Patent Application
20210205435
The present specification makes reference to a Sequence Listing (submitted electronically as a .txt file named “208192-9044_ST25.txt.” The .txt file was generated on Nov. 13, 2018 and is 10,491 bytes in size. The entire contents of the Sequence Listing are hereby incorporated by reference.
Embodiments of the present disclosure pertain generally to cancers associated with human papillomavirus subtype 16 (HPV16) infections. More particularly, the present disclosure provides novel immunogenic epitopes from HPV16 E2, E6 and E7 antigens restricted by common human leukocyte antigen (HLA) alleles for the diagnosis and treatment of HPV16-associated cancers.
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide with close to 600,000 cases diagnosed annually. A subset of HNSCCs caused by the human papillomavirus (HPV), (HPV+HNSCCs), are molecularly and clinically distinct from non-HPV associated HNSCCs (HPV−HNSCCs). In the United States, 70-80% of HPV+HNSCCs are caused by the oncogenic HPV type 16 (HPV16). Incidence of HPV+HNSCC increased 225% from 1984-2004 and has now surpassed the incidence of cervical cancer. Although HPV vaccines effectively prevent HPV-related cancers, the impact of vaccination on HNSCC incidence may not occur until 2060, likely due in part to slow vaccine uptake, and the decades between infection and clinical HPV+HNSCC diagnosis. As a result, over 600,000 cases are predicted in the interim, providing a strong rationale for the development of novel therapeutic strategies against HPV+HNSCC.
The recent development of clinically effective tumor immunotherapies, such as checkpoint blockade (CKB) using PD-1/PD-L1 inhibitors, has led to FDA approval of nivolumab and pembrolizumab for HNSCC. It is now established that the clinical response to CKB is correlated with tumor neo-epitope load. Tumor-specific neo-epitopes have been directly targeted using therapeutic vaccines and/or adoptive T-cell therapy (ACT), and have been shown to enhance cytotoxic T-cell targeting of multiple solid tumors. Thus, there is a renewed interest in defining the human leukocyte antigen (HLA) restricted antigenic repertoire of tumor infiltrating lymphocytes (TILs) to develop targeted therapeutic vaccines, to identify T-cell receptors (TCR) for ACT, and to monitor clinical responses to complex cancer immunotherapies.
Embodiments of the present disclosure pertain generally to cancers associated with human papillomavirus subtype 16 (HPV16) infections. More particularly, the present disclosure provides novel immunogenic epitopes from HPV16 E2, E6 and E7 antigens restricted by common human leukocyte antigen (HLA) alleles for the diagnosis and treatment of HPV16-associated cancers.
Embodiments of the present disclosure include an immunogenic composition for treating a subject having a HPV16-associated disease. In accordance with these embodiments the composition includes a synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens and a pharmaceutically acceptable carrier or excipient. In some embodiments, the immunogenic composition is for treating a subject with head and neck squamous cell carcinoma (HNSCC).
Embodiments of the present disclosure include a method of treating a subject having a HPV16-associated disease. In accordance with these embodiments, the method comprises administering an immunogenic composition described above wherein the administration of the composition induces an immune response against the HPV16-associated disease and treats the subject. In some embodiments the method is used to treat a subject with head and neck squamous cell carcinoma (HNSCC). In some embodiments, the immunogenic composition includes an immune checkpoint inhibitor which can include a programmed cell death protein 1 (PD-1) and an Indoleamine 2,3-dioxygenase 1 (IDO-1) inhibitor.
Embodiments of the present disclosure include an immune cell comprising a T-cell receptor (TCR) capable of binding a synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens.
Embodiments of the present disclosure include a method of detecting an HPV16-associated disease in a subject. In accordance with these embodiments, the method includes obtaining a biological sample comprising T cells from a subject, contacting the biological sample with a MHC class I peptide tetramer composition comprising at least one synthetic MHC class I molecule bound to at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens and detecting the presence of T cells bound to the synthetic polypeptide. In some embodiments the detection comprises flow cytometry or fluorescence-activated cell sorting.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. In case of conflict, the present document, including definitions, will control. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can be used in practice or testing of the present invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.
The terms “comprise(s),” “include(s),” “having,” “has,” “can,” “contain(s),” and variants thereof, as used herein, are intended to be open-ended transitional phrases, terms, or words that do not preclude the possibility of additional acts or structures. The singular forms “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. The present disclosure also contemplates other embodiments “comprising,” “consisting of” and “consisting essentially of,” the embodiments or elements presented herein, whether explicitly set forth or not.
The modifier “about” used in connection with a quantity is inclusive of the stated value and has the meaning dictated by the context (for example, it includes at least the degree of error associated with the measurement of the particular quantity). The modifier “about” should also be considered as disclosing the range defined by the absolute values of the two endpoints. For example, the expression “from about 2 to about 4” also discloses the range “from 2 to 4.” The term “about” may refer to plus or minus 10% of the indicated number. For example, “about 10%” may indicate a range of 9% to 11%, and “about 1” may mean from 0.9-1.1. Other meanings of “about” may be apparent from the context, such as rounding off, so, for example “about 1” may also mean from 0.5 to 1.4.
The use of the terms “a” and “an” and “the” and “at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term “at least one” followed by a list of one or more items (for example, “at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
“Isolated polynucleotide” as used herein may mean a polynucleotide (e.g., of genomic, cDNA, or synthetic origin, or a combination thereof) that, by virtue of its origin, the isolated polynucleotide is not associated with all or a portion of a polynucleotide with which the “isolated polynucleotide” is found in nature; is operably linked to a polynucleotide that it is not linked to in nature; or does not occur in nature as part of a larger sequence.
“Nucleic acid” or “oligonucleotide” or “polynucleotide” as used herein means at least two nucleotides covalently linked together. The depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. Many variants of a nucleic acid may be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. A single strand provides a probe that may hybridize to a target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions.
Nucleic acids may be single stranded or double stranded, or may contain portions of both double stranded and single stranded sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine and isoguanine. Nucleic acids may be obtained by chemical synthesis methods or by recombinant methods.
“Polypeptide” and “isolated polypeptide” as used herein refers to a polymer of amino acids or amino acid derivatives that are connected by peptide bonds. An isolated polypeptide is a polypeptide that is isolated from a source. An isolated polypeptide can be at least 1% pure, at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, and at least 90% pure, as determined by one or more protein biochemistry techniques (e.g., SDS-PAGE).
“Subject” and “patient” as used herein interchangeably refers to any vertebrate, including, but not limited to, a mammal (e.g., cow, pig, camel, llama, horse, goat, rabbit, sheep, hamsters, guinea pig, cat, dog, rat, and mouse, a non-human primate (for example, a monkey, such as a cynomolgous or rhesus monkey, chimpanzee, etc.) and a human). In some embodiments, the subject may be a human or a non-human. The subject or patient may be undergoing other forms of treatment.
“Treat,” “treated,” or “treating,” as used herein, refer to a therapeutic method wherein the object is to slow down (lessen) an undesired physiological condition, disorder or disease, or to obtain beneficial or desired clinical results. In some aspects of the present disclosure, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms; diminishment of the extent of the condition, disorder or disease; stabilization (i.e., not worsening) of the state of the condition, disorder or disease; delay in onset or slowing of the progression of the condition, disorder or disease; amelioration of the condition, disorder or disease state; and remission (whether partial or total), whether detectable or undetectable, or enhancement or improvement of the condition, disorder or disease. Treatment also includes prolonging survival as compared to expected survival if not receiving treatment.
“Variant” used herein with respect to a nucleic acid means (i) a portion or fragment of a referenced nucleotide sequence; (ii) the complement of a referenced nucleotide sequence or portion thereof; (iii) a nucleic acid that is substantially identical to a referenced nucleic acid or the complement thereof; or (iv) a nucleic acid that hybridizes under stringent conditions to the referenced nucleic acid, complement thereof, or a sequences substantially identical thereto.
“Variant” with respect to a peptide or polypeptide that differs in amino acid sequence by the insertion, deletion, or conservative substitution of amino acids, but retain at least one biological activity. Variant may also mean a protein with an amino acid sequence that is substantially identical to a referenced protein with an amino acid sequence that retains at least one biological activity. A conservative substitution of an amino acid, i.e., replacing an amino acid with a different amino acid of similar properties (e.g., hydrophilicity, degree and distribution of charged regions) is recognized in the art as typically involving a minor change. These minor changes may be identified, in part, by considering the hydropathic index of amino acids, as understood in the art. The hydropathic index of an amino acid is based on a consideration of its hydrophobicity and charge. It is known in the art that amino acids of similar hydropathic indexes may be substituted and still retain protein function. In one aspect, amino acids having hydropathic indexes of ±2 are substituted. The hydrophilicity of amino acids may also be used to reveal substitutions that would result in proteins retaining biological function. A consideration of the hydrophilicity of amino acids in the context of a peptide permits calculation of the greatest local average hydrophilicity of that peptide. Substitutions may be performed with amino acids having hydrophilicity values within ±2 of each other. Both the hydrophobicity index and the hydrophilicity value of amino acids are influenced by the particular side chain of that amino acid. Consistent with that observation, amino acid substitutions that are compatible with biological function are understood to depend on the relative similarity of the amino acids, and particularly the side chains of those amino acids, as revealed by the hydrophobicity, hydrophilicity, charge, size, and other properties.
