# Patent

## Title
Generation of HPV-specific T-cells

## Abstract

Embodiments of the disclosure concern methods and compositions for immunotherapy for human papillomavirus infection and diseases associated therewith. In specific embodiments, methods concern production of immune cells that target one or more antigens of HPV16 and/or HPV18, including methods with stimulation steps that employ IL-7 and IL-15, but not IL-6 and/or IL-12. Other specific embodiments utilize stimulations in the presence of certain cells, such as costimulatory cells and certain antigen presenting cells.

## Background
This application claims priority to U.S. Provisional Patent Application Ser. No. 62/395,440, filed Sep. 16, 2016, which is incorporated by reference herein in its entirety.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under P50 CA097007 and PO1 CA94237 awarded by National Cancer Institute. The government has certain rights in the invention.


TECHNICAL FIELD
The present disclosure concerns at least the fields of immunology, cell biology, molecular biology, and medicine, including cancer medicine.
BACKGROUND
Human papillomavirus (HPV) is a DNA virus that establishes productive infections in keratinocytes of the skin or mucous membranes. There are over 170 types of HPV, a subset of which HPV types are carcinogenic, including high-risk sexually transmitted types that can develop into genital neoplasias, including cervical intraepithelial neoplasia (CIN), vulvar intraepithelial neoplasia (VIN), penile intraepithelial neoplasia (PIN), and/or anal intraepithelial neoplasia (AIN), for example. HPV-induced cancers arise when viral sequences are integrated into the cellular DNA of host cells. Some of the HPV “early” genes, such as E6 and E7, act as oncogenes that promote tumor growth and malignant transformation.
Ramos et al., (J Immunother 2013; 36:66-76) describes a method for stimulating peripheral blood mononuclear cells to generate T-cells specific for HPV16 E6 and E7. In brief, the method comprises stimulation of peripheral blood mononuclear cells with dendritic cells in which cells are cultured in CTL medium with or without IL-6, IL-7, IL-12 and IL-15, a second stimulation in which co-cultures are supplemented with IL-2, and weekly stimulation with pepmix-loaded accessory antigen presenting cells (e.g., B-blasts) in the presence of IL-15.
The present disclosure provides relief for a long-felt need in the art to treat HPV-associated diseases, including at least for those associated with HPV16 and HPV18, for example.
BRIEF SUMMARY
The present disclosure is directed to methods and compositions that concern immune system cells that are modified to immunogenically recognize particular targets. In some embodiments, the present disclosure concerns the development of immune cells (including cytotoxic T-lymphocytes (CTLs, also referred to as cytotoxic T-cells)) that target a biological moiety that elicits an immune response in an individual. In specific embodiments, the present disclosure concerns the development of cytotoxic T-cells that target a HPV antigen, including a HPV disease-associated antigen. In some cases, a mixture of cytotoxic T-cells is produced, and the mixture targets more than one HPV antigen, including more than one antigen of more than one HPV type, in some cases.
Embodiments of the disclosure concern methods and compositions for providing therapy to individuals infected with HPV or that have HPV-associated diseases, including cancers, for example. In specific embodiments, the disclosure regards methods and compositions for adoptive cellular immunotherapy that can target HPV-associated, e.g., HPV16-associated and/or HPV18-associated, medical conditions (including cancer) and are therapeutic therefor.
In certain aspects, the present disclosure concerns the development of a plurality of T-cells that target antigens from HPV, e.g., HPV16 and/or HPV18. The present disclosure provides significant and non-obvious improvements on methods for generating T cell lines with specificity against HPV, e.g., HPV16 and/or HPV18 antigens.
In some embodiments of the disclosure, an individual is in need of the methods and/or compositions of the disclosure. In certain embodiments, an individual has been exposed to HPV, e.g., HPV16 and/or HPV18 (the presence of which may or may not be known for the individual), or the individual is suspected of having been exposed to or at risk for being exposed to HPV, e.g., HPV16 and/or HPV18. In certain embodiments, the individual has or is suspected of having or is at risk for having HPV-associated disease, e.g., HPV16-associated and/or HPV18-associated disease, including cancer.
In specific embodiments of part of the method, certain HPV, e.g., HPV16 and/or HPV18, antigen(s) are presented to antigen-presenting cells (APCs) in the form of one or more peptides that span some or all of certain antigen(s). The antigenic peptides may be provided to the antigen-presenting cells in a library of peptide mixtures, which may be referred to as pepmixes. In certain aspects of the disclosure, there is pooling of a variety of pepmixes for exposure to the APCs. APCs that express the antigens may be exposed to peripheral blood T-cells under certain conditions to result in stimulation of T-cells specific for the certain HPV antigen(s).
Some aspects and embodiments of the present disclosure concern the generation and/or expansion of HPV-specific T-cells.
In a first aspect, the present disclosure provides a method for stimulating peripheral blood cells, preferably peripheral blood T-cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and, in at least some cases, in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
In some embodiments a method of producing therapeutic T-cells for human papillomavirus (HPV)-associated disease(s) is provided, the method comprising the step of stimulating peripheral blood T-cells with antigen presenting cells in the presence of one or more of interleukin IL-7 and IL-15 and, in at least some cases, in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein the stimulating produces T-cells therapeutic for HPV-associated diseases.
In some embodiments, the peripheral blood T-cells being stimulated are obtained from a prior stimulation of peripheral blood cells. The prior stimulation may comprise stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in at least some cases in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
As such, prior to stimulating the peripheral blood T-cells, the methods may further comprise stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in at least some cases in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, to produce peripheral blood T-cells.
In some embodiments the one or more peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV16; one or more proteins of HPV18; or both of one or more proteins of HPV16 and one or more proteins of HPV18. In some embodiments the one or more peptides comprise sequence that corresponds to one or more of proteins E5, E6, E7, L1 and L2. In some embodiments the one or more peptides may be a library of peptides, including E1, E2, E3, E4, E5, E6, E7, L1, and/or L2 peptides.
In some embodiments the method may produce immune cells, such as T-cells, specific for HPV or for an HPV antigen. In some embodiments the method may expand a population of T-cells present in the peripheral blood T-cells that are specific for HPV or for at least one HPV antigen. Immune cells other than T cells that may be produced by methods of the disclosure including NK cells and NKT cells.
In some embodiments the antigen presenting cells are activated T-cells, dendritic cells (DC), B-Blasts (BB), or PBMCs, for example.
In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of at least IL-2. In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of at least IL-4. In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of at least IL-6. In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of at least IL-12. In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of at least IL-21. In some embodiments stimulation of peripheral blood T-cells in the presence of IL-7 and IL-15 occurs in the absence of IL-6 and IL-12.
In some particular embodiments stimulation of cells in the method of the first aspect of the present invention occurs in the absence of IL-6 and IL-12.
In some embodiments, peripheral blood T-cells may be present in a population of peripheral blood mononuclear cells (PBMCs) or are obtained or isolated therefrom. The PBMCs in the population may be non-adherent PBMCs. The antigen presenting cells may be activated T-cells, dendritic cells, B-blasts, or PBMCs, for example.
In a second aspect, the present disclosure provides a method for stimulating T-cells specific for HPV or for an HPV antigen, wherein the method comprises stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of IL-7 and IL-15, and optionally in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
In some embodiments a method of producing therapeutic T-cells for human papillomavirus (HPV)-associated diseases is provided, the method comprising the step of stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of one or more of interleukin IL-7 and IL-15, and optionally in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein the stimulating produces T-cells therapeutic for one or more HPV-associated diseases.
In some embodiments the antigen presenting cells are activated T-cells, dendritic cells (DC), B-Blasts (BB) or PBMCs. In particular embodiments the antigen presenting cells are activated T-cells.
In some embodiments the co-stimulatory cells are one or more cell types selected from the group consisting of CD80+ cells, CD86+ cells, CD83+ cells, 4-1BBL+ cells, CD40+ cells, OX40+ cells, and a combination thereof. The co-stimulatory cells may be CD80+/CD86+/CD83+/4-1BBL+ cells.
In some embodiments the stimulation of T-cells specific for HPV or for an HPV antigen is not a first stimulation step. The T-cells being stimulated cells may be the product of a prior stimulation, e.g. using the method of the first aspect of the present disclosure.
In some embodiments the one or more peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV16; one or more proteins of HPV18; or one or more proteins of HPV16 and one or more proteins of HPV18. In some embodiments the one or more peptides comprise sequence that corresponds to one or more of proteins E5, E6, E7, L1 and L2. In some embodiments the one or more peptides may be a library of peptides, including E1, E2, E3, E4, E5, E6, E7, L1, and/or L2 peptides.
In some embodiments the method may produce T-cells specific for HPV or for an HPV antigen. In some embodiments the method may expand a population of T-cells specific for HPV or for an HPV antigen.
In certain embodiments stimulation of T-cells specific for HPV or for an HPV antigen comprises stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of IL-7, IL-15, and in the presence of one or more types of co-stimulatory cells.
In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-2. In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-4. In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-6. In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-7. In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-12. In some embodiments stimulation of T-cells in the presence of IL-7 and IL-15 is in the absence of IL-21. In some embodiments stimulation of T-cells in the method of the first aspect of the present invention is in the absence of IL-6 and IL-12.
Methods according to the first and second aspect of the present disclosure may be methods of producing therapeutic T-cells for HPV-associated diseases. The stimulation of cells may produce T-cells that are therapeutic for HPV-associated diseases.
In a third aspect, the methods of the first and second aspects may be combined to provide a method of producing therapeutic T-cells for HPV-associated diseases, the method comprising:
stimulating peripheral blood cells, preferably peripheral blood T-cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV;
stimulating T-cells obtained from (i) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, and optionally in the presence of one or more types of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
In some embodiments prior to step (ii), T-cells obtained from (i) may be re-stimulated in the presence of IL-7 and IL-15 but not in the presence of co-stimulatory cells, and optionally in the absence of IL-6 and/or IL-12. Such re-stimulation may occur for one, two, three, four, five or more rounds, as required.
In some embodiments the antigen presenting cells used in (i) are dendritic cells (DC), B-Blasts (BB) or PBMCs. In some embodiments the antigen presenting cells used in (ii) are activated T-cells, dendritic cells (DC), B-Blasts (BB) or PBMCs. In some embodiments the antigen presenting cells used in (i) are different to the antigen presenting cells used in (ii), although they may be the same in certain cases. In particular embodiments the antigen presenting cells used in (ii) are activated T-cells.
In some embodiments the co-stimulatory cells are one or more cell types selected from the group consisting of CD80+ cells, CD86+ cells, CD83+ cells, 4-1BBL+ cells, CD40+ cells, OX40+ cells, and a combination thereof. The co-stimulatory cells may be CD80+/CD86+/CD83+/4-1BBL+ cells.
In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-2. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-4. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-6. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-12. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-21. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-6 and IL-12.
In some preferred embodiments stimulation of cells in step (i) is in the absence of IL-6 and IL-12.
In some embodiments stimulation of cells in step (ii) is in the absence of IL-6 and IL-12.
Accordingly, in some embodiments a method of producing therapeutic T-cells for HPV-associated diseases is provided, the method comprising:
(i) stimulating peripheral blood cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV;
(ii) stimulating T-cells obtained from (i) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (ii) is optionally repeated one or more times; and
(iii) stimulating T-cells obtained from (ii) with antigen presenting cells in the presence of IL-7 and IL-15, and optionally in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (iii) is optionally repeated one or more times.
