Administration of Autologous T-Cells Genetically Engineered to Express T-Cell Receptors Reactive Against Mutated Neoantigens in People With Metastatic Cancer

Background:

- The administration of autologous tumor-infiltrating lymphocytes (TIL) can mediate
complete, durable regressions in 20-25% of patients with metastatic melanoma. Recent
studies have shown that these TIL predominantly recognize unique mutated neoantigens
expressed by the cancer not shared by other melanomas.

- Administration of bulk autologous TIL to patients with a variety of other solid cancers,
including cancers of the gastrointestinal tract and genitourinary tract, have little if
any therapeutic impact.

- Recent studies in the National Cancer Institute Surgery Branch, (NCI-SB), have shown
that TIL from non-melanoma solid cancers can also contain T-cells reactive against
non-shared unique mutated neoantigens expressed in the cancer. The frequency of these
T-cells is very low (often < 0.1%) and it is thus difficult to isolate and grow mutation
reactive T-cells to levels required for effective therapy.

- In a single patient with chemo-refractory metastatic cholangiocarcinoma we were able to
grow a relatively pure population of neoantigen reactive TIL and administration of these
cells mediated a near-complete regression of all metastatic disease now lasting 2.5
years.

- We have developed approaches to identify these rare neoantigen reactive T-cells from
common non-melanoma cancers, to isolate their T-cell receptors (TCR), and to genetically
engineer autologous peripheral blood lymphocytes (PBL) to express these TCRs with high
efficiency. The neoantigen TCR gene-modified cells can recognize and destroy the
autologous cancer in vitro.

- We are now proposing a clinical protocol to treat patients with refractory solid cancers
using the adoptive transfer of autologous PBL transduced with genes encoding TCRs that
recognize unique mutated neoantigens expressed by the cancer.

Objectives:

-Primary objective:

--Determine the rate of objective response (using RECIST v1.1 criteria) of patients with
solid cancers who receive autologous PBL that have been transduced with genes encoding T-cell
receptors that recognize mutated neoantigens in the autologous cancer.

Eligibility:

-Patients must be/have:

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

- Measurable solid cancer with at least one lesion that is resectable for TIL generation
with minimal morbidity plus at least one other lesion that can be measured, that falls
into one of four cohorts: (1) gastrointestinal and genitourinary cancers; (2) breast,
ovarian, and other solid cancers; (3) non-small cell lung cancer (NSCLC); and, (4)
glioblastoma. Metastatic disease is required for cohorts 1-3, but not for cohort 4.

- Evaluable solid cancer that has recurred following standard chemotherapy or standard
systemic therapy

- Normal basic laboratory values.

- At least one lesion suitable for surgical resection for the preparation of the cell
product

- No allergies or hypersensitivity to high-dose aldesleukin administration

- No concurrent major medical illnesses or any form of immunodeficiency.

Design:

- Patients will undergo resection or biopsy to obtain tumor for generation of autologous
TIL cultures. 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).

- Patients will be entered into four cohorts: (1) gastrointestinal and genitourinary
cancers, (2) breast, ovarian, and other solid cancers; (3) non-small cell lung cancer
(NSCLC); and, (4) glioblastoma. Exomic sequencing, and often RNA-Seq will be performed
to identify the mutations expressed in the patient s cancer. Multiple autologous TIL
cultures will be grown and tested for reactivity against mutations from the autologous
tumor using assays we have developed that involve the exposure of autologous
antigen-presenting cells to long peptides containing the mutation or tandem mini-genes
encoding the mutation.

- T-cell cultures with reactivity against mutations will be identified and the individual
T-cell receptors that recognize the mutation will be synthesized and used to create a
retrovirus for transduction of the TCR into the patient s autologous PBL.

- Transduced autologous PBL will then be expanded to large numbers using our standard
rapid expansion protocol and administered to the patient following a non-myeloablative,
lymphodepleting preparative regimen of cyclophosphamide and fludarabine. Patients will
then begin high-dose aldesleukin after the infusion of autologous transduced PBL. At the
discretion of the Principal Investigator (PI), patients enrolled in Cohort 3 may receive
low-dose aldesleukin.

- Clinical and immunologic response will be evaluated about 4-6 weeks after cell infusion
and periodically thereafter.

- It is anticipated that approximately one patient per month may enroll on the trial for
each of the four histologic groups. Thus, accrual of up to 4 x 50=200 total evaluable
patients may be completed in approximately 2-4 years. In order to allow for a small
number of inevaluable patients, the accrual ceiling will be set to 210.

- INCLUSION CRITERIA:

- Measurable solid cancer with at least one lesion that is resectable for TIL generation
with minimal morbidity plus at least one other lesion that can be measured that falls
into one of four cohorts: (1) gastrointestinal and genitourinary cancers; (2) breast,
ovarian, and other solid cancers; (3) non-small cell lung cancer (NSCLC); and, (4)
glioblastoma.

