Cancer Vaccine Targeting Brachyury Protein in Tumors

Background:

- Vaccines based on recombinant heat inactivated yeast have been shown to be immunogenic
and well tolerated in animals and humans.

- Using a computer-based differential display analysis tool to conduct global comparison
of expressed sequence tag (EST) clusters in the Unigene database, the gene encoding for
the transcription factor Brachyury was identified as highly represented in tumor-derived
libraries and rarely observed in normal tissue-derived libraries. By using
reverse-transcription followed by polymerase chain reaction (RT-PCR), investigators in
the LTIB have identified the overexpression of Brachyury in gastrointestinal, bladder,
kidney, ovary, uterus, and testicular carcinomas. Similar studies also found
over-expression of Brachyury mRNA in cell lines of lung, colon and prostate cancers, but
not in the majority of normal tissues tested, with the exception of expression in the
testis, thyroid and low levels of expression in B cells pooled from multiple normal
donors.

- Brachyury is a member of the T-box family of transcription factors, characterized by a
highly conserved DNA-binding domain designated as T-domain. Data indicates that the
transcription factor Brachyury confers on the tumor cells a mesenchymal phenotype, as
well as migratory and invasive abilities and enhances tumor cell progression.

- A murine model of MC38 cells engineered to over express human Brachyury gene has
demonstrated increased metastatic potential of Brachyury over-expressing MC38 cells.

- Brachyury specific T cells can lyse human cancer cells expressing Brachyury in an MHC
restricted manner.

- GI-6301 (Yeast-Brachyury vaccine) has been tested in vitro and in the mouse model. These
studies showed Brachyury-specific T cell responses and decreased metastasis in mice
treated with vaccine.

- An ongoing study of a Hepatitis B vaccine (GS-4774) using the yeast platform (heat
killed Saccharomyces cerevisiae) indicated safety of 80 YU dose (4 injection sites at 20
YU injections per site).

Objectives:

-The primary objectives are to:

- Determine the safety and tolerability of escalating doses of GI-6301 (Yeast-Brachyury
vaccine) a heat-killed yeast-based vaccine

- Determine in an expanded cohort if a significant change in Brachyury specific T cells
will be detectable post vaccine.

Eligibility:

- Adults with histologically proven metastatic or locally advanced solid tumors for which
standard curative or palliative measures are no longer effective. Efforts will be made,
as much as possible, to enroll patients with tumor types with known increased expression
of Brachyury (such as lung, breast, ovarian, prostate, colorectal, pancreatic or
chordoma).

- Adequate organ function as defined by liver, kidney, and hematologic laboratory testing.

- Patients with acquired immune defects, systemic autoimmune disease, concurrent use of
steroids, pericardial mass > 1 cm, chronic infections, concurrent tricyclic
antidepressant therapy, or allergy to yeast or yeast-based products will be excluded.

Design:

- This is an open label, phase I trial with sequential dose escalation cohorts of patients
(3-6 patients per dose cohort) for 3 doses of GI-6301 (Yeast-Brachyury vaccine).

- GI-6301 (Yeast-Brachyury vaccine) will be administered subcutaneously at 4 sites
biweekly for 7 visits (day 1, 15, 29, 43, 57, 71, 85), then monthly until patients meet
off-study criteria

(patients who have been on study for one year or more and have had stable disease or better
(PR, CR) have the option to receive vaccine once every 3 months instead of monthly).

- All patients on a given dose level will have completed 28 days on-study without DLT
before enrollment can begin on the next dose level or on the expansion phase (see
statistical analysis section).

- Expansion Phase: 10 additional patients will be enrolled on the MTD dose level (or the
highest dose level explored in the event that a true MTD is not reached), receiving the
same treatment regimen, to assess for immunologic responses and clinical responses.

- Amended dose escalation: 10 patients will be enrolled at an additional dose level (80 YU
per dose, 4 injection sites at 20 YU per site) to determine the safety of this dose
level.

- Up to 33 total patients may be required to complete enrollment of this study.

- INCLUSION CRITERIA:

Participants must meet the following criteria for participation:

- Diagnosis: Patients must have histologically confirmed malignancy by the Laboratory of
Pathology, National Cancer Institute (NCI), that is metastatic or unresectable locally
advanced malignant solid tumor. In the case of Chordoma, unresectable, locally
recurrent, or metastatic tumors are acceptable for enrollment, given that this
represents incurable disease. Efforts will be made, as much as possible, to enroll
patients with tumor types with known increased expression of Brachyury (such as lung,
breast, ovarian, prostate, colorectal, pancreatic, or chordoma).

