Safety and Tolerability of Vorinostat for the Treatment of Moderate-to-Severe Crohn s Disease

Crohn's Disease (CD), a major sub-type of inflammatory bowel disease (IBD), is a chronic,
life-long condition characterized by relapsing inflammation of the gastrointestinal (GI)
tract. Despite recent advances in IBD therapeutics, a significant number of patients with CD
continue to have significant symptoms.

In prior studies, it has been demonstrated that epigenetic modifications of the genome are
associated with and may contribute to the pathogenesis of various disease entities. One type
of epigenetic modification involves acetylation and deacetlyation of histones, mediated by
histone acetyl transferases (HATs) and histone deacetylases (HDACs). Acetylation and
deacetylation of histones regulates the affinity of histones for DNA, thus modulating the
accessibility of transcription factors to gene promoters and enhancer sites. Of interest in
this context is evidence that epigenetic modifications brought about by HDAC inhibitors
(HDACi), i.e., agents that cause hyperacetylation of histones, can limit the course of
gastrointestinal inflammation1-3. One naturally occurring HDAC inhibitor, the bacterial
product butyrate, has been shown to have effects on gene transcription 4,5 that regulate
potentially deleterious pro-inflammatory responses to microbiota in the gut environment. It
has been shown that treatment of dendritic cells and macrophages with butyrate leads to
down-regulation of lipopolysaccharide induced pro-inflammatory mediators such as nitric
oxide, IL-6 and IL-12.6 In addition, butyrate has been shown to enhance the differentiation
of intestinal Foxp3-positive T cells (T regulatory T cell (Treg) development that then
modulates GI inflammation and contributes to mucosal homeostasis7,8. Along the same lines,
another HDAC inhibitor, vorinostat, has been shown to ameliorate graft-vs-host disease (GVHD)
affecting the GI tract in patients undergoing allogeneic bone marrow transplantation9. This
anti-inflammatory effect was also attributable to increased Treg activity, suggesting that
vorinostat, like butyrate, decreases inflammation by enhancing the activity of cells with the
capacity to down-regulate immune responses. The effect of vorinostat on Treg cell expansion
in this study was particularly notable because it suggested that Treg cell numbers can be
increased by agents that have an intrinsic effect on the transcription of key Treg cell
transcription factors. On this basis, treatment of patients with inflammatory and autoimmune
diseases by influencing Treg cell numbers may be more effective than alternative existing
methods of inducing Treg cell expansion such as administration of purified Tregs.

We propose a Phase I/II clinical trial to study the safety and efficacy of vorinostat (100 mg
PO BID for 12 weeks) in treating 20 individuals with moderate-to-severe CD who are not
controlled by standard maintenance therapy. We will assess the effectiveness of vorinostat by
evaluating changes in symptom scores, endoscopic/histologic findings, and
immunologic/laboratory parameters. The participant will return to the NIH CC after starting
treatment on Days 28, 56 and Week 12 for assessing safety and testing of clinical and
immunologic response. They will return again 6 and 9 months post-treatment initiation for
safety and efficacy evaluations.

- INCLUSION CRITERIA:

1. Are 18 to 65 years of age, inclusive, at enrollment date.

2. Have a diagnosis of CD that has been endoscopically or radiographically
confirmed. A colonoscopy will be required at baseline to document mucosal disease
activity. SES-CD will be obtained with minimum score of 7.

3. Have active CD symptoms as defined by a CDAI score between 220 and 350 and
demonstrate active symptoms as defined by continued weight loss, abdominal pain
and/or diarrhea not controlled by standard therapy.

4. The participant must have active CD symptoms and therefore have had an inadequate
response to, loss of response to, or intolerance to at least 1 of the following
agent groups in control of their disease (as defined below for each individual
agent group: Corticosteroids or Immunomodulators or TNF-alpha sign antagonists or
Anti-integrin antibodies)

a. Corticosteroids

i. Signs and symptoms of persistently active disease despite a history of at
least one 4-week induction regimen that included a dose

equivalent to prednisone greater than or equal to 30 mg PO once daily (QD) for 2
weeks or intravenously (IV) for 1 week OR

ii. One failed attempt to taper corticosteroids to below a dose equivalent to
prednisone 10 mg PO QD or to taper to below a dose

of 9 mg of budesonide OR

iii. History of intolerance of corticosteroids at the discretion of the principal
investigator (PI) (including but not limited to Cushing s

syndrome, osteopenia/osteoporosis, hyperglycemia, insomnia, or infection)

