# Patent

## Title
Combination of a PD-1 antagonist and a listeria-based vaccine for treating prostate cancer

## Abstract

The present disclosure describes combination therapies comprising an antagonist of Programmed Death 1 receptor (PD-1) and a Listeria based strain that expresses prostate-tissue specific antigen (PSA), and the use of the combination therapies for the treatment of prostate cancer.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Patent Application No. 62/026,221, filed Jul. 18, 2014 and U.S. Provisional Patent Application No. 62/039,011, filed Aug. 19, 2014, both of which are incorporated in their entirety herein by reference.


FIELD OF THE INVENTION
The present invention relates to combination therapies useful for the treatment of cancer. In particular, the invention relates to the treatment of prostate cancer using an antagonist of a Programmed Death 1 protein (PD-1) in combination with a live attenuated recombinant Listeria strain comprising a fusion protein of a PEST sequence-containing polypeptide or PEST-sequence containing peptide fused to a tumor-associated antigen.
BACKGROUND OF THE INVENTION
PD-1 is recognized as an important player in immune regulation and the maintenance of peripheral tolerance. PD-1 is moderately expressed on naive T, B and NKT cells and up-regulated by T/B cell receptor signaling on lymphocytes, monocytes and myeloid cells (1).
Two known ligands for PD-1, PD-L1 (B7-H1) and PD-L2 (B7-DC), are expressed in human cancers arising in various tissues. In large sample sets of e.g. ovarian, renal, colorectal, pancreatic, liver cancers and melanoma, it was shown that PD-L1 expression correlated with poor prognosis and reduced overall survival irrespective of subsequent treatment (2-13). Similarly, PD-1 expression on tumor infiltrating lymphocytes was found to mark dysfunctional T cells in breast cancer and melanoma (14-15) and to correlate with poor prognosis in renal cancer (16). Thus, it has been proposed that PD-L1 expressing tumor cells interact with PD-1 expressing T cells to attenuate T cell activation and evasion of immune surveillance, thereby contributing to an impaired immune response against the tumor.
Several monoclonal antibodies that inhibit the interaction between PD-1 and one or both of its ligands PD-L1 and PD-L2 are in clinical development for treating cancer. It has been proposed that the efficacy of such antibodies might be enhanced if administered in combination with other approved or experimental cancer therapies, e.g., radiation, surgery, chemotherapeutic agents, targeted therapies, agents that inhibit other signaling pathways that are disregulated in tumors, and other immune enhancing agents.
Listeria monocytogenes (Lm) is a Gram-positive facultative intracellular pathogen that causes listeriolysis. Once invading a host cell, Lm can escape from the phagolysosome through production of a pore-forming protein listeriolysin O (LLO) to lyse the vascular membrane, allowing it to enter the cytoplasm, where it replicates and spreads to adjacent cells based on the mobility of actin-polymerizing protein (ActA). In the cytoplasm, Lm-secreting proteins are degraded by the proteasome and processed into peptides that associate with MHC class I molecules in the endoplasmic reticulum.
SUMMARY OF THE INVENTION
In one embodiment, the invention provides a method for treating a prostate cancer in a human individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to Prostate Specific Antigen (PSA) expressing cells.
In another embodiment, the invention provides a method for treating a prostate cancer in a human individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO).
In yet another embodiment, the invention provides a method for treating a prostate cancer in a human individual comprising administering to the individual a combination therapy, which comprises a PD-1 antagonist and an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain.
In a further embodiment, the invention provides a method for treating a prostate cancer in a human individual comprising administering to the individual a combination therapy, which comprises a PD-1 antagonist and an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain.
In another embodiment, the invention provides a medicament comprising a PD-1 antagonist for use in combination with a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells, for treating a prostate cancer in a patient.
In yet another embodiment, the invention provides a medicament comprising a PD-1 antagonist for use in combination with a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO), for treating a prostate cancer in a patient.
In still another embodiment, the invention provides a medicament comprising a PD-1 antagonist for use in combination with an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain, for treating a prostate cancer in a patient. In a further embodiment, the invention provides a medicament comprising a PD-1 antagonist for use in combination with an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, for treating a prostate cancer in a patient.
In yet another embodiment, the invention provides a medicament comprising a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells for use in combination with a PD-1 antagonist for treating a prostate cancer in a patient.
In yet another embodiment, the invention provides a medicament comprising a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) for use in combination with a PD-1 antagonist for treating a prostate cancer in a patient.
In another embodiment, the invention provides a medicament comprising an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain for use in combination with a PD-1 antagonist for treating a prostate cancer in a patient.
In yet embodiment, the invention provides a medicament comprising an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain for use in combination with a PD-1 antagonist for treating a prostate cancer in a patient.
Other embodiments provide for use of a PD-1 antagonist in the manufacture of medicament for treating a prostate cancer in a human when administered in combination with a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells and use of a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells in the manufacture of a medicament for treating a prostate cancer in a patient when administered in combination with a PD-1 antagonist.
Other embodiments provide for use of a PD-1 antagonist in the manufacture of a medicament for treating a prostate cancer in a human when administered in combination with a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) and use of a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) in the manufacture of a medicament for treating a prostate cancer in a patient when administered in combination with a PD-1 antagonist.
Other embodiments provide for use of a PD-1 antagonist in the manufacture of medicament for treating a prostate cancer in a human when administered in combination with an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain and use of an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain in the manufacture of a medicament for treating a prostate cancer in a patient when administered in combination with a PD-1 antagonist.
Other embodiments provide for use of a PD-1 antagonist in the manufacture of medicament for treating a prostate cancer in a human when administered in combination with an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain and use of an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain in the manufacture of a medicament for treating a prostate cancer in a patient when administered in combination with a PD-1 antagonist.
In a still further embodiment, the invention provides for use of a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA-expressing cells in the manufacture of medicaments for treating a prostate cancer in a patient. In some embodiments, the medicaments comprise a kit, and the kit also comprises a package insert comprising instructions for using the PD-1 antagonist in combination with an a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells to treat a prostate cancer in a patient.
In another embodiment, the invention provides for use of a PD-1 antagonist and a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) in the manufacture of medicaments for treating a prostate cancer in a patient. In some embodiments, the medicaments comprise a kit, and the kit also comprises a package insert comprising instructions for using the PD-1 antagonist in combination with a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) to treat a prostate cancer in a patient.
In yet another embodiment, the invention provides for use of a PD-1 antagonist and an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain in the manufacture of medicaments for treating a prostate cancer in a patient. In some embodiments, the medicaments comprise a kit, and the kit also comprises a package insert comprising instructions for using the PD-1 antagonist in combination with an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain to treat a prostate cancer in a patient.
In still another embodiment, the invention provides for use of a PD-1 antagonist and an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain in the manufacture of medicaments for treating a prostate cancer in a patient. In some embodiments, the medicaments comprise a kit, and the kit also comprises a package insert comprising instructions for using the PD-1 antagonist in combination with an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain to treat a prostate cancer in a patient.
In all of the above treatment method, medicaments and uses, the PD-1 antagonist inhibits the binding of PD-L1 to PD-1, and preferably also inhibits the binding of PD-L2 to PD-1. In some embodiments of the above treatment method, medicaments and uses, the PD-1 antagonist is a monoclonal antibody, or antigen binding fragment thereof, which specifically binds to PD-1 or to PD-L1 and blocks the binding of PD-L1 to PD-1. In one embodiment, the PD-1 antagonist is an anti-PD-1 antibody which comprises a heavy chain and a light chain, and wherein the heavy and light chains comprise the amino acid sequences shown in FIG. 6 (SEQ ID NO:21 and SEQ ID NO:22).
In all of the above embodiments of the treatment method, medicaments and uses, the live-attenuated bacterial strain comprises a recombinant Listeria that is an attenuated auxotrophic strain. In one embodiment, the attenuated strain is Lm dal(−)dat(−) (Lmdd). In another embodiment, the attenuated strains is Lm dal(−)dat(−)ΔactA (LmddA). LmddA is based on a Listeria strain vector which is attenuated due to the deletion of virulence gene actA and retains a plasmid for expression of a trunctated LLO (tLLO) fused to a PSA antigen polypeptide in vivo and in vitro by complementation of dal gene. In some embodiments, the klk3 gene is fused to the hly gene in the chromosome for expression of a tLLO-PSA fusion polypeptide. In some of the above embodiments of the treatment method, medicaments and uses, the Listeria strain is a Listeria monocytogenes. In some of the above embodiments of the treatment method, medicaments and uses, the PSA antigen is fused to a truncated Listeriolysin O (tLLO). In one embodiment, the tLLO is an N-terminal LLO protein fragment. In one embodiment, the N-terminal LLO protein fragment and the PSA antigen are fused directly to one another. In another embodiment, the N-terminal LLO protein fragment and the PSA antigen are operably attached via a linker peptide. In another embodiment, the N-terminal LLO protein fragment and the PSA antigen are attached via a heterologous peptide. In another embodiment, the N-terminal LLO protein fragment is N-terminal to the PSA antigen. In another embodiment, the N-terminal LLO protein fragment is the N-terminal-most portion of the fusion protein. In another embodiment, a truncated LLO is truncated at the C-terminal to arrive at an N-terminal LLO. In all of the above embodiments of the treatment method, medicaments and uses, PSA is a kallikrein serine protease (KLK3) secreted by prostatic epithelial cells, which in one embodiment, is widely used as a marker for prostate cancer. In some embodiments, PSA is the full-length polypeptide. In other embodiment, PSA is a fraction of the full-length polypeptide. In one embodiment, a PSA antigen is encoded by the klk3 gene.
In some embodiments of the above treatment method, medicaments and uses, the live-attenuated bacterial strain is a dal(−) dat(−) actA(−) Listeria monocytogenes strain that episomally expresses the tLLO-PSA fusion protein. In one embodiment, the tLLO consists of about the first 441 AA of the LLO protein. In another embodiment, the LLO fragment is a non-hemolytic form of the LLO protein. In one embodiment, the PSA consists of a full-length protein. In another embodiment, the PSA consists of less than the full-length protein.
In some embodiments of the above treatment method, medicaments and uses of the invention, the prostate cancer is metastatic.
In other embodiments of the above treatment method, medicaments and uses of the invention, the prostate cancer is Castration-Resistant Prostate Cancer (mCRPC).
In still other embodiments of the above treatment method, medicaments and uses of the invention, the patient has been diagnosed with metastatic Castration-Resistant Prostate Cancer (mCRPC) following treatment with at least one previous therapeutic agent.
Also, in some embodiments of any of the above treatment method, medicaments and uses, the prostate cancer tests positive for the expression of one or both of PD-L1 and PD-L2. In some embodiments, the prostate cancer has elevated PD-L1 expression.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows amino acid sequences of the light chain and heavy chain CDRs for an exemplary anti-PD-1 monoclonal antibody useful in the present invention (SEQ ID NOs:1-6).
FIG. 2 shows amino acid sequences of the light chain and heavy chain CDRs for another exemplary anti-PD-1 monoclonal antibody useful in the present invention (SEQ ID NOs:7-12).
FIG. 3 shows amino acid sequences of the heavy chain variable region and full length heavy chain for an exemplary anti-PD-1 monoclonal antibody useful in the present invention (SEQ ID NO:13 and SEQ ID NO:14).
FIG. 4 shows amino acid sequences of alternative light chain variable regions for an exemplary anti-PD-1 monoclonal antibody useful in the present invention (SEQ ID NOs:15-17).
FIGS. 5A and 5B show amino acid sequences of alternative light chains for an exemplary anti-PD-1 monoclonal antibody useful in the present invention (SEQ ID NOs:18-20). FIG. 5A shows the full length sequence of K09A-L-11 light chain (SEQ ID NO: 18) and K09A-L-16 light chain (SEQ ID NO: 19). FIG. 5B shows the full length sequence of K09A-L-17 light chain (SEQ ID NO: 20).
FIG. 6 shows amino acid sequences of the heavy and light chains for MK-3475 (SEQ ID NOs. 21 and 22, respectively).
FIG. 7 shows amino acid sequences of the heavy and light chains for nivolumab (SEQ ID NOs. 23 and 24, respectively).
FIG. 8 shows a schematic representation of the chromosomal region of the Lmdd-143 and LmddA-143 after klk3 integration and actA deletion;
FIGS. 9A-9C. FIG. 9A shows a map of the pADV134 plasmid.
FIGS. 9B and 9C show a map of the antibiotic-independent episomal expression vector for PSA delivery, pADV142 plasmid, wherein the antigen expression cassette consists of a hly promoter and LLO-PSA fusion protein (FIG. 9B) and the nucleotide sequence of pADV142 plasmid, wherein the underline section encodes a Homo sapiens kallikrein 3, (prostate specific antigen) (FIG. 9C).
FIG. 10 shows a diagram of the two parts of the Phase 1-2 study designed to evaluate safety and tolerability of ADXS31-142 (Listeria monocytogenes (10403S dal(−) dat(−) actA(−) pADV142)) as monotherapy and in combination with pembrolizumab (MK-3475) in subjects with mCRPC.
FIG. 11 is a table showing the dose decisions (e.g., escalate, stay, deescalate and unacceptable) for ADSX31-142 Monotherapy based on a sample size of 21 subjects.
FIG. 12 is a table showing the dose decisions (e.g., escalate, stay deescalate and unacceptable) for a combination therapy of ADSX31-142 and pembrolizumab (MK-3475) based on a sample size of 21 subjects.



DETAILED DESCRIPTION
Abbreviations. Throughout the detailed description and examples of the invention the following abbreviations will be used:













APC
antigen presenting cell


BID
One dose twice daily


CBD
Cholesterol Binding Domain


CDR
Complementarity determining region


CFU
Colony-forming units


CHO
Chinese hamster ovary


DFS
Disease free survival


DTR
Dose limiting toxicity


FFPE
formalin-fixed, paraffin-embedded


FR
Framework region


IgG
Immunoglobulin G


IHC
Immunohistochemistry or immunohistochemical


KLK3
Kallikrein-related peptidase 3; also known as APS; PSA; hK3;



KLK2A1


LLO
Listeriolysin O polypeptide


tLLO
truncated Listeriolysin O polypeptide


Lm
Listeria monocytogenes


LmddA-142 
Listeria monocytogenes (10403S dal(−) dat(−) actA(−)



pADV142); also known as ADXS31-142


LmddA-143 
Listeria monocytogenes (10403S dal(−) dat(−) actA(−) with 



klk3 fused to the hly gene in the chromosome)


MTD
Maximum tolerated dose


NCBI
National Center for Biotechnology Information


NCI
National Cancer Institute


OR
Overall response


ORF
Open reading frame


OS
Overall survival


PCR
Polymerase chain reaction


PD
Progressive disease


PSA
Prostate specific antigen


PFS
Progression free survival


PR
Partial response


Q2W
One dose every two weeks


Q3W
One dose every three weeks


Q4W
One dose every four weeks


QD
One dose per day


RECIST
Response Evaluation Criteria in Solid Tumors


SD
Stable disease


SDS-PAGE
Sodium dodecyl sulfate-Polyacrylamide gel electrophoresis


TILs
Tumor infiltrating lymphocytes


VH
Immunoglobulin heavy chain variable region


VK
Immunoglobulin kappa light chain variable region









I. Definitions

So that the invention n may be more readily understood, certain technical and scientific terms are specifically defined below. Unless specifically defined elsewhere in this document, all other technical and scientific terms used herein have the meaning commonly understood by one of ordinary skill in the art to which this invention belongs.
“About” when used to modify a numerically defined parameter (e.g., the dose of a PD-1 antagonist or a live-attenuated bacterial strain that is used to stimulate Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO) or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, or the length of treatment time with a combination therapy described herein) means that the parameter may vary by as much as 10% below or above the stated numerical value for that parameter. For example, a dose of about 200 mg of the PD-1 antagonist, i.e., MK-3475, may vary between 180 mg and 220 mg.
As used herein, including the appended claims, the singular forms of words such as “a,” “an,” and “the,” include their corresponding plural references unless the context clearly dictates otherwise.
“Administration” and “treatment,” as it applies to an animal, human, experimental subject, cell, tissue, organ, or biological fluid, refers to contact of an exogenous pharmaceutical, therapeutic, diagnostic agent, or composition to the animal, human, subject, cell, tissue, organ, or biological fluid. Treatment of a cell encompasses contact of a reagent to the cell, as well as contact of a reagent to a fluid, where the fluid is in contact with the cell. “Administration” and “treatment” also means in vitro and ex vivo treatments, e.g., of a cell, by a reagent, diagnostic, binding compound, or by another cell. The term “subject” includes any organism, preferably an animal, more preferably a mammal (e.g., rat, mouse, dog, cat, rabbit) and most preferably a human.
The term “pharmaceutically acceptable carrier” refers to any inactive substance that is suitable for use in a formulation for the administration to a human of a PD-1 antagonist or a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain.
As used herein, the term “antibody” refers to any form of immunoglobulin molecule that exhibits the desired biological or binding activity. Thus, it is used in the broadest sense and specifically covers, but is not limited to, monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), humanized, human antibodies, chimeric antibodies and camelized single domain antibodies. “Parental antibodies” are antibodies obtained by exposure of an immune system to an antigen prior to modification of the antibodies for an intended use, such as humanization of an antibody for use as a human therapeutic. As used herein, the term “antibody” encompasses not only intact polyclonal or monoclonal antibodies, but also, unless otherwise specified, any antigen binding portion thereof that competes with the intact antibody for specific binding, fusion proteins comprising an antigen binding portion, and any other modified configuration of the immunoglobulin molecule that comprises an antigen recognition site. Antigen binding portions include, for example, Fab, Fab′, F(ab′)2, Fd, Fv, domain antibodies (dAbs, e.g., shark and camelid antibodies), fragments including complementarity determining regions (CDRs), single chain variable fragment antibodies (scFv), maxibodies, minibodies, intrabodies, diabodies, triabodies, tetrabodies, v-NAR and bis-scFv, and polypeptides that contain at least a portion of an immunoglobulin that is sufficient to confer specific antigen binding to the polypeptide. An antibody includes an antibody of any class, such as IgG, IgA, or IgM (or sub-class thereof), and the antibody need not be of any particular class. Depending on the antibody amino acid sequence of the constant region of its heavy chains, immunoglobulins can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2. The heavy-chain constant regions that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.
“Variable regions” or “V region” as used herein means the segment of IgG chains which is variable in sequence between different antibodies. It extends to Kabat residue 109 in the light chain and 113 in the heavy chain. A “variable region” of an antibody refers to the variable region of the antibody light chain or the variable region of the antibody heavy chain, either alone or in combination. Typically, the variable regions of both the heavy and light chains comprise three hypervariable regions, also called complementarity determining regions (CDRs), which are located within relatively conserved framework regions (FR). The CDRs are usually aligned by the framework regions, enabling binding to a specific epitope. In general, from N-terminal to C-terminal, both light and heavy chains variable domains comprise FR1, CDR1, FR2, CDR2, FR3, CDR3 and FR4. The assignment of amino acids to each domain is, generally, in accordance with the definitions of Sequences of Proteins of Immunological Interest, Kabat, et al.; National Institutes of Health, Bethesda, Md.; 5th ed.; NIH Publ. No. 91-3242 (1991); Kabat (1978) Adv. Prot. Chem. 32:1-75; Kabat, et al., (1977) J. Biol. Chem. 252:6609-6616; Chothia, et al., (1987) J Mol. Biol. 196:901-917 or Chothia, et al., (1989) Nature 342:878-883.
As used herein, the term “hypervariable region” refers to the amino acid residues of an antibody that are responsible for antigen-binding. The hypervariable region comprises amino acid residues from a “complementarity determining region” or “CDR” (i.e. CDRL1, CDRL2 and CDRL3 in the light chain variable domain and CDRH1, CDRH2 and CDRH3 in the heavy chain variable domain). See Kabat et al. (1991) Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (defining the CDR regions of an antibody by sequence); see also Chothia and Lesk (1987) J. Mol. Biol. 196: 901-917 (defining the CDR regions of an antibody by structure). As used herein, the term “framework” or “FR” residues refers to those variable domain residues other than the hypervariable region residues defined herein as CDR residues.
As used herein, unless otherwise indicated, “antibody fragment” or “antigen binding fragment” refers to antigen binding fragments of antibodies, i.e. antibody fragments that retain the ability to bind specifically to the antigen bound by the full-length antibody, e.g. fragments that retain one or more CDR regions. Examples of antibody binding fragments include, but are not limited to, Fab, Fab′, F(ab′)2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules, e.g., sc-Fv; nanobodies and multispecific antibodies formed from antibody fragments.
An antibody that “specifically binds to” a specified target protein is an antibody that exhibits preferential binding to that target as compared to other proteins, but this specificity does not require absolute binding specificity. An antibody is considered “specific” for its intended target if its binding is determinative of the presence of the target protein in a sample, e.g. without producing undesired results such as false positives. Antibodies, or binding fragments thereof, useful in the present invention will bind to the target protein with an affinity that is at least two fold greater, preferably at least ten times greater, more preferably at least 20-times greater, and most preferably at least 100-times greater than the affinity with non-target proteins. As used herein, an antibody is said to bind specifically to a polypeptide comprising a given amino acid sequence, e.g. the amino acid sequence of a mature human PD-1 or human PD-L1 molecule, if it binds to polypeptides comprising that sequence but does not bind to proteins lacking that sequence.
“Chimeric antibody” refers to an antibody in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in an antibody derived from a particular species (e.g., human) or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in an antibody derived from another species (e.g., mouse) or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.
“Human antibody” refers to an antibody that comprises human immunoglobulin protein sequences only. A human antibody may contain murine carbohydrate chains if produced in a mouse, in a mouse cell, or in a hybridoma derived from a mouse cell. Similarly, “mouse antibody” or “rat antibody” refer to an antibody that comprises only mouse or rat immunoglobulin sequences, respectively.
“Humanized antibody” refers to forms of antibodies that contain sequences from non-human (e.g., murine) antibodies as well as human antibodies. Such antibodies contain minimal sequence derived from non-human immunoglobulin. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin sequence. The humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. The prefix “hum”, “hu” or “h” is added to antibody clone designations when necessary to distinguish humanized antibodies from parental rodent antibodies. The humanized forms of rodent antibodies will generally comprise the same CDR sequences of the parental rodent antibodies, although certain amino acid substitutions may be included to increase affinity, increase stability of the humanized antibody, or for other reasons.
The terms “cancer”, “cancerous”, or “malignant” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth.
“Biotherapeutic agent” means a biological molecule, such as an antibody or fusion protein, that blocks ligand/receptor signaling in any biological pathway that supports tumor maintenance and/or growth or suppresses the anti-tumor immune response.
“CDR” or “CDRs” as used herein means complementarity determining region(s) in a immunoglobulin variable region, defined using the Kabat numbering system, unless otherwise indicated.
“Chemotherapeutic agent” refers to a chemical or biological substance that can cause death of cancer cells, or interfere with growth, division, repair, and/or function of cancer cells. Classes of chemotherapeutic agents include, but are not limited to: alkylating agents, antimetabolites, kinase inhibitors, spindle poison plant alkaloids, cytoxic/antitumor antibiotics, topisomerase inhibitors, photosensitizers, anti-estrogens and selective estrogen receptor modulators (SERMs), anti-progesterones, estrogen receptor down-regulators (ERDs), estrogen receptor antagonists, leutinizing hormone-releasing hormone agonists, anti-androgens, aromatase inhibitors, EGFR inhibitors, VEGF inhibitors, anti-sense oligonucleotides that inhibit expression of genes implicated in abnormal cell proliferation or tumor growth. Chemotherapeutic agents useful in the treatment methods of the present invention include cytostatic and/or cytotoxic agents.
The antibodies and compositions provided by the present disclosure can be administered via any suitable enteral route or parenteral route of administration. The term “enteral route” of administration refers to the administration via any part of the gastrointestinal tract. Examples of enteral routes include oral, mucosal, buccal, and rectal route, or intragastric route. “Parenteral route” of administration refers to a route of administration other than enteral route. Examples of parenteral routes of administration include intravenous, intramuscular, intradermal, intraperitoneal, intratumor, intravesical, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, transtracheal, intraarticular, subcapsular, subarachnoid, intraspinal, epidural and intrasternal, subcutaneous, or topical administration. The antibodies and compositions of the disclosure can be administered using any suitable method, such as by oral ingestion, nasogastric tube, gastrostomy tube, injection, infusion, implantable infusion pump, and osmotic pump. The suitable route and method of administration may vary depending on a number of factors such as the specific antibody being used, the rate of absorption desired, specific formulation or dosage form used, type or severity of the disorder being treated, the specific site of action, and conditions of the patient, and can be readily selected by a person skilled in the art.
The term “simultaneous administration” as used herein in relation to the administration of medicaments refers to the administration of medicaments such that the individual medicaments are present within a subject at the same time. In addition to the concomitant administration of medicaments (via the same or alternative routes), simultaneous administration may include the administration of the medicaments (via the same or an alternative route) at different times.
The Bliss independence combined response C for two single compounds with effects A and B is C=A+B−A*B, where each effect is expressed as a fractional inhibition between 0 and 1. (Reference: Bliss (1939) Annals of Applied Biology) The Bliss value, defined to be the difference between the experimental response and the calculated Bliss Independence value, indicates whether the two compounds in combination are additive or synergistic.
A Bliss value of zero (0) is considered additive. The term “additive” means that the result of the combination of the two targeted agents is the sum of each agent individually.
“Chothia” as used herein means an antibody numbering system described in Al-Lazikani et al., JMB 273:927-948 (1997).
“Conservatively modified variants” or “conservative substitution” refers to substitutions of amino acids in a protein with other amino acids having similar characteristics (e.g. charge, side-chain size, hydrophobicity/hydrophilicity, backbone conformation and rigidity, etc.), such that the changes can frequently be made without altering the biological activity or other desired property of the protein, such as antigen affinity and/or specificity. Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity (see, e.g., Watson et al. (1987) Molecular Biology of the Gene, The Benjamin/Cummings Pub. Co., p. 224 (4th Ed.)). In addition, substitutions of structurally or functionally similar amino acids are less likely to disrupt biological activity. Exemplary conservative substitutions are set forth in Table 1 below.







