Messenger RNA (mRNA)-Based, Personalized Cancer Vaccine Against Neoantigens Expressed by the Autologous Cancer

Background:

- Therapeutic vaccination against cancer has proven very challenging with little clinical
benefit.

- Vaccines against non-viral tumors have mainly targeted differentiation antigens, cancer
testis antigens, and overexpressed antigens. However, negative selection in the thymus
against these normal non-mutated antigens severely limits the ability to generate high
avidity anti-cancer T-cells. Such depletion can impair their antitumor activity and
limit tumor elimination.

- The National Cancer Institute Surgery Branch (NCI-SB) has developed a pipeline for the
identification of immunogenic T-cell epitopes derived from neoantigens.

- In recent studies, we identified the neoantigens recognized by tumor-infiltrating
lymphocytes (TIL) that mediated regression in patients with metastatic melanoma. Using
whole exome sequencing of a resected metastatic nodule followed by high throughput
immunologic screening, we were able to demonstrate that tumor regressions were
associated with the recognition by the administered TIL of unique somatic mutations that
occurred in the cancer.

- We also found that TIL from 29 of 32 patients with a wide variety of metastatic
gastrointestinal cancers contained lymphocytes that recognized unique mutations
presented in that patient s cancer.

- We, therefore, aim to use this pipeline to identify immunogenic neoantigens and to
predict for neoantigens binding the patient human leukocyte antigen (HLA) molecules from
melanoma or epithelial cancer patients and to use these epitopes for a personalized
therapeutic messenger RNA (mRNA) vaccine.

Objectives

Primary objectives:

- Determine the clinical response rate in patients with metastatic melanoma,
gastrointestinal or genitourinary cancers who receive NCI-4650

- Determine the safety of NCI-4650 in patients with metastatic melanoma, gastrointestinal
or genitourinary cancers

Eligibility

- Age greater than or equal to 18 years and less than or equal to 70 years

- Evaluable metastatic melanoma, gastrointestinal, or genitourinary cancers refractory to
standard of care treatment

- Metastatic cancer lesions suitable for surgical resection to perform whole exome
sequencing and preparation of TIL

Design:

- Patients with metastatic cancer will undergo surgical resection of tumor followed by
exome and RNA sequencing to identify expressed mutations. This will be conducted under
the NCI-SB cell harvest protocol 03-C-0277. (Cell Harvest and Preparation for Surgery
Branch Adoptive Cell Therapy Protocols).

- Immunogenic neoantigens will be identified from TIL by high throughput immunologic
screening using long peptides and tandem minigenes covering all mutated epitopes.

- Up to 15 predicted neoantigens will be selected based on exome and RNA sequencing and
their binding affinity to the patient HLA molecules.

- The mRNA vaccine will be manufactured and supplied as cGMP product by ModernaTX, Inc.

- The patient will be vaccinated with mRNA containing epitopes from immunogenic
neoantigens, predicted neoantigens and mutations in tumor suppressor or driver genes.

- The mRNA vaccine will be administered intramuscularly (IM) for four cycles every two
weeks. A patient may receive a second course for a total of eight cycles given.

- Blood samples will be taken every two weeks (during the vaccination period) and at each
follow-up visit, and patients will be monitored for the quantity and quality of
circulating neoantigen-specific T-cells.

- INCLUSION CRITERIA:

- Measurable (per RECIST v1.1 criteria), metastatic melanoma, gastrointestinal, or
genitourinary cancer with at least one lesion that is resectable. Only patients with
metastatic gastrointestinal cancer will be eligible for enrollment on the Phase I
portion of the study. Patients with metastatic melanoma, gastrointestinal, or
genitourinary cancer will be eligible for enrollment on the Phase II portion of the
study.

- Confirmation of diagnosis of metastatic cancer by the NCI Laboratory of Pathology.

- Patients with 3 or fewer brain metastases that are less than 1 cm in diameter and
asymptomatic are eligible. Lesions that have been treated with stereotactic
radiosurgery must be clinically stable for one month after treatment for the patient
to be eligible. Patients with surgically resected brain metastases are eligible.