“Vector” is used herein to describe a nucleic acid molecule that can transport another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double-stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors can replicate autonomously in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “recombinant expression vectors” (or simply, “expression vectors”). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. “Plasmid” and “vector” may be used interchangeably as the plasmid is the most commonly used form of vector. However, other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions, can be used. In this regard, RNA versions of vectors (including RNA viral vectors) may also find use in the context of the present disclosure.
Before any embodiments of the present disclosure are explained in detail, it is to be understood that the present disclosure is not limited in its application to the details of construction and the arrangement of components set forth in the following description or illustrated in the accompanying drawings. The present disclosure is capable of other embodiments and of being practiced or of being carried out in various ways.
Other aspects of the invention will become apparent by consideration of the detailed description and accompanying drawings.
Embodiments of the present disclosure relate generally to head and neck squamous cell carcinomas (HNSCCs) related to human papillomavirus subtype 16 (HPV16) infections. More particularly, the present disclosure provides novel immunogenic epitopes from HPV16 E2, E6 and E7 antigens restricted by common human leukocyte antigen (HLA) alleles for the diagnosis and treatment of HNSCC. The HPV16 epitopes identified in the present disclosure can be used in combination with blockade of HPV16+HNSCC-specific checkpoints for targeted immunotherapy.
HPV-associated cancers express multiple viral neoantigens. HPV integration into host genome in cervical cancer results in derepression of the oncogenic drivers E6 and E7. Immune therapies targeting E6 and E7 have thus been developed, including peptides, DNA, and ACT therapies. However, in comparison to cervical cancer, HPV+HNSCCs have both lower rates of genome integration, and less interruption of the viral transcriptional regulatory gene E2. Thus, subsets of HPV+HNSCCs also express E2 in addition to E6 and E7. It has been shown that high titers of serum antibodies against HPV16-E2, E6 and E7 are detectable in most HPV+HNSCC patients, indicating immunogenicity and persistence of these antigens. Thus, it is hypothesized that patients with HPV+HNSCC would have pre-existing HPV-specific CTLs, and that HPV-antigen expression levels would influence CTL-dysregulation in tumor microenvironment. The present disclosure identifies the T-cell antigenic landscape of globally frequent HLA class I alleles from HPV16 E2, E6 and E7. By phenotyping HPV-specific CTLs from HPV+HNSCC patients, and analyzing the immune transcriptomes of 119 HNSCCs, intratumoral and peripheral CTL-dysfunction in HPV+HNSCC are demonstrated. Also, CTL-dysfunction can be reversed using targeted HPV-specific T-cell expansion, and synergistic inhibition of IDO-1 and PD-1. Thus, the results of the present disclosure have implications for the development of effective T-cell therapies for HPV+HNSCC.
Strategies enhancing immune-based targeting of tumor cells have come to the forefront of cancer treatments. A subset of head and neck cancers (HNSCCs), caused by HPV16, is an ideal candidate for T-cell cancer immunotherapies. In the present disclosure, immunogenic CD8+ T-cell (CTL) epitopes from 3 HPV16-antigens were identified, and T-cell dysfunction mechanisms in HPV+HNSCC were evaluated. Several novel CTL-epitopes from HPV16-genes E2, E6 and E7 were identified across multiple HLA-alleles in peripheral blood CTLs of HPV+HNSCC patients. It was also found that tumoral viral load largely drives T-cell infiltration and subsequent CTL-exhaustion observed in HPV+HNSCC. Among other things, the present disclosure demonstrates the usefulness of host immune control of HPV, and identifies combination PD-1/IDO-1 inhibition as an efficient and useful strategy to enhance CTL-targeting of HPV+HNSCC.
HPV-driven malignancies can be a useful model system for cancer immunotherapy, due to 1) a long lead time from infection to malignancy; 2) emerging immune and viral biomarkers for early detection; 3) the persistent tissue expression of viral oncogenes; and 4) epidemiologic evidence of the central role of T-cell control of viral persistence. However, the dynamics of viral persistence within immunocompetent individuals and the mechanisms of tumor immune escape remain largely unknown, in particular for HPV+HNSCC. The emerging epidemic of HPV+HNSCC and lack of screening modalities represents a major clinical challenge and opportunity for targeted T-cell immunotherapy.
Embodiments of the present disclosure have expanded the spectrum of HPV+HNSCC-specific immune therapeutic targets at the CTL-epitope level and at the target tumor cell-modulatory level. Previous studies that have attempted to define CTL-immunogenicity from HPV16 have primarily focused on a limited number of HLA-alleles (e.g., A*02:01) and peptides from E6 and E7 (Tables 1-4), with limited data on immunogenic targets in in HPV+HNSCC. The 15 HLA alleles used in the present disclosure are predicted to include 10/12 of HLA supertypes and over 95% of the global population. Viral immune escape by altering HLA-binding CTL epitopes has been documented in HIV-1 and HCV infections, but not as well for DNA viruses such as HPV, where the mutation rates are markedly lower.
The present disclosure has identified several immunogenic CTL-epitopes from the 3 HPV16-antigens (
Despite the addition of CKB antibodies in the ex vivo T-cell stimulation protocol, low levels of E7-CTLs were detected compared to E2 and E6-CTLs. However, the prediction of previously described epitopes from E7 and the successful identification of novel CTL-epitopes from E2 and E6 across various HLA-alleles (
While other studies have shown high levels of immune infiltration in HPV+HNSCCs, results of the present disclosure demonstrate that HPV-antigen load likely drives high CTL-infiltration and CTL-dysfunction (
In addition to the PD-1 checkpoint, it was demonstrated both by computational and experimental in vitro assays that IDO-1 is highly expressed in HPV+HNSCC and other HPV-driven malignancies (
Embodiments of the present disclosure pertain generally to cancers associated with human papillomavirus subtype 16 (HPV16) infections. More particularly, the present disclosure provides novel immunogenic epitopes from HPV16 E2, E6 and E7 antigens restricted by common human leukocyte antigen (HLA) alleles for the diagnosis and treatment of HPV16-associated cancers. The HPV16 epitopes identified in the present disclosure can be used for identification of HPV16 infections and for targeted immunotherapy when used in combination with various immune checkpoint inhibitors.
Human papillomavirus (HPV) is the most common sexually transmitted infection globally. Most people have been unknowingly infected at some point during their lives because many of the infections cause no symptoms and are cleared by the immune system without intervention. When certain subtypes of HPV infection become persistent and unable to be cleared by the immune system it can lead to cancer. HPV subtypes 16 and 18 are considered high-risk for the development of cancer. HPV subtype 16 has been implicated in the majority of HPV-associated cervical cancers, anal cancers, head and neck cancers, vaginal cancers, vulvar cancers, penile cancers, and rectal cancers. A subset of HNSCCs are caused by HPV (HPV+HNSCC), with HPV16 responsible for 70-80% of those cases. Embodiments of the present disclosure pertain to any HPV16-associated diseases, including but not limited to, head and neck squamous cell carcinoma (HNSCC).
The present disclosure identified several novel immunogenic CD8+ T-cell (CTL) epitopes from 3 HPV16 antigens. In one embodiment of the present disclosure, at least one synthetic polypeptide encoding one of the CTL epitopes from E2, E6, or E7 HPV16 antigens are included in an immunogenic composition for treating a HPV16-associated disease. The CTL epitope(s) from the HPV16 E2 antigen can include RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24). The CTL epitope from the HPV16 E6 antigen can include IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43). The CTL epitope from the HPV16 E7 antigen can include LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
The immunogenic compositions disclosed herein can also include one or more pharmaceutically acceptable excipients. As would be appreciated by one of skill in this art based on the present disclosure, excipients can be chosen based on the route of administration, and can be formulated in dosages appropriate for each route of administration. Suitable excipients include diluents, thickening agents, buffer agents, preservatives, surface active agents, adjuvants, detergents, emulsifiers, stabilizers, immunostimulants, and/or others.
Embodiments of the present disclosure also include a method of treating the subject infected with a HPV16-associated disease by administering an immunogenic composition described herein to induce an immune response in the subject. In accordance with these embodiments, the method includes treatment of any HPV16-associated disease, including but not limited to cervical cancer, anal cancer, head and neck cancer, vaginal cancer, vulvar cancer, penile cancer, and rectal cancer.
