
Continuation with 
pembrolizumab is at 
investigator discretion
6.3
Management of hepatic toxicity attributable to both pembrolizumab and nab-paclitaxel

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Hepatotoxicity has been previously described in participants on both single agent pembrolizumab 
and single agent nab-paclitaxel.  Management of this toxicity is addressed in this Section. 
Event
Grade
Action To Be Taken
AST/ALT elevation
2 – first occurrence
Hold both drugs until lab 
elevation is grade 0 or 1, then 
restart both drugs (at the 
previous doses).  Recheck lab 
value weekly or as medically 
indicated.  Recommendations 
for supportive care (steroid 
dosing) are above, in Section 
6.1.  If toxicity takes >12 
weeks to resolve, permanently 
discontinue pembrolizumab.
2- second occurrence and 
beyond
Hold both drugs until lab 
elevation is grade 0 or 1, then 
restart nab-paclitaxel only (at 
the previous dose).  
Permanently discontinue 
pembrolizumab.  Recheck lab 
value weekly or as medically 
indicated.  Recommendations 
for supportive care (steroid 
dosing) are above, in Section 
6.1.  
3
Hold both drugs until lab 
elevation is grade 0 or 1, then 
restart nab-paclitaxel only, at 
dose level -1.  Permanently 
discontinue pembrolizumab.  
Recheck lab value weekly or 
as medically indicated.  
Recommendations for 
supportive care (steroid 
dosing) are above, in Section 
6.1.
4
Discontinue all study 
treatment permanently.  
Recommendations for 
supportive care (steroid 
dosing) are above, in Section 
6.1.  
Total bilirubin elevation (see 
legend for special 
considerations for Gilbert’s 
2 – first occurrence
Hold both drugs until lab 
elevation is grade 0 or 1, then 
restart both drugs (at the 

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Syndrome)1
previous doses).  Recheck lab 
value weekly or as medically 
indicated.  Recommendations 
for supportive care (steroid 
dosing) are above, in Section 
6.1.  If toxicity takes >12 
weeks to resolve, permanently 
discontinue pembrolizumab.
2- second occurrence and 
beyond
Hold both drugs until lab 
elevation is grade 0 or 1, then 
restart nab-paclitaxel only (at 
the previous dose).  
Permanently discontinue 
pembrolizumab.  Recheck lab 
value weekly or as medically 
indicated.  Recommendations 
for supportive care (steroid 
dosing) are above, in Section 
6.1.  
3 and 4
Discontinue all study 
treatment permanently.  
Recommendations for 
supportive care (steroid 
dosing) are above, in Section 
6.1.  
AST or ALT >3.0x upper 
limit of normal (ULN), AND 
total bilirubin >2.0x ULN
Discontinue all study 
treatment permanently.  
Recommendations for 
supportive care (steroid 
dosing) are above, in Section 
6.1.  
1In a patient with known Gilbert’s Syndrome, an additional elevation of 0.5 mg/dL in total bilirubin 
is allowed in each case.
7.
ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial.  The following 
list of reported and/or potential AEs (Section 7.1) and the characteristics of an observed AE 
(Section 7.2) will determine whether the event requires expedited reporting in addition to routine 
reporting.
7.1
Adverse Event Lists
7.1.1
Adverse Event Lists (s) for pembrolizumab
In the pembrolizumab monotherapy trials (P001/P002, P012, P013, and P028, plus the P011
monotherapy arm), the overall incidence of AEs ranged from 83.0% (73 of 88 participants in

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P012) to 100% (10 of 10 participants in P011). The most commonly reported AEs included
fatigue, diarrhea, decreased appetite, nausea, and anemia. The incidence of drug -related
AEs (DRAEs) ranged from 39.8% (35 of 88 participants in P013) to 80.0% (8 of 10 subjects in
P011). The most commonly reported DRAEs across all studies were nausea, fatigue, and
diarrhea. The incidence of Grade 3-5 DRAEs across studies ranged from 6.8% (6 of 88 in
P013) to 12.0% (187 of 1562 participants) in P001/P002. The most commonly reported
Grade 3-5 DRAEs were anemia, alanine aminotransferase increased, and aspartate
aminotransferase increased. Most participants who experienced an AE continued in the study,
with the incidence of AEs leading to discontinuation ranging from 1.9% (8 of 430 participants in
P028) to 12.3% (192 of 1562 participants in P001/P002). The majority of AEs leading to
discontinuation were not considered drug related. Discontinuations due to a DRAE were
infrequent and ranged from 0% (no participants in P011) to 4.5% (4 of 88 participants in P013). 
The
most commonly reported DRAEs leading to discontinuation were pneumonitis, alanine
aminotransferase increased, and aspartate aminotransferase increased.
List of AEs considered expected: 

Endocrine disorders: Adrenal insufficiency, Hyperthyroidism, Hypophysitis, 
Hypopituitarism, Hypothyroidism, Secondary adrenal insufficiency, Thyroid disorder

Eye disorders: Uveitis

Gastrointestinal disorders: Abdominal pain, Colitis, Diarrhea, Pancreatitis

General disorders and administration site conditions: Asthenia, Pyrexia

Hepatobiliary disorders: Autoimmune hepatitis, Hepatitis

Infusion related reaction

Metabolism and nutrition disorders: Diabetic ketoacidosis, Hyponatremia, Type 1 
diabetes mellitus

Musculoskeletal and connective tissue disorders: Arthralgia, Back pain, Myositis

Nervous system disorders: Guillain-Barré syndrome

Renal and urinary disorders: Nephritis

Respiratory, thoracic and mediastinal disorders: Cough, Pneumonitis

Skin and subcutaneous tissue disorders: Pruritis, Rash, Severe skin reaction, Vitiligo
For more details regarding the safety profile of pembrolizumab, please refer to the Pembrolizumab 
(KEYTRUDA) investigator’s brochure.
7.1.1.1
Adverse Event List (s) for Nab-Paclitaxel
In clinical studies, nab-paclitaxel has been associated with alopecia, myelosuppression
(primarily neutropenia), sensory neuropathy, abnormal ECG, fatigue/asthenia, myalgia/arthralgia, 
AST elevation, alkaline phosphatase elevation, anemia, nausea, infections, and diarrhea.
Participants will be monitored for nab-paclitaxel related adverse events, including hematologic, 
GI and hepatic toxicities, and peripheral neuropathy.
For more details regarding the safety profile of nab-paclitaxel, please refer to the ABRAXANE® 

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Package Insert.
7.2
Adverse Event Characteristics

CTCAE term (AE description) and grade:  The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
4.0 will be utilized for AE reporting.  All appropriate treatment areas should have access 
to a copy of the CTCAE version 4.0.  A copy of the CTCAE version 4.0 can be downloaded 
from 
the 
CTEP 
web 
site 

For expedited reporting purposes only:  
-
AEs for the agent(s) that are listed above should be reported only if the adverse event 
varies in nature, intensity or frequency from the expected toxicity information which is 
provided.
-
Other AEs for the protocol that do not require expedited reporting are outlined in the 
next section (Expedited Adverse Event Reporting) under the sub-heading of Protocol-
Specific Expedited Adverse Event Reporting Exclusions.

