Phase I/II Trial of Regorafenib, Hydroxychloroquine, and Entinostat in Metastatic Colorectal Cancer
Phase: PHASE1
Conditions: Colorectal Cancer
Sponsor: Abramson Cancer Center at Penn Medicine

Cover Page for ClinicalTrials.gov 
 
 
 
NCT Number 
 
NCT03215264 
 
 
Protocol 
Official Title 
 
Phase I/II Trial of Regorafenib, Hydroxychloroquine, and Entinostat in 
Metastatic Colorectal Cancer  
 
 
Documents 
Included 
 
 
study protocol and statistical analysis plan embedded within protocol section 
7.0 
Document 
Date 
(mm/dd/yyyy) 
 
06/15/2017 
 
 
 

Phase I/II Trial of Regorafenib, Hydroxychloroquine, and Entinostat 
in Metastatic Colorectal Cancer 
 
 
Principal Investigator:  
Peter J O’Dwyer, MD 
 
 
 
 
Abramson Cancer Center 
 
 
 
 
3400 Civic Center Blvd 
 
 
 
 
Philadelphia, PA 19104 
 
 
 
 
peter.o’dwyer@uphs.upenn.edu 
 
Co-Investigators:   
 
Thomas B. Karasic, MD 
Mark O’Hara, MD 
Ursina Teitelbaum, MD 
Ravi Amaravadi, MD 
Nevena Damjanov, MD 
Kim Reiss-Binder, MD 
Charles J. Schneider, MD 
 
Statistician:    
 
Wei-Ting Hwang, PhD 
 
 
 
 
University of Pennsylvania School of Medicine 
 
 
 
 
Center for Clinical Epidemiology & Biostatistics 
 
 
 
 
628 Blockley Hall 
 
 
 
 
423 Guardian Drive 
 
 
 
 
Philadelphia, PA  19104 
 
Medical Monitor: 
 
Vivek Narayan, MD 
 
Protocol Number: 
 
UPCC 31216 
 
Initial version: 
 
03/24/2017 
Amendment 1: 
 
04/28/2017 
Amendment 2: 
 
06/15/2017 

 
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Title 
A Phase I/II Trial of Regorafenib, Hydroxychloroquine, and 
Entinostat in Metastatic Colorectal Cancer 
Short Title 
Regorafenib/HCQ/Entinostat in colorectal cancer 
IND # 
135547 
IRB Protocol 
Number 
827226 
UPCC Number 
UPCC 31216 
Phase 
Phase I/II 
Methodology 
Single Arm 
Number of Patients 32-44 
Study Duration 
18 months 
Study Center 
University of Pennsylvania Abramson Cancer Center 
Primary Objectives 
Phase I: 
To determine doses of hydroxychloroquine and entinostat with 
acceptable toxicity in combination with regorafenib 
 
Phase II: 
To determine the response rate of the three-drug combination in 
metastatic colorectal cancer that has progressed on standard agents 
 
Secondary 
Objectives 
1.  To measure overall survival, progression-free survival, and 
duration of response 
2.  To describe the toxicity associated with the regimen 
3.  To describe the mutational profiles of responders and non-
responders using next generation sequencing 
4.  To evaluate the pharmacodynamics of entinostat by measuring 
protein lysine acetylation in peripheral blood mononuclear cells 
(PBMCs), and lymphocyte subsets 
5.  To assess and quantitate autophagy pharmacodynamics using 
Western blotting of PBMC extracts and serum markers 
6.  To describe gene expression alterations as result of therapy 
using paired biopsy specimens at baseline and 3 weeks 
7.  To analyze FOXO1 expression and subcellular localization as a 
marker of treatment effect using paired biopsy specimens at 
baseline and 3 weeks 

 
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Main 
Inclusion/Exclusion 
Criteria 
1.  Must have measurable disease by RECIST 1.1 criteria 
2.  ECOG PS 0-1, age at least 18 years 
3.  Sufficient renal, hepatic, and bone marrow function by standard 
laboratory testing 
4.  Must be able to understand and sign written informed consent 
Study Products 
1.  Entinostat: an oral inhibitor of class I histone deacetylases 
2.  Hydroxychloroquine:  an oral inhibitor of autophagy 
Duration of 
Therapy 
 
Until disease progression or unacceptable toxicity 
Statistical Analysis 
Phase I:  Standard 3+3 design, determination of MTD 
Phase II:  Single-arm, overall response rate as primary endpoint 
 
1.0  OBJECTIVES: 
 
1.1  Phase I Primary Endpoint 
1.1.1  To determine doses of hydroxychloroquine and entinostat with acceptable 
toxicity in combination with regorafenib 
 
1.2  Phase II Primary Endpoint 
1.2.1  To determine the response rate of a three drug combination of regorafenib, 
hydroxychloroquine, and entinostat in patients with colorectal cancer that has 
progressed on standard agents 
 
1.3  Secondary Endpoints 
1.3.1  To describe the toxicity profile of the three drug combination 
1.3.2  To measure overall survival, progression-free survival, and duration of 
response 
1.3.3  To describe mutational profiles of responders and non-responders using 
next-generation sequencing 
1.3.4  To evaluate the pharmacodynamics of entinostat by measuring protein 
lysine acetylation in peripheral blood mononuclear cells (PBMCs), and 
lymphocyte subsets 

 
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1.3.5  To assess and quantitate autophagy pharmacodynamics using Western 
blotting of PBMC extracts and serum markers 
1.3.6  To describe gene expression alterations as result of therapy using paired 
biopsy specimens at baseline and 3 weeks (Phase II portion only, when funding 
available) 
1.3.7  To analyze FOXO1 expression and subcellular localization as a marker of 
treatment effect using paired biopsy specimens at baseline and 3 weeks (Phase II 
portion only, when funding available) 
 
2.0  BACKGROUND: 
 
2.1 Antiangiogenic activity in colorectal cancer 
Antiangiogenic therapy has been a mainstay in colon cancer since the approval of 
bevacizumab over a decade ago.1  Angiogenesis is thought of as a hallmark of cancer, 
and microvascular density and other markers of increased angiogenesis have been shown 
to predict worse outcomes in colorectal cancer.2,3  The use of bevacizumab, the 
prototypic antiangiogenic agent, has been shown to decrease tumor perfusion, 
microvascular density, and interstitial fluid pressure in rectal tumors,4 treatment of 
patients with advanced disease is associated with improved survival, both in initial 
therapy, and in second-line, in combination with different chemotherapy.1,5 
 
The role of VEGF pathway inhibition through antibodies and antibody fragments 
continues to expand.  Bevacizumab has now demonstrated benefit in both the first- and 
second-line setting in combination with chemotherapy in colorectal cancer.5,6 Aflibercept, 
a recombinant protein that combines VEGF1R and VEGF2R segments with the Fc 
portion of human IgG, shows survival benefit in the second-line setting.7  Antibody 
targeting of VEGFR2 through ramucirumab, a fully human IgG1 antibody specific to 
VEGFR2, also improves survival in the second-line setting.8 
 
More elusive in colorectal cancer has been the development of oral small molecule 
inhibitors of angiogenesis.  Numerous tyrosine kinase inhibitors (TKIs) have been or are 

 
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currently being developed to target angiogenesis through the VEGF pathway.  Various 
combinations using these drugs have ultimately failed during clinical trials in colorectal 
cancer.9-13  Some considerations to be borne in mind for these drugs include multiple off-
target effects, limited pharmacodynamic grounding, frequent combination with 
chemotherapy, which may not be the optimal setting, and questions about optimal 
scheduling for drugs with short half-lives.   We recently published a randomized phase II 
trial showing lack of effect of the addition of sorafenib to chemotherapy.  Nonetheless, as 
will be described in detail below, regorafenib was FDA-approved for use in colorectal 
cancer, on the basis of a single-agent trial.  It has demonstrated a modest survival benefit 
in the third-line setting as a single agent with very few objective responses, suggesting a 
cytostatic effect14.  Since regorafenib and sorafenib are almost identical in their 
preclinical and clinical characteristics, we expect the combinations proposed here to be 
safe, and any improvement in activity to be readily evident. 
 
2.2 Resistance to Antiangiogenic therapy 
The mechanisms through which angiogenesis inhibitors result in greater tumor cell kill 
have been studied extensively but remain incompletely understood.  The prevailing 
hypothesis is that antiangiogenic therapy works to “normalize” the disrupted vasculature 
of tumors, resulting in increased drug delivery.15,16  In this scenario, the disordered 
angiogenesis that characterizes colon cancers is normalized through inhibition of 
endothelial proliferation, to normalize interstitial pressure and improve chemotherapy 
delivery.  We have proposed an alternative hypothesis, that antiangiogenic therapy 
chokes off the vascular supply of nutrients and oxygen and, by inducing hypoxia, adds to 
the cellular stress of cytotoxic chemotherapy.17,18  Preclinical models respond to 
bevacizumab in vivo proportionally to their susceptibility to hypoxic cell death.17,19 
Additional mechanistic insights have been provided by the work of Kerbel and colleagues 
who have elucidated the contribution of circulating marrow-derived stem cells, which 
may have a profound effect on the tumor microenvironment.20,21  As yet, these proposed 
mechanisms have not yielded useful markers to define the population of patients that may 
benefit from antiangiogenic therapy. 
 

 
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2.3  Autophagy as a mechanism of anti-angiogenic therapy resistance 
Hypoxia and low vascularity environments are frequent obstacles to proliferation 
encountered by tumor cells, and they have developed pathways of resistance.  One such 
pathway is autophagy, in which tumor cells autodigest organelles and cytoplasm to 
generate energy in low nutrient and/or oxygen-poor environments.22,23  Autophagy is a 
multi-step process that involves the vesicular sequestration of cytoplasmic proteins and 
damaged organelles into a structure called the autophagic vesicle (AV). AVs fuse with 
lysosomes and AV contents are degraded by acid-dependent enzymes. This process is 
activated by numerous cell stresses including growth factor or nutrient limitation, 
hypoxia, chemotherapy, and radiation.24  The anti-malarial drugs CQ and HCQ induce 
the death of cells that rely on autophagy for survival by impairing lysosomal function, 
blocking the last step of autophagy.  This strategy has demonstrated early promise in 
multiple tumor types, especially in combination with antiangiogenic therapy.25 
 
We have performed multiple Phase I trials that all show combinations of cytotoxic drugs 
with therapeutic doses of HCQ to be tolerable.  We performed a Phase I/II trial of the 
combination of HCQ and FOLFOX/bevacizumab in patients with metastatic colorectal 
cancer.  Eligible patients had Stage IV colorectal cancer, with no prior therapy for 
metastatic disease, good PS (0,1), and adequate hematologic and biochemical indices.  
We entered 16 patients in the Phase I portion, 6M/10F, median age 57.5, and PS 0 (9) or 
1 (7).  One patient had received prior adjuvant treatment 6 months or more prior to being 
enrolled.  Three patients were treated with 300 mg BID PO continuously in the first 
cohort, 8 patients were treated with 400 mg PO BID, and 5 patients were treated with 
600mg PO BID. No dose-limiting toxicities were seen. The most common adverse events 
were fatigue, nausea, diarrhea, and neuropathy. In the first cohort, one patient had MRSA 
port infection and one patient had a pulmonary embolism, two patients had grade 3 
neutropenia and one had grade 3 fatigue in the second cohort, and in the third cohort 
there was one cardiac arrest and pulmonary embolism and four patients with grade 3 
neutropenia. The adverse events were not thought to be related to the addition of 
hydrochloroquine to FOLFOX and bevacizumab. In all cohorts, 44% of patients had 
partial response, 37% had stable disease, and 19% had progressive disease.  We 

 
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concluded that full doses of FOLFOX/bevacizumab are well-tolerated in combination 
with HCQ 600mg PO BID continuously. 
 
We continued to the Phase II portion of the trial, and again the combination showed no 
unexpected toxicity.  Among the first 25 patients, the response rate was 57%, with 2 CR, and 
many patients were taken to metastatic resection, making interpretation of PFS very difficult.  
Based on the results, a randomized Phase II trial of 160 patients has been proposed for 
ECOG-ACRIN, and will be proposed to the GI Steering Committee in a few months. 
 