In some embodiments, the immunogenic composition includes an immune checkpoint inhibitor. An immune checkpoint inhibitor includes any agent capable inhibiting the function of an immune checkpoint protein and/or pathway. Known immune checkpoint proteins/pathways include PD1 and its ligands PD-L1 and PD-L2, and in addition, IDO-1, CTLA-4, LAG-3, BTLA, B7H3, B7H4, TIMS, KIR. Cancer cells possess mechanisms to exploit these checkpoints and avoid being attacked by the immune system. There are a number of immunotherapeutic agents (immune checkpoint inhibitors) that are known to inhibit immune checkpoint proteins thereby initiating an immune response. Immune checkpoint inhibitors can include antibodies that specifically recognize immune checkpoint proteins. A number of PD1, PDL-1, PD-L2, IDO-1, CTLA-4, LAG-3, BTLA, B7H3, B7H4, 4-1BB (CD137), TEVI3 and KIR inhibitors are known. Examples of PD-1 inhibitors include without limitation humanized antibodies blocking human PD-1 such as Pembrolizumab (formerly Lambrolizumab), or Pidilizumab as well as fully human antibodies such as nivolumab (previously known as MDX-1 106 or BMS-936558). Examples of IDO-1 inhibitors include Epacadostat, Navoximod, Norharmane, and Indiximod. In one embodiment of the present disclosure, the checkpoint inhibitor is the IDO-1 inhibitor Epacadostat. In another embodiment the checkpoint inhibitor is an anti-PD-1 antibody.
Cancer immunotherapy can also include adaptive cell transfer (ACT). ACT involves the transfer of cells into a patient. The cells may originate from the patient or another individual. In some cases, T-cells are isolated from a patient, re-engineered based on the cancer diagnosis, and re-introduced back into the patient to bolster the immune response to the cancer cells. There are several types of immunotherapies that use ACT including tumor-infiltrating lymphocytes (TILs), high affinity T-cell receptors (TCRs), and chimeric antigen receptor (CARs). Both TCR- and CAR-based therapies re-engineer the T-cells to express a modified cell surface receptor capable of recognizing a specific tumor antigen. When these T-cells are reintroduced into the patient, they can recognize and kill cancer cells expressing that specific tumor antigen. One of the differences between TCR- and CAR-based therapies is the type of molecules they recognize. CAR T-cells recognize proteins expressed on the cell surface. TCRs recognize tumor-specific proteins on the inside of cells. When tumor-specific proteins are broken into fragments they show up on the cell surface with another protein called major histocompatibility complex (MHC). TCRs can be engineered to recognize a tumor-specific protein fragment/MHC combination.
Embodiments of the present disclosure also include an immune cell comprising a T-cell receptor (TCR) capable of binding a synthetic polypeptide encoding a CTL epitope derived from E2, E6, or E7 HPV 16 antigen. The CTL epitope from the HPV16 E2 antigen can include RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24). The CTL epitope from the HPV16 E6 antigen can include IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43). The CTL epitope from the HPV16 E7 antigen can include LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
One of the reasons HPV is well-suited for immunotherapy treatment is the early presence of emerging immune and viral biomarkers which allow for early detection. In studies of T-cell responses to viral infection, the predefined antigen repertoire encoded by the virus genome determines the specificity of virus-responsive T cells, which are often present in detectable frequencies following infection. Similarly, in chronic viral infections such T cells are detectable through life. Knowledge of those antigens for a virus and identifying cells expressing the T-cell receptor specific for that given antigen would allow early detection of infection.
Embodiments of the present disclosure include a method of detecting a HPV16-associated disease by quantifying T-cells that are specific for a given HPV antigen within a biological sample using an MHC tetramer assay. MHC tetramers exhibit a substantially higher affinity for a T-cell of interest than MHC monomers or dimers do, and are well-established reagents for the detection of antigen-specific T-cells by flow cytometry or fluorescence activated cell sorting (FACS). Tetramers bind to T-cells that are specific for both the MHC type and peptide being used in the tetramer. Usually cytotoxic T cells express CD8 on their surface, and are activated by binding to a complex of antigenic peptide and Class I MHC molecule. The MHC class I proteins in the present disclosure are bound by one of the synthetic polypeptides encoding epitopes derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens thereby only recognizing T-cells that have encountered the HPV16 virus. MHC tetramers are formed from individual MHC molecules, each bound by a synthetic peptide antigen. In some embodiments the individual MHC molecules each contain a ligand which binds to a polyvalent molecule binding partner to form a tetramer (i.e., a biotin ligand will bind to a streptavidin tetravalent molecule). In some embodiments, individual MHC molecules each contain a self-associating domain that naturally forms a tetramer when in solution.
Flow cytometry, also referred to as fluorescence activated cell sorting (FACS), provides a method for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell. This method can provide fast, objective and quantitative recording of fluorescent signals from individual cells as well as physical separation of cells of particular interest. In an MHC tetramer assay, the fluorescent label can be located on the MHC tetramer, which can allow separation of unlabeled T-cells from those containing the bound MHC tetramer thereby detecting the T-cells expressing the receptor able to identify the epitope specific to the disease antigen. Positive identification of T-cells expressing the epitope-specific receptor demonstrates the presence of the virus within the subject. Other methods for detecting and/or quantifying T cells can also be used, as would be recognized by one of ordinary skill in the art based on the present disclosure.
The following examples are illustrative of disclosed methods. In light of the present disclosure, those of skill in the art will recognize that variations of these examples and other examples of the disclosed method would be possible without undue experimentation.
Frequency and specificity of HPV16 E2, E6 and E7-specific CTLs in HPV+HNSCC. A systematic analysis was performed of potential CTL-epitopes from HPV16 E2, E6 and E7 antigens restricted by 15 globally frequent HLA class I alleles representative of major HLA supertypes (
Tables 1-4: Summary of all predicted candidate HPV16-E2, E6 and E7 epitopes, and cross-reactive epitopes. Peptide pool information from each antigen, relevant information for the epitope's information from HPV T-cell antigen database (cvc.dfci.harvard.edu/hpv/).
Within the 59 candidate HPV16-peptides, E2 had the lowest number of previously defined CTL-epitopes (3/24, 12%), while E6 and E7 had higher number of previously described CTL-epitopes (35% and 46% respectively). The number of predicted HPV16-peptides ranged from 15 peptides (A*02:01), to 0 peptides (B*40:01, B*44:02) among the selected HLA-alleles (
Because HPV-CTLs in peripheral blood mononuclear cells (PBMCs) are not abundant, PBMCs stimulated for 10 days were used with candidate peptides and CKB antibodies aCTLA4 and αPD-1 to enhance HPV-CTL reactivity (
Mapping immunodominant epitopes of HPV16 E2, E6 and E7 in HPV+HNSCCs. To identify novel CTL epitopes from E2, E6 and E7, a second IFNγ Elispot analysis was performed using individual predicted HPV16-peptides against patient-specific HLA-alleles (
HPV16 E2, E6 & E7 epitope distribution and immunogenicity in HPV+HNSCCs.
Landscape of CTL-epitopes from HPV16 E2, E6 and E7 in HPV+HNSCCs. HPV+HNSCC PBMCs from the initial pooled antigen screen (
HPV-specific T-cells exhibit dysfunctional phenotype in HPV+HNSCC patients. The first set of studies interrogated whether responding ex vivo stimulated HPV-specific peripheral CTLs in HPV+HNSCC patients were in naive or memory T-cell compartments. After one round of ex vivo stimulation by autologous antigen-presenting cells (APCs) presenting cognate HPV16-antigen, the majority (>79%) of HPV-specific CTLs detectable by antigen-specific multimers in HLAA*02:01+ patients exhibited memory phenotype distributed between Effector Memory (TEM, CD45ROhiCCR7lo) and Central Memory (TCM, CD45ROhiCCR7hi) compartments (representative examples in
While CTL dysfunction in chronic viral infections and cancers has been described, few studies have focused on the extent of T-cell exhaustion in HPV+HNSCC patients because of the difficulties in studying low-frequency HPV-CTLs. HPV-CTL dysfunction was assessed in HPV+HNSCC patients after ex vivo stimulation by autologous antigen-presenting cells (APCs) presenting cognate HPV16-antigen in the absence of CKB antibodies. The rationale included that activated HPV-specific PD1+CTLs that are poised towards the exhaustion spectrum will become further dysfunctional after APC-stimulation and acquire additional inhibitory markers characteristic of profound dysfunction, such as CD39 and TIM-3.
Chronic EBV-BMLF1 antigen specific HLA-A*02:01-restricted CTLs compared to acute Flu-M1 antigen specific CTLs, displayed a substantially higher DPEx-phenotype (CD39+PD-1+7.5 fold, TIM-3+PD-1+67-fold) indicating the validity of this approach (
HPV16-antigen load correlates with T-cell exhaustion. To provide a broader analysis of immune dysfunction from the tumor side in HPV+HNSCCs, immune signature analysis was performed of publicly available HNSCC transcriptomes (TCGA, UM-cohorts N=119, 51 HPV+, 68 HPV−). Previously-validated immune signatures were used representing tumor infiltrating immune cell subsets and performed single-sample gene set enrichment analysis to score the HPV+ and HPV− subsets. HPV+HNSCC patients in general had higher immune infiltration scores compared to HPV−HNSCCs (
To assess the impact of HPV gene expression on immune cell infiltration, the Spearman correlation coefficients were calculated among ssGSEA scores for the entire gene sets across all patients, including HPV16 genes and performed an unsupervised clustering on the correlation matrix (
HPV16-specific T-cells acquire dysfunctional phenotype upon ex vivo stimulation.