Attribution of the AE:
-
Definite – The AE is clearly related to the study treatment.
-
Probable – The AE is likely related to the study treatment.
-
Possible – The AE may be related to the study treatment.
-
Unlikely – The AE is doubtfully related to the study treatment.
-
Unrelated – The AE is clearly NOT related to the study treatment.
7.3
Expedited Adverse Event Reporting 
7.3.1
Investigators must report to the Overall PI any serious adverse event (SAE) that occurs 
after the initial dose of study treatment, during treatment, or within 30 days of the last dose 
of treatment on the local institutional SAE form. 
7.3.2
DF/HCC Expedited Reporting Guidelines
Investigative sites within DF/HCC will report AEs directly to the DFCI Office for Human 
Research Studies (OHRS) per the DFCI IRB reporting policy. 
7.3.3
Protocol-Specific Expedited Adverse Event Reporting Exclusions
For this protocol only, the AEs/grades listed below do not require expedited reporting to 
the DFCI IRB.  However, they still must be reported through the routine reporting 
mechanism (i.e. case report form) and may require reporting to the FDA and/or Merck.
CTCAE SOC Adverse Event
Grade Expectedness Attribution
Investigations
Neutrophil count 
2 or 3
Unexpected
Possibly, 

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decreased 
(neutropenia)
probably, or 
definitely 
related to study 
treatment
Blood and 
lymphatic 
system 
disorders
Anemia
2 or 3
Unexpected
Possibly, 
probably, or 
definitely 
related to study 
treatment
Investigations
Platelet count 
decreased 
(thrombocytopenia)
2 or 3
Unexpected
Possibly, 
probably, or 
definitely 
related to study 
treatment
Blood and 
lymphatic 
system 
disorders
Blood and 
lymphatic system 
disorders (other)
2 or 3
Unexpected
Possibly, 
probably, or 
definitely 
related to study 
treatment
Nervous 
system 
disorders
Peripheral 
motor/sensory 
neuropathy
2
Unexpected
Possibly, 
probably, or 
definitely 
related to study 
treatment
7.4
Expedited Reporting to the Food and Drug Administration (FDA)
The Overall PI, as study sponsor, will be responsible for all communications with the FDA. The 
Overall PI will report to the FDA, regardless of the site of occurrence, any serious adverse event 
that meets the FDA’s criteria for expedited reporting following the reporting requirements and 
timelines set by the FDA.
7.5
Expedited Reporting to Hospital Risk Management
Participating investigators will report to their local Risk Management office any participant safety 
reports or sentinel events that require reporting according to institutional policy. 
7.6
Routine Adverse Event Reporting
Only ≥ grade 2 Adverse Events must be reported in routine study data submissions to the Overall 
PI on the toxicity case report forms.  AEs reported through expedited processes (e.g., reported 
to the IRB, FDA, etc.) must also be reported in routine study data submissions.
7.7
Immediate Reporting of Adverse Events and Events of Clinical Interest (ECI) to Merck
7.7.1
Serious Adverse Events

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A serious adverse event is any adverse event occurring at any dose or during any use of Merck’s 
product that:

Results in death;

Is life threatening;

Results in persistent or significant disability/incapacity;

Results in or prolongs an existing inpatient hospitalization;

Is a congenital anomaly/birth defect;

Is a new cancer (that is not a condition of the study);

Is associated with an overdose;

Is an other important medical event 
Any serious adverse event, or follow up to a serious adverse event, including death due to any 
cause other than progression of the cancer under study that occurs to any participant from the time 
the consent is signed through 30 days following cessation of treatment, or the initiation of new 
anti-cancer therapy, whichever is earlier, whether or not related to Merck product, must be reported 
within 2 working days to Merck Global Safety. 
Non-serious Events of Clinical Interest will be forwarded to Merck Global Safety and will be handled 
in the same manner as SAEs. 
Additionally, any serious adverse event, considered by an investigator who is a qualified physician 
to be related to Merck product that is brought to the attention of the investigator at any time outside 
of the time period specified in the previous paragraph also must be reported immediately to Merck.
SAE reports and any other relevant safety information should be forwarded to the Merck 
Global Safety facsimile number:  
All participants with serious adverse events must be followed up for outcome until resolution of 
event to grade <1.  If resolution to grade <1 has not occurred within 30 days of the initial event, 
the participant must be followed until stabilization of the event (at a constant grade) for a period 
of at least 2 weeks.
7.7.2
Events of Clinical Interest (ECIs)
Selected non-serious and serious adverse events are also known as Events of Clinical Interest (ECI) 
and must be reported as such on the Adverse Event case report forms/worksheets within 2 working 
days to Merck Global Safety. (
).  Events 
of clinical interest for this trial include:
1. Overdose
For purposes of this trial, an overdose of pembrolizumab will be defined as any dose of 
1,000 mg or greater.  No specific information is available on the treatment of overdose of 
pembrolizumab. Appropriate supportive treatment should be provided if clinically 
indicated. In the event of overdose, the participant should be observed closely for signs of 
toxicity.

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If an adverse event(s) is associated with (“results from”) the overdose of a Merck product, 
the adverse event(s) is reported as a serious adverse event, even if no other seriousness 
criteria are met.
If a dose of Merck’s product meeting the protocol definition of overdose is taken without 
any associated clinical symptoms or abnormal laboratory results, the overdose is reported 
as a non-serious Event of Clinical Interest (ECI), using the terminology “accidental or 
intentional overdose without adverse effect.”
 
2. Elevated AST or ALT Lab value 
An elevated AST or ALT lab value that is greater than or equal to 3X the upper limit of 
normal and an elevated total bilirubin lab value that is greater than or equal to 2X the upper 
limit of normal and, at the same time, an alkaline phosphatase lab value that is less than 
2X the upper limit of normal, 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. 
Additional adverse events:
  
ECIs (both non-serious and serious adverse events) from the date of first dose through 30 days 
following cessation of treatment or the initiation of a new anticancer therapy, whichever is 
earlier, need to be reported within 2 working days to Merck Global Safety. (
 
, regardless of attribution to study treatment, consistent 
with standard SAE reporting guidelines.
Participants should be assessed for possible ECIs prior to each dose.  Lab results should be 
evaluated and subjects should be asked for signs and symptoms suggestive of an immune-
related event.  Participants who develop an ECI thought to be immune-related should have 
additional testing to rule out other etiologic causes.  If lab results or symptoms indicate a 
possible immune-related ECI, then additional testing should be performed to rule out other 
etiologic causes.  If no other cause is found, then it is assumed to be immune-related.
7.7.3
Reporting of Pregnancy and Lactation to Merck
Although pregnancy and lactation are not considered adverse events, it is the responsibility of 
investigators or their designees to report any pregnancy or lactation in a participant 
(spontaneously reported to them) that occurs during the trial.
Pregnancies and lactations that occur after the consent form is signed but before treatment 
allocation must be reported by the investigator if they cause the participant to be excluded from 
the trial, or are the result of a protocol-specified intervention, including but not limited to washout 
or discontinuation of usual therapy, diet, placebo treatment or a procedure.  

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Administer prepared solutions immediately after preparation.  If not administered immediately, 
prepared solutions may be stored refrigerated for up to 20 hours.  Pembrolizumab solutions may 
be stored at room temperature for a cumulative time of up to 4 hours.  This includes room 
temperature storage of liquid drug product solution in vials, room temperature storage of infusion 
solution in the IV bag, and the duration of infusion.
8.1.4
Compatibility
Compatible IV bag materials: PVC plasticized with DEHP, non-PVC (polyolefin), EVA, 
or PE lined polyolefin.
8.1.5
Handling
Qualified personnel, familiar with procedures that minimize undue exposure to themselves 
and the environment, should undertake the preparation, handling, and safe disposal of the 
chemotherapeutic agent in a self-contained and protective environment. 
8.1.6
Availability
Pembrolizumab is an investigational agent and will be supplied free of charge by Merck.
8.1.7
Preparation
Pembrolizumab solution for infusion must be diluted prior to administration.  Allow the 
required number of vials to equilibrate to room temperature.  Do not shake the vials.  Do 
not use if opaque or extraneous particulate matter other than translucent to white 
proteinaceous particles is observed.  Do not use if discolored.  To prepare the infusion 
solution add the dose volume of pembrolizumab to an infusion bag containing 0.9& 
Sodium Chloride Injection, USP of 5% Dextrose Injection, USP.  Gently invert the bag 10-
15 times to mix the solution.  The final concentration must be between 1 mg/mL to 10 
mg/mL.
8.1.8
Administration
Route of administration:  IV infusion only.  Do not administer as an IV push or bolus 
injection.  
Method of administration:  Infuse over approximately 30 minutes (range 25-40 minutes) 
using an infusion set containing a low-protein binding 0.2 to 5 m in-line filter make of 
polyethersulfone or polysulfone.  Infusion rate should not exceed 6.7 mL/min.  A central 
line is not required however if a subject has a central venous catheter in place, it is 
recommended that it be used for the infusion.  Do not co-administer drugs through the same 
infusion line.  Following the infusion, flush the IV line with normal saline.
8.1.9
Ordering

