Patent Application
20190016775
This application is being filed along with a sequence listing in electronic format. The sequence listing is provided as a file in .txt format entitled “PC72354A_FF_SeqList_ST25.txt”, created on Jul. 3, 2018, and having a size of 963 KB. The sequence listing contained in the .txt file is part of the specification and is herein incorporated by reference in its entity.
The present invention relates generally to immunotherapy and specifically to vaccines and methods for treating or preventing neoplastic disorders.
Cancers are a leading cause of mortality worldwide. They may occur in a variety of organs and tissues, such as pancreas, breasts, lungs, stomach, colon, and rectum. Pancreatic cancers are the fourth most common cause of cancer deaths in the United States. Pancreatic cancers may occur in the exocrine or endocrine component of the pancreas. Exocrine cancers include (1) pancreatic adenocarcinoma, which is by far the most common type, (2) acinar cell carcinoma, which represents 5% of exocrine pancreatic cancers, (3) cystadenocarcinomas, which account for 1% of pancreatic cancers, and (4) other rare forms of cancers, such as pancreatoblastoma, adenosquamous carcinomas, signet ring cell carcinomas, hepatoid carcinomas, colloid carcinomas, undifferentiated carcinomas, and undifferentiated carcinomas with osteoclast-like giant cells.
Breast cancer (BrC) is another common cancer among American women and the second leading cause of cancer death in women. Based on various tumor markers such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2), breast cancers can be classified into major subtypes, such as (1) hormone receptor-positive cancers (where the cancer cells contain either estrogen receptors or progesterone receptors); (2) hormone receptor-negative cancers (where the cancer cells don't have either estrogen receptors or progesterone receptors); (3) HER2/neu positive (wherein cancers that have excessive HER2/neu protein or extra copies of the HER2/neu gene); (4) HER2/neu negative cancers (where the cancers don't have excess HER2/neu); (5) triple-negative cancers (wherein the breast cancer cells have neither estrogen receptors, nor progesterone receptors, nor excessive HER2); and (6) triple-positive cancers (where the cancers are estrogen receptor-positive, progesterone receptor-positive, and have too much HER2).
Lung cancer accounts for more than a quarter of all cancer deaths and is the leading cause of cancer-related mortality worldwide. Approximately 85% of cases are histologically classified as non-small cell lung cancers (NSCLC). NSCLC may be further classified into several subtypes, such as squamous cell (epidermoid) carcinoma, adenocarcinoma, large cell (undifferentiated) carcinoma, adenosquamous carcinoma, and sarcomatoid carcinoma. The second common type of lung cancer is small cell lung cancer (SCLC), which accounts for about 10% to 15% of all lung cancers.
Gastric cancer (GaC) is the third most common cause of cancer-related death in the world. About 90-95% of gastric cancers are adenocarcinomas; other less common types include lymphoma, GISTs, and carcinoid tumors.
Colorectal cancer (CRC) is also a leading cause of cancer-related deaths in the United States. Adenocarcinomas are the most common type of CRC, which accounts for more than 95% of colorectal cancers. Other less common types of CRC include Carcinoid tumors, gastrointestinal stromal tumors (GISTs), lymphomas, and sarcomas.
Traditional regimens of cancer management have been successful in the management of a selective group of circulating and solid cancers. However, many types of cancers are resistant to traditional approaches. In recent years, immunotherapy for cancers has been explored, particularly cancer vaccines and antibody therapies. One approach of cancer immunotherapy involves the administering an immunogen to generate an active systemic immune response towards a tumor-associated antigen (TAA) on the target cancer cell. While a large number of tumor-associated antigens have been identified and many of these antigens have been explored as viral-, bacterial-, protein-, peptide-, or DNA-based vaccines for the treatment or prevention of cancers, most clinical trials so far have failed to produce a therapeutic product. Therefore, there exists a need for an immunogen or vaccine that may be used in the treatment or prevention of cancers.
The present disclosure relates to immunogenic polypeptides derived from the tumor-associated antigens MUC1, CEA, or TERT, nucleic acid molecules encoding such immunogenic polypeptides, compositions comprising such an immunogenic polypeptide or nucleic acid molecule, such as vaccines, and uses of the polypeptides, nucleic acid molecules, and compositions.
The human mucin 1 protein (MUC1; also known as episialin, PEM, H23Ag, EMA, CA15-3, and MCA) is a polymorphic transmembrane glycoprotein expressed on the apical surfaces of simple and glandular epithelia. The MUC1 gene encodes a single polypeptide chain precursor that includes a signal peptide sequence. Immediately after translation the signal peptide sequence is removed and the remaining portion of the MUC1 precursor is further cleaved into two peptide fragments: the longer N-terminal subunit (MUC1-N or MUC1α) and the shorter C-terminal subunit (MUC1-C or MUC1β). The mature MUC1 comprises a MUC1-N and a MUC1-C associated through stable hydrogen bonds. MUC1-N, which is an extracellular domain, contains variable number tandem repeats (VNTR) of 20 amino acid residues, with the number of repeats varying from 20 to 125 in different individuals. The region of the MUC1 protein that is composed of the variable number tandem repeats is also referred to in the present disclosure as “VNTR region.” MUC1-C contains a short extracellular region (approximately 53 amino acids), a transmembrane domain (approximately 28 amino acid), and a cytoplasmic tail (approximately 72 amino acids). The cytoplasmic tail of MUC1 (MUC1-CT) contains highly conserved serine and tyrosine residues that are phosphorylated by growth factor receptors and intracellular kinases. Human MUC1 exists in multiple isoforms resulting from different types of MUC1 RNA alternative splicing. The amino acid sequence of full length human MUC1 isoform 1 protein precursor (isoform 1, Uniprot P15941-1) is provided in SEQ ID NO: 1 (“MUC1 Reference Polypeptide”). At least 16 other isoforms of human MUC-1 have been reported so far (Uniprot P15941-2 through P15941-17), which include various insertions, deletions, or substitutions as compared to the sequence of isoform 1. These isoforms are known as isoform 2, 3, 4, 5, 6, Y, 8, 9, F, Y-LSP, S2, M6, ZD, T10, E2, and J13 (Uniprot P15941-2 through P15941-17, respectively). The full length human MUC1 isoform 1 precursor protein consists of 1255 amino acids, which includes a signal peptide sequence at amino acids 1-23. The MUC1-N and MUC1-C domains of the mature MUC1 protein consist of amino acids 24-1097 and 1098-1255, respectively.
Carcinoembryonic antigen-related cell adhesion molecules (also known as CEACAMs) are a group of glycoproteins in the immunoglobulin (Ig) superfamily group. Structurally, the CEACAM group consists of a single N-terminal domain and a maximum of six disulfide-linked internal domains similar to C2-type Ig domains. The group contains 12 proteins (CEACAM1, 3-8, 16, 18-21), several of which, such as CEACAM1, CEACAM5, and CEACAM6, have been considered valid clinical markers and promising therapeutic targets in various cancers such as melanoma, lung, colorectal, and pancreatic cancers. Overexpression of CEACAM5, also referred to herein and known in the art as CEA, has been found to be in the majority of human carcinomas. CEACAM5 is expressed as a 702-amino acid precursor protein consisting of: (1) a signal peptide (amino acids 1-34); (2) the N-domain (amino acids 35-144); (3) three repeating units comprising six constant C2-like domains termed as A1 (amino acids 146-237), B1 (amino acids 238-322), A2 (amino acids 324-415), and B2 (amino acids 416-498), A3 (amino acids 502-593), and B3 (amino acids 594-677); and (4) a propeptide (amino acids 686-702). The signal peptide is cleaved off from the mature protein during transport to the cell surface. The amino acid sequence of a full length human CEA precursor protein is available at UniProt (Accession No. P06731) and is also set forth herein in SEQ ID NO:2 (“CEA Reference Polypeptide”).
Telomerase reverse transcriptase (or TERT) is the catalytic component of the telomerase, which is a ribonucleoprotein polymerase responsible for maintaining telomere ends by addition of the telomere repeat TTAGGG. In addition to TERT, telomerase also includes an RNA component which serves as a template for the telomere repeat. Human TERT gene encodes an 1132 amino acid protein. Several isoforms of human TERT exist, which result from alternative splicing. The amino acid sequences of isoform 1, isoform 2, isoform 3, and isoform 4 are available at Uniprot (<www.uniprot.org>; Uniprot identifiers O14746-1, O14746-2, O14746-3, and O14746-4, respectively). The amino acid sequence of human full length TERT isoform 1 protein (isoform 1, Genbank AAD30037, Uniprot O14746-1) is also provided herein in SEQ ID NO:3 (“TERT Reference Polypeptide”). As compared with TERT isoform 1 (O14746-1), isoform 2 (O14746-2) has replacement of amino acids 764-807 (STLTDLQPYM . . . LNEASSGLFD→LRPVPGDPAG . . . AGRAAPAFGG) and deletion of C-terminal amino acids 808-1132), isoform 3 (O14746-3) has deletion of amino acids 885-947, and isoform 4 (O14746-4) has deletions of amino acids 711-722 and 808-1132, and replacement of amino acids 764-807 (STLTDLQPYM . . . LNEASSGLFD→LRPVPGDPAG . . . AGRAAPAFGG).
In some aspects, the present disclosure provides isolated immunogenic polypeptides derived from tumor-associated antigen (TAA) MUC1, CEA, or TERT, which is useful, for example, in eliciting an immune response in vivo (e.g. in an animal, including humans), or for use as a component in pharmaceutical compositions, including vaccines, for the treatment of cancer.
In other aspects, the present disclosure provides nucleic acid molecules (also referred to as “antigen constructs”) that each encode one or more immunogenic polypeptides provided by the present disclosure. In some embodiments, the present disclosure provides multi-antigen nucleic acid constructs that each encode two, three, or more different immunogenic TAA polypeptides, such as: (1) one immunogenic CEA polypeptide and one immunogenic MUC1 polypeptide; (2) one immunogenic CEA polypeptide and one immunogenic TERT polypeptide; and (3) one immunogenic CEA polypeptide, one immunogenic MUC1 polypeptide, and one immunogenic TERTpolypeptide.
The disclosure also provides vectors (such as plasmid vectors and virual vectors) that contain one or more antigen constructs provided by the present disclosure. The vectors are useful for cloning or expressing the encoded immunogenic TAA polypeptides, or for delivering the antigen constructs in a composition, such as a vaccine, to a host cell or to a host animal or a human.
The present disclosure further provides compositions comprising one or more of the immunogenic polypeptides, isolated antigen constructs encoding one or more immunogenic TAA polypeptides, or vectors containing an antigen construct encoding one or more immunogenic TAA polypeptides. In some embodiments, the composition is an immunogenic composition useful for eliciting an immune response against a TAA in a mammal, such as a mouse, dog, monkey, or human. In some embodiments, the composition is a vaccine composition useful for immunization of a mammal, such as a human, for inhibiting abnormal cell proliferation, for providing protection against the development of cancer (used as a prophylactic), or for treatment of disorders (used as a therapeutic) associated with TAA over-expression, such as cancer, particularly pancreatic, ovarian, lung, colorectal, gastric, and breast cancer.
In some further aspects, the present disclosure provides a method of eliciting an immune response against tumor-associated antigen (TAA) CEA, MUC1, or TERT, which comprises administering to the mammal an effective amount of (1) an immunogenic CEA polypeptide, an immunogenic MUC1 polypeptide, and/or an immunogenic TERT polypeptide, (2) an antigen construct encoding one or more immunogenic TAA polypeptides provided by the present disclosure, (3) vectors (such as viral vectors and plasmid vectors) that contain one or more antigen constructs, or (4) compositions containing one or more immunogenic TAA polypeptides, one or more antigen constructs, or one or more vectors as disclosed herein. Examples of the mammals in each of htemehtods include mouse, dog, monkey, or human.
In some further aspects, the present disclosure provides a method of inhibiting abnormal cell proliferation, a method of providing protection against the development of cancer, a method for treatment of cancer, and a method for treatment of a disorder associated with over-expression of a TAA in a mammal, each of which comprises administering to the mammal an effective amount of (1) an immunogenic CEA polypeptide, an immunogenic MUC1 polypeptide, an immunogenic TERT polypeptide, or a combination of any of these immunogenic polypeptides, (2) an antigen construct encoding one or more of these immunogenic TAA polypeptides, (3) vectors (such as viral vectors and plasmid vectors) that contain one or more antigen constructs, or (4) compositions containing one or more of these immunogenic TAA polypeptides, one or more antigen constructs, or one or more vectors as disclosed herein. Examples of the mammals in each of htemehtods include mouse, dog, monkey, or human. In the methods related to cancer management, examples of cancers include pancreatic, ovarian, lung, colorectal, gastric, or breast cancer.
In an aspect of the present invention, the following embodiments, each described by a numbered clause, are contemplated:
1. An antigen construct, comprising a nucleotide sequence encoding an immunogenic CEA polypeptide as disclosed herein.
2. The antigen construct according to clause 1, further comprising a nucleotide sequence encoding an immunogenic MUC1 polypeptide as disclosed herein.
3. The antigen construct according to clause 1 or 2, further comprising a nucleotide sequence encoding an immunogenic TERT polypeptide as disclosed herein.
4. The antigen construct according to clause 1, further comprising a nucleotide sequence encoding an immunogenic MUC1 polypeptide as disclosed herein and a nucleotide sequence encoding an immunogenic TERT polypeptide as disclosed herein.
5. The antigen construct according to any one of clauses 2, 3, or 4, further comprising a spacer nucleotide sequence as disclosed herein.
6. The antigen construct according to clause 5, wherein the spacer nucleotide sequence encodes a 2A peptide.
7. The antigen construct according to clause 5, wherein the spacer nucleotide sequence encodes a 2A peptide selected from the group consisting of EMC2A, ERA2A, ERB2A, and T2A.
8. The antigen construct according to any one of clauses 1-7, wherein the immunogenic CEA polypeptide is selected from the group consisting of:
(1) a polypeptide comprising or consisting of amino acids 2-702 of SEQ ID NO:2, amino acids 323-702 of SEQ ID NO:2, or amino acids 323-677 of SEQ ID NO:2;
(2) a polypeptide comprising or consisting of amino acid sequence of SEQ ID NO:15 or amino acids 4-704 of SEQ ID NO:15;
(3) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:17 or amino acids 4-526 of SEQ ID NO:17;
(4) a polypeptide comprising or consisting of the sequence of SEQ ID NO:19 or amino acids 4-468 of SEQ ID NO:19; or
(5) a polypeptide that is a functional variant of any of the polypeptides of (1)-(4) above.
9. The antigen construct according to any one of clauses 3-8, wherein the immunogenic TERT polypeptide is selected from the group consisting of:
(1) a polypeptide comprising the amino acid sequence of SEQ ID NO:9 or amino acids 2-893 of SEQ ID NO:9;
(2) a polypeptide comprising the amino acid sequence of SEQ ID NO:11 or amino acids 3-791 of SEQ ID NO:11;
(3) a polypeptide comprising the amino acid sequence of SEQ ID NO:13 or amino acids 4-594 of SEQ ID NO:13; and
(4) a polypeptide that is a functional variant of any of the polypeptides of (1)-(3) above.
10. The antigen construct according to any one of clauses 2, and 4-9, wherein the immunogenic MUC1 polypeptide is selected from the group consisting of:
(1) a polypeptide comprising the amino acid sequence of SEQ ID NO:5 or amino acids 4-537 of SEQ ID NO:5;
(2) a polypeptide comprising the amino acid sequence of SEQ ID NO:7 or amino acids 4-517 of SEQ ID NO:7; and
(3) a functional variant of the polypeptide of (1) or (2) above.
11. The antigen construct according to any one of clauses 1-10, which comprises a nucleotide sequence encoding an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:31 or an amino acid sequence comprising amino acids 4-1088 of SEQ ID NO:31;
(2) the amino acid sequence of SEQ ID NO:33 or an amino acid sequence comprising amino acids 4-1081 of SEQ ID NO:33;
(3) the amino acid sequence of SEQ ID NO:35 or an amino acid sequence comprising amino acids 4-1085 of SEQ ID NO:35;
(4) the amino acid sequence of SEQ ID NO:37 or an amino acid sequence comprising an amino acid sequence comprising amino acids 4-1030 of SEQ ID NO:37;
(5) the amino acid sequence of SEQ ID NO:39 or an amino acid sequence comprising amino acids 4-1381 of SEQ ID NO:39; and
(6) the amino acid sequence of SEQ ID NO:41 or an amino acid sequence comprising amino acids 4-1441 of SEQ ID NO:41.
12. The antigen construct according to any one of clauses 1-11, which comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(2) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(3) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(4) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(5) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(6) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; and
(7) a nucleotide sequences that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
13. The antigen construct according to any one of clauses 1-12, which comprises a nucleotide sequence encoding an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:43 or an amino acid sequence comprising amino acids 4-2003 of SEQ ID NO:43;
(2) the amino acid sequence of SEQ ID NO:45 or an amino acid sequence comprising amino acids 4-2001 of SEQ ID NO:45;
(3) the amino acid sequence of SEQ ID NO:47 or an amino acid sequence comprising amino acids 4-2008 of SEQ ID NO:47;
(4) the amino acid sequence of SEQ ID NO:49 or an amino acid sequence comprising amino acids 4-1996 of SEQ ID NO: 49;
(5) the amino acid sequence of SEQ ID NO:51 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:51; and
(6) the amino acid sequence of SEQ ID NO:53 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:53.
14. The antigen construct according to any one of clauses 1-13, which comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(2) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(3) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(4) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(5) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50;
(6) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
15. The antigen construct according to any one of clauses 1-14, which comprises:
(1) a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92; or
(2) a degenerate variant of a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92.
16. A pharmaceutical composition comprising: (i) an antigen construct according to any one of clauses 1-15 and (ii) a pharmaceutically acceptable carrier.
17. The pharmaceutical composition according to clause 16, which is a vaccine.
18. A method of treating cancer in a human in need of treatment, comprising administering to the human an effective amount of the pharmaceutical composition according to clause 16 or clause 17.
19. The method according to clause 18, wherein the cancer over-expresses one or more tumor-associated antigens selected from MUC1, CEA, or TERT.
20. The method according to clause 18, wherein the cancer is pancreatic cancer, ovarian cancer, breast cancer, gastric cancer, lung cancer, or colorectal cancer.
21. The method according to clause 18, wherein the cancer is triple negative breast cancer, estrogen receptor positive breast cancer, or HER2 positive breast cancer.
22. The method according to clause 18, further comprising administering to the patient an effective amount of an immune modulator.
23. The method according to clause 22, wherein the immune modulator is a CTLA-4 inhibitor, an 001 inhibitor, a PD-1 inhibitor, or a PD-L1 inhibitor.
24. The method according to clause 18, further comprising administering to the human an adjuvant.
25. A vector, comprising an antigen construct according to any one of clauses 1-15.
26. The vector according to clause 25, which is a plasmid vector.
27. The vector according to clause 26, which comprises a nucleotide sequence of any of SEQ ID NOs:57, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, and 74.
28. The vector according to clause 25, which is a viral vector.
29. The vector according to clause 28, which comprises a nucleotide sequence of any of SEQ ID NOs:58, 60, 62, 64, 66, and 68.
30. A method for the treatment of cancer in a human, comprising administering to the human an effective amount of (1) an antigen construct according to any one of clauses 1-15, (2) a pharmaceutical composition according to clause 16 or clause 17, or (3) a vector according to any one of clauses 25-29.
The term “adjuvant” refers to a substance that, when administered to a host mammal, such as human, is capable of enhancing, accelerating, or prolonging an antigen-specific immune response elicited by a vaccine or an immunogen in the host.
The term “agonist” refers to a substance which promotes (induces, causes, enhances or increases) the activity of another molecule (such as a receptor). The term agonist encompasses substances which bind a receptor and substances which promote receptor function without binding thereto.
The term “antagonist” or “inhibitor” refers to a substance that partially or fully blocks, inhibits, or neutralizes a biological activity of another molecule or a receptor.
The term “antigen” refers to a substance that, when introduced to a host mammal (directly or upon expression as in, e.g., DNA vaccines), is capable of being recognized by the immune system of the host mammal, such as binding to an antibody or to antigen receptors on T cells. Antigens can be proteins or protein fragments, carbohydrates, gangliosides, haptens, or nucleic acids. A substance is termed “antigenic” when it is capable of specifically interacting with an antigen recognition molecule of the immune system, such as antibody or T cell antigen receptor. The term “tumor-associated antigen” or “TAA” refers to an antigen which is specifically expressed by tumor cells or expressed at a higher frequency or density by tumor cells than by non-tumor cells of the same tissue type. TAA may be molecules that are not normally expressed by the host, or mutated, truncated, misfolded, or otherwise abnormal manifestations of molecules normally expressed by the host. Examples of TAA include CEA, TERT, and MUC1.
The term “co-administration” refers to administration of two or more agents to the same subject as part of a treatment regimen. The two or more agents may be encompassed in a single formulation and thus be administered simultaneously. Alternatively, the two or more agents may be in separate physical formulations and administered separately, either sequentially or simultaneously to the subject. The term “administered simultaneously” or “simultaneous administration” means that the administration of the first agent and that of a second agent overlap in time with each other, while the term “administered sequentially” or “sequential administration” means that the administration of the first agent and that of a second agent do not overlap in time with each other.
The term “cytosolic” or “cytoplasmic” means that after a nucleotide sequence encoding a particular polypeptide is expressed by a host cell, the expressed polypeptide is expected to be retained inside the host cell.
The term “degenerate variants” refers to nucleic acid sequences that have substitutions of bases but encode the same polypeptide or amino acid sequence.
The term “effective amount” refers to an amount administered to a mammal that is sufficient to cause a desired effect in the mammal.
The term “functional variant” of an amino acid sequence or an immunogenic TAA polypeptide (collectively “reference polypeptide”) refers to an amino acid sequence or a polypeptide that comprises from 90% to 100% of the number of amino acids of the reference polypeptide, has lower than 100% but higher than 95% identity to the amino acid sequence of the reference polypeptide, and possess the same or similar immunogenic properties of the reference polypeptide.