T-cell exhaustion signatures correlate with HPV16-antigen expression. 119 HNSCC transcriptomes (68 HPV−HNSCCs and 51 HPV+HNSCCS), were analyzed for immune cell infiltration by ssGSEA. In
IDO-1 represents a novel HPV+HNSCC specific immune target. Differential expression of constituent genes was analyzed within the exhaustion gene set between HPV+HNSCCs and HPV−HNSCCs (
IDO-1 inhibition enhances T-cell targeting of HPV+HNSCCs. IDO-1 inhibitors are being evaluated in pre-clinical and clinical settings to enhance tumor immunity. The possibility of exploiting IDO-1 inhibition to overcome HPV-CTL dysfunction, especially using E7-CTLs, was tested. HLA-A*02:01+HPV+HNSCC cell line UM-SCC-104 (SCC-104) was fluorescently labeled, which has high IDO-1, E7 and PD-L1 expression (
IDO-1 is an HPV-specific immune target and can enhance HPV-T-cell cytotoxicity Shown in
HPV16 candidate CTL-epitope prediction. HPV16-candidate CTL epitopes were predicted using previously described prediction strategies (Krishna S, Anderson K S. Methods Mol Biol. 2016; 1403:779-96 and Chowell D, et al. Proc Natl Acad Sci USA. 2015; 112:E1754-62), except for the incorporation of immunogenicity scores. For the 15 HLA-class I alleles, 9-mer and 10-mer candidate epitopes derived from the HPV16 proteins E2, E6, and E7 were predicted from 5 independent prediction algorithms and normalized. HLA-class I restricted 9-mer and 10-mer candidate epitopes derived from the HPV16 proteins E2, E6, and E7 were predicted for the HLAs A*01:01, A*02:01, A*03:01, A*11:01, A*24:02, B*07:02, B*08:01, B*15:01, B*27:05, B*35:01, B*40:01, B*40:02, B*44:02 B*51:01, and B*57:01. Top 4-5 candidate peptides/HLA-allele were used for experiments.
The protein reference sequences for each of HPV16 proteins were obtained from Papillomavirus Episteme (PAVE) and were then entered into 5 different prediction algorithms; 3 MHC-binding: IEDB-consensus binding, NetMHCpan binding, Syfpeithi and 2 antigen-processing algorithms: IEDB-consensus processing, ANN processing. The individual scores from each of the prediction algorithms were then normalized within the pool of predicted peptides after removal of poor-binders, and the mean normalized binding scores were used to re-rank the candidate peptides. Top 4-5 candidate peptides satisfying binding percentile scores >80% (
Ex vivo stimulation and epitope mapping of HPV+HNSCC PBMCs. PBMCs were obtained from stage III or stage IV HPV+HNSCC patients (MSSM cohort). All HPV16-peptides (>80% purity) were synthesized by Proimmune, UK. HPV+HNSCC PBMCs were thawed, rested with 1 μg/mL of CKB antibodies anti-PD1 (eBosciences, USA), anti-CTLA4 (eBosciences, USA) for 1 hour at 37° C. HPV16-peptides in pool or individually were added subsequently in biological triplicates, along with recombinant human IL-2 (20 U/mL), human IL-7 (5 ng/mL). On day 5, half the media was removed and replaced with fresh IL-2 and peptide pool. On day 8, half the media was removed and fresh media, IL-2 and peptide was added to the cells and replated into a 96-well multiscreen elispot plate for Elispot detection.
PBMCs were obtained from stage III or stage IV HPV+HNSCC patients (MSSM cohort) as described previously. All human PBMCs were obtained using informed consent under clinical protocol HSM 10-00585. PBMCs were stimulated as previously described. Briefly, HPV16-peptide pools shown in
HPV-CTL stimulation for phenotyping. HPV-specific T-cells were generated by stimulating autologous HPV+HNSCC patient B-cell APCs. APCs were either peptide pulsed with HPV16-epitopes, or transfected with whole HPV-antigen encoded in mammalian expression plasmid pCDNA3.2 (Invitrogen, CA, USA). APCs were washed and incubated with thawed whole HPV+HNSCC PBMCs at a ratio of 1:2 (200,000 APCs: 400,000 PBMCs) supplemented with 20 U/mL recombinant human IL-2 (R&D Systems, MN, USA), 5 ng/mL IL-7 (R&D Systems, MN, USA). On day 5, partial media exchange was performed. On day 10, expanded HPV-CTLs were restimulated with peptide-pulsed, transfected APCs similar to day 1. HPV-CTLs were used for cytolytic assays or immunophenotyped after day 20.
Tetramer staining, HPV-CTL and HPV+cell line phenotyping. HPV16-tetramers were obtained from NIH Tetramer Core Facility at Emory University. For tetramer staining, cells were re-suspended in 100 μL staining buffer with 5% human serum and 1 mM Dasatanib (ThermoFisher Scientific, MA, USA), and each tetramer was added at concentration of 1:100 for 30 minutes at room temperature. Cells were washed twice and restained with anti-CD8-PC5, anti-CD4-FITC, anti-CD14-FITC and anti-CD19-FITC for exclusion gates, and either a combination of anti-PD1-BV605 and anti-CD39-BV-405 or anti-PD1-BV-605 and anti-TIM3-BV-405 for 30 minutes on ice. HPV+cell line PD-L1 staining was done for 30 minutes on ice. Samples were then washed twice in 1×PBS, and analyzed by Attune flow cytometer (ThermoFisher Scientific, MA, USA).
Flow cytometry staining for T-cell and tumor immunophenotyping. Cells were washed once in MACs buffer (containing 1λ PBS, 1% BSA, 0.5 mM EDTA), centrifuged at 550 g, 5 minutes, and re-suspended in 200 μL MACS buffer. Cells were stained in 100 μL of staining buffer containing anti-CD137, conjugated with phycoerythrin (PE, clone 4B4-1; BD Biosciences, USA), anti-CD8-PC5 (clone B9.11; Beckman Coulter 1:100), anti-CD4 (clone SK3; BioLegend, 1:200), anti-CD14 (clone 63D3; BioLegend, 1:200) and anti-CD19 (clone HIB19; BioLegend, 1:200), all conjugated to Fluorescein isothiocyanate (FITC) for exclusion gates, and either a combination of anti-PD1-Brilliant Violet 605 (BV605, clone EH12.2H7; BioLegend, 1:50) and anti-CD39-BV-405 (clone A1; BioLegend, 1:200) or anti-PD1-BV-605 and anti-TIM3-BV-405 (clone F38-2E2; BioLegend, 1:50) for 30 minutes on ice. PD-L1 staining on HPV+HNSCC and cervical cancer cell lines were done using 50_, PD-L1 antibody (clone MIH1, ThermoFisher Scientific, MA, USA) in 100 μL MACS buffer. Samples were covered and incubated for 30 min on ice then washed twice in 1×PBS, and resuspended in 1 mL 1×PBS prior to analysis.
Tetramer staining for T-cell immunophenotyping. The following HLA-A*02:01 HPV16 tetramers were obtained from NIH Tetramer Core Facility at Emory University: TLQDVSLEV E2(93-101), YICEEASVTV E2(138-147), ALQAIELQL E2(69-77), KLPQLCTEL E6(18-26), TIHDIILECV E6(29-38), FAFRDLCIV E6(52-60), YMLDLQPET E7(11-19), and YMLDLQPETT E7(11-20). Cells were washed (550 g, 5 min) twice in MACS buffer with 5% human serum. After washing, cells were re-suspended in 100 μL staining buffer (MACS buffer, with 5% human serum and 1 mM Dasatanib (ThermoFisher Scientific, MA, USA). Each of the eight HLA-A*02:01 HPV16 tetramers (NIH Tetramer Core, Emory University, Atlanta, USA), all conjugated with phycoerythrin (PE) was added to each respective sample at concentration of 1:100. Samples were incubated at room temperature for 30 minutes under dark. After incubation, cells were washed 2× in MACS buffer. Cells were stained in 100 μL MACS buffer with anti-CD8-PC5, anti-CD4-FITC, anti-CD14-FITC and anti-CD19-FITC for exclusion gates, and either a combination of anti-PD1-BV605 and anti-CD39-BV-405 or anti-PD1-BV-605 and anti-TIM3-BV-405 for 30 minutes on ice. Samples were then washed twice in 1×PBS, and analyzed by flow cytometry. For flow cytometric analysis, all samples were acquired with Attune flow cytometer (ThermoFisher Scientific, MA, USA) and analyzed using Attune-software. Gates for expression of different markers and tetramers were determined based on flow minus one (FMO) samples for each color after doublet discrimination. Only samples with >50 CD8+Tetramer+ or CD8+CD137+ events were considered. Percentages from each of the gated population were used for the analysis.