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Pembrolizumab will be obtained directly from Merck, the study sponsor.
8.1.10 Accountability
The investigator, or a responsible party designated by the investigator, should maintain a 
careful record of the inventory and disposition of the agent using the NCI Drug 
Accountability Record Form (DARF) or another comparable drug accountability form.  
(See the NCI Investigator’s Handbook for Procedures for Drug Accountability and 
Storage.)
8.1.11 Destruction and Return
At the end of the study, unused supplies of Pembrolizumab should be destroyed according to 
institutional policies.  Destruction will be documented per Institutional policies.
8.2
Nab-Paclitaxel
Please refer to the FDA-approved package insert for nab-paclitaxel for product information, 
extensive preparation instructions, and a comprehensive list of adverse events.
8.2.1
Description
ABRAXANE® for Injectable Suspension (paclitaxel protein-bound particles for injectable 
suspension) (albumin-bound) is an albumin- bound form of paclitaxel with a mean particle 
size of approximately 130 nanometers. Paclitaxel exists in the particles in a non crystalline, 
amorphous state.  ABRAXANE® is free of solvents.
The active agent in ABRAXANE® is paclitaxel, a microtubule inhibitor. The chemical 
name for paclitaxel is 5β,20-Epoxy 1,2α,4,7β,10β,13α-hexahydroxytax-11-en-9-one 4,10-
diacetate 2-benzoate 13-ester with (2R,3S)-N-benzoyl-3-phenylisoserine. 
Paclitaxel has the following structural formula:

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Paclitaxel is a white to off-white crystalline powder with the empirical formula 
C47H51NO14 and a molecular weight of 853.91. It is highly lipophilic, insoluble in water, 
and melts at approximately 216°C to 217°C. 
8.2.2
Form
Nab-paclitaxel is available in single use vials containing 100 mg of paclitaxel as a 
lyophilized powder.
8.2.3
Storage and Stability
Store vials in original cartons at room temperature (20°C-25°C; 68°F-77°F). Retain the 
original package to protect from bright light. Unopened vials of albumin-bound paclitaxel 
are stable until the date indicated on the package when stored at the above temperature in 
the original package.
Reconstituted vials of nab-paclitaxel may be refrigerated at (2°C-8°C; 38°F-46°F) for a
maximum of 8 hours and should be protected from bright light.
8.2.4
Handling
Qualified personnel, familiar with procedures that minimize undue exposure to themselves 
and the environment, should undertake the preparation, handling, and safe disposal of the 
chemotherapeutic agent in a self-contained and protective environment. 
8.2.5
Availability
Nab-paclitaxel is commercially available and will be obtained from the Institutional 
pharmacy.

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8.2.6
Preparation
Reconstitute each vial with 20 mL of 0.9% Sodium Chloride Injection, USP injected over 
at least 1 minute. Direct the NaCl onto the inside wall of the vial, and not directly onto the 
lyophilized cake, as this will result in foaming. Following reconstitution, allow the vial to 
sit for a minimum of 5 (five) minutes to ensure proper wetting of the lyophilized 
cake/powder. Gently swirl and/or invert the vial slowly for at least 2 minutes until complete 
dissolution of any cake/powder occurs. Rapid agitation or shaking will result in foaming. 
If foaming or clumping occurs, stand solution for at least 15 minutes until foam subsides. 
The reconstituted suspension should appear milky and homogeneous without visible 
particulates. If unsuspended powder is visible, the vial should be gently inverted again to 
ensure complete resuspension, prior to use.  Each mL of reconstituted product will contain 
5 mg of paclitaxel. Withdraw the desired volume and inject the suspension into an empty 
sterile PVC container.
Parenteral drug products should be inspected visually for particulate matter and 
discoloration before administration whenever the solution and container permit. The 
reconstituted sample should be milky and homogenous, without visible particulates. If 
particulates are visible or settling occurs, the vial should be gently inverted to ensure 
complete resuspension before use.
8.2.7
Administration
Nab-paclitaxel will be administered intravenous infusion over 30 minutes. Filters are not
required for preparation or administration of nab-paclitaxel. If filters are used as part of
institutional procedure, the pore size must be > 15 micron.
8.2.8
Ordering
Nab-paclitaxel is commercially available and will be ordered per the standard practices of 
the Institutional pharmacy.
8.2.9
Accountability
Nab-paclitaxel is a commercially available product.  Accountability will be handled per 
institutional polices regarding commercial products.
  
8.2.10 Destruction and Return
Nab-paclitaxel is a commercially available product.  Destruction and return will be 
handled per institutional policies regarding commercial products.
9.
BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES
A baseline research biopsy (biopsy 1) prior to study therapy is required on this trial, in addition 
to two on-treatment biopsies (biopsy 2 and biopsy 3).  Tissue will be collected at the time of 
surgery for research purposes.  For patients who are determined to have evidence of clinically 

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significant residual disease by physical exam or imaging after completion of protocol treatment 
and who wish to continue with additional chemotherapy, an image-guided biopsy is mandatory 
prior to the initiation of additional therapy. In these cases, fresh and archival tissue at surgery 
will also be collected. All patients will also submit an archived tissue sample from their 
diagnostic biopsy and breast surgery. We plan to use this tissue to perform a number of immune 
profiling assays, detailed below.  Background information on the pre-clinical and clinical 
rationale for these investigations is discussed in Section 2.5 and Section 2.6.  On tumor tissue, 
we will perform characterization based on histology (TILs), protein expression, mRNA 
expression, and single cell RNA sequencing.  Additionally, we will bank specimens for possible 
future DNA analysis, and other further testing.
If any of the biomarkers are inevaluable based on testing of tissue from biopsy 1, the assay may 
be attempted on the patient’s archival tumor tissue, if feasible.
Four blood draws for correlative science are required on this trial; blood draws will be performed 
just prior to week 1 day 1 infusion of study drugs, just prior to week 3 day 1 infusion of study 
drugs, just prior to week 7 day 1 infusion of study, and at the time of the last dose of chemotherapy 
(or up to 2 weeks after the last dose of chemotherapy).   On each blood draw, we will perform flow 
cytometry to characterize protein expression of immune mediators, detailed below, and additional 
blood will be stored for future testing.
All patients will additionally be asked to provide a stool sample at three separate timepoints: 
prior to treatment, after exposure to either nab-paclitaxel or pembrolizumab alone (after W1, 
both arms), and after exposure to both nab-paclitaxel and pembrolizumab together (after W4). A 
fourth collection may be requested from patients who experience grade ≥ 2 diarrhea after 
discussion with the PI. This collection is not required, but is strongly encouraged. These samples 
will be analyzed for microbiota content.
Please refer to the separate laboratory manual for additional correlative details including 
collection, processing, and shipping instructions.
9.1
Archival Tissue Requirements
All participants will have archival tissue collected at baseline from their diagnostic biopsy as 
well as from their surgical procedure. 
9.1.1
Collection, handling, and shipping of archival tissue
Diagnostic biopsy and breast surgery archival tissue requirements: 20 unstained slides at 4-5um 
are required. For the surgical sample, a sample containing residual tumor or tissue from the tumor 
bed (in the case of a pathologic complete response) should be collected.
Tissue will be stored with the current CRC for this trial, but may at some point, be transitioned to 
storage within the DF/HCC Clinical Trials Core Laboratory or the Breast Tumor Immunology 
Lab (BTIL). Any samples leftover after correlative projects for this trial have been completed 
will become property of the DF/HCC Clinical Trials Core Laboratory (Dr. Deborah Dillon).  