2.4 Epigenetic regulation and autophagy 
Adaptive responses to tumor stress such as autophagy require complex coordination, 
influenced by numerous tumor suppressor genes (e.g. TP53, PTEN) and oncogenes (e.g. 
EGFR) as well as epigenetic modification of gene expression.25  While the mutational 
profiles of tumors have been increasingly well described through efforts such as The Cancer 
Genome Atlas, the role of epigenetic modification in many tumors remains incompletely 
understood.  Histone deacetylases (HDACs) are a family of proteins that influence gene 
expression through multiple mechanisms and have been demonstrated to be pathogenic in a 
variety of tumors, including colorectal cancer.27  The HDACs have been classified based on 
homology to yeast proteins into classes I, II, and IV, and at least 11 separate human HDAC 
proteins have been identified.  They initially were shown to alter gene expression through 
cleavage of acetyl-lysine bonds on histones, with resultant alterations in chromatin structure 
and DNA promoter access.28  Additionally, they have been shown to interact with a variety 
of non-histone proteins, including p53, E2F, NF-κB, α-tubulin, and heat shock protein 90 
(HSP90), which may further alter cell-signaling pathways.29 
 
Despite incomplete understanding of the different mechanisms through which HDACs 
exert their effects in vivo, small molecule inhibitors of HDACs have shown efficacy in a 
variety of tumor types.  Three HDAC inhibitors, vorinostat, belinostat and romidepsin, 
are approved in cutaneous T cell lymphoma, and a fourth HDAC inhibitor, panobinostat, 
is approved in multiple myeloma.   Preclinical mechanistic studies have demonstrated 
multiple antitumor effects, including increased apoptotic death, G1/S cell cycle arrest, 
downregulation of angiogenesis, and modification of tumor immunogenicity.29  The 

 
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relative importance of each of these effects varies considerably based on tumor type and 
specificity of the HDAC inhibitor for the various HDAC isotypes.30  Additionally, the 
alterations in cell signaling are highly dependent upon the cellular environment, and 
stressors such as nutrient deprivation, hypoxia, or chemotherapy.  This variability 
hampers the applicability of preclinical models and makes combination therapy effects 
less predictable.  Nevertheless, the benefit of HDAC inhibitor monotherapy in solid 
tumors is modest, and promising combinations are emerging.31  Entinostat, also known as 
MS-275, is an HDAC inhibitor that selectively inhibits class I HDACs, resulting in a 
more favorable side effect profile.32  It is currently undergoing investigation as 
monotherapy and in combination in a variety of tumor types. 
 
Studies in our lab at Penn have shown that HDAC inhibitors are strong inducers of autophagy 
in colon cancer cells lines, especially under hypoxia, and that IC50 values are variable among 
the lines.  Coadministration of the autophagy inhibitor CQ markedly sensitizes the cell lines to 
HDAC inhibition, with CI values that demonstrate marked synergy.  This positive interaction 
is even more enhanced under hypoxic conditions.  The combination of hydroxychloroquine 
and vorinostat was recently shown to be safe in phase I clinical trial.33 
 
Table 1:  Interaction of HDAC inhibition with Autophagy Inhibition 
Cell Line 
IC50 SAHA 
(M) 
Oxic 
IC50 SAHA 
(M) 
Hypoxic 
IC50 CQ 
(M) 
Oxic 
IC50 CQ 
(M) 
Hypoxic 
CI S + H* 
Oxic 
CI S + H* 
Hypoxic 
1.HT29 
0.35 
1.57 
3.9 
2.1 
0.54 
0.45 
2.HCT116 0.12 
0.32 
10.8 
7.2 
0.45 
0.33 
3.HCT15 
3.42 
7.14 
10.4 
6.3 
0.25 
0.18 
4.RKO 
1.89 
4.52 
12 
6.7 
0.3 
0.15 
5.DLD1 
0.82 
0.98 
11.5 
9.2 
0.65 
0.09 
6.SW620 
0.54 
1.62 
10.1 
7.2 
0.22 
0.22 
7.Colo205 0.26 
0.31 
9.0 
5.4 
0.8 
0.37 
*Combinatorial Index.  A CI value <0.9 is defined as synergistic, 0.9-1.1 additive, and 
>1.1 antagonistic 
 

 
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An extensive literature documents a positive interaction between HDAC inhibitors and 
DNA damaging drugs, but for various reasons this has never been translated effectively to 
the clinic.  These interactions will be explored more fully in a front-line trial with FOLFOX. 
 
2.5  Regorafenib Clinical Experience 
Regorafenib is a multikinase inhibitor with effects on angiogenesis via the VEGF 
pathway as well as various cell growth pathways.  It is closely related to sorafenib, 
differing in structure by a single fluorine molecule.  The principle tyrosine kinase targets 
of regorafenib include VEGFR1-3, PDGR-β, KIT, RAF-1, B-RAF, B-RAFV600E, RET, 
and to a lesser extent FGFR2 and TIE2.34 
 
Phase I trials established a dosing regimen of 160 mg daily for 21 days of a 28 day cycle 
and demonstrated hand-foot syndrome, fatigue, diarrhea, and hypertension as the 
predominant side effects.35  Regorafenib demonstrated consistent bioavailability between 
subjects.  T1/2 ranged from 20-40 hours, with relative stability of plasma concentrations 
between doses.  It is metabolized into two pharmacologically active compounds, M2 and 
M5, which reach similar concentrations as the parent compound at steady state. 
 
Regorafenib is an FDA-approved therapy for metastatic colorectal cancer that has 
progressed on prior therapy with 5-fluorouracil, oxaliplatin, irinotecan, anti-angiogenic 
therapy, and, if KRAS wild-type, anti-EGFR therapy.  This approval was based on a 
proven survival benefit from the phase III CORRECT trial, which compared regorafenib 
to placebo in a 2:1 ratio in colorectal cancer that had progressed on all standard 
therapies.36  Participants randomized to regorafenib in that trial received 160 mg daily for 
three weeks out of a four-week cycle.  Overall survival improved in the regorafenib arm 
to 6.4 months, compared to 5.0 months in the placebo arm (hazard ratio 0.77, 95% CI 
0.64-0.94, p=0.0052.  Grade 3-4 toxicities in this trial with regorafenib included hand-
foot syndrome (17%), fatigue (10%), diarrhea (7%), hypertension (7%), and rash (6%).  
Very few objective responses were seen with regorafenib (1% versus 0.4% with placebo), 
implying a cytostatic effect on the tumor. 
 

 
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A second phase III trial conducted in Asia, the CONCUR study, identical in design to the 
CORRECT trial, confirmed the results.37  In this study, overall survival improved with 
regorafenib (8.8 months) compared to placebo (6.3 months) (HR 0.55, CI 0.40-0.77, 
p=0.00016).   The objective response rate was 4% in the regorafenib arm.  Grade 3-4 
adverse events were similar to those seen in the CORRECT trial, including hand-foot 
syndrome (16%), hypertension (11%), liver abnormalities (7% hyperbilirubinemia, 7% 
elevated ALT, 6% elevated AST), hypophosphatemia (7%), lipase elevation (6%), and 
rash (6%).  Additionally, two grade 5 adverse events (cardiac arrest and death NOS) were 
possibly attributable to the drug. 
 
2.6  Hydroxychloroquine Clinical Experience 
Chloroquine (CQ) is a synthetic 4-aminoquinoline that has been used for 60 years in 
humans for malaria prophylaxis and treatment,38 rheumatoid arthritis,39 and human 
immunodeficiency virus (HIV)40. It is an inexpensive orally available drug that has CNS 
penetration. It has a large therapeutic index, and its most predictable cumulative toxicity 
is retinopathy, which can be prevented by discontinuation of the drug.41 It is this toxicity 
and worldwide malarial resistance to CQ that lead to discontinuation of extensive 
research into CQ’s non-malarial applications. Chloroquine derivatives such as HCQ are 
still used extensively in rheumatoid arthritis and lupus erythematosis and have a larger 
therapeutic index. The chemical structure of CQ derivatives allows them to serve as a 
weak base which is trapped in acidic cellular compartments.42 Thus chloroquine 
deacidifies lysosomes, inhibiting the last step in autophagy. With this last step blocked, a 
cell reliant on autophagy will increase the generation of autophagosomes and will 
eventually undergo either apoptotic or non-apoptotic cell death. Evidence in mouse 
models and human cancer cell lines suggest CQ may have significant anti- tumor activity 
by inhibiting autophagy induced by cancer therapy.43 
 
Adding chloroquine to improve the efficacy of anticancer therapy has already been tested 
in a randomized clinical trial. A small single-institution placebo-controlled phase III trial 
testing the addition of CQ at an oral daily dose of 150 mg to RT and carmustine in 
patients with newly diagnosed glioblastoma multiforme (GBM) yielded surprising 

 
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results.44  Median overall survival was significantly longer in the CQ-treated patients (24 
months) than in controls (11 months). At the end of the observation period, six patients 
(40%) treated with CQ were alive at 59, 45, 30, 20 (1 each) and 27 (2 patients) months 
after surgery. In contrast, patients in the control group survived 32, 25, and 22 months. 
Although not statistically significantly different, the rate of death over time was almost 
half as large in the CQ group compared to the placebo group (hazard ratio, 0.52 [95% CI, 
0.21 to 1.26]; p= 0.139). 
 
Hydroxychloroquine (HCQ) is commonly prescribed for rheumatoid arthritis and lupus at 
doses of 400 mg po daily. A pharmacokinetic/pharmacodynamic study of escalating 
doses of HCQ at 400 mg/800 mg/1200 mg po daily in patients with rheumatoid arthritis 
followed by maintenance doses of 400 mg po daily found that doses of up to 1200 mg po 
daily were well tolerated.45 Dose limiting toxicities of nausea, vomiting and abdominal 
pain were observed at 800 and 1200 mg po daily. This toxicity correlated with blood 
HCQ levels, but not to blood levels of the other active metabolites, 
desethylhydroxychloroquine (DHCQ), desethylchloroquine (DCQ), or 
bisdesethylchloroquine (BDCQ). Improvement of symptoms in rheumatoid arthritis 
correlated with blood DHCQ levels, suggesting a dose-response relationship. 
Chloroquine derivatives are metabolized through the p450 enzyme system and CQ may 
inhibit the metabolism of CYP2D6- metabolized drugs.45,46 
 
A predictable cumulative toxicity associated with CQ is retinopathy, and this is another 
reason why dose escalation with CQ would be limited. While a link between HCQ and 
retinopathy has also been made, it occurs infrequently and only after a prolonged 
exposure. A study using multifocal electroretinography to detect early pre-clinical retinal 
changes in long-term HCQ users, found that 10 out of 11 patients that developed early 
pre-clinical changes had been taking HCQ at doses of 400 mg po daily for greater than 5 
years.47 No overt retinopathy was noted in the 19 patients followed. This suggests that at 
a cumulative dose of 730 g, the risk of retinal changes increases, but techniques such as 
multifocal electroretinography can detect early changes and prevent overt visual loss. 
 

 
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We have previously conducted several trials of HCQ in combination with anticancer 
agents ranging from HCQ/alkylating therapy for glioblastoma, through 
HCQ/temsirolimus in Phase I, as well as FOLFOX/bevacizumab/HCQ in colorectal 
cancer. A CNS consortium trial (led from the University of Pennsylvania) to test the 
addition of HCQ at escalating doses to RT/temozolomide found excessive 
myelosuppression compared to temozolomide alone and reached a daily dose of only 
600mg HCQ, which incompletely inhibited autophagy and was ineffective in the phase II 
portion.48  With temsirolimus, tolerable doses of HCQ have been higher, and a dose level 
of 1200 mg is currently being explored. Dermatologic effects and fatigue associated with 
mTOR inhibitors do not appear to be worsened by HCQ at doses up to 1000 mg daily. In 
the frontline setting for metastatic colorectal cancer, 600mg twice daily dosing was used 
along with FOLFOX as the phase II dose without any additional toxicity. 
 
The pharmacokinetics of hydroxychloroquine (HCQ) studied in patients with rheumatoid 
arthritis, malaria, and healthy volunteers demonstrate marked intra- and interpatient 
variability, with a two-fold range in total clearance (4-10 L/h) (26-8). The variability in 
the rate of absorption from oral dosing has been reported to be as high as 87%, 
contributing to differences in peak blood concentrations (Cmax) and time to peak 
concentration (Tmax) among patients receiving identical doses (26-8). Due to its long 
terminal elimination half-life of approximately 40 days, at least 120 days of continuous 
dosing are required before blood HCQ levels reach 90% of steady-state concentrations. 
Predicted blood concentrations are 898 ng/mL and 1796 ng/mL for patients receiving 200 
mg and 400 mg daily of HCQ sulfate, respectively.49  A one- compartment population 
pharmacokinetic model with a lag time was developed to estimate individual HCQ 
pharmacokinetic parameters in 36 patients who participated in a dose-escalation trial of 
HCQ in conjunction with radiation therapy and temozolomide for glioblastoma 
multiforme48. Population values for apparent volume of distribution (Vd) and total 
clearance were 604 L and 10.7 L/hr, with CV% of 23% and 5%, respectively. Mean 
individual estimated HCQ pharmacokinetic values for Vd were 573 L (range, 205-1291 
L) and clearance 10.5 L/hr (range, 6.8-13.7 L/hr). Mean estimated Cmax values were 
linear and proportional to total daily oral HCQ sulfate doses at 200, 400, 600, and 800 mg 

 
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daily and consistent with predicted and observed blood concentrations from the published 
literature.50-52  The population pharmacokinetic estimates are comparable to data from a 
population pharmacokinetic study in patients with rheumatoid arthritis where the Vd was 
605 L and total clearance was 9.9 L/h.53  Although pharmacokinetic analyses of HCQ 
sulfate at doses up to 1200 mg daily combined with other agents in phase I and II trials at 
the University of Pennsylvania have not been completed, dose-proportional HCQ 
concentrations and concentration-response relationships for daily doses between 400 and 
1200 mg daily have been reported.50 
 
2.7 Entinostat Clinical Experience 
Entinostat, also known as MS-275, is a synthetic benzamide derivative that has been 
demonstrated to preferentially inhibit class I HDACs, especially HDAC type 1.  
Preclinical animal models of entinostat demonstrated a Tmax of 30-40 minutes and T1/2 of 
one hour.  Based on this data, the initial phase I trial of entinostat started dosage at 2 
mg/m2 daily for the first 28 days of a 42 day cycle.54  Both patients on this daily protocol 
experienced dose-limiting toxicity during the first cycle, and pharmacokinetic data 
suggested a half-life of 30-50 times longer than that observed in the animal models.   As a 
result, dosing was changed to biweekly, and all subsequent phase I trials used either 
weekly or biweekly dosing strategies.  Plasma clearance of entinostat in humans follows 
bi-exponential kinetics suggestive of enterohepatic circulation with a T1/2 of 
approximately 50 hours.  Pharmacodynamic studies have used measurement of histone 
H3 acetylation in peripheral-blood mononuclear cells (PMBCs) as a surrogate for HDAC 
inhibition, although this does not nearly reflect the full spectrum of HDAC inhibitor 
activity.55  Western blot and flow cytometric assays of this using entinostat demonstrated 
significant interpatient variability in both magnitude and timing of H3 hyperacetylation 
but no clear dose-dependence.56 
 
The most common side effects observed in the initial phase I study were fatigue (100%), 
nausea (83%), anorexia (56%), myelosuppression (neutropenia 74%, thrombocytopenia 
61%, anemia 26%), headache (52%), hypoalbuminemia (48%), and electrolyte 
abnormalities (hypocalcemia 43%, hyponatremia 35%, hypophosphatemia 26%).  The 

 
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most frequent grade 3 toxicities in the 23 patients were nausea (4), hypophosphatemia 
(4), fatigue (3), diarrhea (3), and neutropenia (3).  The only grade 4 event was leukopenia 
and neutropenia in a single patient.  The MTD in this study was 10 mg/m2 every 2 weeks. 
 