Cell lines and immunoblotting experiments. Cervical cancer cell lines SiHa and Caski were obtained from ATCC (Manassas, Va., USA). HPV+HNSCC cell lines were obtained from the following sources: UPCI:SCC90 (SCC90) was obtained from ATCC (Manassas, USA), UM-SCC-47 (SCC47) and UM-SCC-104 (SCC104) from Merck Millipore (Billerica, Mass., USA). All cell lines contained integrated HPV-16 DNA, and were maintained in the following media: Caski was maintained in RPMI-1640 (ATCC) with 10% heat inactivated fetal bovine serum (FBS), SiHa in Eagle's Minimum Essential Medium (EMEM, ATCC, USA) with 10% FBS, SCC90 and, SCC47 in Dulbecco's Modified Eagle's Medium (DMEM, ATCC, USA) with 10% FBS, SCC104 cells were maintained in Iscove's Modified Dulbecco's Medium (IMDM, Gibco, NY, USA) with 10% human serum. Cells were harvested by trypsinization (0.25% Trypsin, GE Healthcare, IL, USA), and resuspended in 1 mL RIPA buffer (Invitrogen, CA, USA) containing a cocktail of protease inhibitors (Roche Diagnostics, IN, USA). Equal amounts of cell lysates were loaded on a 4-20% SDS-polyacrylamide gel (Invitrogen, CA, USA) and transferred to a Polyvinylidene fluoride membrane (GE Healthcare, IL, USA). The membrane was blocked with 5% nonfat dry milk in PBS-1% Tween (PBST) for 1 hour at room temperature. Primary antibodies and concentrations were as follows: GAPDH (Cell Signalling Technologies, MA, USA, clone 14C10, 1:2000), IDO-1 antibody (ThermoFisher Scientific, clone PAS-29819, 1:1000), anti-HPV16-E7 antibody (Fitzgerald industries, MA, USA, clone 10-7987, 1:1000). Visualization was done with Dura Western Blotting Kit (Thermo Scientific, USA) according to the manufacturer's instructions.
HPV-CTL cytotoxicity assays. HLA-A*02:01+HPV+HNSCC+SCC-104 cells were pre-labelled with 0.5 μM CellTracker Green CMFDA (ThermoFisher Scientific, MA, USA) for 1 hour and washed. HPV-specific CTLs were pooled by HPV-antigen, washed and resuspended in media supplemented with 20 U/mL IL-2, with 1 μg/mL isotype IgG or anti-PD1 antibody, DMSO, and 1 μM IDO-1 inhibitor Epacadostat (Selleck Chemicals, MA, USA) in various combinations as described. HPV-CTLs were added at ratio of 5:1 to SCC-104 cells and incubated for 48 hours at 37 C, 5% CO2. Cocultured cells were harvested, neutralized with media supernatant from each well containing dead cells and centrifuged for 850 g, 10 minutes. Cell pellets were washed twice with sterile 1×PBS, resuspended with 1 mL 1×PBS, and 2 uL Propidium Iodide (ThermoFisher Scientific, MA, USA) and cell death was assessed by flow cytometry. All samples were acquired with Attune flow cytometer (ThermoFisher Scientific, MA, USA) in blue-violet configuration and analyzed using Attune-software.
HLA-A*02:01 expressing HPV+HNSCC cell line SCC-104 was used for cytotoxicity assays. SCC-104 cells were plated at a density of 50,000 cells per well in a flat bottom 96-well sterile treated plate (Corning, USA). Twenty four hours later, cells were pre-labelled with 0.5 μM CellTracker Green CMFDA (ThermoFisher Scientific, MA, USA) for one hour, washed thrice with sterile 1×PBS. HPV-specific CTLs generated by either peptide pulsing or transfected antigens were pooled by HPV-antigen, washed and resuspended in BCM supplemented with 20 U/mL IL-2 along with 1 μg/mL isotype IgG antibody, anti-PD1 antibody (eBosciences, USA), DMSO, and 1 μM IDO-1 inhibitor Epacadostat (Selleck Chemicals, MA, USA) in various combinations as described. HPV-CTLs were added at ratio of 5:1 to SCC-104 cells and incubated for 48 hours at 37° C., 5% CO2. The cocultured cells were harvested by trypsinization, neutralized with media supernatant from each well containing dead cells and centrifuged for 850 g, 10 minutes. Cell pellets were washed twice with sterile 1×PBS, resuspended with 1 mL 1×PBS, and 2 uL Propidium Iodide (ThermoFisher Scientific, MA, USA) and cell death was assessed by flow cytometry. All samples were acquired with Attune flow cytometer (ThermoFisher Scientific, MA, USA) in blue-violet configuration and analyzed using Attune-software.
RNASeq data alignment. RNA-Seq reads for each sample were quality checked using FastQC (version 0.10.1, Babraham bioinformatics, Babraham Institute, Cambridge, UK) and aligned to the human genome build 38 (GRCh38, CF_000001405.33_GRCh38.p7_genomic.fna) primary assembly and HPV16 genome (GCF_000863945.1_ViralProj15505_genomic.fna) simultaneously using STAR (version 2.5.2B). After alignment, variants were discovered following GATK Best Practices workflow for RNAseq (gatkforums.broadinstitute.org/gatk/discussion/3892/the-gatk-best-practices-for-variant-calling-on-rnaseq-in-full-detail). Raw RNAseq reads were pre-processed by adding read groups, indexing, marking duplicates and sorting, Split‘N’Trim, reassigning mapping quality and base recalibration.
RNASeq datasets and gene signature sources. Transcriptome data for HNSCC patient samples (n=119) were obtained from TCGA (TCGA-cohort), and University of Michigan study (UM-cohort). In total, there were 34 and 18 HPV+HNSCC samples from TCGA-cohort and UM-cohort respectively. HPV−HNSCC dataset comprised of 18 tumors from UM-cohort and 49 tumors from TCGA dataset that were both HPV-negative by p16 status and HPV−FISH. For ssGSEA analysis, immune signatures, comprising of 509 genes were obtained from previous studies. Additional gene signatures were obtained as follows: Custom HPV gene sets were grouped into HPV (All 8 HPV genes), HPV. Onco (E6, E7) and HPV. Early (E2, E4, E5). TIGIT gene signature (50 genes) was obtained from Johnston et al., TIL.Treg (309 genes) and Exhaust gene sets (49 genes) were obtained from De Simone et al., and CYT (GZMA, PRF) from Rooney et al.
HLA typing. For MSSM-cohort, HLA-typing was performed by Proimmune HLA-tissue typing services, UK. For HLA-calling from RNAseq data (TCGA and UM cohorts), PHLAT (Bai et al., 2014) was used to infer the HLA typing of the three major MHC class I (HLA-A, -B, -C) alleles. The method employs a read mapping based selection of candidate allele followed by a likelihood based scoring over all pairwise combinations of selected alleles and infers the first four digits with a high accuracy. For HLA-odds ratio calculations, HLA-allele typing from all 3 cohorts (MSSM, TCGA and UM) were combined resulting in 64 HPV−HNSCC (TCGA) and 77 HPV+HNSCCs.
HPV16 epitope prediction from RNAseq data. HLA types obtained from PHLAT were used to predict the epitopes binding to patient-specific HLA alleles. Binding affinities were predicted using IEDB recommended algorithm from the Immune Epitope Database (IEDB) tool. Reference fasta files for HPV protein sequences were used to predict peptide lengths of 8, 9, 10, 11 for each patient's allele and peptide combination. If the matching HLA allele of the patient did not exist in the current IEDB list, the closest allele was identified by keeping the first two digits the same and searching for the nearest available match for the third and fourth digit. To retain only high affinity binding epitopes with the patient-specific HLA alleles, epitopes with a binding affinity greater than 500 nM were not considered in downstream analyses.