In some embodiments the antigen presenting cells used in (i) and (ii) are dendritic cells (DC) B-Blasts (BB) or PBMCs. In some embodiments the antigen presenting cells used in (iii) are activated T-cells, dendritic cells (DC), B-Blasts (BB) or PBMCs. In some embodiments the antigen presenting cells used in (iii) are different to the antigen presenting cells used in (i) and/or (ii). In preferred embodiments the antigen presenting cells used in (iii) are activated T-cells.
In preferred embodiments the stimulation in (iii) is in the presence of co-stimulatory cells. In some embodiments the co-stimulatory cells are one or more cell types selected from the group consisting of CD80+ cells, CD86+ cells, CD83+ cells, 4-1BBL+ cells, CD40+ cells, OX40+ cells, and a combination thereof. The co-stimulatory cells may be CD80+/CD86+/CD83+/4-1BBL+ cells.
In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-2. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-4. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-6. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-12. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-21. In some embodiments stimulation of cells in the presence of IL-7 and IL-15 is in the absence of IL-6 and IL-12.
In some embodiments stimulation of cells in step (i) is in the absence of IL-6 and IL-12. In some other embodiments stimulation of cells in step (i) is in the presence of IL-6 and IL-12.
In some particular embodiments stimulation of cells in step (ii) is in the absence of IL-6 and IL-12. In some particular embodiments stimulation of cells in step (iii) is in the absence of IL-6 and IL-12.
In some particular embodiments methods of the present disclosure are for producing T-cells specific for HPV16 and/or HPV18. In some particular embodiments methods of the present invention are for producing T-cells specific for HPV16-associated and/or HPV18-associated diseases.
In some embodiments, peripheral blood T-cells may be obtained from an individual that is known to be infected or suspected of being infected with HPV; HPV16 or HPV18; or both HPV16 and HPV18.
In some embodiments, antigen presenting cells may be obtained from an individual that is known to be infected or suspected of being infected with HPV; HPV16 or HPV18; or both HPV16 and HPV18.
In some embodiments, the method may occur in the absence of exposing the T-cells produced by the method to activated B cells that were previously exposed to a library of peptides.
In some embodiments, antigen presenting cells may be autologous or allogeneic to an individual intended to be treated with the therapeutic T-cells obtained.
In some embodiments, the one or more peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV16; one or more proteins of HPV18; or one or more proteins of HPV16 and one or more proteins of HPV18. In some embodiments the one or more peptides comprise sequence that corresponds to one or more of proteins E1, E2, E3, E4, E5, E6, E7, L1, and/or L2 that come from HPV16, HPV18, or HPV16 and HPV18.
In embodiments of the present disclosure the peptides may comprise sequence that corresponds to one or more of HPV proteins E1, E2, E3, E4, E5, E6, E7, L1, and/or L2. The peptides may correspond to a contiguous amino acid sequence present within said HPV protein. A peptide may have a length of at least or no more than 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids in length, or of 15 amino acids in length. The collection of peptides may form a library and peptides in the library may overlap in sequence with other peptides by any suitable amount, including 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, or 14 amino acids, for example. The peptides may comprise sequence that corresponds to: a) the HPV18 E6 protein and/or the HPV18 E7 protein, and/or b) the HPV16 E6 protein and/or the HPV16 E7 protein.
In embodiments of the present disclosure the HPV may be HPV16 or HPV18, or both. In embodiments concerned with treatment of an HPV-associated disease, the disease may be cancer and the peptides may comprise a sequence that corresponds to one or both of E6 and E7. When the HPV-associated disease is a pre-cancerous lesion, the peptides may comprise sequence that corresponds to one, some, or all of E1, E2, E3, E4, E5, E6, E7, L1, and L2.
T-cells produced by the methods of the present disclosure may be isolated and/or purified, e.g., isolated/purified from other cells.
In some embodiments, a therapeutically effective amount of T-cells produced by the methods of the present disclosure are provided to an individual that has been exposed to HPV, or that has HPV-associated disease. In a related aspect T-cells produced by the method of the present disclosure are provided for use in the treatment of HPV-associated disease. In another related aspect the use of T-cells produced by the method of the present disclosure are provided for use in the manufacture of a medicament for use in the treatment of HPV-associated disease.
In one aspect of the present invention T-cells for use in a method of adoptive cellular immunotherapy are provided, wherein the T-cells are obtained by, obtainable by, or are the product of, a method for stimulating peripheral blood or T-cells or a method of producing therapeutic T-cells described herein, the method of adoptive cellular immunotherapy comprising administering the T-cells to the subject.
In one aspect of the present invention the use of T-cells in the manufacture of a medicament for use in a method of adoptive cellular immunotherapy comprising administering the T-cells to the subject is provided, wherein the T-cells are obtained by, obtainable by, or are the product of, a method for stimulating peripheral blood or T-cells or a method of producing therapeutic T-cells described herein.
In one aspect of the present invention a method of preparing a pharmaceutical composition, medicament or vaccine is provided, the method comprising stimulating peripheral blood or T-cells according to a method described herein, or producing therapeutic T-cells according to a method described herein, and mixing the cells obtained, with a pharmaceutically acceptable carrier, adjuvant, diluent or excipient.
The disease to be treated may be a neoplasm. The neoplasm may be a cancer. The cancer may be an HPV-positive cancer, HPV16-positive cancer and/or HPV18-positive cancer.
The individual to be treated may be a human. The individual may be a patient. The individual may have been exposed to HPV, such as HPV16, HPV18, or both HPV16 and HPV18, or has an HPV-, HPV16- and/or HPV18-associated disease. The HPV-, HPV16- and/or HPV18-associated disease may be a neoplasm. The neoplasm may be a cancer.
A cancer may be of any kind. In some embodiments the cancer is a cervical cancer, anal cancer, vulvar cancer, vaginal cancer, penile cancer, or oropharyngeal cancer. In some embodiments the cancer is a HPV-related carcinoma, HPV-positive oropharyngeal carcinoma, HPV-positive cervical carcinoma, HPV-positive anal carcinoma, HPV-positive vulvar carcinoma, nasopharyngeal carcinoma, HPV-positive penile carcinoma, HPV-positive dysplasias of any site, or laryngeal papillomatosis.
The individual or subject may have received, be receiving, or will receive an additional cancer therapy. The additional cancer therapy may be surgery, radiation, hormone therapy, chemotherapy, immunotherapy, or a combination thereof.
The individual or subject may be determined as having HPV-associated cancer or HPV-positive cancer. The individual may be determined as having HPV16-associated cancer or HPV16-positive cancer. The individual may be determined as having HPV18-associated cancer or HPV18-positive cancer. The individual or subject may be any animal or human. The individual or subject is preferably mammalian, more preferably human. The individual or subject may be a non-human mammal, but is more preferably human. The individual or subject may be male or female. The individual or subject may be a patient.
Methods according to the present disclosure that involve steps of cell stimulation may be performed in vitro or ex vivo. The term “in vitro” is intended to encompass studies with materials, biological substances, cells and/or tissues in laboratory conditions or in culture. “Ex vivo” refers to something present or taking place outside an organism, e.g. outside the human or animal body, which may be on tissue (e.g. whole organs) or cells taken from the organism.
In one embodiment, there is a method for stimulating peripheral blood cells, the method comprising stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of human papillomavirus (HPV). The peripheral blood T-cells may be obtained from a prior stimulation of peripheral blood cells, such as wherein the prior stimulation of peripheral blood cells comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV. In specific cases, prior to stimulating the peripheral blood T-cells, the method further comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, to produce peripheral blood T-cells.
In an embodiment, there is a method of producing therapeutic T-cells for HPV-associated diseases, the method comprising the step of: stimulating peripheral blood T-cells with antigen presenting cells in the presence of one or more of IL-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein the stimulating produces T-cells therapeutic for HPV-associated diseases. The peripheral blood T-cells may be obtained from a prior stimulation of peripheral blood cells, such as wherein the prior stimulation of peripheral blood cells comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV. In specific cases, prior to stimulating the peripheral blood T-cells, the method further comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, to produce peripheral blood T-cells.
In embodiments of methods encompassed by the disclosure, antigen presenting cells are activated T-cells, dendritic cells, B-blasts, or PBMCs. Peripheral blood T-cells may be present in a population of peripheral blood mononuclear cells (PBMCs) or are obtained or isolated therefrom, in at least some cases, and the PBMCs in the population may be non-adherent PBMCs. When employed, co-stimulatory cells may be CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells, or a combination thereof.
In a particular embodiment, there is a method for stimulating T-cells specific for HPV or for an HPV antigen, the method comprising stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of IL-7 and IL-15 and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
In certain embodiments, there is a method of producing therapeutic T-cells for HPV-associated diseases, the method comprising the step of stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of one or more of IL-7 and IL-15 and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein the stimulating produces T-cells therapeutic for HPV-associated diseases.
In one embodiment, there is a method of producing therapeutic T-cells for HPV-associated diseases, the method comprising: (i) stimulating peripheral blood cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of IL-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV; and (ii) stimulating T-cells obtained from (i) with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV. In specific embodiments, prior to step (ii) T-cells obtained from (i) may be re-stimulated in the presence of IL-7 and IL-15 but not in the presence of co-stimulatory cells.
In an embodiment, a method of producing therapeutic T-cells for HPV-associated diseases is provided, the method comprising: (i) stimulating peripheral blood cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV; (ii) stimulating T-cells obtained from (i) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (ii) is optionally repeated one or more times; and (iii) stimulating T-cells obtained from (ii) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (iii) is optionally repeated one or more times.
In any method of the disclosure, the HPV may be HPV16 or HPV18. Peptides comprising sequence that corresponds to one or more of E1, E2, E3, E4, E5, E6, E7, L1, and L2 may be utilized in any method of the disclosure. The peptides may comprise sequence that corresponds to: a) the HPV18 E6 protein and/or the HPV18 E7 protein, and/or b) the HPV16 E6 protein and/or the HPV16 E7 protein. In some cases, an individual being provided with an effective amount of cells as described herein has an HPV-associated disease, such as cancer, and the peptides comprise sequence that corresponds to one or both of E6 and E7. In specific aspects, the one or more peptides comprises peptides of at least or no more than 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids in length, and in particular the one or more peptides comprises peptides of 15 amino acids in length. In specific embodiments, one or more peptides form a library and peptides in the library overlap in sequence with other peptides by 11 amino acids.
In particular embodiments, a therapeutically effective amount of T-cells produced by the method are provided to an individual that has been exposed to HPV or that has HPV-associated disease. In specific embodiments, an HPV-associated disease comprises a neoplasm.
A therapeutically effective amount of T-cells produced by a method of the disclosure may be provided to an individual that has been exposed to HPV16, HPV18, or both, or that has HPV16-associated and/or HPV18-associated disease, including a neoplasm such as cancer.
In particular embodiments, the cancer is a cervical cancer, anal cancer, vulvar cancer, vaginal cancer, penile cancer, oropharyngeal cancer, nasopharyngeal carcinoma, laryngeal papillomatosis, laryngeal cancer, head and neck cancer, or a dysplasia of any site thereof.
In some cases, an individual that has received and/or will receive cells of the disclosure has also received, is receiving, or will receive an additional cancer therapy, such as surgery, radiation, hormone therapy, chemotherapy, immunotherapy, or a combination thereof.
In certain aspects, an individual that has received and/or will receive cells of the disclosure is determined as having HPV-associated cancer, such as HPV16-associated cancer or HPV18-associated cancer.
The following numbered paragraphs contain statements of broad combinations of the inventive technical features herein disclosed:
1. A method for stimulating peripheral blood cells, the method comprising stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of human papillomavirus (HPV).
2. A method of producing therapeutic T-cells for HPV-associated diseases, the method comprising the step of:

    
    
        stimulating peripheral blood T-cells with antigen presenting cells in the presence of one or more of IL-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV,
        wherein the stimulating produces T-cells therapeutic for HPV-associated diseases.
    
    


3. The method of paragraph 1 or 2, wherein the peripheral blood T-cells are obtained from a prior stimulation of peripheral blood cells.
4. The method of paragraph 3, wherein the prior stimulation of peripheral blood cells comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
5. The method of paragraph 1 or 2, wherein prior to stimulating said peripheral blood T-cells, the method further comprises stimulating peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, to produce peripheral blood T-cells.
6. The method of any one of paragraphs 1-7, wherein the antigen presenting cells are dendritic cells, B-blasts, or PBMCs.
7. The method of any one of paragraphs 1-6, wherein the peripheral blood T-cells are present in a population of peripheral blood mononuclear cells (PBMCs) or are obtained or isolated therefrom.
8. The method of paragraph 7, wherein the PBMCs in the population are non-adherent PBMCs.
9. A method for stimulating T-cells specific for HPV or for an HPV antigen, the method comprising stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of IL-7 and IL-15 and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
10. A method of producing therapeutic T-cells for HPV-associated diseases, the method comprising the step of stimulating T-cells specific for HPV or for an HPV antigen with antigen presenting cells in the presence of one or more of IL-7 and IL-15 and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein the stimulating produces T-cells therapeutic for HPV-associated diseases.
11. The method of paragraph 9 or 10, wherein the antigen presenting cells are activated T cells, dendritic cells, B-blasts, or PBMCs.
12. The method of any one of paragraphs 9 to 11, wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells, or a combination thereof.
13. A method of producing therapeutic T-cells for HPV-associated diseases, the method comprising:

    
    
        (i) stimulating peripheral blood cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of IL-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV; and
        (ii) stimulating T-cells obtained from (i) with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV.
    
    


14. The method of paragraph 13, wherein prior to step (ii) T-cells obtained from (i) may be re-stimulated in the presence of IL-7 and IL-15 but not in the presence of co-stimulatory cells.
15. The method of paragraph 13 or 14, wherein the antigen presenting cells used in (i) are dendritic cells (DC), B-Blasts (BB) or PBMCs.
16. The method of any one of paragraphs 13 to 15, wherein the antigen presenting cells used in (ii) are activated T cells, dendritic cells (DC) or B-Blasts (BB).
17. The method of any one of paragraphs 13 to 16, wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells, or a combination thereof.
18. A method of producing therapeutic T-cells for HPV-associated diseases is provided, the method comprising:

    
    
        (i) stimulating peripheral blood cells, wherein the method comprises stimulating peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV;
        (ii) stimulating T-cells obtained from (i) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and optionally in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (ii) is optionally repeated one or more times; and
        (iii) stimulating T-cells obtained from (ii) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least part of the sequence of one or more proteins of HPV, wherein (iii) is optionally repeated one or more times.
    
    


19. The method of paragraph 18, wherein the antigen presenting cells used in (i) and (ii) are DC, BB, or PBMCs.
20. The method of paragraph 18 or 19, wherein the antigen presenting cells used in (iii) are activated T cells, DC, BB, or PBMCs.
21. The method of any one of paragraphs 18 to 20, wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells or a combination thereof.
22. The method of any one of paragraphs 1-21, wherein the HPV is HPV16 or HPV18.
23. The method of any one of paragraphs 1-22, wherein the peptides comprise sequence that corresponds to one or more of E1, E2, E3, E4, E5, E6, E7, L1, and L2.
24. The method of any one of paragraphs 1-23, wherein the HPV-associated disease is cancer and the peptides comprise sequence that corresponds to one or both of E6 and E7.
25. The method of any one of paragraphs 1-25, wherein the peptides comprise sequence that corresponds to:

    
    
        a) the HPV18 E6 protein and/or the HPV18 E7 protein, and/or
        b) the HPV16 E6 protein and/or the HPV16 E7 protein.
    
    


26. The method of any one of paragraphs 1-25, wherein the one or more peptides comprises peptides of at least or no more than 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acids in length.
27. The method of any one of paragraphs 1-26, wherein the one or more peptides comprises peptides of 15 amino acids in length.
28. The method of any one of paragraphs 1-27, wherein one or more peptides form a library and peptides in the library overlap in sequence with other peptides by 11 amino acids.
29. The method of any one of paragraphs 1-28, wherein a therapeutically effective amount of T-cells produced by the method are provided to an individual that has been exposed to HPV or that has HPV-associated disease.
30. The method of paragraph 29, wherein the HPV-associated disease comprises a neoplasm.
31. The method of any one of paragraphs 1 to 30, wherein a therapeutically effective amount of T-cells produced by the method are provided to an individual that has been exposed to HPV16, HPV18 or both, or that has HPV16-associated and/or HPV18-associated disease.
32. The method of paragraph 31, wherein the HPV16-associated and/or HPV18-associated disease comprises a neoplasm.
33. The method of paragraph 31 or 32, wherein the neoplasm is cancer.
34. The method of paragraph 33, wherein the cancer is cervical cancer, anal cancer, vulvar cancer, vaginal cancer, penile cancer, oropharyngeal cancer, nasopharyngeal carcinoma, laryngeal papillomatosis, laryngeal cancer, head and neck cancer, or a dysplasia of any of site thereof.
35. The method of paragraph 33 or 34, wherein the individual has received, is receiving, or will receive an additional cancer therapy.
36. The method of paragraph 35, wherein the additional cancer therapy is surgery, radiation, hormone therapy, chemotherapy, immunotherapy, or a combination thereof.
37. The method of any one of paragraphs 33 to 36, wherein the individual is determined as having HPV-associated cancer.
38. The method of any one of paragraphs 33 to 37, wherein the individual is determined as having HPV16-associated cancer.
39. The method of any one of paragraphs 33 to 38, wherein the individual is determined as having HPV18-associated cancer.
40. T-cells for use in a method of adoptive cellular immunotherapy, wherein the T-cells are obtained by, obtainable by, or are the product of, a method for stimulating peripheral blood or T-cells or a method of producing therapeutic T-cells according to any one of paragraphs 1 to 39, wherein the method of adoptive cellular immunotherapy comprises administering the T-cells to the subject.
41. Use of T-cells in the manufacture of a medicament for use in a method of adoptive cellular immunotherapy comprising administering the T-cells to the subject, wherein the T-cells are obtained by, obtainable by, or are the product of, a method for stimulating peripheral blood or T-cells or a method of producing therapeutic T-cells according to any one of claims 1 to 39.
42. A method of preparing a pharmaceutical composition, medicament or vaccine, the method comprising stimulating peripheral blood or T-cells or producing therapeutic T-cells according to any one of claims 1 to 39, and mixing the cells obtained with a pharmaceutically acceptable carrier, adjuvant, diluent or excipient.
The foregoing has outlined rather broadly the features and technical advantages of the present invention in order that the detailed description of the invention that follows may be better understood. Additional features and advantages of the invention will be described hereinafter which form the subject of the claims of the invention. It should be appreciated by those skilled in the art that the conception and specific embodiment disclosed may be readily utilized as a basis for modifying or designing other structures for carrying out the same purposes of the present invention. It should also be realized by those skilled in the art that such equivalent constructions do not depart from the spirit and scope of the invention as set forth in the appended claims. The novel features which are believed to be characteristic of the invention, both as to its organization and method of operation, together with further objects and advantages will be better understood from the following description when considered in connection with the accompanying figures. It is to be expressly understood, however, that each of the figures is provided for the purpose of illustration and description only and is not intended as a definition of the limits of the present invention.
The invention includes the combination of the aspects and preferred features described except where such a combination is clearly impermissible or expressly avoided.
The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
Aspects and embodiments of the present invention will now be illustrated, by way of example, with reference to the accompanying figures. Further aspects and embodiments will be apparent to those skilled in the art. All documents mentioned in this text are incorporated herein by reference.
Throughout this specification, including the claims which follow, unless the context requires otherwise, the word “comprise,” and variations such as “comprises” and “comprising,” will be understood to imply the inclusion of a stated integer or step or group of integers or steps but not the exclusion of any other integer or step or group of integers or steps.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A demonstrates a method in the art that utilizes certain conditions for the production of HPV16-specific T-cells. FIG. 1A is a bar chart showing production of spot forming colonies (SFC) on stimulation of PBMCs from three HPV-associated cancer patients (identified as OCV, HND and HNC) with autologous DCs loaded with no pepmix (Neg), HPV16 E6 pepmix (HPV16 E6) or HPV16 E7 pepmix (HPV16 E7). For patient OCV the three bars present from left to right are Neg, HPV16 E6 and HPV16 E7. For patients HND and HNC the two bars present from left to right are HPV16 E6 and HPV16 E7.
FIG. 1B demonstrates a method of the disclosure that utilizes, under certain novel conditions, the production of a mixture of T-cells specific for HPV16 or HPV18 by stimulation of T-cells in the presence of IL-7 and IL-15 and in the absence of IL-6 and IL-12. FIG. 1B is a bar chart showing production of spot forming colonies (SFC) on stimulation of PBMCs from three HPV-associated cancer patients (identified as OCV, PCV and HND). For patient OCV the five bars present from left to right are no pepmix (Neg), HPV16 E6 pepmix (HPV16 E6), HPV16 E7 pepmix (HPV16 E7), HPV18 E6 pepmix (HPV18 E6), and HPV18 E7 pepmix (HPV18 E7). For patient PCD the two bars present from left to right are HPV16 E6 and HPV16 E7. For patient HND the four bars present from left to right are HPV16 E6, HPV16 E7, HPV18 E6 and HPV18 E7.
FIG. 2 is a chart showing in vivo expansion and persistence of infused HPV stimulated T-cells transduced with a dominant negative receptor for TGF-beta (DNRII) in patient #1 at time points post infusion.
FIG. 3 is a chart showing in vivo expansion and persistence of infused HPV stimulated T cells transduced with a dominant negative receptor for TGF-beta (DNRII) in patient #2 at time points post infusion.
FIG. 4 shows PET scans (left and center) and photographs of physical examination (right) for patient #2. Top row: pre-treatment. Bottom row: 6 weeks after treatment with HPV stimulated T cells produced according to the present invention.