TABLE 1







Exemplary Conservative Amino Acid Substitutions










Original residue
Conservative substitution







Ala (A)
Gly; Ser



Arg (R)
Lys; His



Asn (N)
Gln; His



Asp (D)
Glu; Asn



Cys (C)
Ser; Ala



Gln (Q)
Asn



Glu (E)
Asp; Gln



Gly (G)
Ala



His (H)
Asn; Gln



Ile (I)
Leu; Val



Leu (L)
Ile; Val



Lys (K)
Arg; His



Met (M)
Leu; Ile; Tyr



Phe (F)
Tyr; Met; Leu



Pro (P)
Ala



Ser (S)
Thr



Thr (T)
Ser



Trp (W)
Tyr; Phe



Tyr (Y)
Trp; Phe



Val (V)
Ile; Leu










“Consists essentially of,” and variations such as “consist essentially of” or “consisting essentially of,” as used throughout the specification and claims, indicate the inclusion of any recited elements or group of elements, and the optional inclusion of other elements, of similar or different nature than the recited elements, that do not materially change the basic or novel properties of the specified dosage regimen, method, or composition. As a non-limiting example, an antibody that consists essentially of a recited amino acid sequence may also include the addition and/or substitution of one or more amino acids that do not materially affect the properties of the antibody.
“Diagnostic anti-PD-L monoclonal antibody” means a mAb which specifically binds to the mature form of the designated PD-L (PD-L1 or PDL2) that is expressed on the surface of certain mammalian cells. A mature PD-L lacks the presecretory leader sequence, also referred to as leader peptide The terms “PD-L” and “mature PD-L” are used interchangeably herein, and shall be understood to mean the same molecule unless otherwise indicated or readily apparent from the context.
As used herein, a diagnostic anti-human PD-L1 mAb or anti-hPD-L1 mAb refers to a monoclonal antibody that specifically binds to mature human PD-L1. Specific examples of diagnostic anti-human PD-L1 mAbs useful as diagnostic mAbs for immunohistochemistry (IHC) detection of PD-L1 expression in formalin-fixed, paraffin-embedded (FFPE) tumor tissue sections are antibody 20C3 and antibody 22C3, which are described in WO2014/100079. Another anti-human PD-L1 mAb that has been reported to be useful for IHC detection of PD-L1 expression in FFPE tissue sections (Chen, B. J. et al., Clin Cancer Res 19: 3462-3473 (2013)) is a rabbit anti-human PD-L1 mAb publicly available from Sino Biological, Inc. (Beijing, P. R. China; Catalog number 10084-R015).
“Framework region” or “FR” as used herein means the immunoglobulin variable regions excluding the CDR regions.
“Homology” refers to sequence similarity between two polypeptide sequences when they are optimally aligned. When a position in both of the two compared sequences is occupied by the same amino acid monomer subunit, e.g., if a position in a light chain CDR of two different Abs is occupied by alanine, then the two Abs are homologous at that position. The percent of homology is the number of homologous positions shared by the two sequences divided by the total number of positions compared ×100. For example, if 8 of 10 of the positions in two sequences are matched or homologous when the sequences are optimally aligned then the two sequences are 80% homologous. Generally, the comparison is made when two sequences are aligned to give maximum percent homology. For example, the comparison can be performed by a BLAST algorithm wherein the parameters of the algorithm are selected to give the largest match between the respective sequences over the entire length of the respective reference sequences.
The following references relate to BLAST algorithms often used for sequence analysis: BLAST ALGORITHMS: Altschul, S. F., et al., (1990) J. Mol. Biol. 215:403-410; Gish, W., et al., (1993) Nature Genet. 3:266-272; Madden, T. L., et al., (1996) Meth. Enzymol. 266:131-141; Altschul, S. F., et al., (1997) Nucleic Acids Res. 25:3389-3402; Zhang, J., et al., (1997) Genome Res. 7:649-656; Wootton, J. C., et al., (1993) Comput. Chem. 17:149-163; Hancock, J. M. et al., (1994) Comput. Appl. Biosci. 10:67-70; ALIGNMENT SCORING SYSTEMS: Dayhoff, M. O., et al., “A model of evolutionary change in proteins.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3. M. O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found., Washington, D.C.; Schwartz, R. M., et al., “Matrices for detecting distant relationships.” in Atlas of Protein Sequence and Structure, (1978) vol. 5, suppl. 3.” M. O. Dayhoff (ed.), pp. 353-358, Natl. Biomed. Res. Found., Washington, D.C.; Altschul, S. F., (1991) J. Mol. Biol. 219:555-565; States, D. J., et al., (1991) Methods 3:66-70; Henikoff, S., et al., (1992) Proc. Natl. Acad. Sci. USA 89:10915-10919; Altschul, S. F., et al., (1993) J. Mol. Evol. 36:290-300; ALIGNMENT STATISTICS: Karlin, S., et al., (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268; Karlin, S., et al., (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877; Dembo, A., et al., (1994) Ann Prob. 22:2022-2039; and Altschul, S. F. “Evaluating the statistical significance of multiple distinct local alignments.” in Theoretical and Computational Methods in Genome Research (S. Suhai, ed.), (1997) pp. 1-14, Plenum, New York.
“Isolated antibody” and “isolated antibody fragment” refers to the purification status and in such context means the named molecule is substantially free of other biological molecules such as nucleic acids, proteins, lipids, carbohydrates, or other material such as cellular debris and growth media. Generally, the term “isolated” is not intended to refer to a complete absence of such material or to an absence of water, buffers, or salts, unless they are present in amounts that substantially interfere with experimental or therapeutic use of the binding compound as described herein.
“Kabat” as used herein means an immunoglobulin alignment and numbering system pioneered by Elvin A. Kabat ((1991) Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md.).
“Monoclonal antibody” or “mAb” or “Mab”, as used herein, refers to a population of substantially homogeneous antibodies, i.e., the antibody molecules comprising the population are identical in amino acid sequence except for possible naturally occurring mutations that may be present in minor amounts. In contrast, conventional (polyclonal) antibody preparations typically include a multitude of different antibodies having different amino acid sequences in their variable domains, particularly their CDRs, which are often specific for different epitopes. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, a monoclonal antibody to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al. (1975) Nature 256: 495, or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567). The monoclonal antibody may also be isolated from phage antibody libraries using the techniques described in Clackson et al. (1991) Nature 352: 624-628 and Marks et al. (1991) J. Mol. Biol. 222: 581-597, for example. See also Presta (2005) J. Allergy Clin. Immunol. 116:731.
“Patient” or “subject” refers to any single human subject for which therapy is desired or that is participating in a clinical trial, epidemiological study or used as a control.
“PD-1 antagonist” means any chemical compound or biological molecule that blocks binding of human PD-L1 expressed on a cancer cell to human PD-1 expressed on an immune cell (T cell, B cell or NKT cell) and preferably also blocks binding of human PD-L2 expressed on a cancer cell to the immune-cell expressed PD-1. Alternative names or synonyms for PD-1 and its ligands include: PDCD1, PD1, CD279 and SLEB2 for PD-1; PDCD1L1, PDL1, B7H1, B7-4, CD274 and B7-H for PD-L1; and PDCD1L2, PDL2, B7-DC, Btdc and CD273 for PD-L2. Exemplary human PD-1 amino acid sequences can be found in NCBI Locus No.: NP_005009. Exemplary human PD-L1 and PD-L2 amino acid sequences can be found in NCBI Locus No.: NP_054862 and NP_079515, respectively.
PD-1 antagonists useful in the any of the treatment method, medicaments and uses of the present invention include a monoclonal antibody (mAb), or antigen binding fragment thereof, which specifically binds to human PD-1 or human PD-L1. The mAb may be a human antibody, a humanized antibody or a chimeric antibody, and may include a human constant region. In some embodiments, the human constant region is selected from the group consisting of IgG1, IgG2, IgG3 and IgG4 constant regions, and in some embodiments, the human constant region is an IgG1 or IgG4 constant region. In some embodiments, the antigen binding fragment is selected from the group consisting of Fab, Fab′-SH, F(ab′)2, scFv and Fv fragments.
Examples of mAbs that bind to human PD-1, and useful in the treatment method, medicaments and uses of the present invention, are described in U.S. Pat. Nos. 7,488,802, 7,521,051, 8,008,449, 8,354,509, 8,168,757, WO2004/004771, WO2004/072286, WO2004/056875, and US2011/0271358. Specific anti-human PD-1 mAbs useful as the PD-1 antagonist in the treatment method, medicaments and uses of the present invention include: MK-3475, a humanized IgG4 mAb with the structure described in WHO Drug Information, Vol. 27, No. 2, pages 161-162 (2013) and which comprises the heavy and light chain amino acid sequences shown in FIG. 6, nivolumab (BMS-936558), a human IgG4 mAb with the structure described in WHO Drug Information, Vol. 27, No. 1, pages 68-69 (2013) and which comprises the heavy and light chain amino acid sequences shown in FIG. 7; the humanized antibodies h409A11, h409A16 and h409A17, which are described in WO2008/156712, and AMP-514, which is being developed by MedImmune.
Examples of mAbs that bind to human PD-L1, and useful in the treatment method, medicaments and uses of the present invention, are described in WO2013/019906, WO2010/077634 A1 and U.S. Pat. No. 8,383,796. Specific anti-human PD-L1 mAbs useful as the PD-1 antagonist in the treatment method, medicaments and uses of the present invention include MPDL3280A, BMS-936559, MEDI4736, MSB0010718C and an antibody which comprises the heavy chain and light chain variable regions of SEQ ID NO:24 and SEQ ID NO:21, respectively, of WO2013/019906.
Other PD-1 antagonists useful in the any of the treatment method, medicaments and uses of the present invention include an immunoadhesin that specifically binds to human PD-1 or human PD-L1, e.g., a fusion protein containing the extracellular or PD-1 binding portion of PD-L1 or PD-L2 fused to a constant region such as an Fc region of an immunoglobulin molecule. Examples of immunoadhesion molecules that specifically bind to PD-1 are described in WO2010/027827 and WO2011/066342. Specific fusion proteins useful as the PD-1 antagonist in the treatment method, medicaments and uses of the present invention include AMP-224 (also known as B7-DCIg), which is a PD-L2-FC fusion protein and binds to human PD-1.
In some embodiments of the treatment method, medicaments and uses of the present invention, the PD-1 antagonist is a monoclonal antibody, or antigen binding fragment thereof, which comprises: (a) light chain CDRs SEQ ID NOs: 1, 2 and 3 and heavy chain CDRs SEQ ID NOs: 4, 5 and 6; or (b) light chain CDRs SEQ ID NOs: 7, 8 and 9 and heavy chain CDRs SEQ ID NOs: 10, 11 and 12.
In other embodiments of the treatment method, medicaments and uses of the present invention, the PD-1 antagonist is a monoclonal antibody, or antigen binding fragment thereof, which specifically binds to human PD-1 and comprises (a) a heavy chain variable region comprising SEQ ID NO:13 or a variant thereof, and (b) a light chain variable region comprising an amino acid sequence selected from the group consisting of SEQ ID NO:15 or a variant thereof; SEQ ID NO:16 or a variant thereof; and SEQ ID NO: 17 or a variant thereof. A variant of a heavy chain variable region sequence is identical to the reference sequence except having up to 17 conservative amino acid substitutions in the framework region (i.e., outside of the CDRs), and preferably has less than ten, nine, eight, seven, six or five conservative amino acid substitutions in the framework region. A variant of a light chain variable region sequence is identical to the reference sequence except having up to five conservative amino acid substitutions in the framework region (i.e., outside of the CDRs), and preferably has less than four, three or two conservative amino acid substitution in the framework region.
In another embodiment of the treatment method, medicaments and uses of the present invention, the PD-1 antagonist is a monoclonal antibody which specifically binds to human PD-1 and comprises (a) a heavy chain comprising SEQ ID NO: 14 and (b) a light chain comprising SEQ ID NO:18, SEQ ID NO:19 or SEQ ID NO:20.
In yet another embodiment of the treatment method, medicaments and uses of the present invention, the PD-1 antagonist is a monoclonal antibody which specifically binds to human PD-1 and comprises (a) a heavy chain comprising SEQ ID NO: 14 and (b) a light chain comprising SEQ ID NO:18.
Table 2 below provides a list of the amino acid sequences of exemplary anti-PD-1 mAbs for use in the treatment method, medicaments and uses of the present invention, and the sequences are shown in FIGS. 1-5.