The term “identical” refers to two or more nucleic acids, or two or more polypeptides, that share the exact same sequence of nucleotides or amino acids, respectively. The term “percent identity” describes the level of similarity between two or more nucleic acids or polypeptides. When two sequences are aligned by bioinformatics software, “percent identity” is calculated by multiplying the number of exact nucleotide/amino acid matches between the sequences by 100, and dividing by the length of the aligned region, including gaps. For example, two 100-amino acid long polypeptides that exhibit 10 mismatches when aligned would be 90% identical.
The term “immune-effector-cell enhancer” or “IEC enhancer” refers to a substance capable of increasing and/or enhancing the number, quality, and/or function of one or more types of immune effector cells of a mammal. Examples of immune effector cells include cytolytic Dendiritic cells, CD8 T cells, CD4 T cells, NK cells, and B cells.
The term “immune modulator” refers to a substance capable of altering (e.g., inhibiting, decreasing, increasing, enhancing or stimulating) the working or function of any component of the innate, humoral, or cellular immune system of a mammal. Thus, the term “immune modulator” encompasses the “immune-effector-cell enhancer” as defined herein and the “immune-suppressive-cell inhibitor” as defined herein, as well as substance that affects any other components of the immune system of a mammal.
The term “immune response” refers to any detectable response to a particular substance (such as an antigen or immunogen) by the adaptive immune system of a host mammal, including cell-mediated immune responses (e.g., responses mediated by T cells, such as antigen-specific T cells, and non-specific cells of the immune system) and humoral immune responses (e.g., responses mediated by B cells, such as generation and secretion of antibodies into the plasma, lymph, and/or tissue fluids). Examples of immune responses include an alteration (e.g., increase) in release of cytokines (e.g., Th1, Th2 or Th17 type cytokines) or chemokine, macrophage activation, dendritic cell activation, T cell (e.g., CD4+ or CD8+ T cell) activation, induction of B cell response (e.g., antibody production), induction of a cytotoxic T lymphocyte (“CTL”) response, and expansion (e.g., growth of a population of cells) of cells of the immune system (e.g., T cells and B cells).
The term “immunogenic” or “immunogenicity” refers to the ability of a substance upon administration to a host mammal (such as a human) to cause, elicit, stimulate, or induce an immune response, or to improve, enhance, increase or prolong a pre-existing immune response, in the host mammal, whether alone or when linked to a carrier, in the presence or absence of an adjuvant. Such a substance is referred to as “immunogen.”
The term “immunogenic composition” refers to a composition that is immunogenic.
The term “immunogenic MUC1 polypeptide” refers to a polypeptide that is immunogenic against a human native MUC1 protein or against cells expressing the human native MUC1 protein. The polypeptide may have the same amino acid sequence as that of a human native MUC1 protein or display one or more mutations as compared to the amino acid sequence of a human native MUC1 protein.
The term “immunogenic CEA polypeptide” refers to a polypeptide that is immunogenic against a human native CEA protein or against cells expressing a human native CEA protein and displays one or more mutations, such as deletion of one or more amino acids, as compared to the amino acid sequence of the human native CEA protein.
The term “immunogenic TERT polypeptide” refers to a polypeptide that is immunogenic against a human native TERT protein or against cells expressing a human native TERT protein. The polypeptide may have the same amino acid sequence as that of a human native TERT protein or displays one or more mutations as compared to the amino acid sequence of a human native TERT protein.
The term “immunogenic TAA polypeptide” refers to an “immunogenic CEA polypeptide,” an “immunogenic MUC1 polypeptide, or an “immunogenic TERT polypeptide,” each as defined herein above.
The term “immune-suppressive-cell inhibitor” or “ISC inhibitor” refers to a substance capable of reducing and/or suppressing the number and/or function of immune suppressive cells of a mammal. Examples of immune suppressive cells include regulatory T cells (“Tregs”), myeloid-derived suppressor cells, and tumor-associated macrophages.
The term “mammal” refers to any animal species of the Mammalia class. Examples of mammals include: humans; non-human primates such as monkeys; laboratory animals such as rats, mice, guinea pigs; domestic animals such as cats, dogs, rabbits, cattle, sheep, goats, horses, and pigs; and captive wild animals such as lions, tigers, elephants, and the like.
The term “membrane-bound” means that after a nucleotide sequence encoding a particular polypeptide is expressed by a host cell, the expressed polypeptide is bound to, attached to, or otherwise associated with, the membrane of the cell.
The term “neoplastic disorder” refers to a condition in which cells proliferate at an abnormally high and uncontrolled rate, the rate exceeding and uncoordinated with that of the surrounding normal tissues. It usually results in a solid lesion or lump known as “tumor.” This term encompasses benign and malignant neoplastic disorders. The term “malignant neoplastic disorder”, which is used interchangeably with the term “cancer” in the present disclosure, refers to a neoplastic disorder characterized by the ability of the tumor cells to spread to other locations in the body (known as “metastasis”). The term “benign neoplastic disorder” refers to a neoplastic disorder in which the tumor cells lack the ability to metastasize.
The term “mutation” refers to deletion, addition, or substitution of amino acid residues in the amino acid sequence of a protein or polypeptide as compared to the amino acid sequence of a reference protein or polypeptide.
The term “pharmaceutical composition” refers to a solid or liquid composition suitable for administration to a subject (e.g. a human patient) for eliciting a desired physiological, pharmacological, or therapeutic effect. In addition to containing one or more active ingredients, a pharmaceutical composition may contain one or more pharmaceutically acceptable excipients.
The term “pharmaceutically acceptable excipient” refers to a substance in pharmaceutical composition, such as a vaccine, other than the active ingredients (e.g., the antigen, antigen-coding nucleic acid, immune modulator, or adjuvant) that is compatible with the active ingredients and does not cause significant untoward effect in subjects to whom it is administered.
The term “excipient” as used in the context of a pharmaceutical composition refers to a substance that generally has no medicinal properties and is included in the composition for purpose of streamlining the manufacture of the drug product and/or facilitating stabilization, delivery, and absorption of the active drug substance. The term “pharmaceutically acceptable excipient” refers to an excipient in a pharmaceutical composition, such as a vaccine composition, that is compatible with the active ingredients (e.g., the antigen or immunogen, antigen-coding nucleic acid, immune modulator, or adjuvant) in the composition and does not cause significant untoward effects in subjects to whom it is administered.
The terms “peptide,” “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids linked together by peptide bonds. They may be of any length and can include coded and non-coded amino acids, chemically, or biochemically modified, or derivatized amino acids.
The term “preventing” or “prevent” refers to (a) keeping a disorder from occurring, (b) delaying the onset of a disorder or onset of symptoms of a disorder, or (c) minimizing the incidence or effects of a disorder.
The term “secreted” in the context of a polypeptide means that after a nucleotide sequence encoding the polypeptide is expressed by a host cell, the expressed polypeptide is secreted outside of the host cell.
The term “suboptimal dose” when used to describe the amount of an immune modulator, such as a protein kinase inhibitor, refers to a dose of the immune modulator that is below the minimum amount required to produce the desired therapeutic effect for the disease being treated when the immune modulator is administered alone to a patient.
The term “treating,” “treatment,” or “treat” refers to abrogating a disorder, reducing the severity of a disorder, or reducing the severity or occurrence frequency of a symptom of a disorder.
The term “vaccine” refers to an immunogenic composition for administration to a mammal (such as a human) for eliciting a protective immune response against a particular antigen or antigens. The primary active ingredient of a vaccine is the immunogen(s). A vaccine that comprises an immunogenic polypeptide as immunogen is also referred to as “peptide vaccine.” A vaccine that does not contain an immunogenic polypeptide but rather contains a nucleic acid molecule that encodes an immunogenic polypeptide is referred to as a “DNA vaccine” or “RNA vaccine” (depending on the case it may be). Upon delivery of the DNA or RNA vaccine into host cells, the immunogenic polypeptide encoded by the nucleic acid molecule will be expressed by the host cells, producing a protective immune response. The nucleic acid molecule in a DNA or RNA vaccine may be in the form of naked nucleic acid, plasmid, or virus vector, or any other form suitable for delivering the nucleic acid.
The term “vector” refers to a nucleic acid molecule, or a modified microorganism, that is capable of transporting or transferring a foreign nucleic acid molecule into a host cell. The foreign nucleic acid molecule is referred to as “insert” or “transgene.” A vector generally consists of an insert and a larger sequence that serves as the backbone of the vector. Based on the structure or origin of vectors, major types of vectors include plasmid vectors, cosmid vectors, phage vectors (such as lambda phage), viral vectors (such as adenovirus vectors), artificial chromosomes, and bacterial vectors.
In some aspects, the present disclosure provides isolated immunogenic TAA polypeptides, which are useful, for example, for eliciting an immune response in vivo (e.g. in an animal, including humans) or in vitro, activating effector T cells, or generating antibodies specific for the TAA or for use as a component in a pharmaceutical composition, including a vaccine, for the treatment of a cancer, such as pancreatic, lung cancer, colorectal cancer, gastric cancer, or breast cancer.
These immunogenic TAA polypeptides can be prepared by methods known in the art in light of the present disclosure. The capability of the polypeptides to elicit an immune response can be measured in in vitro assays or in vivo assays. In vitro assays for determining the capability of a polypeptide or DNA construct to elicit immune responses are known in the art. One example of such in vitro assays is to measure the capability of the polypeptide or nucleic acid expressing a polypeptide to stimulate T cell response as described in U.S. Pat. No. 7,387,882, the disclosure of which is incorporated in this application. The assay method comprises the steps of: (1) contacting antigen presenting cells in culture with an antigen thereby the antigen can be taken up and processed by the antigen presenting cells, producing one or more processed antigens; (2) contacting the antigen presenting cells with T cells under conditions sufficient for the T cells to respond to one or more of the processed antigens; (3) determining whether the T cells respond to one or more of the processed antigens. The T cells used may be CD8+ T cells or CD4+ T cells. T cell response may be determined by measuring the release of one or more cytokines, such as interferon-gamma and interleukin-2, and lysis of the antigen presenting cells (tumor cells). B cell response may be determined by measuring the production of antibodies.
B-1. Immunogenic MUC1 Polypeptides
In one aspect, the present disclosure provides immunogenic MUC1 polypeptides derived from a human native MUC1 by introducing one or more mutations to the human native MUC1 protein. Examples of mutations include deletion of some, but not all, of the tandem repeats of 20 amino acids in the VNTR region of the MUC1 protein, deletion of the signal peptide sequence in whole or in part, and deletion of amino acids of non-consensus amino acid sequences found in the MUC1 isoforms. Thus, in some embodiments, the immunogenic MUC1 polypeptides comprise (1) the amino acid sequence of 3 to 30 tandem repeats of 20 amino acids of a human MUC1 protein and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some particular embodiments, the immunogenic MUC1 polypeptides comprise (1) the amino acid sequence of 5 to 25 tandem repeats of the human MUC1 and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some embodiments, the immunogenic MUC1 polypeptides consist of (1) the amino acid sequence of 3 to 30 tandem repeats of 20 amino acids of a human MUC1 protein and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some particular embodiments, the immunogenic MUC1 polypeptides consist of (1) the amino acid sequence of 5 to 25 tandem repeats of the human MUC1 and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some further embodiments, the immunogenic MUC1 polypeptides are in cytoplasmic form (or “cMUC1”). The term “cytoplasmic form” refers to an immunogenic MUC1 polypeptide that lacks in whole or in part the secretory sequence (amino acids 1-23; also known as “signal peptide sequence”) of the human native MUC1 protein. The deletion of amino acids of the secretory sequence is expected to prevent the polypeptide from entering the secretory pathway as it is expressed in the cells. In some other embodiments, the immunogenic MUC1 polypeptides are in membrane-bound form. The immunogenic MUC1 polypeptides can be derived, constructed, or prepared from the amino acid sequence of any of the human MUC1 isoforms known in the art or discovered in the future, including, for example, Uniprot isoforms 1, 2, 3, 4, 5, 6, Y, 8, 9, F, Y-LSP, S2, M6, ZD, T10, E2, and J13 (Uniprot P15941-1 through P15941-17, respectively). In some embodiments, the immunogenic MUC1 polypeptides comprise an amino acid sequence that is part of human MUC1 isoform 1 wherein the amino acid sequence of the human MUC1 isoform 1 is set forth in SEQ ID NO: 1. In some embodiments, the immunogenic MUC1 polypeptides consist of an amino acid sequence that is part of human MUC1 isoform 1 wherein the amino acid sequence of the human MUC1 isoform 1 is set forth in SEQ ID NO: 1. In a specific embodiment, the immunogenic MUC1 polypeptide comprises amino acids 22-225 and 946-1255 of the amino acid sequence of SEQ ID NO:1. In some other specific embodiments, the present disclosure provides an immunogenic MUC1 polypeptide selected from:
(1) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:5 (Plasmid 1027 polypeptide);
(2) a polypeptide comprising or consisting of amino acids 4-537 of SEQ ID NO:5;
(3) a polypeptide comprising or consisting of amino acids 24-537 of SEQ ID NO:5;
(4) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:7 (Plasmid 1197 polypeptide);
(5) a polypeptide comprising or consisting of amino acids 4-517 of SEQ ID NO:7;
(6) a polypeptide comprising or consisting of amino acids 4-517 of SEQ ID NO:7, wherein in SEQ ID NO:7 the amino acid at position 513 is T; and
(7) a functional variant of any of the polypeptides of (1)-(6) above.
In some specific embodiments, the immunogenic MUC1 polypeptides comprise the amino acid sequence of SEQ ID NO:5 (Plasmid 1027 polypeptide) or SEQ ID NO:7 (Plasmid 1197 polypeptide). In some specific embodiments, the immunogenic MUC1 polypeptides consists of the amino acid sequence of SEQ ID NO:5 (Plasmid 1027 polypeptide) or SEQ ID NO:7 (Plasmid 1197 polypeptide).
In one aspect, the present invention provides a functional variant of any of the immunogenic MUC1 polypeptides disclosed herein.
B-2. Immunogenic TERT Polypeptides
In another aspect, the present disclosure provides immunogenic TERT polypeptides derived from a human TERT protein by deletion of up to 600 of the N-terminal amino acids of the TERT protein. Thus, an immunogenic TERT polypeptide may comprise the C-terminal amino acid sequence starting from position 601 of any human TERT protein isoform. In some embodiments, the immunogenic TERT polypeptides comprise the amino acid sequence of TERT isoform 1 set forth in SEQ ID NO:3, wherein up to about 600 amino acids from the N-terminus (amino terminus) of the amino acid sequence of TERT isoform 1 are absent. Any number of amino acids up to 600 from the N-terminus of the TERT isoform 1 may be absent in the immunogenic TERT polypeptide. For example, the N-terminal amino acids from position 1 through position 50, 100, 50, 200, 250, 300, 350, 400, 450, 500, 550, or 600 of the TERT isoform 1 of SEQ ID NO:3 may be absent from the immunogenic TERT polypeptide. Thus, an immunogenic TERT polypeptide may comprise amino acids 51-1132, 101-1132, 151-1132, 201-1132, 251-1132, 301-1132, 351-1132, 401-1132, 451-1132, 501-1132, or 551-1132 of SEQ ID NO:3. In one embodiment, the immunogenic TERT polypeptide comprises amino acids 601-1132 of the amino acid sequence of SEQ ID NO:3. In another embodiment, the present disclosure provides an immunogenic TERT polypeptide that comprises amino acids 241-1132 of the amino acid sequence of SEQ ID NO:3.
An immunogenic TERT polypeptide may consist of amino acids 51-1132, 101-1132, 151-1132, 201-1132, 251-1132, 301-1132, 351-1132, 401-1132, 451-1132, 501-1132, or 551-1132 of SEQ ID NO:3. In one embodiment, the immunogenic TERT polypeptide consists of amino acids 601-1132 of the amino acid sequence of SEQ ID NO:3. In another embodiment, the present disclosure provides an immunogenic TERT polypeptide that consists of amino acids 241-1132 of the amino acid sequence of SEQ ID NO:3.
The immunogenic TERT polypeptides may also be constructed from other TERT isoforms. Where the immunogenic TERT polypeptides are constructed from TERT isoforms with C-terminal truncations, such as isoform 2, 3, or 4, it is preferred that fewer amino acids are deleted from the N-terminus of the protein.
In some further embodiments, the immunogenic TERT polypeptide further comprises one or more amino acid mutations that inactivate the TERT catalytic domain. Examples of such amino acid mutations include substitution of aspartic acid with alanine at position 712 of SEQ ID NO:3 (D712A) and substitution of valine with isoleucine at position 713 of SEQ ID NO:3 (V713I). In some embodiments the immunogenic TERT polypeptide comprises both mutations D712A and V713I. In an embodiment said mutations include a substitution of aspartic acid at position 712 of SEQ ID NO:3 and/or substitution of valine at position 713 of SEQ ID NO:3 (V713I) wherein said mutation(s) inactivates the TERT catalytic domain. In another embodiment said mutation consists of a substitution of aspartic acid at position 712 of SEQ ID NO:3 and/or substitution of valine at position 713 of SEQ ID NO:3 (V713I) wherein said mutation(s) inactivates the TERT catalytic domain. In still another embodiment said mutation consists of a substitution of aspartic acid with alanine at position 712 of SEQ ID NO:3 (D712A) and/or a substitution of valine with isoleucine at position 713 of SEQ ID NO:3 (V713I).
In some specific embodiments, the present disclosure provides an immunogenic TERT polypeptide selected from:
(1) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:9 (Plasmid 1112 Polypeptide) or amino acids 2-893 of SEQ ID NO:9;
(2) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:11 (Plasmid 1326 Polypeptide) or amino acids 3-791 of SEQ ID NO:11;
(3) a polypeptide comprising or consisting of the amino acid sequence of SEQ ID NO:13 (Plasmid 1330 Polypeptide) or amino acids 4-594 of SEQ ID NO:13; or
(4) a polypeptide that is a functional variant of any of the polypeptides of (1)-(3) above.
In one aspect, the present invention provides a functional variant of any of the immunogenic TERT polypeptides disclosed herein.
B-3. Immunogenic CEA Polypeptides
In another aspect, the present disclosure provides isolated immunogenic CEA polypeptides derived from a human native CEA by introducing one or more mutations to the human native CEA precursor protein. Examples of the introduced mutations include deletion of one, two, three, four, or five of the C2-like domains, deletion of the signal peptide sequence in whole or in part, and deletion of some or all of the amino acids of the propeptide. Thus, in some embodiments, the immunogenic CEA polypeptides provided by the present disclosure comprise (1) the amino acid sequence of the N-domain and (2) the amino acid sequence of 1 to 5 C2-like domains of a human CEA protein. In some particular embodiments, the immunogenic CEA polypeptides comprise (1) the amino acid sequence of at least four C2-like domains, such as A2, B2, A3, and B3, and (2) the amino acid sequence of the N-domain. In some further embodiments, the immunogenic CEA polypeptides are in cytoplasmic form (or “cCEA”). The term “cytoplasmic form” refers to an immunogenic CEA polypeptide that lacks in whole or in part the signal peptide sequence (amino acids 1-34) of the human native CEA precursor protein. The deletion of amino acids of the signal peptide is expected to prevent the polypeptide from entering the secretory pathway as it is expressed in the cells. In some other embodiments, the immunogenic CEA polypeptides are in the membrane-bound form (or “mCEA”). An immunogenic mCEA polypeptide includes amino acids of the signal peptide and, after expressed by a host cell, remains bound to, or otherwise associated with, the membrane of the host cell.
The immunogenic CEA polypeptides provided by the present disclosure can be derived, constructed, or prepared from the amino acid sequence of any of the human CEA isoforms known in the art or discovered in the future. In some embodiments, the immunogenic CEA polypeptides comprise an amino acid sequence that is part of human CEA isoform 1 precursor protein having amino acid sequence of SEQ ID NO:2.
In some specific embodiments, the present disclosure provides any of the following immunogenic CEA polypeptides:
(1) a polypeptide comprising amino acids 2-702 of SEQ ID NO:2, amino acids 323-702 of SEQ ID NO:2, or amino acids 323-677 of SEQ ID NO:2;
(2) a polypeptide consisting of amino acids 2-702 of SEQ ID NO:2, amino acids 323-702 of SEQ ID NO:2, or amino acids 323-677 of SEQ ID NO:2;
(3) a polypeptide comprising amino acids of SEQ ID NO:15 (amino acid sequence encoded by Plasmid 1361) or amino acids 4-704 of SEQ ID NO:15;
(4) a polypeptide consisting of amino acids of SEQ ID NO:15 (amino acid sequence encoded by Plasmid 1361) or amino acids 4-704 of SEQ ID NO:15;
(5) a polypeptide comprising the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386) or amino acids 4-526 of SEQ ID NO:17;
(6) a polypeptide consisting of the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386) or amino acids 4-526 of SEQ ID NO:17;
(7) a polypeptide comprising the sequence of SEQ ID NO:19 (amino acid sequence encoded by Plasmid 1390) or amino acids 4-468 of SEQ ID NO:19;
(8) a polypeptide consisting of the sequence of SEQ ID NO:19 (amino acid sequence encoded by Plasmid 1390) or amino acids 4-468 of SEQ ID NO:19; or
(9) a polypeptide that is a functional variant of any of the polypeptides of (1)-(8) above.
In one aspect, the present invention provides a functional variant of any of the immunogenic TERT polypeptides disclosed herein.
In some aspects, the present disclosure provides an isolated nucleic acid molecule that encodes one, two, three, or more separate immunogenic TAA polypeptides. Such a nucleic acid molecule is also referred to as “antigen construct” in the present disclosure. A nucleic acid molecule that encodes only one immunogenic TAA polypeptide is also referred to herein as a “single-antigen construct” and a nucleic acid molecule that encodes more than one immunogenic TAA polypeptide is also referred to as a “multi-antigen construct.” A nucleic acid molecule that encodes two different immunogenic TAA polypeptides is also referred to as a “dual-antigen construct” and a nucleic acid molecule that encodes three different immunogenic TAA polypeptides is also referred to as a “triple-antigen construct.” The nucleic acid molecules can be deoxyribonucleic acids (DNA) or ribonucleic acids (RNA). Thus, a nucleic acid molecule can comprise a nucleotide sequence disclosed herein wherein thymidine (T) can also be uracil (U), which reflects the differences between the chemical structures of DNA and RNA. In reference to a nucleotide sequence of a RNA which corresponds to a nucleotide sequence of a DNA in the present disclosure, the term “correspond” or “corresponding” refers to a nucleotide sequence of the RNA that is identical to the reference nucleotide sequence of the DNA except that thymidine (T) in the DNA nucleotide sequence is replaced with uracil (U) in the RNA nucleotide sequence. The nucleic acid molecules can be in modified forms, single or double stranded forms, or linear or circular forms.