Additional phase I studies have explored alternative dosing schedules without clear 
definition of an optimal regimen.  A dose of 2 mg/m2 twice weekly was excessively toxic 
and discontinued in favor of weekly or biweekly dosing in a phase I trial in patients with 
solid tumors and lymphoma.56  All subsequent studies have of entinostat have used 
weekly or biweekly dosing.  In a phase I trial in patients with refractory leukemia, 8 
mg/m2 weekly for the first 4 weeks of a 6-week cycle was determined to be the MTD57  
In a phase I trial in patients with refractory solid tumors, the MTD was 6 mg/m2 weekly 
for the first 4 weeks of a 6-week cycle.58  Later phase II trials used fixed dose instead of 
weight-based dosing of entinostat, with a range of doses and weekly or biweekly 
scheduling.59-61  Most recently, a phase I trial of entinostat in combination with sorafenib 
in solid tumors demonstrated tolerability of standard full doses of sorafenib (400mg twice 
daily) with entinostat 10 mg every 2 weeks.62  The toxicity profile in this trial was similar 
to that of the initial phase I study, with few events of grade 3 or higher. Therefore the 
combination with regorafenib, an almost identical VEGF-R2 inhibitor, is expected to be 
tolerable. 
 
2.8 Rationale for Clinical Trial 
In summary, previous studies have indicated that autophagy may be a mechanism of 
resistance to both antiangiogenic and cytotoxic drugs.  Multiple phase I trials have shown 
that HCQ is well-tolerated with multiple forms of chemotherapy, and specifically with 
the combination of FOLFOX/bevacizumab in colorectal cancer, as well as with sorafenib.  
Based on very striking (Table 1) preclinical data that support the further addition of 
HDAC inhibition, this trial is proposed as a test of principle that augmented autophagy 
inhibition can render a purely antiangiogenic therapy more effective.  Since regorafenib 
alone is associated with a 1% response rate, we would view a 15% response rate with the 
combination as promising and worth developing further. 
 

 
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3.0  ELIGIBILITY 
 
3.1 Inclusion Criteria 
 
3.1.1 Histologic or cytologic confirmation of metastatic colorectal cancer 
 
3.1.2 Measurable disease based on modified RECIST 1.1 criteria 
3.1.3 Patients should have received adequate therapy with prior 5-fluorouracil, 
oxaliplatin, and irinotecan, unless contra-indicated, not tolerated or declined. 
3.1.4 No prior therapy with regorafenib or other anti-angiogenic tyrosine kinase 
inhibitor 
3.1.5 No prior or current therapy with an HDAC inhibitor 
 
3.1.6 Age 18 years or older 
 
3.1.7 ECOG performance status of 0 or 1 
3.1.8 
If a female of childbearing potential, has a negative serum blood pregnancy test 
during  screening and a negative urine pregnancy test within 3 days prior to 
receiving the first dose of study drug. If the screening serum test is done within 3 
days prior to receiving the first dose of study drug, a urine test is not required. If 
a patient is of childbearing potential the patient must agree to use effective 
contraception (see Appendix C for acceptable methods) during the study and for 
120 days after the last dose of study drug.  Non-childbearing potential is defined 
as (by other than medical reasons): 
 ≥45 years of age and has not had menses for >2 years 
 Amenorrheic for <2 years without a hysterectomy and oophorectomy 
and a follicle-stimulating hormone value in the postmenopausal range 
upon pre-study (screening) evaluation 
• 
Post hysterectomy, oophorectomy or tubal ligation. Documented 
hysterectomy or oophorectomy must be confirmed with medical 
records of the actual procedure or confirmed by an ultrasound. Tubal 
ligation must be confirmed with medical records of the actual 
procedure otherwise the patient must be willing to use 2 adequate 
barrier methods throughout the study, starting with the screening visit 
through 120 days after the last dose of study drug 

 
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3.1.9 If male, agrees to use an adequate method of contraception (see Appendix C) 
starting with the first dose of study drug through 120 days after the last dose 
of study drug 
3.1.10 Life expectancy of greater than 3 months 
3.1.11 Patients must have the ability to understand and the willingness to sign a 
written informed consent document. 
3.1.12 Adequate bone-marrow, liver, and renal function as assessed by the 
following laboratory requirements within 4 weeks of starting treatment 
• 
Absolute neutrophil count >1,500 per uL 
• 
Hemoglobin > 9 g/dL 
• 
Platelets >100,000 per uL 
• 
Creatinine < 1.5 x ULN OR Creatinine clearance (CrCl) > 60 by Cockcroft-
Gault Equation if Creatinine >1.5 
• 
AST and ALT < 2.5 x ULN (< 5 x ULN if documented liver metastases) 
• 
Total bilirubin <1.5 ULN OR direct bilirubin < ULN if total bilirubin > 1.5 x ULN 
• 
INR < 2.0 
3.1.13 Experienced resolution of toxic effect(s) of the most recent prior anti-
cancer therapy to Grade <1 (except alopecia or neuropathy). If patient 
underwent major surgery or radiation therapy of >30 Gy, they must have 
recovered from the toxicity and/or complications from the intervention. 
 
3.2  Exclusion Criteria 
3.2.1 History or current evidence of any condition, therapy, or laboratory 
abnormality that might confound the results of the study, interfere with the 
patient’s participation for the full duration of the study, or is not in the best 
interest of the patient to participate, in the opinion of the treating 
Investigator, including, but not limited to: 
a) Myocardial infarction or arterial thromboembolic events within 6 months 
prior to screening or severe or unstable angina, New York Heart Association  
(NYHA) Class III or IV disease, or a QTc interval > 470 msec. 
b) Uncontrolled hypertension or diabetes mellitus. 
c) Another known malignancy that is progressing or requires active treatment. 

 
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d) Any prior history of other cancer within the prior 5 years with the exception 
of adequately treated basal cell carcinoma or cervical intraepithelial neoplasia 
[CIN]/cervical carcinoma in situ or melanoma in situ).  
e) Active infection requiring systemic therapy 
f) Known active central nervous system (CNS) metastases and/or 
carcinomatous meningitis. 
3.2.2 Any contraindication to oral agents or significant nausea and vomiting, 
malabsorption, or significant small bowel resection that, in the opinion of 
the investigator, would preclude adequate absorption. 
3.2.3 Allergy to benzamide, inactive components of entinostat, or any of the 
other administered therapies 
3.2.4 
Known psychiatric or substance abuse disorders that would interfere with 
cooperation with the requirements of the study. 
3.2.5 
Currently participating and receiving study therapy or has participated in a study 
of an investigational agent and received study therapy or used an investigational 
device within 4 weeks of the first dose of study drug. 
 
 3.2.6 If female, is pregnant or breastfeeding. 
3.2.7 Known G6PD deficiency, severe psoriasis, porphyria, macular 
degeneration, or severe diabetic retinopathy due to greater potential HCQ 
toxicity 
3.2.8 Patients with pre-existing hypertension should be on a stable 
antihypertensive regimen and have a blood pressure ≤ 150/100 mmHg at 
the time of enrollment. 
3.2.9 Evidence or history of bleeding diathesis. Any hemorrhage or bleeding event 
of CTCAE grade 3 or higher within 4 weeks of start of study medication 
 
3.2.10 Non-healing wound, ulcer, or bone fracture 
3.2.11 Patients using warfarin are excluded.  Patients using other oral or 
parenteral anticoagulation are not excluded provided they are on a stable 
dose of anticoagulant but must undergo more frequent platelet count 
monitoring (see section 4.8). 
 
 

 
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4.0  TREATMENT PLAN 
Table 2:  Dosing Schedule 
Drug 
Dose 
Route 
Schedule 
Regorafenib 
160 mg daily 
Oral 
Daily for 21 days of each 
28-day cycle 
Entinostat 
2-5 mg weekly 
Oral 
Days 1, 8, 15, and 22 of 
each 28-day cycle 
Hydroxychloroquine 
400-1200 mg daily 
Oral 
Days 1-28 of each 28-day 
cycle 
 
4.1  Regorafenib Dosing 
All patients will receive regorafenib at the FDA-approved dose of 160 mg by mouth daily 
for days 1-21 of a 28-day cycle.  As noted below, dose decreases of regorafenib are often 
required in the initial cycle, followed by tolerance of full doses in subsequent cycles: 
such manipulations of the regorafenib dose are standard, and will not be taken into 
account in determining the MTD.  Should excess toxicity attributable to regorafenib be 
repeatedly observed, the principal investigator may institute a standard initial dose 
escalation period.  This will consist of regorafenib 80mg daily for the first 7 days of 
therapy, followed by increase to 120 mg for days 8-14 if 80mg tolerated, and 160 mg for 
days 15 and beyond if 120 mg tolerated. 
 
4.2  Phase I Dose Escalation of Hydroxychloroquine and Entinostat 
We expect that the full doses of each drug will be well-tolerated based on previous 
studies.  Patients will begin treatment with weekly oral entinostat and daily oral HCQ 
given in divided doses, per Table 3 below. The starting phase I total daily dose for HCQ 
is 600 mg, based on our previous Phase I trials. Weekly dosing of entinostat has been 
established as the best balance between toxicity due to accumulation and drug 
pharmacodynamics.  Entinostat is currently undergoing study at a dose of 5mg weekly in 
a phase III trial in breast cancer, and 5mg weekly will be the target dose for this study.  
Given the potential for overlapping toxicities in this combination, an initial dose of 3 mg 
will be used, with subsequent escalation. 
 

 
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Three patients will be treated at the starting doses, with escalation to an entinostat dose of 
5mg at dose level 2 followed by dose escalation of HCQ to 1200 mg/daily at dose level 3, 
with expansion to a total of 6 patients once safety has been established.  Dose levels 2A 
and 2B will not be used during the dose escalation phase, they will be used only if de-
escalation from dose level 3 is required.  Toxicity attributable to hydroxychloroquine is 
not expected given its excellent tolerability in multiple phase II studies with combination 
chemotherapy using 1200 mg per day.  In the event that dose level 3 exceeds the MTD 
(as described below), provision is made for stepwise dose de-escalation by 200 mg to 
dose levels 2B (1000 mg total daily dose HCQ) then 2A (800 mg total daily dose HCQ). 
 
Before accrual to the next dose level may begin, all patients in the first cohort must 
complete the first 4 weeks of treatment, permitting toxicities to be assessed. The target 
DLT rate is ≤ 33%. The MTD will be defined as a) the dose producing DLT in 1 out of 6 
patients, or b) the dose level below the dose which produced DLT in ≥ 2 out of 3 patients, 
or in ≥ 2 out of 6 patients. The rules for dose escalation and cohort size are outlined in 
Table 3. No intra-patient dose escalation is planned. 
 
Table 3: Hydroxychloroquine and Entinostat Phase I: Dose Escalation Schema 
Dose 
Level 
Dose Hydroxychloroquine 
(mg/day) 
Schedule of HCQ 
Administration 
Dose 
Entinostat 
-1 
400 mg 
200 mg q12h 
2 mg weekly 
1 
600 mg 
200 mg qAM/ 400 mg qPM 
3 mg weekly 
2 
600 mg 
200 mg qAM/ 400 mg qPM 
5 mg weekly 
2A 
800 mg 
400mg qAM/400mg qPM 
5 mg weekly 
2B 
1000 mg 
400mg qAM/600mg qPM 
5 mg weekly 
3 
1200 mg 
600 mg q12h 
5 mg weekly 
 
Tablets of HCQ are available in 200 mg strengths. HCQ will be administered in two 
divided doses daily. When taking HCQ twice daily, the two daily doses should be taken 
as close as possible to 12 hours apart. Patients will be instructed to swallow the whole 
tablet in rapid succession without chewing.  Patients receiving antacids, sucralfate, 
cholestyramine, and/or bicarbonate should have the HCQ and entinostat drug doses 
administered at least 1 hour before or 2 hours after these medications. 
 