TABLE 2





EXEMPLARY ANTI-HUMAN PD-1 MONOCLONAL


ANTIBODIES







A. Comprises light and heavy chain CDRs 


of hPD-1.08A in WO2008/156712








CDRL1
SEQ ID NO: 1


CDRL2
SEQ ID NO: 2


CDRL3
SEQ ID NO: 3 


CDRH1
SEQ ID NO: 4


CDRH2
SEQ ID NO: 5


CDRH3
SEQ ID NO: 6







B. Comprises light and heavy chain 


CDRs of hPD-1.09A in WO2008/156712








CDRL1
SEQ ID NO: 7


CDRL2
SEQ ID NO: 8


CDRL3
SEQ ID NO: 9


CDRH1
SEQ ID NO: 10


CDRH2
SEQ ID NO: 11


CDRH3
SEQ ID NO: 12







C. Comprises the mature h109A heavy chain 


variable region and one of the mature K09A 


light chain variable regions in WO2008/156712








Heavy chain VR
SEQ ID NO: 13


Light chain VR
SEQ ID NO: 15 or SEQ ID NO: 16 or SEQ ID NO: 17







D. Comprises the mature 409 heavy chain and one of the 


mature K09A light chains in WO2008/156712








Heavy chain
SEQ ID NO: 14


Light chain
SEQ ID NO: 18 or SEQ ID NO: 19 or SEQ ID NO: 20









“PD-L1” expression or “PD-L2” expression as used herein means any detectable level of expression of the designated PD-L protein on the cell surface or of the designated PD-L mRNA within a cell or tissue. PD-L protein expression may be detected with a diagnostic PD-L antibody in an IHC assay of a tumor tissue section or by flow cytometry. Alternatively, PD-L protein expression by tumor cells may be detected by PET imaging, using a binding agent (e.g., antibody fragment, affibody and the like) that specifically binds to the desired PD-L target, e.g., PD-L1 or PD-L2. Techniques for detecting and measuring PD-L mRNA expression include RT-PCR and realtime quantitative RT-PCR.
Several approaches have been described for quantifying PD-L1 protein expression in IHC assays of tumor tissue sections. See, e.g., Thompson, R. H., et al., PNAS 101 (49); 17174-17179 (2004); Thompson, R. H. et al., Cancer Res. 66:3381-3385 (2006); Gadiot, J., et al., Cancer 117:2192-2201 (2011); Taube, J. M. et al., Sci Transl Med 4, 127ra37 (2012); and Toplian, S. L. et al., New Eng. J Med. 366 (26): 2443-2454 (2012).
One approach employs a simple binary end-point of positive or negative for PD-L1 expression, with a positive result defined in terms of the percentage of tumor cells that exhibit histologic evidence of cell-surface membrane staining. A tumor tissue section is counted as positive for PD-L1 expression if IHC staining is observed in at least 1%, and preferably 5% of total tumor cells. In an embodiment, a prostate tumor sample is designated as having weak PD-L1 expression if 1% to 49% of the total tumor cells in the sample exhibit membrane staining and is designated as having strong PD-L1 expression if at least 50% of the tumor cells in the sample exhibit membrane staining, in each case as determined by IHC assay using the antibody 22C3 described in WO2014/100079.
In another approach, PD-L1 expression in the tumor tissue section is quantified in the tumor cells as well as in infiltrating immune cells, which predominantly comprise lymphocytes. The percentage of tumor cells and infiltrating immune cells that exhibit membrane staining are separately quantified as <5%, 5 to 9%, and then in 10% increments up to 100%. For tumor cells, PD-L1 expression is counted as negative if the score is <5% score and positive if the score is ≧5%. PD-L1 expression in the immune infiltrate is reported as a semi-quantitative measurement called the adjusted inflammation score (AIS), which is determined by multiplying the percent of membrane staining cells by the intensity of the infiltrate, which is graded as none (0), mild (score of 1, rare lymphocytes), moderate (score of 2, focal infiltration of tumor by lymphohistiocytic aggregates), or severe (score of 3, diffuse infiltration). A tumor tissue section is counted as positive for PD-L1 expression by immune infiltrates if the AIS is ≧5.
The level of PD-L mRNA expression may be compared to the mRNA expression levels of one or more reference genes that are frequently used in quantitative RT-PCR, such as ubiquitin C.
In some embodiments, a level of PD-L1 expression (protein and/or mRNA) by malignant cells and/or by infiltrating immune cells within a tumor is determined to be “overexpressed” or “elevated” based on comparison with the level of PD-L1 expression (protein and/or mRNA) by an appropriate control. For example, a control PD-L1 protein or mRNA expression level may be the level quantified in nonmalignant cells of the same type or in a section from a matched normal tissue. In some embodiments, PD-L1 expression in a tumor sample is determined to be elevated if PD-L1 protein (and/or PD-L1 mRNA) in the sample is at least 10%, 20%, or 30% greater than in the control.
“Prostate Cancer Working Group 2 (PCWG2) criteria” as used herein has the meaning as presented in Scher et al., (2008) “Design and End Points of Clinical Trials for Patients With Progressive Prostate Cancer and Castrate Levels of Testosterone: Recommendations of the Prostate Cancer Clinical Trials Working Group” J. Clin. Oncol. 26(7):1148-159, incorporated in its entirety herein.
“RECIST 1.1 Response Criteria” as used herein means the definitions set forth in Eisenhauer et al., E. A. et al., Eur. J Cancer 45:228-247 (2009) for target lesions or nontarget lesions, as appropriate based on the context in which response is being measured.
“Sustained response” means a sustained therapeutic effect after cessation of treatment with a therapeutic agent, or a combination therapy described herein. In some embodiments, the sustained response has a duration that is at least the same as the treatment duration, or at least 1.5, 2.0, 2.5 or 3 times longer than the treatment duration.
The terms “synergy” or “synergistic” are used to mean that the response of the combination of the two agents is more than the sum of each agent's individual response. More specifically, in the in vitro setting one measure of synergy is known as “Bliss synergy.” Bliss synergy refers to “excess over Bliss independence”, as determined by the Bliss value defined above. When the Bliss value is greater than zero (0), or more preferably greater than 0.2, it is considered indicative of synergy. Of course, the use of “synergy” herein also encompasses in vitro synergy as measured by additional and/or alternate methods. References herein to a combination's in vitro biological effects, including but not limited to anti-cancer effects, being greater than, or equal to, the sum of the combination's components individually, may be correlated to Bliss values. Again, the use of “synergy” herein, including whether a combination of components demonstrates activity equal to or greater than the sum of the components individually, may be measured by additional and/or alternate methods and are known, or will be apparent, to those skilled in this art. In one embodiment, the combination of a Listeria based immunotherapy, as described herein, with an anti-PD-1 antibody, as described herein, provides synergistic antitumor activities.
“Tissue Section” refers to a single part or piece of a tissue sample, e.g., a thin slice of tissue cut from a sample of a normal tissue or of a tumor.
“Treat” or “treating” a cancer as used herein means to administer a combination therapy of a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain to a subject having a prostate cancer, or diagnosed with a prostate cancer, to achieve at least one positive therapeutic effect, such as for example, reduced number of cancer cells, reduced tumor size, reduced rate of cancer cell infiltration into peripheral organs, or reduced rate of tumor metastasis or tumor growth. Positive therapeutic effects in cancer can be measured in a number of ways (See, W. A. Weber, J. Nucl. Med. 50:1S-10S (2009)). For example, with respect to tumor growth inhibition, according to NCI standards, a T/C≦42% is the minimum level of anti-tumor activity. A T/C<10% is considered a high anti-tumor activity level, with T/C (%)=Median tumor volume of the treated/Median tumor volume of the control×100. In some embodiments, the treatment achieved by a combination of the invention is any of PR, CR, OR, PFS, DFS and OS. PFS, also referred to as “Time to Tumor Progression” indicates the length of time during and after treatment that the cancer does not grow, and includes the amount of time patients have experienced a CR or PR, as well as the amount of time patients have experienced SD. DFS refers to the length of time during and after treatment that the patient remains free of disease. OS refers to a prolongation in life expectancy as compared to naive or untreated individuals or patients. In some embodiments, response to a combination of the invention is any of PR, CR, PFS, DFS, OR or OS that is assessed using RECIST 1.1 response criteria. The treatment regimen for a combination of the invention that is effective to treat a cancer patient may vary according to factors such as the disease state, age, and weight of the patient, and the ability of the therapy to elicit an anti-cancer response in the subject. While an embodiment of any of the aspects of the invention may not be effective in achieving a positive therapeutic effect in every subject, it should do so in a statistically significant number of subjects as determined by any statistical test known in the art such as the Student's t-test, the chi2-test, the U-test according to Mann and Whitney, the Kruskal-Wallis test (H-test), Jonckheere-Terpstra-test and the Wilcoxon-test.
The terms “treatment regimen”, “dosing protocol” and dosing regimen are used interchangeably to refer to the dose and timing of administration of each therapeutic agent in a combination of the invention.
“Tumor” as it applies to a subject diagnosed with, or suspected of having, a cancer refers to a malignant or potentially malignant neoplasm or tissue mass of any size, and includes primary tumors and secondary neoplasms. A solid tumor is an abnormal growth or mass of tissue that usually does not contain cysts or liquid areas. Different types of solid tumors are named for the type of cells that form them. Examples of solid tumors are sarcomas, carcinomas, and lymphomas. Leukemias (cancers of the blood) generally do not form solid tumors (National Cancer Institute, Dictionary of Cancer Terms).
“Tumor burden” also referred to as “tumor load”, refers to the total amount of tumor material distributed throughout the body. Tumor burden refers to the total number of cancer cells or the total size of tumor(s), throughout the body, including lymph nodes and bone narrow. Tumor burden can be determined by a variety of methods known in the art, such as, e.g. by measuring the dimensions of tumor(s) upon removal from the subject, e.g., using calipers, or while in the body using imaging techniques, e.g., ultrasound, bone scan, computed tomography (CT) or magnetic resonance imaging (MRI) scans.
The term “tumor size” refers to the total size of the tumor which can be measured as the length and width of a tumor. Tumor size may be determined by a variety of methods known in the art, such as, e.g. by measuring the dimensions of tumor(s) upon removal from the subject, e.g., using calipers, or while in the body using imaging techniques, e.g., bone scan, ultrasound, CT or MRI scans.
In some embodiment, this invention provides an immunogenic composition comprising a live attenuated bacteria strain, for example a Listeria vaccine strain comprises a nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding fusion polypeptide, wherein said fusion polypeptide comprises a PEST sequence-containing polypeptide or a PEST sequence-containing peptide fused to a PSA antigen or fragment thereof. In one embodiment, an immunogenic composition comprises a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells. In another embodiment, an immunogenic composition comprises a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO. In yet another embodiment, an immunogenic composition comprises an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain. In still another embodiment, an immunogenic composition comprises an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain. In some embodiments, the present invention provides methods of treating, protecting against, and inducing an immune response against a tumor or a cancer, for example treating a prostate cancer comprising the step of administering to a subject an immunogenic composition provided herein.
In some embodiments, the immunogenic compositions comprising a live attenuated bacteria strain, for example a Listeria vaccine strain comprises a nucleic acid molecule, wherein the nucleic acid molecule comprises a first open reading frame encoding fusion polypeptide, wherein said fusion polypeptide comprises a PEST sequence-containing polypeptide or a PEST sequence-containing peptide fused to a PSA antigen or fragment thereof may be used in a method of preventing or treating a tumor or cancer in a human subject, for example a prostate cancer, comprising the step of administering to the subject the immunogenic composition strain provided herein, the recombinant Listeria strain comprising a recombinant polypeptide comprising an N-terminal fragment of an LLO protein and tumor-associated antigen, whereby the recombinant Listeria strain induces an immune response against the tumor-associated antigen, thereby treating a tumor or cancer in a human subject. In another embodiment, the immune response is a T-cell response. In another embodiment, the T-cell response is a CD4+FoxP3−T cell response. In another embodiment, the T-cell response is a CD8+T cell response. In another embodiment, the T-cell response is a CD4+FoxP3− and CD8+T cell response.
In some embodiments, the live-attenuated Listeria strain comprises a nucleic acid molecule, the nucleic acid molecule comprising a first open reading frame encoding a fusion polypeptide, wherein said fusion polypeptide comprises a PEST sequence-containing polypeptide or a PEST sequence-containing peptide fused to a PSA antigen or fragment thereof. In some embodiments, the nucleic acid molecule is comprised in an episomal expression vector. In other embodiments, the nucleic acid molecule is integrated into the chromosomal DNA.
In one embodiment, the nucleic acid molecule comprising a first open reading frame encoding a fusion polypeptide is integrated into the Listeria genome. In another embodiment, the nucleic acid is in a plasmid in said attenuated Listeria vaccine strain. In another embodiment, the nucleic acid molecule is in a bacterial artificial chromosome in said attenuated Listeria vaccine strain.
It will be well appreciated an “immunogenic composition” may comprise the recombinant Listeria provided herein, and an adjuvant. In another embodiment, an immunogenic composition comprises a recombinant Listeria provided herein. In another embodiment, an immunogenic composition comprises an adjuvant known in the art or as provided herein. It is also to be understood that such compositions enhance an immune response, or increase a T effector cell to regulatory T cell ratio or elicit an anti-tumor immune response, as further provided herein. As used throughout, the term “immunogeneic composition” and “composition” may be used interchangeably having all the same meanings and qualities.
Following the administration of the immunogenic compositions provided herein, the methods provided herein induce the expansion of T effector cells in peripheral lymphoid organs, leading to an enhanced presence of T effector cells at the tumor site. In another embodiment, the methods provided herein induce the expansion of T effector cells in peripheral lymphoid organs, leading to an enhanced presence of T effector cells at the periphery. Such expansion of T effector cells leads to an increased ratio of T effector cells to regulatory T cells in the periphery and at the tumor site without affecting the number of Tregs. It will be appreciated by the skilled artisan that peripheral lymphoid organs include, but are not limited to, the spleen, peyer's patches, the lymph nodes, the adenoids, etc. In one embodiment, the increased ratio of T effector cells to regulatory T cells occurs in the periphery without affecting the number of Tregs. In another embodiment, the increased ratio of T effector cells to regulatory T cells occurs in the periphery, the lymphoid organs and at the tumor site without affecting the number of Tregs at these sites. In another embodiment, the increased ratio of T effector cells decrease the frequency of Tregs, but not the total number of Tregs at these sites. The term “attenuation” as used herein, is meant a diminution in the ability of the bacterium to cause disease in an animal. In other words, the pathogenic characteristics of the attenuated Listeria strain have been lessened compared with wild-type Listeria, although the attenuated Listeria is capable of growth and maintenance in culture. Using as an example the intravenous inoculation of Balb/c mice with an attenuated Listeria, the lethal dose at which 50% of inoculated animals survive (LD50) is preferably increased above the LD50 of wild-type Listeria by at least about 10-fold, more preferably by at least about 100-fold, more preferably at least about 1,000 fold, even more preferably at least about 10,000 fold, and most preferably at least about 100,000-fold. An attenuated strain of Listeria is thus one which does not kill an animal to which it is administered, or is one which kills the animal only when the number of bacteria administered is vastly greater than the number of wild type non-attenuated bacteria which would be required to kill the same animal. An attenuated bacterium should also be construed to mean one which is incapable of replication in the general environment because the nutrient required for its growth is not present therein. Thus, the bacterium is limited to replication in a controlled environment wherein the required nutrient is provided. The attenuated strains of the present invention are therefore environmentally safe in that they are incapable of uncontrolled replication.
In one embodiment, the attenuated Listeria strain provided herein lacks antibiotic resistance genes. In another embodiment, the attenuated Listeria strain provided herein comprises a plasmid comprising a nucleic acid encoding an antibiotic resistance gene. In another embodiment, an attenuated Listeria strain expressing a PSA polypeptide in which the nucleic acid encoding the polypeptide is operably integrated into the Listeria genome in an open reading frame with an LLO gene.
In one embodiment, the attenuated Listeria provided herein is capable of escaping the phagolysosome.
In one embodiment, the Listeria genome comprises a deletion of the endogenous ActA gene, which in one embodiment is a virulence factor. In one embodiment, such a deletion provides a more attenuated and thus safer Listeria strain for human use. According to this embodiment, the PSA antigen or fragment thereof is integrated in frame with LLO in the Listeria chromosome. In another embodiment, the integrated nucleic acid molecule is integrated into the ActA locus.
In one embodiment, an exression vector comprises at nucleic acid molecule comprising a recombinant polypeptide comprising a PSA antigen or fragment thereof. In another embodiment, the recombinant polypeptide further comprises a truncated LLO protein, a truncated ActA protein or a PEST sequence peptide fused to the PSA antigen. In another embodiment, the truncated LLO protein is a N-terminal LLO or fragment thereof. In another embodiment, the truncated ActA protein is a N-terminal ActA protein or fragment thereof.
In another embodiment the attenuated strain is LmddA. In another embodiment, the attenuated strain is LmΔactA. In another embodiment, the attenuated strain is LmΔPrfA. In another embodiment, the attenuated strain is LmΔPlcB. In another embodiment, the attenuated strain is LmΔPlcA. In another embodiment, the strain is the double mutant or triple mutant of any of the above-mentioned strains. In another embodiment, this strain exerts a strong adjuvant effect which is an inherent property of Listeria-based strains. In another embodiment, this strain is constructed from the EGD Listeria backbone. In another embodiment, the strain used in the invention is a Listeria strain that expresses a non-hemolytic LLO.
In another embodiment, the Listeria strain is an auxotrophic mutant. In another embodiment, the Listeria strain is deficient in a gene encoding a vitamin synthesis gene. In another embodiment, the Listeria strain is deficient in a gene encoding pantothenic acid synthase.
In one embodiment, the generation of AA strains of Listeria deficient in D-alanine, for example, may be accomplished in a number of ways that are well known to those of skill in the art, including deletion mutagenesis, insertion mutagenesis, and mutagenesis which results in the generation of frameshift mutations, mutations which cause premature termination of a protein, or mutation of regulatory sequences which affect gene expression. In another embodiment, mutagenesis can be accomplished using recombinant DNA techniques or using traditional mutagenesis technology using mutagenic chemicals or radiation and subsequent selection of mutants. In another embodiment, deletion mutants are preferred because of the accompanying low probability of reversion of the auxotrophic phenotype. In another embodiment, mutants of D-alanine which are generated according to the protocols presented herein may be tested for the ability to grow in the absence of D-alanine in a simple laboratory culture assay. In another embodiment, those mutants which are unable to grow in the absence of this compound are selected for further study.
In another embodiment, in addition to the aforementioned D-alanine associated genes, other genes involved in synthesis of a metabolic enzyme, as provided herein, may be used as targets for mutagenesis of Listeria. 
In another embodiment, the metabolic enzyme complements an endogenous metabolic gene that is lacking in the remainder of the chromosome of the recombinant bacterial strain. In one embodiment, the endogenous metabolic gene is mutated in the chromosome. In another embodiment, the endogenous metabolic gene is deleted from the chromosome. In another embodiment, said metabolic enzyme is an amino acid metabolism enzyme. In another embodiment, said metabolic enzyme catalyzes a formation of an amino acid used for a cell wall synthesis in said recombinant Listeria strain. In another embodiment, said metabolic enzyme is an alanine racemase enzyme. In another embodiment, said metabolic enzyme is a D-amino acid transferase enzyme. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In one embodiment, said auxotrophic Listeria strain comprises an episomal expression vector comprising a metabolic enzyme that complements the auxotrophy of said auxotrophic Listeria strain. In another embodiment, the construct is contained in the Listeria strain in an episomal fashion. In another embodiment, the foreign antigen is expressed from a vector harbored by the recombinant Listeria strain. In another embodiment, said episomal expression vector lacks an antibiotic resistance marker. In one embodiment, an antigen of the methods and compositions as provided herein is fused to an polypeptide comprising a PEST sequence. In another embodiment, said polypeptide comprising a PEST sequence is a truncated LLO. In another embodiment, said polypeptide comprising a PEST sequence is ActA.
In another embodiment, the Listeria strain is deficient in an AA metabolism enzyme. In another embodiment, the Listeria strain is deficient in a D-glutamic acid synthase gene. In another embodiment, the Listeria strain is deficient in the dat gene. In another embodiment, the Listeria strain is deficient in the dal gene. In another embodiment, the Listeria strain is deficient in the dga gene. In another embodiment, the Listeria strain is deficient in a gene involved in the synthesis of diaminopimelic acid. CysK. In another embodiment, the gene is vitamin-B12 independent methionine synthase. In another embodiment, the gene is trpA. In another embodiment, the gene is trpB. In another embodiment, the gene is trpE. In another embodiment, the gene is asnB. In another embodiment, the gene is gltD. In another embodiment, the gene is gltB. In another embodiment, the gene is leuA. In another embodiment, the gene is argG. In another embodiment, the gene is thrC. In another embodiment, the Listeria strain is deficient in one or more of the genes described hereinabove.
In another embodiment, the Listeria strain is deficient in a synthase gene. In another embodiment, the gene is an AA synthesis gene. In another embodiment, the gene is folP. In another embodiment, the gene is dihydrouridine synthase family protein. In another embodiment, the gene is ispD. In another embodiment, the gene is ispF. In another embodiment, the gene is phosphoenolpyruvate synthase. In another embodiment, the gene is hisF. In another embodiment, the gene is hisH. In another embodiment, the gene is fliI. In another embodiment, the gene is ribosomal large subunit pseudouridine synthase. In another embodiment, the gene is ispD. In another embodiment, the gene is bifunctional GMP synthase/glutamine amidotransferase protein. In another embodiment, the gene is cobS. In another embodiment, the gene is cobB. In another embodiment, the gene is cbiD. In another embodiment, the gene is uroporphyrin-III C-methyltransferase/uroporphyrinogen-III synthase. In another embodiment, the gene is cobQ. In another embodiment, the gene is uppS. In another embodiment, the gene is truB. In another embodiment, the gene is dxs. In another embodiment, the gene is mvaS. In another embodiment, the gene is dapA. In another embodiment, the gene is ispG. In another embodiment, the gene is folC. In another embodiment, the gene is citrate synthase. In another embodiment, the gene is argJ. In another embodiment, the gene is 3-deoxy-7-phosphoheptulonate synthase. In another embodiment, the gene is indole-3-glycerol-phosphate synthase. In another embodiment, the gene is anthranilate synthase/glutamine amidotransferase component. In another embodiment, the gene is menB. In another embodiment, the gene is menaquinone-specific isochorismate synthase. In another embodiment, the gene is phosphoribosylformylglycinamidine synthase I or II. In another embodiment, the gene is phosphoribosylaminoimidazole-succinocarboxamide synthase. In another embodiment, the gene is carB. In another embodiment, the gene is carA. In another embodiment, the gene is thyA. In another embodiment, the gene is mgsA. In another embodiment, the gene is aroB. In another embodiment, the gene is hepB. In another embodiment, the gene is rluB. In another embodiment, the gene is ilvB. In another embodiment, the gene is ilvN. In another embodiment, the gene is alsS. In another embodiment, the gene is fabF. In another embodiment, the gene is fabH. In another embodiment, the gene is pseudouridine synthase. In another embodiment, the gene is pyrG. In another embodiment, the gene is truA. In another embodiment, the gene is pabB. In another embodiment, the gene is an atp synthase gene (e.g. atpC, atpD-2, aptG, atpA-2, etc).
In another embodiment, the gene is phoP. In another embodiment, the gene is aroA. In another embodiment, the gene is aroC. In another embodiment, the gene is aroD. In another embodiment, the gene is plcB.
In another embodiment, the Listeria strain is deficient in a peptide transporter. In another embodiment, the gene is ABC transporter/ATP-binding/permease protein. In another embodiment, the gene is oligopeptide ABC transporter/oligopeptide-binding protein. In another embodiment, the gene is oligopeptide ABC transporter/permease protein. In another embodiment, the gene is zinc ABC transporter/zinc-binding protein. In another embodiment, the gene is sugar ABC transporter. In another embodiment, the gene is phosphate transporter. In another embodiment, the gene is ZIP zinc transporter. In another embodiment, the gene is drug resistance transporter of the EmrB/QacA family. In another embodiment, the gene is sulfate transporter. In another embodiment, the gene is proton-dependent oligopeptide transporter. In another embodiment, the gene is magnesium transporter. In another embodiment, the gene is formate/nitrite transporter. In another embodiment, the gene is spermidine/putrescine ABC transporter. In another embodiment, the gene is Na/Pi-cotransporter. In another embodiment, the gene is sugar phosphate transporter. In another embodiment, the gene is glutamine ABC transporter. In another embodiment, the gene is major facilitator family transporter. In another embodiment, the gene is glycine betaine/L-proline ABC transporter. In another embodiment, the gene is molybdenum ABC transporter. In another embodiment, the gene is techoic acid ABC transporter. In another embodiment, the gene is cobalt ABC transporter. In another embodiment, the gene is ammonium transporter. In another embodiment, the gene is amino acid ABC transporter. In another embodiment, the gene is cell division ABC transporter. In another embodiment, the gene is manganese ABC transporter. In another embodiment, the gene is iron compound ABC transporter. In another embodiment, the gene is maltose/maltodextrin ABC transporter. In another embodiment, the gene is drug resistance transporter of the Bcr/CflA family. In another embodiment, the gene is a subunit of one of the above proteins.
In one embodiment, provided herein is a nucleic acid molecule that is used to transform the Listeria in order to arrive at a recombinant Listeria. In another embodiment, the nucleic acid provided herein used to transform Listeria lacks a virulence gene. In another embodiment, the nucleic acid molecule is integrated into the Listeria genome and carries a non-functional virulence gene. In another embodiment, the virulence gene is mutated in the recombinant Listeria. In yet another embodiment, the nucleic acid molecule is used to inactivate the endogenous gene present in the Listeria genome. In yet another embodiment, the virulence gene is an actA gene, an inlA gene, and inlB gene, an inlC gene, inlJ gene, a plbC gene, a bsh gene, or a prfA gene. It is to be understood by a skilled artisan, that the virulence gene can be any gene known in the art to be associated with virulence in the recombinant Listeria. 
In yet another embodiment the Listeria strain is an inlA mutant, an inlB mutant, an inlC mutant, an inlJ mutant, prfA mutant, actA mutant, a dal/dat mutant, a prfA mutant, a plcB deletion mutant, or a double mutant lacking both plcA and plcB. In another embodiment, the Listeria comprise a deletion or mutation of these genes individually or in combination. In another embodiment, the Listeria provided herein lack each one of genes. In another embodiment, the Listeria provided herein lack at least one and up to ten of any gene provided herein, including the actA, prfA, and dal/dat genes. In another embodiment, the prfA mutant is a D133V prfA mutant.
In one embodiment, the live attenuated Listeria is a recombinant Listeria. In another embodiment, the recombinant Listeria comprises a mutation or a deletion of a genomic internalin C (inlC) gene. In another embodiment, the recombinant Listeria comprises a mutation or a deletion of a genomic actA gene and a genomic internalin C gene. In one embodiment, translocation of Listeria to adjacent cells is inhibited by the deletion of the actA gene and/or the inlC gene, which are involved in the process, thereby resulting in unexpectedly high levels of attenuation with increased immunogenicity and utility as a strain backbone. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the metabolic gene, the virulence gene, etc. is lacking in a chromosome of the Listeria strain. In another embodiment, the metabolic gene, virulence gene, etc. is lacking in the chromosome and in any episomal genetic element of the Listeria strain. In another embodiment, the metabolic gene, virulence gene, etc. is lacking in the genome of the virulence strain. In one embodiment, the virulence gene is mutated in the chromosome. In another embodiment, the virulence gene is deleted from the chromosome. Each possibility represents a separate embodiment of the present invention
In one embodiment, the recombinant Listeria strain provided herein is attenuated. In another embodiment, the recombinant Listeria lacks the actA virulence gene. In another embodiment, the recombinant Listeria lacks the prfA virulence gene. In another embodiment, the recombinant Listeria lacks the inlB gene. In another embodiment, the recombinant Listeria lacks both, the actA and inlB genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA gene. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous inlB gene. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous inlC gene. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA and inlB genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA and inlC genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA, inlB, and inlC genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA, inlB, and inlC genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation of the endogenous actA, inlB, and inlC genes. In another embodiment, the recombinant Listeria strain provided herein comprise an inactivating mutation in any single gene or combination of the following genes: actA, dal, dat, inlB, inlC, prfA, plcA, plcB.
It will be appreciated by the skilled artisan that the term “mutation” and grammatical equivalents thereof, include any type of mutation or modification to the sequence (nucleic acid or amino acid sequence), and includes a deletion mutation, a truncation, an inactivation, a disruption, or a translocation. These types of mutations are readily known in the art.
In one embodiment, in order to select for an auxotrophic bacteria comprising a plasmid encoding a metabolic enzyme or a complementing gene provided herein, transformed auxotrophic bacteria are grown on a media that will select for expression of the amino acid metabolism gene or the complementing gene. In another embodiment, a bacteria auxotrophic for D-glutamic acid synthesis is transformed with a plasmid comprising a gene for D-glutamic acid synthesis, and the auxotrophic bacteria will grow in the absence of D-glutamic acid, whereas auxotrophic bacteria that have not been transformed with the plasmid, or are not expressing the plasmid encoding a protein for D-glutamic acid synthesis, will not grow. In another embodiment, a bacterium auxotrophic for D-alanine synthesis will grow in the absence of D-alanine when transformed and expressing the plasmid of the present invention if the plasmid comprises an isolated nucleic acid encoding an amino acid metabolism enzyme for D-alanine synthesis. Such methods for making appropriate media comprising or lacking necessary growth factors, supplements, amino acids, vitamins, antibiotics, and the like are well known in the art, and are available commercially (Becton-Dickinson, Franklin Lakes, N.J.). Each method represents a separate embodiment of the present invention.
In another embodiment, once the auxotrophic bacteria comprising the plasmid of the present invention have been selected on appropriate media, the bacteria are propagated in the presence of a selective pressure. Such propagation comprises growing the bacteria in media without the auxotrophic factor. The presence of the plasmid expressing an amino acid metabolism enzyme in the auxotrophic bacteria ensures that the plasmid will replicate along with the bacteria, thus continually selecting for bacteria harboring the plasmid. The skilled artisan, when equipped with the present disclosure and methods herein will be readily able to scale-up the production of the Listeria strain vector by adjusting the volume of the media in which the auxotrophic bacteria comprising the plasmid are growing.
The skilled artisan will appreciate that, in another embodiment, other auxotroph strains and complementation systems are adopted for the use with this invention.
In one embodiment, the N-terminal LLO protein fragment and PSA antigen are fused directly to one another. In another embodiment, the genes encoding the N-terminal LLO protein fragment and PSA antigen are not fused directly to one another. In another embodiment, the N-terminal LLO protein fragment and PSA antigen are operably attached via a linker peptide. In another embodiment, the N-terminal LLO protein fragment and PSA antigen are attached via a heterologous peptide. In another embodiment, the N-terminal LLO protein fragment is N-terminal to the PSA antigen. In another embodiment, the N-terminal LLO protein fragment is the N-terminal-most portion of the fusion protein. In another embodiment, a truncated LLO is truncated at the C-terminal to arrive at an N-terminal LLO. Each possibility represents a separate embodiment of the present invention.
The term “linker”, as used herein refers to an amino acid sequence that joins two heterologous polypeptides, or fragments or domains thereof. For example, linking a tLLO and a PSA polypeptide. In general, as used herein, a linker is an amino acid sequence that covalently links the polypeptides to form a fusion polypeptide. A linker typically includes the amino acids translated from the remaining recombination signal after removal of a reporter gene from a display vector to create a fusion protein comprising an amino acid sequence encoded by an open reading frame and the display protein. As appreciated by one of skill in the art, the linker can comprise additional amino acids, such as glycine and other small neutral amino acids.
The term “operably linked” as used herein means that the transcriptional and translational regulatory nucleic acid, is positioned relative to any coding sequences in such a manner that transcription is initiated. Generally, this will mean that the promoter and transcriptional initiation or start sequences are positioned 5′ to the coding region.
The term “open reading frame” or “ORF” is a portion of an organism's genome which contains a sequence of bases that could potentially encode a protein. In another embodiment, the start and stop ends of the ORF are not equivalent to the ends of the mRNA, but they are usually contained within the mRNA. In one embodiment, ORFs are located between the start-code sequence (initiation codon) and the stop-codon sequence (termination codon) of a gene. Thus, in one embodiment, a nucleic acid molecule operably integrated into a genome as an open reading frame with an endogenous polypeptide is a nucleic acid molecule that has integrated into a genome in the same open reading frame as an endogenous polypeptide.
In one embodiment, the attenuated Listeria strain provided herein expresses a recombinant polypeptide. In another embodiment, the attenuated Listeria strain comprises a plasmid that encodes a recombinant polypeptide. In another embodiment, a recombinant nucleic acid provided herein is in a plasmid in the attenuated Listeria strain provided herein. In another embodiment, the plasmid is an episomal plasmid that does not integrate into said attenuated Listeria strain's chromosome. In another embodiment, the plasmid is an integrative plasmid that integrates into said Listeria strain's chromosome. In another embodiment, the plasmid is a multicopy plasmid.
In one embodiment, the attenuated Listeria strain of the compositions and methods as provided herein comprise a first or second nucleic acid molecule that encodes a Prostate Specific Antigen (PSA), which in one embodiment, is a marker for prostate cancer that is highly expressed by prostate tumors. In one embodiment, PSA is a kallikrein serine protease (KLK3) secreted by prostatic epithelial cells, which in one embodiment, is widely used as a marker for prostate cancer.
In one embodiment, the recombinant Listeria strain as provided herein comprises a nucleic acid molecule encoding KLK3 protein.
In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPL


 


YDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGT


 


TCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAG


 


RWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYR


 


KWIKDTIVANP 


 


(SEQ ID No: 25; GenBank Accession No. CAA32915).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 25. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 25. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 25. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 25. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







(SEQ ID No: 26)


IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVIL


 


LGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLL


 


RLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCV


 


DLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCYGVLQ


 


GITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP.






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 26. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 26. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 26. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 26. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVIL


 


LGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLL


 


RLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCV


 


DLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQ


 


GITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP 


 


(SEQ ID No: 27; GenBank Accession No. AAA59995.1).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 27. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 27. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 27. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 27. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







ggtgtcttaggcacactggtcttggagtgcaaaggatctaggcacgtga


 


ggctttgtatgaagaatcggggatcgtacccaccccctgtttctgatca


 


tcctgggcatgtctcctctgcctagtcccctagatgaagtctccatgag


 


ctacaagggcctggtgcatccagggtgatctagtaattgcagaacagca


 


agtgctagctctccctccccttccacagctctgggtgtgggagggggtt


 


gtccagcctccagcagcatggggagggccttggtcagcctctgggtgcc


 


agcagggcaggggcggagtcctggggaatgaaggttttatagggctcct


 


gggggaggctccccagccccaagcttaccacctgcacccggagagctgt


 


gtcaccatgtgggtcccggagtatcctcaccctgtccgtgacgtggatt


 


ggtgagaggggccatggttggggggatgcaggagagggagccagccctg


 


actgtcaagctgaggctctttcccccccaacccagcaccccagcccaga


 


cagggagctgggctatactgtctctcccagccccacttcaagcccatac


 


ccccagtcccctccatattgcaacagtcctcactcccacaccaggtccc


 


cgctccctcccacttaccccagaactacttcccatttgcccagccagct


 


ccctgctcccagctgattactaaaggggaagacctgggcatctccgtga


 


tctctagtggggctcaaaacctccaaggacctctctcaatgccattgga


 


ccaggaccgtatcactggtccatctcctgagcccctcaatcctatcaca


 


gtctactgacttacccattcagctgtgagtgtccaaccctatcccagag


 


accttgatgatggcctcccaatcagccctaggatacccagatgccaacc


 


agacacctcatattcctagccaggctatctggcctgagacaacaaatgg


 


gtccctcagtctggcaatgggactctgagaactcctcattccctgactc


 


ttagccccagactcttcattcagtggcccacattttccttaggaaaaac


 


atgagcatccccagccacaactgccagctctctgagtccccaaatctgc


 


atccattcaaaacctaaaaacaaaaagaaaaacaaataaaacaaaacca


 


actcagaccagaactgattctcaacctgggacttcctaaactaccaaaa


 


ccacctcaccagcaactgaacctcgccataaggcacttatccctggacc


 


tagcaccccttatcccctcagaatccacaacttgtaccaagtacccact


 


cccagtccaagaccccaaatcaccacaaaggacccaatccccagactca


 


agatatggtctgggcgctgtcttgtgtctcctaccctgatccctgggtt


 


caactctgctcccagagcatgaagcctctccaccagcaccagccaccaa


 


cctgcaaacctagggaagattgacagaattcccagcctacccagctccc


 


cctgcccatgtcccaggactcccagccaggactctgcccccgtgtattt


 


caaacccacatcctaaatccatctcctatccgagtcccccagaccccct


 


gtcaaccctgattcccctgatctagcaccccctctgcaggcgctgcgcc


 


cctcatcctgtctcggattgtgggaggctgggagtgcgagaagcattcc


 


caaccctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcg


 


gtgttctggtgcacccccagtgggtcctcacagctgcccactgcatcag


 


gaagtgagtaggggcctggggtctggggagcaggtgtctgtgtcccaga


 


ggaataacagctgggcattaccccaggataacctctaaggccagccagg


 


gactgggggagagagggaaagactggacaggtcacatggggaggcaggg


 


aggggctggaccaccctccccatggctgcctgggtctccatctgtgtcc


 


ctctatgtctctagtgtcgattcattatgtctcaggtaactggcttcgg


 


agtgtctctccgtgtgactattagactctctctccctctcactctgtct


 


tcagtctccatatctccccctctctctgtccactctggtccctctctag


 


ccagtgtgtctcaccctgtatctctctgccaggctctgtctctcggtct


 


ctgtctcacctgtgccttctccctactgaacacacgcacgggatgggcc


 


tgggggaccctgagaaaaggaagggctaggctgggcgcggtggctcaca


 


cctgtaatcccagcactagggaggccaaggcaggtagatcacctgaggt


 


caggagttcgagaccagcctggccaactggtgaaaccccatctctacta


 


aaaatacaaaaaattagccaggcgtggtggcgcatgcctgtagtcccag


 


ctactcaggagctgagggaggagaattgcattgaacctggaggagagga


 


gcagtgagccgagaccgtgccactgcactccagcctgggtgacagagtg


 


agactccgcctcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaagaaaaga


 


aaagaaaagaaaaggaagtgattatccctgatgtgtgtgggtatgaggg


 


tatgagagggcccctctcactccattccactccaggacatccctccact


 


cagggagacacagagaagggctggaccagctggagctgggaggggcaat


 


tgagggaggaggaaggagaagggggaaggaaaacagggtatgggggaaa


 


ggaccctggggagcgaagtggaggatacaaccagggcctgcaggcaggc


 


tacctacccacttggaaacccacgccaaagccgcatctacagctgagcc


 


actctgaggcctcccctccccggcggtccccactcagctccaaagtctc


 


tctccatactctcccacactttatcatcccccggattcctctctacttg


 


gactcattcttcattgacttcctgatccctactcattcatctgatctca


 


ctactgcctggattgacttctctctctcatctctggcccatgtctgatc


 


tctatgtactgtcattctactcatcctgtgtattacggctcaccagtag


 


tcactgactcccctctgccattcattctctctgccatttaccctatcct


 


tacccaggactctcagactgtatctgcccacaccctctcacactgctga


 


tcccaactcgagtctgtattaggcctgaactgtgtatcccaaccctgtg


 


attctcactgatctattctataggagcctcctccttgctcctctgtcca


 


tctctattccttatcatcctcgctcctcattcctgcgtctgatcctccc


 


cagcaaaagcgtgatcttgctgggtcggcacagcctgatcatcctgaag


 


acacaggccaggtatttcaggtcagccacagatcccacacccgctctac


 


gatatgagcctcctgaagaatcgattcctcaggccaggtgatgactcca


 


gccacgacctcatgctgctccgcctgtcagagcctgccgagctcacgga


 


tgctgtgaaggtcatggacctgcccacccaggagccagcactggggacc


 


acctgctacgcctcaggctggggcagcattgaaccagaggagtgtacgc


 


ctgggccagatggtgcagccgggagcccagatgcctgggtctgagggag


 


gaggggacaggactcctgggtctgagggaggagggccaaggaaccaggt


 


ggggtccagcccacaacagtgatttgcctggcccgtagtcttgacccca


 


aagaaacttcagtgtgtggacctccatgttataccaatgacgtgtgtgc


 


gcaagttcaccctcagaaggtgaccaagttcatgctgtgtgctggacgc


 


tggacagggggcaaaagcacctgctcggtgagtcatccctactcccaag


 


atcttgagggaaaggtgagtgggaccttaattctgggctggggtctaga


 


agccaacaaggcgtctgcctcccctgctccccagctgtagccatgccac


 


ctccccgtgtctcatctcattccctccaccctatattgactccctcaag


 


gcaataggttattcttacagcacaactcatctgacctgcgttcagcaca


 


cggttactaggcacctgctatgcacccagcactgccctagagcctggga


 


catagcagtgaacagacagagagcagcccctccatctgtagcccccaag


 


ccagtgaggggcacaggcaggaacagggaccacaacacagaaaagctgg


 


agggtgtcaggaggtgatcaggctctcggggagggagaaggggtgggga


 


gtgtgactgggaggagacatcctgcagaaggtgggagtgagcaaacacc


 


tgcgcaggggaggggagggcctgcggcacctgggggagcagagggaaca


 


gcatctggccaggcctgggaggaggggcctagagggcgtcaggagcaga


 


gaggaggttgcctggctggagtgaaggatcggggcagggtgcgagaggg


 


aacaaaggacccctcctgcagggcctcacctgggccacaggaggacact


 


gcttacctctgaggagtcaggaactgtggatggtgctggacagaagcag


 


gacagggcctggctcaggtgtccagaggctgcgctggcctcctatggga


 


tcagactgcagggagggagggcagcagggatgtggagggagtgatgatg


 


gggctgacctgggggtggctccaggcattgtccccacctgggcccttac


 


ccagcctccctcacaggctcctggccctcagtctctcccctccactcca


 


ttctccacctacccacagtgggtcattctgatcaccgaactgaccatgc


 


cagccctgccgatggtcctccatggctccctagtgccctggagaggagg


 


tgtctagtcagagagtagtcctggaaggtggcctctgtgaggagccacg


 


gggacagcatcctgcagatggtcctggcccttgtcccaccgacctgtct


 


acaaggactgtcctcgtggaccctcccctctgcacaggagctggaccct


 


gaagtcccacctaccggccaggactggagcccctacccctctgaggaat


 


ccctgcccaccacttctggaagtcggctctggagacatactctcttcac


 


caaagctgggaactgctatctgttatctgcctgtccaggtctgaaagat


 


aggattgcccaggcagaaactgggactgacctatctcactctctccctg


 


cattacccttagggtgattctgggggcccacttgtctgtaatggtgtgc


 


ttcaaggtatcacgtcatggggcagtgaaccatgtgccctgcccgaaag


 


gccttccctgtacaccaaggtggtgcattaccggaagtggatcaaggac


 


accatcgtggccaacccctgagcacccctatcaagtccctattgtagta


 


aacttggaaccaggaaatgaccaggccaagactcaagcctccccagact


 


actgaccatgtccttaggtgtgaggtccagggagctaggaaaagaaatc


 


agcagacacaggtgtagaccagagtgatcttaaatggtgtaattagtcc


 


tctctgtgtcctggggaatactggccatgcctggagacatatcactcaa


 


tactctgaggacacagttaggatggggtgtctgtgttatagtgggatac


 


agagatgaaagaggggtgggatcc 


 


(SEQ ID No: 28; GenBank Accession No. X14810).