DETAILED DESCRIPTION
The scope of the present application is not intended to be limited to the particular embodiments of the process, machine, manufacture, composition of matter, means, methods and steps described in the specification.
In keeping with long-standing patent law convention, the words “a” and “an” when used in the present specification in concert with the word comprising, including the claims, denote “one or more.” Some embodiments of the invention may consist of or consist essentially of one or more elements, method steps, and/or methods of the invention. It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein.
The present disclosure concerns the production and use of therapeutic T-cells for individuals that are in need of HPV-specific T-cells, e.g., HPV16- and/or HPV18-specific T-cells, including for treating HPV infection and HPV-associated medical conditions. In particular embodiments, the methods and compositions are useful for treating neoplasms that are indirectly or directly related to HPV infection, and such neoplasms may be benign or malignant. Between 13 and 18 HPV strains have been characterized as conferring a high oncogenic risk, with 12 of these strains belonging to the HPV species 7 (HPV-18, -39, -45, -59, -68) and species 9 (HPV-16, -31, -33, -35, -52, -58, -67). HPV Types 6 and 11 cause laryngeal papillomatisis.
I. HPV Antigen(s) and Generation of Pepmixes
Methods of the disclosure utilize antigen-presenting cells that present mixtures of peptides to T-cells. Such “loaded” APCs are generated prior to exposure to peripheral blood T-cells for stimulation of the peripheral blood T-cells, and the generation of the loaded APCs may or may not be performed by the individual or entity that performs the stimulation step for the peripheral blood T-cells. Thus, in some embodiments, an effective amount of a library of peptides is provided to APCs as part of methods that ultimately generate therapeutic CTLs. In methods of the disclosure, prior to a stimulation step, APCs are exposed to a sufficient amount of the library of peptides. The library, in particular cases, comprises a mixture of peptides (“pepmixes”) that span part or all of the same antigen, although in some cases the library comprises pepmixes that span part or all of one or more antigens, and the one or more antigens may or may not be from the same HPV. In particular embodiments, peptides for the APCs are non-natural, and they may or may not be chemically synthesized or produced by recombinant means.
In utilizing a library of mixtures of peptides from one or more HPV antigens, the various peptides may come from any part of a given protein, but in specific cases the peptides collectively span the length of the majority or all of the protein, wherein the sequence of the peptides overlap at least in part to facilitate coverage of the entire desired region of the specific antigen(s). In some cases the peptides span the length of one or more known epitopes or domains of the respective antigen to which the peptides correspond. Certain regions may be covered by peptides that span the length of the region, including a region such as a N-terminal domain, C-terminal domain, extracellular domain, or intracellular domain, for example.
The antigens from which the peptides are derived may be antigens for HPVs that may be of any kind, but in specific embodiments the antigens are such that they allow for direction of cytotoxic T-cells to neoplasms, including cancers, associated with HPV infection. In particular embodiments, the peptides are derived from, or have sequence that corresponds to, at least part of one or more antigens of at least one HPV type, including HPV16 and/or HPV18. For example, in late stage cervical cancer, the HPV virus integrates into a tumor cell genome and loses all of its other genes except E6 and E7, so in some cases these antigens are targeted. In embodiments wherein one would treat an earlier stage of cancer, such as before the virus integrated, one could utilize peptides from antigens other than E6 and E7, including E5 and L1 and L2, for example. However, given that the two primary oncoproteins of high risk HPV types are E6 and E7, in specific embodiments the sequence of the peptides are obtained from E6 and/or E7 from any HPV, but HPV16 and/or HPV18, in particular. Peptides from any of antigens E1, E2, E3, E4, E5, E6, E7, L1, and/or L2 may be utilized in methods of the disclosure.
In some cases, a pepmix library includes peptides corresponding to one or more antigens from a single type of HPV virus, and those peptides may or may not provide sequence coverage across the entire antigen(s) in question. In other cases, a pepmix library includes peptides corresponding to one or more antigens from more than one HPV virus, and those peptides may or may not provide sequence coverage across the entire antigen(s) in question. The pepmix may or may not be enriched for peptides corresponding to one or more certain regions of one or more certain antigens or corresponding to the entirety of one or more certain antigens.
Pepmixes utilized in the disclosure may be from commercially available peptide libraries or may be synthetically generated, for example. Examples of available libraries include those from JPT Technologies (Springfield, Va.) or Miltenyi Biotec (Auburn, Calif.). The skilled artisan, based on known sequences of HPV16 E6, HPV16 E7, HPV18 E6, and HPV18 E7, for example, would have sufficient information to be able to generate peptides that correspond to their exemplary, respective sequences. An example of sequence of the HPV16 E6 protein is available at the National Center for Biotechnology Information's GenBank® database at GenBank® Accession No. AIQ82776.1 GI:688010703. An example of sequence of the HPV16 E7 protein is at GenBank® Accession No. AIQ82814.1 GI:688010789. An example of sequence of the HPV18 E6 protein is at GenBank® Accession No. AGU90423.1 GI:537801975. An example of sequence of the HPV18 E7 protein is at GenBank® Accession No. AGU90424.1 GI:537801976.
In particular embodiments, a library is comprised of peptides of a certain length that correspond to their respective antigens, although in some cases a library is comprised of a mixture of peptides with two or more different lengths. The peptides may be of a certain length(s) and they may overlap in sequence of a certain amount, although there may be variability of length of overlap in some libraries. In particular embodiments, the peptides are at least 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 or more amino acids in length, for example. In particular embodiments, there is overlap among the peptides of at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34 amino acids in length, for example. In specific embodiments, the peptides are 15 amino acids long and overlap one another by 11 amino acids. A mixture of different peptides may include any ratio of the different peptides, although in some embodiments each particular peptide is present at substantially the same numbers in the mixture as another particular peptide. Although coverage of an antigen in sequence for the peptides may be random and substantially even over a given region of an antigen, in some embodiments a library may be enriched for one or more particular peptides, such as one or more peptides that are known to encode an epitope or a part thereof, for example.
In particular embodiments, the pepmix for a particular antigen protein comprise all possible HLA class I epitopes that are 8 to 10 amino acids long, for example. In specific embodiments, longer peptides are utilized to cover all class II epitopes for a particular peptide. In certain aspects, the peptides are at a maximum of 30 amino acids in length with overlapping of 25 amino acids.
II. Methods of Producing and Using Therapeutic T-Cells
A. Producing Therapeutic T-Cells
In certain aspects, the present disclosure concerns the development of immune cells, such as cytotoxic T-cells, that target one or more antigens from at least one HPV virus.
Methods disclosed herein may involve the stimulation and/or expansion of immune cells. The methods may involve the stimulation and/or expansion of peripheral blood cells, such as peripheral blood mononuclear cells. The methods may involve the stimulation and/or expansion of T cells. The cells may have been obtained from the patient to be treated (i.e., autologous cells), or from another individual (i.e., allogeneic cells). The methods involve stimulation and/or expansion of isolated immune cells, in certain embodiments. That is, specific methods may be performed on a population of cells that contains substantially no non-immune cells, such as erythrocytes. In some cases, the immune cells are isolated PBMCs, or isolated T cells. The cells may have been obtained from a sample of blood, such as a sample of blood obtained from the patient or individual. Certain methods disclosed herein involve a step of obtaining PBMCs and/or T cells from a sample obtained from the patient. Certain embodiments of methods do not involve the step of obtaining a sample of blood or cells from the patient or individual, but instead are performed on a sample or cells that have been previously obtained. The method may involve processing the sample, such as enriching the sample for immune cells, such as PBMCs and/or T cells. Such methods may involve removing or substantially reducing the amount of, erythrocytes, platelets, serum and/or plasma in a sample. This may result in a population of immune cells containing substantially no other cells, such as erythrocytes. Methods disclosed herein may be performed on isolated immune cells, or a sample containing immune cells in addition to other cells.
In methods of producing the T-cells, peripheral blood T-cells may be initially stimulated with APCs that have been exposed to one or more peptides that span some or all of at least one HPV antigen. The antigenic peptides may be provided to the APCs in a library of peptide mixtures, and multiple libraries of pepmixes may be provided to the same collection of APCs. In some embodiments, the collection includes both immunodominant and subdominant antigens.
In embodiments of the disclosure, therapeutic T-cells are generated and may be provided to an individual that has an HPV infection or is at risk of having an HPV-associated medical condition that results indirectly or directly from an HPV infection. In methods of producing the therapeutic T-cells, under certain conditions peripheral blood T-cells are mixed with APCs that are loaded with a library of peptides that span part or all of one or more antigens, including part or all of a HPV16 and/or HPV18 antigen, including E6 and/or E7, for example. In specific embodiments, for the stimulating step the T-cells reside within a population of PBMCs.
In some embodiments, the APCs used in certain steps may be dendritic cells (DCs). Methods for generation of DCs are well known in the art, e.g. see Ramos et al., supra. Monocytes may be isolated from PBMCs by CD14 selection and cultured in DC medium and 2 mM alanyl-glutamine with 800 U/ml granulocyte/macrophage colony stimulating factor (GM-CSF) and 1000 U/ml interleukin 4 (IL-4) for 5 days. GM-CSF and IL-4 may be replenished on day 3. On day 5, DCs are matured in DC media with 10 ng/ml interleukin-1β (IL-1β), 100 ng/ml interleukin 6 (IL-6), 10 ng/ml prostaglandin E2, 800 U/ml GM-CSF and 1000 U/ml IL-4. DC maturation may be assessed by flow cytometry to detect upregulation of CD80. CD83, CD86 and HLA-DR.
In some embodiments, the APCs used in certain steps are activated T-cells. Activated T-cells may be polyclonal T-cells (T-APCs) generated using a portion of the autologous PBMC isolated from the venesected blood. The cells may be activated by culturing in cell culture plates that are coated with anti-CD3 and anti-CD28 antibodies. The cells are then cultured to expand in the presence of IL-2 for 2 weeks. The expanded T-APC can be cryopreserved for later use. 2-3 days prior to using T-APC for stimulation (e.g., for the 3rd cycle of stimulation and optionally for subsequent stimulations), cryopreserved cells are thawed and re-stimulated in anti-CD3 and anti-CD28 antibody-coated cell culture plates. On the day of stimulation, the T-APC cells are harvested and pulsed with the HPV E6/E7 peptides, followed by adding to the on-going culture of HPV stimulated T-cells at 1:1 ratio.
In some embodiments, the APCs used in certain steps and/or methods may be B-blasts (BBs). B-blasts may be generated from a patient's autologous PBMC, for example. The B lymphocytes within the PBMCs are activated by co-culturing with an irradiated allogeneic CD40L-expressing MRC5 epithelial cell line and expanded in media containing 100 U/ml IL-4 and 1 microgram/ml cyclosporin A.
In some embodiments, there is a method of generating T-cells that target at least one antigen from one or both of HPV16 and HPV18, and this occurs generally by contacting a plurality of PBMCs with a plurality of APCs loaded for peptides from a library of peptides that correspond to one or more particular HPV16 and/or HPV18 viral antigens. In specific embodiments, the exposure of the two populations of cells allows for expansion of the T-cells. In particular embodiments, the stimulation step(s) occurs in the presence of one or more particular cytokines, which may be mammalian (e.g. murine, human) or human cytokines. In certain embodiments, the one or more cytokines are IL-7 and IL-15, although in alternative embodiments the cytokine(s) are selected from the group consisting of IL-15, IL-7, IL-21, IL-12, IL-6, IL-4, and a combination thereof. In specific embodiments, one or more steps of the methods do not occur in the presence of IL-2, IL-4, IL-6, IL-7, IL-12, and/or IL-21, although alternatively IL-2, IL-4, IL-6, IL-7, IL-12, and/or IL-21 may be utilized. Reference to the presence of a cytokine is to presence of exogenously added cytokine, i.e. excluding any cytokine present within or secreted by the culture of cells. In some embodiments, the peptides are further defined as peptides that overlap in sequence to span part or all of a HPV antigen. For example, in certain aspects the peptides overlap by at least 10 amino acids, and particularly 11, and in some embodiments the peptides are at least 12 or more amino acids in length, and particularly 15 amino acids in length.
The selection of an appropriate amount or concentration of a given cytokine for inclusion in a cell culture is within the ability of the person or ordinary skill in the art. By way of example, the following is a list of certain interleukins and examples of appropriate concentrations that may be used:
Interleukin 6 (IL-6): 50 to 150 ng/ml, one of about 50 ng/ml, 60 ng/ml, 70 ng/ml, 80 ng/ml, 90 ng/ml, 100 ng/ml, 110 ng/ml, 120 ng/ml, 130 ng/ml, 140 ng/ml or 150 ng/ml;
Interleukin 7 (IL-7): 5 to 15 ng/ml, one of about 5 ng/ml, 6 ng/ml, 7 ng/ml, 8 ng/ml, 9 ng/ml, 10 ng/ml, 11 ng/ml, 12 ng/ml, 13 ng/ml, 14 ng/ml or 15 ng/ml;
Interleukin 12 (IL-12): 5 to 15 ng/ml, one of about 5 ng/ml, 6 ng/ml, 7 ng/ml, 8 ng/ml, 9 ng/ml, 10 ng/ml, 11 ng/ml, 12 ng/ml, 13 ng/ml, 14 ng/ml or 15 ng/ml;
Interleukin 15 (IL-15): 5 to 15 ng/ml, one of about 5 ng/ml, 6 ng/ml, 7 ng/ml, 8 ng/ml, 9 ng/ml, 10 ng/ml, 11 ng/ml, 12 ng/ml, 13 ng/ml, 14 ng/ml or 15 ng/ml.
Table 1 below provides examples of certain embodiments of methods of the disclosure.