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9.2
Procedures for obtaining breast tissue for study
9.2.1
Collection, handling, and shipping of non-surgical biopsy specimens
Research core biopsies of the primary breast lesion will be obtained at the indicated timepoints 
from all participants.
Biopsies should not be performed on Friday afternoons, as there may not be time for processing 
of the fresh tissue.  If a biopsy must be performed on Friday morning, the lab of Mariano 
Severgnini must be notified in advance to ensure that there will be adequate time for processing 
fresh tissue, since fresh tissue cannot be stored over the weekend. Specimens in RNALater and 
formalin should be stored at room temperature until shipment. Specimens in RNALater and 
formalin may be stored over the weekend and shipped on Monday. 
It is mandatory that core biopsies be image-guided.  A clip should be placed in the biopsy site at 
the time of the research biopsy if a clip was not placed during diagnostic biopsy. Pre- and post-
procedure 90-degree lateral and craniocaudal mammogram is recommended to ensure that the 
correct lesion has been biopsied and to determine the relationship of the clip to the lesion that was 
visualized prebiopsy. Clip migration following biopsy has been reported and the distance from the 
original biopsy cavity can be measured36. If sufficiently far away from the biopsy cavity, then an 
addendum should be made to the report documenting that the clip should NOT be used to guide 
post-treatment tumor sampling.  Experience with NeoALTTO and I-SPY1 suggest that taking four 
core biopsy samples from one area is feasible and acceptable to participants and ethics 
committees37.  
Ideally five core biopsies will be obtained:

Two cores should be placed in 10% neutral buffered formalin tube.

One core should be placed in RNAlater

Two cores should be placed in sterile DMEM
The order of specimen collection should be:

First core: 10% neutral buffered formalin

Second core: Sterile DMEM

Third core: RNAlater

Fourth core: Sterile DMEM

Fifth core: 10% neutral buffered formalin
For up to the next 12 patients enrolled, the order of specimen collection will be: 

First core: 10% neutral buffered formalin

Second core: RPMI with Hepes

Third core: RPMI with Hepes

Fourth core: RNA later

Fifth core: RPMI with Hepes
If additional cores are obtained, they should be processed as follows:

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9.8
Hypotheses for secondary/correlative objectives

We hypothesize that all ER+ breast tumors can be placed in a category of general “immune 
activity” level based on histologic, protein-based, and RNA-based analyses.  We will assess 
this with (1) a “core” set of markers (PD-L1 expression; PD-L1 expression; PD-L2 
expression; CD8 expression; and stromal TILs) and, (2) an expanded, exploratory set of 
markers.

We hypothesize that an ER+ tumor’s “immune activity” will increase over the course of 
treatment with nab-paclitaxel/pembrolizumab monotherapy, followed by combination 
therapy, but that the magnitude of this increase will be greatest when nab-paclitaxel therapy 
precedes combination therapy.

We hypothesize that breast tumors with a higher level of “immune activity” at baseline, or 
a greater degree of increase from baseline to on-treatment tissue sampling, will have a 
higher likelihood of achieving more favorable RCB as well as pCR after treatment with 
both nab-paclitaxel and pembrolizumab.

We hypothesize that the immune marker profile in the peripheral blood will change from 
baseline to surgery on nab-paclitaxel/pembrolizumab monotherapy or combination 
therapy.

We hypothesize that a serially measured immune marker or composite of markers in the 
peripheral blood will correspond to changes in peri-tumoral immune activity as assessed 
on serial tumor biopsies.

The structure and function of the gut microbiome before starting any treatment can be 
predictive of response to therapy, with a greater microbial diversity, estimated by 
Shannon index, being predictive of efficacy.

The structure and function of gut microbiome changes in response to each treatment 
alone, and also in response to the combination of both Nab-paclitaxel and pembrolizumab 
therapy and can predict the likelihood of response to therapy.

The abundance and functional profile of specific gut bacteria is associated with response 
to therapy.
9.9
Immunohistochemistry for primary endpoint (PD-L1 expression) and secondary/exploratory 
endpoints
Immunohistochemistry will be used to evaluate biomarkers for purposes of all primary and 
secondary objectives (see Section 1.2 and 1.3).  Assessment of TILs by histology will also be a 
part of analyses of secondary objectives.  The primary objective will be assessed based on 
immunohistochemistry for PD-L1.
PD-L1, as measured by immunohistochemistry (IHC), is an integral biomarker on this trial.  The 
procedure for quantifying PD-L1 expression by IHC, as well as quantifying other exploratory 
biomarkers by IHC, is described below.
Tissue will be collected and fixed by 10% neutral buffered formalin overnight, dehydrated, and 
paraffin embedded.  Four micrometer-thick sections will be cut.  The paraffin blocks and unstained 
slides will be stored at room temperature.  All immunohistochemical staining will be performed in 

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(for PD-Ligands) or number of positive cells per unit area (for PD-1+ lymphocytes).  
Intensity of staining is also captured automatically using the above algorithms and assigned 
a score (0, 1, 2, or 3) based upon the average optical density of the region or cells.  All 
results are exported into an Excel spreadsheet.
4. Individual scoring data will be compared to clinical parameters to determine if there is an 
association with outcome.  Scores using a combination of biomarker data will also be 
considered.
For overall biomarker analysis:
The semi-quantitative scoring for this study is in accordance with those published previously and, 
as described above, will include scores for both the neoplastic and non-neoplastic cells within the 
tumor microenvironment.  Data derived from pathologist visual scoring (semi-quantitative, but 
with increased specificity for delineating neoplastic and non-neoplastic cells) and pathologist-
assisted, automated scoring (quantitative, but without accurately delineating neoplastic and non-
neoplastic cells) for each marker of interest will be assessed for its clinical value.  As necessary, 
the data from combinations of markers will also be considered (i.e. combined scores from PD-L1 
and PD-L2 expression).  All data will be analyzed in conjunction with the biostatistics group.
Overall, for purposes of PD-L1 assessment for the primary objective of this trial: PD-L1 staining 
will be quantified as described, via visual evaluation by two separate pathologists to calculate the 
H-score for PD-L1 on tumor cells.
Further details of the immunohistochemical assay and assessment are described in protocol lab 

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manual.
It should be noted that the above staining protocols are based on standard methods used at the time 
of protocol writing.  It is possible that at the time protein expression assays are conducted, novel 
and improved methods for staining or its quantification will exist.  In this case, we plan to use the 
best available, best validated experimental method available at the time for all secondary and 
exploratory analyses.  This does not apply to the analysis of PD-L1 expression by H-score for 
purposes of the primary endpoint, which will be carried out as described above.
9.10
Tumor infiltrating lymphocyte (TIL) percentage and determination of lymphocyte predominant 
breast cancer (LPBC)
Paraffinized, hematoxylin and eosin-stained slides taken from two tissue planes will be derived 
from each biopsy and will be reviewed by certified pathologists.  In the research setting, all cases 
are reviewed by two pathologists and any discordant results resolved by consensus review.  The 
extent of lymphocytic infiltrate in tumor tissue will be assessed and stromal TIL percentage will 
be determined.  More detailed guidelines for the quantification of stromal TILs in breast cancer 
can be found in the recommendations from the International TILs Working Group 2014.22
After assessment of the TIL percentage, the pathologists will categorize the specimen as 
lymphocyte predominant breast cancer (LPBC), defined as a tumor that contains >60% stromal 
lymphocytes, or non-LPBC.
Again, it should be noted that the above TIL assessment methods are based on standard methods 
used at the time of protocol writing.  It is possible that at the time assessments are conducted, there 
will be a different, accepted method of TIL quantification.  In this case, we plan to use the best 
available, best validated method available at the time for all secondary and exploratory analyses.
9.11
Exploratory correlative analyses of tumor tissue
9.11.1 Flow cytometry of tumor infiltrating lymphocytes
TILs will be isolated from the biopsy specimen as described in the protocol lab manual.
Surface staining followed by flow cytometry on the resultant TILs will then be performed as 
described in the protocol lab manual.  The following antibodies may be used on all specimens: 
(core set)
CD8
PD-1
PD-L1
PD-L2
A selection of the following antibodies may also be used, and additional antibodies may be used 
as well, as deemed appropriate and informative based on the state of the immune profiling literature 
at the time of correlative science performance:
CD4

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FOXP3
CD127
(Other antibodies as listed in the protocol lab manual)
9.11.2 RNA and DNA analysis
RNA analysis will be performed, and tissue for RNA analysis will be stored, in the 
 