 
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4.3  Phase II Dose Expansion 
To determine the recommended phase II dose (RP2D), at least 6 patients must be treated 
at the MTD for 2 cycles.  In order to fulfill this criterion, patients who go off study before 
the completion of 2 cycles for reasons other than toxicity (e.g. disease progression) will 
be replaced in this cohort.  The RP2D will be defined as a dose in which fewer than 33% 
of patients have a DLT and at which chronic administration is tolerated.  To evaluate for 
chronic toxicity, tolerability is defined as 4 out of 6 patients treated for 2 cycles at the 
RP2D receiving during cycle 2: 
1) At least 80% (in total mg per cycle) of the regorafenib dose at which the patient 
begins cycle 2 
2) At least 75% of entinostat doses, with no more than one dose reduction 
3) At least 80% (in total mg per cycle) of the HCQ doses 
 
Should chronic tolerability fail to be demonstrated at the initial RP2D, the previous dose 
level (or a lower dose level at the discretion of the principal investigator) will be 
expanded until at least 6 patients have been treated at this new RP2D for 2 cycles. 
Evaluation for chronic tolerability will be performed as above after 2 cycles until the 
RP2D is determined. 
 
After determination of the RP2D, an additional 20 patients will be enrolled at this dose 
level in the Phase II portion. 
 
4.4  Experimental Drug Compliance 
Treatment compliance to entinostat and HCQ will be assessed at the end of each cycle. 
Patients will complete a diary to document their weekly intakes. They will be instructed 
to return all unused drugs (partially used and empty containers) and their diary at each 
visit. Site staff will perform accountability of the returned drug and will assess patient 
compliance. Site staff must ensure that the patient clearly understands the directions for 
self-medication and follows the schedule. 
 
 

 
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4.5  DLT Definition and Escalation Decision Process 
Dose Limiting Toxicities will be defined by toxicity occurring during the first 4 weeks of 
this study. Any non-hematologic AE of Grade 3 or higher that is judged to be probably 
treatment-related will be considered a DLT with the exceptions of fatigue; rash 
attributable to regorafenib; or nausea, vomiting, or diarrhea that has improved to Grade < 
1 within 72 hours.  Any non-hematologic AE of Grade 4 or higher of any duration that is 
judged to be probably treatment-related will be considered a DLT except for elevations of 
lipase and/or amylase in the absence of clinical pancreatitis. 
 
The following hematologic DLT will be considered if any occurs in the first cycle: 
1) grade 4 neutropenia lasting more than 7 days 
2)  febrile neutropenia (T > 100.4 F in presence of ANC <500) 
3)  platelet count less than 25,000/mm3 
4)  platelet count less than 50,000/mm3 with clinically significant hemorrhage 
 
If a DLT is observed in exactly 1 patient in the first cohort of 3, the cohort will be 
expanded to 6. If a DLT occurs in 2 or more patients per cohort, then the cohort one dose 
below will be the declared the MTD provided that at least 6 patients have been treated at 
that level with fewer than one third having DLTs. The rules for dose escalation and 
cohort size are outlined in Table 3. No intra-patient dose escalation is planned. 
 
Evaluable Patients: Patients will be evaluable for toxicity if they have taken one dose of 
HCQ and entinostat.  Patients who experience a dose-limiting toxicity will be evaluable 
for the cohort after at least one dose of HCQ and one dose of entinostat.  To be 
considered for evaluability in a Phase I cohort in the absence of dose-limiting toxicity, 
patients should have completed > 85% of HCQ doses, and at least 3 of 4 entinostat doses.  
Phase II patients will be evaluable for response if they have completed 85% of their 
expected dose of HCQ and at least 3 doses of entinostat in the initial 4 weeks, in the 
absence of progression. Patients who do not meet these criteria will be replaced. In the 
unexpected event of excess toxicity at dose level 1, there is provision (Table 3) for a dose 
reduction of both HCQ and entinostat. 
 

 
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Table 4: Phase I: Criteria for Dose Escalation and Cohort Size 
Number of patients with DLT 
Rule 
0/3 DLT 
Escalate 
1/3 DLT 
Increase cohort to 6 patients 
≥ 2/3 DLT 
De-escalate dose 
 
If the cohort size is increased to 6 patients, the following rules apply 
 
 
Number of patients with DLT 
Rule 
1/6 DLT 
Escalate 
2/6 DLT 
MTD is next lower dose 
≥ 3/6 DLT 
De-escalate dose 
The doses of entinostat and HCQ will remain the same for each patient throughout 
treatment unless there is a need for a dose decrease for toxicity.  These DLT decisions are 
assuming the toxicity is characteristic of entinostat or HCQ. 
 
DLT determination is complex in this three-drug combination, and should the DLT 
toxicities be more likely associated with regorafenib, a lower dose of regorafenib may be 
required. 
 
4.6 Duration of Treatment 
Patients will continue therapy on 28-day cycles until disease progression or the 
constraints of this therapy are deemed to be detrimental to the patient’s health. In this 
event, the protocol should be discontinued. Furthermore, the protocol will be 
discontinued should the patient withdraw consent.  All patients in whom protocol therapy 
has been discontinued will be followed for progression of disease and survival. 
 
4.7  Measurement of Response 
Patients will be assessed on regularly prescribed intervals in order to determine if there is 
evidence of disease progression. A CT or MRI of the abdomen/pelvis and chest (if 
thoracic disease is present) will be obtained at 8 and 16 weeks, then every 8-12 weeks per 
standard practice. 
 
 

 
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4.8  Laboratory Testing 
Patients will have laboratory testing at the pre-treatment screening visit, cycle 1 day 1, and 
cycle 1 day 15 as described in the schedule of events (Appendix A), including complete 
blood count with differential and comprehensive metabolic panel with magnesium and 
phosphorous.  Complete blood counts will be continued every two weeks until week 8, and 
then every four weeks if the hematologic toxicity is tolerable.  Comprehensive metabolic 
panel, magnesium, and phosphorous will be checked every 4 weeks after the initial testing 
unless there is concerning toxicity.  CEA will be checked at baseline, and, if it is elevated 
above the laboratory upper limit of normal, will be checked on day 1 of each 28-day cycle.  
Prothrombin time (PT) and activated prothromboplastin time (aPTT) will be checked at 
baseline.  Patients on non-prophylactic anticoagulation will have a complete blood count 
weekly for cycles 1 and 2, and every 2 weeks with subsequent cycles. 
 
For correlative pharmacodynamic testing, blood samples for peripheral blood mononuclear 
cells (PBMCs) will be obtained on cycle 1 day 1 (prior to therapy administration), cycle 1 
day 2, and cycle 1 day 15.  As in our previous study, autophagy inhibition will be assessed 
using western analysis of autophagy markers in PBMCs.   HDAC inhibition will be 
measured through multiparametric flow cytometric analysis of histone and non-histone 
targets of de-acetylation enzymes in PBMCs63 in collaboration with Dr Jane Trepel, NIH.  
In addition, the effects of the treatment on lymphocyte subsets will be analyzed by flow 
cytometry.64  The procedures for this are further described in the laboratory manual. 
 
4.9  Tumor Biopsy 
All patients receiving treatment on this trial should have available archival tumor tissue 
for analysis.  This tissue should be that which was procured at the time of diagnosis and 
prior to treatment either through colonoscopic biopsy, surgical excision, or core biopsy of 
a metastatic site.  Formalin-fixed, paraffin-embedded tissue will suffice. About 20 
unstained slides, 5 microns thick will be requested.  During the phase II portion of the 
study, additional tumor biopsy samples will be obtained in consenting patients with 
accessible disease between day 15 and day 22 of cycle 1, as permitted by scheduling of 
the procedure.  In these paired biopsy samples, analysis of antigens including FOXO1 

 
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expression, localization, phosphorylation, and acetylation will be performed before and 
after treatment.  Gene expression will also be analyzed in these patients by RNA-Seq and 
cytokine analysis will be performed in collaboration with Drs Downes and Evans at Salk. 
 
4.10  Gene Expression Profiling 
For the tumor genomic characterization, we plan to submit all patients’ baseline tumor 
biopsies for NGS analysis in a CLIA-approved test developed in the Department of 
Pathology at Penn (CPD Solid Tumor Panel, version 2), or equivalent, or more in-depth 
analysis as funding may permit. 
 
5.0  DOSE MODIFICATIONS 
Toxicity will be graded using the NCI Common Toxicity Criteria, CTCAE v. 4.03, which 
is available on the NCI website www.ctep.cancer.gov.  As specified in the following 
tables, dose modification should be based upon the worst grade of toxicity experienced. 
Dose reductions should be continued for subsequent cycles.  Exceptions may be made 
after discussion with the Principal Investigator. 
 
5.1.  Regorafenib 
Interrupt regorafenib for the following: 
• NCI CTCAE Version 4.03 grade 2 hand-foot skin reaction (HFSR) [palmar-plantar 
erythrodysesthesia (PPE)] that is recurrent or does not improve within 7 days despite 
dose reduction; interrupt therapy for a minimum of 7 days for grade 3 HFSR 
• Symptomatic Grade 2 hypertension 
• Any NCI CTCAE v4.03 Grade 3 or 4 adverse reaction attributable to regorafenib 
 
Reduce the dose of regorafenib to 120 mg: 
• For the first occurrence of Grade 2 HFSR of any duration 
• After recovery of any Grade 3 or 4 adverse reaction attributed to regorafenib 
• For Grade 3 aspartate aminotransferase (AST)/ alanine aminotransferase (ALT) 
elevation (see Note below) 
 

 
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Reduce the dose of regorafenib to 80 mg: 
• For re-occurrence of Grade 2 HFSR at the 120 mg dose 
• After recovery of any Grade 3 or 4 adverse reaction at the 120 mg dose (except 
hepatotoxicity) 
 
Discontinue regorafenib permanently for the following: 
• Failure to tolerate 80 mg dose 
• Any occurrence of AST or ALT more than 20 times the upper limit of normal (ULN) 
Grade 4 
• Any occurrence of AST or ALT more than 3 times ULN with concurrent bilirubin more 
than 2 times ULN 
• For any of the following complications:  gastrointestinal perforation/fistula, hemorrhage 
(severe or life-threatening), reversible posterior leukoencephalopathy syndrome (RPLS), 
wound dehiscence 
 
Note:  With regorafenib, as many as a third of patients may require dose decreases.  
These can often be temporary and patients can often be re-dosed at starting doses after 
resolution of toxicity. 
 
5.2  Entinostat 
All dose modifications should be based on the AE requiring the greatest modification and 
should be properly documented in source documents. Investigators may take a more 
conservative approach than the guidelines outlined below on the basis of clinical 
judgment that is in the best interest of the subject. 
 
Management of toxicities that are at least possibly related to entinostat, with toxicities 
graded by the Investigator according to the NCI, CTCAE, version 4.03 should be 
managed as follows: 
 

 
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P
Table 5:  Dose Reductions for Entinostat-Related Non-Hematologic Toxicity1 
Non-hematologic Toxicity 
Toxicity 
Dose Modifications 
Grade 4 
Administer symptomatic remedies/ start prophylaxis. 
Hold doseP   until recovery to Grade 1 or baseline under the following 
directions: 
1. 
If recovered within 4 weeks of onset (ie: ≤3 missed doses) , 
resume study drug as follows: 
 
If receiving 5 mg, restart study drug at 3 mg 
 
If receiving 3 mg, restart study drug at 2 mg 
 
If receiving 2 mg, discontinue study treatment 
2. 
If not recovered within 4 weeks, permanently discontinue study drug. 
Grade 3 
Administer symptomatic remedies/ start prophylaxis. Hold dose until recovery 
to Grade 1 or baseline under the following directions: 
1. If recovered within 1 week, resume study drug at prior dose. If not 
recovered within 1 week, continue to hold dose. 
2. If recovered within 2-4 weeks, resume study drug as follows: 
 
If receiving 5 mg, restart study drug at 3 mg 
 
If receiving 3 mg, restart study drug at 2 mg 
 
If receiving 2 mg, permanently discontinue study drug 
3. If not recovered within 4 weeks, permanently discontinue study drug.  
Recurrence of 
the same ≥ 
Grade 3 toxicity 
despite dose 
reduction 
 
If the same ≥ Grade 3 event recurs: 
1. Administer symptomatic remedies/ start prophylaxis. Hold1 dose until 
recovery to Grade 1 or baseline. 
2. If recovered within 2 weeks, resume study drug as follows: 
 If receiving 5 mg, restart study drug at 3 mg 
 If receiving 3 mg, restart study drug at 2 mg 
 If receiving 2 mg, permanently discontinue study drug 
3. If the same ≥ Grade 3 event recurs (i.e., third occurrence) despite 
entinostat dose reduction to 2 mg, as described above, discontinue 
study drug. 
≤Grade 2 
Administer symptomatic remedies / start prophylaxis. 
Dosing of study drug may be interrupted at the Investigator’s discretion. 
 If dose is held for 4 consecutive weeks, permanently discontinue 
study drug.
1
 
 If toxicity resolves, resume entinostat at the original dose. 
 