- Patients may have disease that is measurable or non-measurable but evaluable disease

- Eastern Cooperative Oncology Group (ECOG) performance status of 0 to 1 at study entry
(Karnofsky greater than or equal to 70)

- Age greater than or equal to 18 years. Because no dosing or adverse event data are
currently available on the use of Yeast Brachyury vaccine in patients <18 years of
age, children are excluded from this study, but will be eligible for future pediatric
trials.

- Prior Therapy: Completed or had disease progression on at least one prior line of
diseaseappropriate therapy for metastatic disease, or not be a candidate for therapy
of proven efficacy for their disease.

- Patients must have normal organ and marrow function as defined below:

- Serum creatinine 1.5 times upper limit of normal OR creatinine clearance on a
24-h urine collection of 60 mL/min.

- Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) 2.5 times the
upper limits of normal.

- Total bilirubin less than or equal to 1.5 times upper limit of normal OR in
patients with Gilbert's syndrome, a total bilirubin 3.0.

- Hematological eligibility parameters (within16 days of starting therapy):

- Granulocyte count 1,500/mm(3)

- Platelet count 100,000/m(3)

- Patients must have baseline pulse oximetry > 90% on room air.

- Recovered completely (Grade 1 or baseline) from any reversible toxicity associated
with recent therapy. Typically this is 3 4 weeks for patients who most recently
received cytotoxic therapy, except for the nitrosoureas and mitomycin C for which 6
weeks is needed for recovery.

- There should be a minimum of 2 weeks from any prior chemotherapy, immunotherapy and/or
radiation.

- Prior immune therapy is allowed.

- Men and women of child-bearing potential must agree to use effective birth control or
abstinence during and for a period of 4 months after the last vaccination therapy.

- Patients with prostate cancer must continue to receive gonadotropin-releasing hormone
(GnRH) agonist therapy (unless orchiectomy has been done). If a patient has refused
GnRH therapy, they may be enrolled on a dose level for which the safety has already
been determined.

- Patients with estrogen-receptor positive (ER+) breast cancer being treated with
adjuvant hormonal therapy (selective estrogen receptor modulator or aromatase
inhibitor) who have rising tumor markers as evidence of disease progression or
metastatic disease on scans may continue on hormonal therapy while being treated with
vaccine.

- Patients must be negative for yeast allergy skin test

- Ability to understand and the willingness to sign a written informed consent document.

EXCLUSION CRITERIA:

Patients with any of the following will not be eligible for participation in this study:

- Patients should have no evidence of immune dysfunction as listed below.

- Human immunodeficiency virus (HIV) positivity due to the potential for decreased
immune response to the vaccine.

- Active autoimmune diseases requiring treatment or a history of autoimmune disease that
might be stimulated by vaccine treatment. This requirement is due to the potential
risks of exacerbating autoimmunity. However, patients with vitiligo, diabetes
mellitus, and hashimoto s thyroiditis on appropriate replacement therapy may be

enrolled.

--Concurrent use of systemic steroids, except for physiologic doses of systemic steroid
replacement or local (topical, nasal, or inhaled) steroid use. Limited doses of systemic
steroids (e.g., in patients with exacerbations of reactive airway disease or to prevent
intravenous (IV) contrast allergic reaction or anaphylaxis in patients who have known
contrast allergies) are allowed.

- History of allergy or untoward reaction to yeast-based products (any hypersensitivity
to yeast-based products will be excluded).

- Pregnant or breast-feeding women, due to the unknown effects of the Yeast Brachyury
vaccine on the fetus or infant.

- Serious intercurrent medical illness which would interfere with the ability of the
patient to carry out the treatment program, including, but not limited to,
inflammatory bowel disease, Crohn's disease, ulcerative colitis, or active
diverticulitis.

- Untreated brain metastases (or local treatment of brain metastases within the last 6
months) and or spinal cord metastasis.

- Patients with pericardial masses >1 cm will be excluded.

- Concurrent chemotherapy. (However, the following anti-tumor therapies will be allowed:
Trastuzumab for human epidermal growth factor receptor 2 (HER2+) breast cancer and
hormonal therapy for breast (e.g., selective estrogen receptor modulators, aromatase
inhibitors) and prostate cancer (e.g., GnRH antagonists/agonists or antagonists and
androgen receptor antagonists).

- Chronic hepatitis infection, including B and C, because potential immune impairment
caused by these disorders may diminish the effectiveness of this immunologic therapy.

- Patients requiring continuous tricyclic antidepressant therapy should be excluded due
to the interference with the yeast skin test in creating false negative test results.

- Participation in another interventional clinical trial within 28 days before start of
study treatment.

- Any significant disease that, in the opinion of the investigator, may impair the
patient s tolerance of study treatment.

- Significant dementia, altered mental status, or any psychiatric condition that would
prohibit the understanding or rendering of informed consent.