The antigen constructs, including both DNA and RNA constructs, can be prepared using methods known in the art in light of the present disclosure. Method for making single-antigen constructs and multi-antigen constructs is further described herein below. Additionally, it's well established that the injection of mRNA into host cells leads to expression of encoded proteins and immunological responses. The in vitro transcribed mRNA can be produced stably and the encoded protein can be translated efficiently through the use of various elements/systems known in the art (such as UTR's, PolyA, capping system, and codon optimization). Further, the fusion of lysosomal or endosomal targeting signals to mRNA encoded polypeptides can enhance the T-cell immune responses. mRNA can be delivered unformulated or through EP or formulated in lipids or other vehicles.
C-1. CEA Single-Antigen Constructs
In some embodiments, the present disclosure provides antigen constructs that encode any of the immunogenic CEA polypeptides described herein above.
In some specific embodiments, the antigen construct encodes an immunogenic CEA polypeptide selected from:
(1) a polypeptide comprising amino acids 2-702 of SEQ ID NO:2, amino acids 323-702 of SEQ ID NO:2, or amino acids 323-677 of SEQ ID NO:2;
(2) a polypeptide comprising amino acids of SEQ ID NO:15 (amino acid sequence encoded by Plasmid 1361) or amino acids 4-704 of SEQ ID NO:15;
(3) a polypeptide comprising the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386) or amino acids 4-526 of SEQ ID NO:17;
(4) a polypeptide comprising the sequence of SEQ ID NO:19 (amino acid sequence encoded by Plasmid 1390) or amino acids 4-468 of SEQ ID NO:19; or
(5) a polypeptide that is a functional variant of any of the polypeptides of (1)-(4) above.
In some specific embodiments, the antigen construct encodes an immunogenic CEA polypeptide selected from:
(1) a polypeptide consisting of amino acids 2-702 of SEQ ID NO:2, amino acids 323-702 of SEQ ID NO:2, or amino acids 323-677 of SEQ ID NO:2;
(2) a polypeptide consisting of amino acids of SEQ ID NO:15 (amino acid sequence encoded by Plasmid 1361) or amino acids 4-704 of SEQ ID NO:15;
(3) a polypeptide consisting of the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386) or amino acids 4-526 of SEQ ID NO:17;
(4) a polypeptide consisting of the sequence of SEQ ID NO:19 (amino acid sequence encoded by Plasmid 1390) or amino acids 4-468 of SEQ ID NO:19; or
(5) a polypeptide that is a functional variant of any of the polypeptides of (1)-(4) above.
In some particular embodiments, the present disclosure provides an antigen construct that is a DNA and comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:14 (Plasmid 1361 open reading frame) or a nucleotide sequence comprising nucleotides 10-2112 of SEQ ID NO:14;
(2) the nucleotide sequence of SEQ ID NO:16 (Plasmid 1386 open reading frame) or a nucleotide sequence comprising nucleotides 10-1578 of SEQ ID NO:16;
(3) the nucleotide sequence of SEQ ID NO:18 (Plasmid 1390 open reading frame) or a nucleotide sequence comprising nucleotides 10-1404 of SEQ ID NO:18; and
(4) a nucleotide sequence that is a degenerate variant of the nucleotide sequences of (1)-(3).
In some other particular embodiments, the present disclosure provides an antigen construct that is a DNA and consists of a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:14 (Plasmid 1361 open reading frame) or a nucleotide sequence consisting of nucleotides 10-2112 of SEQ ID NO:14;
(2) the nucleotide sequence of SEQ ID NO:16 (Plasmid 1386 open reading frame) or a nucleotide sequence consisting of nucleotides 10-1578 of SEQ ID NO:16;
(3) the nucleotide sequence of SEQ ID NO:18 (Plasmid 1390 open reading frame) or a nucleotide sequence consisting of nucleotides 10-1404 of SEQ ID NO:18; and
(4) a nucleotide sequence that is a degenerate variant of the nucleotide sequences of (1)-(3). In some other particular embodiments, the present disclosure provides an antigen construct that is a RNA and comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:14 (Plasmid 1361 open reading frame) or a nucleotide sequence comprising nucleotides 10-2112 of SEQ ID NO:14;
(2) the nucleotide sequence of SEQ ID NO:16 (Plasmid 1386 open reading frame) or a nucleotide sequence comprising nucleotides 10-1578 of SEQ ID NO:16;
(3) the nucleotide sequence of SEQ ID NO:18 (Plasmid 1390 open reading frame) or a nucleotide sequence comprising nucleotides 10-1404 of SEQ ID NO:18; and
(4) a nucleotide sequence that is a degenerate variant of the nucleotide sequences of (1)-(3).
C-2. Multi-Antigen Constructs
In another aspect, the present disclosure provides antigen constructs that each encode two, three, or more different immunogenic TAA polypeptides.
Methods and techniques for construction of vectors for co-expression of two or more polypeptides from a single nucleic acid (also known in the art as “multicistronic vectors”) are known in the art. The multi-antigen constructs provided by the present disclosure can be prepared using such techniques in light of the disclosure. For example, a multi-antigen construct can be constructed by incorporating multiple independent promoters into a single plasmid (Huang, Y., Z. Chen, et al. (2008). “Design, construction, and characterization of a dual-promoter multigenic DNA vaccine directed against an HIV-1 subtype C/B′ recombinant.” J Acquir Immune Defic Syndr 47(4): 403-411; Xu, K., Z. Y. Ling, et al. (2011). “Broad humoral and cellular immunity elicited by a bivalent DNA vaccine encoding HA and NP genes from an H5N1 virus.” Viral Immunol 24(1): 45-56). The plasmid can be engineered to carry multiple expression cassettes, each consisting of a) a eukaryotic promoter for initiating RNA polymerase dependent transcription, with or without an enhancer element, b) a gene encoding a target antigen, and c) a transcription terminator sequence. Upon delivery of the plasmid to the transfected cell nucleus, transcription will be initiated from each promoter, resulting in the production of separate mRNAs, each encoding one of the target antigens. The mRNAs will be independently translated, thereby producing the desired antigens.
Multi-antigen constructs provided by the present disclosure can also be constructed through the use of viral 2A peptides (Szymczak, A. L. and D. A. Vignali (2005). “Development of 2A peptide-based strategies in the design of multicistronic vectors.” Expert Opin Biol Ther 5(5): 627-638; de Felipe, P., G. A. Luke, et al. (2006). “E unum pluribus: multiple proteins from a self-processing polyprotein.” Trends Biotechnol 24(2): 68-75; Luke, G. A., P. de Felipe, et al. (2008). “Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes.” J Gen Virol 89 (Pt 4): 1036-1042; Ibrahimi, A., G. Vande Velde, et al. (2009). “Highly efficient multicistronic lentiviral vectors with peptide 2A sequences.” Hum Gene Ther 20(8): 845-860; Kim, J. H., S. R. Lee, et al. (2011). “High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice.” PLoS One 6(4): e18556). These peptides, also called cleavage cassettes or CHYSELs (cis-acting hydrolase elements), are approximately 20 amino acids long with a highly conserved carboxy terminal D-V/I-EXNPGP motif. These peptides are rare in nature, most commonly found in viruses such as Foot-and-mouth disease virus (FMDV), Equine rhinitis A virus (ERAV), Equine rhinitis B virus (ERBV), Encephalomyocarditis virus (EMCV), Porcine teschovirus (PTV), and Thosea asigna virus (TAV) (Luke, G. A., P. de Felipe, et al. (2008). “Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes.” J Gen Virol 89 (Pt 4): 1036-1042). An amino acid sequence of some of these peptides is provided in Table 17. With a 2A-based multi-antigen expression strategy, genes encoding multiple target antigens are linked together in a single open reading frame (ORF), separated by sequences encoding viral 2A peptides. The entire open reading frame can be cloned into a vector with a single promoter and terminator. Upon delivery of the constructs to a host cell, mRNA encoding the multiple antigens will be transcribed and translated as a single polyprotein. During translation of the 2A peptides, ribosomes skip the bond between the C-terminal glycine and proline. The ribosomal skipping acts like a cotranslational autocatalytic “cleavage” that releases the peptide sequences upstream of the 2A peptide from those downstream. The incorporation of a 2A peptide between two protein antigens may result in the addition of ˜20 amino acids onto the C-terminus of the upstream polypeptide and 1 amino acid (proline) to the N-terminus of downstream protein. In an adaptation of this methodology, protease cleavage sites can be incorporated at the N terminus of the 2A cassette such that ubiquitous proteases will cleave the cassette from the upstream protein (Fang, J., S. Yi, et al. (2007). “An antibody delivery system for regulated expression of therapeutic levels of monoclonal antibodies in vivo.” Mol Ther 15(6): 1153-1159). Examples of specific 2A-peptide sequences that may be used in construction of the multi-antigen constructs of the present disclosure include those that are disclosed in Andrea L. Szymczak & Darrio AA Vignali: Development of 2A peptide-based strategies in the design of multicistronic vectors. Expert Opinion Biol. Ther. (2005) 5(5) 627-638, as well as in international patent application WO2015/063674, the disclosure of which is incorporated herein by reference.
Another method that may be used for constructing the multi-antigen constructs involves the use of an internal ribosomal entry site, or IRES. Internal ribosomal entry sites are RNA elements found in the 5′ untranslated regions of certain RNA molecules (Bonnal, S., C. Boutonnet, et al. (2003). “IRESdb: the Internal Ribosome Entry Site database.” Nucleic Acids Res 31(1): 427-428). They attract eukaryotic ribosomes to the RNA to facilitate translation of downstream open reading frames. Unlike normal cellular 7-methylguanosine cap-dependent translation, IRES-mediated translation can initiate at AUG codons far within an RNA molecule. The highly efficient process can be exploited for use in multi-cistronic expression vectors (Bochkov, Y. A. and A. C. Palmenberg (2006). “Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location.” Biotechniques 41(3): 283-284, 286, 288). Typically, two transgenes are inserted into a vector between a promoter and transcription terminator as two separate open reading frames separated by an IRES. Upon delivery of the constructs to a host cell, a single long transcript encoding both transgenes will be transcribed. The first ORF will be translated in the traditional cap-dependent manner, terminating at a stop codon upstream of the IRES. The second ORF will be translated in a cap-independent manner using the IRES. In this way, two independent proteins can be produced from a single mRNA transcribed from a vector with a single expression cassette. Examples of IRES sequences includes poliovirus (PV) IRES, encephalomyocarditis virus (EMCV) IRES, Foot-and-mouth disease virus (FMDV) IRES, Hepatitis A virus IRES, Hepatitis B virus IRES, Kaposi's sarcoma-associated herpesvirus (KSHV) IRES, and classical swine fever virus IRES. A nucleotide sequence of the EMCV IRES is disclosed in WO2013/165754 (
The nucleotide sequence that is inserted between two coding sequences or transgenes in an open reading frame (ORF) of a nucleic acid molecule and functions to allow co-expression or translation of two separate gene products from the nucleic acid molecule is referred to as “spacer nucleotide sequence” in the present disclosure. Examples of specific spacer nucleotide sequences that may be used in the multi-antigen constructs include eukaryotic promoters, nucleotide sequences encoding a 2A peptide, and internal ribosomal entry site (IRES) sequences. Examples of specific 2A peptides include 2A peptides of acute bee paralysis virus (ABP2A), cricket paralysis virus (CrP2A), equine rhinitis A virus (ERA2A), equine rhinitis B virus (ERB2A), encephalomyocarditis virus (EMC2A), foot-and-mouth disease virus (FMD2A or F2A), human rotavirus (HT2A), Infectious flacherie virus (IF2A), porcine teschovirus (PT2A or P2A), porcine rotavirus (PR2A), and Thosea asigna virus (T2A, TA2A, or TAV2A).
In some aspects, the present disclosure provides an antigen construct comprising (i) at least one coding nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) one or more nucleotide sequences encoding one or more other immunogenic TAA polypeptides, such as an immunogenic TERT polypeptide, an immunogenic MUC1 polypeptide, an immunogenic MSLN polypeptide, an immunogenic PSA polypeptide, an immunogenic PSMA polypeptide, or an immunogenic PSCA polypeptide.
In some embodiments, the present disclosure provides an antigen construct comprising (i) at least one coding nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one coding nucleotide sequence encoding either an immunogenic TERT polypeptide or an immunogenic MUC1 polypeptide. The nucleotide sequence encoding the immunogenic CEA polypeptide may be either upstream or downstream of the other coding nucleotide sequence. The construct may further comprise a spacer nucleotide sequence between the coding nucleotide sequences. The structure of such a dual antigen construct is shown in formula (I) and formula (II):
TAA-SPACER-CEA (I)
CEA-SPACER-TAA (II)
wherein in each of formulas (I) and (II): (i) CEA represents a nucleotide sequence encoding an immunogenic CEA polypeptide; (ii) TAA represents a nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide; and (iii) SPACER is a spacer nucleotide sequence and may be absent. Examples of spacer nucleotide sequences that may be included in the dual-antigen constructs include nucleotide sequences encoding a foot-and-mouth disease virus 2A peptide (FMD2A or FMDV2A), equine rhinitis A virus 2A peptide (ERA2A), Equine rhinitis B virus 2A peptide (ERB2A), encephalomyocarditis virus 2A peptide (EMC2A or EMCV2A), porcine teschovirus 2A peptide (PT2A), and Thosea asigna virus 2A peptide (T2A, TA2A, or TAV2A). In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In some other aspects, the present disclosure provides a multi-antigen construct comprising (i) at least one coding nucleotide sequence encoding an immunogenic CEA polypeptide, (ii) at least one coding nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (iii) at least one coding nucleotide sequence encoding an immunogenic TERT polypeptide. In some embodiments, the multi-antigen construct further comprises a spacer nucleotide sequence. The structure of a multi-antigen construct is shown in formula (III):
TAA1-SPACER1-TAA2-SPACER2-TAA3 (III)
wherein in formula (III): (i) TAA1, TAA2, and TAA3 each represent a nucleotide sequence encoding an immunogenic TAA polypeptide selected from the group consisting of an immunogenic MUC1 polypeptide, an immunogenic CEA polypeptide, and an immunogenic TERT polypeptide, wherein TAA1, TAA2, and TAA3 encode different immunogenic TAA polypeptides; and (ii) SPACER1 and SPACER2 each represent a spacer nucleotide sequence, wherein (a) SPACER1 and SPACER2 may be the same or different and (b) one of or both of SPACER1 and SPACER2 may be absent. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In some embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic CEA polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic TERT polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In some other embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic TERT polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic CEA polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In still other embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic CEA polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic TERT polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In some further embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic CEA polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic TERT polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In still other embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic TERT polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic CEA polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In still other embodiments, the present disclosure provides a multi-antigen construct of formula (III), wherein in formula (III): (i) TAA1 is a nucleotide sequence encoding an immunogenic TERT polypeptide; (ii) TAA2 is a nucleotide sequence encoding an immunogenic CEA polypeptide; and (iii) TAA3 is a nucleotide sequence encoding an immunogenic MUC1 polypeptide. In some embodiments, SPACER1 and SPACER2 are, independently, a nucleotide sequence encoding a 2A peptide, or a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding a 2A peptide. In some embodiments, SPACER1 and SPACER2 are a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding a 2A peptide and SPACER2 is a nucleotide sequence encoding GGSGG. In some embodiments, SPACER1 is a nucleotide sequence encoding GGSGG and SPACER2 is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
In some specific embodiments, the present disclosure provides a multi-antigen construct of a formula selected from the group consisting of:
(1) MUC1-2A-CEA-2A-TERT (IV)
(2) MUC1-2A-TERT-2A-CEA (V)
(3) CEA-2A-MUC1-2A-TERT (VI)
(4) CEA-2A-TERT-2A-MUC1 (VII)
(5) TERT-2A-MUC1-2A-CEA (VIII)
(6) TERT-2A-CEA-2A-MUC1 (IX)
wherein in each of formulas (IV)-(IX): (i) MUC1, CEA, and TERT represent a nucleotide sequence encoding an immunogenic MUC1 polypeptide, an immunogenic CEA polypeptide, and an immunogenic TERT polypeptide, respectively; and (ii) 2A is a nucleotide sequence encoding a 2A peptide. In some embodiments, the antigen construct encodes any of the immunogenic CEA polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic TERT polypeptides described herein above. In some embodiments, the antigen construct encodes any of the immunogenic MUC1 polypeptides described herein above.
The immunogenic CEA polypeptide, immunogenic MUC1 polypeptide, and immunogenic TERT polypeptide encoded by a multi-antigen construct, including dual antigen constructs and triple-antigen constructs, may be in membrane-bound form or cytoplasmic form. In some specific embodiments, the immunogenic TAA polypeptide is in cytoplasmic form.
In some embodiments, the immunogenic CEA polypeptide encoded by a multi-antigen construct comprises (1) the amino acid sequence of the N-domain and (2) the amino acid sequence of 1, 2, 3, 4, or 5 C-like domains of a human CEA protein. In some particular embodiments, the immunogenic CEA polypeptides comprise (1) the amino acid sequence of at least four C-like domains, such as A2, B2, A3, and B3, and (2) the amino acid sequence of the N-domain. In some further embodiments, the immunogenic CEA polypeptides are in cytoplasmic form (or “cCEA”) or the membrane-bound form (or “mCEA”).
In some specific embodiments, the immunogenic CEA polypeptide encoded by a multi-antigen construct comprises an amino acid sequence selected from:
(1) an amino acid sequence comprising or consisting of (i) amino acids 323-677 of SEQ ID NO:2 or (ii) amino acids 35-144 and 323-677 of SEQ ID NO:2;
(2) an amino acid sequence comprising or consisting of (i) amino acids 323-702 of SEQ ID NO:2 or (ii) amino acids 2-144 and 323-702 of SEQ ID NO:2;
(3) the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386 (mCEA) or amino acids 4-526 of SEQ ID NO:17;
(4) the amino acid sequence of SEQ ID NO:19 (amino acid sequence encoded Plasmid 1390 (cCEA) or amino acids 4-468 of SEQ ID NO:19; or
(5) a functional variant of any of the amino acid sequences of (1)-(4) above.
In some specific embodiments, the immunogenic CEA polypeptide encoded by a multi-antigen construct consists of an amino acid sequence selected from:
(1) an amino acid sequence comprising or consisting of (i) amino acids 323-677 of SEQ ID NO:2 or (ii) amino acids 35-144 and 323-677 of SEQ ID NO:2;
(2) an amino acid sequence comprising or consisting of (i) amino acids 323-702 of SEQ ID NO:2 or (ii) amino acids 2-144 and 323-702 of SEQ ID NO:2;
(3) the amino acid sequence of SEQ ID NO:17 (amino acid sequence encoded by Plasmid 1386 (mCEA) or amino acids 4-526 of SEQ ID NO:17;
(4) the amino acid sequence of SEQ ID NO:19 (amino acid sequence encoded Plasmid 1390 (cCEA) or amino acids 4-468 of SEQ ID NO:19; or
(5) a functional variant of any of the amino acid sequences of (1)-(4) above.
In some particular embodiments, the multi-antigen construct is a DNA and comprises (1) the nucleotide sequence of SEQ ID NO:14, (2) the nucleotide sequence of SEQ ID NO:16, (3) the nucleotide sequence of SEQ ID NO:18, or (4) a degenerate variant of the nucleotide sequence of SEQ ID NO:14, 16, or 18. In some other particular embodiments, the multi-antigen construct is a RNA and comprises a nucleotide sequence that corresponds to: (1) the nucleotide sequence of SEQ ID NO:14; (2) the nucleotide sequence of SEQ ID NO:16; (3) the nucleotide sequence of SEQ ID NO:18; or (4) a degenerate variant of the nucleotide sequence of SEQ ID NO:14, 16, or 18.
In some embodiments, the immunogenic MUC1 polypeptide encoded by a multi-antigen construct comprises (1) an amino acid sequence of 3 to 30 tandem repeats of 20 amino acids of a human MUC1 protein and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some specific embodiments, the immunogenic MUC1 polypeptide encoded by a multi-antigen construct comprises an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:5 (Plasmid 1027 polypeptide);
(2) an amino acid sequence comprising amino acids 4-537 of SEQ ID NO:5;
(3) an amino acid sequence comprising amino acids 24-537 of SEQ ID NO:5;
(4) the amino acid sequence of SEQ ID NO:7 (Plasmid 1197 polypeptide);
(5) an amino acid sequence comprising amino acids 4-517 of SEQ ID NO:7; and
(6) an amino acid sequence comprising amino acids 4-517 of SEQ ID NO:7, with the proviso that the amino acid at position 513 is T.
In some embodiments, the immunogenic MUC1 polypeptide encoded by a multi-antigen construct consists of (1) an amino acid sequence of 3 to 30 tandem repeats of 20 amino acids of a human MUC1 protein and (2) the amino acid sequences of the human MUC1 protein that flank the VNTR region. In some specific embodiments, the immunogenic MUC1 polypeptide encoded by a multi-antigen construct consists of an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:5 (Plasmid 1027 polypeptide);
(2) an amino acid sequence comprising amino acids 4-537 of SEQ ID NO:5;
(3) an amino acid sequence comprising amino acids 24-537 of SEQ ID NO:5;
(4) the amino acid sequence of SEQ ID NO:7 (Plasmid 1197 polypeptide);
(5) an amino acid sequence comprising amino acids 4-517 of SEQ ID NO:7; and
(6) an amino acid sequence comprising amino acids 4-517 of SEQ ID NO:7, with the proviso that the amino acid at position 513 is T.
In some specific embodiments, the immunogenic MUC1 polypeptide encoded by a multi-antigen construct consists of an amino acid sequence selected from the group consisting of:
(1) an amino acid sequence consisting of amino acids 4-537 of SEQ ID NO:5;
(2) an amino acid sequence consisting of amino acids 24-537 of SEQ ID NO:5;
(3) an amino acid sequence consisting of amino acids 4-517 of SEQ ID NO:7;
and
(4) an amino acid sequence consisting of amino acids 4-517 of SEQ ID NO:7, with the proviso that the amino acid at position 513 is T.