Messenger RNA (mRNA) expression within tumor biopsy specimens will be assessed using the 
most current and informative methodologies at the time that correlative science is performed on 
all specimens.  NanoString signatures and comprehensive RNA sequencing may be used.  Potential 
genes of interest, based on prior immune profiling of breast tumors,18 include CXCL9, CCL5, 
CD8ACD80, CXCL13, IGKC, CD21, IDO1, PD-1, PD-L1, PD-L2, CTLA4, and FOXP3.
Additional RNA analysis, and specifically use of single cell RNA sequencing techniques, will be 
performed in collaboration with Dr. Eliezer Van Allen at the Broad Institute.  DNA analysis may 
also be performed to assess parameters such as mutational load and neoantigen burden.
For a subset of patients, single-cell RNA sequencing will be performed on fresh tumor biopsies 
and surgical tissue. These studies will determine whether changes in RNA expression signatures 
at the level of individual tumor and immune cells correlate with treatment response and resistance. 
The analyses will also investigate whether particular immune cell subsets are enriched in 
responders compared to non-responders, as suggested by studies in other tumors treated with 
checkpoint inhibitors.
9.12
Exploratory correlative analyses of peripheral blood: flow cytometry to characterize immune markers 
in peripheral blood mononuclear cells (PBMCs) prior to, during, and after therapy with nab-paclitaxel 
and pembrolizumab
PBMCs will be generated as described in the protocol lab manual, and used to assess immune cell 
populations.
Surface staining with a panel of antibodies (see below, and protocol lab manual) and flow 
cytometry on PBMCs will then be performed as described in the protocol lab manual.  The 
following antibodies may be used on all specimens: (core set)
CD8
PD-1
PD-L1
PD-L2
A selection of the following antibodies may also be used, and additional antibodies may be used 
as well, as deemed appropriate and informative based on the state of the immune profiling literature 
at the time of correlative science performance:
CD4
FOXP3

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CD127
9.13
Additional analysis
The above-mentioned analyses may be altered based on novel developments in the field of cancer 
immune profiling at the time of correlative science.  Additional markers or alternative technologies 
(based on scientific developments and/or novel technologies) may also be used, to explore 
potential prognostic or predictive candidate markers/panels or markers related to treatment benefit 
and/or safety, to improve diagnostic tests, or to understand breast cancer biology.  Some of the 
above-mentioned markers for secondary/correlative objectives may be eliminated, if they are no 
longer deemed biologically relevant at the time analyses are performed.
9.14
Analysis of DNA extraction from stool samples
Under the supervision of 
, total genomic DNA will be isolated from 0.25g of 
feces using the PowerSoil DNA isolation kit (Mo Bio, USA) 
 
. Purified DNA will be separated on a 1% 
agarose gel and quantified by densitometry and spectrophotometry (NanoDrop 1000; Thermo 
Scientific, USA).
9.15
Analysis of RNA Extraction from stool samples
Under 
 supervision, 16S rRNA analysis will be performed at The V4–V5 region of the 
16S rRNA gene will be amplified and sequenced on an Illumina MiSeq platform at 
 
 For each stool sample, replicate PCR reactions will be performed using modified 
universal bacterial primers designed to amplify the V4-V5 16S rRNA region: 563F (59-
nnnnnnnn-NNNNNNNNNNNN-AYTGGGYDTAAAGN G-39) and 926R (59-nnnnnnnn-
NNNNNNNNNNNN-CCGTCAATTYHTTTR AGT-39). 
Using the Illumina TruSeq Sample Preparation procedure, PCR products will be quantified and 
pooled at equimolar amounts before Illumina barcodes and adaptors will be ligated on. The 
completed library will be sequenced on an Ilumina Miseq platform according to the Illumina 
recommended protocol. Sequences will be analysed using mothur version 1.31.115. Sequences 
were aligned using the Silva reference alignment as a template and potentially chimeric 
sequences were eliminated using the UChime algorithm16. Five thousand sequences per patient 
were selected (mean 4,974, s.d. 150) and sequences with a distance-based similarity of Z97% 
were grouped into OTUs using the furthest-neighbour algorithm. OTUs were classified using the 
Greengenes 16S rRNA reference database. OTU-based microbial diversity was estimated by 
calculating two diversity indices, Shannon and Inverse Simpson. OTU-based richness was 
determined by calculating the Chao richness estimate and constructing rarefaction curves. OTUs 
were grouped at different levels of classification (phylum, class, order, family and genus); at 
each level, OTUs that did not have a classification were grouped together by the highest 
available resolution. Feature selection of the intestinal microbia’s composition was performed on 
OTUs with an average abundance 40.01% in either patient group and grouped by phylotype.

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COHORT A CALENDAR
Pre-studya
W1 D1
W2 D1
W3 D1
W4 D1
W5 D1
W6 D1
W7 D1
W8 D1
W9 D1
W10 D1
W11 D1
W12 D1
W15 D1
Surgerym
Post-surgery
Follow-up
Informed consent
X
Demographics
X
Medical history
X
Performance statusb
X
Concomitant medications
X
X
X
X
X
X
X
X
Adverse event evaluation
X
X
X
X
X
X
X
Physical examf
X
X
X
X
X
X
X
X
Vital signs (including 
weight/height)p
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
Hematology (CBC with 
diff) and, chemistry 
panelq
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
PT/PTT
X
TSH/free T4
X
X
X
X
X
X
Cortisols
X
X
X
X
X
X
Pregnancy testc
X
EKG
X
Mammogram, breast
US, or breast MRIe
X
Xr
CT scan 
(chest/abd/pelvis) and
bone scan or PET-CT
scang
X
Surgical assessmenth
X
Xr
Axillary assessmenti
X
Nab-paclitaxel 
administration
X
X
X
X
X
X
X
X
X
X
X
X
Pembrolizumab 
administration
X
X
X
X
X
Image-guided Research 
biopsyd,n
Xd
Xd
Xd
Xn
Research Blood 
collectionj
X
X
X
Xr
Research Stool 
Collectiont
X
X
X
Stool Questionnaireu
X
X
X
Archival tumor tissueo
X
X
Assessment for residual 
cancer burdenk
X
Assessment for 
progressive 
disease/survivali
X

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COHORT B CALENDAR 
Pre-studya
W1 D1
W3 D1
W4 D1
W5/6 D1
W7 D1
W8/9 D1
W10 D1
W11/12 D1
W13 D1
W14 D1
Surgerym
Post-surgery
Follow-up
Informed consent
X
Demographics
X
Medical history
X
Performance statusb
X
Concomitant medications
X
X
X
X
X
X
X
Adverse event evaluation
X
X
X
X
X
X
Physical examf
X
X
X
X
X
X
X
Vital signs (including 
weight/height)p
X
X
X
X
X
X
X
X
X
X
X
X
Hematology (CBC with diff) 
and chemistry panelq
X
X
X
X
X
X
X
X
X
X
X
X
PT/PTT
X
TSH/free T4
X
X
X
X
X
Cortisols
X
X
X
X
X
X
Pregnancy testc
X
EKG
X
Mammogram, breast
US, or breast MRIe
X
Xr
CT scan (chest/abd/pelvis) and
bone scan or PET-CT
scang
X
Surgical assessmenth
X
Xr
Axillary assessmenti
X
Nab-paclitaxel administration
X
X
X
X
X
X
X
X
X
Pembrolizumab administration
X
X
X
X
X
Image-guided Research biopsyd,n
Xd
Xd
Xd
Xn
Research Blood collectionj
X
X
X
Xr
Research Stool Collectiont
X
X
X
Stool Questionnaireu
X
X
X
Archival tumor tissueo
X
X
Assessment for residual cancer 
burdenk
X
Assessment for progressive 
disease/survivall
X
Abbreviations: W: Week; D: Day
a.
Baseline evaluations are to be conducted within 28 days prior to start of protocol therapy unless otherwise noted.  If screening 
assessments occur within 3 days before start of study treatment, then they may serve as the Week 1 Day 1 values.
b.
See Appendix A.
c.
In female participants of child-bearing potential, urine or serum pregnancy test must be performed within 7 days before the first dose of 
study medication.  If the urine test is positive or cannot be confirmed as negative, then a serum test is required.
d.
Baseline research biopsy obtained within 14 days before starting protocol therapy is required.  See Section 5.2.4 for more information 
regarding the timing of the biopsies and Section 9.1.1 for biopsy handling and processing instructions.  A biopsy should also be obtained 
in participants who go off study for progressive disease, or in whom the treating physician chooses to administer additional non-protocol 
therapy prior to surgery.  
e.
See Section 5.2.4 regarding breast imaging recommendations.  Affected breast imaging that measures the tumor must be done within 28 
days prior to enrollment; MRI is strongly recommended, although other imaging modalities (mammogram, ultrasound) are permitted if 
practical or financial considerations preclude MRI, as long as the target lesion can be adequately measured.   This same imaging modality 
should be performed again prior to surgery (2-3 weeks after the last dose of study treatment) to assess tumor response.
f.
Tumor measurements should be ascertained by physical exam (not required at Post-Surgery visit)..
g.
It is recommended, but not required that participants with anatomic Stage IIa disease and above (AJCC 8th edition) will have CT scans 
of chest, abdomen and pelvis and bone scans or PET-CT scans performed during screening to rule out metastatic disease. 
h.
All participants will be seen and examined by the treating surgeon at Screening and at the Pre-Operative visit.  See Section 5.2.4 for 
further details of the surgical assessment.
i.
See guidelines for axillary assessment in Section 5.2.4.
j.
See Section 9.3 for specific timing of research blood draws and handling and processing instructions.
k.
Assessment of residual cancer burden (RCB) is described in Section 11.5.