1:  If greater than 50% of doses are missed during any 6 week period, patients may be 
discontinued from study drug treatment, in the absence of extenuating circumstances. 
 

 
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Table 6:  Dose Reductions for Entinostat-Related Hematologic Toxicity1 
Hematologic Toxicity 
Toxicity 
Dose Modifications 
≥Grade 3 
neutropenia, 
≥Grade 3 
uncomplicated 
thrombocytopenia, 
or Grade 2 
complicated 
thrombocytopenia 
 
Administer symptomatic remedies/ start prophylaxis. 
Hold dose1P until recovery to Grade 1 or study baseline under the following 
direction: 
1. If not recovered by next scheduled dose, skip the dose. If recovered 
by next scheduled dose, resume study drug at prior dose. 
2. If receiving 2 mg dose, and not recovered by either of the next 2 
scheduled 
doses, 
permanently 
discontinue 
study 
treatment. 
Otherwise, skip each dose. If recovered for either of these doses, 
resume study drug as follows: 
 
If receiving 5 mg, restart study drug at 3 mg. 
 
If receiving 3 mg, restart study drug at 2 mg. 
3. If not recovered within 4 weeks, permanently discontinue study drug. 
Recurrence of the 
same hematologic 
toxicity 
If the same hematologic toxicity recurs: 
1. Administer symptomatic remedies/ start prophylaxis. Hold1 dose until 
recovery to Grade 1 or baseline. 
2. If recovered within 2 weeks, resume study drug as follows: 
 If receiving 5 mg, restart study drug at 3 mg 
 If receiving 3 mg, restart study drug at 2 mg 
 If receiving 2 mg, permanently discontinue study drug 
3. If the same ≥ Grade 3 event recurs (i.e., third occurrence) despite 
entinostat dose reduction to 2 mg, as described above, permanently 
discontinue study drug. 
1:  If greater than 50% of doses are missed during any 6 week period, patients may be 
discontinued from study drug treatment, in the absence of extenuating circumstances. 
 
5.3  Hydroxychloroquine 
 
5.3.1  Dose Modification for Hydroxychloroquine 
Any AE of ≥ Grade 3 and attributed as possibly, probably or definitely related to HCQ 
will result in the dose being held until the AE has resolved to ≤ grade 1 or baseline. If the 
AE resolves, reinstitution of treatment can occur at either the previous or reduced dose as 
described in Table 2 at the discretion of the investigator. 
 
If the AE recurs at the reduced dose, treatment will be held until the AE has resolved to ≤ 
grade 1 and when resolved treatment can be reinstituted at the next lower dose level. 

 
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Toxicities that may be attributable to HCQ include nausea, vomiting, diarrhea, rash, and 
visual field deficit. If any of these AEs occur at grade ≤ 2, HCQ may be continued and 
the AE managed with supportive care. For any AE with a grade ≥ 3, the dose of HCQ 
should be held until the toxicity resolves to grade 1 (or is found to be unrelated to HCQ). 
 
With particular regard to visual field deficits patients should be cautioned to report any 
visual symptoms, particularly difficulty seeing entire words or faces, intolerance to glare, 
decreased night vision, or loss of peripheral vision. These symptoms of peripheral 
retinal toxicity should prompt drug discontinuation and ophthalmologic evaluation. 
 
Table 7:  Dose Reductions for Regorafenib 
Drug 
Starting Dose 
Dose Level -1 
Dose Level -2 
Regorafenib 
160 mg daily 
120 mg daily 
80 mg daily 
 
6.0  DRUG INFORMATION 
6.1  Regorafenib 
6.1.1 Other names:  BAY 73-4506 
 
6.1.2 Commericial name:  Stivarga 
6.1.3 Availability:   Regorafenib is commercially available as 40 mg tablets and 
is available through the hospital pharmacy 
6.1.4 Route of administration:  Oral 
6.1.5 Storage and Stability:  Regorafenib tablets are supplied in packages 
containing three bottles, with each bottle containing 28 tablets, for a total of 84 
tablets per package.  Store regorafenib at 25°C (77°F); excursions are permitted 
from 15 to 30°C (59 to 86°F).  Store tablets in the original bottle and do not 
remove the desiccant. Keep the bottle tightly closed after first opening.  Discard 
any unused tablets 28 days after opening the bottle. Dispose of unused tablets in 
accordance with local requirements 
6.1.6 Nursing/Patient Instructions:  Take regorafenib at the same time each day 
with a low-fat breakfast. 
 

 
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6.1.7  Table 8:  Potential Toxicities of Regorafenib (from Stivarga Package Insert) 
Adverse Reactions 
STIVARGA 
(N=500) 
Placebo 
(N=253) 
Grade 
Grade 
All % 
≥ 3 % 
All % 
≥ 3 % 
General disorders and administration 
site conditions 
Asthenia/fatigue 
Pain 
Fever 
 
 
64 
29 
28 
 
 
15 
3 
2 
 
 
46 
21 
15 
 
 
9 
2 
0 
Metabolism and nutrition disorders 
Decreased appetite and food intake 
 
47  
 
5  
 
28  
 
4 
Skin and subcutaneous tissue disorders 
HFSR/PPES 
Rash 
 
45 
26 
 
17 
6 
 
7 
4 
 
0 
<1 
Gastrointestinal disorders 
Diarrhea 
Mucositis 
 
43 
33 
 
8 
4 
 
17 
5 
 
2 
0 
Investigations 
Weight loss 
 
32 
 
<1 
 
10 
 
0 
Infections and infestations 
Infection 
 
31 
 
9  
 
17 
 
6 
Vascular disorders 
Hypertension 
Hemorrhage* 
 
30 
21 
 
8 
2 
 
8 
8 
 
<1 
<1 
Respiratory, thoracic and mediastinal 
disorders 
Dysphonia 
30 
0 
6 
0 
Nervous system disorders 
Headache 
10 
 <1 
7 
0 
 
* Fatal outcomes observed. 
 
Other clinically important adverse reactions observed more commonly in less than 10% 
of Stivarga-treated patients and at a higher incidence than in placebo-treated patients 
included the following: alopecia (7.6% vs. 1.6%), taste disorder (7.6% vs. 2.4%), 
musculoskeletal stiffness (6.0% vs. 2.0%), dry mouth (4.8% vs. 2.0%), hypothyroidism 
(4.2% vs. 0.4%), tremor (2.0% vs. 0.0), gastroesophageal reflux (1.4% vs. 0.0), and 
gastrointestinal fistula (0.8% vs. 0.4%). 
 
Keratoacanthoma/squamous cell carcinoma of the skin occurred in 0.09% of 1100 
Stivarga-treated patients across open-label or placebo-controlled clinical trials. 
 
**For complete information about regorafenib, please see the FDA package insert 
 

 
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6.2  Entinostat 
 
6.2.1 Other names:  MS-275, SNDX0275 
6.2.2 Availability:  Entinostat is not commercially available and will be supplied 
by Syndax at no cost to participants 
6.2.3 Route of administration:  Oral 
6.2.4 Nursing/Patient Instructions:  Entinostat is to be taken on an empty 
stomach, at least 2 hours after a meal and at least 1 hour before the next 
meal.  If entinostat is vomited, dosing should not be re-administered but 
instead the dose should be skipped. 
 
For weekly (or less frequent) dosing: 
 
If an entinostat dose is missed, it may be taken up to 48 hours after the 
scheduled dosing time. If it is not taken within the 48 hour window, the 
dose should not be taken and should be counted as a missed dose. The 
patient should take the next scheduled dose per protocol. 
6.2.5 Storage and Stability:  Entinostat is an oral drug supplied by Syndax as 
pink to light red (1 mg) or yellow (5 mg) as polymorph B coated tablets. 
Each tablet contains mannitol, sodium starch glycolate, hydroxypropyl 
cellulose, potassium bicarbonate, and magnesium stearate as inert fillers. 
The film coating consists of hypromellose, talc, titanium dioxide, and 
ferric oxide pigments (red and yellow) as colorants. Entinostat is to be 
stored at controlled room temperature (15ºC to 25ºC) in a secure, locked 
storage area to which access is limited.  Entinostat is to be protected from 
light and not to be exposed to extremes of temperature (greater than 30ºC 
or less than 5ºC). The pharmacist should dispense the investigational 
material to the patient at appropriate intervals throughout the study in 
childproof containers. 
 
 
 

 
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6.2.6 Table 9:  Potential Toxicities of Entinostat 
Adverse Events with Possible 
Relationship to MS-275 (SNDX-275, entinostat) 
 (CTCAE 4.0 Term) 
[n= 215] 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
Anemia 
 
 
 
Febrile neutropenia 
 
GASTROINTESTINAL DISORDERS 
 
Abdominal pain 
 
 
Constipation 
 
Diarrhea 
 
 
 
Dyspepsia 
 
 
Flatulence 
 
Nausea 
 
 
Vomiting 
 
 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
 
Edema limbs 
 
Fatigue 
 
 
 
Fever 
 
 
Non-cardiac chest pain 
 
INFECTIONS AND INFESTATIONS 
 
Infection2 
 
INVESTIGATIONS 
 
Alanine aminotransferase increased 
 
 
Alkaline phosphatase increased 
 
 
Aspartate aminotransferase increased 
 
 
Blood bilirubin increased 
 
 
Creatinine increased 
 
 
Lymphocyte count decreased 
 
Neutrophil count decreased  
 
Platelet count decreased 
 
 
 
Weight loss 
 
 
White blood cell decreased 
 

 
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Adverse Events with Possible 
Relationship to MS-275 (SNDX-275, entinostat) 
 (CTCAE 4.0 Term) 
[n= 215] 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
 
METABOLISM AND NUTRITION DISORDERS 
Anorexia 
 
 
 
Dehydration 
 
 
Hyperglycemia 
 
Hypoalbuminemia 
 
 
 
Hypocalcemia 
 
 
Hypokalemia 
 
 
Hypomagnesemia 
 
Hyponatremia 
 
 
Hypophosphatemia 
 
 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
 
Arthralgia 
 
 
Back pain 
 
 
Generalized muscle weakness 
 
 
Myalgia 
 
 
Pain in extremity 
 
NERVOUS SYSTEM DISORDERS 
 
Dysgeusia 
 
Headache 
 
 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
 
Cough 
 
Dyspnea 
 
 
 
Epistaxis 
 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
 
 
Erythema multiforme 
SURGICAL AND MEDICAL PROCEDURES 
 
Surgical and medical procedures - Other 
(packed RBC transfusion) 
 
 
 
 

 
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6.2.7  Prohibited Concomitant Medications 
 
The following medications are excluded while the patient is receiving entinostat: 
 
Any other HDAC inhibitor, including valproic acid 
 
DNA methyltransferase inhibitors 
 
Any additional anticancer agents, such as chemotherapy, immunotherapy, targeted 
therapy, biological response modifiers, or endocrine therapy, will not be allowed, even if 
utilized as treatment of non-cancer indications. 
 
Any investigational agents 
 
Radiation therapy 
Note: Radiation therapy to a symptomatic solitary lesion or to the brain may be 
considered on an exceptional case-by-case basis after consultation with Sponsor. The 
patient must have clear measurable disease outside the radiated field. Administration 
of palliative radiation therapy will be considered clinical progression. 
 
Traditional herbal medicines; these therapies are not fully studied and their use may result in 
unanticipated drug-drug interactions that may cause or confound the assessment of toxicity 
 
Medications to be Avoided During the Study: 
 
Sensitive substrates of CYP1A2, CYP2C8, CYP3A with a narrow therapeutic window  
(see Appendix) 
 
Drugs that are known to inhibit or induce P-gp (see Appendix B) 
 
6.3  Hydroxychloroquine 
 
6.3.1 Generic name:  Hydroxychloroquine sulfate 
 
6.3.2 Commercial name:  Plaquenil 
6.3.2 Availability:  Hydroxychloroquine is commercially available and patients 
will be given prescriptions to be filled at their local pharmacy 
6.3.4 Route of administration:  Oral 
6.3.5 Nursing/Patient Instructions:  Hydroxychloroquine should be taken by 
swallowing the whole tablet in rapid succession without chewing.  Patients 
receiving antacids, sucralfate, cholestyramine, and/or bicarbonate should 
have the HCQ drug dose administered at least 1 hour before or 2 hours 
after these medications. 
 