TABLE 1







Examples of Elements of a Method








Embodiments
Examples for Embodiments












First Stimulation
Source of T-cells
Peripheral blood mononuclear cells (PBMC)




Non-adherent PBMC



Antigen-presenting
Dendritic cells (DC)s, PBMCs or B-blasts



cells (APC)



Cytokines
Combinations of IL-15 and IL-7, optionally




with IL-6 and/or IL-12 and/or IL-21 and/or IL-4



Antigen
Viral pepmixes for HPV


Second stimulation
Source of T-cells
Product of first stimulation



APCs
DC




PBMCs




Autologous activated T-cells (AATC)



Cytokines
IL-15 and IL-7, preferably no IL-6 or IL-12




and optionally IL-15 and IL-7 are the only




interleukins



Antigen
Viral pepmixes for HPV


Third stimulation
Source of T-cells
Product of second stimulation


(and subsequent


stimulations as


desired)



APCs
Pepmix-loaded AATCs + costimulatory cells



Cytokines
IL-15 and IL-7, preferably no IL-6 or IL-12




and optionally IL-15 and IL-7 are the only




interleukins



Costimulatory cells
Cells expressing CD86, 4-1BB, and CD83,




e.g., K562 cells









Thus, in particular embodiments, a population of T-cells (wherein the population may comprise substantially all T-cells or wherein the population of T-cells is within another population of cells, such as within PBMCs) is exposed to a population of APCs to generate T cell lines having particular characteristics, including at least: a) effectiveness at targeting HPV16 E6 and/or E7 and/or effectiveness at targeting HPV18 E6 and/or E7; b) polyclonality; c) TH1 bias; or d) a combination thereof. The generated T cell lines may be produced to be effective at targeting HPV species 7 (HPV-18, -39, -45, -59, -68) and species 9 (HPV-16, -31, -33, -35, -52, -58, -67), and types 6 and 11, and this may be the results of pepmixes directed to any one or more of the following antigens: E1, E2, E3, E4, E5, E6, E7, L1, and/or L2.
In some cases, T-cells are stimulated more than once, and different stimulation steps may or may not expose the population of cells to the same conditions. In specific embodiments, a first stimulation has conditions different from a subsequent stimulation, including a second stimulation and/or a third stimulation. In specific embodiments, a first stimulation step of the method utilizes APCs that are pepmix-loaded DCs or pepmix-loaded PBMCs and utilizes IL-7 and IL-15. This stimulation step may optionally be repeated one or more times.
In certain embodiments of the methods, between days 8 and 10 following an initial exposure of the peripheral blood T-cells (or PBMCs) to the pepmix or APCs, there may be a re-stimulation of the PBMCs on day 8, day 9, or day 10, but not later, and then a subsequent re-stimulation may occur on day 15, day 16, or day 17.
In a stimulation step that is subsequent to the first stimulation step (including optional repeats of the first stimulation step), the resultant T-cells obtained after the first stimulation (and which may be in a heterogeneous population of cells) are exposed to pepmix-loaded DCs or pepmix-loaded PBMCs and/or autologous activated T-cells. In a stimulation that is subsequent to first and second stimulation steps, T-cells obtained after the second or later stimulation (and which may reside in a heterogeneous population of cells) are exposed to pepmix-autologous activated T-cells. Costimulatory cells that may be utilized in any stimulation step include at least cells that express CD86, 4-1BB, CD83, CD40, OX40, and/or CD80. In specific cases, the costimulatory cells may be K562 cells.
In some embodiments, during the steps of the method the cells in culture are modified. In specific embodiments, the cells are modified to harbor a polynucleotide that expresses a gene product that renders the cells effective or more effective for a specific purpose or function, such as effective or more effective for targeting a particular target and/or enhanced in function for T-cell-mediated cytotoxicity, and/or modified to resist tumor antigen-specific cellular immunity, for example.
In some embodiments, the cells are modified to express a certain non-natural receptor that allows the T-cells to effectively or more effectively target a desired target cell, such as one that expresses a certain antigen. The cells may be modified to express a chimeric antigen receptor (CAR), an αβ T-cell receptor, and so forth. The cells may be modified to express an expression vector (that may be viral (including retroviral, lentiviral, adenoviral, adeno-associated viral, and so forth) or non-viral) during the method at specific time points, such as the vector being introduced between day 2 and 5 of culture, for example. In some embodiments the cells are exposed to the expression vector within about 3 days after each stimulation, but in such cases the modification occurs in more differentiated T-cells that have less long term potential (which in specific circumstances is desirable).
In specific embodiments, the cells are modified to express a CAR that targets a cancer antigen, such as EphA2, HER2, GD2, Glypican-3, 5T4, 8H9, αvβ6 integrin, B cell maturation antigen (BCMA) B7-H3, B7-H6, CAIX, CA9, CD19, CD20, CD22, kappa light chain, CD30, CD33, CD38, CD44, CD44v6, CD44v7/8, CD70, CD123, CD138, CD171, CEA, CSPG4, EGFR, EGFRvIII, EGP2, EGP40, EPCAM, ERBB3, ERBB4, ErbB3/4, FAP, FAR, FBP, fetal AchR, Folate Receptor α, GD2, GD3, HLA-AI MAGE A1, HLA-A2, IL11Ra, IL13Ra2, KDR, Lambda, Lewis-Y, MCSP, Mesothelin, Muc1, Muc16, NCAM, NKG2D ligands, NY-ESO-1, PRAME, PSCA, PSC1, PSMA, ROR1, Sp17, SURVIVIN, TAG72, TEM1, TEM8, VEGRR2, carcinoembryonic antigen, HMW-MAA, VEGF receptors, and/or other exemplary antigens that are present with in the extracellular matrix of tumors, such as oncofetal variants of fibronectin, tenascin, or necrotic regions of tumors and other tumor-associated antigens or actionable mutations that are identified through genomic analysis and or differential expression studies of tumors, for example.
In some embodiments the cells are modified to resist tumor antigen-specific cellular immunity, e.g. mediated by transforming growth factor beta (TGF-β). For example, the cells may be modified to express a dominant negative receptor for TGF-beta (DNRII), e.g. as described in Foster et al., (Antitumor activity of EBV-specific T lymphocytes transduced with a dominant negative TGF-beta receptor. J Immunother. 2008; 31:500-505, incorporated herein by reference). This may comprise transfecting the cells with a retroviral expression vector encoding a dominant negative TGF-β type II receptor (DNRII) modified by removal of the immunogenic hemagglutinin tag. Such modified T-cells have been shown to have a functional advantage over unmodified T-cells in the presence of TGF-β-secreting tumor, including enhanced antitumor activity (Foster et al., supra).
Methods according to the present invention may improve the rate of expansion for populations of virus-specific T-cells as compared to prior art methods. The rate of expansion for a T-cell population can be analysed by methods well known to the skilled person. Methods include measuring the number of T-cells at one or more time points. For example, the number of T-cells can be determined after performing a method according to the invention and compared to the number of T-cells at the beginning of the method; fold expansion in the number of T-cells can then be calculated.
Rates of expansion can also be determined by analysing cell division by T-cells over a period of time. Cell division for a given population of T-cells can be analysed, for example, by in vitro analysis of incorporation of 3H-thymidine or by CFSE dilution assay, e.g. as described in Fulcher and Wong, Immunol Cell Biol (1999) 77(6): 559-564, hereby incorporated by reference in entirety.
The improvement in the rate of expansion achieved by the methods according to the present invention can be determined by performing a method according to the invention, and comparing the expansion for T-cells in that method to a comparable, control method, e.g. as per the method of Ramos et al., (J Immunother 2013; 36:66-76).
In some embodiments, the rate of expansion for a population of T-cells in a method according to the present invention is one of at least 1.001 times, 1.002 times, 1.003 times, 1.004 times, 1.005 times, 1.006 times, 1.007 times, 1.008 times, 1.009 times, 1.01 times, 1.02 times, 1.03 times, 1.04 times, 1.05 times, 1.06 times, 1.07 times, 1.08 times, 1.09 times, 1.1 times, 1.2 times, 1.3 times, 1.4 times, 1.5 times, 1.6 times, 1.7 times, 1.8 times, 1.9 times, or 2 times the rate of expansion in a comparable control method.
The rate of expansion may be of the virus-specific T-cell population, or the total T-cell population.
The virus-specific T-cells generated/expanded according to the method of the present invention may at least retain the same functional properties as virus-specific T-cells generated/expanded according to prior art methods. That is, the accelerated rate of expansion does not negatively influence the functional properties of the expanded T-cells.
For example, in embodiments wherein the methods generate/expand a population of virus-specific T-cells, the T-cells display similar cytotoxicity to cells infected with or comprising/expressing a peptide of the virus as virus-specific T-cells expanded according to prior art methods.
Cytotoxicity of expanded T-cells can be analysed e.g. by culturing the expanded T-cell population with APCs presenting a peptide of the virus for which the T-cell is specific at different effector (i.e. T-cell) to target (i.e. APC) ratios, and measuring specific lysis of the APCs. For example, cytotoxicity of an HPV-specific CTL population can be analysed by measuring specific lysis of HPV-transformed LCL cells at different effector to target ratios.
B. Using Therapeutic T-Cells
In certain embodiments, cells produced by methods of the disclosure are provided to an individual in need thereof for treatment of a medical condition, including one caused by a viral infection, or to target a viral infection in which no symptoms of a medical condition are detectable or have manifested. As used herein “treatment” or “treating,” includes any beneficial or desirable effect on the symptoms or pathology of a disease or pathological condition, and may include even minimal reductions in one or more measurable markers of the disease or condition being treated, e.g., cancer. Treatment can involve optionally either the reduction or amelioration of symptoms of the disease or condition, or the delaying of the progression of the disease or condition. “Treatment” does not necessarily indicate complete eradication or cure of the disease or condition, or associated symptoms thereof.