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l.
Post-surgical follow-up information will be collected at assessments every 6 months until 5 years after surgery.  See Section 5.7. No 
tests or procedures are required during follow-up; however clinical data will be collected on CRFs. These data should be based on 
exams, tests, or procedures done at the registering institution or at a local facility.
m.
Surgery should take place no more than 42 days from the last dose of study treatment.
n.
The procedure for surgical collection is described in Section 9.1.2.
o.
Patients will submit an archived sample from their diagnostic biopsy and from their surgery.See Section9.0. Can be obtained at any time 
during the life of the trial and does not have to be performed as a screening or surgery assessment. 
p.
Height needed at week 1 day 1 only.  Weight not required at Pre-Surgery, Surgery, or Follow-up visits.  See sections 5.2.2 and 5.2.3 
regarding dosing changes for weight fluctuation while on therapy.
q.
Sodium, potassium, chloride, bicarbonate, BUN, creatinine, total protein, albumin, total bilirubin, SGOT (AST), SGPT (ALT), 
Alkaline Phosphatase. PT and PTT at screening only.
r.
Pre-surgical assessments to be done at the time of the last dose of chemotherapy or within 2 weeks after the last dose of protocol 
therapy.
s.
Cortisol to be drawn at baseline, W3D1, W6D1, W9D1, W12D1, and W14D1 on Cohort B.
t.
Baseline stool collection should be obtained within 28 days before starting protocol therapy. The W1 stool collection should be 
performed after dosing on W1, but prior to dosing on W2. The W4 stool collection should be performed after dosing on W4, but prior 
to dosing on W5. An optional stool sample may be collected at the time of grade ≥ 2 diarrhea after discussion with the PI. As these 
collections are for exploratory correlative purposes, failure to provide a sample at these timepoints will not constitute a protocol 
violation. See section 9 and/or stool collection guidance document for more details.
u.
Each stool collection kit will contain a questionnaire for the patients to complete regarding the conditions surrounding their collection. 
These will be a part of the kit and are not to be administered in clinic. Failure to complete these questionnaires at the required or 
optional timepoints will not constitute a protocol violation. 

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11. MEASUREMENT OF EFFECT
11.1
Antitumor Effect – Solid Tumors
A baseline and pre-surgical radiographic study of the breast is required; MRI is recommended. 
The same radiographic modality should be used consistently. The baseline scan must be obtained 
within 28 days of beginning therapy. The pre-surgical imagining should occur at the time of the 
last dose ofchemotherapy or within 2 weeks after the last dose of chemotherapy. If the participant 
clinically progresses, repeat imaging is required. If there is discordance (clinical progression, but 
radiographic stable disease or response), contact the study chair.
11.2
Radiographic assessment
Each participant will have pre- and post-therapy radiographic tumor measurements, preferably by 
MRI, however if logistic or practical issues preclude MRI use, mammogram or ultrasound may be 
substituted. The longest diameter (LD) of the target lesion at the time of study initiation will be 
reported as the baseline LD. The baseline LD of the target lesion will be used as reference to further 
characterize the objective tumor response of the measureable dimension of the disease. 
Response criteria are based on the RECIST 1.1 criteria:
Radiographic Complete Response (CR): Complete disappearance of the target lesion
Radiographic Partial Response (PR): Greater than or equal to 30% decrease in the longest 
diameter (LD) of the target lesion taking as reference the baseline LD.
Radiographic Progressive Disease (PD): Greater than or equal to 20% increase in the LD of 
target lesion taking as reference the baseline LD or the appearance of one or more new lesions.
Radiographic Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD taking as reference the baseline LD 
11.3
Other radiographic response parameters:  Immune-Related Response Criteria (irRECIST)
11.3.1 Definition of Tumor Response Using Immune-Related Response Criteria (irRECIST)
irRECIST is RECIST 1.1 adapted as described below to account for the unique tumor
response seen with immuno-therapeutics.
irRECIST may be used by site investigators and local radiology review to assess tumor
response and progression, and make treatment decisions. This data will be collected in the
clinical database.
irRECIST takes into account the clinical condition/stability of participants, as described in the 
table below, in addition to response or progression via tumor imaging.
Clinically stable is defined by the following criteria:

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 Absence of symptoms and signs indicating clinically significant progression of
disease, including worsening of laboratory values
 No decline in ECOG performance status
 Absence of rapid progression of disease
 Absence of progressive tumor at critical anatomical sites (e.g., cord compression)
requiring urgent alternative medical intervention
Table: irRECIST: Tumor Imaging and Treatment after 1st Radiologic Evidence of PD or SD, CR, 
or PR
In determining whether or not the tumor burden has increased, decreased or remained stable,
site investigators should consider all target lesions as well as non-target lesions.
Any subject deemed clinically unstable should be discontinued from trial treatment at first

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evidence of progressive disease by tumor imaging and is not required to have repeat tumor
imaging for confirmation.
For a clinically stable subject with first radiologic evidence of progressive disease (i.e.,
unconfirmed progression of disease), it is at the discretion of the site investigator to
continue treating the subject with the assigned treatment per protocol until progression of
disease is confirmed at least 28 days from the date of the tumor imaging first suggesting PD.
If progression is not confirmed on the subsequent tumor imaging, the subject should continue
to receive study therapy and have tumor imaging performed per protocol, or sooner if clinically 
indicated, to monitor disease status. If radiologic progression is confirmed by subsequent tumor 
imaging, then the subject will be discontinued from trial treatment.
NOTE: If a subject with confirmed progression by tumor imaging (i.e. 2 scans at least 28
days apart demonstrating progressive disease) is clinically stable or clinically improved, and
there is no further increase in the tumor burden at the confirmatory scan, an exception may
be considered to continue treatment upon consultation with the Sponsor.
The same imaging modality (i.e., CT or MRI), acquisition and technical parameters should
be used throughout the study for a given subject.
11.4
Clinical assessments
Both target and, in the event of multifocal or multicentric invasive cancer, nontarget lesions should 
be followed clinically and their clinical size recorded at baseline. Measurements thereafter are 
required; these lesions should be categorized at subsequent visits regarding whether there is 
evidence of progression. If “yes”, the study chair should be notified in order to determine whether 
the participant should come off protocol treatment.
11.5
Pathologic Response
Pathologic response will be reported using the Residual Cancer Burden11 calculator from M.D 
Anderson: 
 
The following parameters are required from pathologic examination in order to calculate Residual 
Cancer Burden (RCB) after neoadjuvant treatment:

The largest two dimensions (mms) of the residual tumor bed in the breast (largest tumor 
bed if multicentric disease)

Histologic assessment of the percentage of the tumor bed area that contains carcinoma (all 
carcinoma, i.e. invasive and in situ), select one of the following: 0%, 1%, 5%, 10%, 20%, 
30%, 40%, 50%, 60%, 70%, 80%, 90%

To assess cellularity it is helpful to scan across the sections of tumor bed and then estimate 
the average cellularity from the different microscopic fields.