In some particular embodiments, the multi-antigen construct is a DNA and comprises: (1) the nucleotide sequence of SEQ ID NO:4 or a nucleotide sequence comprising nucleotides 10-1611 of SEQ ID NO:4; (2) the nucleotide sequence of SEQ ID NO:6 or a nucleotide sequence comprising nucleotides 10-1551 of SEQ ID NO:6; or (3) a degenerate variant of the nucleotide sequence of SEQ ID NO:4 or SEQ ID NO:6.
In some other particular embodiments, the multi-antigen construct is a RNA and comprises a nucleotide sequence that corresponds to (1) the nucleotide sequence of SEQ ID NO:4, (2) the nucleotide sequence of SEQ ID NO:6, or (3) a degenerate variant of the nucleotide sequence of SEQ ID NO:4 or SEQ ID NO:6.
The immunogenic TERT polypeptide encoded by a multi-antigen construct may be the full length TERT protein or any truncated or mutated form of the TERT protein. The full length TERT protein is expected to generate stronger immune responses than a truncated form. However, depending on the specific vector chosen to deliver the construct, the vector may not have the capacity to carry the gene encoding the full TERT protein. Therefore, deletions of some amino acids from the protein may be made such that the transgenes would fit into a particular vector. The deletions of amino acids can be made from the N-terminus, C-terminus, or anywhere in the sequence of the TERT protein (e.g. from the TERT protein of SEQ ID NO:3). Additional deletions may be made in order to remove the nuclear localization signal, thereby rendering the polypeptides cytoplasmic, increasing access to cellular antigen processing/presentation machinery. In some embodiments, the amino acids up to position 200, 300, 400, 500, or 600 of the N-terminus of the TERT protein are absent from the immunogenic TERT polypeptides (e.g. from the TERT protein of SEQ ID NO:3).
In some specific embodiments, amino acids 1-343 (TERT343), 1-240 (TERT240), or 1-541 (TERT541) of the N-terminus of the TERT protein of SEQ ID NO:3 are absent. Thus, in an embodiment, the amino acid sequence of the immunogenic TERT polypeptide encoded by a multi-antigen construct of the invention is any of the following:
(1) an amino acid sequence comprising amino acids 51-1132 of SEQ ID NO:3 and lacking amino acids 1 to 50 of SEQ ID NO:3;
(2) an amino acid sequence comprising amino acids 101-1132 of SEQ ID NO:3 and lacking amino acids 1 to 100 of SEQ ID NO:3;
(3) an amino acid sequence comprising amino acids 151-1132 of SEQ ID NO:3 and lacking amino acids 1 to 150 of SEQ ID NO:3;
(4) an amino acid sequence comprising amino acids 201-1132 of SEQ ID NO:3 and lacking amino acids 1 to 200 of SEQ ID NO:3;
(5) an amino acid sequence comprising amino acids 241-1132 of SEQ ID NO:3 and lacking amino acids 1 to 240 of SEQ ID NO:3;
(6) an amino acid sequence comprising amino acids 301-1132 of SEQ ID NO:3 and lacking amino acids 1 to 300 of SEQ ID NO:3;
(7) an amino acid sequence comprising amino acids 351-1132 of SEQ ID NO:3 and lacking amino acids 1 to 350 of SEQ ID NO:3;
(8) an amino acid sequence comprising amino acids 401-1132 of SEQ ID NO:3 and lacking amino acids 1 to 400 of SEQ ID NO:3;
(9) an amino acid sequence comprising amino acids 451-1132 of SEQ ID NO:3 and lacking amino acids 1 to 450 of SEQ ID NO:3;
(10) an amino acid sequence comprising amino acids 501-1132 of SEQ ID NO:3 and lacking amino acids 1 to 500 of SEQ ID NO:3;
(11) an amino acid sequence comprising amino acids 551-1132 of SEQ ID NO:3 and lacking amino acids 1 to 550 of SEQ ID NO:3; or
(12) an amino acid sequence comprising amino acids 601-1132 of SEQ ID NO:3 and lacking amino acids 1-600 of SEQ ID NO:3.
In an embodiment, the amino acid sequence of the immunogenic TERT polypeptide encoded by a multi-antigen construct of the invention is any of the following:
(1) an amino acid sequence consisting of amino acids 51-1132, 101-1132, 151-1132, 201-1132, 251-1132, 301-1132, 351-1132, 401-1132, 451-1132, 501-1132, or 551-1132 of SEQ ID NO:3;
(2) an amino acid sequence consisting of amino acids 601-1132 of SEQ ID NO:3;
(3) an amino acid sequence consisting of amino acids 542-1132 of SEQ ID NO:3;
(4) an amino acid sequence consisting of amino acids 344-1132 of SEQ ID NO:3; and
(5) an amino acid sequence consisting of amino acids 241-1132 of SEQ ID NO:3.
Mutations of additional amino acids may be introduced in order to inactivate the TERT catalytic domain. Examples of such mutations include substitution of aspartic acid at position 712 of SEQ ID NO:3, such as D712A, and substitution of valine at position 713 of SEQ ID NO:3, such as V713I. Therefore, in an embodiment, the immunogenic TERT polypeptide encoded by a multi-antigen construct consists of any of the above disclosed TERT polypeptides wherein a substitution at position corresponding to aspartic acid 712 of SEQ ID NO:3 and/or substitution at position corresponding to valine 713 of SEQ ID NO:3 and wherein said mutation(s) inactivates the TERT catalytic domain. In an embodiment said mutation consists of a substitution of aspartic acid at position corresponding to position 712 of SEQ ID NO:3 and substitution of valine at position corresponding to position 713 of SEQ ID NO:3 wherein said mutation(s) inactivate the TERT catalytic domain. In an embodiment said mutation consists of a substitution of aspartic acid with alanine at position corresponding to position 712 of SEQ ID NO:3 (D712A) and a substitution of valine with isoleucine at position corresponding to position 713 of SEQ ID NO:3 (V713I).
In some specific embodiments, the immunogenic TERT polypeptide encoded by a multi-antigen construct comprises an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:9 (Plasmid 1112 Polypeptide) or an amino acid sequence comprising amino acids 2-893 of SEQ ID NO:9;
(2) the amino acid sequence of SEQ ID NO:11 (Plasmid 1326 Polypeptide) or an amino acid sequence comprising amino acids 4-791 of SEQ ID NO:11;
(3) the amino acid sequence of SEQ ID NO:13 (Plasmid 1330 Polypeptide) or an amino acid sequence comprising amino acids 4-594 of SEQ ID NO:13; or
(4) an amino acid sequence that is a functional variant of any of the amino acid sequences (1)-(3) above.
In some specific embodiments, the immunogenic TERT polypeptide encoded by a multi-antigen construct consists of an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:9 (Plasmid 1112 Polypeptide) or an amino acid sequence comprising amino acids 2-893 of SEQ ID NO:9;
(2) the amino acid sequence of SEQ ID NO:11 (Plasmid 1326 Polypeptide) or an amino acid sequence comprising amino acids 4-791 of SEQ ID NO:11;
(3) the amino acid sequence of SEQ ID NO:13 (Plasmid 1330 Polypeptide) or an amino acid sequence comprising amino acids 4-594 of SEQ ID NO:13; or
(4) an amino acid sequence that is a functional variant of any of the amino acid sequences (1)-(3) above.
In some specific embodiments, the immunogenic TERT polypeptide encoded by a multi-antigen construct consists of an amino acid sequence selected from the group consisting of:
(1) an amino acid sequence consisting of amino acids 2-893 of SEQ ID NO:9;
(2) an amino acid sequence consisting of amino acids 4-791 of SEQ ID NO:11;
(3) an amino acid sequence consisting of amino acids 4-594 of SEQ ID NO:13; or
(4) an amino acid sequence that is a functional variant of any of the amino acid sequences (1)-(3) above.
In some particular embodiments, the multi-antigen construct is a DNA and comprises: (1) the nucleotide sequence of SEQ ID NO:8 or a nucleotide sequence comprising nucleotides 4-2673 of SEQ ID NO:8; (2) the nucleotide sequence of SEQ ID NO:10 or a nucleotide sequence comprising nucleotides 10-2373 of SEQ ID NO:10; (3) the nucleotide sequence of SEQ ID NO:12 or a nucleotide sequence comprising nucleotides 10-1782 of SEQ ID NO:12; or (4) a degenerate variant of the nucleotide sequence of SEQ ID NO:8, SEQ ID NO:10, or SEQ ID NO:12.
In some other particular embodiments, the multi-antigen construct is a RNA and comprises a nucleotide sequence that corresponds to (1) the nucleotide sequence of SEQ ID NO:8, (2) the nucleotide sequence of SEQ ID NO:10, (3) the nucleotide sequence of SEQ ID NO:12, or (4) a degenerate variant of the nucleotide sequence of SEQ ID NO:8, 10, or 12.
In some particular embodiments, the present disclosure provides a multi-antigen construct that comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the multi-antigen construct encodes an amino acid sequence comprising:
(1) the amino acid sequence of SEQ ID NO:31 or amino acids 4-1088 of SEQ ID NO:31;
(2) the amino acid sequence of SEQ ID NO:33 or amino acids 4-1081 of SEQ ID NO:33;
(3) the amino acid sequence of SEQ ID NO:35 or amino acids 4-1085 of SEQ ID NO:35;
(4) the amino acid sequence of SEQ ID NO:37 or amino acids 4-1030 of SEQ ID NO:37;
(5) the amino acid sequence of SEQ ID NO:39 or amino acids 4-1381 of SEQ ID NO:39; or
(6) the amino acid sequence of SEQ ID NO:41 or amino acids 4-1441 of SEQ ID NO:41.
In some particular embodiments, the present disclosure provides a multi-antigen construct that comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the multi-antigen construct encodes an amino acid sequence consisting of:
(1) the amino acid sequence of SEQ ID NO:31 or amino acids 4-1088 of SEQ ID NO:31;
(2) the amino acid sequence of SEQ ID NO:33 or amino acids 4-1081 of SEQ ID NO:33;
(3) the amino acid sequence of SEQ ID NO:35 or amino acids 4-1085 of SEQ ID NO:35;
(4) the amino acid sequence of SEQ ID NO:37 or amino acids 4-1030 of SEQ ID NO:37;
(5) the amino acid sequence of SEQ ID NO:39 or amino acids 4-1381 of SEQ ID NO:39, or
(6) the amino acid sequence of SEQ ID NO:41 or amino acids 4-1441 of SEQ ID NO:41.
In some specific embodiments, the present disclosure provides a multi-antigen construct that is a DNA and comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the a multi-antigen construct comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(2) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(3) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(4) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(5) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(6) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; or
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some specific embodiments, the present disclosure provides a multi-antigen construct that is a DNA and comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the a multi-antigen construct comprises a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-3264 of SEQ ID NO:30;
(2) a nucleotide sequence consisting of nucleotides 10-3243 of SEQ ID NO:32;
(3) a nucleotide sequence consisting of nucleotides 10-3255 of SEQ ID NO:34;
(4) a nucleotide sequence consisting of nucleotides 10-3090 of SEQ ID NO:36;
(5) a nucleotide sequence consisting of nucleotides 10-4143 of SEQ ID NO:38;
(6) a nucleotide sequence consisting of nucleotides 10-4323 of SEQ ID NO:40; or
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some other specific embodiments, the present disclosure provides a multi-antigen construct that is a RNA (e.g. mRNA) and comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the a multi-antigen construct comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(2) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(3) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(4) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(5) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(6) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; or
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some other specific embodiments, the present disclosure provides a multi-antigen construct that is a RNA (e.g. mRNA) and comprises (i) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (ii) at least one nucleotide sequence encoding either an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide, wherein the a multi-antigen construct comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-3264 of SEQ ID NO:30;
(2) a nucleotide sequence consisting of nucleotides 10-3243 of SEQ ID NO:32;
(3) a nucleotide sequence consisting of nucleotides 10-3255 of SEQ ID NO:34;
(4) a nucleotide sequence consisting of nucleotides 10-3090 of SEQ ID NO:36;
(5) a nucleotide sequence consisting of nucleotides 10-4143 of SEQ ID NO:38;
(6) a nucleotide sequence consisting of nucleotides 10-4323 of SEQ ID NO:40; or
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some other embodiments, the present disclosure provides a multi-antigen construct that comprises (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct comprises a nucleotide sequence encoding an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:43 or an amino acid sequence comprising amino acids 4-2003 of SEQ ID NO:43;
(2) the amino acid sequence of SEQ ID NO:45 or an amino acid sequence comprising amino acids 4-2001 of SEQ ID NO:45;
(3) the amino acid sequence of SEQ ID NO:47 or an amino acid sequence comprising amino acids 4-2008 of SEQ ID NO:47;
(4) the amino acid sequence of SEQ ID NO:49 or an amino acid sequence comprising amino acids 4-1996 of SEQ ID NO: 49;
(5) the amino acid sequence of SEQ ID NO:51 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:51;
(6) the amino acid sequence of SEQ ID NO:53 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:53; or
(7) a functional variant of any of the amino acid sequences (1)-(6) above.
In some other embodiments, the present disclosure provides a multi-antigen construct that comprises (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct comprises a nucleotide sequence encoding an amino acid sequence selected from the group consisting of:
(1) an amino acid sequence consisting of amino acids 4-2003 of SEQ ID NO:43;
(2) an amino acid sequence consisting of amino acids 4-2001 of SEQ ID NO:45;
(3) an amino acid sequence consisting of amino acids 4-2008 of SEQ ID NO:47;
(4) an amino acid sequence consisting of amino acids 4-1996 of SEQ ID NO: 49;
(5) an amino acid sequence consisting of amino acids 4-1943 of SEQ ID NO:51;
or
(6) an amino acid sequence consisting of amino acids 4-1943 of SEQ ID NO:53.
In some particular embodiments, the present disclosure provides a multi-antigen construct that comprises (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct is a DNA and comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(2) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(3) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(4) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(5) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50;
(6) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some particular embodiments, the present disclosure provides a multi-antigen construct that comprises (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct is a DNA and comprises a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-6009 of SEQ ID NO:42;
(2) a nucleotide sequence consisting of nucleotides 10-6003 of SEQ ID NO:44;
(3) a nucleotide sequence consisting of nucleotides 10-6024 of SEQ ID NO:46;
(4) a nucleotide sequence consisting of nucleotides 10-5988 of SEQ ID NO:48;
(5) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:50;
(6) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some other particular embodiments, the present disclosure provides a multi-antigen construct, wherein the multi-antigen construct is a RNA (e.g. mRNA) and comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(2) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(3) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(4) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(5) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50;
(6) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In some other particular embodiments, the present disclosure provides a multi-antigen construct, wherein the multi-antigen construct is a RNA (e.g. mRNA) and comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-6009 of SEQ ID NO:42;
(2) a nucleotide sequence consisting of nucleotides 10-6003 of SEQ ID NO:44;
(3) a nucleotide sequence consisting of nucleotides 10-6024 of SEQ ID NO:46;
(4) a nucleotide sequence consisting of nucleotides 10-5988 of SEQ ID NO:48;
(5) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:50;
(6) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences (1)-(6) above.
In still other particular embodiments, the present disclosure provides a multi-antigen construct comprising (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct is an RNA (e.g. mRNA) and comprises a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:87;
(2) the nucleotide sequence of SEQ ID NO:88;
(3) the nucleotide sequence of SEQ ID NO:89;
(4) the nucleotide sequence of SEQ ID NO:90;
(5) the nucleotide sequence of SEQ ID NO:91;
(6) the nucleotide sequence of SEQ ID NO:92; and
(7) a degenerate variant of any of the nucleotide sequence of SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, or SEQ ID NO:92.
In still other particular embodiments, the present disclosure provides a multi-antigen construct comprising (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide, (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide, and (3) at least one nucleotide sequence encoding an immunogenic TERT polypeptide, wherein the multi-antigen construct is an RNA (e.g. mRNA) and consists of a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:87;
(2) the nucleotide sequence of SEQ ID NO:88;
(3) the nucleotide sequence of SEQ ID NO:89;
(4) the nucleotide sequence of SEQ ID NO:90;
(5) the nucleotide sequence of SEQ ID NO:91;
(6) the nucleotide sequence of SEQ ID NO:92; and
(7) a degenerate variant of any of the nucleotide sequence of SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:89, SEQ ID NO:90, SEQ ID NO:91, or SEQ ID NO:92.
Another aspect of the invention relates to vectors containing one or more of any of the antigen constructs provided by the present disclosure, including single antigen constructs, dual-antigen constructs, triple-antigen constructs, and other multi-antigen constructs. The vectors are useful for cloning or expressing the immunogenic TAA polypeptides encoded by the antigen constructs, or for delivering the antigen construct in a composition, such as a vaccine, to a host cell or to a host animal, such as a human.
A wide variety of vectors may be prepared to contain and express an antigen construct provided by the present disclosure, such as plasmid vectors, cosmid vectors, phage vectors, and viral vectors. In addition to the transgene insert sequence (i.e., the single-antigen construct or multi-antigen constructs provided by the present disclosure), which is also referred to as open reading frame (ORF), the structure of a vector typically comprises other components or elements that enable or facilitate the expression, such as origin of replication, multi-cloning site, and a selectable marker.
In some embodiments, the disclosure provides a plasmid vector containing an antigen construct provided by the present disclosure. Examples of suitable plasmid vectors include pBR325, pUC18, pSKF, pET23D, and pGB-2. Other examples of plasmid vectors, as well as method of constructing such vectors, are described in U.S. Pat. Nos. 5,589,466, 5,688,688, and 5,814,482. Construction of specific exemplary plasmid vectors comprising a single-antigen construct, dual-antigen construct, or triple-antigen construct is also described in the present disclosure.
In some specific embodiments, the disclosure provides a plasmid vector comprising a nucleotide sequence of any of SEQ ID NOs:54, 55, 56, 57, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, and 74.
In other embodiments, the present invention provides vectors that are constructed from viruses (i.e., viral vectors), including DNA viruses and RNA viruses (retroviruses). Examples of DNA viruses that may be used to construct a vector include herpes simplex virus, parvovirus, vaccinia virus, and adenoviruses. Examples of RNA viruses that may be used to construct a vector include alphavirus, flavivirus, pestivirus, influenzavirus, lyssavirus, and vesiculovirus. Construction of vectors from various viruses is known in the art. Examples of retroviral vectors are described in U.S. Pat. Nos. 5,716,613, 5,716,832, and 5,817,491. Examples of vectors that can be generated from alphaviruses are described in U.S. Pat. Nos. 5,091,309, 5,843,723, and 5,789,245. Examples of other vectors include: (1) pox viruses, such as canary pox virus or vaccinia virus (U.S. Pat. Nos. 4,603,112, 4,769,330 and 5,017,487; WO 89/01973); (2) SV40 (Mulligan et al., Nature 277:108-114, 1979); (3) herpes (Kit, Adv. Exp. Med. Biol. 215:219-236, 1989; U.S. Pat. No. 5,288,641); and (4) lentivirus such as HIV (Poznansky, J. Virol. 65:532-536, 1991).
In some particular embodiments, the present disclosure provides adenoviral vectors derived from non-human primate adenoviruses, such as simian adenoviruses. Examples of such adenoviral vectors, as well as their preparation, are described in PCT application publications WO2005/071093 and WO2010/086189, and include non-replicating vectors constructed from simian adenoviruses, such as ChAd3, ChAd4, ChAdS, ChAd7, ChAd8, ChAd9, ChAd10, ChAd11, ChAd16, ChAd17, ChAd19, ChAd20, ChAd22, ChAd24, ChAd26, ChAd30, ChAd31, ChAd37, ChAd38, ChAd44, ChAd63, ChAd68, ChAd82, ChAd55, ChAd73, ChAd83, ChAd146, ChAd147, PanAd1, Pan Ad2, and Pan Ad3, and replication-competent vectors constructed from adenoviruses Ad4 or Ad7. It is preferred that in constructing the adenoviral vectors from the simian adenoviruses one or more of the early genes from the genomic region of the virus selected from E1A, E1B, E2A, E2B, E3, and E4 are either deleted or rendered non-functional by deletion or mutation. In a particular embodiment, the vector is constructed from ChAd68. The chimpanzee adenovirus ChAd68 is also referred to in the literature as simian adenovirus 25, C68, AdC68, Chad68, SAdV25, PanAd9, or Pan9. A method of constructing vectors from ChAd68 for expressing multi-antigen constructs is described in international patent application publication WO2015/063647. Expression vectors typically include one or more control elements that are operatively linked to the nucleic acid sequence to be expressed. The term “control elements” refers collectively to promoter regions, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites (“IRES”), enhancers, and the like, which collectively provide for the replication, transcription, and translation of a coding sequence in a recipient cell. Not all of these control elements need always be present so long as the selected coding sequence is capable of being replicated, transcribed, and translated in an appropriate host cell. The control elements are selected based on a number of factors known to those skilled in that art, such as the specific host cells and source or structures of other vector components. For enhancing the expression of an immunogenic TAA polypeptide, a Kozak sequence can be provided upstream of the sequence encoding the immunogenic TAA polypeptide. For vertebrates, a known Kozak sequence is (GCC)NCCATGG, wherein N is A or G and GCC is less conserved. Exemplary Kozak sequences that can be used include GAACATGG, ACCAUGG and ACCATGG.
In some embodiments, the vector comprises a multi-antigen construct encoding (i) at least one immunogenic CEA polypeptide and (ii) at least one immunogenic MUC1 polypeptide or at least one immunogenic TERT polypeptide. The vector may be a DNA plasmid vector, DNA virus vector, RNA plasmid vector, or RNA virus vector. In some specific embodiments, the vector comprises a multi-antigen construct which encodes an amino acid sequence comprising:
(1) the amino acid sequence of SEQ ID NO:31 or amino acids 4-1088 of SEQ ID NO:31;
(2) the amino acid sequence of SEQ ID NO:33 or amino acids 4-1081 of SEQ ID NO:33;
(3) the amino acid sequence of SEQ ID NO:35 or amino acids 4-1085 of SEQ ID NO:35;
(4) the amino acid sequence of SEQ ID NO:37 or amino acids 4-1030 of SEQ ID NO:37;
(5) the amino acid sequence of SEQ ID NO:39 or amino acids 4-1381 of SEQ ID NO:39;
(6) the amino acid sequence of SEQ ID NO:41 or amino acids 4-1441 of SEQ ID NO:41; or
(7) a functional variant of any of the amino acid sequences (1)-(6) above.