In the methods encompassed by the disclosure, the therapeutic T-cells are utilized to treat viral-associated disease caused directly or indirectly by a single non-HPV virus or are otherwise provided to an individual that is seropositive for a single non-HPV virus. In other cases, the therapeutic T-cells are utilized to treat viral-associated disease(s) caused directly or indirectly by more than one virus or are otherwise provided to an individual that is seropositive for more than one virus. In the collection of therapeutic T-cells, each T-cell and its progeny has specificity for only one peptide in one antigen from one virus, and upon production of the collection of therapeutic T-cells, one expands a population of T-cell clones that together have multi-specificity, such as for multiple epitopes in each viral antigen, for example.
In at least some methods of the disclosure, a therapeutically effective amount of the CTLs generated thereby are administered to an individual, for example, an individual known to have or suspected of having or susceptible to having HPV16 and/or HPV18-associated disease. In specific embodiments, the cells are administered by injection, such as intravenous, intramuscular, intradermal, subcutaneous, intraperitoneal injection, and so forth, for example. In some embodiments, the CTLs are further defined as polyclonal CD4+ and CD8+ CTLs. The PBMCs may be allogeneic to the individual or may be autologous to the individual.
In certain cases, neoplasms are treated with cells of the disclosure, and the neoplasm may be benign, malignant, or a premalignant lesion that can lead to cancer. Thus, an individual may be treated with cells produced by methods of the disclosure at the premalignant lesion stage and/or after the lesion becomes malignant. The individual may have early or late stage cancer, and the skilled artisan is aware that the methods of producing the cells may be tailored for such different stages of cancer, such as by utilizing peptides for the APCs that are from antigens associated with early vs. late stage cancer. In specific embodiments, the cancer may be primary, metastatic, recurrent, refractory, and so forth.
In certain cases, premalignant lesions that can lead to cancers, such as premalignant lesions of the cervix, vulva, vagina, penis, larynx, oropharynx anus, and other upper aerodigestive areas, for example, are treated with cells produced by methods of the disclosure. Thus, an individual may be treated with cells produced by methods of the disclosure at the premalignant lesion stage and/or after the lesion becomes malignant. HPV-associated medical conditions that may be treated with cells produced by methods of the disclosure include at least dysplasias of the genital area(s), cervical intraepithelial neoplasia, vulvar intraepithelial neoplasia, penile intraepithelial neoplasia, anal intraepithelial neoplasia, cervical cancer, anal cancer, vulvar cancer, vaginal cancer, penile cancer, genital cancers, oropharyngeal cancer, nasopharyngeal carcinoma, oral papillomas and other upper aerodigestive lesions.
In some cases, one can determine the serotype that is associated with a cancer before administration of the cells, although in some cases the serotype is not determined. In specific embodiments, HPV16-specific or HPV18-specific cells have activity for tumors that are HPV16 or HPV18-positive, respectively, although in some cases there is cross-reactivity with different HPV serotypes. The ability to cross-react may or may not be known, and in certain cases, for example, an individual with HPV16 infection or HPV16-associated medical condition is administered HPV18-specific T-cells, and vice versa. In such cases, an individual may be treated with cells specific for a serotype in which it is unknown if the individual has that serotype, yet the cells still are therapeutically effective because of cross-reactivity.
In cases wherein the APCs of the stimulation steps of the method are loaded with HPV16 and HPV18 pepmixes together, the outcome of administration of T-cells expanded through such APCs is determined by whether the individual has been exposed to the virus in question. For example, if an individual is infected with HPV18 and not HPV16, only HPV18-specific T-cells will respond, and this is because the infection will initially have stimulated a T-cell response to HPV 18. Those T-cells will expand in the individual and then become memory T-cells and would be at higher numbers than T-cells specific for HPV16 that have never been activated, for example.
The individual being treated may be known to have cancer, suspected of having cancer, or at risk for having cancer (such as personal or family history; being sexual active, including sexually promiscuous; and/or having a genetic predisposition, including one or more specific markers). An individual being treated may have the presence of the HPV virus but there are not yet any deleterious symptoms of a HPV-related medical condition. The individual may have a benign or malignant neoplasm. The individual may have early or late stage cancer, and the skilled artisan is aware that the methods of producing the cells may be tailored for such different stages of cancer, such as by utilizing peptides for the APCs that are from antigens associated with early vs. late stage cancer. In specific embodiments, the HPV-associated disease is malignant cancer of the mouth or genital region. In specific embodiments, the cancer may be primary, metastatic, recurrent, refractory, and so forth. The individual may be infected with HPV16 and/or HPV18 as a result of sexual acts of any kind or intimate physical contact of any kind.
Any stage of HPV infection may be treated with cells encompassed by the disclosure. The individual with established HPV-associated cancer being treated with methods of the disclosure include Carcinoma in Situ (Stage 0), Stage I, Stage II, Stage III, or Stage IV (which may be determined by MRI, CT scan, PET scan, etc.). Additionally, individuals with pre-cancer lesions (dysplasia) may also be treated.
In some embodiments, one or more administrations of the cells produced by methods of the disclosure are provided to an individual in need thereof. The length of time between different administrations may be of any suitable duration, including on the order of 1-7 days, 1-4 weeks, 1-12 months, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more years. Multiple infusions within about a year may be employed, in some cases. In cases wherein more than one administration of cells are provided to the individual, the antigen to which the cells are targeted may or may not be the same antigen that was targeted with the cells utilized in earlier administration(s). For example, in a first administration of cells, the cells may target HPV18 E6, whereas in another administration of cells, the cells target HPV18 E7, or vice versa. Additional administration(s) may be required in cancers that become refractory, for example. Additional stimulations may be employed in conjunction with one or more other types of cancer treatments.
In some cases, an individual is optionally determined to have HPV infection by any suitable means in the art. Because HPV cannot be cultured in cell cultures, one may utilize HPV infection diagnosis methods such as DNA tests utilizing PCR, Southern blot hybridization, and/or in situ hybridization, and these methods may or may not be used in conjunction with colposcopy; acetic acid test; biopsy; physical examination; and/or Pap smear, for example.
In specific embodiments, a male individual is provided an effective amount of cells produced by methods of the disclosure to target HPV with which he is infected, and in such a case the individual thereafter has a reduced chance of infecting another, such as a female individual through sexual activity. The male individual may or may not be determined to be infected with HPV prior to exposure to the cells of the methods of the disclosure. In some cases, if an individual is shown to be infected with an oncogenic HPV, it would be worth treating him with cells to eliminate his risk. If the cells were effective, they would also reduce the chances of him transmitting the virus to his partner.
In specific embodiments, the individual is immunocompromised (which for example, may be defined as an individual whose ability to fight infectious disease or cancer with the immune system is compromised or entirely absent). In specific embodiments, the immunocompromised individual has had a stem cell transplant (including hematopoietic stem cell transplantation), has had an organ transplant and/or has received one or more cancer treatments, including chemotherapy or radiation, for example. In some cases, the individual has acquired or inherited immune deficiency disorder. In some embodiments, those that are immunocompromised by their disease and/or its treatment are provided methods and/or compositions of the disclosure.
Methods of medical treatment may involve treatment of cancer by a method of ameliorating, treating, or preventing a malignancy in a human subject wherein the steps of the method assist or boost the immune system in eradicating cancerous cells. Such methods may include the administration of cells, according to the present invention that invoke an active (or achieve a passive) immune response to destroy cancerous cells. Methods of treatment may optionally include the co-administration of biological adjuvants (e.g., interleukins, cytokines, Bacillus Comette-Guerin, monophosphoryl lipid A, etc.) in combination with conventional therapies for treating cancer such as chemotherapy, radiation, or surgery. Methods of treatment may involve administering a composition according to the present invention as a vaccine that works by activating the immune system to prevent or destroy cancer cell growth. Methods of medical treatment may also involve in vivo, ex vivo, and adoptive immunotherapies, including those using autologous and/or heterologous cells or immortalized cell lines.
III. Pharmaceutical Compositions
In accordance with this disclosure, the term “pharmaceutical composition” relates to a composition for administration to an individual. In a particular embodiment, the pharmaceutical composition comprises a composition comprising therapeutic immune cells for parenteral, transdermal, intraluminal, intra-arterial, intrathecal or intravenous administration or for direct injection into a neoplasm, such as a cancer. It is in particular envisaged that the pharmaceutical composition is administered to the individual via infusion or injection. Administration of the suitable compositions may be effected by different ways, e.g., by intravenous, subcutaneous, intraperitoneal, intramuscular, topical or intradermal administration.
The pharmaceutical composition of the present disclosure may further comprise a pharmaceutically acceptable carrier. Examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil/water emulsions, various types of wetting agents, sterile solutions, etc. Compositions comprising such carriers can be formulated by well-known conventional methods. These pharmaceutical compositions can be administered to the subject at a suitable dose.