ssGSEA analysis of HPV and immune gene signatures. Log transformed transcripts per million (Log2 TPM+1) from each HNSCC sample, after subtraction of low expression genes was used for ssGSEA as previously described in Senbabaoglu et al. Pre-defined immune signatures, have been extensively validated in Senbabaoglu et al., and Mandal et al. ssGSEA scores were computed for each tumor sample using the R package GSVA, and Z-transformed across the cohort prior to analysis. To assess impact of HPV-gene expression on immune signatures, a correlation matrix was built using the R-library Corrplot with the Z-transformed ssGSEA scores and were displayed by hierarchical clustering of correlations. (Clustered correlation matrix values for each gene-set correlations not shown but available upon request). Individual gene expression analysis was performed by unsupervised hierarchical clustering methods and were used for heatmap analysis in
Elispot detection of IFNγ secretion. Elispot detection assay was performed as previously described. Briefly, sterile multiscreen Elispot plates, (Merck Millipore, Billerica, Mass., USA) precoated overnight with 5 μg/well anti-IFNγ capture antibody (clone D1K, Mabtech, USA) in sterile 1×PBS. Eight days after stimulation, HPV+HNSCC PBMCs were subject to media change and IL-2, peptide (pools or individual) were added. Cells in each well were transferred to the Elispot plate and incubated at 37° C. 5% CO2 incubator for 48 hours. Plates were washed with elispot buffer (PBS+0.5% FBS) and incubated with 1 μg/mL anti-IFNγ secondary detection antibody (clone 7-B6-1, Mabtech, USA) for 2 hours at room temperature, washed and reincubated with 1 μg/mL Streptavidin ALP conjugate for 1 hour at room temperature. The wells were washed again with elispot buffer and spots were developed by incubating for 8-10 minutes with detection buffer (33 μL NBT, 16.5 μL BCIP, in 100 mM Tris-HCl pH 9, 1 mM MgCl2, 150 mM NaCl). Plates were dried for 2 days and spots were read using the AID Elispot reader (Autoimmun Diagnostika GmbH, Germany). Average number of spot forming units for the triplicates were calculated for each test peptide/pool and subtracted from background (either HIV-control peptide pool or PBS-DMSO controls).
RAPID-ELISA for E2, E6 and E7 seroreactivity in HPV+HNSCC patients. RAPID-ELISA was performed as described previously. Briefly, patient sera were diluted 1:100 and blocked with E. coli lysate. Each antigen was expressed from template cDNA and captured onto 96-well plates coated with anti-GST Ab (GE Healthcare, Piscataway, N.J.) in duplicates. Horseradish peroxidase (HRP) anti-human IgG Abs (Jackson ImmunoResearch Laboratories, West Grove, Pa.) were added at 1:10,000, and detected using Supersignal ELISA Femto Chemiluminescent substrate (Thermo Scientific). Luminescence was detected as relative light units (RLU) on a Glomax 96 Microplate Luminometer (Promega, Madison, Wis.) at 425 nm. To control for nonspecific and GST-specific antibodies, the ratio of RLU for individual HPV-specific Abs to the RLU for the control GST-antigen was measured.
Autologous APC generation from HPV+HNSCC patient PBMCs. Autologous CD40L-activated B-cell APCs were generated from specific HPV+HNSCC patients by incubating whole PBMCs with irradiated (32 Gy) K562-cell line expressing human CD40L (KCD40L) at a ratio of 4:1 (800,000 PBMCs to 200,000 irradiated KCD40Ls) in each well. The cells were maintained in B-cell media (BCM) consisting of IMDM (Gibco, USA), 10% heat inactivated human serum (Gemini Bio Products, CA, USA), Antibiotic-Antimycotic (Anti-Anti, Gibco, USA). BCM was supplemented with 10 ng/mL recombinant human IL-4 (R&D Systems, MN, USA), 2 μg/mL Cyclosporin A (Sigma-Aldrich, CA, USA), 1× insulin transferrin supplement (ITES, Lonza, MD, USA). APCs were re-stimulated with fresh irradiated KCD40Ls on days 5 and 10, after washing with 1×PBS and expanding into a whole 24-well plate. After two weeks, APC purity was assessed by CD19+CD86+ expressing cells by flow cytometry, and were generally used for T-cell stimulation after >90% purity. APCs were either restimulated up to 4 weeks or frozen and re-expanded as necessary.
HPV-CTL stimulation by autologous APCs. Antigen-specific T-cells were generated by stimulating HPV+HNSCC patient B-cell APCs by either peptide pulsing of specific HPV16-epitopes, or by transfecting whole antigen encoded in mammalian expression plasmid pCDNA3.2 (Invitrogen, CA, USA). Peptide pulsing of APCs was done under BCM 5% human serum, with recombinant IL-4. Transfection of APCs were done using the Lonza 4D Nucleofector, primary P3 buffer, program EO117 (Lonza, MD, USA) and incubated in BCM-10% human serum, IL-4 without any Anti-Anti. Twenty four hours later, on day 1, APCs were washed and incubated with thawed whole HPV+HNSCC PBMCs at a ratio of 1:2 (200,000 APCs: 400,000 PBMCs) in a 24-well plate in BCM supplemented with 20 U/mL recombinant human IL-2 (R&D Systems, MN, USA), 5 ng/mL IL-7 (R&D Systems, MN, USA). On day 5, partial media exchange was performed by replacing half the well with fresh B-cell media and IL-2. On day 10, fresh APCs were either peptide pulsed or transfected as described above in a new 24-well plate. On day 11, expanded T-cells were restimulated with peptide-pulsed, transfected APCs similar to day 1. T-cells were used for cytolytic assays or immunophenotyped after day 20.
Statistical Analysis. Categorical variables, such as Elispot data, and Flow cytometric data were summarized as SFUs, and percentages. Continuous variables (RNAseq data) were presented with mean with standard error of mean (SEM). Unpaired T-test with Welch's correction was used for all categorical variable analyses, and for continuous variable analyses non-parametric Mann-Whitney's test was used. For heatmaps of T-cell frequencies and ssGSEA RNASeq analyses, Z-transformation was performed to normalize the data across the cohorts. R statistical software V3.4.0 and Prism software (GraphPad Software) were used for data managements and statistical analyses. Significance levels were set at 0.1 (*), and P-values of 0.01 (**) or 0.001 (***) for all tests are indicated.
Various features and advantages of the invention are set forth in the following claims.
All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
As described herein, polypeptides, compositions, and methods can include any of the following SEQ ID NOs.
E2 Pool 1
A01-A03-B57-E2
E2(329-338)
HLA-A*01:01
KSAIVTLTY
E2(329-338)
HLA-A*11:01
KSAIVTLTY
E2(329-338)
HLA-A*03:01
KSAIVTLTY
E2(329-338)
HLA-B*35:01
KSAIVTLTY
A02-E2-1
E2(93-101)
HLA-A*02:01
TLQDVSLEV
(SEQ ID NO: 2)
A02-E2-2
E2(138-147)
HLA-A*02:01
YICEEASVTV
(SEQ ID NO: 3)
A11-E2-1
E2(284-292)
HLA-A*11:01
NTTPIVHLK
(SEQ ID NO: 5)
B07-E2-1
E2(207-215)
HLA-B*07:02
SPEIIRQHL
(SEQ ID NO: 7)
E2 Pool 2
A02-E2-3
E2(69-77)
HLA-A*02:01
ALQAIELQL
(SEQ ID NO: 10)
A03-E2-2
E2(267-276)
HLA-A*03:01
ILTAFNSSHK
(SEQ ID NO: 12)
A11-E2-2
E2(103-112)
HLA-A*03:01
LTAPTGCIKK
E2 Pool 3
A02-E2-6
E2(191-199)
HLA-A*02:01
QVILCPTSV
(SEQ ID NO: 19)
A02-E2-6
E2(297-306)
HLA-A*03:01
TLKCLRYRFK
B07-E2-3
E2(249-257)
HLA-B*07:02
NPCHTTKLL
(SEQ ID NO: 22)
B35-E2-2
E2(158-167)
HLA-B*35:01
YYVHEGIRTY
E6-Pool-1
A03-E6-1
E6(33-41)
HLA-A*11:01
IILECVYCK
A02-E6-1
E6(18-26)
HLA-A*02:01
KLPQLCTEL
(SEQ ID NO: 29)
B07-E6-1
E6(15-24)
HLA-B*07:02
RPRKLPQLCT
(SEQ ID NO: 30)
A11-E6-1
E6(93-101)
HLA-A*11:01
TTLEQQYNK
(SEQ ID NO: 31)
E6-Pool-2
A03-E6-2
E6(68-77)
HLA-A*11:01
AVCDKCLKFY
(SEQ ID NO: 32)
B07-E6-2
E6(65-74)
HLA-B*07:02
NPYAVCDKCL
(SEQ ID NO: 35)
A02-E6-2
E6(29-38)
HLA-A*02:01
TIHDIILECV
(SEQ ID NO: 36)
B35-E6-1
E6(67-76)
HLA-B*35:01
YAVCDKCLKF
(SEQ ID NO: 38)
E6-Pool-3
B07-E6-3
E6(119-126)
HLA-B*07:02
CPEEKQRHL
(SEQ ID NO: 39)
A02-E6-3
E6(52-60)
HLA-A*02:01
FAFRDLCIV
(SEQ ID NO: 42)
A03-E6-3
E6(106-116)
HLA-A*03:01
LLIRCINCQK
(SEQ ID NO: 43)
B35-E6-2
E6(82-90)
HLA-B*35:01
YGTTLEQQY
(SEQ ID NO: 44)
E7-Pool-1
A02-E7-1
E7(82-90)
HLA-A*02:01
LLMGTLGIV
(SEQ ID NO: 48)
A03/A11-E7-3
E7(88-97)
HLA-A*03:01
GIVCPICSQK
B07-B08-B35-E7
E7(5-13)
HLA-B*07:02
TPTLHEYML
(SEQ ID NO: 51)
E7-Pool-2
A02-E7-2
E7(85-93)
HLA-A*02:01
GTLGIVCPI
(SEQ ID NO: 55)
A03/A11-E7-2
E7(89-97)
HLA-A*11:01
IVCPICSQK
(SEQ ID NO: 56)
E7 11-19
E7(11-19)
HLA-A*02:01
YMLDLQPET
(SEQ ID NO: 59)
E7 11-20
E7(11-20)
HLA-A*02:01
YMLDLQPETT
(SEQ ID NO: 60)
The occurrence of the disclosed HPV16-Antigens E2, E7, and E8 were examined in other HPV genomes by blasting the Papillomavirus database available from URL: pave.niaid.nih.gov/#home (see Tables 6-8).