In some other specific embodiments, the vector is a DNA vector and comprises a multi-antigen construct comprising a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(2) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(3) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(4) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(5) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(6) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; and
(7) a nucleotide sequences that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some other specific embodiments, the present disclosure provides a RNA vector, which comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(2) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(3) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(4) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(5) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(6) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some other embodiments, the vector contains a multi-antigen construct encoding (i) at least one immunogenic MUC1 polypeptide, (ii) at least one immunogenic CEA polypeptide, and (iii) at least one immunogenic TERT polypeptide. The vector may be a DNA plasmid vector, DNA virus vector, RNA plasmid vector, or RNA virus vector. In some specific embodiments, the vector comprises a multi-antigen construct which encodes an amino acid sequence selected from the group consisting of:
(1) the amino acid sequence of SEQ ID NO:43 or an amino acid sequence comprising amino acids 4-2003 of SEQ ID NO:43;
(2) the amino acid sequence of SEQ ID NO:45 or an amino acid sequence comprising amino acids 4-2001 of SEQ ID NO:45;
(3) the amino acid sequence of SEQ ID NO:47 or an amino acid sequence comprising amino acids 4-2008 of SEQ ID NO:47;
(4) the amino acid sequence of SEQ ID NO:49 or an amino acid sequence comprising amino acids 4-1996 of SEQ ID NO: 49;
(5) the amino acid sequence of SEQ ID NO:51 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:51;
(6) the amino acid sequence of SEQ ID NO:53 or an amino acid sequence comprising amino acids 4-1943 of SEQ ID NO:53; or
(7) a functional variant of any of the amino acid sequences of (1)-(6) above.
In some other specific embodiments, the present disclosure provides a DNA vector, which comprises a multi-antigen construct comprising a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(2) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(3) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(4) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(5) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50; or
(6) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some other specific embodiments, the present disclosure provides a RNA vector, which comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(2) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(3) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(4) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(5) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50;
(6) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some specific embodiments, the present disclosure provides a DNA viral vector comprising a nucleotide sequence of any of SEQ ID NOs:58, 60, 62, 64, 66, and 68. In some other specific embodiments, the present disclosure provides a DNA plasmid vector comprising the a nucleotide sequence of any of SEQ ID NOs:57, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, and 74.
In some specific embodiments, the vector is a DNA vector and comprises a multi-antigen construct comprising a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-3264 of SEQ ID NO:30;
(2) a nucleotide sequence consisting of nucleotides 10-3243 of SEQ ID NO:32;
(3) a nucleotide sequence consisting of nucleotides 10-3255 of SEQ ID NO:34;
(4) a nucleotide sequence consisting of nucleotides 10-3090 of SEQ ID NO:36;
(5) a nucleotide sequence consisting of nucleotides 10-4143 of SEQ ID NO:38;
(6) a nucleotide sequence consisting of nucleotides 10-4323 of SEQ ID NO:40; and
(7) a nucleotide sequences that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some other specific embodiments, the present disclosure provides a RNA vector, which comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-3264 of SEQ ID NO:30;
(2) a nucleotide sequence consisting of nucleotides 10-3243 of SEQ ID NO:32;
(3) a nucleotide sequence consisting of nucleotides 10-3255 of SEQ ID NO:34;
(4) a nucleotide sequence consisting of nucleotides 10-3090 of SEQ ID NO:36;
(5) a nucleotide sequence consisting of nucleotides 10-4143 of SEQ ID NO:38;
(6) a nucleotide sequence consisting of nucleotides 10-4323 of SEQ ID NO:40; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some other embodiments, the vector contains a multi-antigen construct encoding (i) at least one immunogenic MUC1 polypeptide, (ii) at least one immunogenic CEA polypeptide, and (iii) at least one immunogenic TERT polypeptide. The vector may be a DNA plasmid vector, DNA virus vector, RNA plasmid vector, or RNA virus vector. In some specific embodiments, the present disclosure provides a DNA vector, which comprises a multi-antigen construct comprising a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-6009 of SEQ ID NO:42;
(2) a nucleotide sequence consisting of nucleotides 10-6003 of SEQ ID NO:44;
(3) a nucleotide sequence consisting of nucleotides 10-6024 of SEQ ID NO:46;
(4) a nucleotide sequence consisting of nucleotides 10-5988 of SEQ ID NO:48;
(5) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:50; or
(6) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
In some specific embodiments, the present disclosure provides a DNA viral vector consisting of a nucleotide sequence of any of SEQ ID NOs:58, 60, 62, 64, 66, and 68. In some other specific embodiments, the present disclosure provides a DNA plasmid vector consisting of the a nucleotide sequence of any of SEQ ID NOs:57, 59, 61, 63, 65, 67, 69, 70, 71, 72, 73, and 74.
In some other specific embodiments, the present disclosure provides a RNA vector, which comprises a nucleotide sequence that corresponds to a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-6009 of SEQ ID NO:42;
(2) a nucleotide sequence consisting of nucleotides 10-6003 of SEQ ID NO:44;
(3) a nucleotide sequence consisting of nucleotides 10-6024 of SEQ ID NO:46;
(4) a nucleotide sequence consisting of nucleotides 10-5988 of SEQ ID NO:48;
(5) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:50;
(6) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(6) above.
The present disclosure also provides compositions, which comprise an isolated nucleic acid molecule (i.e., an antigen construct) or a vector provided by the present disclosure. A composition may comprise only one individual antigen construct, such as a dual-antigen construct or a triple-antigen construct. It may also comprise two or more different individual antigen constructs, such as a combination of a single-antigen construct and a dual-antigen construct, or a combination of three or more single-antigen constructs encoding different immunogenic TAA polypeptides. The compositions are useful for eliciting an immune response against a TAA protein in vitro or in vivo in a mammal, including a human. In some embodiments, the compositions are immunogenic compositions or pharmaceutical compositions. In some particular embodiments, the composition is a vaccine composition for administration to humans for (1) inhibiting abnormal cell proliferation, providing protection against the development of cancer (used as a prophylactic), (2) treatment of cancer (used as a therapeutic) associated with TAA over-expression, or (3) eliciting an immune response to a particular human TAA, such as CEA, MUC1, and TERT.
In some embodiments, a composition provided by the present disclosure comprises a multi-antigen construct or a vector comprising a multi-antigen construct, wherein the multi-antigen construct encodes two or more immunogenic TAA polypeptides. For example, a multi-antigen construct may encode two or more immunogenic TAA polypeptides in any of the following combinations:
(1) an immunogenic CEA polypeptide and an immunogenic MUC1 polypeptide;
(2) an immunogenic CEA polypeptide and an immunogenic TERT polypeptide; and
(3) an immunogenic CEA polypeptide, an immunogenic MUC1 polypeptide, and an immunogenic TERT polypeptide.
In some particular embodiments, the composition provided by the present disclosure comprises a dual-antigen construct or a vector comprising a dual-antigen construct, wherein the dual-antigen construct comprises a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:31 or amino acids 4-1088 of SEQ ID NO:31;
(2) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:33 or amino acids 4-1081 of SEQ ID NO:33;
(3) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:35 or amino acids 4-1085 of SEQ ID NO:35;
(4) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:37 or amino acids 4-1030 of SEQ ID NO:37;
(5) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:39 or amino acids 4-1381 of SEQ ID NO:39;
(6) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:41 or amino acids 4-1441 of SEQ ID NO:41;
(7) the nucleotide sequence of SEQ ID NO:30 or a nucleotide sequence comprising nucleotides 10-3264 of SEQ ID NO:30;
(8) the nucleotide sequence of SEQ ID NO:32 or a nucleotide sequence comprising nucleotides 10-3243 of SEQ ID NO:32;
(9) the nucleotide sequence of SEQ ID NO:34 or a nucleotide sequence comprising nucleotides 10-3255 of SEQ ID NO:34;
(10) the nucleotide sequence of SEQ ID NO:36 or a nucleotide sequence comprising nucleotides 10-3090 of SEQ ID NO:36;
(11) the nucleotide sequence of SEQ ID NO:38 or a nucleotide sequence comprising nucleotides 10-4143 of SEQ ID NO:38;
(12) the nucleotide sequence of SEQ ID NO:40 or a nucleotide sequence comprising nucleotides 10-4323 of SEQ ID NO:40; and
(13) a nucleotide sequences that is a degenerate variant of any of the nucleotide sequences of (1)-(12) above.
In some other particular embodiments, the compositions provided by the present disclosure comprise (1) a triple-antigen construct, or (2) a vector comprising a triple-antigen construct, wherein the triple antigen construct comprises a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:43 or amino acids 4-2003 of SEQ ID NO:43;
(2) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:45 or amino acids 4-2001 of SEQ ID NO:45;
(3) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:47 or amino acids 4-2008 of SEQ ID NO:47;
(4) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:49 or amino acids 4-1996 of SEQ ID NO: 49;
(5) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:51 or amino acids 4-1943 of SEQ ID NO:51;
(6) a nucleotide sequence encoding the amino acid sequence of SEQ ID NO:53 or amino acids 4-1943 of SEQ ID NO:53;
(7) the nucleotide sequence of SEQ ID NO:42 or a nucleotide sequence comprising nucleotides 10-6009 of SEQ ID NO:42;
(8) the nucleotide sequence of SEQ ID NO:44 or a nucleotide sequence comprising nucleotides 10-6003 of SEQ ID NO:44;
(9) the nucleotide sequence of SEQ ID NO:46 or a nucleotide sequence comprising nucleotides 10-6024 of SEQ ID NO:46;
(10) the nucleotide sequence of SEQ ID NO:48 or a nucleotide sequence comprising nucleotides 10-5988 of SEQ ID NO:48;
(11) the nucleotide sequence of SEQ ID NO:50 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:50;
(12) the nucleotide sequence of SEQ ID NO:52 or a nucleotide sequence comprising nucleotides 10-5829 of SEQ ID NO:52; and
(13) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(12) above.
In some other particular embodiments, the compositions provided by the present disclosure comprise a triple-antigen construct, or a vector comprising a triple-antigen construct, wherein the triple antigen construct comprises a nucleotide sequence selected from the group consisting of:
(1) a nucleotide sequence consisting of nucleotides 10-6009 of SEQ ID NO:42;
(2) a nucleotide sequence consisting of nucleotides 10-6003 of SEQ ID NO:44;
(3) a nucleotide sequence consisting of nucleotides 10-6024 of SEQ ID NO:46;
(4) a nucleotide sequence consisting of nucleotides 10-5988 of SEQ ID NO:48;
(5) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:50;
(6) a nucleotide sequence consisting of nucleotides 10-5829 of SEQ ID NO:52; and
(7) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of (1)-(7 above.
In other particular embodiments, the compositions provided by the present disclosure comprises a RNA triple-antigen construct, or a RNA vector comprising a triple-antigen construct, wherein the triple antigen construct comprises a nucleotide sequence that corresponds to (1) any of the sequences of SEQ ID NOs:42, 44, 46, 48, 50, 52 or (2) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of SEQ ID NOs:42, 44, 46, 48, 50, 52.
In other particular embodiments, the compositions provided by the present disclosure comprise a RNA triple-antigen construct, or a RNA vector comprising a triple-antigen construct, wherein the triple antigen construct consists of a nucleotide sequence that corresponds to (1) any of the sequences of SEQ ID NOs:42, 44, 46, 48, 50, 52 or (2) a nucleotide sequence that is a degenerate variant of any of the nucleotide sequences of SEQ ID NOs:42, 44, 46, 48, 50, 52.
In still other particular embodiments, the compositions provided by the present disclosure comprise a triple-antigen construct, or a vector comprising a triple-antigen construct, wherein the triple antigen construct comprises (1) a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92 or (2) degenerate variant of a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92. In some other particular embodiments, the present disclosure provides a composition comprising a plasmid, wherein the plasmid comprises a nucleotide sequence of any of SEQ ID Nos: 57, 59, 61, 63, 65, and 67. In still other particular embodiments, the present disclosure provides a composition comprising a vector, wherein the vector comprises a nucleotide sequence of any of SEQ ID Nos: 58, 60, 62, 64, 66, and 68.
In still other particular embodiments, the compositions provided by the present disclosure comprise a triple-antigen construct, or a vector comprising a triple-antigen construct, wherein the triple antigen construct consists of (1) a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92 or (2) degenerate variant of a nucleotide sequence of any of SEQ ID NOS: 87, 88, 89, 90, 91, and 92. In some other particular embodiments, the present disclosure provides a composition comprising a plasmid, wherein the plasmid consists of a nucleotide sequence of any of SEQ ID Nos: 57, 59, 61, 63, 65, and 67. In still other particular embodiments, the present disclosure provides a composition comprising a vector, wherein the vector consists of a nucleotide sequence of any of SEQ ID Nos: 58, 60, 62, 64, 66, and 68.
The compositions, such as a pharmaceutical composition or a vaccine composition, may further comprise a pharmaceutically acceptable excipient. Pharmaceutically acceptable excipients for nucleic acid compositions, including DNA vaccine and RNA vaccine compositions, are well known to those skilled in the art. Such excipients may be aqueous or nonaqueous solutions, suspensions, and emulsions. Examples of non-aqueous excipients include propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Examples of aqueous excipient include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Suitable excipients also include agents that assist in cellular uptake of the polynucleotide molecule. Examples of such agents are (i) chemicals that modify cellular permeability, such as bupivacaine, (ii) liposomes or viral particles for encapsulation of the polynucleotide, or (iii) cationic lipids or silica, gold, or tungsten microparticles which associate themselves with the polynucleotides. Anionic and neutral liposomes are well-known in the art (see, e.g., Liposomes: A Practical Approach, RPC New Ed, IRL press (1990), for a detailed description of methods for making liposomes) and are useful for delivering a large range of products, including polynucleotides.
An immunogenic composition, pharmaceutical composition, or vaccine composition provided by the present disclosure may be used in conjunction or combination with one or more immune modulators. The composition may also be used in conjunction or combination with one or more adjuvants. Further, the composition may be used in conjunction or combination with one or more immune modulators and one or more adjuvants. The immune modulators or adjuvants may be formulated separately from the antigen construct or vector, or they may be part of the same composition formulation. Thus, in some embodiments, the present disclosure provides a pharmaceutical composition that comprises (1) an antigen construct provided by the present disclosure or vector containing such an antigen construct and (2) an immune modulator. In some further embodiments, the pharmaceutical composition further comprises an adjuvant. Examples of immune modulators and adjuvants are provided herein below.
The compositions, including vaccine compositions, can be prepared in any suitable dosage forms, such as liquid forms (e.g., solutions, suspensions, or emulsions) and solid forms (e.g., capsules, tablets, or powder), and by methods known to one skilled in the art.
In other aspects, the present disclosure provides (1) use of the antigen constructs, vectors, and compositions as medicament, (2) use of the antigen constructs, vectors, and compositions in the manufacture of a medicament for eliciting an immune response against a TAA, for inhibiting abnormal cell proliferation, or for treating a cancer, and (3) methods of using the antigen constructs, vectors, and compositions, wherein the antigen constructs, vectors, and compositions are as described herein above.
In one aspect, the present disclosure provides use of (1) an antigen construct encoding one or more immunogenic TAA polypeptides, (2) a vector containing such an antigen construct, or (3) a composition containing such as antigen-construct or vector for eliciting an immune response against a TAA in a mammal, such as a human. In some embodiments, the disclosure provides a method of eliciting an immune response against a TAA in a mammal, particularly a human, which method comprises administering to the mammal an effective amount of a composition comprising (1) an antigen construct encoding one or more immunogenic TAA polypeptides or (2) a vector containing an antigen construct encoding one or more immunogenic TAA polypeptides. In some embodiments, the disclosure provides a method of eliciting an immune response against CEA in a mammal, particularly a human, comprising administering to the mammal an effective amount of a composition comprising an antigen construct provided by the present disclosure, wherein the antigen construct comprises (1) at least one nucleotide sequence encoding an immunogenic CEA polypeptide and (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide or an immunogenic TERT polypeptide. In some other embodiments, the disclosure provides a method of eliciting an immune response against MUC1 in a mammal, particularly a human, comprising administering to the mammal an effective amount of a composition comprising an antigen construct provided by the present disclosure, wherein the antigen construct comprises (1) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide and (2) at least one nucleotide sequence encoding an immunogenic CEA polypeptide or an immunogenic TERT polypeptide. In some further embodiments, the disclosure provides a method of eliciting an immune response against TERT in a mammal, particularly a human, comprising administering to the mammal an effective amount of a composition comprising an antigen construct provided by the present disclosure, wherein the antigen construct comprises (1) at least one nucleotide sequence encoding an immunogenic TERT polypeptide and (2) at least one nucleotide sequence encoding an immunogenic MUC1 polypeptide or an immunogenic CEA polypeptide.
In another aspect, the present disclosure provides use of (1) an antigen construct encoding one or more immunogenic TAA polypeptides, (2) a vector containing such an antigen construct, or (3) a composition containing such as antigen-construct or vector for inhibiting abnormal cell proliferation in a mammal, such as a human. In some embodiments, the present disclosure provides a method of inhibiting abnormal cell proliferation in a mammal, particularly a human, comprising administering to the mammal an effective amount of a composition comprising (1) an antigen construct encoding one or more immunogenic TAA polypeptides or (2) a vector containing an antigen construct encoding one or more immunogenic TAA polypeptides, wherein the abnormal cell proliferation is associated with over-expression of the tumor-associated antigen CEA, MUC1, or TERT. The abnormal cell proliferation may be in any organ or tissues of a human, such as breast, stomach, ovaries, lungs, bladder, large intestine (e.g., colon and rectum), kidneys, pancreas, and prostate. In some embodiments, the method is for inhibiting abnormal cell proliferation in the breast, ovaries, pancreas, colon, lung, stomach, and rectum. The antigen construct or vector in the composition administered encodes at least one immunogenic polypeptide that is derived from, or immunogenic against, the over-expressed tumor-associated antigen. The antigen construct may be a single-antigen construct or a multi-antigen construct, such as a dual-antigen construct or a triple-antigen construct. In some specific embodiments, the composition comprises a triple-antigen construct encoding an immunogenic CEA polypeptide, an immunogenic MUC1 polypeptide, and an immunogenic TERT polypeptide.
In a further aspect, the present disclosure provides use of (1) an antigen construct encoding one or more immunogenic TAA polypeptides, (2) a vector containing such an antigen construct, or (3) a composition containing such as antigen-construct or vector as a medicament for treatment of a cancer in a mammal, particularly a human. In some embodiments, the present disclosure provides a method of treating a cancer in a human, wherein the cancer is associated with over-expression of one or more of the tumor-associated antigen CEA, MUC1, and TERT. The method comprises administering to the human an effective amount of a composition that comprises an antigen construct encoding at least one immunogenic polypeptide that is derived from, or immunogenic against, the over-expressed tumor-associated antigen in the particular cancer. The antigen construct may be a single-antigen construct or a multi-antigen construct, such as a dual-antigen construct or a triple-antigen construct. In some specific embodiments, the composition comprises a triple-antigen construct encoding an immunogenic CEA polypeptide, an immunogenic MUC1 polypeptide, and an immunogenic TERT polypeptide. Any cancer that over-expresses the tumor-associate antigen MUC1, CEA, and/or TERT may be treated by a method provided by the present disclosure. Examples of cancers include breast cancer, ovarian cancer, lung cancer (such as small cell lung cancer and non-small cell lung cancer), colorectal cancer, gastric cancer, and pancreatic cancer. In some particular embodiments, the present disclosure provide a method of treating cancer in a human, which comprises administering to the human an effective amount of a composition comprising a triple-antigen construct, wherein the cancer is (1) breast cancer, such as estrogen-receptor and/or progesterone-receptor positive breast cancer, HER2 positive breast cancer, or triple-negative breast cancer, (2) lung cancer, such as NSCLC or SCLC, (3) gastric cancer, (4) pancreatic cancer, or (5) colorectal cancer.
In some specific embodiments, the present disclosure provides a method of eliciting an immune response against a TAA, a method of inhibiting abnormal cell proliferation, or a method of treating a cancer in a mammal, particularly a human, which method comprises administering to the mammal an effective amount of a composition comprising a multi-antigen construct or vector comprising a multi-antigen construct, wherein the multi-antigen construct comprises a nucleotide sequence encoding any of the amino acid sequence of SEQ ID Nos: 43, 45, 47, 49, 51, and 53. In other specific embodiments, the present disclosure provides a method of eliciting an immune response against a TAA, a method of inhibiting abnormal cell proliferation, or a method of treating a cancer in a mammal, particularly a human, which method comprises administering to the mammal an effective amount of a composition comprising a multi-antigen construct, wherein the multi-antigen construct comprises a nucleotide sequence of any of SEQ ID Nos: 42, 44, 46, 48, 50, 52, and 87-92. In other specific embodiments, the present disclosure provides a method of eliciting an immune response against a TAA, a method of inhibiting abnormal cell proliferation, or a method of treating a cancer in a mammal, particularly a human, which method comprises administering to the mammal an effective amount of a composition comprising a vector, wherein the vector comprises a nucleotide sequence of any of SEQ ID Nos: 57-68.
The compositions can be administered to a mammal, including human, by a number of suitable methods known in the art. Examples of suitable methods include: (1) intramuscular, intradermal, intraepidermal, or subcutaneous administration, (2) oral administration, and (3) topical application (such as ocular, intranasal, and intravaginal application). One particular method of intradermal or intraepidermal administration of a nucleic acid vaccine composition, particularly composition containing a DNA plasmid, is gene gun delivery using the Particle Mediated Epidermal Delivery (PMED™) vaccine delivery device marketed by PowderMed. PMED is a needle-free method of administering vaccines to animals or humans. The PMED system involves the precipitation of DNA onto microscopic gold particles that are then propelled by helium gas into the epidermis. The DNA-coated gold particles are delivered to the APCs and keratinocytes of the epidermis, and once inside the nuclei of these cells, the DNA elutes off the gold and becomes transcriptionally active, producing encoded protein. Another particular method for intramuscular administration of a nucleic acid vaccine involves electroporation. Electroporation uses controlled electrical pulses to create temporary pores in the cell membrane, which facilitates cellular uptake of the nucleic acid vaccine injected into the muscle. Where a CpG is used in combination with a nucleic acid vaccine, the CpG and nucleic acid vaccine may be co-formulated in one formulation and the formulation is administered intramuscularly by electroporation.