 
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6.3.6  Table 10:  Potential Toxicities of Hydroxychloroquine 
Central Nervous 
System 
Irritability, nervousness, emotional changes, nightmares, 
psychosis, headache, dizziness, vertigo, seizure, ataxia, lassitude 
Dermatologic 
Bleaching of hair, alopecia, pigmentation changes (skin and 
mucosal; black-blue color), rash (urticarial, morbilliform, 
lichenoid, maculopapular, purpuric, erythema annulare 
centrifugum, Stevens-Johnson syndrome, acute generalized 
exanthematous pustulosis, and exfoliative dermatitis) 
Gastrointestinal 
Anorexia, nausea, vomiting, diarrhea, abdominal cramping 
Hematologic 
Aplastic anemia, agranulocytosis, leukopenia, thrombocytopenia, 
hemolysis (in patients with glucose-6-phosphate deficiency) 
Hepatic 
Abnormal liver function/hepatic failure (isolated cases) 
Neuromuscular & 
Skeletal 
Myopathy leading to progressive weakness and atrophy of 
proximal muscle groups (may be associated with mild sensory 
changes, loss of deep tendon reflexes, and abnormal nerve 
conduction) 
Ocular 
Disturbance in accommodation, keratopathy, corneal 
changes/deposits (visual disturbances, blurred vision, photophobia 
- reversible on discontinuation), macular edema, atrophy, 
abnormal pigmentation, retinopathy (early changes reversible - 
may progress despite discontinuation if advanced), optic disc 
pallor/atrophy, attenuation of retinal arterioles, pigmentary 
retinopathy, scotoma, decreased visual acuity, nystagmus 
 
**For complete information about hydroxychloroquine, please see the FDA package insert 
 
7.0  STATISTICS 
7.1  Primary Endpoints 
7.1.1  Phase I 
The Phase I methodology will be a standard Phase I escalating trial with three patients 
per level, expanding to six patients per level in the event of dose-limiting toxicity at any 
level, and provision for expansion to 20 additional patients at the recommended Phase II 
dose to better characterize the optimal dose and the variation in toxicity at that level. A 
minimum of 4 weeks of combination therapy with hydroxychloroquine, entinostat, and 
regorafenib are required in the third patient before escalation to the next dose is initiated. 
At the MTD, at least 6 patients must be treated for 2 cycles to evaluate chronic toxicity 
and determine the RP2D (see section 4.3 for details). 
 

 
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We will calculate the percentage of subjects with toxicities at each dose level. We expect 
that doses close to full single agent doses will be tolerable.  Three patients will be 
initially treated at each dose level.  The plan for escalation is described below: 
 
Three patients will initially be treated at each dose level. 
 
If 0/3 patients experience DLT, then the dose will be escalated. 
 
If 2-3/3 patients experience DLT, then the MTD has been exceeded. Three additional 
patients are treated at the previous dose (if only 3 had been treated) as a total of 6 patients 
must be treated at the MTD. 
 
If 1/3 patients experience DLT, then 3 additional patients are treated. If none of the 
additional patients develop DLT, then the dose will be escalated, otherwise escalation 
ceases and the previous dose will be expanded to a total of 6 patients. 
 
To assure safety in this phase I study, the operating characteristics of the escalation rule 
to be employed have been determined. The operating characteristics denote the 
probability of escalation to the next dose level, for a given true DLT rate. For a true DLT 
that is high, we desire the probability of escalation to be low. As noted in the table, the 
probability of escalating beyond a certain dose level, if that dose level truly has a 10% 
DLT rate, is 0.91. On the other hand, if the true DLT rate is 40%, there is only a 31% 
chance of dose escalation. 
 
Table 11:  Operating Characteristics of the Escalation Rule 
True DLT Rate 
Probability of Escalation 
.1 
.91 
.2 
.71 
.3 
.49 
.4 
.31 
.5 
.17 
.6 
.08 
.7 
.03 
.8 
.01 
 

 
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7.1.2  Phase II 
Single agent regorafenib showed ORR of 1% in phase III trials in advanced colorectal cancers. 
We anticipate being able to improve this response rate substantially, perhaps to 15% or more. 
We will enroll a total 26 patients at the RP2D, including those treated during the phase I 
portion of the study.  Sample size calculations are based on an assumption of at least 20 
evaluable patients.  With 20 patients, an exact binomial test with a 0.05 one-sided significance 
level will have 84% power to detect an improvement from the historical rate (null hypothesis 
proportion) of 1% to an improved rate (alternative proportion) of 15%. 
 
7.2  Secondary endpoints 
Progression-free survival, overall survival, and duration of response will be calculated 
with 95% confidence intervals.  Toxicity rates will also be calculated by category with 
95% confidence intervals.  With 20 subjects, we have a 88% chance of observing, at least 
once, any toxicity occurring at a rate of 10% or higher. 
 
We will use response as the primary efficacy marker to investigate the relationship 
between changes in autophagy and protein lysine acetylation markers and the efficacy of 
treatment.  We will summarize time-to-event outcomes (time to progression, survival 
time and duration of response) with Kaplan-Meier survival curves. We will also analyze 
toxicity including changes in counts, and degree of non-hematologic toxicity, according 
to the pharmacodynamic markers.  Analyses of mutational profiles and correlatives from 
tumor biopsies (if obtained) will be exploratory. 
 
7.3  Sample Size/Accrual Rate 
Phase I: The phase I study will involve six possible dose levels, although accrual at more 
than 3 or 4 levels is very unlikely. The total sample size will range from a minimum of 12 
to a maximum of 24 patients. We expect accrual to be completed within 6-9 months. 
 
Phase II: During the Phase II portion we will enroll up to 20 additional patients and 
expect an accrual time of approximately 1 year. 
 
7.4  Statistical Software 
All analyses, except as otherwise noted, will be performed using either SAS or STATA. 
 

 
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8.0  SAFETY AND ADVERSE EVENTS 
8.1 Definitions 
8.1.1  Adverse Event 
An adverse event (AE) is any symptom, sign, illness or experience that develops or 
worsens in severity during the course of the study. The CTC version 4.0 will be used to 
grade toxicity. Intercurrent illnesses or injuries should be regarded as adverse events. 
Abnormal results of diagnostic procedures are considered to be adverse events if the 
abnormality: 
 
Results in study withdrawal 
 
Is associated with a serious adverse event 
 
Is associated with clinical signs or symptoms 
 
Leads to additional treatment or to further diagnostic tests 
 
Is considered by the investigator to be of clinical significance 
8.1.2.  Serious Adverse Event 
Adverse events are classified as serious or non-serious. A serious adverse event is any 
AE that is: 
 
Fatal 
 
Life-threatening 
 
Requires or prolongs hospital stay 
 
Results in persistent or significant disability or incapacity 
 
A congenital anomaly or birth defect 
 
An important medical event 
 
Pregnancy 
8.1.3  Important Medical Events 
Important medical events are those that may not be immediately life threatening, but are 
clearly of major clinical significance. They may jeopardize the patient, and may require 
intervention to prevent one of the other serious outcomes noted above. All adverse events 
that do not meet any of the criteria for serious should be regarded as non-serious adverse 
events. 
 

 
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8.2.  Post-study 
All unresolved adverse events should be followed by the investigator until the events are 
resolved, the patient is lost to follow-up, or the adverse event is otherwise explained. At 
the last scheduled visit, the investigator should instruct each patient to report any 
subsequent event(s) that the patient, or the patient’s personal physician, believes might 
reasonably be related to participation in this study. 
 
8.3  Abnormal Laboratory Values 
A clinical laboratory abnormality should be documented as an adverse event if the 
abnormality is of a degree, typically at least grade 2 and not present as grade 1 or higher 
at baseline, that requires active management; e.g. change of dose, discontinuation of the 
drug, more frequent follow-up assessments, further diagnostic investigation. 
 
8.4  Hospitalization, Prolonged Hospitalization or Surgery 
Any adverse event that results in hospitalization or prolonged hospitalization should be 
documented and reported as a serious adverse event unless specifically instructed 
otherwise in this protocol. Any condition responsible for surgery should be documented 
as an adverse event if the condition meets the criteria for an adverse event. 
 
Neither the condition, hospitalization, prolonged hospitalization, nor surgery are reported 
as an adverse event in the following circumstances: 
 
Hospitalization or prolonged hospitalization for diagnostic or elective surgical procedures 
for a preexisting condition. Surgery should not be reported as an outcome of an adverse 
event if the purpose of the surgery was elective or diagnostic and the outcome was 
uneventful. 
 
Hospitalization or prolonged hospitalization required to allow efficacy measurement for 
the study. 
 
Hospitalization or prolonged hospitalization for therapy of the target disease of the study, 
unless it is a worsening or increase in frequency of hospital admissions as judged by the 
clinical investigator. 
 

 
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8.5 Recording of Adverse Events 
At each contact with the patient, the investigator must seek information on adverse events by 
specific questioning and, as appropriate, by examination. Information on all adverse events 
should be recorded immediately in the source document, and also in the appropriate adverse 
event module of the case report form (CRF). All clearly related signs, symptoms, and 
abnormal diagnostic procedures results should recorded in the source document, though 
should be grouped under one diagnosis. All adverse events occurring during the study period 
must be recorded. The clinical course of each event should be followed until resolution, 
stabilization, or until it has been determined that the study treatment or participation is not the 
cause. Serious adverse events that are still ongoing at the end of the study period must be 
followed up to determine the final outcome. Any serious adverse event that occurs after the 
study period and is considered to be possibly related to the study treatment or study 
participation should be recorded and reported immediately. 
 
8.6 Reporting of Serious Adverse Events 
8.6.1 Study Sponsor Notification by Investigator 
A serious adverse event must be reported to the study sponsor within 24 hours of the 
event. Report serious adverse events by phone and facsimile to: 
Peter O’Dwyer, MD 
Phone: 215-360-0716 
Fax: 215-349-8551 
or via the HUP page operator at 215-662-4000 
 
At the time of the initial report, the following information should be provided: 
• Study identifier 
• Study Center 
• Patient number 
• A description of the event 
• Date of onset 
• Current status 
• Whether study treatment was discontinued 
• The reason why the event is classified as serious 
• Investigator assessment of the association between the event and study treatment 
 

 
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8.6.2 IRB Notification by Investigator-sponsor 
Reports of all serious adverse events (including follow-up information) must be 
submitted to the IRB within 10 working days, according to IRB guidelines. 
 
Reporting Process to IRB 
Principal Investigators are required to submit reports of unanticipated problems posing 
risks to subjects or others that are probably or definitely study related via the HS-ERA 
system within 10 working days of the event. 
 
For reportable deaths, the initial submission to the IRB may be made by contacting the 
appropriate IRB coordinator as soon as the death is known, with a report via HS-ERA 
within 10 days if death is from underlying disease and within 24 hours if study related 
activity is considered contributory to the death. 
 
8.6.3 FDA Notification by Investigator-sponsor, Voluntary 
The study sponsor shall notify the FDA by telephone or by facsimile transmission of any 
unexpected fatal or life-threatening experience associated with the use of the drug as soon 
as possible but no later than 7 calendar days from the sponsor’s original receipt of the 
information. If a previous adverse event that was not initially deemed reportable is later 
found to fit the criteria for reporting, the study sponsor will submit the adverse event in a 
written report to the FDA as soon as possible, but no later than 15 calendar days from the 
time the determination is made. 
 
8.6.4  Sponsor Notification 
The investigator must inform Syndax in writing using a SAE form or MEDWATCH 
3500A form of any SAE within 24 hours of being aware of the event.  The date of 
awareness should be noted on the report.  The written report must be completed and 
supplied to Syndax within 24 hours/1 business day at the latest on the following working 
day.  The initial report must be as complete as possible, including details of the current 
illness and (serious) adverse event, and an assessment of the causal relationship between 
the event and the investigational product(s).  Information not available at the time of the 
initial report (e.g., an end date for the adverse event or laboratory values received after 
the report) must be documented on a follow-up report.  A final report to document 

 
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resolution of the SAE is required.  If this is a multicenter trial, participating study sites 
must report SAEs to Syndax as described and within 24 hours of awareness.  
Participating sites should also report SAEs to the primary study site. 
 
SAES should be sent via email or fax to: 
aereporting@syndax.com 
1-781-419-1420 
9.0. DATA HANDLING AND RECORD KEEPING 
9.1  Confidentiality 
Information about study subjects will be kept confidential and managed according to the 
requirements of the Health Insurance Portability and Accountability Act of 1996 (HIPAA). 
Those regulations require a signed subject authorization informing the subject of the following: 
 
What protected health information (PHI) will be collected from subjects in this study 
 
Who will have access to that information and why 
 
Who will use or disclose that information 
 
The rights of a research subject to revoke their authorization for use of their PHI 
In the event that a subject revokes authorization to collect or use PHI, the investigator, by 
regulation, retains the ability to use all information collected prior to the revocation of 
subject authorization. For subjects that have revoked authorization to collect or use PHI, 
attempts should be made to obtain permission to collect at least vital status (i.e. that the 
subject is alive) at the end of their scheduled study period 
 
9.2  Source Documents 
Source data is all information, original records of clinical findings, observations, or other 
activities in a clinical trial necessary for the reconstruction and evaluation of the trial. 
Source data are contained in source documents.  Examples of these original documents, 
and data records include: hospital records, clinical and office charts, laboratory notes, 
memoranda, subjects’ diaries or evaluation checklists, pharmacy dispensing records, 
recorded data from automated instruments, copies or transcriptions certified after 
verification as being accurate and complete, microfiches, photographic negatives, 
microfilm or magnetic media, x-rays, subject files, and records kept at the pharmacy, at 
the laboratories, and at medico-technical departments involved in the clinical trial. 
 