In another embodiment, the KLK3 protein is encoded by residues 401 . . . 446, 1688 . . . 1847, 3477 . . . 3763, 3907 . . . 4043, and 5413 . . . 5568 of SEQ ID No: 28. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 28. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 28. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 28. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 28. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAV


 


CGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPH


 


PLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPA


 


LGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFM


 


LCAGRWTGGKSTCSWVILITELTMPALPMVLHGSLVPWRGGV 


 


(SEQ ID No: 29; GenBank Accession No. NP_001025218)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 29. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 29. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 29. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 29. Each possibility represents a separate embodiment as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







agccccaagcttaccacctgcacccggagagctgtgtcaccatgtgggt


 


cccggagtatcctcaccctgtccgtgacgtggattggtgctgcacccct


 


catcctgtctcggattgtgggaggctgggagtgcgagaagcattcccaa


 


ccctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcggtg


 


actggtgcacccccagtgggtcctcacagctgcccactgcatcaggaac


 


aaaagcgtgatcttgctgggtcggcacagcctgatcatcctgaagacac


 


aggccaggtatttcaggtcagccacagatcccacacccgctctacgata


 


tgagcctcctgaagaatcgattcctcaggccaggtgatgactccagcca


 


cgacctcatgctgctccgcctgtcagagcctgccgagctcacggatgct


 


gtgaaggtcatggacctgcccacccaggagccagcactggggaccacct


 


gctacgcctcaggctggggcagcattgaaccagaggagacttgacccca


 


aagaaacttcagtgtgtggacctccatgttataccaatgacgtgtgtgc


 


gcaagttcaccctcagaaggtgaccaagttcatgctgtgtgctggacgc


 


tggacagggggcaaaagcacctgctcgtgggtcattctgatcaccgaac


 


tgaccatgccagccctgccgatggtcctccatggctccctagtgccctg


 


gagaggaggtgtctagtcagagagtagtcctggaaggtggcctctgtga


 


ggagccacggggacagcatcctgcagatggtcctggcccttgtcccacc


 


gacctgtctacaaggactgtcctcgtggaccctcccctctgcacaggag


 


ctggaccctgaagtcccttccccaccggccaggactggagcccctaccc


 


ctctgttggaatccctgcccaccttcttctggaagtcggctctggagac


 


atttctctcttcttccaaagctgggaactgctatctgttatctgcctgt


 


ccaggtctgaaagataggattgcccaggcagaaactgggactgacctat


 


ctcactctctccctgcttttacccttagggtgattctgggggcccactt


 


gtctgtaatggtgtgcttcaaggtatcacgtcatggggcagtgaaccat


 


gtgccctgcccgaaaggccttccctgtacaccaaggtggtgcattaccg


 


gaagtggatcaaggacaccatcgtggccaacccctgagcacccctatca


 


accccctattgtagtaaacttggaaccttggaaatgaccaggccaagac


 


tcaagcctccccagttctactgacctttgtccttaggtgtgaggtccag


 


ggttgctaggaaaagaaatcagcagacacaggtgtagaccagagtgttt


 


cttaaatggtgtaattttgtcctctctgtgtcctggggaatactggcca


 


tgcctggagacatatcactcaatttctctgaggacacagataggatggg


 


gtgtctgtgttatttgtggggtacagagatgaaagaggggtgggatcca


 


cactgagagagtggagagtgacatgtgctggacactgtccatgaagcac


 


tgagcagaagctggaggcacaacgcaccagacactcacagcaaggatgg


 


agctgaaaacataacccactctgtcctggaggcactgggaagcctagag


 


aaggctgtgagccaaggagggagggtcttcctttggcatgggatgggga


 


tgaagtaaggagagggactggaccccctggaagctgattcactatgggg


 


ggaggtgtattgaagtcctccagacaaccctcagatttgatgatttcct


 


agtagaactcacagaaataaagagctgttatactgtg 


 


(SEQ ID No: 30; GenBank Accession No.


 


NM_001030047).






In another embodiment, the KLK3 protein is encoded by residues 42-758 of SEQ ID No: 30. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 30. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 30. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 30. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 30. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGR


 


AVCGGVLVHPQWVLTAAHCIRK (SEQ ID No: 31; GenBank


 


Accession No. NP_001025221).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 31. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 31. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID No: 31. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 31. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 31. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







(SEQ ID No: 32)


agccccaagcttaccacctgcacccggagagctgtgtcaccatgtgggt


 


cccggagtcacctcacccaccgtgacgtggattggtgctgcacccctca


 


tcctgtctcggattgtgggaggctgggagtgcgagaagcattcccaacc


 


ctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcggtgac


 


tggtgcacccccagtgggtcctcacagctgcccactgcatcaggaagtg


 


agtaggggcctggggtctggggagcaggtgtctgtgtcccagaggaata


 


acagctgggcattttccccaggataacctctaaggccagccttgggact


 


gggggagagagggaaagttctggttcaggtcacatggggaggcagggtt


 


ggggctggaccaccctccccatggctgcctgggtctccatctgtgacct


 


ctatgtctctagtgtcgattcattatgtctcaggtaactggcttcggag


 


tgtctctccgtgtgactattagactctctctccctctcttctctgtctt


 


cagt.






In another embodiment, the KLK3 protein is encoded by residues 42-758 of SEQ ID No: 32. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 32. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 32. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 32. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 32. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein that is the source of the KLK3 peptide has the sequence:







(SEQ ID No: 33)


MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAV


 


CGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPH


 


PLYDMSLLKNRFLRPGDDSSIEPEEFLTPKKLQCVDLHVISNDVCAQVH


 


PQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALP


 


ERPSLYTKVVHYRKWIKDTIVANP.






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 33. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 33. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 33. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 33. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







(SEQ ID No: 34)


agccccaagcttaccacctgcacccggagagctgtgtcaccatgtgggt


 


cccggagtcacctcaccctgtccgtgacgtggattggtgctgcacccct


 


catcctgtctcggattgtgggaggctgggagtgcgagaagcattcccaa


 


ccctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcggtg


 


actggtgcacccccagtgggtcctcacagctgcccactgcatcaggaac


 


aaaagcgtgatcttgctgggtcggcacagcctgatcatcctgaagacac


 


aggccaggtatttcaggtcagccacagcacccacacccgctctacgata


 


tgagcctcctgaagaatcgattcctcaggccaggtgatgactccagcat


 


tgaaccagaggagttcttgaccccaaagaaacttcagtgtgtggacctc


 


catgttataccaatgacgtgtgtgcgcaagttcaccctcagaaggtgac


 


caagttcatgctgtgtgctggacgctggacagggggcaaaagcacctgc


 


tcgggtgattctgggggcccacttgtctgtaatggtgtgcttcaaggta


 


tcacgtcatggggcagtgaaccatgtgccctgcccgaaaggccaccctg


 


tacaccaaggtggtgcattaccggaagtggatcaaggacaccatcgtgg


 


ccaacccctgagcacccctatcaaccccctattgtagtaaacttggaac


 


caggaaatgaccaggccaagactcaagcctccccagactactgacctag


 


tccttaggtgtgaggtccagggagctaggaaaagaaatcagcagacaca


 


ggtgtagaccagagtgatcttaaatggtgtaattagtcctctctgtgtc


 


ctggggaatactggccatgcctggagacatatcactcaatactctgagg


 


acacagataggatggggtgtctgtgttatagtggggtacagagatgaaa


 


gaggggtgggatccacactgagagagtggagagtgacatgtgctggaca


 


ctgtccatgaagcactgagcagaagctggaggcacaacgcaccagacac


 


tcacagcaaggatggagctgaaaacataacccactctgtcctggaggca


 


ctgggaagcctagagaaggctgtgagccaaggagggagggtatcctagg


 


catgggatggggatgaagtaaggagagggactggaccccctggaagctg


 


attcactatggggggaggtgtattgaagtcctccagacaaccctcagat


 


ttgatgatacctagtagaactcacagaaataaagagctgaatactgtg.






In another embodiment, the KLK3 protein is encoded by residues 42-758 of SEQ ID No: 34. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 34. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 34. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 34. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 34. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRKPGDDSSHDLMLLRLSEPAELTDAVKVMDLPT


 


QEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVT


 


KFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLY


 


TKVVHYRKWIKDTIVANP (SEQ ID No: 35; GenBank


 


Accession No. NP_001025219).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 35. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 35. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 35. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 35. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







agccccaagcttaccacctgcacccggagagctgtgtcaccatgtgggt


 


cccggagtatcctcaccctgtccgtgacgtggattggtgctgcacccct


 


catcctgtctcggattgtgggaggctgggagtgcgagaagcattcccaa


 


ccctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcggtg


 


actggtgcacccccagtgggtcctcacagctgcccactgcatcaggaag


 


ccaggtgatgactccagccacgacctcatgctgctccgcctgtcagagc


 


ctgccgagctcacggatgctgtgaaggtcatggacctgcccacccagga


 


gccagcactggggaccacctgctacgcctcaggctggggcagcattgaa


 


ccagaggagttcttgaccccaaagaaacttcagtgtgtggacctccatg


 


ttataccaatgacgtgtgtgcgcaagttcaccctcagaaggtgaccaag


 


ttcatgctgtgtgctggacgctggacagggggcaaaagcacctgctcgg


 


gtgattctgggggcccacttgtctgtaatggtgtgcttcaaggtatcac


 


gtcatggggcagtgaaccatgtgccctgcccgaaaggccaccctgtaca


 


ccaaggtggtgcattacccaaggacaccatcgtggccaacccctgagca


 


cccctatcaaccccctaagtagtaaacttggaaccaggaaatgaccagg


 


ccaagactcaagcctccccagactactgacctagtccttaggtgtgagg


 


tccagggagctaggaaaagaaatcagcagacacaggtgtagaccagagt


 


gatcttaaatggtgtaattagtcctctctgtgtcctggggaatactggc


 


catgcctggagacatatcactcaatactctgaggacacagataggatgg


 


ggtgtctgtgttatagtggggtacagagatgaaagaggggtgggatcca


 


cactgagagagtggagagtgacatgtgctggacactgtccatgaagcac


 


tgagcagaagctggaggcacaacgcaccagacactcacagcaaggatgg


 


agctgaaaacataacccactctgtcctggaggcactgggaagcctagag


 


aaggctgtgagccaaggagggagggtcttcctttggcatgggatgggga


 


tgaagtaaggagagggactggaccccctggaagctgattcactatgggg


 


ggaggtgtattgaagtcctccagacaaccctcagatttgatgataccta


 


gtagaactcacagaaataaagagctgttatactgtg (SEQ


 


ID No: 36; GenBank Accession No. NM_001030048).






In another embodiment, the KLK3 protein is encoded by residues 42-758 of SEQ ID No: 36. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 36. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 36. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 36. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 36. Each possibility represents a separate embodiment of the methods and compositions as provided herein

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAV


 


CGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPH


 


PLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPA


 


LGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFM


 


LCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTK


 


VVHYRKWIKDTIVANP (SEQ ID No: 37; GenBank Accession


 


No. NP_001639).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 37. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 37. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 37. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 37. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







agccccaagcttaccacctgcacccggagagctgtgtcaccatgtgggt


 


cccggagtcacctcaccctgtccgtgacgtggattggtgctgcacccct


 


catcctgtctcggattgtgggaggctgggagtgcgagaagcattcccaa


 


ccctggcaggtgcttgtggcctctcgtggcagggcagtctgcggcggtg


 


actggtgcacccccagtgggtcctcacagctgcccactgcatcaggaac


 


aaaagcgtgatcttgctgggtcggcacagcctgatcatcctgaagacac


 


aggccaggtatttcaggtcagccacagcacccacacccgctctacgata


 


tgagcctcctgaagaatcgattcctcaggccaggtgatgactccagcca


 


cgacctcatgctgctccgcctgtcagagcctgccgagctcacggatgct


 


gtgaaggtcatggacctgcccacccaggagccagcactggggaccacct


 


gctacgcctcaggctggggcagcattgaaccagaggagacttgacccca


 


aagaaacttcagtgtgtggacctccatgttataccaatgacgtgtgtgc


 


gcaagttcaccctcagaaggtgaccaagttcatgctgtgtgctggacgc


 


tggacagggggcaaaagcacctgctcgggtgattctgggggcccacttg


 


tctgtaatggtgtgcttcaaggtatcacgtcatggggcagtgaaccatg


 


tgccctgcccgaaaggccaccctgtacaccaaggtggtgcattaccgga


 


agtggatcaaggacaccatcgtggccaacccctgagcacccctatcaac


 


cccctattgtagtaaacttggaaccaggaaatgaccaggccaagactca


 


agcctccccagttctactgacctttgtccttaggtgtgaggtccagggt


 


tgctaggaaaagaaatcagcagacacaggtgtagaccagagtgtttctt


 


aaatggtgtaattngtcctctctgtgtcctggggaatactggccatgcc


 


tggagacatatcactcaatttctctgaggacacagataggatggggtgt


 


ctgtgttatttgtggggtacagagatgaaagaggggtgggatccacact


 


gagagagtggagagtgacatgtgctggacactgtccatgaagcactgag


 


cagaagctggaggcacaacgcaccagacactcacagcaaggatggagct


 


gaaaacataacccactctgtcctggaggcactgggaagcctagagaagg


 


ctgtgagccaaggagggagggtcttcctttggcatgggatggggatgaa


 


gtaaggagagggactggaccccctggaagctgattcactatggggggag


 


gtgtattgaagtcctccagacaaccctcagatttgatgatttcctagta


 


gaactcacagaaataaagagctgttatactgtg (SEQ ID No: 38;


 


GenBank Accession No. NM_001648).






In another embodiment, the KLK3 protein is encoded by residues 42-827 of SEQ ID No: 38. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 38. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 38. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 38. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 38. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAV


 


CGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPH


 


PLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPA


 


LGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFM


 


LCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTK


 


VVHYRKWIKDTIVANP (SEQ ID No: 39 GenBank Accession


 


No. AAX29407.1).






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 39. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 39. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 39. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID No: 39. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 39. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







gggggagccccaagcttaccacctgcacccggagagctgtgtcaccatg


 


tgggtcccggttgtcttcctcaccctgtccgtgacgtggattggtgctg


 


cacccctcatcctgtctcggattgtgggaggctgggagtgcgagaagca


 


ttcccaaccctggcaggtgcttgtggcctctcgtggcagggcagtctgc


 


ggcggtgttctggtgcacccccagtgggtcctcacagctgcccactgca


 


tcaggaacaaaagcgtgatcttgctgggtcggcacagcctgatcatcct


 


gaagacacaggccaggtatttcaggtcagccacagcacccacacccgct


 


ctacgatatgagcctcctgaagaatcgattcctcaggccaggtgatgac


 


tccagccacgacctcatgctgctccgcctgtcagagcctgccgagctca


 


cggatgctgtgaaggtcatggacctgcccacccaggagccagcactggg


 


gaccacctgctacgcctcaggctggggcagcattgaaccagaggagact


 


tgaccccaaagaaacttcagtgtgtggacctccatgttataccaatgac


 


gtgtgtgcgcaagttcaccctcagaaggtgaccaagttcatgctgtgtg


 


ctggacgctggacagggggcaaaagcacctgctcgggtgattctggggg


 


cccacttgtctgtaatggtgtgcttcaaggtatcacgtcatggggcagt


 


gaaccatgtgccctgcccgaaaggccttccctgtacaccaaggtggtgc


 


attaccggaagtggatcaaggacaccatcgtggccaacccctgagcacc


 


cctatcaactccctattgtagtaaacttggaaccaggaaatgaccaggc


 


caagactcaggcctccccagactactgacctagtccttaggtgtgaggt


 


ccagggagctaggaaaagaaatcagcagacacaggtgtagaccagagtg


 


atcttaaatggtgtaattagtcctctctgtgtcctggggaatactggcc


 


atgcctggagacatatcactcaatactctgaggacacagataggatggg


 


gtgtctgtgttatttgtggggtacagagatgaaagaggggtgggatcca


 


cactgagagagtggagagtgacatgtgctggacactgtccatgaagcac


 


tgagcagaagctggaggcacaacgcaccagacactcacagcaaggatgg


 


agctgaaaacataacccactctgtcctggaggcactgggaagcctagag


 


aaggctgtgagccaaggagggagggtcttcctttggcatgggatgggga


 


tgaagtagggagagggactggaccccctggaagctgattcactatgggg


 


ggaggtgtattgaagtcctccagacaaccctcagatttgatgataccta


 


gtagaactcacagaaataaagagctgttatactgcgaaaaaaaaaaaaa


 


aaaaaaaaaaaaa (SEQ ID No: 40;


 


GenBank Accession No. BC056665).






In another embodiment, the KLK3 protein is encoded by residues 47-832 of SEQ ID No: 40. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 40. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 40. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 40. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 40. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRA


 


VCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSF


 


PHPLYDMSLLKNRFLRPGDDSSIEPEEFLTPKKLQCVDLHVISNDVCA


 


QVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEP


 


CALPERPSLYTKVVHYRKWIKDTIVA.


 


(SEQ ID No: 41; GenBank Accession No. AJ459782)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 41. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 41. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 41. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 41. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAV


 


CGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPH


 


PLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPA


 


LGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFM


 


LCAGRWTGGKSTCSVSHPYSQDLEGKGEWGP. 


 


(SEQ ID No: 42, GenBank Accession No. AJ512346)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 42. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 42. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 42. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID No: 42. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 42. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGERGHGWGDAGEGASPDCQAEALSPPTQHPSPDRE


 


LGSFLSLPAPLQAHTPSPSILQQSSLPHQVPAPSHLPQNFLPIAQPAPCS


 


QLLY.


 


(SEQ ID No: 43 GenBank Accession No. AJ459784)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No 43. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 43. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID No: 43. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 43. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 43. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPL


 


YDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGT


 


TCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAG


 


RWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYR


 


KWIKDTIVANP.


 


(SEQ ID NO: 44 GenBank Accession No. AJ459783)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 44. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 44. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 44. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 44. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein is encoded by a nucleotide molecule having the sequence:







aagtacccactcccagtccaagaccccaaatcaccacaaaggacccaa


 


tccccagactcaagatatggtctgggcgctgtcagtgtctcctaccct


 


gatccctgggttcaactctgctcccagagcatgaagcctctccaccag


 


caccagccaccaacctgcaaacctagggaagattgacagaattcccag


 


cctttcccagctccccctgcccatgtcccaggactcccagccttggtt


 


ctctgcccccgtgtcttttcaaacccacatcctaaatccatctcctat


 


ccgagtcccccagacctcctgtcaaccctgattcccctgatctagcac


 


cccctctgcaggtgctgcacccctcatcctgtctcggattgtgggagg


 


ctgggagtgcgagaagcattcccaaccctggcaggtgcttgtagcctc


 


tcgtggcagggcagtctgcggcggtgactggtgcacccccagtgggtc


 


ctcacagctacccactgcatcaggaacaaaagcgtgatcttgctgggt


 


cggcacagcctgatcatcctgaagacacaggccaggtatttcaggtca


 


gccacagcacccacacccgctctacgatatgagcctcctgaagaatcg


 


attcctcaggccaggtgatgactccagccacgacctcatgctgctccg


 


cctgtcagagcctgccgagctcacggatgctatgaaggtcatggacct


 


gcccacccaggagccagcactggggaccacctgctacgcctcaggctg


 


gggcagcattgaaccagaggagacttgaccccaaagaaacttcagtgt


 


gtggacctccatgttatttccaatgacgtgtgtgcgcaagttcaccct


 


cagaaggtgaccaagttcatgctgtgtgctggacgctggacagggggc


 


aaaagcacctgctcgggtgattctgggggcccacttgtctgtaatggt


 


gtgcttcaaggtatcacgtcatggggcagtgaaccatgtgccctgccc


 


gaaaggccttccctgtacaccaaggtggtgcattaccggaagtggatc


 


aaggacaccatcgtggccaacccctgagcacccctatcaactccctat


 


tgtagtaaacttggaaccaggaaatgaccaggccaagactcaggcctc


 


cccagactactgacctagtccttaggtgtgaggtccagggagctagga


 


aaagaaatcagcagacacaggtgtagaccagagtgatcttaaatggtg


 


taattagtcctctctgtgtcctggggaatactggccatgcctggagac


 


atatcactcaatactctgaggacacagataggatggggtgtctgtgtt


 


atttgtggggtacagagatgaaagaggggtgggatccacactgagaga


 


gtggagagtgacatgtgctggacactgtccatgaagcactgagcagaa


 


gctggaggcacaacgcaccagacactcacagcaaggatggagctgaaa


 


acataacccactctgtcctggaggcactgggaagcctagagaaggctg


 


tgaaccaaggagggagggtatcctaggcatgggatggggatgaagtaa


 


ggagagggactgaccccctggaagctgattcactatggggggaggtgt


 


attgaagtcctccagacaaccctcagatttgatgatacctagtagaac


 


tcacagaaataaagagctgttatactgtgaa.