The dosage regimen will be determined by the attending physician and clinical factors. As is well known in the medical arts, dosages for any one patient depends upon many factors, including the patient's size, body surface area, age, the particular compound to be administered, sex, time and route of administration, general health, and other drugs being administered concurrently. A particular dosage for administration might be in the range of 2×107 cells per m2 to 1×1010 cells per m2 of body surface area. Progress can be monitored by periodic assessment.
The compositions of the disclosure may be administered locally or systemically. In a preferred embodiment, the pharmaceutical composition is administered subcutaneously and in an even more preferred embodiment intravenously. Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishes, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. In addition, the pharmaceutical composition of the present disclosure might comprise proteinaceous carriers, like, e.g., serum albumin or immunoglobulin, preferably of human origin. It is envisaged that the pharmaceutical composition of the disclosure might comprise, in addition to the cells as described in this disclosure, further biologically active agents, depending on the intended use of the pharmaceutical composition.
IV. Combination Therapy
In certain embodiments of the disclosure that concern CTLs generated against HPV antigen(s), methods of the present disclosure for clinical aspects are combined with other agents effective in the treatment of hyperproliferative disease, such as anti-cancer agents. An “anti-cancer” agent is capable of negatively affecting cancer in a subject, for example, by killing cancer cells, inducing apoptosis in cancer cells, reducing the growth rate of cancer cells, reducing the incidence or number of metastases, reducing tumor size, inhibiting tumor growth, reducing the blood supply to a tumor or cancer cells, promoting an immune response against cancer cells or a tumor, preventing or inhibiting the progression of cancer, or increasing the lifespan of a subject with cancer. More generally, these other compositions may be provided in a combined amount effective to kill or inhibit proliferation of the cell. This may be achieved by contacting the cancer cell with a single composition or pharmacological formulation that includes both agents, or by contacting the cancer cell with two distinct compositions or formulations, at the same time, wherein one composition includes the expression construct and the other includes the second agent(s). In other cases, administration of the cells and a second composition may be separate and may have separate administration routes and/or carriers.
Tumor cell resistance to chemotherapy and radiotherapy agents represents a major problem in clinical oncology. One goal of current cancer research is to find ways to improve the efficacy of chemo- and/or radiotherapy by combining it with additional therapy. In the context of the present disclosure, it is contemplated that cell therapy could be used similarly in conjunction with chemotherapeutic, radiotherapeutic, and/or immunotherapeutic intervention, for example.
Alternatively, the present inventive therapy may precede or follow the other agent treatment by intervals ranging from minutes to weeks, months, or years. In embodiments where the other agent and present invention are applied separately to the individual, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the agent and inventive therapy would still be able to exert an advantageously combined effect on the cell. In such instances, it is contemplated that one may contact the cell with both modalities within about 12-24 h of each other and, more preferably, within about 6-12 h of each other. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or 8) lapse between the respective administrations.
It is expected that the treatment cycles would be repeated as necessary. It also is contemplated that various standard therapies, as well as surgical intervention, may be applied in combination with the inventive cell therapy.
Examples of HPV-associated cancer treatments (as an example) that may be used in conjunction with cells produced from methods of the disclosure include at least the following: 1) surgery (tumor resection, neck dissection, conization, hysterectomy, and so forth); 2) drug therapy that may include Avastin® (Bevacizumab); Blenoxane (Bleomycin); Hycamtin® (Topotecan Hydrochloride); or a combination thereof; 3) radiotherapy; 4) immunotherapy other than that of the disclosure; 5) hormone therapy; or 6) a combination thereof.
V. Kits of the Disclosure
Any of the compositions described herein may be comprised in a kit. In a non-limiting example, a library of pepmixes may be comprised in a kit, any type of cells may be provided in the kit, and/or reagents for manipulation of pepmixes and/or cells may be provided in the kit. Cytokine(s) or means of producing them (such as vectors that encode them) may be included in the kit. Cell culture reagents and/or apparatus(es) may be included. The component(s) are provided in suitable container means.
In one embodiment a kit may comprise a container comprising a quantity of T-cells obtained by a method of the present invention formulated for administration to a subject (e.g. by admixture with a suitable carrier, excipient, diluent, or adjuvant) preferably by infusion, more preferably for administration by infusion in a method of autologous adoptive cellular immunotherapy. The kit may be maintained at a predetermined temperature, e.g. less than about 4° C., less than about −2° C. or less than about −50° C. The kit may further comprise instructions for the storage and/or transport of the kit and/or for the administration of the T-cells.
The kits may comprise a suitably aliquoted compositions of the present invention. The components of the kits may be packaged either in aqueous media or in lyophilized form. The container means of the kits will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there are more than one component in the kit, the kit also will generally contain a second, third or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a vial. The kits of the present invention also will typically include a means for containing the components in close confinement for commercial sale. Such containers may include injection or blow molded plastic containers into which the desired vials are retained.
However, the components of the kit may be provided as dried powder(s). When reagents and/or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means.
In some cases, reagents and/or devices to detect HPV infection may be included in the kit. Examples include swabs, spatulas, cytobrushes, slides, cover slips, cytology sample collection receptacle(s), and so forth. Additional drugs for HPV infection or cancer may be included in the kit, such as Bevacizumab; Bleomycin; Topotecan Hydrochloride; or a combination thereof.
EXAMPLES
The following examples are presented in order to more fully illustrate the preferred embodiments of the invention. They should in no way, however, be construed as limiting the broad scope of the invention.
Example 1
Production of Therapeutic T-Cells
In some embodiments of the disclosure, there is a mechanism by which one can rapidly generate a single preparation of T-cells, including polyclonal (for example, CD4+ and CD8+) CTLs, that are consistently specific for a variety of antigens derived from one or more human papillomaviruses that can prove fatal. The disclosure is readily adaptable to clinical implementation and can be used as an “off the shelf” HPV antiviral agent. The methods and compositions are readily adaptable to clinical implementation and are useful as a safe and effective HPV antiviral agent for individuals.
In specific embodiments, peripheral blood T-cells were stimulated with monocyte-derived dendritic cells loaded with pepmixes [peptide libraries of 15-mers overlapping by 11 amino acids (aa)] spanning E6/E7, in the presence or absence of specific accessory cytokines. The resulting T-cell lines were further expanded with pepmix-loaded activated B-cell blasts. There was successfully reactivation and expansion (>1200-fold) of E6-specific/E7-specific T-cells from 8/16 cervical and 33/52 oropharyngeal cancer patients.
The presence of the cytokines interleukin (IL)-6, IL-7, IL-12, and IL-15 is useful in the method, in specific embodiments of the methods. The produced T-cell lines possess the desirable characteristics of polyclonality, multiple T-cell subset representation (including the memory compartment) and a TH1 bias, and eliminate E6/E7 targets. The disclosure has shown that it is possible to robustly generate HPV16 E6/E7-directed T-cell lines from patients with HPV16-associated cancers. Because the technique is scalable and good-manufacturing procedures-compliant, these lines are useful for adoptive cellular immunotherapy of patients with HPV16 cancers and may be applied to HPV18 cancers also.
Known methods for producing T-cells for HPV16 are demonstrated in FIG. 1A, showing results for 3 HPV-associated cancer patients (γIFN ELISpot assay obtained in cell lines obtained after stimulation of PBMCs by DCs loaded with only HPV16-pepmix). In FIG. 1B, results are shown for 2 of the patients whose results are also demonstrated in FIG. 1A, in addition to a third individual. FIG. 1B shows results of γIFN ELISpot assay for cell lines obtained after stimulation of PBMCs by DCs loaded with HPV16-pepmix and HPV18-pepmix. Reactivity against both HPV16 and HPV18 antigens can be detected (not all patients will have reactivity against both serotypes).
Turning to specifics of the methods, in certain cases DCs are loaded with HPV16-E6/E7 and HPV18-E6/E7 pepmix libraries. In such cases, the cell lines are able to recognize both HPV16 and HPV18 E6 and E7 antigens (instead of only HPV16 antigens, for example). In at least certain cases, expansion of the T-cells occurs in the presence of IL-7 and IL-15 but not IL-2. The presence of IL-7 and IL-15 in conditions for the method may or may not be at each step of stimulation and expansion. In some embodiments, expansion of the HPV-specific T-cells after initial generation/expansion with DCs occurs not with autologous B-blasts loaded with pepmixes in the presence of IL-15 but instead utilizes autologous, polyclonal activated T-cells loaded with pepmix, in the presence of costimulatory cells (CD80/CD86/CD83/4-1BBL), and IL-7 and IL-15. Employing these conditions, T-cell expansion occurs at a more rapid rate, at least 10-fold as that obtained by known methods, with successful demonstration having occurred after 3 rounds of stimulation and without loss of specificity.
Summary of fold cellular expansion using the known method with 3 HPV-associated cancer patients is provided in Table 2.