b. Immunomodulators

i. Signs and symptoms of persistently active disease despite a history of at
least one 12-week regimen of oral azathioprine (AZA) (greater than or wqual to
2.5 mg/kg/Day) or 6-MP (greater than or equal to 1.5 mg/kg/Day) OR

ii. Signs and symptoms of persistently active disease despite a history of at
least one 12-week regimen of MTX (greater than or equal to 25 mg/week) OR

iii. History of intolerance of at least one immunomodulator (including but not
limited to nausea/vomiting leading to discontinuation,

abdominal pain, pancreatitis, liver function test abnormalities, lymphopenia,
thiopurine methyltransferase genetic mutation, or

serious infection)

c. TNF-alpha sign antagonists with signs and symptoms of persistently active
disease despite a history of receiving infliximab, adalimumab, or certolizumab at
a dose approved for the treatment of CD and:

i. Patient had an inadequate response after completing the full induction
regimen, per approved product labeling

ii. Responded initially but then lost response with continued therapy

iii. Patient had a significant adverse event response which precluded further use
including but not exclusion of infusion reaction, serum

sickness and/or lupus-like rash.

d. Anti-integrin antibodies: with signs and symptoms of persistently active
disease despite a history of receiving an anti-integrin antibody agent
(natalizumab or vedolizumab) at a dose approved for the treatment of CD and:

i. Patient had an inadequate response after completing the full induction
regimen, per approved product labeling

ii. Responded initially but then lost response with continued therapy

iii. Patient had a significant adverse event response which precluded further use
including but not exclusion of infusion reaction, serum

sickness and/or lupus-like reaction.

5. At the discretion of the PI, concomitant medications will be permitted if the
following conditions are met prior to baseline assessment (Day-1):

a. 5-aminosalicylic acid (ASA)-based compounds are permissible if:

i. Oral 5-ASA-based compounds must be at a stable dose for at least 3 weeks prior
to baseline or

ii. Recently discontinued oral 5-ASA-based compounds must have been discontinued
at least 3 weeks prior to baseline or

iii. Rectal 5-ASA-based compounds are not permissible during the study and must
have been discontinued at least 3 weeks prior to baseline.

b. Corticosteroids (e.g., prednisone, budesonide) are permissible if:

i. Oral corticosteroids must be at a prednisone-equivalent dose of less than or
equal to 40 mg/day, or 9 mg/day of budesonide, and have been at a stable dose for
at least 3 weeks prior to baseline or

ii. Discontinuation of oral corticosteroids must have been completed at least 3
weeks prior to baseline or

iii. Parenteral (subcutaneous, intramuscular, or IV) or rectal corticosteroids
are not permitted during the study and must not have been used within a 3-week
period prior to baseline

c. CD-specific antibiotics are permissible if using an antibiotic for treatment
of CD ( a CD-specific antibiotic i.e., metronidazole, ciprofloxacin, rifaximin,
ampicillin, sulfonamide and tetracycline)

i. Participants must have been using the antibiotic for at least 3 weeks before
baseline at a stable dose or

ii. If not currently using a CD-specific antibiotic, the stop date must have been
at least 3 weeks prior to baseline.

d. Immunomodulators are permissible if:

i. Participants receiving chronic (i.e., greater than or equal to 12 weeks)
treatment with AZA, 6-MP, or MTX prior to baseline must be on a stable dose for
at least 6- 8 weeks prior to baseline and must continue on this same dose during
the study. OR

ii. Participants who have discontinued therapy with AZA, 6-MP, or MTX must have
stopped the medication at least 4 weeks prior to baseline. OR

iii. Participants must not have received therapy with other known
immunomodulators (e.g., cyclosporine, tacrolimus, sirolimus, pentoxifylline, or
mycophenolate mofetil) or experimental agents (e.g., granulocyte- or macrophage
colony stimulating factor) for at least

8 weeks or 5 half-lives of agent from baseline, whichever is longer.

e. The use of Anti-TNF and Anti-integrin therapy or other biological therapy listed
below will not be permitted and the following washout period will be required in order
for participant to be eligible:

i. Three months washout prior to baseline for certolizumab or natalizumab.

ii. Two months washout prior to baseline for adalimumab, infliximab, and vedolizumab.

iii. 8 week washout prior to baseline for cyclosporine, pimecrolimus, tacrolimus, and any
other systemic immunosuppressant.

6. Participants must agree to have samples of their blood and tissue stored for potential
future research use.

7. Participants must have a primary medical care provider.

8. Male participants must agree to employ birth control measures to prevent pregnancy in
female partners from start of treatment, and continuing through 8 weeks post treatment.