 


(SEQ ID No: 45; GenBank Accession No. X07730)






In another embodiment, the KLK3 protein is encoded by residues 67-1088 of SEQ ID No: 45. In another embodiment, the KLK3 protein is encoded by a homologue of SEQ ID No: 45. In another embodiment, the KLK3 protein is encoded by a variant of SEQ ID No: 45. In another embodiment, the KLK3 protein is encoded by an isomer of SEQ ID No: 45. In another embodiment, the KLK3 protein is encoded by a fragment of SEQ ID No: 45. Each possibility represents a separate embodiment of the methods and compositions as provided herein.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRK.


 


(SEQ ID No: 63; GenBank Accession No. NM_001030050)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 63. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 63. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID No: 63. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 63. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 63. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the KLK3 protein that is the source of the KLK3 peptide has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPL


 


YDMSLLKNRFLRPGDDSSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQK


 


VTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPS


 


LYTKVVHYRKWIKDTIVANP.


 


(SEQ ID No: 64; GenBank Accession No. NM_001064049)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 64. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 64. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 64. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 64. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRKPGDDSSHDLMLLRLSEPAELTDAVKVMDLPT


 


QEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVT


 


KFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLY


 


TKVVHYRKWIKDTIVANP.


 


(SEQ ID No: 65; GenBank Accession No. NM_001030048)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 65. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 65. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 65. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 65. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPL


 


YDMSLLKNRFLRPGDDSSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQK


 


VTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPS


 


LYTKVVHYRKWIKDTIVA.


 


(SEQ ID No: 66; GenBank Accession No. AJ459782)






In another embodiment, the KLK3 protein is a homologue of SEQ ID No: 66. In another embodiment, the KLK3 protein is a variant of SEQ ID No: 66. In another embodiment, the KLK3 protein is an isomer of SEQ ID No: 66. In another embodiment, the KLK3 protein is a fragment of SEQ ID No: 66. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVC


 


GGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPL


 


YDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGT


 


TCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAG


 


RWTGGKSTCSVSHPYSQDLEGKGEWGP.


 


(SEQ ID NO: 50 GenBank Accession No. AJ512346)






In another embodiment, the KLK3 protein is a homologue of SEQ ID NO: 50. In another embodiment, the KLK3 protein is a variant of SEQ ID NO: 50. In another embodiment, the KLK3 protein is an isomer of SEQ ID NO: 50. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID NO: 50. In another embodiment, the KLK3 protein is a fragment of SEQ ID NO: 50. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the KLK3 protein has the sequence:







MWVPVVFLTLSVTWIGERGHGWGDAGEGASPDCQAEALSPPTQHPSPDRE


 


LGSFLSLPAPLQAHTPSPSILQQSSLPHQVPAPSHLPQNFLPIAQPAPCS


 


QLLY.


 


(SEQ ID NO: 51 GenBank Accession No. AJ459784)






In another embodiment, the KLK3 protein is a homologue of SEQ ID NO: 51. In another embodiment, the KLK3 protein is a variant of SEQ ID NO: 51. In another embodiment, the sequence of the KLK3 protein comprises SEQ ID NO: 51. In another embodiment, the KLK3 protein is an isomer of SEQ ID NO: 51. In another embodiment, the KLK3 protein is a fragment of SEQ ID NO: 51.

In another embodiment, the KLK3 protein is encoded by a sequence set forth in one of the following GenBank Accession Numbers: BC005307, AJ310938, AJ310937, AF335478, AF335477, M27274, and M26663. In another embodiment, the KLK3 protein is encoded by a sequence set forth in one of the above GenBank Accession Numbers. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 protein is encoded by a sequence set forth in one of the following GenBank Accession Numbers: NM_001030050, NM_001030049, NM_001030048, NM_001030047, NM_001648, AJ459782, AJ512346, or AJ459784. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In one embodiment, the KLK3 protein is encoded by a variation of any of the sequences described herein wherein the sequence lacks









(SEQ ID NO: 52)



MWVPVVFLTLSVTWIGAAPLILSR.






In another embodiment, the KLK3 protein has the sequence that comprises a sequence set forth in one of the following GenBank Accession Numbers: X13943, X13942, X13940, X13941, and X13944. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 protein is any other KLK3 protein known in the art. Each KLK3 protein represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 peptide is any other KLK3 peptide known in the art. In another embodiment, the KLK3 peptide is a fragment of any other KLK3 peptide known in the art. Each type of KLK3 peptide represents a separate embodiment of the methods and compositions as provided herein.
“KLK3 peptide” refers, in another embodiment, to a full-length KLK3 protein. In another embodiment, the term refers to a fragment of a KLK3 protein. In another embodiment, the term refers to a fragment of a KLK3 protein that is lacking the KLK3 signal peptide. In another embodiment, the term refers to a KLK3 protein that contains the entire KLK3 sequence except the KLK3 signal peptide. “KLK3 signal sequence” refers, in another embodiment, to any signal sequence found in nature on a KLK3 protein. In another embodiment, a KLK3 protein of methods and compositions as provided herein does not contain any signal sequence. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the kallikrein-related peptidase 3 (KLK3 protein) that is the source of a KLK3 peptide for use in the methods and compositions as provided herein is a PSA protein. In another embodiment, the KLK3 protein is a P-30 antigen protein. In another embodiment, the KLK3 protein is a gamma-seminoprotein protein. In another embodiment, the KLK3 protein is a kallikrein 3 protein. In another embodiment, the KLK3 protein is a semenogelase protein. In another embodiment, the KLK3 protein is a seminin protein. In another embodiment, the KLK3 protein is any other type of KLK3 protein that is known in the art. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 protein is a splice variant 1 KLK3 protein. In another embodiment, the KLK3 protein is a splice variant 2 KLK3 protein. In another embodiment, the KLK3 protein is a splice variant 3 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 1 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 2 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 3 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 4 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 5 KLK3 protein. In another embodiment, the KLK3 protein is a transcript variant 6 KLK3 protein. In another embodiment, the KLK3 protein is a splice variant RP5 KLK3 protein. In another embodiment, the KLK3 protein is any other splice variant KLK3 protein known in the art. In another embodiment, the KLK3 protein is any other transcript variant KLK3 protein known in the art. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 protein is a mature KLK3 protein. In another embodiment, the KLK3 protein is a pro-KLK3 protein. In another embodiment, the leader sequence has been removed from a mature KLK3 protein of methods and compositions as provided herein. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, the KLK3 protein that is the source of a KLK3 peptide of methods and compositions as provided herein is a human KLK3 protein. In another embodiment, the KLK3 protein is a primate KLK3 protein. In another embodiment, the KLK3 protein is a KLK3 protein of any other species known in the art. In another embodiment, one of the above KLK3 proteins is referred to in the art as a “KLK3 protein.” Each possibility represents a separate embodiment of the methods and compositions as provided herein.
The term “isoform” refers to a version of a molecule, for example, a protein, with only slight differences compared to another isoform, or version, of the same protein. In one embodiment, isoforms may be produced from different but related genes, or in another embodiment, may arise from the same gene by alternative splicing. In another embodiment, isoforms are caused by single nucleotide polymorphisms.
The term, “fragment” refers to a protein or polypeptide that is shorter or comprises fewer amino acids than the full length protein or polypeptide. In another embodiment, fragment refers to a nucleic acid that is shorter or comprises fewer nucleotides than the full length nucleic acid. In another embodiment, the fragment is an N-terminal fragment. In another embodiment, the fragment is a C-terminal fragment. In one embodiment, the fragment is an intrasequential section of the protein, peptide, or nucleic acid. In one embodiment, the fragment is a functional fragment. In another embodiment, the fragment is an immunogenic fragment. In one embodiment, a fragment has 10-20 nucleic or amino acids, while in another embodiment, a fragment has more than 5 nucleic or amino acids, while in another embodiment, a fragment has 100-200 nucleic or amino acids, while in another embodiment, a fragment has 100-500 nucleic or amino acids, while in another embodiment, a fragment has 50-200 nucleic or amino acids, while in another embodiment, a fragment has 10-250 nucleic or amino acids.
The term, “immunogenicity” or “immunogenic” is used herein to refer to the innate ability of a protein, peptide, nucleic acid, antigen or organism to elicit an immune response in an animal when the protein, peptide, nucleic acid, antigen or organism is administered to the animal. Thus, “enhancing the immunogenicity” in one embodiment, refers to increasing the ability of a protein, peptide, nucleic acid, antigen or organism to elicit an immune response in an animal when the protein, peptide, nucleic acid, antigen or organism is administered to an animal. The increased ability of a protein, peptide, nucleic acid, antigen or organism to elicit an immune response can be measured by, in one embodiment, a greater number of antibodies to a protein, peptide, nucleic acid, antigen or organism, a greater diversity of antibodies to an antigen or organism, a greater number of T-cells specific for a protein, peptide, nucleic acid, antigen or organism, a greater cytotoxic or helper T-cell response to a protein, peptide, nucleic acid, antigen or organism, and the like.
In one embodiment, a PSA antigen comprises a truncated PSA open reading frame (GenBank Accession Number NM_001648), lacking its secretory signal sequence the first 24 AA. The truncated PSA may be amplified using the primers: Adv60-PSA(XhoI-no ATG)F: gtgCTCGAGattgtgggaggctgggagtg (SEQ ID No: 46) and Adv61-PSA(SpeI-Stop)R: gatACTAGTttaggggttggccacgatgg (SEQ ID No: 47) and may be subcloned in-frame with the first 441 amino acids of LLO to create a tLLO-PSA fusion polypeptide of this invention. The AA sequence of LLO-PSA is as follows:







MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASP


 


KTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEY


 


IVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPV


 


KRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQA


 


YPNVSAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQ


 


EEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYIS


 


SVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSF


 


KAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFL


 


KDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYD


 


LEIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKS


 


VILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHD


 


LMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPK


 


KLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLV


 


CYGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP


 


(SEQ ID No: 48; PSA sequence is underlined).






In some embodiments, a live-attenuated Listeria monocytogenes comprises a tLLO-PSA fusion polypeptide comprising the sequence SEQ ID NO: 48. In some embodiments, a live-attenuated Listeria monocytogenes comprises a tLLO-PSA fusion polypeptide consisting essentially of the sequence SEQ ID NO: 48. In some embodiments, a live-attenuated Listeria monocytogenes comprises a tLLO-PSA fusion polypeptide consisting of the sequence SEQ ID NO: 48.

There is one AA difference between this PSA and the sequence in NM_001648, at position N 221 Y).
In one embodiment, a recombinant fusion polypeptide of methods and compositions of the present invention is an LLO-KLK3 fusion polypeptide. In another embodiment, the fusion polypeptide has the sequence set forth in SEQ ID No: 48. In another embodiment, the fusion polypeptide is homologous to the sequence set forth in SEQ ID No: 48. In another embodiment, the fusion polypeptide is a variant of the sequence set forth in SEQ ID No: 48. In another embodiment, “homology” refers to identity to one of SEQ ID No: 48 of greater than 72%. In another embodiment, the homology is greater than 75%. In another embodiment, “homology” refers to identity to a sequence of greater than 78%. In another embodiment, the homology is greater than 80%. In another embodiment, the homology is greater than 82%. In another embodiment, “homology” refers to identity to a sequence of greater than 83%. In another embodiment, the homology is greater than 85%. In another embodiment, the homology is greater than 87%. In another embodiment, “homology” refers to identity to a sequence of greater than 88%. In another embodiment, the homology is greater than 90%. In another embodiment, the homology is greater than 92%. In another embodiment, “homology” refers to identity to a sequence of greater than 93%. In another embodiment, the homology is greater than 95%. In another embodiment, “homology” refers to identity to a sequence of greater than 96%. In another embodiment, the homology is greater than 97%. In another embodiment, the homology is greater than 98%. In another embodiment, the homology is greater than 99%. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the truncated LLO comprises a PEST amino acid (AA) sequence. In another embodiment, the PEST amino acid sequence is KENSISSMAPPASPPASPKTPIEKKHADEIDK (SEQ ID NO: 49). In another embodiment, fusion of an antigen to other LM PEST AA sequences from Listeria will also enhance immunogenicity of the antigen.
The N-terminal LLO protein fragment of methods and compositions of the present invention comprises, in another embodiment, SEQ ID No: 54. In another embodiment, the fragment comprises an LLO signal peptide. In another embodiment, the fragment comprises SEQ ID No: 55. In another embodiment, the fragment consists approximately of SEQ ID No: 55. In another embodiment, the fragment consists essentially of SEQ ID No: 54. In another embodiment, the fragment corresponds to SEQ ID No: 55. In another embodiment, the fragment is homologous to SEQ ID No: 55. In another embodiment, the fragment is homologous to a fragment of SEQ ID No: 55. In some embodiments, the ALLO fused to a PSA antigen is 416 AA long (exclusive of the signal sequence), as 88 residues from the amino terminus which is inclusive of the activation domain containing cysteine 484 were truncated. It will be clear to those skilled in the art that any ALLO without the activation domain, and in particular without cysteine 484, are suitable for methods and compositions of the present invention. In another embodiment, fusion of a heterologous antigen to any ALLO, including the PEST AA sequence, SEQ ID NO: 49, enhances cell mediated and anti-tumor immunity of the antigen. Each possibility represents a separate embodiment of the present invention.
The LLO protein utilized to construct strains of the present invention has, in another embodiment, the sequence:







MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASP


 


KTPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEY


 


IVVEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPV


 


KRDSLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQA


 


YPNVSAKIDYDDEMAYSESQLIAKFUTAFKAVNNSLNVNFGAISEGKMQ


 


EEVISFKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYIS


 


SVAYGRQVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSF


 


KAVIYGGSAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFL


 


KDNELAVIKNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYD


 


PEGNEIVQHKNWSENNKSKLAHETSSIYLPGNARNINVYAKECTGLAWE


 


WWRTVIDDRNLPLVKNRNISIWGTTLYPKYSNKVDNPIE 


 


(GenBank Accession No. P13128; SEQ ID NO: 53; 


 


nucleic acid sequence is set forth in GenBank 


 


Accession No. X15127).






The first 25 AA of the proprotein corresponding to this sequence are the signal sequence and are cleaved from LLO when it is secreted by the bacterium. Thus, in this embodiment, the full length active LLO protein is 504 residues long. In another embodiment, the above LLO fragment is used as the source of the LLO fragment incorporated in a strain of the present invention. Each possibility represents a separate embodiment of the present invention.

In another embodiment, the N-terminal fragment of an LLO protein utilized in compositions and methods of the present invention has the sequence:







(SEQ ID NO: 54)


MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSVAPPASPPASPK


 


TPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIV


 


VEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRD


 


SLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYSNV


 


SAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVIS


 


FKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGR


 


QVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGG


 


SAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVI


 


KNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYD.






In another embodiment, the LLO fragment corresponds to about AA 20-442 of an LLO protein utilized herein.
In another embodiment, the LLO fragment has the sequence:







(SEQ ID NO: 55)


MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSVAPPASPPASPK


 


TPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIV


 


VEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRD


 


SLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYSNV


 


SAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVIS


 


FKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGR


 


QVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGG


 


SAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVI


 


KNNSEYIETTSKAYTD.