--Note: Metastatic disease is required for cohorts 1-3, but not required for cohort 4.
NSCLC includes but is not limited to squamous cell carcinoma, adenosquamous carcinoma
or adenocarcinomas. Neuroendocrine tumors are not eligible.

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

- Refractory to approved standard systemic therapy. Specifically:

- Patients with metastatic colorectal cancer must have received oxaliplatin or
irinotecan.

- Patients with breast and ovarian cancer must be refractory to both first and
second line treatments.

- Patients with NSCLC must have received at least one platinum-based chemotherapy
regimen and at least one FDA approved targeted treatment (when appropriate).

- Patients with glioblastoma must have progression of disease after radiotherapy
(including patients that undergo surgery for recurrent disease and are rendered
NED). This includes recurrent glioblastoma after receiving all standard
first-line treatment, including surgery (if feasible due to neurosurgical and
neuro-anatomical considerations) and adjuvant radiotherapy +/- chemotherapy.

- For cohorts 1-3: patients with 3 or fewer brain metastases that are less than or equal
to 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.

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

- For cohorts 1-3: clinical performance status of ECOG 0 or 1.

- For cohort 4: Patients must have Karnofsky performance status greater than or equal to
60.

- Patients of both genders must be willing to practice birth control from the time of
enrollment on this studyand for four months after treatment.

- Women of child-bearing potential must have a negative pregnancy test because of the
potentially dangerous effects of the treatment on the fetus.

- 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 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 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 filgrastim

- 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 x ULN

- Serum creatinine less than or equal to 1.6 mg/dl.

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

- More than four weeks must have elapsed since any prior systemic therapy at the time
the patient receives the preparative regimen, and patients' toxicities must have
recovered to a grade 1 or less.

Note: Patients may have undergone minor surgical procedures within the past three weeks, as
long as all toxicities have recovered to grade 1 or less.

- For cohort 3: more than two weeks must have elapsed since any prior palliation for
major bronchial occlusion or bleeding at the time the patient receives the preparative
regimen, and patient s toxicities must have recovered to a grade 1 or less.

- For cohort 4: patients must be at least four weeks from radiation therapy.
Additionally, patients must be at least six weeks from nitrosoureas, four weeks from
temozolomide, three weeks from procarbazine, two weeks from vincristine and four weeks
from last bevacizumab administration. Patients must be at least four weeks from other
cytotoxic therapies not listed above and two weeks for non-cytotoxic agents (e.g.,
interferon) including investigative agents.

- For Cohort 4: Patients must either not be receiving steroids, or be on a stable dose
of steroids, for at least five days prior to registration.

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

- Willing to sign a durable power of attorney.

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

EXCLUSION CRITERIA:

- Women of child-bearing potential who are pregnant or breastfeeding because of the
potentially dangerous effects of the treatment on the fetus or infant.

- Concurrent systemic steroid therapy, except for patients with glioblastoma (cohort 4).

- Active systemic infections requiring anti-infective treatment, coagulation disorders,
or any other active or uncompensated major medical illnesses.

- For cohort 3: Any major bronchial occlusion or bleeding not amenable to palliation.

- For cohort 4: Clinically significant hemorrhagic or ischemic stroke, including
transient ischemic attacks and other central nervous system bleeding in the preceding
six months that were not related to glioma surgery.

Note: History of prior intratumoral bleeding is not an exclusion criterion; however,
patients with a history of prior intratumoral bleeding, will need to undergo a non-contrast
head CT to exclude acute bleeding.

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

- 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.)

- History of severe immediate hypersensitivity reaction to cyclophosphamide,
fludarabine, or aldesleukin.

- For cohorts 1, 2, or 4: Clinically significant patient history which in the judgment
of the Principal Investigator (PI) would compromise the patients' ability to tolerate
high-dose aldesleukin.

Note: At the discretion of the PI, patients enrolled in cohort 3 may receive low-dose
aldesleukin.

- History of coronary revascularization or ischemic symptoms.

- Any patient known to have an LVEF less than or equal to 45%.

- Documented LVEF less than or equal to 45% tested in patients:

- Age greater than or equal to 65 years

- With clinically significant atrial and/or ventricular arrhythmias including but
not limited to: atrial fibrillation, ventricular tachycardia, second- or
third-degree heart block or have a history of ischemic heart disease and/or chest
pain

- Documented FEV1 less than or equal to 50% predicted tested in patients with:

- A prolonged history of cigarette smoking (greater than or equal to 20 pack-year
smoking history, with cessation within the past two years).

- Symptoms of respiratory dysfunction

- Patients who are receiving any other investigational agents.