The effective amount of the composition to be administered in a given method can be readily determined by a person skilled in the art and will depend on a number of factors. In a method of treating cancer, such as pancreatic cancer, ovarian cancer, lung cancer, colorectal cancer, gastric cancer, and breast cancer, factors that may be considered in determining the effective amount include the subject to be treated, including the subject's immune status and health, the severity or stage of the cancer to be treated, the specific immunogenic TAA polypeptides expressed, the degree of protection or treatment desired, the administration method and schedule, and other therapeutic agents (such as adjuvants or immune modulators) used. The method of formulation and delivery are among the key factors for determining the dose of the nucleic acid required to elicit an effective immune response. For example, the effective amounts of the nucleic acid in a vaccine may be in the range of 2 μg/dose-10 mg/dose when the vaccine is formulated as an aqueous solution and administered by hypodermic needle injection or pneumatic injection, whereas only 16 ng/dose-16 μg/dose may be required when the nucleic acid is prepared as coated gold beads and delivered using a gene gun technology. The dose range for a nucleic acid in a vaccine by electroporation is generally in the range of 0.5-10 mg/dose. In the case where the nucleic acid vaccine is administered together with a CpG by electroporation in a co-formulation, the dose of the nucleic acid vaccine may be in the range of 0.5-5 mg/dose and the dose of CpG is typically in the range of 0.05 mg-5 mg/dose, such as 0.05, 0.2, 0.6, or 1.2 mg/dose per person.
The vaccine compositions provided by the present disclosure can be used in a prime-boost strategy to induce robust and long-lasting immune response. Priming and boosting vaccination protocols based on repeated injections of the same immunogenic construct are well known. In general, the first dose of the vaccine may not be able to produce protective immunity, but only “primes” the immune system. A protective immune response develops after the second, third, or subsequent doses (the “boosts”). The boosts are performed according to conventional techniques, and can be further optimized empirically in terms of schedule of administration, route of administration, choice of adjuvant, dose, and potential sequence when administered with another vaccine. In one embodiment, the vaccine compositions are used in a conventional homologous prime-boost strategy, in which the same vaccine is administered to the animal in both the prime and boosts doses. For example, the same vaccine composition containing a plasmid vector is administered in both the initial doses (“prime’) and subsequent doses (“boost”). In another embodiment, the vaccine compositions are used in a heterologous prime-boost vaccination, in which different types of vaccines expressing the same immunogenic TAA polypeptide(s) are administered at predetermined time intervals. For example, an antigen construct is administered in the form of a plasmid vector in the prime dose and in the form of a viral vector in the boost doses, or vice versa.
The vaccine compositions may be used together with one or more adjuvants. Examples of suitable adjuvants include: (1) oil-in-water emulsion formulations, such as MF59 and AS03, (2) saponin adjuvants, such as QS21 and Iscomatrix® (Commonwealth Serum Laboratories, Australia); (3) Complete Freund's Adjuvant (CFA) and Incomplete Freund's Adjuvant (IFA); (4) cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, interferons (e.g. gamma interferon), macrophage colony stimulating factor (M-CSF), and tumor necrosis factor (TNF); (5) monophosphoryl lipid A (MPL) or 3-O-deacylated MPL (3dMPL); (6) oligonucleotides comprising CpG motifs; and (7) metal salt, including aluminum salts (alum), such as aluminum phosphate and aluminum hydroxide.
Further, for the treatment of a neoplastic disorder, including a cancer, in a mammal, including human, the compositions may be administered in combination with one or more immune modulators. The immune modulator may be an immune-suppressive-cell inhibitor (ISC inhibitor) or an immune-effector-cell enhancer (IEC enhancer). Further, one or more ISC inhibitors may be used in combination with one or more IEC enhancers. The immune modulators may be administered by any suitable methods and routes, including (1) systemic administration such as intravenous, intramuscular, or oral administration, and (2) local administration such intradermal and subcutaneous administration. Where appropriate or suitable, local administration is generally preferred over systemic administration. Local administration of any immune modulators can be carried out at any location of the body of the mammal that is suitable for local administration of pharmaceuticals; however, it is more preferable that these immune modulators are administered locally at close proximity to the vaccine draining lymph node.
The compositions, such as a vaccine, may be administered simultaneously or sequentially with any or all of the immune modulators used. Similarly, when two or more immune modulators are used, they may be administered simultaneously or sequentially with respect to each other. In some embodiments, a vaccine is administered simultaneously (e.g., in a mixture) with respect to one immune modulator, but sequentially with respect to one or more additional immune modulators. Co-administration of the vaccine and the immune modulators can include cases in which the vaccine and at least one immune modulator are administered so that each is present at the administration site, such as vaccine draining lymph node, at the same time, even though the antigen and the immune modulators are not administered simultaneously. Co-administration of the vaccine and the immune modulators also can include cases in which the vaccine or the immune modulator is cleared from the administration site, but at least one cellular effect of the cleared vaccine or immune modulator persists at the administration site, such as vaccine draining lymph node, at least until one or more additional immune modulators are administered to the administration site. In cases where a nucleic acid vaccine is administered in combination with a CpG, the vaccine and CpG may be contained in a single formulation and administered together by any suitable method. In some embodiments, the nucleic acid vaccine and CpG in a co-formulation (mixture) is administered by intramuscular injection in combination with electroporation.
In some embodiments, the immune modulator is an ISC inhibitor. Examples of ISC inhibitors include (1) protein kinase inhibitors, such as imatinib, sorafenib, lapatinib, BIRB-796, and AZD-1152, AMG706, Zactima (ZD6474), MP-412, sorafenib (BAY 43-9006), dasatinib, CEP-701 (lestaurtinib), XL647, XL999, Tykerb (lapatinib), MLN518, (formerly known as CT53518), PKC412, ST1571, AEE 788, OSI-930, OSI-817, sunitinib malate (Sutent), axitinib (AG-013736), erlotinib, gefitinib, axitinib, bosutinib, temsirolismus and nilotinib (AMN107). In some particular embodiments, the tyrosine kinase inhibitor is sunitinib, sorafenib, or a pharmaceutically acceptable salt or derivative (such as a malate or a tosylate) of sunitinib or sorafenib; (2) cyclooxygenase-2 (COX-2) inhibitors, such as celecoxib and rofecoxib; (3) phosphodiesterase type 5 (PDES) inhibitors, such as avanafil, lodenafil, mirodenafil, sildenafil, tadalafil, vardenafil, udenafil, and zaprinast, (4) DNA crosslinkers, such as cyclophosphamide, (5) PARP inhibitors, such as talazoparib, and (6) CDK inhibitors, such palbocyclib.
In some embodiments, the immune modulator that is used in combination with a nucleic acid composition is an IEC enhancer. Two or more IEC enhancers may be used together. Examples of IEC enhancers that may be used include: (1) TNFR agonists, such as agonists of OX40, 4-1BB (such as BMS-663513), GITR (such as TRX518), and CD40 (such as CD40 agonistic antibodies); (2) CTLA-4 inhibitors, such as is Ipilimumab and Tremelimumab; (3) TLR agonists, such as CpG 7909 (5′ TCGTCGTTTTGTCGTTTTGTCGTT3′), CpG 24555 (5′ TCGTCGTTTTTCGGTGCTTTT3′ (CpG 24555); and CpG 10103 (5′ TCGTCGTTTTTCGGTCGTTTT3′); (4) programmed cell death protein 1 (PD-1) inhibitors, such as nivolumab and pembrolizumab; and (5) PD-L1 inhibitors, such as atezolizumab, durvalumab, and velumab; and (6) 001 inhibitors.
In some embodiments, the IEC enhancer is CD40 agonist antibody, which may be a human, humanized or part-human chimeric anti-CD40 antibody. Examples of specific CD40 agonist antibodies include the G28-5, mAb89, EA-5 or S2C6 monoclonal antibody, and CP870,893. CP-870,893 is a fully human agonistic CD40 monoclonal antibody (mAb) that has been investigated clinically as an anti-tumor therapy. The structure and preparation of CP870,893 is disclosed in WO2003041070 (where the antibody is identified by the internal identified “21.4.1” and the amino acid sequences of the heavy chain and light chain of the antibody are set forth in SEQ ID NO: 40 and SEQ ID NO: 41, respectively). For use in combination with a composition present disclosure, CP-870,893 may be administered by any suitable route, such as intradermal, subcutaneous, or intramuscular injection. The effective amount of CP870893 is generally in the range of 0.01-0.25 mg/kg. In some embodiment, CP870893 is administered at an amount of 0.05-0.1 mg/kg.
In some other embodiments, the IEC enhancer is a CTLA-4 inhibitor, such as Ipilimumab and Tremelimumab. Ipilimumab (also known as MEX-010 or MDX-101), marketed as YERVOY, is a human anti-human CTLA-4 antibody. Ipilimumab can also be referred to by its CAS Registry No. 477202-00-9, and is disclosed as antibody 10DI in PCT Publication No. WO 01/14424. Tremelimumab (also known as CP-675,206) is a fully human IgG2 monoclonal antibody and has the CAS number 745013-59-6. Tremelimumab is disclosed in U.S. Pat. No. 6,682,736, incorporated herein by reference in its entirety, where it is identified as antibody 11.2.1 and the amino acid sequences of its heavy chain and light chain are set forth in SEQ ID NOs:42 and 43, respectively. For use in combination with a composition provided by the present disclosure, Tremelimumab may be administered locally, particularly intradermally or subcutaneously. The effective amount of Tremelimumab administered intradermally or subcutaneously is typically in the range of 5-200 mg/dose per person. In some embodiments, the effective amount of Tremelimumab is in the range of 10-150 mg/dose per person per dose. In some particular embodiments, the effective amount of Tremelimumab is about 10, 25, 50, 75, 100, 125, 150, 175, or 200 mg/dose per person.
In some other embodiments, the immune modulator is a PD-1 inhibitor or PD-L1 inhibitor. Examples of PD-1 inhibitors include nivolumab (trade name Opdivo), pembrolizumab (trade name Keytruda), RN888 (anti-PD-1 antibody), pidilizumab (Cure Tech, AMP-224 (GSK), AMP-514 (GSK), and PDR001 (Novartis). Examples of PD-L1 inhibits include atezolizumab (PD-L1-specific mAbs; trade name Tecentriq), durvalumab (PD-L1-specific mAbs; trade name Imfinzi), and avelumab (PD-L1-specific mAbs; trade name Bavencio), and BMS-936559 (BMS). See also Okazaki T et al., International Immunology (2007); 19,7:813-824 and Sunshine J et al., Curr Opin Pharmacol. 2015 August; 23:32-8). In some specific embodiment, the PD-1 inhibitor is RN888. RN888 is a monoclonal antibody that specifically binds to PD-1. RN888 is disclosed in international patent application publication WO2016/092419, in which the antibody is identified as mAb7 having a full-length heavy chain amino acid sequence of SEQ ID NO:29 and full-length light chain amino acid sequence of SEQ ID NO:39.
In other embodiments, the immune modulator is an inhibitor of indoleamine 2,3-dioxygenase 1 (also known as “IDO1”). IDO1 was found to modulate immune cell function to a suppressive phenotype and was, therefore, believed to partially account for tumor escape from host immune surveillance. The enzyme degrades the essential amino acid tryptophan into kynurenine and other metabolites. It was found that these metabolites and the paucity of tryptophan leads to suppression of effector T-cell function and augmented differentiation of regulatory T cells. The 001 inhibitors may be large molecules, such as an antibody, or a small molecule, such as a chemical compound.
In some particular embodiments, the polypeptide or nucleic acid composition provided by the present disclosure is used in combination with a 1,2,5-oxadiazole derivative 001 inhibitor disclosed in WO2010/005958. Examples of specific 1,2,5-oxadiazole derivative IDO1 inhibitors include the following compounds:
The 1,2,5-oxadiazole derivative IDO1 inhibitors are typically administered orally once or twice per day and effective amount by oral administration is generally in the range of 25 mg-1000 mg per dose per patient, such as 25 mg, 50 mg, 100 mg, 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, or 1000 mg. In a particular embodiment, the polypeptide or nucleic acid composition provided by the present disclosure is used in combination with 4-({2-[(aminosulfonyl)amino]ethyl}amino)-N-(3-bromo-4-fiuorophenyl)-N′-hydroxy-1,2,5-oxadiazole-3-carboximidamide administered orally twice per day at 25 mg or 50 mg per dose. The 1,2,5-oxadiazole derivatives may be synthesized as described in U.S. Pat. No. 8,088,803, which is incorporated herein by reference in its entirety.
In some other specific embodiments, the polypeptide or nucleic acid composition provided by the present disclosure is used in combination with a pyrrolidine-2,5-dione derivative 001 inhibitor disclosed in WO2015/173764. Examples of specific pyrrolidine-2,5-dione derivative inhibitors include the following compounds:
The pyrrolidine-2,5-dione derivative 001 inhibitors are typically administered orally once or twice per day and the effective amount by oral administration is generally in the range of 50 mg-1000 mg per dose per patient, such as 125 mg, 250 mg, 500 mg, 750 mg, or 1000 mg. In a particular embodiment, the polypeptide or nucleic acid composition provided by the present disclosure is used in combination with 3-(5-fluoro-1H-indol-3-yl)pyrrolidine-2,5-dione administered orally once per day at 125-100 mg per dose per patient. The pyrrolidine-2,5-dione derivatives may be synthesized as described in U.S. patent application publication US2015329525, which is incorporated herein by reference in its entirety.
The following examples are provided to illustrate certain embodiments of the invention. They should not be construed to limit the scope of the invention in any way. From the discussion above and these examples, one skilled in the art can ascertain the essential characteristics of the invention and, without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usage and conditions.
Example 1 illustrates the construction of plasmid vectors containing a single-antigen construct, a dual-antigen construct, or a triple antigen construct. Unless as otherwise noted, reference to amino acid positions or residues of MUC1, CEA, and TERT protein refers to the amino acid sequence of human MUC1 isoform 1 precursor protein as set forth in SEQ ID NO:1, the amino acid sequence of human carcinoembryonic antigen (CEA) isoform 1 precursor protein as set forth in SEQ ID NO:2, and the amino acid sequence of human TERT isoform 1 precursor protein as set forth in SEQ ID NO:3, respectively. Structures of some of the primers used in the plasmid constructions are provided in Table 16.
1A. Plasmids Containing a Single-Antigen Construct
Plasmid 1027 (MUC1).
Plasmid 1027 was generated using the techniques of gene synthesis and restriction fragment exchange. The amino acid sequence of human MUC1 with a 5× tandem repeat VNTR region was submitted to GeneArt for gene optimization and synthesis. The gene encoding the polypeptide was optimized for expression, synthesized, and cloned. The MUC-1 open reading frame was excised from the GeneArt vector by digestion with NheI and BglII and inserted into similarly digested plasmid pPJV7563. The open reading frame (ORF) nucleotide sequence of Plasmid 1027 is set forth in SEQ ID NO:4. The amino acid sequence encoded by Plasmid 1027 is set for in SEQ ID NO:5.
Plasmid 1361 (CEA).
Plasmid 1361 was constructed using the techniques of gene synthesis, PCR and Seamless cloning. First, the gene encoding the CEA reference sequence was codon optimized for expression at DNA2.0. The sequence encoding amino acids 2-702 was amplified by PCR with primers ID1361-1362_PCRF and ID1361-1362_PCRR. The amplicon was cloned into the NheI/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1361 is set forth in SEQ ID NO:14. The amino acid sequence encoded by Plasmid 1361 is set for in SEQ ID NO:15.
Plasmid 1386 (mCEA).
Plasmid 1386, which encodes a membrane-bound immunogenic CEA polypeptide (mCEA), was constructed using the techniques of PCR and Seamless cloning. First, the gene fragment encoding CEA amino acids 2-144 was amplified by PCR from plasmid 1361 with primers f pmed CEA SS and r CEA D1. Second, the gene fragment encoding CEA amino acids 323-702 was amplified by PCR from plasmid 1361 with primers f CEA D1-D4 and r pmed CEA GPI. The amplicons were ligated and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1386 is set forth in SEQ ID NO:16. The amino acid sequence encoded by Plasmid 1386 is set for in SEQ ID NO:17.
Plasmid 1390 (cCEA).
Plasmid 1390, which encodes a cytoplasmic immunogenic CEA polypeptide (cCEA), was constructed using the techniques of PCR and Seamless cloning. First, the gene fragment encoding CEA amino acids 35-144 was amplified by PCR from plasmid 1361 with primers f pmed CEA D1 and r CEA D1. Second, the gene fragment encoding CEA amino acids 323-677 was amplified by PCR from plasmid 1361 with primers f CEA D1-D4 and r pmed CEA D7. The amplicons were ligated and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1390 is set forth in SEQ ID NO:18. The amino acid sequence encoded by Plasmid 1390 is set for in SEQ ID NO:19.
Plasmid 1065 (Full Length TERT D712A/V713I).
Plasmid 1065 was generated using the techniques of gene synthesis and restriction fragment exchange. The amino acid sequence of human TERT with two mutations (D712A/V713I) designed to inactivate enzymatic activity was submitted to DNA2.0 for gene optimization and synthesis. The gene encoding the polypeptide was optimized for expression, synthesized, and cloned. The TERT open reading frame was excised from the DNA2.0 vector by digestion with NheI and BglII and inserted into similarly digested plasmid pPJV7563. The amino acid sequence encoded by Plasmid 1065 is set for in SEQ ID NO:81. The open reading frame (ORF) nucleotide sequence of Plasmid 1065 is set forth in SEQ ID NO:82.
Plasmid 1112 (TERT240).
Plasmid 1112 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding TERT amino acids 241-1132 was amplified by PCR from plasmid 1065 with primers f pmed TERT 241G and r TERT co# pMed. The amplicon was cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1112 is set forth in SEQ ID NO:8. The amino acid sequence encoded by Plasmid 1112 is set for in SEQ ID NO:9.
Plasmid 1197 (cMUC1).
Plasmid 1197, which encodes a cytoplasmic immunogenic MUC1 polypeptide (cMUC1), was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding MUC1 amino acids 22-225, 946-1255 was amplified by PCR from plasmid 1027 with primers ID1197F and ID1197R. The amplicon was cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1197 is set forth in SEQ ID NO:6. The amino acid sequence encoded by Plasmid 1197 is set for in SEQ ID NO:7.
Plasmid 1326 (TERT343).
Plasmid 1326 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding TERT amino acids 344-1132 was amplified by PCR from plasmid 1112 with primers TertΔ343-F and Tert-R. The amplicon was cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1326 is set forth in SEQ ID NO:10. The amino acid sequence encoded by Plasmid 1326 is set for in SEQ ID NO:11.
Plasmid 1330 (TERT541).
Plasmid 1330 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding TERT amino acids 542-1132 was amplified by PCR from plasmid 1112 with primers TertΔ541-F and Tert-R. The amplicon was cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1330 is set forth in SEQ ID NO:12. The amino acid sequence encoded by Plasmid 1330 is set for in SEQ ID NO:13.
1B. Plasmids Containing a Dual-Antigen Construct
Plasmid 1269 (Muc1-Tert240).
Plasmid 1269 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f tg link Ter240 and r pmed Bgl Ter240. The gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f pmed Nhe Muc and r link muc. PCR resulted in the addition of an overlapping GGSGG linker at the 5′ end of Tert and 3′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1269 is set forth in SEQ ID NO:20. The amino acid sequence encoded by Plasmid 1269 is set for in SEQ ID NO:21.
Plasmid 1270 (Muc1-ERB2A-Tert240).
Plasmid 1270 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f2 ERBV2A, f1 ERBV2A Ter240, and r pmed Bgl Ter240. The gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f pmed Nhe Muc and r ERB2A Bamh Muc. PCR resulted in the addition of overlapping ERBV 2A sequences at the 5′ end of Tert and 3′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1270 is set forth in SEQ ID NO:22. The amino acid sequence encoded by Plasmid 1270 is set for in SEQ ID NO:23.
Plasmid 1271 (Tert240-ERB2A-Muc1).
Plasmid 1271 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f pmed Nhe Ter240 and r ERB2A Bamh Ter240. The gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f2 ERBV2A, f1 ERBV2A Muc, and r pmed Bgl Muc. PCR resulted in the addition of overlapping ERBV 2A sequences at the 3′ end of Tert and 5′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1271 is set forth in SEQ ID NO:24. The amino acid sequence encoded by Plasmid 1271 is set for in SEQ ID NO:25.
Plasmid 1286 (cMuc1-ERB2A-Tert240).
Plasmid 1286 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f2 ERBV2A, f1 ERBV2A Ter240, and r pmed Bgl Ter240. The gene encoding human Mucin-1 amino acids 22-225, 946-1255 was amplified by PCR from plasmid 1197 with primers f pmed Nhe cytMuc and r ERB2A Bamh Muc. PCR resulted in the addition of overlapping ERBV 2A sequences at the 5′ end of Tert and 3′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1286 is set forth in SEQ ID NO:26. The amino acid sequence encoded by Plasmid 1286 is set for in SEQ ID NO:27.
Plasmid 1287 (Tert240-ERB2A-cMuc1).
Plasmid 1287 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f pmed Nhe Ter240 and r ERB2A Bamh Ter240. The gene encoding human Mucin-1 amino acids 22-225, 946-1255 was amplified by PCR from plasmid 1197 with primers f2 ERBV2A, f1 ERBV2A cMuc, and r pmed Bgl Muc. PCR resulted in the addition of overlapping ERBV 2A sequences at the 3′ end of Tert and 5′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1287 is set forth in SEQ ID NO:28. The amino acid sequence encoded by Plasmid 1287 is set for in SEQ ID NO: 29.