In another embodiment, “truncated LLO” or “ALLO” refers to a fragment of LLO that comprises the PEST-like domain. In another embodiment, the terms refer to an LLO fragment that comprises a PEST amino acid sequence.
In another embodiment, the terms refer to an LLO fragment that does not contain the activation domain at the amino terminus and does not include cysteine 484. In another embodiment, the terms refer to an LLO fragment that is not hemolytic. In another embodiment, the LLO fragment is rendered non-hemolytic by deletion or mutation of the activation domain. In another embodiment, the LLO fragment is rendered non-hemolytic by deletion or mutation of cysteine 484. In another embodiment, the LLO fragment is rendered non-hemolytic by deletion or mutation at another location. In another embodiment, the LLO is rendered non-hemolytic by a deletion or mutation of the cholesterol binding domain (CBD) as detailed in U.S. Pat. No. 8,771,702, which is incorporated by reference herein. In another embodiment, there is a mutation in a cholesterol-binding domain (CBD) of the LLO or a fragment thereof, wherein said mutation comprises a substitution of a 1-50 amino acid peptide comprising a CBD. In one embodiment, there is a mutation in a CBD of the LLO or a fragment thereof, wherein said mutation comprises a substitution of residue C484, W491, W492 of SEQ ID NO: 53, alone or in combination, wherein said recombinant protein exhibits a greater than 100-fold reduction in hemolytic activity relative to wild-type LLO. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the LLO fragment consists of about the first 441 AA of the LLO protein. In another embodiment, the LLO fragment consists of about the first 420 AA of LLO. In another embodiment, the LLO fragment is a non-hemolytic form of the LLO protein.
In another embodiment, the LLO fragment consists of about residues 1-25. In another embodiment, the LLO fragment consists of about residues 1-50. In another embodiment, the LLO fragment consists of about residues 1-75. In another embodiment, the LLO fragment consists of about residues 1-100. In another embodiment, the LLO fragment consists of about residues 1-125. In another embodiment, the LLO fragment consists of about residues 1-150. In another embodiment, the LLO fragment consists of about residues 1175. In another embodiment, the LLO fragment consists of about residues 1-200. In another embodiment, the LLO fragment consists of about residues 1-225. In another embodiment, the LLO fragment consists of about residues 1-250. In another embodiment, the LLO fragment consists of about residues 1-275. In another embodiment, the LLO fragment consists of about residues 1-300. In another embodiment, the LLO fragment consists of about residues 1-325. In another embodiment, the LLO fragment consists of about residues 1-350. In another embodiment, the LLO fragment consists of about residues 1-375. In another embodiment, the LLO fragment consists of about residues 1-400. In another embodiment, the LLO fragment consists of about residues 1-425. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the LLO fragment contains residues of a homologous LLO protein that correspond to one of the above AA ranges. The residue numbers need not, in another embodiment, correspond exactly with the residue numbers enumerated above; e.g. if the homologous LLO protein has an insertion or deletion, relative to an LLO protein utilized herein, then the residue numbers can be adjusted accordingly. In another embodiment, the LLO fragment is any other LLO fragment known in the art.
In another embodiment, a homologous LLO refers to identity to an LLO sequence (e.g. to one of SEQ ID No: 53-55) of greater than 70%. In another embodiment, a homologous LLO refers to identity to one of SEQ ID No: 53-55 of greater than 72%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 75%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 78%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 80%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 82%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 83%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 85%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 87%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 88%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 90%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 92%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 93%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 95%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 96%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 97%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 98%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of greater than 99%. In another embodiment, a homologous refers to identity to one of SEQ ID No: 53-55 of 100%. Each possibility represents a separate embodiment of the present invention.
The amino acid and nucleotide sequences from United States Publication Nos. US-2007-0253976-A1 and US-2011-0129499-A1 are incorporated herein in their entirety.
The term “homologue” refers to a nucleic acid or amino acid sequence which shares a certain percentage of sequence identity with a particular nucleic acid or amino acid sequence. In one embodiment, a sequence useful in the composition and methods as provided herein may be a homologue of a particular LLO sequence or N-terminal fragment thereof. In another embodiment, a sequence useful in the composition and methods as provided herein may be a homologue of an antigenic polypeptide, which in one embodiment, is KLK3 or a functional fragment thereof. In one embodiment, a homolog of a polypeptide and, in one embodiment, the nucleic acid encoding such a homolog, of the present invention maintains the functional characteristics of the parent polypeptide. For example, in one embodiment, a homolog of an antigenic polypeptide of the present invention maintains the antigenic characteristic of the parent polypeptide. In another embodiment, a sequence useful in the composition and methods as provided herein may be a homologue of any sequence described herein. In one embodiment, a homologue shares at least 70% identity with a particular sequence. In another embodiment, a homologue shares at least 72% identity with a particular sequence. In another embodiment, a homologue shares at least 75% identity with a particular sequence. In another embodiment, a homologue shares at least 78% identity with a particular sequence. In another embodiment, a homologue shares at least 80% identity with a particular sequence. In another embodiment, a homologue shares at least 82% identity with a particular sequence. In another embodiment, a homologue shares at least 83% identity with a particular sequence. In another embodiment, a homologue shares at least 85% identity with a particular sequence. In another embodiment, a homologue shares at least 87% identity with a particular sequence. In another embodiment, a homologue shares at least 88% identity with a particular sequence. In another embodiment, a homologue shares at least 90% identity with a particular sequence. In another embodiment, a homologue shares at least 92% identity with a particular sequence. In another embodiment, a homologue shares at least 93% identity with a particular sequence. In another embodiment, a homologue shares at least 95% identity with a particular sequence. In another embodiment, a homologue shares at least 96% identity with a particular sequence. In another embodiment, a homologue shares at least 97% identity with a particular sequence. In another embodiment, a homologue shares at least 98% identity with a particular sequence. In another embodiment, a homologue shares at least 99% identity with a particular sequence. In another embodiment, a homologue shares 100% identity with a particular sequence. Each possibility represents a separate embodiment as provided herein.
Homology is, in one embodiment, determined by computer algorithm for sequence alignment, by methods well described in the art. For example, computer algorithm analysis of nucleic acid sequence homology may include the utilization of any number of software packages available, such as, for example, the BLAST, DOMAIN, BEAUTY (BLAST Enhanced Alignment Utility), GENPEPT and TREMBL packages.
In another embodiment, homology is determined via determination of candidate sequence hybridization, methods of which are well described in the art (See, for example, “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., Eds. (1985); Sambrook et al., 2001, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al., 1989, Current Protocols in Molecular Biology, Green Publishing Associates and Wiley Interscience, N.Y). For example methods of hybridization may be carried out under moderate to stringent conditions, to the complement of a DNA encoding a native caspase peptide. Hybridization conditions being, for example, overnight incubation at 42° C. in a solution comprising: 10-20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA.
In one embodiment, it is to be understood that a homolog of any of the sequences as provided herein and/or as described herein is considered to be a part of the invention.
In another embodiment, a recombinant Listeria strain of the methods and compositions as provided herein comprise a nucleic acid molecule encoding a PSA fussion polypeptide operably integrated into the Listeria genome as an open reading frame with an endogenous ActA sequence. In another embodiment, a recombinant Listeria strain of the methods and compositions as provided herein comprise an episomal expression vector comprising a nucleic acid molecule encoding PSA fusion protein comprising an antigen fused to an ActA or a truncated ActA. In one embodiment, the expression and secretion of the antigen is under the control of an actA promoter and ActA signal sequence and it is expressed as fusion to 1-233 amino acids of ActA (truncated ActA or tActA). In another embodiment, the truncated ActA consists of the first 390 amino acids of the wild type ActA protein as described in U.S. Pat. No. 7,655,238, which is incorporated by reference herein in its entirety. In another embodiment, the truncated ActA is an ActA-N100 or a modified version thereof (referred to as ActA-N100*) in which a PEST motif has been deleted and containing the nonconservative QDNKR substitution as described in US Patent Publication Serial No. 2014/0186387.
The term “functional” within the meaning of the invention, is used herein to refer to the innate ability of a protein, peptide, nucleic acid, fragment or a variant thereof to exhibit a biological activity or function. In one embodiment, such a biological function is its binding property to an interaction partner, e.g., a membrane-associated receptor, and in another embodiment, its trimerization property. In the case of functional fragments and the functional variants of the invention, these biological functions may in fact be changed, e.g., with respect to their specificity or selectivity, but with retention of the basic biological function.
In another embodiment, a “functional fragment” is an immunogenic fragment and elicits an immune response when administered to a subject alone or in a strain composition provided herein. In another embodiment, a functional fragment has biological activity as will be understood by a skilled artisan and as further provided herein.
The term “nucleic acids” or “nucleotide” refers to a string of at least two base-sugar-phosphate combinations. The term includes, in one embodiment, DNA and RNA. “Nucleotides” refers, in one embodiment, to the monomeric units of nucleic acid polymers. RNA may be, in one embodiment, in the form of a tRNA (transfer RNA), snRNA (small nuclear RNA), rRNA (ribosomal RNA), mRNA (messenger RNA), anti-sense RNA, small inhibitory RNA (siRNA), micro RNA (miRNA) and ribozymes. The use of siRNA and miRNA has been described (Caudy A A et al, Genes & Devel 16: 2491-96 and references cited therein). DNA may be in form of plasmid DNA, viral DNA, linear DNA, or chromosomal DNA or derivatives of these groups. In addition, these forms of DNA and RNA may be single, double, triple, or quadruple stranded. The term also includes, in another embodiment, artificial nucleic acids that may contain other types of backbones but the same bases. In one embodiment, the artificial nucleic acid is a PNA (peptide nucleic acid). PNA contain peptide backbones and nucleotide bases and are able to bind, in one embodiment, to both DNA and RNA molecules. In another embodiment, the nucleotide is oxetane modified. In another embodiment, the nucleotide is modified by replacement of one or more phosphodiester bonds with a phosphorothioate bond. In another embodiment, the artificial nucleic acid contains any other variant of the phosphate backbone of native nucleic acids known in the art. The use of phosphothiorate nucleic acids and PNA are known to those skilled in the art, and are described in, for example, Neilsen P E, Curr Opin Struct Biol 9:353-57; and Raz N K et al Biochem Biophys Res Commun 297:1075-84. The production and use of nucleic acids is known to those skilled in art and is described, for example, in Molecular Cloning, (2001), Sambrook and Russell, eds. and Methods in Enzymology: Methods for molecular cloning in eukaryotic cells (2003) Purchio and G. C. Fareed. Each nucleic acid derivative represents a separate embodiment as provided herein.
The terms “polypeptide,” “peptide” and “recombinant peptide” refer, in another embodiment, to a peptide or polypeptide of any length. In another embodiment, a peptide or recombinant peptide as provided herein has one of the lengths enumerated above for an HMW-MAA fragment. Each possibility represents a separate embodiment of the methods and compositions as provided herein. In one embodiment, the term “peptide” refers to native peptides (either degradation products, synthetically synthesized peptides or recombinant peptides) and/or peptidomimetics (typically, synthetically synthesized peptides), such as peptoids and semipeptoids which are peptide analogs, which may have, for example, modifications rendering the peptides more stable while in a body or more capable of penetrating into cells. Such modifications include, but are not limited to N terminus modification, C terminus modification, peptide bond modification, including, but not limited to, CH2-NH, CH2-S, CH2-S═O, O═C—NH, CH2-O, CH2-CH2, S═C—NH, CH═CH or CF═CH, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified, for example, in Quantitative Drug Design, C. A. Ramsden Gd., Chapter 17.2, F. Choplin Pergamon Press (1992), which is incorporated by reference as if fully set forth herein. Further details in this respect are provided hereinunder.
The term “antigenic polypeptide” is used herein to refer to a polypeptide, peptide or recombinant peptide as described hereinabove that is foreign to a host and leads to the mounting of an immune response when present in, or, in another embodiment, detected by, the host.
In one embodiment, “antigenic polypeptide” is used herein to refer to a polypeptide, peptide recombinant polypeptide or recombinant peptide as described herein that is processed and presented on MHC class I and/or class II molecules present in a subject's cells leading to the mounting of an immune response when present in, or, in another embodiment, detected by, the host. In one embodiment, the antigen may be foreign to the host. In another embodiment, the antigen might be present in the host but the host does not elicit an immune response against it because of immunologic tolerance.
In one embodiment, the antigen is a tumor-associated antigen. In one embodiment, the tumor-associated antigen is PSA. In one embodiment, the recombinant attenuated Listeria strain of the compositions and methods as provided herein express a PSA polypeptide that is expressed by a tumor cell. In one embodiment, the recombinant Listeria strain of the compositions and methods as provided herein comprise a first or second nucleic acid molecule that encodes a PSA, which in one embodiment, is a marker for prostate cancer that is highly expressed by prostate tumors. In one embodiment, PSA is a kallikrein serine protease (KLK3) secreted by prostatic epithelial cells, which in one embodiment, is widely used as a marker for prostate cancer.
Peptide bonds (—CO—NH—) within the peptide may be substituted, for example, by N-methylated bonds (—N(CH3)-CO—), ester bonds (—C(R)H—C—O—O—C(R)—N—), ketomethylen bonds (—CO—CH2-), *-aza bonds (—NH—N(R)—CO—), wherein R is any alkyl, e.g., methyl, carba bonds (—CH2-NH—), hydroxyethylene bonds (—CH(OH)—CH2-), thioamide bonds (—CS—NH—), olefinic double bonds (—CH═CH—), retro amide bonds (—NH—CO—), peptide derivatives (—N(R)—CH2-CO—), wherein R is the “normal” side chain, naturally presented on the carbon atom.
These modifications can occur at any of the bonds along the peptide chain and even at several (2-3) at the same time. Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted for synthetic non-natural acid such as TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o-methyl-Tyr.
In addition to the above, the peptides as provided herein may also include one or more modified amino acids or one or more non-amino acid monomers (e.g. fatty acids, complex carbohydrates etc).
The term “oligonucleotide” is interchangeable with the term “nucleic acid”, and may refer to a molecule, which may include, but is not limited to, prokaryotic sequences, eukaryotic mRNA, cDNA from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and even synthetic DNA sequences. The term also refers to sequences that include any of the known base analogs of DNA and RNA.
It will be appreciated by the skilled artisan that the term “PEST sequence-containing polypeptide” or “PEST sequence-containing protein” may encompass a truncated LLO protein, which in one embodiment is a N-terminal LLO, and a truncated ActA protein which in one embodiment is an N-terminal LLO, or fragments thereof. It will also be appreciated by the skilled artisan that the term “PEST-sequence containing peptide” may encompass a PEST sequence peptide or peptide fragments of an LLO protein or an ActA protein thereof. PEST sequence peptides are known in the art and are described in U.S. Pat. No. 7,635,479, and in US Patent Publication Serial No. 2014/0186387, both of which are hereby incorporated in their entirety herein.
In another embodiment, a PEST sequence of prokaryotic organisms can be identified routinely in accordance with methods such as described by Rechsteiner and Roberts (TBS 21:267-271, 1996) for L. monocytogenes. Alternatively, PEST amino acid sequences from other prokaryotic organisms can also be identified based by this method. Other prokaryotic organisms wherein PEST amino acid sequences would be expected to include, but are not limited to, other Listeria species. For example, the L. monocytogenes protein ActA contains four such sequences. These are KTEEQPSEVNTGPR (SEQ ID NO: 56), KASVTDTSEGDLDSSMQSADESTPQPLK (SEQ ID NO: 57), KNEEVNASDFPPPPTDEELR (SEQ ID NO: 58), and RGGIPTSEEFSSLNSGDFTDDENSETTEEEIDR (SEQ ID NO: 59). Also Streptolysin O from Streptococcus sp. contain a PEST sequence. For example, Streptococcus pyogenes Streptolysin O comprises the PEST sequence KQNTASTETTTTNEQPK (SEQ ID NO: 60) at amino acids 35-51 and Streptococcus equisimilis Streptolysin O comprises the PEST-like sequence KQNTANTETTTTNEQPK (SEQ ID NO: 61) at amino acids 38-54. Further, it is believed that the PEST sequence can be embedded within the antigenic protein. Thus, for purposes of the present invention, by “fusion” when in relation to PEST sequence fusions, it is meant that the antigenic protein comprises both the antigen, for example PSA, and the PEST amino acid sequence either linked at one end of the antigen or embedded within the antigen.
In another embodiment, the construct or nucleic acid molecule is expressed from an episomal or plasmid vector, with a nucleic acid sequence encoding a PEST sequence-containing polypeptide or a PEST-sequence peptide. In another embodiment, the plasmid is stably maintained in the recombinant Listeria strain strain in the absence of antibiotic selection. In another embodiment, the plasmid does not confer antibiotic resistance upon the recombinant Listeria. In another embodiment, the fragment is a functional fragment. In another embodiment, the fragment is an immunogenic fragment.
The term “Stably maintained” refers, in another embodiment, to maintenance of a nucleic acid molecule or plasmid in the absence of selection (e.g. antibiotic selection) for 10 generations, without detectable loss. In another embodiment, the period is 15 generations. In another embodiment, the period is 20 generations. In another embodiment, the period is 25 generations. In another embodiment, the period is 30 generations. In another embodiment, the period is 40 generations. In another embodiment, the period is 50 generations. In another embodiment, the period is 60 generations. In another embodiment, the period is 80 generations. In another embodiment, the period is 100 generations. In another embodiment, the period is 150 generations. In another embodiment, the period is 200 generations. In another embodiment, the period is 300 generations. In another embodiment, the period is 500 generations. In another embodiment, the period is more than 500 generations. In another embodiment, the nucleic acid molecule or plasmid is maintained stably in vitro (e.g. in culture). In another embodiment, the nucleic acid molecule or plasmid is maintained stably in vivo. In another embodiment, the nucleic acid molecule or plasmid is maintained stably both in vitro and in vitro. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
The term “amino acid” or “amino acids” is understood to include the 20 naturally occurring amino acids; those amino acids often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acids including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, nor-valine, nor-leucine and ornithine. Furthermore, the term “amino acid” may include both D- and L-amino acids.
The term “nucleic acid” or “nucleic acid sequence” refers to a deoxyribonucleotide or ribonucleotide oligonucleotide in either single- or double-stranded form. The term encompasses nucleic acids, i.e., oligonucleotides, containing known analogues of natural nucleotides which have similar or improved binding properties, for the purposes desired, as the reference nucleic acid. The term also includes nucleic acids which are metabolized in a manner similar to naturally occurring nucleotides or at rates that are improved thereover for the purposes desired. The term also encompasses nucleic-acid-like structures with synthetic backbones. DNA backbone analogues provided by the invention include phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3′-thioacetal, methylene(methylimino), 3′-N-carbamate, morpholino carbamate, and peptide nucleic acids (PNAs); see, e.g., Oligonucleotides and Analogues, a Practical Approach, edited by F. Eckstein, IRL Press at Oxford University Press (1991); Antisense Strategies, Annals of the New York Academy of Sciences, Volume 600, Eds. Baserga and Denhardt (NYAS 1992); Mulligan (1993) J. Med. Chem. 36:1923-1937; Antisense Research and Applications (1993, CRC Press). PNAs contain non-ionic backbones, such as N-(2-aminoethyl) glycine units. Phosphorothioate linkages are described, e.g., in WO 97/03211; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol. 144:189-197. Other synthetic backbones encompasses by the term include methyl-phosphonate linkages or alternating methylphosphonate and phosphodiester linkages (Strauss-Soukup (1997) Biochemistry 36:8692-8698), and benzylphosphonate linkages (Samstag (1996) Antisense Nucleic Acid Drug Dev. 6:153-156). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide primer, probe and amplification product.
In another embodiment, the construct or nucleic acid molecule provided herein is integrated into the Listerial chromosome using homologous recombination. Techniques for homologous recombination are well known in the art, and are described, for example, in Baloglu S, Boyle S M, et al (Immune responses of mice to vaccinia virus recombinants expressing either Listeria monocytogenes partial listeriolysin or Brucella abortus ribosomal L7/L12 protein. Vet Microbiol 2005, 109(1-2): 11-7); and Jiang L L, Song H H, et al., (Characterization of a mutant Listeria monocytogenes strain expressing green fluorescent protein. Acta Biochim Biophys Sin (Shanghai) 2005, 37(1): 19-24). In another embodiment, homologous recombination is performed as described in U.S. Pat. No. 6,855,320. In another embodiment, a temperature sensitive plasmid is used to select the recombinants. Each technique represents a separate embodiment of the present invention.
In another embodiment, the construct or nucleic acid molecule is integrated into the Listerial chromosome using transposon insertion. Techniques for transposon insertion are well known in the art, and are described, inter alia, by Sun et al. (Infection and Immunity 1990, 58: 3770-3778) in the construction of DP-L967. Transposon mutagenesis has the advantage, in another embodiment, that a stable genomic insertion mutant can be formed but the disadvantage that the position in the genome where the foreign gene has been inserted is unknown.
In another embodiment, the construct or nucleic acid molecule is integrated into the Listerial chromosome using phage integration sites (Lauer P, Chow M Y et al, Construction, characterization, and use of two Listeria monocytogenes site-specific phage integration vectors. J Bacteriol 2002; 184(15): 4177-86). In certain embodiments of this method, an integrase gene and attachment site of a bacteriophage (e.g. U153 or PSA listeriophage) is used to insert the heterologous gene into the corresponding attachment site, which may be any appropriate site in the genome (e.g. comK or the 3′ end of the arg tRNA gene). In another embodiment, endogenous prophages are cured from the attachment site utilized prior to integration of the construct or heterologous gene. In another embodiment, this method results in single-copy integrants. In another embodiment, the present invention further comprises a phage based chromosomal integration system for clinical applications, where a host strain that is auxotrophic for essential enzymes, including, but not limited to, d-alanine racemase can be used, for example Lmdal(−)dat(−). In another embodiment, in order to avoid a “phage curing step,” a phage integration system based on PSA is used. This requires, in another embodiment, continuous selection by antibiotics to maintain the integrated gene. Thus, in another embodiment, the current invention enables the establishment of a phage based chromosomal integration system that does not require selection with antibiotics. Instead, an auxotrophic host strain can be complemented. Each possibility represents a separate embodiment of the present invention.
The term “recombination site” or “site-specific recombination site” refers to a sequence of bases in a nucleic acid molecule that is recognized by a recombinase (along with associated proteins, in some cases) that mediates exchange or excision of the nucleic acid segments flanking the recombination sites. The recombinases and associated proteins are collectively referred to as “recombination proteins” see, e.g., Landy, A., (Current Opinion in Genetics & Development) 3:699-707; 1993).
The term “phage expression vector” or “phagemid” refers to any phage-based recombinant expression system for the purpose of expressing a nucleic acid sequence of the methods and compositions as provided herein in vitro or in vivo, constitutively or inducibly, in any cell, including prokaryotic, yeast, fungal, plant, insect or mammalian cell. A phage expression vector typically can both reproduce in a bacterial cell and, under proper conditions, produce phage particles. The term includes linear or circular expression systems and encompasses both phage-based expression vectors that remain episomal or integrate into the host cell genome.
The term “episomal expression vector” as described herein refers to a nucleic acid vector which may be linear or circular, and which is usually double-stranded in form. In one embodiment, an episomal expression vector comprises a gene of interest. In another embodiment, the inserted gene of interest is not interrupted or subjected to regulatory constraints which often occur from integration into cellular DNA. In another embodiment, the presence of the inserted heterologous gene does not lead to rearrangement or interruption of the cell's own important regions. In another embodiment, episomal vectors persist in multiple copies in the bacterial cytoplasm, resulting in amplification of the gene of interest, and, in another embodiment, viral trans-acting factors are supplied when necessary. In another embodiment, in stable transfection procedures, the use of episomal vectors often results in higher transfection efficiency than the use of chromosome-integrating plasmids (Belt, P. B. G. M., et al (1991) Efficient cDNA cloning by direct phenotypic correction of a mutant human cell line (HPRT2) using an Epstein-Barr virus-derived cDNA expression vector. Nucleic Acids Res. 19, 4861-4866; Mazda, O., et al. (1997) Extremely efficient gene transfection into lympho-hematopoietic cell lines by Epstein-Barr virus-based vectors. J. Immunol. Methods 204, 143-151). In one embodiment, the episomal expression vectors of the methods and compositions as provided herein may be delivered to cells in vivo, ex vivo, or in vitro by any of a variety of the methods employed to deliver DNA molecules to cells. The vectors may also be delivered alone or in the form of a pharmaceutical composition that enhances delivery to cells of a subject.