When estimating percentage cancer cellularity in any microscopic field, compare the 
involved area with obvious standards, e.g. more or less than half, one quarter, one fifth, 
one tenth, one twentieth, etc.

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
Expect there to be variable cellularity within the cross section of any tumor bed, but 
estimate the overall cellularity from the average of the estimates in different microscopic 
fields of the tumor bed. E.g., if cellularity in different fields of the tumor bed were estimated 
as 20%, 10%, 20%, 0%, 20%, 30%, then an average estimate of overall cellularity would 
be 20%.

Histologic estimate of the percentage of the carcinoma in the tumor bed that is in situ, select 
one of the following: 0%, 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 
100%

The number of positive (metastatic) lymph nodes

The largest diameter (mm) of the largest nodal metastasis
For the purpose of this study pCR will be defined as RCB=0.
12. DATA REPORTING / REGULATORY REQUIREMENTS
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 7.0 
(Adverse Events: List and Reporting Requirements).
12.1
Data Reporting
12.1.1 Method
ODQ will collect, manage, and perform quality checks on the data for this study.
12.1.2 Responsibility for Data Submission
Investigative sites within DF/HCC or DF/PCC are responsible for submitting data 
according to the schedule set by ODQ.
12.2
Data Safety Monitoring
The 
 will review and monitor toxicity 
and accrual data from this study. The committee is composed of clinical specialists with experience 
in oncology and who have no direct relationship with the study. Information that raises any 
questions about participant safety will be addressed with the Overall PI and study team.
The DSMC will review each protocol up to four times a year or more often if required to review 
toxicity and accrual data. Information to be provided to the committee may include: up-to-date 
participant accrual; current dose level information; DLT information; all grade 2 or higher 
unexpected adverse events that have been reported; summary of all deaths occurring with 30 days 
of intervention for Phase I or II protocols; for gene therapy protocols, summary of all deaths while 
being treated and during active follow-up; any response information; audit results, and a summary 
provided by the study team. Other information (e.g. scans, laboratory values) will be provided 
upon request. 

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12.3
Multicenter Guidelines
N/A
12.4
Collaborative Research and Future Use of Data and Biospecimens
Tissue, blood, stool, bodily fluids, and other materials derived from these will be collected in this 
study to analyze genes, DNA, RNA, proteins and cells for the study’s correlative endpoints and 
potential future research, utilizing new types of biomarker testing as it becomes available. 
These samples and any data generated as a part of these clinical trials may be used for future 
research studies and may be provided to collaborating investigators both within and outside of the 
DF/HCC for either correlative endpoints or secondary use. Samples and data may be shared with 
outside non-profit academic investigators, as well as with for-profit pharmaceutical investigators 
or commercial entities, with whom we collaborate. When samples or data are sent to collaborators 
and when any research is performed on them, all information will be identified with a code, and 
will not contain any PHI, such as name, birthday, or MRNs. 
In order to allow the greatest amount of research to be performed on the specimens and 
information generated as a part of this trial, researchers in this study may share results of genetic 
sequencing with other scientists. De-identified specimen or genetic data may be placed into one 
of more publicly-accessible scientific databases, such as the National Institutes of Health’s 
Database for Genotypes and Phenotypes (dbGaP). The results from the correlative research on 
this study will be shared with these public databases. Through such databases, researchers from 
around the world will have access to de-identified samples or data for future research. More 
detailed information, beyond the public database, may only be accessed by scientists at other 
research centers who have received special permission to review de-identified data.
13. STATISTICAL CONSIDERATIONS
13.1
Study Design/Endpoints
This is a randomized open label study examining biomarker changes over the course of treatment 
with nab-paclitaxel, pembrolizumab, or both in HR+ breast cancer.  Participants will be accrued 
in one stage with completion of a safety analysis of the first 6 patients per arm.  Participants will 
be registered and randomized by the Office of Data Quality (ODQ).  Participants will be 
randomized 1:1 to receive a run-in of either two weeks of nab-paclitaxel (cohort A) or one dose of 
pembrolizumab (cohort B) monotherapy.  Participants will then receive combination nab-
paclitaxel (administered weekly) and pembrolizumab (administered every 3 weeks) for a total of 
15 weeks (cohort A) or 14 weeks (cohort B).  At completion, each patient will have received 12 
doses of weekly nab-paclitaxel, and 5 doses of every-3-week pembrolizumab.  Three research 
biopsies are required over the course of therapy: one at pre-treatment baseline (biopsy 1), one post-
monotherapy (biopsy 2), and one post-doublet therapy (biopsy 3).  Additional tissue collection at 
surgery will be performed if residual disease is present.

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All participants who receive at least one dose of either study drug will be evaluated for the 
biomarker and clinical endpoints.
Primary endpoint:

Change in PD-L1 expression by immunohistochemistry from baseline biopsy (biopsy 1) to 
biopsy after 2-week treatment with either nab-paclitaxel or pembrolizumab (biopsy 2), 
assessed as a dichotomous variable (H-score ≥ 100 versus 0-99). Secondary analysis of the 
endpoint will evaluate change in PD-L1 expression as a continuous variable (absolute 
change in H-score).
Secondary endpoints:
Secondary biomarker endpoints

The absolute change in expression of core immune biomarkers (stromal TILs;) from 
baseline biopsy (biopsy 1) to biopsy after 2-week treatment with either nab-paclitaxel or 
pembrolizumab (biopsy 2).
Secondary safety endpoint

Safety and tolerability profile: maximum grade of all treatment-related adverse events 
using CTCAE v4.0
Secondary efficacy endpoints

Pathologic complete response rate, defined as RCB 0,11 following treatment with 
combination nab-paclitaxel and pembrolizumab in the neoadjuvant setting for HR+ breast 
cancer.

Overall response rate, assessed radiographically by both RECIST 1.1 and irRECIST, 
following treatment with combination nab-paclitaxel and pembrolizumab in the 
neoadjuvant setting

Disease-free survival following treatment with combination nab-paclitaxel and 
pembrolizumab in the neoadjuvant setting for HR+ breast cancer.
Blood and Tissue correlative science endpoints

The absolute change in PD-L1 expression by immunohistochemistry from baseline biopsy 
(biopsy 1) to biopsy after treatment with nab-paclitaxel or pembrolizumab monotherapy, 
followed by doublet therapy (biopsy 3, and surgery in participants with residual disease) , 
assessed as a dichotomous variable (H-score ≥ 100 versus 0-99) and as a continuous 
variable (absolute change in H-score)

The absolute change in expression of core immune biomarkers (stromal TILs) from 
baseline biopsy (biopsy 1) to biopsy after treatment with nab-paclitaxel or pembrolizumab 
monotherapy, followed by doublet therapy (biopsy 3, and surgery in participants with 
residual disease). 

Characterization of an expanded set of immune biomarkers (based on histology, protein 
expression, and mRNA expression) in HR+ breast tumors both pre-treatment and on serial 
biopsies.

Characterization of the immune biomarker profile in PBMCs both pre-treatment and on 