Plasmid 1409 (Muc1-EMC2A-mCEA).
Plasmid 1409 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f pmed Nhe Muc and r EM2A Bamh Muc. The gene encoding CEA amino acids 2-144, 323-702 was amplified by PCR from plasmid 1386 with primers f2 EMCV2A, f1 EMC2a CEAss, and r pmed CEA GPI. PCR resulted in the addition of overlapping EMCV 2A sequences at the 5′ end of CEA and 3′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1409 is set forth in SEQ ID NO:30. The amino acid sequence encoded by Plasmid 1409 is set for in SEQ ID NO:31.
Plasmid 1410 (mCEA-T2A-Muc1).
Plasmid 1410 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding CEA amino acids 2-144, 323-702 was amplified by PCR from plasmid 1386 with primers f pmed CEA SS and r T2A CEA. The gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f2 T2A 63, f1 T2a Muc, and r pmed Bgl Muc. PCR resulted in the addition of overlapping T2A sequences at the 3′ end of CEA and 5′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1410 is set forth in SEQ ID NO:32. The amino acid sequence encoded by Plasmid 1410 is set for in SEQ ID NO:33.
Plasmid 1411 (mCEA-Furin-T2A-Muc1). Plasmid 1411 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding CEA amino acids 2-144, 323-702 was amplified by PCR from plasmid 1386 with primers f pmed CEA SS and r T2A furin CEA. The gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f2 T2A 63, f1 T2a Muc, and r pmed Bgl Muc. PCR resulted in the addition of overlapping furin cleavage site and T2A sequences at the 3′ end of CEA and 5′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1411 is set forth in SEQ ID NO:34. The amino acid sequence encoded by Plasmid 1411 is set for in SEQ ID NO:35.
Plasmid 1431 (Muc1-EMC2A-cCEA).
Plasmid 1431 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding human Mucin-1 amino acids 2-225, 946-1255 was amplified by PCR from plasmid 1027 with primers f pmed Nhe Muc and r EM2A Bamh Muc. The gene encoding CEA amino acids 35-144, 323-677 was amplified by PCR from plasmid 1390 with primers f2 EMCV2A, f EMC2a CEA d1, and r pmed CEA D7. PCR resulted in the addition of overlapping EMCV 2A sequences at the 5′ end of CEA and 3′ end of Muc1. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1431 is set forth in SEQ ID NO:36. The amino acid sequence encoded by Plasmid 1431 is set for in SEQ ID NO:37.
Plasmid 1432 (cCEA-T2A-Tert240). Plasmid 1432 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding the CEA amino acids 35-144, 323-677 was amplified by PCR from plasmid 1390 with primers f pmed CEA D1 and r T2a CEA D7. The gene encoding human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f2 T2A 63, f1 T2A Tert240, and r pmed Bgl Ter240. The PCR resulted in the addition of overlapping TAV 2A sequences at the 5′ end of Tert and 3′ end of CEA. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1432 is set forth in SEQ ID NO:38. The amino acid sequence encoded by Plasmid 1432 is set for in SEQ ID NO:39.
Plasmid 1440 (Tert240-ERA2A-mCEA). Plasmid 1440 was constructed using the techniques of PCR and Seamless cloning. First, the gene encoding human telomerase amino acids 241-1132 was amplified by PCR from plasmid 1112 with primers f pmed Nhe tert240 and r ERA2A Tert. The gene encoding CEA amino acids 2-144, 323-702 was amplified by PCR from plasmid 1386 with primers f2 ERAV2A, f1 ERA2A ssCEA, and r pmed CEA GPI. The PCR resulted in the addition of overlapping ERAV 2A sequences at the 3′ end of Tert and 5′ end of CEA. The amplicons were mixed together and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1440 is set forth in SEQ ID NO:40. The amino acid sequence encoded by Plasmid 1440 is set for in SEQ ID NO:41.
1C. Plasmids Containing a Triple-Antigen Construct
Plasmid 1424 (Muc1-ERB2A-Tert240-ERA2A-mCEA). Plasmid 1424 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human Mucin-1 amino acids 2-225, 946-1255, an ERBV 2A peptide, and the amino terminal half of human Tert240 were amplified by PCR from plasmid 1270 with primers f pmed Nhe Muc and r tert 1602-1579. The genes encoding the carboxy terminal half of Tert240, an ERAV 2A peptide, and human CEA amino acids 2-144, 323-702 were amplified by PCR from plasmid 1440 with primers f tert 1584-1607 and r pmed CEA GPI. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1424 is set forth in SEQ ID NO:42. The amino acid sequence encoded by Plasmid 1424 is set for in SEQ ID NO:43.
Plasmid 1425 (mCEA-T2A-Muc1-ERB2A-Tert240). Plasmid 1425 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human CEA amino acids 2-144, 323-702, a TAV 2A peptide, and the amino terminal half of human Mucin-1 were amplified by PCR from plasmid 1410 with primers f pmed CEA SS and r muc 986-963. The genes encoding the carboxy terminal half of human Mucin-1, an ERBV 2A peptide, and human telomerase amino acids 241-1132 were amplified by PCR from plasmid 1270 with primers f Muc 960-983 and r pmed Bgl Ter240. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1425 is set forth in SEQ ID NO:44. The amino acid sequence encoded by Plasmid 1425 is set for in SEQ ID NO:45.
Plasmid 1426 (Tert240-ERB2A-Muc1-EMC2A-mCEA). Plasmid 1426 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human telomerase amino acids 241-1132, an ERBV 2A peptide, and the amino terminal half of human Mucin-1 were amplified by PCR from plasmid 1271 with primers f pmed Nhe Ter240 and r muc 986-963. The genes encoding the carboxy terminal half of human Mucin-1, an EMCV 2A peptide, and CEA amino acids 2-144, 323-702 were amplified by PCR from plasmid 1409 with primers f Muc 960-983 and r pmed CEA GPI. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1426 is set forth in SEQ ID NO:46. The amino acid sequence encoded by Plasmid 1426 is set for in SEQ ID NO:47.
Plasmid 1427 (Tert240-ERA2A-mCEA-T2A-Muc1). Plasmid 1427 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human telomerase amino acids 241-1132, an ERAV 2A peptide, and the amino terminal half of mCEA were amplified by PCR from plasmid 1440 with primers f pmed Nhe Ter240 and R CEA SR2. The genes encoding the carboxy terminal half of mCEA, a TAV 2A peptide, and human Mucin-1 amino acids 2-225, 946-1255 were amplified by PCR from plasmid 1410 with primers f cCEA 562-592 and r pmed Bgl Muc. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1427 is set forth in SEQ ID NO:48. The amino acid sequence encoded by Plasmid 1427 is set for in SEQ ID NO:49.
Plasmid 1428 (Muc1-EMC2A-cCEA-T2A-Tert240). Plasmid 1428 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human Mucin-1 amino acids 2-225, 946-1255, an EMCV 2A peptide, and the amino terminal half of cCEA were amplified by PCR from plasmid 1431 with primers f pmed Nhe Muc and r cCEA 849-820. The genes encoding the carboxy terminal half of cCEA, a TAV 2A peptide, and human telomerase amino acids 241-1132 were amplified by PCR from plasmid 1432 with primers f CEA 833-855 and r pmed Bgl Ter240. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1428 is set forth in SEQ ID NO:50. The amino acid sequence encoded by Plasmid 1428 is set for in SEQ ID NO:51.
Plasmid 1429 (cCEA-T2A-Tert240-ERB2A-Muc1). Plasmid 1429 was constructed using the techniques of PCR and Seamless cloning. First, the genes encoding human CEA amino acids 35-144, 323-677, a TAV 2A peptide, and the amino terminal half of human Tert240 were amplified by PCR from plasmid 1432 with primers f pmed CEA D1 and r tert 1602-1579. The genes encoding the carboxy terminal half of human Tert240, an ERBV 2A peptide, and human Mucin-1 amino acids 2-225, 946-1255 were amplified by PCR from plasmid 1271 with primers f tert 1584-1607 and r pmed Bgl Muc. The partially overlapping amplicons were digested with Dpn I, mixed together, and cloned into the Nhe I/Bgl II sites of pPJV7563 by Seamless cloning. The open reading frame nucleotide sequence of Plasmid 1429 is set forth in SEQ ID NO:52. The amino acid sequence encoded by Plasmid 1429 is set for in SEQ ID NO:53.
1D. Vector Construction
This example illustrates the construction of vectors carrying a multi-antigen construct. Vectors carrying the same triple-antigen construct (open reading frame) as that carried by each of plasmids 1424, 1425, 1426, 1427, 1428, and 1429 were constructed from chimpanzee adenovirus AdC68 genomic sequences as described in international patent application publication WO2015/063647. These vectors are referred to as AdC68Y-1424, AdC68Y-1425, AdC68Y-1426, AdC68Y-1427, AdC68Y-1428, and AdC68Y-1429, respectively. The organizations of these vectors are provided in
The full length genomic sequence of AdC68 is available from Genbank having Accession Number AC_000011.1 and is also provided in WO2015/063647. The AdC68 backbone without transgenes (the “empty vector”) was designed in silico with E1 and E3 deletions engineered into the virus to render it replication incompetent and create space for transgene insertion. Vector AdC68Y, having deletions of bases 456-3256 and 27476-31831, was engineered to have improved growth properties over previous AdC68 vectors. The empty vector was biochemically synthesized in a multi-stage process utilizing in vitro oligo synthesis and subsequent recombination-mediated intermediate assembly as artificial chromosomes in Escherichia coli (E. coli) and/or yeast. Open reading frames encoding the various immunogenic TAA polypeptides were amplified by PCR from plasmids 1424, 1425, 1426, 1427, 1428, and 1429 using primer sets Muc1-20 bp-F-98/mCEA-20 bp-R-100, Y-mCEA-S2/Y-Tert-A2, Y-Tert-S/Y-CEA-A, Y-Tert-S/Y-MUC-A, Y-MUC-S2/Y-Tert-A2, and cCEA-20 bp-F-106/Muck 20BP-R-108, respectively. The amplicons were then inserted into the empty vector backbone. Recombinant viral genomes were released from the bacterial artificial chromosomes by digestion with Pacl and the linearized nucleic acids were transfected into an E1 complimenting adherent HEK293 cell line. Upon visible cytopathic effects and adenovirus foci formation, cultures were harvested by multiple rounds of freezing/thawing to release virus from the cells. Viruses were amplified and purified by standard techniques.
Study in HLA-A2/DR1 Mice
Study Design.
Twelve mixed gender HLA-A2/DR1 mice were primed on day 0 and boosted on day 14 with DNA construct Plasmid 1027 (which encodes the membrane-bound immunogenic MUC1 polypeptide of SEQ ID NO:5) or Plasmid 1197 (which encodes the cytosolic immunogenic MUC1 polypeptide of SEQ ID NO:7) using the PMED method. On day 21, mice were sacrificed and splenocytes assessed for MUC1-specific cellular immunogenicity in an interferon-gamma (IFN-γ) ELISpot and intracellular cytokine staining (ICS) assay.
Particle Mediated Epidermal Delivery (PMED).
PMED is a needle-free method of administering vaccines to animals or to patients. The PMED system involves the precipitation of DNA onto microscopic gold particles that are then propelled by helium gas into the epidermis. The ND10, a single use device, uses pressurized helium from an internal cylinder to deliver gold particles and the X15, a repeater delivery device, uses an external helium tank which is connected to the X15 via high pressure hose to deliver the gold particles. Both of these devices were used in studies to deliver the MUC1 DNA plasmids. The gold particle was usually 1-3 μm in diameter and the particles were formulated to contain 2 μg of antigen DNA plasmids per 1 mg of gold particles. (Sharpe, M. et al.: P. Protection of mice from H5N1 influenza challenge by prophylactic DNA vaccination using particle mediated epidermal delivery. Vaccine, 2007, 25(34): 6392-98: Roberts L K, et al.: Clinical safety and efficacy of a powdered Hepatitis B nucleic acid vaccine delivered to the epidermis by a commercial prototype device. Vaccine, 2005; 23(40):4867-78).
IFN-γ ELISpot Assay.
Splenocytes from individual animals were co-incubated in triplicate with individual Ag-specific peptides (each peptide at 2-10 ug/ml, 2.5-5e5 cells per well) or pools of 15mer Ag-specific peptides (overlapping by 11 amino acids, covering the entire Ag-specific amino acid sequence; see Table 15; each peptide at 2-5 ug/ml, 1.25-5e5 cells per well) in IFN-γ ELISpot plates. The plates were incubated for ˜16 hours at 37° C., 5% CO2, then washed and developed, as per manufacturer's instruction. The number of IFN-γ spot forming cells (SFC) was counted with a CTL reader. The average of the triplicates was calculated and the response of the negative control wells, which contained no peptides, subtracted. The SFC counts were then normalized to describe the response per 1e6 splenocytes. The antigen-specific responses in the tables represent the sum of the responses to the Ag-specific peptides or peptide pools.
ICS Assay.
Splenocytes from individual animals were co-incubated with H-2b-, HLA-A2-, or HLA-A24-restricted Ag-specific peptides (each peptide at 5-10 ug/ml, 1-2e6 splenocytes per well) or pools of 15mer Ag-specific peptides (overlapping by 11 amino acids, covering the entire Ag-specific amino acid sequence; see Table 15; each peptide at 2-5 ug/ml, 1-2e6 splenocytes per well) in U-bottom 96-well-plate tissue culture plates. The plates were incubated ˜16 hrs at 37° C., 5% CO2. The cells were then stained to detect intracellular IFN-γ expression from CD8+ T cells and fixed. Cells were acquired on a flow cytometer. The data was presented per animal as frequency of peptide(s) Ag- or peptide pool Ag-specific IFN-γ+ CD8+ T cells after subtraction of the responses obtained in the negative control wells, which contained no peptide.
Sandwich ELISA Assay.
The standard sandwich ELISA assay was done using the Tecan Evo, Biomek FxP, and BioTek 405 Select TS automation instruments. The 384 well microplates (flat-well, high binding) were coated at 25 μl/well with 1.0 μg/mL human MUC1 or human CEA protein (antigen) in 1×PBS, and incubated overnight at 4° C. The next morning, plates were blocked for one hour at RT with 5% FBS in PBS with 0.05% Tween 20 (PBS-T). Mouse serum was prepared at a 1/100 starting dilution in PBS-T in 96 U-bottom well plates. The Tecan Evo performed ½ log serial dilutions in PBS-T over 9 dilution increment points, followed by stamping of 25 μl/well of diluted serum from the 96 well plates to 384 well plates. The 384 well plates were incubated for 1 hour at RT on a shaker at 600 RPM, then, using the BioTek EL 405 Select TS plate washer, the plates were washed 4 times in PBS-T. Secondary mouse anti-IgG-HRP antibody was diluted to an appropriate dilution and stamped by Biomek FxP at 25 μl/well into 384 well plates, and incubated for 1 hour at RT on a shaker at 600 RPM, followed by 5 repeated washes. Using the Biomek FxP, plates were stamped at 25 μl/well of RT TMB substrate and incubated in the dark at RT for 30 minutes, followed by 25 μl/well stamping of 1N H2SO4 acid to stop the enzymatic reaction. Plates were read on the Molecular Devices, Spectramax 340PC/384 Plus at 450 nm wavelength. Data were reported as calculated titers at OD of 1.0 with a limit of detection of 99.0. The antigen-specific commercial monoclonal antibody was used in each plate as a positive control to track plate-to-plate variation performance; irrelevant vaccinated mouse serum was used as a negative control, and PBS-T only wells were used to monitor non-specific binding background. Titers in the tables represent antigen-specific IgG titers elicited from individual animals.
Results.
Table 1 shows ELISpot and ICS data from HLA-A2/DR1 splenocytes cultured with peptide pools derived from the MUC1 peptide library (see Table 15) or MUC1 peptide aa516-530, respectively. Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with MUC1 peptide pools, and background subtraction. Numbers in column 4 represent the frequency of CD8+ T cells being IFN-γ+ after restimulation with MUC1 peptide aa516-530 and background subtraction. A positive response is defined as having SFC>100 and a frequency of IFN-γ+ CD8+ T cells>0.1%. As shown in Table 1, the immunogenic MUC1 polypeptides made with the full-length membrane-bound (Plasmid 1027) and cytosolic (Plasmid 1197) MUC1 constructs were capable of inducing MUC1-specific T cell responses including HLA-A2-restricted MUC1 peptide aa516-530-specific CD8+ T cell responses. The cytosolic MUC1 antigen format induced the highest magnitude of T cell responses. Importantly, T cell responses derived from cancer patients against the MUC1 peptide aa516-530 have been shown to correlate with anti-tumor efficacy in vitro (Jochems C et al., Cancer Immunol Immunother (2014) 63:161-174) demonstrating the importance of raising cellular responses against this specific epitope.
Study in HLA-A24 Mice
Study design. Mixed gender HLA-A24 mice were primed on day 0 and boosted on days 14, 28 and 42 with DNA construct Plasmid 1027 by PMED administration. On day 21, mice were sacrificed and splenocytes assessed for MUC1-specific cellular immunogenicity (ELISpot).
Results.
Table 2 shows ELISpot data from HLA-A24 splenocytes cultured with peptide pools derived from the MUC1 peptide library (see Table 15). Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with MUC1 peptide pools and background subtraction. The number in bold font indicates that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. A positive response is defined as having SFC>100. As shown in Table 2, membrane-bound MUC1 construct was capable of inducing MUC1-specific cellular responses.
6207
Study in Monkeys
Study Design.
14 Chinese-sourced cynomolgus macaques were primed with an adenovirus vector AdC68W encoding the cytosolic MUC1 polypeptide (same polypeptide as encoded by Plasmid 1197) or full-length membrane-bound MUC1 polypeptide (same polypeptide as encoded by Plasmid 1027) at 2e11 viral particles by bilateral intramuscular injection (1 mL total). 29 days later, animals were boosted with Plasmid 1197 or Plasmid 1027 delivered intramuscularly bilaterally via electroporation (2 mL total). Anti-CTLA-4 was administered subcutaneously on days 1 (32 mg) and 29 (50 mg). 14 days after the last immunization, animals were bled and PBMCs and sera isolated to assess MUC1-specific cellular (ELISpot, ICS) and humoral (ELISA) responses, respectively. The adenovirus vector AdC68W used in this and other examples of the present disclosure was constructed from the chimpanzee adenovirus AdC68 according to the method described in international patent application WO2015/063647. NHP-specific immune assays.
EL/Spot Assay.
PBMCs from individual animals were co-incubated in duplicate with pools of 15mer Ag-specific peptides (overlapping by 11 amino acids, covering the entire Ag-specific amino acid sequence), each peptide at 2 ug/ml, 4e5 cells per well, in IFN-γ ELISpot plates (see Table 15). The plates were incubated for ˜16 hrs at 37° C., 5% CO2, then washed and developed, as per manufacturers instruction. The number of IFN-γ spot forming cells (SFC) was counted with a CTL reader. The average of the duplicates was calculated and the response of the negative control wells, which contained no peptides, subtracted. The SFC counts were then normalized to describe the response per 1e6 PBMCs. The antigen-specific responses in the tables represent the sum of the responses to the Ag-specific peptide pools.
ICS Assay.
PBMCs from individual animals were co-incubated with pools of 15mer MUC1 peptides (overlapping by 11 amino acids, covering the entire native full-length MUC1 amino acid sequence; see Table 15), each peptide at 2 ug/mL, 1.5-2e6 PBMCs per well, in U-bottom 96-well-plate tissue culture plates. The plates were incubated for ˜16 hours at 37° C., 5% CO2, and then stained to detect intracellular IFN-γ expression from CD8 T cells. After fixation, the cells were acquired on a flow cytometer. The results are presented per individual animal as number of MUC1, CEA, or TERT-specific IFN-γ+ CD8+ T cells after subtraction of the responses obtained in the negative control wells, which contained no peptide, and normalized to 1e6 CD8+ T cells.
Sandwich ELISA Assay.
The standard sandwich ELISA assay was done using the Tecan Evo, Biomek FxP, and BioTek 405 Select TS automation instruments. The 384 well microplates (flat-well, high binding) were coated at 25 μl/well with 1.0 μg/mL human MUC1 or human CEA protein (antigen) in 1×PBS, and incubated overnight at 4° C. The next morning, plates were blocked for one hour at RT with 5% FBS in PBS with 0.05% Tween 20 (PBS-T). Sera from Chinese-sourced cynomolgus macaques were prepared at a 1/100 starting dilution in PBS-T in 96 U-bottom well plates. The Tecan Evo performed ½ log serial dilutions in PBS-T over 9 dilution increment points, followed by stamping of 25 μl/well of diluted serum from the 96 well plates to 384 well plates. The 384 well plates were incubated for 1 hour at RT on a shaker at 600 RPM, then, using the BioTek EL 405 Select TS plate washer, the plates were washed 4 times in PBS-T. Secondary rhesus anti-IgG-HRP antibody, which cross-reacts with cynomolgus IgG, was diluted to an appropriate dilution and stamped by Biomek FxP at 25 μl/well into 384 well plates, and incubated for 1 hour at RT on a shaker at 600 RPM, followed by 5 repeated washes. Using the Biomek FxP, plates were stamped at 25 μl/well of RT TMB substrate and incubated in the dark at RT for 30 minutes, followed by 25 μl/well stamping of 1N H2SO4 acid to stop the enzymatic reaction. Plates were read on the Molecular Devices, Spectramax 340PC/384 Plus at 450 nm wavelength. Data were reported as calculated titers at OD of 1.0 with a limit of detection of 99.0. The antigen-specific commercial monoclonal antibody was used in each plate as a positive control to track plate-to-plate variation performance; irrelevant vaccinated mouse serum was used as a negative control, and PBS-T only wells were used to monitor non-specific binding background. Titers in the tables represent antigen-specific IgG titers elicited from individual animals.
Results.