TABLE 2







Fold expansion at the end of each stimulation with known method











After 1st stimulation
After 2nd stimulation
After 3rd stimulation


Patient
(with DC and IL-
(with DC and IL-
(with B-blasts


ID
2/15)
2/15)
and IL-2/15)













OPA
3.38
2.63
4.96


OPE
1.59
4.60
1.60


OPY
2.20
2.50
0.38









A summary of fold cellular expansion using a novel method of the disclosure with 3 HPV-associated cancer patients is shown in Table 3. Fold expansion after 3 rounds of stimulation is on average approximately 50 times higher than using a known method. Specificity is maintained (illustrated in #1).







TABLE 3







Fold expansion at the end of each stimulation with a


method of the disclosure













After 3rd stimulation



After 1st stimulation
After 2nd stimulation
(with activated T-


Patient
(with DC and IL-
(with DC and IL-
cells, costim cells


ID
7/15)
7/15)
and IL-7/15)













PDC
2.60
5.35
151.20


PGD
5.00
6.36
120.00


PJK
3.58
5.53
60.00









Example 2
Protocol for the Expansion of HPV T-Cells
HPV stimulated T-cells (HPVST) are first activated by HPV E6/E7 peptide-pulsed autologous dendritic cells (DCs) at 10-20:1 PBMC:DC ratio, and cultured for 8 days in culture medium containing IL-6 (100 ng/ml), IL-7 (10 ng/ml), IL-12 (10 ng/ml), IL-15 (10 ng/ml) (e.g. per the first stimulation step described by Ramos et al., (J Immunother 2013; 36:66-76)).
A second stimulation step on day 9 is carried out using peptide-pulsed DCs at 5-10:1 PBMC:DC ratio in media containing IL-7 (10 ng/ml) and IL-15 (100 ng/ml).
Subsequent weekly stimulation/expansion steps are then carried to achieve a desired number of HPVSTs out using HPV E6/E7 peptide-pulsed autologous T-APC at 1:1 ratio, in the presence of equal number of irradiated allogeneic K562-cs co-stimulatory cells, and in media containing IL-7 (10 ng/ml) and IL-15 (100 ng/ml). The polyclonal T cells (T-APCs) are generated using a portion of the autologous PBMC isolated from the venesected blood. The cells are activated by culturing in cell culture plates that are coated with anti-CD3 and anti-CD28 antibodies. The cells are then cultured to expand in the presence of IL-2 for 2 weeks. The expanded T-APC can be cryopreserved for later use. 2-3 days prior to using T-APC for HPVST re-stimulation (3rd cycle of HPVST re-stimulation and onward), cryopreserved cells are thawed and re-stimulated in anti-CD3 and anti-CD28 antibody-coated cell culture plates. On the day of HPVST re-stimulation, the T-APC cells are harvested and pulsed with the HPV E6/E7 peptides, followed by adding to the on-going culture of HPVST at 1:1 ratio.
Example 3
In Vivo Expansion and Persistence of Infused HPVSTs in Human Patients
HPVSTs obtained from Example 2 were transduced with a dominant negative receptor for TGF-beta (DNRII) [see Foster et al., Antitumor activity of EBV-specific T lymphocytes transduced with a dominant negative TGF-beta receptor. J Immunother. 2008; 31:500-505].
The HPVSTs were administered to two human patients and tested for in vivo expansion and persistence. Patient #1 had widely metastatic oropharyngeal cancer and had discontinued prior therapy. Patient #2 had oropharyngeal cancer metastatic to the neck and was receiving concomitant nivolumab treatment, without prior response to nivolumab alone.
In vivo expansion and persistence of infused HPVSTs was assessed by qPCR for the DNRII gene performed in PBMCs isolated from peripheral blood from the patient. Data points in FIGS. 2 and 3 represent critical post-infusion intervals after the infusion of HPVSTs.
In patient #1 progressive expansion was observed (FIG. 2). In patient #2 although expansion was limited (FIG. 3), with a peak at 6 weeks coinciding with re-infusion of HPVSTs, the patient had a partial clinical response. Six weeks after HPVST infusion patient #2 exhibited a decrease in disease burden measured by PET scan and physical examination compared to a pre-treatment baseline (FIG. 4).
Although the present invention and its advantages have been described in detail, it should be understood that various changes, substitutions and alterations can be made herein without departing from the spirit and scope of the invention as defined by the appended claims. Moreover, the scope of the present application is not intended to be limited to the particular embodiments of the process, machine, manufacture, composition of matter, means, methods and steps described in the specification. As one of ordinary skill in the art will readily appreciate from the disclosure of the present invention, processes, machines, manufacture, compositions of matter, means, methods, or steps, presently existing or later to be developed that perform substantially the same function or achieve substantially the same result as the corresponding embodiments described herein may be utilized according to the present invention. Accordingly, the appended claims are intended to include within their scope such processes, machines, manufacture, compositions of matter, means, methods, or steps.

## Claims

1. A method of treating a human papillomavirus (HPV)-positive cancer in a subject, the method comprising:
(1) generating or expanding a population of T cells specific for a HPV by a method comprising: (a) obtaining peripheral blood T-cells from a subject with HPV-positive cancer; and (b) stimulating the peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV; and (2) administering the generated or expanded population of T cells to a subject with HPV-positive cancer.

2. The method of claim 1, wherein after (1)(a) and before (1)(b) the method further comprises stimulating the peripheral blood cells with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV.

3. The method of claim 1, wherein after (1) and before (2) the method further comprises stimulating the population of T-cells obtained from (1) with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV.

4. The method of claim 3 wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells, or a combination thereof.

5. The method of claim 1, wherein after (1) and before (2) the method further comprises (i) re-stimulating the population of T-cells obtained from (1) in the presence of IL-7 and IL-15 but not in the presence of co-stimulatory cells, and (ii) stimulating the T-cells obtained after (i) with antigen presenting cells in the presence of IL-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV.

6. The method of claim 1, wherein the antigen presenting cells are dendritic cells (DC), B-blasts (BB), or peripheral blood mononuclear cells (PBMCs).

7. The method of claim 1, wherein the cancer is cervical cancer, anal cancer, vulvar cancer, vaginal cancer, penile cancer, oropharyngeal cancer, nasopharyngeal carcinoma, laryngeal papillomatosis, laryngeal cancer, head and neck cancer, or a dysplasia of any of site thereof.

8. A method of treating a HPV-positive cancer in a subject, the method comprising:
(1) generating or expanding a population of T cells specific for a HPV by a method comprising:
(i) (a) obtaining peripheral blood T-cells from a subject with HPV-positive cancer; and (b) stimulating the peripheral blood T-cells with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV;
(ii) stimulating the peripheral blood T-cells obtained from (i) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15 and in the absence of IL-6 and/or IL-12, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV, wherein (ii) is optionally repeated one or more times; and
(iii) stimulating T-cells obtained from (ii) with antigen presenting cells in the presence of interleukin (IL)-7 and IL-15, and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV, wherein (iii) is optionally repeated one or more times;
(2) administering the generated or expanded population of T cells to a subject with HPV-positive cancer.

9. The method of claim 8, wherein stimulation of T-cells in (i) is in the presence of IL-6 and/or IL-12.

10. The method of claim 8, wherein the antigen presenting cells used in (i) and (ii) are dendritic cells (DC), B-blasts (BB), or peripheral blood mononuclear cells (PBMCs).

11. The method of claim 8, wherein the antigen presenting cells used in (iii) are activated T cells, dendritic cells (DC), B-blasts (BB), or peripheral blood mononuclear cells (PBMCs).

12. The method of claim 8, wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells or a combination thereof.

13. A method of treating a cancer in a HPV-positive subject, the method comprising:
(1) generating or expanding a population of T cells specific for a HPV by a method comprising: (a) obtaining peripheral blood T-cells from a subject with HPV-positive cancer; and (b) stimulating T-cells specific for HPV or for an HPV antigen in the peripheral blood with antigen presenting cells in the presence of IL-7 and IL-15 and in the absence of IL-6 and/or IL-12 and in the presence of co-stimulatory cells, wherein the antigen presenting cells were previously exposed to one or more peptides, wherein the peptides comprise sequence that corresponds to at least 8 contiguous amino acids of the sequence of one or both of E6 and E7 of HPV; and
(2) administering the generated or expanded population of T cells to a subject with HPV-positive cancer.

14. The method of claim 13, wherein the antigen presenting cells are activated T cells, dendritic cells (DC), B-blasts (BB), or peripheral blood mononuclear cells (PBMCs).

15. The method of claim 13, wherein the co-stimulatory cells are CD80+, CD86+, CD83+, 4-1BBL+, CD40+ cells, OX40+ cells, or a combination thereof.