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serial blood draws.
Stool and Microbiome correlative science endpoints
Overall, we plan to describe the landscape of gut microbiota in patients with BC who will 
receive pembrolizumab plus Nab-paclitaxel, and the changes in their gut microbiota after each 
treatment alone, and after the combined regimen. Statistical analyses of intestinal microbiota 
samples will be performed using R Statistical Language (v3.1.1) and GraphPad Prism (version 
6.0e) software packages. Unpaired Mann–Whitney rank sum test (two-tailed) will be used for 
comparisons of continuous variables between two groups. Bar plots will be used to represent the 
data’s mean at the center values, with error bars to indicate standard deviation.  In order to 
explore the association of PD-L1 change to baseline microbiota diversity, and changes from 
baseline in microbiota, inference will be based on Wilcoxon rank sum tests and estimates of 
predictive value along the continuous scales will be visualized using receiver operating 
characteristic (ROC) curves and reported with c-index and confidence intervals derived from 
variance estimates of Somers rank correlation. Unadjusted P-values will be considered 
significant for the Mann–Whitney rank sum test. 
We will quantify microbiome features from amplicon, metagenome, metatranscriptome using 
established pipelines to identify strain-level taxonomic, functional gene, transcriptional, and 
microbially-mediated metabolite profiles associated with BC patients with and without 
immunotherapy70-76. We will use modified multivariate linear modeling to identify statistically 
significant features associated with outcomes. Statistical tests for association with these 
outcomes and covariates will be performed using the sparse generalized linear model MaAsLin, 
which provides random effects models for both log-Gaussian and zero-inflated negative binomial 
link functions. Computational workflows for these steps are implemented as AnADAMA2 
(http://huttenhower.sph.harvard.edu/anadama) workflows, a reproducible data handling 
environment that captures all provenance during the analysis process.
An initial safety review is planned for each cohort.  Accrual will be paused after 6 participants 
are enrolled on each arm and a formal monitoring of safety will be conducted when the 6 
participants per arm have completed the period of DLT evaluation. If >1 patient in either arm 
develops a dose limiting toxicity, enrollment will be halted and there will be a discussion with 
the DSMC to determine whether modifications are required to proceed with the study.  The 
following table gives the probability of continuing after 6 patients under varying true rates of 
dose-limiting toxicity.
Dose acceptance using 6 subjects
True DLT rate
0.1
0.2
0.3
0.4
0.5
0.6
0.7
Probability
89%
66%
42%
23%
11%
4%
1%
13.2
Sample Size, Accrual Rate and Study Duration
The target accrual is 50 participants (25 per arm). The sample size was chosen to have adequate 

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power for detecting changes in PD-L1 expression within each arm. The null hypothesis is no 
change in the amount of PD-L1 expression from baseline to after a two-week run in of nab-
paclitaxel or pembrolizumab, and the primary analysis will be tested in each arm using one-sided 
alpha (type I error) of 0.05 using a McNemar’s test (changes from H-score 0-99 to ≥100). As a 
secondary analysis, a Wilcoxon signed rank test will be used to evaluate absolute change in H-
score using an alpha (type I error) of 0.05.  With an anticipated 15% assay failure rate, 25 patients 
per arm will provide 21 evaluable paired specimens for each treatment. Under the assumption that 
positive PD-L1 expression occurs in 20.1% of cases,28 and that there is a 0.1% probability of PD-
L1 expression changing from positive to negative, there will be 80% power to see an increase in 
PD-L1 positive expression to 50% of the cases after the two-week run-in of monotherapy.  Power 
calculations for the exact non-parametric test for small sample sizes was performed in East v6.3 
(Cytel Inc.). 
Expected accrual is 0-1 participants per month; therefore, it will take approximately 75 months to 
complete accrual.  An additional 6 months of follow-up will be required after the last participant 
is accrued to cover the time from initial enrollment to the first post-surgical follow-up visit, for a 
total study duration of approximately 80 months.
13.3
Stratification Factors
No stratification factors are planned.
13.4
Interim Monitoring Plan
During the safety run-in phase, the first 6 patients within a dosing cohort need to complete 21 
days of treatment and the safety data will be reviewed before enrolling additional patients.  
Toxicity will also be monitored by the DF/HCC DSMC as described in Section 12.2
13.5
Analysis of Primary Endpoints
Descriptive statistics will be used to summarize the distribution of H-scores of PD-L1 expression 
by immunohistochemistry that are observed at baseline and after 2 weeks of monotherapy (e.g. 
mean, standard deviation, median, and inter-quartile range). The primary evaluation of change in 
PD-L1 expression within each arm will be based on an exact McNemar’s test (H-score 0-99 versus 
100) and Wilcoxon signed rank test (absolute change in H-score) using a one-sided alpha = 0.05 
for each test. No statistical inferences will made to compare the change in PD-L1 expression across 
arms.
13.6
Analysis of Secondary Endpoints
Secondary endpoints of additional core immune biomarkers and of changes in all markers from 
baseline to post-neoadjuvant treatment will similarly use descriptive statistics and test for changes 
within arm using the Wilcoxon signed rank test with two-sided alpha = 0.05. Exploratory analyses 
will evaluate whether log fold-change in marker levels removed skewness in the empirical 
distribution of changes from baseline. In addition, exploratory analysis will evaluate the Spearman 

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correlation in marker levels at each timepoint and changes from baseline.  With an anticipated 15% 
assay failure rate, 42 evaluable paired specimen are anticipated for detecting changes in biomarker 
levels from baseline to post-neoadjuvant treatment. This will provide 90% power to detect a 0.47 
shift in standardized units under an assumption of an additive shift model with a Gaussian common 
density function.  
For the secondary safety endpoint, treatment-related toxicities will be summarized by maximum 
grade and by term using CTCAE v4.0 and reported with 90% binomial exact confidence intervals.
The overall pCR rate will be reported using 95% Binomial exact confidence intervals, and RCB 
levels will be summarized for all patients using frequency tables. With 50 patients receiving 
protocol treatment, the maximum width of any confidence interval will be 0.21. To explore the 
association of pCR to baseline marker levels, and changes from baseline in biomarkers, inference 
will be based on Wilcoxon rank sum tests and estimates of predictive value along the continuous 
scales will be visualized using receiver operating characteristic (ROC) curves and reported with c-
index and confidence intervals derived from variance estimates of Somers rank correlation. 
Disease-free survival will be summarized using Kaplan-Meier estimates and 95% confidence 
bands. 
Single-cell RNA sequencing will be performed on fresh tumor biopsies and surgical tissue for a 
subset of patients to assess the relationship of timepoint-specific tumor and immune cell 
subpopulations with clinical outcomes in exploratory analyses. In addition, changes in single-cell 
RNA expression signatures from baseline will be correlated with response. Standard 
preprocessing and quality control algorithms will be performed to filter out low quality cells and 
to normalize the expression data. Differentially expressed genes will be identified using the 
Benjamini-Hochberg procedure to control the false discovery rate for multiple comparisons. 
Descriptive statistics and clustering techniques, including principal component analysis and t-
distributed stochastic neighbor embedding, will be employed to summarize the distributions of 
the expression data and identify tumor and immune cell subpopulations. Changes in cell 
subpopulations between timepoints will be assessed with Wilcoxon signed-rank tests, while 
differences in cell subpopulations between responders and non-responders will be compared with 
Mann-Whitney tests. Preliminary associations of tumor and immune cell subpopulations with 
disease-free survival will be explored using Cox proportional hazard models. 
13.7
Reporting and Exclusions
13.7.1 Evaluation of Toxicity
All participants will be evaluable for toxicity from the time of their first treatment.  Participants 
who never start protocol therapy will be considered inevaluable. 
13.7.2 Evaluation of the Primary Efficacy Endpoint
All Participants who receive at least one dose of either study drug will be evaluable for efficacy 
endpoints.  Participants who never start protocol therapy will be considered inevaluable and will 
be replaced.  Biomarker analyses will be conducted in all Participants with evaluable biospecimen 

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within arm that is defined by the treatment received (per protocol).
14. PUBLICATION PLAN
The Primary Investigator will be the final arbiter of the manuscript content.  

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

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APPENDIX B
NEW YORK HEART ASSOCIATION (NYHA) CLASSIFICATIONS
The New York Heart Association (NYHA) Cardiac Disease Classification provides a functional 
and therapeutic classification for the prescription of physical activity for cardiac participants.  
Based on NYHA definitions, participants are to be classified as follows:

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APPENDIX C
STRONG CYP3A INDUCERS/INHIBITORS
The list provided below is not exhaustive.  For a more comprehensive, frequently updated list, 
please visit: 
Medications that strongly inhibit CYP3A:
Amprenavir
Atazanavir
Boceprevir
Clarithromycin
Conivaptan
Delavirdine
Diltiazem
Erythromycin
Fosamprenavir
Indinavir
Itraconazole
Ketoconazole
Lopinavir
Mibefradil
Miconazole
Nefazodone
Nelfinavir
Posaconazole
Ritonavir
Saquinavir
Telaprevir
Telithromycin
Verapamil
Voriconazole
Grapefruit, grapefruit juice, or any product containing grapefruit
Medications that strongly induce CYP3A:
Carbamazepine
Felbamate
Nevirapine
Phenobarbital
Phenytoin
Primidone
Rifabutin
Rifampin
Rifapentin
St. John’s wort