For reasons of completeness, various aspects of the invention are set out in the following numbered clauses, as well as the following claims:
Clause 1. An immunogenic composition for treating a subject having a HPV16-associated disease, the composition comprising at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, and a pharmaceutically acceptable carrier or excipient.
Clause 2. The immunogenic composition of clause 1, wherein the HPV16-associated disease is selected from the group consisting of cervical cancers, anal cancers, head and neck cancers, vaginal cancers, vulvar cancers, penile cancers, and rectal cancers.
Clause 3. The immunogenic composition of clause 2, wherein the HPV16-associated disease is a head and neck squamous cell carcinoma (HNSCC).
Clause 4. The immunogenic composition of clause 1, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 5. The immunogenic composition of clause 4, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 6. The immunogenic composition of clause 1, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E6 antigen.
Clause 7. The immunogenic composition of clause 6, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 8. The immunogenic composition of clause 1, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 9. The immunogenic composition of clause 8, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 10. A method of treating a subject having a HPV16-associated disease, the method comprising administering an immunogenic composition comprising at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, and a pharmaceutically acceptable carrier or excipient; wherein administration of the composition to the subject induces an immune response against the HPV16-associated disease and treats the subject.
Clause 11. The method of clause 10, wherein the HPV16-associated disease is selected from the group consisting of cervical cancers, anal cancers, head and neck cancers, vaginal cancers, vulvar cancers, penile cancers, and rectal cancers.
Clause 12. The method of clause 11, wherein the HPV16-associated disease is a head and neck squamous cell carcinoma (HNSCC).
Clause 13. The method of clause 10, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 14. The method of clause 13, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 15. The method of clause 10, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E6 antigen.
Clause 16. The method of clause 15, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 17. The method of clause 10, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 18. The method of clause 17, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 19. The method of clause 10, wherein the immunogenic composition further comprises an immune checkpoint inhibitor.
Clause 20. The method of clause 19, wherein the immune checkpoint inhibitor is a programmed cell death protein 1 (PD-1) inhibitor.
Clause 21. The method of clause 10, wherein the immunogenic composition further comprises an Indoleamine 2,3-dioxygenase 1 (IDO-1) inhibitor.
Clause 22. An immune cell comprising a T-cell receptor (TCR) capable of binding a synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens; wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24); wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43); and wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 23. A method of detecting an HPV16-associated disease in a subject, the method comprising obtaining a biological sample from a subject, wherein the biological sample comprises T cells; contacting the biological sample with a MHC class I peptide tetramer composition comprising at least one synthetic MHC class I molecule and at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, wherein the at least one synthetic MHC class I molecule is bound to the at least one synthetic polypeptide encoding the CTL epitope derived from E2, E6, or E7 HPV16 antigens; detecting the presence of T cells bound to the synthetic polypeptide encoding the CTL epitope derived from E2, E6, or E7 HPV16 antigens.
Clause 24. The method of clause 23, wherein detecting the presence of T cells comprises flow cytometry or fluorescence-activated cell sorting.
Clause 25. The method of clause 23, wherein the at least one synthetic peptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 26. The method of clause 25, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 27. The method of clause 23, wherein the at least one synthetic peptide encodes CTL epitope from the HPV16 E6 antigen.
Clause 28. The method of clause 27, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 29. The method of clause 23, wherein the at least one synthetic peptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 30. The method of clause 29, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 31. The method of clause 23, wherein the MHC class I peptide tetramer composition further comprises a ligand.
Clause 32. The method of clause 23, wherein the MHC class I peptide tetramer composition further comprises a label.
Clause 33. The method of clause 32, wherein the label comprises a fluorescent molecule, a luminescent molecule, or a radioactive molecule.
Clause 34. The method of clause 23, wherein the MHC class I molecule comprises a self-assembling protein domain.
Clause 35. An immunogenic composition for treating a subject having a human papillomavirus (HPV)-associated disease, the composition comprising at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, and a pharmaceutically acceptable carrier or excipient.
Clause 36. The immunogenic composition of clause 35, wherein the HPV-associated disease is selected from the group consisting of cervical cancers, anal cancers, head and neck cancers, vaginal cancers, vulvar cancers, penile cancers, and rectal cancers.
Clause 37. The immunogenic composition of clause 35 or 36, wherein the HPV-associated disease is a head and neck squamous cell carcinoma (HNSCC).
Clause 38. The immunogenic composition of any one of clauses 35-37, wherein the HPV-associated disease is caused by HPV subtype 1, HPV subtype 2, HPV subtype 6, HPV subtype 7, HPV subtype 11, HPV subtype 16, HPV subtype 18, HPV subtype 22, HPV subtype 23, HPV subtype 26, HPV subtype 31, HPV subtype 33, HPV subtype 34, HPV subtype 35, HPV subtype 37, HPV subtype 38, HPV subtype 39, HPV subtype 41, HPV subtype 42, HPV subtype 43, HPV subtype 44, HPV subtype 45, HPV subtype 51, HPV subtype 52, HPV subtype 53, HPV subtype 54, HPV subtype 56, HPV subtype 58, HPV subtype 59, HPV subtype 62, HPV subtype 63, HPV subtype 66, HPV subtype 67, HPV subtype 68, HPV subtype 69, HPV subtype 70, HPV subtype 71, HPV subtype 73, HPV subtype 77, HPV subtype 81, HPV subtype 82, HPV subtype 85, HPV subtype 86, HPV subtype 89, HPV subtype 91, HPV subtype 92, HPV subtype 96, HPV subtype 97, HPV subtype 100, HPV subtype 106, HPV subtype 108, HPV subtype 109, HPV subtype 110, HPV subtype 111, HPV subtype 113, HPV subtype 120, HPV subtype 121, HPV subtype 122, HPV subtype 133, HPV subtype 139, HPV subtype 150, HPV subtype 151, HPV subtype 155, HPV subtype 156, HPV subtype 180, or HPV subtype 204.
Clause 39. The immunogenic composition of any one of clauses 35-38, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 40. The immunogenic composition of clause 39, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 41. The immunogenic composition of clause 39 or 40, wherein the HPV-associated disease is caused by HPV1, HPV2, HPV16, HPV18, HPV22, HPV23, HPV26, HPV31, HPV33, HPV34, HPV35, HPV37, HPV38, HPV39, HPV41, HPV42, HPV43, HPV44, HPV45, HPV51, HPV52, HPV53, HPV54, HPV56, HPV59, HPV62, HPV63, HPV66, HPV67, HPV68, HPV69, HPV70, HPV71, HPV77, HPV81, HPV82, HPV85, HPV86, HPV89, HPV91, HPV92, HPV96, HPV97, HPV100, HPV106, HPV108, HPV109, HPV110, HPV111, HPV113, HPV120, HPV121, HPV122, HPV133, HPV139, HPV150, HPV151, HPV155, HPV156, HPV180, or HPV204.
Clause 42. The immunogenic composition of any one of clauses 35-38, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E6 antigen.
Clause 43. The immunogenic composition of clause 42, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 44. The immunogenic composition of clause 42 or 43, wherein the HPV-associated disease is caused by HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV53, HPV56, HPV58, HPV67, HPV68, HPV70, HPV73, HPV82, HPV85, or HPV97.
Clause 45. The immunogenic composition of any one of clauses 35-38, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 46. The immunogenic composition of clause 45, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 47. The immunogenic composition of clause 45 or 46, wherein the HPV-associated disease is caused by HPV6, HPV7, HPV11, HPV16, HPV31, HPV33, HPV35, HPV52, HPV58, HPV67, HPV71, HPV73, or HPV106.
Clause 48. A method of treating a subject having a human papillomavirus (HPV)-associated disease, the method comprising administering an immunogenic composition comprising at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, and a pharmaceutically acceptable carrier or excipient; wherein administration of the composition to the subject induces an immune response against the HPV16-associated disease and treats the subject.
Clause 49. The method of clause 48, wherein the HPV16-associated disease is selected from the group consisting of cervical cancers, anal cancers, head and neck cancers, vaginal cancers, vulvar cancers, penile cancers, and rectal cancers.