Table 3 shows the ELISpot and ICS data from Chinese-sourced cynomolgus macaque PBMCs cultured with peptide pools derived from the MUC1 peptide library (Table 15), and the ELISA data from Chinese-sourced cynomolgus macaque sera. Numbers in column 3 represent # IFN-γ spots/106 PBMCs after restimulation with MUC1 peptide pools and background subtraction. Numbers in column 4 represent # IFN-γ+ CD8+ T cells/106 CD8+ T cells after restimulation with MUC1 peptide pools and background subtraction. Numbers in column 5 represent the anti-MUC1 IgG titer (Optical Density (O.D)=1, Limit of Detection (L.O.D)=99.0). A positive response is defined as having SFC>50, IFN-γ+ CD8+ T cells/1e6 CD8+ T cells>50, and IgG titers>99. As shown in Table 3, the immunogenic MUC1 polypeptides made with the cytosolic (Plasmid 1197) and native full-length membrane-bound (Plasmid 1027) MUC1 constructs were capable of inducing MUC1-specific T and B cell responses. The native full-length membrane-bound MUC1 construct (Plasmid 1027) was shown to induce the overall best MUC1-specific cellular and humoral response.
Immune Response Study in Pasteur (HLA-A2/DR 1) Mice
Study Design.
Mixed gender HLA-A2/DR1 mice were primed on day 0 and boosted on day 14 with a plasmid carrying a single-antigen construct encoding the human membrane-bound (Plasmid 1386) or cytosolic CEA polypeptide (Plasmid 1390) by electroporation. The antigen-specific T cell response was measured seven days later in an IFN-γ ELISpot and ICS assay.
Results.
Table 4 shows ELISpot and ICS data from HLA-A2/DR1 splenocytes cultured with peptide pools derived from the CEA peptide library composed of aa1-699 for mice immunized with construct 1386, and aa37-679 (removal of signal sequence and GPI sequence) for mice immunized with Plasmid 1390 (see also Table 15). Numbers in columns 3 and 4 represent # IFN-γ+ spots/1e6 splenocytes and the frequency of IFN-γ+ CD8+ T cells respectively, elicited after restimulation with relevant CEA peptides pools and background subtraction Table 5 shows ELISpot data from HLA-A2/DR1 splenocytes cultured with the CEA peptide aa693-701. A positive response is defined as having SFC>100 and a frequency of IFN-γ+ CD8+ T cells>0.1%. As shown in Table 4, the immunogenic CEA polypeptides made with the membrane-bound (Plasmid 1386) and cytosolic (Plasmid 1390) CEA constructs described in Example 1A above were capable of inducing CEA-specific T cell responses. Comparable magnitudes of CEA-specific T cell responses were induced by both membrane-bound and cytosolic CEA antigen formats. As shown in Table 5, immunization with the membrane-bound construct 1386 induced an HLA-A2 restricted T cell response against CEA peptide aa693-701, which has been shown in the literature to be processed and presented by HLA-A2 (Conforti A et al., J Immunother (2009) 32:744-754).
Immune Response Study in HLA A24 Mice
Study Designs.
Sixteen mixed-gender HLA-A24 mice were primed on day 0 and boosted on day 14 with human membrane-bound (Plasmid 1386) or cytosolic CEA (Plasmid 1390) DNA constructs via DNA electroporation. CEA-specific T cell responses were measured 7 days after the last immunization in an IFN-γ ELISpot and ICS assay.
Results.
Table 6 shows ELISpot and ICS data from HLA-A24 splenocytes cultured with peptide pools derived from the CEA peptide library (see also Table 15). Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with CEA peptide pools encompassing aa1-699 and background subtraction. Numbers in column 4 represent the frequency of CD8+ T cells being IFN-γ+ after restimulation with CEA peptide pools encompassing aa37-679, and background subtraction. A positive response is defined as having SFC>100 and a frequency of IFN-γ+ CD8+ T cells>0.1%. The number in bold font indicates that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. As shown in Table 6, the immunogenic CEA polypeptides made with the membrane-bound (Plasmid 1386) and cytosolic CEA (Plasmid 1390) constructs were capable of inducing comparable CEA-specific cellular responses as measured via ELISpot. Vaccination with the cytosolic CEA construct (Plasmid 1390), however, induced higher CEA-specific IFN-γ+ CD8+ T cell responses measured via ICS.
3723
3081
3031
Immune Responses Study in HLA-A2/DR1 Mice
Study Design.
Six mixed gender HLA-A2/DR1 mice were primed with an AdC68W adenovirus vector encoding the truncated (Δ240) cytosolic immunogenic TERT polypeptide (Plasmid 1112) at 1e10 viral particles by intramuscular injection (50 ul). 28 days later, animals were boosted intramuscularly with 50 ug DNA delivered bilaterally via electroporation (2×20 ul) encoding the truncated (Δ240) cytosolic TERT antigen (Plasmid 1112). The antigen-specific T cell response was measured seven days later in an IFN-γ ELISpot and ICS assay.
Results.
Table 7 shows ELISpot and ICS data from HLA-A2/DR1 splenocytes cultured with peptide pools derived from the TERT peptide library (see also Table 15) or TERT peptide aa861-875, respectively. Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with TERT peptide pools and background subtraction. Numbers in column 4 represent the frequency of CD8+ T cells being IFN-γ+ after restimulation with TERT peptide aa861-875 and background subtraction. A positive response is defined as having SFC>100 and a frequency of IFN-γ+ CD8+ T cells>0.1%. As shown in Table 7, the immunogenic TERT polypeptide made with the truncated (Δ240) cytosolic TERT construct was capable of inducing HLA-A2-restricted TERT-specific CD8 T cell responses.
Immune Responses Study in HLA-A24 Mice
Study Designs.
Eight mixed gender HLA-A24 mice were primed with an AdC68W adenovirus vector encoding the truncated (Δ240) cytosolic TERT polypeptide (same polypeptide as encoded by Plasmid 1112) at 1e10 viral particles total by bilateral intramuscular injection (50 ul into each tibialis anterior muscle). 14 days later, animals were boosted intramuscularly with 50 ug DNA (Plasmid 1112) delivered bilaterally via electroporation (2×20 ul) encoding the truncated (Δ240) cytosolic TERT polypeptide. The antigen-specific T cell response was measured seven days later in an IFN-γ ELISpot and ICS assay.
Results.
Table 8 shows IFN-γ ELISpot and ICS data from HLA-A24 splenocytes cultured with peptide pools derived from the TERT peptide library (see also Table 15) or TERT peptide aa841-855), respectively. Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with TERT peptide pools and background subtraction. Numbers in column 4 represent the frequency of CD8+ T cells being IFN-γ+ after restimulation with TERT peptides aa841-855, and background subtraction. Numbers in bold font indicate that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. A positive response is defined as having SFC>100 and a frequency of IFN-γ+ CD8+ T cells>0.1%. As shown in Table 8, the immunogenic TERT polypeptide made with the truncated (Δ240) cytosolic TERT (Plasmid 1112) construct is capable of inducing HLA-A24-restricted TERT-specific CD8+ T cell responses.
4233
3407
3213
Immune Responses Study in Monkeys
Study Design.
Eight Chinese-sourced cynomolgus macaques were primed with an AdC68W adenovirus vector encoding the truncated (A240) cytosolic TERT antigen (Plasmid 1112) at 2e11 viral particles by bilateral intramuscular injection (1 mL total). 30 and 64 days later, animals were boosted with DNA (Plasmid 1112) encoding truncated (Δ240) cytosolic TERT antigen delivered intramuscularly bilaterally via electroporation (2 mL total). Anti-CTLA-4 was administered subcutaneously on days 1 (32 mg), 31 (50 mg) and 65 (75 mg). 14 days after the last immunization, animals were bled and PBMCs isolated to assess TERT-specific cellular (ELISpot, ICS) responses.
Results.
Table 9 shows the ELISpot and ICS data from Chinese-sourced cynomolgus macaques' PBMCs cultured with peptide pools derived from the TERT peptide library (see also Table 15). Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with TERT peptide pools and background subtraction. Numbers in column 4 represent # IFN-γ+ CD8+ T cells/106 CD8+ T cells after restimulation with TERT peptide pools and background subtraction. A positive response is defined as having SFC>50 and IFN-γ+ CD8+ T cells/1e6 CD8+ T cells>50. As shown in Table 9, the immunogenic TERT polypeptide made with the truncated (A240) cytosolic (Plasmid 1112) TERT construct was capable of inducing TERT-specific T cell responses.
Immune Response Study in Monkeys
Study Design.
24 Chinese-sourced cynomolgus macaques were primed with dual-antigen adenoviral AdC68W vectors encoding human native full-length membrane-bound MUC1 (MUC1) and human truncated (Δ240) cytosolic TERT (TERTΔ240) polypeptides (Plasmids 1270, 1271, and 1269) at 2e11 viral particles by bilateral intramuscular injection (1 mL total). 30 and 64 days later, animals were boosted with dual-antigen DNA constructs (Plasmids 1270, 1271, and 1269) encoding the same two antigens delivered intramuscularly bilaterally via electroporation (2 mL total). Anti-CTLA-4 was administered subcutaneously on days 1 (32 mg), 31 (50 mg) and 65 (75 mg). 14 days after the last immunization, animals were bled and PBMCs and serum isolated to assess MUC1- and TERT-specific cellular (ELISpot, ICS) and MUC1-specific humoral (ELISA) responses, respectively. In total, three different dual-antigen vaccine constructs, which co-expressed both antigens, were evaluated: a) MUC1-2A-TERTΔ240 (Plasmid 1270), an AdC68W vector and DNA plasmid encoding MUC1 and TERT linked by a 2A peptide; b) TERTΔ240-2A-MUC1 (Plasmid 1271), an AdC68W vector and DNA plasmid encoding TERT and MUC1 linked by a 2A peptide; c) MUC1-TERTΔ240 (Plasmid 1269), an AdC68W vector and DNA plasmid encoding the MUC1-TERT fusion protein.
Results.
Table 10 shows the ELISpot and ICS data from Chinese-sourced cynomolgus macaque PBMCs cultured with peptide pools derived from the MUC1 and TERT peptide libraries (see also Table 15), and the ELISA data from Chinese-sourced cynomolgus macaque sera. A positive response is defined as having SFC>50, IFN-γ+ CD8+ T cells/1e6 CD8+ T cells>50, and IgG titers>99. Numbers in columns 3 and 6 represent # IFN-γ spots/106 splenocytes after restimulation with MUC1 and TERT peptide pools and background subtraction, respectively. Numbers in bold font indicate that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. Numbers in columns 4 and 7 represent # IFN-γ+ CD8+ T cells/106 CD8+ T cells after restimulation with MUC1 peptide pools and TERT peptide pools, respectively, and background subtraction. Numbers in column 5 represent the anti-MUC1 IgG titer (Optical Density (O.D)=1, Limit of Detection (L.O.D)=99.0). As shown in Table 10, the immunogenic MUC1 and TERT polypeptides made with the MUC1- and TERT-expressing dual-antigen constructs (Plasmids 1270, 1271, and 1269) were capable of inducing MUC1- and TERT-specific T cell responses, and MUC1-specific B cell responses. The dual-antigen construct 1269 encoding a MUC1-TERT fusion protein was shown to induce the strongest overall MUC1-specific cellular response; in contrast, dual-antigen construct Plasmid 1271 (TERT-2A-MUC1) was shown to induce the strongest overall TERT-specific cellular response. All three dual-antigen constructs were shown to induce a comparable MUC1-specific humoral response.
2937
2138
3794
2955
4402
2875
Example 6 illustrates the capability of plasmid and adenoviral vectors that carry a triple-antigen construct expressing the human native full-length membrane-bound MUC1 polypeptide (MUC1), human membrane-bound or cytosolic CEA polypeptide (mCEA or cCEA), and human truncated (Δ240) cytosolic TERT polypeptide (TERTΔ240) to elicit Ag-specific T and B cell responses to all three encoded cancer antigens.
Immune Response Study in C57BL/6J Mice Using DNA Electroporation
Study Design.
48 female C57BL/6J mice were immunized with triple-antigen DNA constructs encoding human MUC1, mCEA or cCEA, and TERTΔ240. The triple-antigen DNA vaccine (50 ug) was delivered intramuscularly bilaterally (20 ul total into each tibialis anterior muscle) with concomitant electroporation in a prime/boost regimen, two weeks apart between each vaccination. MUC1-, CEA-, and TERT-specific cellular responses, and MUC1- and CEA-specific humoral responses were measured 7 days after the last immunization in an IFN-γ ELISpot assay and ELISA assay, respectively. In total, six different plasmids carrying triple-antigen DNA constructs each encoding three TAA polypeptides linked by 2A peptides were used as follows: MUC1-2A-TERTΔ240-2A-mCEA (Plasmid 1424), mCEA-2A-MUC1-2A-TERTΔ240 (Plasmid 1425), TERTΔ240-2A-MUC1-2A-mCEA (Plasmid 1426), TERTΔ240-2A-mCEA-2A-MUC1 (Plasmid 1427), MUC1-2A-cCEA-2A-TERTΔ240 (Plasmid 1428), cCEA-2A-TERTΔ240-2A-MUC1 (Plasmid 1429).
Results.
Tables 11A-C show the ELISpot data from C57BL/6J splenocytes cultured with peptide pools derived from the MUC1, CEA, and TERT peptide libraries (see also Table 15), the ICS data from C57BL/6J splenocytes cultured with TERT peptide aa1025-1039, and the ELISA data from C57BL/6J mouse sera. A positive response is defined as having SFC>100, a frequency of IFN-γ+ CD8+ T cells>0.1%, and IgG titers>99. Numbers in column 3 of Tables 11A-C represent # IFN-γ spots/106 splenocytes after restimulation with MUC1, CEA, or TERT peptide pools and background subtraction, respectively. Numbers in bold font indicate that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. Numbers in column 4 of Tables 11A-B represent the anti-MUC1 and CEA IgG titer, respectively (Optical Density (O.D)=1, Limit of Detection (L.O.D)=99.0). Numbers in column 4 of Table 110 represent the frequency of CD8+ T cells being IFN-γ+ after restimulation with TERT-specific peptide TERT aa1025-1039, and background subtraction. As shown in Tables 11A-C, the immunogenic MUC1, CEA, and TERT polypeptides made with the MUC1-, CEA-, and TERT-expressing triple-antigen constructs were capable of inducing T cell responses against all three antigens, and B cell responses against MUC1. In contrast, while mCEA containing triple-antigen constructs (Plasmids 1424-1427) were capable of inducing B cell responses against CEA, cCEA containing triple-antigen constructs (Plasmids 1428-1429) induced either weaker or no CEA-specific B cell responses.
4739
4469
4142
Immune Response Study in C57BL/6J Mice Using Adenoviral Vectors
Study Design.
48 female C57BL/6J mice were primed with triple-antigen adenoviral vectors encoding human MUC1, mCEA or cCEA, and TERTΔ240, at 1e10 viral particles by intramuscular injection (50 ul into each tibialis anterior muscle). 14 days later, animals were boosted with triple-antigen DNA constructs (50 ug) delivered intramuscularly bilaterally (20 ul into each tibialis anterior muscle) with concomitant electroporation. MUC1-, CEA-, and TERT-specific cellular responses, and MUC1- and CEA-specific humoral responses were measured 7 days after the last immunization in an IFN-γ ELISpot and ICS assay, and an ELISA assay, respectively. In total, six triple-antigen adenoviral and DNA constructs encoding MUC1, mCEA or cCEA, and TERTΔ240 linked by 2A peptides were used as follows: MUC1-2A-TERTΔ240-2A-mCEA (Plasmid 1424), mCEA-2A-MUC1-2A-TERTΔ240 (Plasmid 1425), TERTΔ240-2A-MUC1-2A-mCEA (Plasmid 1426), TERTΔ240-2A-mCEA-2A-MUC1 (Plasmid 1427), MUC1-2A-cCEA-2A-TERTΔ240 (Plasmid 1428), cCEA-2A-TERTΔ240-2A-MUC1 (Plasmid 1429).
Results.
Tables 12A-C shows the ELISpot data from C57BL/6J splenocytes cultured with peptide pools derived from the MUC1, CEA, and TERT peptide libraries (see also Table 15), the ICS data from C57BL/6J splenocytes cultured with TERT peptide aa1025-1039, and the ELISA data from C57BL/6J mouse sera. A positive response is defined as having SFC>100, a frequency of IFN-γ+ CD8+ T cells>0.1%, and IgG titers>99. Numbers in column 3 in Tables 12A-C represent # IFN-γ spots/106 splenocytes after restimulation with MUC1, CEA, or TERT peptide pools, and background subtraction, respectively. Numbers in bold font indicate that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. Numbers in column 4 in Table 12C represent # IFN-γ+ CD8+ T cells/106 CD8+ T cells after restimulation with TERT-specific peptide TERT aa1025-1039, and background subtraction. Numbers in column 4 in Tables 12A-B represent the anti-MUC1 and anti-CEA IgG titer, respectively (Optical Density (O.D)=1, Limit of Detection (L.O.D)=99.0). As shown in Tables 12A-C, the immunogenic MUC1, CEA, and TERT polypeptides made with MUC1-, CEA-, and TERT-expressing triple-antigen constructs were capable of inducing T cell responses against all three antigens, and B cell responses against MUC1. In contrast, while mCEA containing triple-antigen constructs (Plasmids 1424-1427) were capable of inducing B cell responses against CEA, cCEA containing triple-antigen constructs (Plasmids 1428-1429) induced either weaker or no CEA-specific B cell responses.
4556
4184
4530
4406
5134
4199
4088
5060
4251
Immune Response Study in HLA-A24 Mice
Study Design.
Sixteen mixed gender HLA-A24 mice were primed with an adenoviral AdC68Y triple-antigen construct (Plasmid 1426: TERTΔ240-2A-MUC1-2A-mCEA or Plasmid 1428: MUC1-2A-cCEA-2A-TERTΔ240) encoding human MUC1, mCEA or cCEA, and TERTΔ240 at 1e10 viral particles by intramuscular injection (50 ul into each tibialis anterior muscle). 14 days later, animals were boosted intramuscularly with 50 ug triple-antigen DNA construct (Plasmid 1426 or 1428) encoding the same three antigens (20 ul delivered into each tibialis anterior muscle with concomitant electroporation). HLA-A24-restricted MUC1-specific cellular responses were measured 7 days after the last immunization in an IFN-γ ELISpot assay.
Results.
Table 13 shows the ELISpot data from HLA-A24 splenocytes cultured with the MUC1 peptide aa524-532. A positive response is defined as having SFC>50. Numbers in column 3 represent # IFN-γ spots/106 splenocytes after restimulation with MUC1 peptide aa524-532 and background subtraction. As shown in Table 13, the immunogenic MUC1 polypeptides made with the MUC1-, CEA-, and TERT-expressing triple-antigen constructs 1426 and 1428 were capable of inducing HLA-A24-restricted MUC1 peptide aa524-532-specific CD8+ T cell responses. Importantly, T cell responses derived from cancer patients against this specific MUC1 peptide have been shown to correlate with anti-tumor efficacy in vitro (Jochems C et al., Cancer Immunol Immunother (2014) 63:161-174) demonstrating the importance of raising cellular responses against this specific epitope.
Immune Response Study in Monkeys
Study Design.
42 Chinese-sourced cynomolgus macaques were primed on day 1 with AdC68Y adenoviral vectors encoding human native full-length membrane-bound MUC1 (MUC1), human membrane-bound or cytoplasmic CEA (mCEA or cCEA), and human truncated (Δ240) cytosolic TERT (TERTΔ240 antigens at 2e11 viral particles by bilateral intramuscular injection (1 mL total). On day 30 and day 57 animals were boosted with DNA encoding the same three antigens delivered intramuscularly bilaterally via electroporation (2 mL total). Anti-CTLA-4 was administered subcutaneously on days 1 (32 mg), 30 (50 mg) and 57 (75 mg). 15 days after the last immunization, animals were bled and PBMCs and serum isolated to assess MUC1-, CEA-, and TERT-specific cellular (ELISpot, ICS) and MUC1- and CEA-specific humoral (ELISA) responses, respectively. In total, six triple-antigen adenoviral and DNA constructs encoding MUC1, mCEA or cCEA, and TERTΔ240 linked by 2A peptides were evaluated: MUC1-2A-TERTΔ240-2A-mCEA (Plasmid 1424), mCEA-2A-MUC1-2A-TERTΔ240 (Plasmid 1425), TERTΔ240-2A-MUC1-2A-mCEA (Plasmid 1426), TERTΔ240-2A-mCEA-2A-MUC1 (Plasmid 1427), MUC1-2A-cCEA-2A-TERTΔ240 (Plasmid 1428), cCEA-2A-TERTΔ240-2A-MUC1 (Plasmid 1429).
Results.
Tables 14A, 14B, and 14C show the ELISpot and ICS data from Chinese-sourced cynomolgus macaque PBMCs cultured with peptide pools derived from the MUC1, CEA, and TERT peptide libraries (see also Table 15), and the ELISA data from Chinese-sourced cynomolgus macaque sera. A positive response is defined as having SFC>50, IFN-γ+ CD8+ T cells/1e6 CD8+ T cells>50, and IgG titers>99. Numbers in column 3 in Tables 14A-C represent # IFN-γ spots/106 splenocytes after restimulation with MUC1, CEA, or TERT peptide pools, and background subtraction, respectively. Numbers in bold font indicate that at least 1 peptide pool tested was too numerous to count, therefore the true figure is at least the value stated. Numbers in column 4 in Tables 14A-C represent # IFN-γ+ CD8+ T cells/106 CD8+ T cells after restimulation with MUC1, CEA, or TERT peptide pools, respectively, and background subtraction. Numbers in column 5 in Tables 14A-B represent the anti-MUC1 and anti-CEA IgG titer (Optical Density (O.D)=1, Limit of Detection (L.O.D)=99.0), respectively. As shown in Tables 14A-C, the immunogenic MUC1, CEA, and TERT polypeptides made with MUC1-, CEA-, and TERT-expressing triple-Ag constructs were capable of inducing cellular responses against all three antigens, and humoral responses against MUC1. However, triple-antigen constructs containing mCEA induced greater CEA-specific B cell responses than those containing cCEA.
2065
1808
2957
2082
Drosophilia C (DrosC)
T. brucei TSR1
T. cruzi AP endonuclease
This application claims the benefit of U.S. Provisional Application No. 62/531,227 filed on Jul. 11, 2017 and U.S. Provisional Application No. 62/682,044 filed on Jun. 7, 2018. The entire content of each of the forgoing applications is incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 62531227 | Jul 2017 | US | |
| 62682044 | Jun 2018 | US |