9. Females of childbearing potential must not be breast-feeding, possibly or actually
pregnant, must not have had unprotected intercourse for one month prior to dosing, and must
agree not to become pregnant beginning from enrollment in the study to at least 8 weeks
after the end of treatment. Participants must remain completely abstinent of potentially
reproductive sexual intercourse (e.g. due to a committed lifestyle) or to consistently use
BOTH a barrier method with a spermicide (male or female condom) AND ALSO one of the below
listed methods of birth control:

1. Continuous/daily hormonal methods including oral contraceptive pills, patch,
implant/injection, etc.

2. Surgical sterilization of either partner, of sufficient duration to be effective, and
NOT known to have failed.

3. Intrauterine device.

EXCLUSION CRITERIA:

1. Presence of clinically significant systemic infection (e.g., chronic or acute
infection, urinary tract infection, or upper respiratory tract infection) within three
months of screening.

2. History or presence of recurrent or chronic infection (e.g., viral infection
[including hepatitis B or C, human immunodeficiency virus (HIV)], bacterial infection,
systemic fungal infection, or syphilis).

3. Positive for tuberculosis via PPD or QFT-G. Individuals who are known to have received
the tuberculosis vaccine will be administered the QFT-G (QuantiFERON-TB Gold), all
others will undergo PPD skin test to rule out TB.

4. A conduction abnormality on baseline electrocardiogram (ECG) that in the opinion of a
cardiologist, is deemed significant.

5. At the discretion of the investigator, off-label use of any small molecule
therapeutics that are immune modulators (e.g., naltrexone) within 90 days of beginning
screening or at any time during the 30 days of the screening window.

6. Presence of abnormal hematological and biochemical parameters, including:

1. Neutrophil count < 1500 cells/mm3.

2. Hemoglobin < 9 g/dL.

3. Platelet count less than or equal to 150,000 cells/mm3.

4. Creatinine greater than or equal to 1.2 times the upper limit of normal (ULN).

5. Alanine aminotransferase (ALT) and/or aspartate aminotransferase (AST) greater
than or equal to 1.5 times ULN.

6. Prothrombin time-international normalized ratio (PT-INR) > 1.0 ULN

7. Serum bilirubin level > 1.0 times ULN.

7. Individuals on chronic anticoagulation medications.

8. Stool sample for GI pathogens (FilmArray GI Panel testing for 22 viral, bacterial and
parasitic GI pathogens that cause infectious diarrhea) If a stool sample determined
positive for acute gastrointestinal infection with impact of occurrence on
gastrointestinal inflammation as determined by principal investigator during
screening. In addition, stool samples positive for GI pathogens will be discussed with
an infectious disease physician to determine impact of occurrence on gastrointestinal
inflammation. If the organism is thought to be pathogenic the patient will receive
appropriate treatment. This will be documented in the participant s medical record.

9. Presence of cytomegalovirus (CMV) infection as defined by positive immunohistochemical
staining on tissue intestine biopsy.

10. History of low-grade or high-grade colonic mucosal dysplasia.

11. History of bowel surgery other than perianal (e.g., fistulotomy, seton placement, or
abscess drainage) within 6 months prior to beginning the CDAI screening diary or
drawing screening blood samples.

12. Presence of surgical changes to gut anatomy that preclude administration of clinical
activity indices; this includes but is not limited to ileostomy, colostomy, or
subtotal colectomy with ileorectal anastomosis.

13. Known or suspected short bowel syndrome.

14. Requirement of parenteral, total parenteral, elemental oral, or nasogastric nutrition.

15. History of cancer, other than non-melanomatous cancer of the skin, within the past 5
years.

16. Unwillingness or inability to comply with study requirements.

17. Presence of only small bowel CD that is inaccessible by standard colonoscopy for
harvest of research biopsies. Individuals with only upper gastrointestinal CD or only
perianal fistulizing CD are also excluded for this reason.

18. Refusal to abstain from using COX-2 inhibitors or non-steroidal anti-inflammatory
drugs (NSAIDs) throughout the study agent administration period.

19. Has uncontrolled diabetes

20. Is taking anti-seizure medication, such as valproic acid or its derivative (i.e.,
Depakote)

21. Presence of any condition that, in the opinion of the investigator, contraindicates
participation in this study.

22. Has participated in another investigational trial within 8 weeks (or 5 half-lives of
any investigational study agent), whichever is greater, prior to the pre-trial
(screening) visit. The window will be derived from the last date of treatment on the
previous trial.