Clause 50. The method of clause 48 or 49, wherein the HPV16-associated disease is a head and neck squamous cell carcinoma (HNSCC).
Clause 51. The immunogenic composition of any one of clauses 48-50, wherein the HPV-associated disease is caused by HPV subtype 1, HPV subtype 2, HPV subtype 6, HPV subtype 7, HPV subtype 11, HPV subtype 16, HPV subtype 18, HPV subtype 22, HPV subtype 23, HPV subtype 26, HPV subtype 31, HPV subtype 33, HPV subtype 34, HPV subtype 35, HPV subtype 37, HPV subtype 38, HPV subtype 39, HPV subtype 41, HPV subtype 42, HPV subtype 43, HPV subtype 44, HPV subtype 45, HPV subtype 51, HPV subtype 52, HPV subtype 53, HPV subtype 54, HPV subtype 56, HPV subtype 58, HPV subtype 59, HPV subtype 62, HPV subtype 63, HPV subtype 66, HPV subtype 67, HPV subtype 68, HPV subtype 69, HPV subtype 70, HPV subtype 71, HPV subtype 73, HPV subtype 77, HPV subtype 81, HPV subtype 82, HPV subtype 85, HPV subtype 86, HPV subtype 89, HPV subtype 91, HPV subtype 92, HPV subtype 96, HPV subtype 97, HPV subtype 100, HPV subtype 106, HPV subtype 108, HPV subtype 109, HPV subtype 110, HPV subtype 111, HPV subtype 113, HPV subtype 120, HPV subtype 121, HPV subtype 122, HPV subtype 133, HPV subtype 139, HPV subtype 150, HPV subtype 151, HPV subtype 155, HPV subtype 156, HPV subtype 180, or HPV subtype 204.
Clause 52. The method of any one of clauses 48-51, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 53. The method of clause 52, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 54. The immunogenic composition of clause 52 or 53, wherein the HPV-associated disease is caused by HPV1, HPV2, HPV16, HPV18, HPV22, HPV23, HPV26, HPV31, HPV33, HPV34, HPV35, HPV37, HPV38, HPV39, HPV41, HPV42, HPV43, HPV44, HPV45, HPV51, HPV52, HPV53, HPV54, HPV56, HPV59, HPV62, HPV63, HPV66, HPV67, HPV68, HPV69, HPV70, HPV71, HPV77, HPV81, HPV82, HPV85, HPV86, HPV89, HPV91, HPV92, HPV96, HPV97, HPV100, HPV106, HPV108, HPV109, HPV110, HPV111, HPV113, HPV120, HPV121, HPV122, HPV133, HPV139, HPV150, HPV151, HPV155, HPV156, HPV180, or HPV204.
Clause 55. The method of any one of clauses 48-51, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E6 antigen.
Clause 56. The method of clause 55, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 57. The immunogenic composition of clause 55 or 56, wherein the HPV-associated disease is caused by HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV53, HPV56, HPV58, HPV67, HPV68, HPV70, HPV73, HPV82, HPV85, or HPV97.
Clause 58. The method of any one of clauses 48-51, wherein the at least one synthetic polypeptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 59. The method of clause 58, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 60. The immunogenic composition of clause 58 or 59, wherein the HPV-associated disease is caused by HPV6, HPV7, HPV11, HPV16, HPV31, HPV33, HPV35, HPV52, HPV58, HPV67, HPV71, HPV73, or HPV106.
Clause 61. The method of any one of clauses 48-60, wherein the immunogenic composition further comprises an immune checkpoint inhibitor.
Clause 62. The method of clause 61, wherein the immune checkpoint inhibitor is a programmed cell death protein 1 (PD-1) inhibitor.
Clause 63. The method of any one of clauses 48-60, wherein the immunogenic composition further comprises an Indoleamine 2,3-dioxygenase 1 (IDO-1) inhibitor.
Clause 64. A method of detecting a human papillomavirus (HPV)-associated disease in a subject, the method comprising obtaining a biological sample from a subject, wherein the biological sample comprises T cells; contacting the biological sample with a MHC class I peptide tetramer composition comprising at least one synthetic MHC class I molecule and at least one synthetic polypeptide encoding a cytotoxic T lymphocyte (CTL) epitope derived from E2, E6, or E7 human papillomavirus subtype 16 (HPV16) antigens, wherein the at least one synthetic MHC class I molecule is bound to the at least one synthetic polypeptide encoding the CTL epitope derived from E2, E6, or E7 HPV16 antigens; detecting the presence of T cells bound to the synthetic polypeptide encoding the CTL epitope derived from E2, E6, or E7 HPV16 antigens.
Clause 65. The method of clause 64, wherein detecting the presence of T cells comprises flow cytometry or fluorescence-activated cell sorting.
Clause 66. The method of clause 64 or 65, wherein the at least one synthetic peptide encodes a CTL epitope from the HPV16 E2 antigen.
Clause 67. The method of clause 66, wherein the CTL epitope from the HPV16 E2 antigen is selected from the group consisting of RLECAIYYK (SEQ ID NO:4), VYLTAPTGCI (SEQ ID NO:6), SPEIIRQHL (SEQ ID NO:7), VVEGQVDYY (SEQ ID NO:9), ILTAFNSSHK (SEQ ID NO:12), LTAPTGCIKK (SEQ ID NO:13), HPAATHTKAV (SEQ ID NO:14), LAVSKNKAL (SEQ ID NO:15), DSAPILTAF (SEQ ID NO:16), LQDVSLEVY (SEQ ID NO:17), YLTAPTGCI (SEQ ID NO:18), QVILCPTSV (SEQ ID NO:19), NPCHTTKLL (SEQ ID NO:22), GIRTYFVQF (SEQ ID NO:23), and YYVHEGIRTY (SEQ ID NO:24).
Clause 68. The immunogenic composition of clause 66 or 67, wherein the HPV-associated disease is caused by HPV1, HPV2, HPV16, HPV18, HPV22, HPV23, HPV26, HPV31, HPV33, HPV34, HPV35, HPV37, HPV38, HPV39, HPV41, HPV42, HPV43, HPV44, HPV45, HPV51, HPV52, HPV53, HPV54, HPV56, HPV59, HPV62, HPV63, HPV66, HPV67, HPV68, HPV69, HPV70, HPV71, HPV77, HPV81, HPV82, HPV85, HPV86, HPV89, HPV91, HPV92, HPV96, HPV97, HPV100, HPV106, HPV108, HPV109, HPV110, HPV111, HPV113, HPV120, HPV121, HPV122, HPV133, HPV139, HPV150, HPV151, HPV155, HPV156, HPV180, or HPV204.
Clause 69. The method of clause 64 or 65, wherein the at least one synthetic peptide encodes CTL epitope from the HPV16 E6 antigen.
Clause 70. The method of clause 69, wherein the CTL epitope from the HPV16 E6 antigen is selected from the group consisting of IILECVYCK (SEQ ID NO:26), ISEYRHYCY (SEQ ID NO:27), IVYRDGNPY (SEQ ID NO:28), TTLEQQYNK (SEQ ID NO:31), CPEEKQRHL (SEQ ID NO:39), and LLIRCINCQK (SEQ ID NO:43).
Clause 71. The immunogenic composition of clause 69 or 70, wherein the HPV-associated disease is caused by HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV53, HPV56, HPV58, HPV67, HPV68, HPV70, HPV73, HPV82, HPV85, or HPV97.
Clause 72. The method of clause 64 or 65, wherein the at least one synthetic peptide encodes a CTL epitope from the HPV16 E7 antigen.
Clause 73. The method of clause 72, wherein the CTL epitope from the HPV16 E7 antigen is selected from the group consisting of LQPETTDLY (SEQ ID NO:46), HGDTPTLHEY (SEQ ID NO:47), TPTLHEYML (SEQ ID NO:51), and QPETTDLYCY (SEQ ID NO:52).
Clause 74. The immunogenic composition of clause 72 or 73, wherein the HPV-associated disease is caused by HPV6, HPV7, HPV11, HPV16, HPV31, HPV33, HPV35, HPV52, HPV58, HPV67, HPV71, HPV73, or HPV106.
Clause 75. The method of any one of clauses 64-74, wherein the MHC class I peptide tetramer composition further comprises a ligand.
Clause 76. The method of any one of clauses 64-74, wherein the MEW class I peptide tetramer composition further comprises a label.
Clause 77. The method of clause 76, wherein the label comprises a fluorescent molecule, a luminescent molecule, or a radioactive molecule. 100.1811 Clause 78. The method of any one of clauses 64-74, wherein the MEW class I molecule comprises a self-assembling protein domain.
This application claims the benefit of U.S. Provisional Patent Application No. 62/586,517, filed on Nov. 15, 2017, the entire content of which is fully incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US18/61362 | 11/15/2018 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62586517 | Nov 2017 | US |