 
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9.3  Case Report Forms 
The study case report form (CRF) is the primary data collection instrument for the study. 
All data requested on the CRF must be recorded. All missing data must be explained. 
Data will be collected using CRFs designed, stored and secured in Velos. 
 
9.4  Study Monitoring, Auditing and Inspecting 
The investigator will permit study-related monitoring, audits, and inspections by the IRB, 
the sponsor, government regulatory bodies, and the ACC CRU monitors of all study 
related documents (e.g. source documents, regulatory documents, data collection 
instruments, study data etc.). The investigator will ensure the capability for inspections of 
applicable study-related facilities (e.g. pharmacy, diagnostic laboratory, etc.).   
Participation as an investigator in this study implies acceptance of potential inspection by 
government regulatory authorities and applicable University compliance and quality 
assurance offices. Vivek Narayan, MD will act as medical monitor for this study. 
 
10.0  MEASUREMENT OF EFFECT 
Response and progression will be evaluated in this study using the new international 
criteria proposed by the revised Response Evaluation Criteria in Solid Tumors (RECIST) 
guideline (version 1.1) [Eur J Ca 45:228-247, 2009]. Changes in the largest diameter 
(unidimensional measurement) of the tumor lesions and the shortest diameter in the case 
of malignant lymph nodes are used in the RECIST criteria. 
 
10.1 Definitions 
Evaluable for toxicity: All patients will be evaluable for toxicity from the time of their 
first treatment on study. 
 
Evaluable for objective response: Only those patients who have measurable disease present at 
baseline, have received at least one cycle of therapy, and have had their disease re-evaluated 
will be considered evaluable for response. These patients will have their response classified 
according to the definitions stated below. (Note: Patients who exhibit objective disease 
progression prior to the end of cycle 1 will also be considered evaluable.) 
 

 
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Evaluable Non-Target Disease Response: Patients who have lesions present at baseline 
that are evaluable but do not meet the definitions of measurable disease, have received at 
least one cycle of therapy, and have had their disease re- evaluated will be considered 
evaluable for non-target disease. The response assessment is based on the presence, 
absence, or unequivocal progression of the lesions. 
 
10.2 Disease Parameters 
Measurable disease: Measurable lesions are defined as those that can be accurately 
measured in at least one dimension (longest diameter to be recorded) as >20 mm by chest 
x-ray, as >10 mm with CT scan, or >10 mm with calipers by clinical exam. All tumor 
measurements must be recorded in millimeters (or decimal fractions of centimeters). 
 
Malignant lymph nodes: To be considered pathologically enlarged and measurable, a 
lymph node must be >15 mm in short axis when assessed by CT scan (CT scan slice 
thickness recommended to be no greater than 5 mm). At baseline and in follow-up, only 
the short axis will be measured and followed. 
 
Non-measurable disease: All other lesions (or sites of disease), including small lesions 
(longest diameter <10 mm or pathological lymph nodes with ≥ 10 to <15 mm short axis), 
are considered non-measurable disease. Bone lesions, leptomeningeal disease, ascites, 
pleural/pericardial effusions, lymphangitis cutis/pulmonitis, inflammatory breast disease, 
and abdominal masses (not followed by CT or MRI), are considered as non-measurable. 
Note: Cystic lesions that meet the criteria for radiographically defined simple cysts 
should not be considered as malignant lesions (neither measurable nor non- measurable) 
since they are, by definition, simple cysts. 
 
‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable 
lesions, if they meet the definition of measurability described above. However, if non-
cystic lesions are present in the same patient, these are preferred for selection as target 
lesions. 
 

 
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Target lesions: All measurable lesions up to a maximum of 2 lesions per organ and 5 lesions 
in total, representative of all involved organs, should be identified as target lesions and 
recorded and measured at baseline. Target lesions should be selected on the basis of their 
size (lesions with the longest diameter), be representative of all involved organs, but in 
addition should be those that lend themselves to reproducible repeated measurements. It 
may be the case that, on occasion, the largest lesion does not lend itself to reproducible 
measurement in which circumstance the next largest lesion which can be measured 
reproducibly should be selected. A sum of the diameters (longest for non-nodal lesions, 
short axis for nodal lesions) for all target lesions will be calculated and reported as the 
baseline sum diameters. If lymph nodes are to be included in the sum, then only the short 
axis is added into the sum. The baseline sum diameters will be used as reference to further 
characterize any objective tumor regression in the measurable dimension of the disease. 
 
Non-target lesions: All other lesions (or sites of disease) including any measurable 
lesions over and above the 5 target lesions should be identified as non-target lesions and 
should also be recorded at baseline. Measurements of these lesions are not required, but 
the presence, absence, or in rare cases unequivocal progression of each should be noted 
throughout follow-up. 
 
10.3 Methods for Evaluation of Measurable Disease 
All measurements should be taken and recorded in metric notation using a ruler or calipers. All 
baseline evaluations should be performed as closely as possible to the beginning of treatment 
and never more than 4 weeks before the beginning of the treatment. 
 
The same method of assessment and the same technique should be used to characterize 
each identified and reported lesion at baseline and during follow-up. Imaging-based 
evaluation is preferred to evaluation by clinical examination unless the lesion(s) being 
followed cannot be imaged but are assessable by clinical exam. 
 
10.3.1 Clinical lesions 
Clinical lesions will only be considered measurable when they are superficial (e.g., skin 
nodules and palpable lymph nodes) and <10 mm diameter as assessed using calipers (e.g., 

 
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skin nodules). In the case of skin lesions, documentation by color photography, including 
a ruler to estimate the size of the lesion, is recommended. 
 
10.3.2  Conventional CT and MRI 
This guideline has defined measurability of lesions on CT scan based on the assumption 
that CT slice thickness is 5 mm or less. If CT scans have slice thickness greater than 5 
mm, the minimum size for a measurable lesion should be twice the slice thickness. MRI 
is also acceptable in certain situations (e.g. for body scans). 
 
Use of MRI remains a complex issue. MRI has excellent contrast, spatial, and temporal 
resolution; however, there are many image acquisition variables involved in MRI, which 
greatly impact image quality, lesion conspicuity, and measurement. Furthermore, the 
availability of MRI is variable globally. As with CT, if an MRI is performed, the 
technical specifications of the scanning sequences used should be optimized for the 
evaluation of the type and site of disease. Furthermore, as with CT, the modality used at 
follow-up should be the same as was used at baseline and the lesions should be 
measured/assessed on the same pulse sequence. It is beyond the scope of the RECIST 
guidelines to prescribe specific MRI pulse sequence parameters for all scanners, body 
parts, and diseases. Ideally, the same type of scanner should be used and the image 
acquisition protocol should be followed as closely as possible to prior scans. Body scans 
should be performed with breath-hold scanning techniques, if possible. 
 
10.3.3 PET-CT 
At present, the low dose or attenuation correction CT portion of a combined PET-CT is 
not always of optimal diagnostic CT quality for use with RECIST measurements. 
However, if the site can document that the CT performed as part of a PET-CT is of 
identical diagnostic quality to a diagnostic CT (with IV and oral contrast), then the CT 
portion of the PET-CT can be used for RECIST measurements and can be used 
interchangeably with conventional CT in accurately measuring cancer lesions over time. 
Note, however, that the PET portion of the CT introduces additional data which may bias 
an investigator if it is not routinely or serially performed. 
 

 
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10.3.4 Ultrasound 
Ultrasound is not useful in assessment of lesion size and should not be used as a method 
of measurement. Ultrasound examinations cannot be reproduced in their entirety for 
independent review at a later date and, because they are operator dependent, it cannot be 
guaranteed that the same technique and measurements will be taken from one assessment 
to the next. If new lesions are identified by ultrasound in the course of the study, 
confirmation by CT or MRI is advised. If there is concern about radiation exposure at 
CT, MRI may be used instead of CT in selected instances. 
 
10.3.5 Tumor markers 
Tumor markers alone cannot be used to assess response. If markers are initially above the 
upper normal limit, they must normalize for a patient to be considered in complete 
clinical response. 
 
10.3.6 Cytology, Histology 
The cytological confirmation of the neoplastic origin of any effusion that appears or 
worsens during treatment when the measurable tumor has met criteria for response or 
stable disease is mandatory to differentiate between response or stable disease (an 
effusion may be a side effect of the treatment) and progressive disease. 
 
10.3.7 FDG-PET 
While FDG-PET response assessments need additional study, it is sometimes reasonable 
to incorporate the use of FDG-PET scanning to complement CT scanning in assessment 
of progression (particularly possible 'new' disease). New lesions on the basis of FDG-
PET imaging can be identified according to the following algorithm: 
• 
Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of 
PD based on a new lesion. 
• 
No FDG-PET at baseline and a positive FDG-PET at follow-up: If the positive 
FDG-PET at follow-up corresponds to a new site of disease confirmed by CT, this 
is PD. If the positive FDG-PET at follow-up is not confirmed as a new site of 
disease on CT, additional follow-up CT scans are needed to determine if there is 
truly progression occurring at that site (if so, the date of PD will be the date of the 

 
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initial abnormal FDG-PET scan). If the positive FDG-PET at follow-up 
corresponds to a pre-existing site of disease on CT that is not progressing on the 
basis of the anatomic images, this is not PD. 
 
Note: A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake 
greater than twice that of the surrounding tissue on the attenuation corrected image. 
 
10.4 Response Criteria 
10.4.1.  Evaluation of Target Lesions 
Complete Response (CR):  Disappearance of all target lesions. Any pathological lymph 
nodes (whether target or non-target) must have reduction in short axis to <10 mm. 
 
Partial Response (PR):  At least a 30% decrease in the sum of the diameters of target 
lesions, taking as reference the baseline sum diameters 
 
Progressive Disease (PD):  At least a 20% increase in the sum of the diameters of target 
lesions, taking as reference the smallest sum on study (this includes the baseline sum if 
that is the smallest on study). In addition to the relative increase of 20%, the sum must 
also demonstrate an absolute increase of at least 5 mm. (Note: the appearance of one or 
more new lesions is also considered progressions). 
 
Stable Disease (SD):  Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD, taking as reference the smallest sum diameters while on study 
 
10.4.2 Evaluation of Non-Target Lesions 
Complete Response (CR):  Disappearance of all non-target lesions and normalization of tumor 
marker level. All lymph nodes must be non-pathological in size (<10 mm short axis) 
 
Note: If tumor markers are initially above the upper normal limit, they must normalize 
for a patient to be considered in complete clinical response. 
 
Non-CR/Non-PD:  Persistence of one or more non-target lesion(s) and/or maintenance of 
tumor marker level above the normal limits 
 

 
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Progressive Disease (PD):  Appearance of one or more new lesions and/or unequivocal 
progression of existing non-target lesions. Unequivocal progression should not normally 
trump target lesion status. It must be representative of overall disease status change, not a 
single lesion increase. 
 
Although a clear progression of “non-target” lesions only is exceptional, the opinion of 
the treating physician should prevail in such circumstances, and the progression status 
should be confirmed at a later time by the review panel (or Principal Investigator). 
 
10.4.3  Evaluation of Best Overall Response 
The best overall response is the best response recorded from the start of the treatment until 
disease progression/recurrence (taking as reference for progressive disease the smallest 
measurements recorded since the treatment started). The patient's best response assignment 
will depend on the achievement of both measurement and confirmation criteria. 
 
Table 12:  Evaluation of Patients with Measurable Disease 
Target 
Lesions 
Non-Target 
Lesions 
New 
Lesions 
Overall 
Response 
Best Overall Response when 
Confirmation is Required* 
CR 
CR 
No 
CR 
>4 wks. Confirmation** 
CR 
Non- CR/Non-
PD 
No 
PR 
>4 wks. Confirmation** 
 
CR 
Not evaluated 
No 
PR 
PR 
Non- CR/Non- 
PD/not evaluated 
No 
PR 
SD 
Non- CR/Non- 
PD/not evaluated 
No 
SD 
documented at least once >4 
wks. from baseline** 
PD 
Any 
Yes or No 
PD 
no prior SD, PR or CR 
 
Any 
PD*** 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
* See RECIST 1.1 manuscript for further details on what is evidence of a new lesion. ** Only 
for non-randomized trials with response as primary endpoint.*** In exceptional circumstances, 
unequivocal progression in non-target lesions may be accepted as disease progression. 
Note: Patients with a global deterioration of health status requiring discontinuation of treatment 
without objective evidence of disease progression at that time should be reported as 
“symptomatic deterioration.” Every effort should be made to document the objective 
progression even after discontinuation of treatment. 
 

 
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Table 13:  Evaluation of Patients with Non-Measurable Disease 
Non-Target Lesions 
New Lesions 
Overall Response 
CR 
No 
CR 
Non-CR/non-PD 
No 
Non-CR/non-PD* 
Not all evaluated 
No 
not evaluated 
Unequivocal PD 
Yes or No 
PD 
Any 
Yes 
PD 
* ‘Non-CR/non-PD’ is preferred over ‘stable disease’ for non-target disease since 
SD is increasingly used as an endpoint for assessment of efficacy in some trials so 
to assign this category when no lesions can be measured is not advised 
 
10.4.3 Duration of Response 
Duration of overall response: The duration of overall response is measured from the time 
measurement criteria are met for CR or PR (whichever is first recorded) until the first 
date that recurrent or progressive disease is objectively documented (taking as reference 
for progressive disease the smallest measurements recorded since the treatment started). 
The duration of overall CR is measured from the time measurement criteria are first met 
for CR until the first date that progressive disease is objectively documented. 
 
