Methods of isolating t cells having antigenic specificity for a cancer-specific mutation

A method of treating a tumor in a patient, the method comprising:

• identifying more than one gene in the nucleic acid of tumor cells in the tumor of the patient, each gene containing a cancer-specific mutation that encodes a mutated amino acid sequence;
• separately inducing autologous antigen presenting cells (APCs) of the patient to present the mutated amino acid sequence for each of the more than one identified genes;
• obtaining separate cultures of autologous T cells from multiple fragments of the patient's tumor;
• separately co-culturing each of the APCs presenting a mutated amino acid sequence with each of the separate cultures of autologous T cells;
• assessing each co-culture for autologous T cells having antigenic specificity for the mutated amino acid sequence presented in the context of an MHC class I molecule of the patient;
• assessing each co-culture for autologous T cells having antigenic specificity for the mutated amino acid sequence presented in the context of an MHC class II molecule of the patient;
• selecting the autologous T cells having antigenic specificity for a mutated amino acid sequence presented in the context of major histocompatibility complex (MHC) molecule(s) expressed by the patient and isolating the selected autologous T cells;
• expanding the number of isolated T cells to obtain a population of T cells that have antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation;
• and
• administering to the patient the population of T cells in an amount effective to treat the tumor in the patient,
• wherein the T cells administered to the patient have antigenic specificity for a mutated amino acid sequence expressed by the tumor in the patient, and
• wherein the tumor is a tumor of any one of the following cancers:
• acute lymphocytic cancer;
• acute myeloid leukemia;
• bone cancer;
• brain cancer;
• breast cancer;
• cancer of the anus, anal canal, or anorectum;
• cancer of the eye;
• cancer of the joints;
• cancer of the neck, gallbladder, or pleura;
• cancer of the nose, nasal cavity, or middle ear;
• cancer of the oral cavity;
• cancer of the penis;
• cancer of the uterus;
• cancer of the vagina;
• cancer of the vulva;
• cholangiocarcinoma;
• chronic lymphocytic leukemia;
• chronic myeloid cancer;
• colon cancer;
• esophageal cancer;
• Hodgkin lymphoma;
• liver cancer;
• lung cancer;
• malignant mesothelioma;
• multiple myeloma;
• non-Hodgkin lymphoma;
• ovarian cancer;
• pancreatic cancer;
• peritoneum, omentum, and mesentery cancer;
• prostate cancer;
• rectal cancer;
• renal cancer;
• skin cancer;
• small intestine cancer;
• soft tissue cancer;
• stomach cancer;
• testicular cancer;
• thyroid cancer;
• ureter cancer;
• urinary bladder cancer;
• and uterine cervical cancer.