- Prior therapy with at least one first-line standard of care treatment or second-line
treatment of proven effectiveness. Patients must have progressive disease after prior
treatment. Prior first-or second-line treatments would include the following:

- Patients with metastatic melanoma: Receipt of a checkpoint inhibitor as
first-line therapy

- Patients with metastatic melanoma with an activating mutation of KIT: Receipt of
Imatinib

- Patients with a BRAF V600 activating mutation: Receipt of appropriate targeted
therapy

- Patients with metastatic gastrointestinal cancer: Receipt of up to two forms of
approved first- and/or second-line chemotherapy regimens

- Patients with metastatic genitourinary cancers: Receipt of a first- or
second-line therapy appropriate for their histologic subtype

- Age greater than or equal to 18 years and less than or equal to 70 years.

- Clinical performance status of ECOG 0 or 1.

- Serology

- Seronegative for HIV antibody. (The experimental treatment being evaluated in
this protocol depends on an intact immune system. Patients who are HIV
seropositive may have decreased immune-competence and thus may be less responsive
to the experimental treatment and more susceptible to its toxicities.)

- Seronegative for hepatitis B antigen, and seronegative for hepatitis C antibody.
If hepatitis C antibody test is positive, then the patient must be tested for the
presence of antigen by RT-PCR and be HCV RNA negative.

- Hematology

- ANC > 1000/mm(3) without the support of growth factors.

- WBC greater than or equal to 3000/mm(3)

- Platelet count greater than or equal to 100.000/mm(3)

- Hemoglobin > 8.0 g/dl. Subjects may be transfused to reach this cut-off.

- Chemistry

- Serum ALT/AST less than or equal to 5.0 times ULN

- Serum creatinine <1.5 times ULN or measured creatinine clearance (calculated
using Cockcroft-Gault formula) > 40 ml/min

- Total bilirubin less than or equal to 2.0 mg/dl, except in patients with Gilbert
s Syndrome, who must have a total bilirubin < 3.0 mg/dl.

- More than four weeks must have elapsed since any prior systemic therapy at the time
the patient receives the immunization regimen, and patients toxicities must have
recovered to a grade 1 or less (except for toxicities such as alopecia or vitiligo).

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

- Subjects must be co-enrolled on protocol 03-C-0277.

EXCLUSION CRIETERIA:

- Pregnant or breastfeeding women who do not consent to stop breast-feeding while on
study treatment and for 30 days after the use of the investigational vaccine where
pregnancy is confirmed by a positive, rising hCG laboratory test.

- Women of child-bearing potential, defined as all women capable of becoming
pregnant, unless they agree to use an appropriate method of contraception during
dosing and for 120 days after the last dose (i.e., final vaccine). Effective
contraception methods include a combination of any two of the following (unless
method is abstinence or sterilization, in which only one method is required):

- Use of oral, injected or implanted hormonal methods of contraception or
other forms of hormonal contraception that have comparable efficacy (failure
rate <1%). In case of use of oral contraception, women should have been
stable on the same pill for a minimum of 6 months before taking study
treatment.

- Placement of an intrauterine device or intrauterine system.

- Barrier methods of contraception: condom or occlusive cap (diaphragm or
cervical/vault caps) with spermicidal foam/gel/film/cream/vaginal
suppository.

- Total abstinence

- Female sterilization at least eight weeks before taking study treatment.

- Male sterilization (at least six months prior to screening).

- Sexually active males must use a condom during intercourse during dosing and for 120
days after the last dose (i.e., final vaccine), and should not father a child in this
period.

- Any systemic steroid therapy or other form of immunosuppressive therapy within 7 days
of the first dose of the vaccine. A physiologic dose of systemic corticosteroids may
be approved. Inhaled or topical steroids, and less than or equal to 10 mg daily
prednisone equivalent, are permitted in the absence of active autoimmune disease.

- Active systemic infections requiring anti-infective treatment, coagulation disorders,
or any other active or uncompensated major medical illnesses of the cardiovascular,
respiratory, or immune system.

- Any form of primary immunodeficiency (such as Severe Combined Immunodeficiency
Disease).

- Concurrent opportunistic infections (the experimental treatment being evaluated in
this protocol depends on an intact immune system. Patients who have decreased immune
competence may be less responsive to the experimental treatment and more susceptible
to its toxicities).

- Any vaccinations four weeks prior to the first vaccination cycle or live vaccines at
any time during the study.