Duration of stable disease: Stable disease is measured from the start of the treatment until 
the criteria for progression are met, taking as reference the smallest measurements 
recorded since the treatment started, including the baseline measurements. 
 
11.0  ETHICAL CONSIDERATIONS 
This study is to be conducted according to US and international standards of Good 
Clinical Practice (FDA Title 21 part 312 and International Conference on Harmonization 
guidelines), applicable government regulations and Institutional research policies and 
procedures. 
 
This protocol and any amendments will be submitted to a properly constituted 
independent Ethics Committee (EC) or Institutional Review Board (IRB), in agreement 
with local legal prescriptions, for formal approval of the study conduct. The decision of 

 
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the EC/IRB concerning the conduct of the study will be made in writing to the 
investigator and a copy of this decision will be provided to the sponsor before 
commencement of this study. The investigator should provide a list of EC/IRB members 
and their affiliate to the sponsor. 
 
All subjects for this study will be provided a consent form describing this study and 
providing sufficient information for subjects to make an informed decision about their 
participation in this study. This consent form will be submitted with the protocol for review 
and approval by the EC/IRB for the study. The formal consent of a subject, using the 
EC/IRB-approved consent form, must be obtained before that subject is submitted to any 
study procedure. This consent form must be signed by the subject or legally acceptable 
surrogate, and the investigator- designated research professional obtaining the consent. 
 
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15.  Jain RK. Normalization of tumor vasculature: an emerging concept in antiangiogenic 
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27.  Weichert W, Röske A, Niesporek S, et al.  Class I histone deacetylase expression has 
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33.  Mahalingam D, Mita M, Sarantopoulos J, et al. Combined autophagy and HDAC 
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26;381(9863):303-12. 
 

 
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37.  Li J, Qin S, Xu R, et al. Regorafenib plus best supportive care versus placebo plus 
best supportive care in Asian patients with previously treated metastatic colorectal cancer 
(CONCUR): a randomised, double-blind, placebo-controlled, phase 3 trial.  Lancet 
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rheumatoid arthritis. Ann Intern Med 2001;134(8):695-706. 
 
40.  Romanelli F, Smith KM, Hoven AD. Chloroquine and hydroxychloroquine as 
inhibitors of human immunodeficiency virus (HIV-1) activity. Curr Pharm Des 
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41.  Toler SM. Oxidative stress plays an important role in the pathogenesis of drug-
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42.  Poole B, Ohkuma S. Effect of weak bases on the intralysosomal pH in mouse 
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44.   Sotelo J, Briceno E, Lopez-Gonzalez MA. Adding chloroquine to conventional 
treatment for glioblastoma multiforme: a randomized, double-blind, placebo-controlled 
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45.  Munster T, Gibbs JP, Shen D, et al. Hydroxychloroquine concentration-response 
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46.  Projean D, Baune B, Farinotti R, et al. In vitro metabolism of chloroquine: 
identification of CYP2C8, CYP3A4, and CYP2D6 as the main isoforms catalyzing N-
desethylchloroquine formation. Drug Metab Dispos 2003;31(6):748-54. 
 
47.  Somer M, Kallio J, Pesonen U, et al. Influence of hydroxychloroquine on the 
bioavailability of oral metoprolol. Br J Clin Pharmacol 2000;49(6):549-54. 
 
48.  Maturi RK, Yu M, Weleber RG. Multifocal electroretinographic evaluation of long-
term hydroxychloroquine users. Arch Ophthalmol 2004;122(7):973-81. 

 
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49.  Rosenfeld MR, Ye X, Supko JG, et al. A phase I/II trial of hydroxychloroquine in 
conjunction with radiation therapy and concurrent and adjuvant temozolomide in patients 
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51.  Lim HS, Im JS, Cho JY, et al. Pharmacokinetics of hydroxychloroquine and its 
clinical implications in chemoprophylaxis against malaria caused by Plasmodium vivax. 
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52.  Tett S, Cutler DJ, Day RO, et al. Bioavailability of hydroxychloroquine tablets in 
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53.  Carmichael SJ, Charles B, Tett SE. Population pharmacokinetics of 
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54.  Ryan QC, Headlee D, Acharya M, et al. Phase I and pharmacokinetic study of MS-
275, a histone deacetylase  inhibitor, in patients with advanced and refractory solid 
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55.  Prince HM, Bishton MJ, Harrison SJ. Clinical studies of histone deacetylase 
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56.  Gore L, Rothenberg ML, O'Bryant CL, et al. A phase I and pharmacokinetic study of 
the oral histone deacetylase inhibitor, MS-275, in patients with refractory solid tumors 
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57.  Gojo I, Jiemjit A, Trepel JB, et al. Phase 1 and pharmacologic study of MS-275, a 
histone deacetylase inhibitor, in adults with refractory and relapsed acute leukemias. 
Blood. 2007 Apr 1;109(7):2781-90. 
 
58.  Kummar S, Gutierrez M, Gardner ER, et al. Phase I trial of MS-275, a histone 
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59.  Yardley DA, Ismail-Khan RR, Melichar B, et al. Randomized phase II, double-blind, 
placebo-controlled study of exemestane with or without entinostat in postmenopausal 

 
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women with locally recurrent or metastatic estrogen receptor-positive breast cancer 
progressing on treatment with a nonsteroidal aromatase inhibitor. J Clin Oncol. 2013 Jun 
10;31(17):2128-35. 
 
60.  Witta SE, Jotte RM, Konduri K, et al. Randomized phase II trial of erlotinib with and 
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61.  Hauschild A, Trefzer U, Garbe C, et al. Multicenter phase II trial of the histone 
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Erratum in: Lancet Oncol. 2015 Mar;16(3):e105. 
 
 
 
 

 
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Appendix A:  Schedule of Events 
Pre-study evaluations including scans are to be conducted within 28 days prior to start of 
protocol therapy. Laboratory assessments are to be done within 5 days of scheduled date.  If 
correlative biopsies are not obtained due to lack of funding, these omissions will not be 
considered protocol deviations. 
 
Pre- 
Study 
Cycle 1 (28 days) 
 
Cycle 2 (28 days) 
Cycle 3 and later 
cycles (28 days) 
Day 1 
Day 2 
Day 15 
Day 1 
Day 15 
Day 1 
Office Visit1 
X 
X 
 
X 
X 
 
X 
 
Treatment 
HCQA 
 
X---------------------------------------------------------------------------X 
RegorafenibB 
 
X---------------------------------------------------------------------------X 
EntinostatC 
 
X---------------------------------------------------------------------------X 
 
Tests and Observations 
Informed consent 
X 
 
 
 
 
 
 
Inclusion/exclusion criteria 
X 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
Medical history 
X 
 
 
 
 
 
 
Concurrent meds 
X 
X 
 
X 
X 
 
X 
Physical exam2 
X 
X 
 
X 
X 
 
X 
Vital signs3 
X 
X 
 
X 
X 
 
X 
Height 
X 
 
 
 
 
 
 
Weight 
X 
X 
 
X 
X 
 
X 
Performance status 
X 
X 
 
X 
X 
 
X 
Adverse event evaluation 
 
X 
 
X 
X 
 
X 
 
Laboratory Studies 
Complete blood count with 
differential4 
X 
X 
 
X 
X 
X 
X 
PT/aPTT5 
X 
 
 
 
 
 
 
Chemistry profile6  
X 
X 
 
X 
X 
 
X 
CEA7 
X 
X 
 
 
X 
 
X 
Urine or Serum B-HCG 
(women of childbearing 
potential)8 
X 
X8 
 
 
 
 
 
 
Radiologic Evaluations 
CT/MRI9 
X 
 
 
 
 
 
X 
 
Research Correlates 
PBMCs for PD Analysis10 
 
X 
X 
X 
 
 
 
Tumor Biopsies11 
 
 
 
X 
 
 
 
 
 
 

 
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A:  HCQ will be administered according to Section 4.2 (days 1-28).  See Section 5.0 for dose modifications. 
B:  Regorafenib will be administered at 160 mg (Days 1-21), unless adjusted as per Section 4.1.  See 
Section 5.0 for dose modifications. 
C:  Entinostat will be administered according to Section 4.2 (Days 1, 8, 15, 22).  See Section 5.0 for dose 
modifications. 
1:  The pre-study visit must be within 28 days of starting therapy (Cycle 1 Day 1).  Office visits should 
occur within 1 week of the originally scheduled date.  Longer delays should be discussed with the 
principal investigator. 
2:  Complete physical exam will be completed at baseline; focused physical examinations will be 
conducted thereafter. 
3:  Blood pressure, heart rate, oxygen saturation, temperature 
4:  After Cycle 2, done Day 1 of each cycle, provided that hematologic toxicity is tolerable.  Patients on 
non-prophylactic anticoagulation must have CBC weekly for cycles 1 and 2 and every 2 weeks with 
subsequent cycles. 
5:  Screening or Cycle 1 Day 1 only. 
6:  Na, K, Ca, Mg, phosphorus, BUN, creatinine, glucose, alkaline phosphatase, AST, ALT, total 
bilirubin, albumin, total protein.   After Cycle 1, done Day 1 of each cycle unless concerning toxicity 
7:  CEA will be checked at baseline.  If it is elevated, it will be checked on day 1 of each cycle, otherwise 
it will not be routinely followed. 
8:  Serum B-HCG will be checked at screening and either urine or serum B-HCG must be checked within 
3 days of initiation of study drug 
9:  Radiologic evaluations (CT preferred, MRI acceptable; PET/CT only if required per treating 
physician) of the abdomen/pelvis and chest (if thoracic disease is present) and tumor measurements will 
be performed at baseline (within 4 weeks of study therapy), at Cycle 3 Day 1 and Cycle 5 Day 1 (or 
within 2 weeks), then every 8-12 weeks per standard practice. Scans may be evaluated for texture analysis 
as a baseline for exploratory radiomic endpoints. 
10:  Sample handling as in Laboratory Manual. 
11:  Tumor biopsies to be taken in phase II portion (when funding obtained) in subjects who meet 
eligibility at Cycle 1 between day 15 and day 22 if possible.  Archived tumor material prior to treatment 
will also be analyzed, as discussed in section 4.9. 
 
 

 
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Appendix B:  Concomitant Medications to Avoid 
 
Examples of sensitive in vivo CYP substrates and CYP substrates with narrow therapeutic range 
are summarized below. 
 
Examples of substrates that may be affected by entinostat 
CYP Enzymes   
 
Substrates with narrow therapeutic range1 
CYP1A2  
Theophylline, tizanidine 
CYP2C8   
 
Paclitaxel 
CYP3A2  
Alfentanil, astemizole3, cisapride3, cyclosporine, dihydroergotamine, 
ergotamine, fentanyl, pimozide, quinidine, sirolimus, tacrolimus, 
terfenadine3  
 
1   CYP substrates with narrow therapeutic range refers to drugs whose exposure-response 
relationship indicates that small increases in their exposure levels by the concomitant use of 
CYP inhibitors may lead to serious safety concerns (e.g., Torsades de Pointes). 
2   Because a number of CYP3A substrates (e.g., darunavir, maraviroc) are also substrates of P-
gp, the observed increase in exposure could be due to inhibition of both CYP3A and P-gp. 
3    Withdrawn from the United States market because of safety reasons. 
 
P-gp Inhibitors and Inducers 
 
Inhibitors 
Inducers 
Amiodarone, azithromycin, captopril, carvedilol, 
clarithromycin, conivaptan, diltiazem, dronedarone, 
felodipine, lopinavir,quercetin, ranolazine,ticagrelor, 
ritonavir, cyclosporine, verapamil erythromycin, 
ketoconazole,  itraconazole, quinidine 
Avasimibe, carbamazepine, phenytoin, 
rifampin, St John’s Wort, 
tipranavir/ritonavir 
 
 
 
 
 

 
UPCC 31216 (IRB # 827226) 
 
Protocol Amendment 2:   06/15/2017 
60 
Appendix C:  Medically Acceptable Methods of Birth Control 
 
Females: 
Women of child-bearing potential (as per section 3.1.8) must agree to use 2 of the following 
forms of contraception OR completely refrain from intercourse during the study and for at least 
120 days following the last dose of study drug. 
 
Males: 
Men with partners of child-bearing potential (as per section 3.1.8) must agree along with their 
partner to use 2 of the following forms of contraception OR completely refrain from intercourse 
during the study and for at least 120 days following the last dose of study drug. 
 
Acceptable methods include: 
 
Condoms 
 
Diaphragm 
 
Cervical cap 
 
Intra-uterine device 
 
Surgical sterilization (tubal ligation or vasectomy) 
 
Oral contraceptives 
 
Abstinence at certain times of the cycle, such as during ovulation or after ovulation, or 
withdrawal are not acceptable methods.  The list of methods is not exhaustive and additional 
contraception methods not included above may also be acceptable.  The study doctor must 
approve the contraceptive methods in subjects with child-bearing potential.