Methods of isolating T cells having antigenic specificity for a cancer-specific mutation
Inventors
Tran, Eric • Lu, Yong-Chen • Robbins, Paul • Rosenberg, Steven A.
Assignees
US Department of Health and Human Services
Publication Number
US-10973894-B2
Publication Date
2021-04-13
Expiration Date
2034-10-02
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Abstract
Disclosed are methods of isolating T cells having antigenic specificity for a mutated amino acid sequence encoded by a cancer-specific mutation, the method comprising: identifying one or more genes in the nucleic acid of a cancer cell of a patient, each gene containing a cancer-specific mutation that encodes a mutated amino acid sequence; inducing autologous APCs of the patient to present the mutated amino acid sequence; co-culturing autologous T cells of the patient with the autologous APCs that present the mutated amino acid sequence; and selecting the autologous T cells. Also disclosed are related methods of preparing a population of cells, populations of cells, pharmaceutical compositions, and methods of treating or preventing cancer.
Core Innovation
The invention provides methods of isolating T cells having antigenic specificity for mutated amino acid sequences encoded by cancer-specific mutations by identifying one or more genes in the nucleic acid of a cancer cell of a patient that contain cancer-specific mutations encoding mutated amino acid sequences. The method then induces autologous antigen presenting cells (APCs) of the patient to present these mutated amino acid sequences, co-cultures the patient's autologous T cells with these APCs, and selects T cells that exhibit antigenic specificity for the mutated sequences presented in the context of major histocompatibility complex (MHC) molecules expressed by the patient.
The problem addressed by the invention arises from the challenges in adoptive cell therapy (ACT) for cancer treatment, notably the difficulty in identifying and isolating T cells that specifically recognize cancer antigens. Traditional methods for identifying cancer antigens, such as using cDNA libraries, are time-consuming, laborious, and may have technical biases. There is a need for improved methods to efficiently obtain cancer-reactive T cells that target cancer-specific mutations, thereby improving the efficacy and applicability of ACT.
The invention further provides advantages such as rapidly assessing a large number of mutations restricted by all of the patient's MHC molecules simultaneously, thereby identifying the full repertoire of mutation-reactive T cells. It discerns immunogenic cancer mutations from silent or non-immunogenic mutations, enabling isolation of personalized T cells unique to the patient. The method avoids the need to co-culture T cells with tumor cell lines, which can be difficult to generate, especially for epithelial cancers, and minimizes potential toxicity by selecting T cells that specifically target mutated amino acid sequences.
Claims Coverage
The patent claims cover multiple inventive features related to methods of isolating T cells specific for mutated amino acid sequences encoded by cancer-specific mutations, methods for preparing populations of these T cells, and methods of treating tumors using these cells.
Identification of genes containing cancer-specific mutations
Identifying more than one gene in the nucleic acid of tumor cells of a patient, each gene containing a cancer-specific mutation encoding a mutated amino acid sequence.
Presentation of mutated amino acid sequences by autologous APCs
Separately inducing autologous antigen presenting cells of the patient to present the mutated amino acid sequences, including methods such as peptide pulsing or introducing nucleotide sequences encoding the mutated amino acid sequences, optionally using tandem gene sequence constructs.
Separate co-culture and assessment of autologous T cells
Obtaining separate cultures of autologous T cells from multiple tumor fragments and separately co-culturing each with APCs presenting mutated amino acid sequences, assessing the T cells for antigenic specificity in the context of MHC class I and class II molecules expressed by the patient.
Selection and isolation of antigen-specific T cells
Selecting autologous T cells with antigenic specificity based on expression of activation markers (e.g., PD-1, LAG-3, TIM-3, 4-1BB, OX40, CD107a) or cytokine secretion profiles, and isolating these cells from non-specific T cells.
Expansion of antigen-specific T cells
Expanding the isolated antigen-specific T cells to obtain populations for therapeutic use, for example, culturing with feeder PBMC, IL-2, and OKT3 antibody.
Treatment of tumors using autologous antigen-specific T cells
Administering to the patient a therapeutically effective amount of the prepared autologous T cells having antigenic specificity for mutated amino acid sequences expressed by the tumor, for treating epithelial cancers or specific cancers such as cholangiocarcinoma, melanoma, colon cancer, or rectal cancer.
The patent claims comprehensively cover the identification of cancer-specific mutated genes, presentation of mutated epitopes by autologous APCs, selective co-culture and identification of antigen-specific autologous T cells, their expansion, and therapeutic administration for cancer treatment, encompassing MHC class I and II contexts and various antigen presentation approaches.
Stated Advantages
The methods rapidly assess a large number of mutations restricted by all of the patient's MHC molecules at once, identifying the full repertoire of mutation-reactive T cells.
They distinguish immunogenic cancer mutations from silent or non-immunogenic mutations, allowing targeted identification of effective antigens.
They enable isolation of personalized T cell populations unique to the patient, useful for adoptive cell therapy.
They avoid reliance on tumor cell lines for co-culture, which may be difficult to generate, especially for epithelial cancers.
They potentially minimize toxicity by selecting T cells that specifically target mutated sequences, sparing normal cells.
Documented Applications
Methods of treating or preventing cancer in a mammal by administering populations of isolated T cells having antigenic specificity for mutated amino acid sequences encoded by cancer-specific mutations.
Preparation of pharmaceutical compositions comprising populations of isolated T cells with antigenic specificity for mutated amino acid sequences for therapeutic use.
Use in treating various cancers including acute lymphocytic leukemia, acute myeloid leukemia, epithelial cancers such as cholangiocarcinoma, melanoma, colon cancer, rectal cancer, and a broad range of solid and liquid tumors.
Adoptive cell therapy protocols involving infusion of expanded autologous T cells reactive to patient-specific cancer mutations.
Interested in licensing this patent?