The term “fused” refers to linkage by covalent bonding.
The term “Transforming,” refers to engineering a bacterial cell to take up a plasmid or other heterologous DNA molecule. In another embodiment, “transforming” refers to engineering a bacterial cell to express a gene of a plasmid or other heterologous DNA molecule. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In another embodiment, conjugation is used to introduce genetic material and/or plasmids into bacteria. Methods for conjugation are well known in the art, and are described, for example, in Nikodinovic J et al (A second generation snp-derived Escherichia coli-Streptomyces shuttle expression vector that is generally transferable by conjugation. Plasmid. 2006 November; 56(3):223-7) and Auchtung J M et al (Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response. Proc Natl Acad Sci USA. 2005 Aug. 30; 102(35):12554-9). Each method represents a separate embodiment of the methods and compositions as provided herein.
In one embodiment, the expression vector comprising a nucleic acid molecule provided herein further comprises a second open reading frame encoding a metabolic enzyme. In another embodiment, the metabolic enzyme complements an endogenous gene that is lacking in the chromosome of the recombinant Listeria strain. In another embodiment, the metabolic enzyme encoded by the open reading frame is an alanine racemase enzyme (dal). In another embodiment, the metabolic enzyme encoded by the open reading frame is a D-amino acid transferase enzyme (dat). In another embodiment, the Listeria strains provided herein comprise a mutation in the endogenous dal/dat genes. In another embodiment, the Listeria lacks the dal/dat genes. In another embodiment, the Listeria lacks the dal/dat/and actA genes.
In another embodiment, a nucleic acid molecule of the methods and compositions of the present invention is operably linked to a promoter/regulatory sequence. In another embodiment, the nucleic acid sequence encoding PSA of methods and compositions of the present invention is operably linked to a promoter/regulatory sequence. In another embodiment, the second open reading frame of methods and compositions of the present invention is operably linked to a promoter/regulatory sequence. In another embodiment, each of the open reading frames are operably linked to a promoter/regulatory sequence. Each possibility represents a separate embodiment of the present invention.
The term “Metabolic enzyme” refers, in one embodiment, to an enzyme involved in synthesis of a nutrient required by the host bacteria. In another embodiment, the term refers to an enzyme required for synthesis of a nutrient required by the host bacteria. In another embodiment, the term refers to an enzyme involved in synthesis of a nutrient utilized by the host bacteria. In another embodiment, the term refers to an enzyme involved in synthesis of a nutrient required for sustained growth of the host bacteria. In another embodiment, the enzyme is required for synthesis of the nutrient. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In one embodiment, the PSA antigen used in the invention is associated with prostate cancer.
In one embodiment, strains as provided herein generate effector T cells that are able to infiltrate the tumor, destroy tumor cells and eradicate the disease. In one embodiment, naturally occurring tumor infiltrating lymphocytes (TILs) are associated with better prognosis in several tumors. Moreover, the infiltration of the tumor by T cells has been associated with success of immunotherapeutic approaches in both pre-clinical and human trials. In one embodiment, the infiltration of lymphocytes into the tumor site is dependent on the up-regulation of adhesion molecules in the endothelial cells of the tumor vasculature, generally by proinflammatory cytokines, such as IFN-γ, TNF-α and IL-1. Several adhesion molecules have been implicated in the process of lymphocyte infiltration into tumors, including intercellular adhesion molecule 1 (ICAM-1), vascular endothelial cell adhesion molecule 1 (V-CAM-1), vascular adhesion protein 1 (VAP-1) and E-selectin. However, these cell-adhesion molecules are commonly down-regulated in the tumor vasculature. Thus, in one embodiment, strains as provided herein increase TILs, up-regulate adhesion molecules (in one embodiment, ICAM-1, V-CAM-1, VAP-1, E-selectin, or a combination thereof), up-regulate pro-inflammatory cytokines (in one embodiment, IFN-γ, TNF-α, IL-1, or a combination thereof), or a combination thereof.
The attenuated Listeria strain of methods and compositions of the present invention is, in another embodiment, a attenuated Listeria monocytogenes strain. In another embodiment, the Listeria strain is a attenuated Listeria seeligeri strain. In another embodiment, the Listeria strain is a attenuated Listeria grayi strain. In another embodiment, the Listeria strain is a attenuated Listeria ivanovii strain. In another embodiment, the Listeria strain is a attenuated Listeria murrayi strain. In another embodiment, the Listeria strain is a attenuated Listeria welshimeri strain. In another embodiment, the Listeria strain is a attenuated strain of any other Listeria species known in the art. Each possibility represents a separate embodiment of the present invention.
In another embodiment, a recombinant Listeria strain of the present invention has been passaged through an animal host. In another embodiment, the passaging maximizes efficacy of the strain as a strain vector. In another embodiment, the passaging stabilizes the immunogenicity of the Listeria strain. In another embodiment, the passaging stabilizes the virulence of the Listeria strain. In another embodiment, the passaging increases the immunogenicity of the Listeria strain. In another embodiment, the passaging increases the virulence of the Listeria strain. In another embodiment, the passaging removes unstable sub-strains of the Listeria strain. In another embodiment, the passaging reduces the prevalence of unstable sub-strains of the Listeria strain. In another embodiment, the Listeria strain contains a genomic insertion of the gene encoding the antigen-containing recombinant peptide. In another embodiment, the Listeria strain carries a plasmid comprising the gene encoding the antigen-containing recombinant peptide. In another embodiment, the passaging is performed as described herein. In another embodiment, the passaging is performed by any other method known in the art. Each possibility represents a separate embodiment of the present invention.
It is understood that wherever embodiments are described herein with the language “comprising”, otherwise analogous embodiments described in terms of “consisting of” and/or “consisting essentially of” are also provided.
Where aspects or embodiments of the invention are described in terms of a Markush group or other grouping of alternatives, the present invention encompasses not only the entire group listed as a whole, but each member of the group individually and all possible subgroups of the main group, but also the main group absent one or more of the group members. The present invention also envisages the explicit exclusion of one or more of any of the group members in the claimed invention.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present specification, including definitions, will control. Throughout this specification and claims, the word “comprise,” or variations such as “comprises” or “comprising” will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Any example(s) following the term “e.g.” or “for example” is not meant to be exhaustive or limiting.
Exemplary methods and materials are described herein, although methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention. The materials, methods, and examples are illustrative only and not intended to be limiting.
II. Methods, Uses And Medicaments
In one aspect of the invention, the invention provides a method for treating a cancer in an individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells. In another aspect of the invention, the invention provides a method for treating a cancer in an individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO. In yet another aspect of the invention, the invention provides a method for treating a cancer in an individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain. In still another aspect of the invention, the invention provides a method for treating a cancer in an individual comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain.
The combination therapy may also comprise one or more additional therapeutic agents. The additional therapeutic agent may be, e.g., a chemotherapeutic, a biotherapeutic agent (including but not limited to antibodies to VEGF, VEGFR, EGFR, Her2/neu, other growth factor receptors, CD20, CD40, CD-40L, CTLA-4, OX-40, 4-1BB, and ICOS), an immunogenic agent (for example, attenuated cancerous cells, tumor antigens, antigen presenting cells such as dendritic cells pulsed with tumor derived antigen or nucleic acids, immune stimulating cytokines (for example, IL-2, IFNα2, GM-CSF), and cells transfected with genes encoding immune stimulating cytokines such as but not limited to GM-C SF).
Examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CBI-TMI); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; antibiotics such as the enediyne antibiotics (e.g. calicheamicin, especially calicheamicin gamma1I and calicheamicin phiI1, see, e.g., Agnew, Chem. Intl. Ed. Engl., 33:183-186 (1994); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromomophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycins, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin (including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidamine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidamol; nitracrine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2′,2′′-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxoids, e.g. paclitaxel and doxetaxel; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. Also included are anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen, raloxifene, droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LY117018, onapristone, and toremifene (Fareston); aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands, such as, for example, 4(5)-imidazoles, aminoglutethimide, megestrol acetate, exemestane, formestane, fadrozole, vorozole, letrozole, and anastrozole; and anti-androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; and pharmaceutically acceptable salts, acids or derivatives of any of the above.
Each therapeutic agent in a combination therapy of the invention may be administered either alone or in a medicament (also referred to herein as a pharmaceutical composition) which comprises the therapeutic agent and one or more pharmaceutically acceptable carriers, excipients and diluents, according to standard pharmaceutical practice.
Each therapeutic agent in a combination therapy of the invention may be administered simultaneously (i.e., in the same medicament), concurrently (i.e., in separate medicaments administered one right after the other in any order) or sequentially in any order. Sequential administration is particularly useful when the therapeutic agents in the combination therapy are in different dosage forms (one agent is a tablet or capsule and another agent is a sterile liquid) and/or are administered on different dosing schedules, e.g., a chemotherapeutic that is administered at least daily and a biotherapeutic that is administered less frequently, such as once weekly, once every two weeks, or once every three weeks.
In another embodiment, administration of a combination therapy comprising Pembrolizumab (MK-3475) and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells provides synergistic antitumor activity. In another embodiment, administration of a combination therapy comprising Pembrolizumab (MK-3475) and a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO provides synergistic antitumor activity. In another embodiment, administration of a combination therapy comprising Pembrolizumab (MK-3475) and an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain provides synergistic antitumor activity. In another embodiment, administration of a combination therapy comprising Pembrolizumab (MK-3475) and an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain provides synergistic antitumor activity.
Dosage units for a PD-1 antagonist (e.g., MK-3475) may be expressed as a flat dose, i.e., 100 mg, 200 mg, 300 mg, or as a patient-specific dose, i.e., mg/kg (mg therapeutic agent/kg of body weight) or mg/m2 (quantity in milligrams per square meter of body surface area).
In one embodiment, the dose of the attenuated Listeria strain comprised by the immunogenic composition provided herein is administered to a subject at a dose of 1×107-3.31×1010 CFU. In another embodiment, the dose is 1×108-3.31×1010 CFU. In another embodiment, the dose is 1×109-3.31×1010 CFU. In another embodiment, the dose is 5-500×108 CFU. In another embodiment, the dose is 7-500×108 CFU. In another embodiment, the dose is 10-500×108 CFU. In another embodiment, the dose is 20-500×108 CFU. In another embodiment, the dose is 30-500×108 CFU. In another embodiment, the dose is 50-500×108 CFU. In another embodiment, the dose is 70-500×108 CFU. In another embodiment, the dose is 100-500×108 CFU. In another embodiment, the dose is 150-500×108 CFU. In another embodiment, the dose is 5-300×108 CFU. In another embodiment, the dose is 5-200×108 CFU. In another embodiment, the dose is 5-150×108 CFU. In another embodiment, the dose is 5-100×108 CFU. In another embodiment, the dose is 5-70×108 CFU. In another embodiment, the dose is 5-50×108 CFU. In another embodiment, the dose is 5-30×108 CFU. In another embodiment, the dose is 5-20×108 CFU. In another embodiment, the dose is 1-30×109 CFU. In another embodiment, the dose is 1-20×109CFU. In another embodiment, the dose is 2-30×109 CFU. In another embodiment, the dose is 1-10×109 CFU. In another embodiment, the dose is 2-10×109 CFU. In another embodiment, the dose is 3-10×109 CFU. In another embodiment, the dose is 2-7×109 CFU. In another embodiment, the dose is 2-5×109 CFU. In another embodiment, the dose is 3-5×109 CFU. In another embodiment, the dose is 0.5×109 CFU. In another embodiment, the dose is 1×109 CFU. In another embodiment, the dose is 5×109 CFU. In another embodiment, the dose is 1×1010 CFU.
In another embodiment, the dose is 1×107 organisms. In another embodiment, the dose is 1×108 organisms. In another embodiment, the dose is 1×109 organisms. In another embodiment, the dose is 1.5×109 organisms. In another embodiment, the dose is 2×109 organisms. In another embodiment, the dose is 3×109 organisms. In another embodiment, the dose is 4×109 organisms. In another embodiment, the dose is 5×109 organisms. In another embodiment, the dose is 6×109 organisms. In another embodiment, the dose is 7×109 organisms. In another embodiment, the dose is 8×109 organisms. In another embodiment, the dose is 10×109 organisms. In another embodiment, the dose is 1.5×1010 organisms. In another embodiment, the dose is 2×1010 organisms. In another embodiment, the dose is 2.5×1010 organisms. In another embodiment, the dose is 3×1010 organisms. In another embodiment, the dose is 3.3×1010 organisms. In another embodiment, the dose is 4×1010 organisms. In another embodiment, the dose is 5×1010 organisms. Each dose and range of doses represents a separate embodiment of the present invention.
It will be appreciated by the skilled artisan that the term “Boosting” may encompass administering an additional strain or immunogenic composition or recombinant Listeria strain dose or immune checkpoint inhibitor alone or in combination to a subject. In another embodiment of methods of the present invention, 2 boosts (or a total of 3 inoculations) are administered. In another embodiment, 3 boosts are administered. In another embodiment, 4 boosts are administered. In another embodiment, 5 boosts are administered. In another embodiment, 6 boosts are administered. In another embodiment, more than 6 boosts are administered. Each possibility represents a separate embodiment of the present invention.
In another embodiment, a method of present invention further comprises the step of boosting the subject with a recombinant Listeria strain or immune checkpoint inhibitor as provided herein. In another embodiment, the recombinant Listeria strain used in the booster inoculation is the same as the strain used in the initial “priming” inoculation. In another embodiment, the booster strain is different from the priming strain. In another embodiment, the recombinant immune checkpoint inhibitor used in the booster inoculation is the same as the inhibitor used in the initial “priming” inoculation. In another embodiment, the booster inhibitor is different from the priming inhibitor. In another embodiment, the same doses are used in the priming and boosting inoculations. In another embodiment, a larger dose is used in the booster. In another embodiment, a smaller dose is used in the booster. In another embodiment, the methods of the present invention further comprise the step of administering to the subject a booster vaccination. In one embodiment, the booster vaccination follows a single priming vaccination. In another embodiment, a single booster vaccination is administered after the priming vaccinations. In another embodiment, two booster vaccinations are administered after the priming vaccinations. In another embodiment, three booster vaccinations are administered after the priming vaccinations. In one embodiment, the period between a prime and a boost strain is experimentally determined by the skilled artisan. In another embodiment, the period between a prime and a boost strain is 1 week, in another embodiment it is 2 weeks, in another embodiment, it is 3 weeks, in another embodiment, it is 4 weeks, in another embodiment, it is 5 weeks, in another embodiment it is 6-8 weeks, in yet another embodiment, the boost strain is administered 8-10 weeks after the prime strain.
In another embodiment, a method of the present invention further comprises boosting the subject with a immunogenic composition comprising an attenuated Listeria strain provided herein. In another embodiment, a method of the present invention comprises the step of administering a booster dose of the immunogenic composition comprising the attenuated Listeria strain provided herein. In another embodiment, the booster dose is an alternate form of said immunogenic composition. In another embodiment, the methods of the present invention further comprise the step of administering to the subject a booster immunogenic composition. In one embodiment, the booster dose follows a single priming dose of said immunogenic composition. In another embodiment, a single booster dose is administered after the priming dose. In another embodiment, two booster doses are administered after the priming dose. In another embodiment, three booster doses are administered after the priming dose. In one embodiment, the period between a prime and a boost dose of an immunogenic composition comprising the attenuated Listeria provided herein is experimentally determined by the skilled artisan. In another embodiment, the dose is experimentally determined by a skilled artisan. In another embodiment, the period between a prime and a boost dose is 1 week, in another embodiment it is 2 weeks, in another embodiment, it is 3 weeks, in another embodiment, it is 4 weeks, in another embodiment, it is 5 weeks, in another embodiment it is 6-8 weeks, in yet another embodiment, the boost dose is administered 8-10 weeks after the prime dose of the immunogenic composition.
Heterologous “prime boost” strategies have been effective for enhancing immune responses and protection against numerous pathogens. Schneider et al., Immunol. Rev. 170:29-38 (1999); Robinson, H. L., Nat. Rev. Immunol. 2:239-50 (2002); Gonzalo, R. M. et al., Strain 20:1226-31 (2002); Tanghe, A., Infect. Immun 69:3041-7 (2001). Providing antigen in different forms in the prime and the boost injections appears to maximize the immune response to the antigen. DNA strain priming followed by boosting with protein in adjuvant or by viral vector delivery of DNA encoding antigen appears to be the most effective way of improving antigen specific antibody and CD4+T-cell responses or CD8+T-cell responses respectively. Shiver J. W. et al., Nature 415: 331-5 (2002); Gilbert, S. C. et al., Strain 20:1039-45 (2002); Billaut-Mulot, O. et al., Strain 19:95-102 (2000); Sin, J. I. et al., DNA Cell Biol. 18:771-9 (1999). Recent data from monkey vaccination studies suggests that adding CRL1005 poloxamer (12 kDa, 5% POE), to DNA encoding the HIV gag antigen enhances T-cell responses when monkeys are vaccinated with an HIV gag DNA prime followed by a boost with an adenoviral vector expressing HIV gag (Ad5-gag). The cellular immune responses for a DNA/poloxamer prime followed by an Ad5-gag boost were greater than the responses induced with a DNA (without poloxamer) prime followed by Ad5-gag boost or for Ad5-gag only. Shiver, J. W. et al. Nature 415:331-5 (2002). U.S. Patent Appl. Publication No. US 2002/0165172 A1 describes simultaneous administration of a vector construct encoding an immunogenic portion of an antigen and a protein comprising the immunogenic portion of an antigen such that an immune response is generated. The document is limited to hepatitis B antigens and HIV antigens. Moreover, U.S. Pat. No. 6,500,432 is directed to methods of enhancing an immune response of nucleic acid vaccination by simultaneous administration of a polynucleotide and polypeptide of interest. According to the patent, simultaneous administration means administration of the polynucleotide and the polypeptide during the same immune response, preferably within 0-10 or 3-7 days of each other. The antigens contemplated by the patent include, among others, those of Hepatitis (all forms), HSV, HIV, CMV, EBV, RSV, VZV, HPV, polio, influenza, parasites (e.g., from the genus Plasmodium), and pathogenic bacteria (including but not limited to M. tuberculosis, M. leprae, Chlamydia, Shigella, B. burgdorferi, enterotoxigenic E. coli, S. typhosa, H. pylori, V. cholerae, B. pertussis, etc.). All of the above references are herein incorporated by reference in their entireties.
In another embodiment, the recombinant polypeptide of methods of the present invention is expressed by the recombinant Listeria strain. In another embodiment, the expression is mediated by a nucleotide molecule carried by the recombinant Listeria strain. Each possibility represents a separate embodiment of the present invention.
As used herein, the term “recombinant Listeria” in some embodiments refers to an attenuated Listeria having all the same meanings and qualities described throughout.
In another embodiment, a composition comprising a strain of the present invention further comprises an adjuvant. In yet another embodiment, a strain of the present invention may be administered with an adjuvant. The adjuvant utilized in methods and compositions of the present invention is, in another embodiment, a granulocyte/macrophage colony-stimulating factor (GM-CSF) protein. In another embodiment, the adjuvant comprises a GM-CSF protein. In another embodiment, the adjuvant is a nucleotide molecule encoding GM-CSF. In another embodiment, the adjuvant comprises a nucleotide molecule encoding GM-CSF. In another embodiment, the adjuvant is saponin QS21. In another embodiment, the adjuvant comprises saponin QS21. In another embodiment, the adjuvant is monophosphoryl lipid A. In another embodiment, the adjuvant comprises monophosphoryl lipid A. In another embodiment, the adjuvant is SBAS2. In another embodiment, the adjuvant comprises SBAS2. In another embodiment, the adjuvant is an unmethylated CpG-containing oligonucleotide. In another embodiment, the adjuvant comprises an unmethylated CpG-containing oligonucleotide. In another embodiment, the adjuvant is an immune-stimulating cytokine. In another embodiment, the adjuvant comprises an immune-stimulating cytokine. In another embodiment, the adjuvant is a nucleotide molecule encoding an immune-stimulating cytokine. In another embodiment, the adjuvant comprises a nucleotide molecule encoding an immune-stimulating cytokine. In another embodiment, the adjuvant is or comprises a quill glycoside. In another embodiment, the adjuvant is or comprises a bacterial mitogen. In another embodiment, the adjuvant is or comprises a bacterial toxin. In another embodiment, the adjuvant is or comprises any other adjuvant known in the art. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the method provided herein further comprises the step of co-administering with, prior to or following the administration of said recombinant Listeria strain an an immune checkpoint protein inhibitor. In one embodiment, an adjuvant is selected from the group comprising Montanide ISA 51, GM-CSF, KLH, a cytokine, a growth factor, a cell population, QS21, Freund's incomplete adjuvant, aluminum phosphate, aluminum hydroxide, BCG, alum, an interleukin, an unmethylated CpG oligonucleotide, quill glycosides, monophosphoryl lipid A, a liposome, a bacterial mitogen, a bacterial toxin, or a chemokine, or any combination thereof.
In some instances, the PD-1 antagonist and the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells are combined in a single dosage form. In some instances, the PD-1 antagonist and the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO are combined in a single dosage form. In some instances, the PD-1 antagonist and the an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain are combined in a single dosage form. In some instances, the PD-1 antagonist and the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain are combined in a single dosage form.
Although the simultaneous administration of the PD-1 antagonist and the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells may be maintained throughout a period of treatment or prevention, anti-cancer activity may also be achieved by subsequent administration of one compound in isolation (for example, PD-1 antagonist without the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells, following combination treatment, or alternatively the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells, without PD-1 antagonist, following combination treatment). In addition, although the simultaneous administration of the PD-1 antagonist and the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO may be maintained throughout a period of treatment or prevention, anti-cancer activity may also be achieved by subsequent administration of one compound in isolation (for example, PD-1 antagonist without the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO, following combination treatment, or alternatively the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO, without PD-1 antagonist, following combination treatment). Further, although the simultaneous administration of the PD-1 antagonist and the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain may be maintained throughout a period of treatment or prevention, anti-cancer activity may also be achieved by subsequent administration of one compound in isolation (for example, PD-1 antagonist without the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain, following combination treatment, or alternatively the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain, without PD-1 antagonist, following combination treatment). In addition, although the simultaneous administration of the PD-1 antagonist and the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain may be maintained throughout a period of treatment or prevention, anti-cancer activity may also be achieved by subsequent administration of one compound in isolation (for example, PD-1 antagonist without the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, following combination treatment, or alternatively the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, without PD-1 antagonist, following combination treatment).
In some embodiments, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered before administration of the PD-1 antagonist, while in other embodiments, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered after administration of the PD-1 antagonist. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In some embodiments, at least one of the therapeutic agents in the combination therapy is administered using the same dosage regimen (dose, frequency and duration of treatment) that is typically employed when the agent is used as monotherapy for treating the same cancer. In other embodiments, the patient receives a lower total amount of at least one of the therapeutic agents in the combination therapy than when the agent is used as monotherapy, e.g., smaller doses, less frequent doses, and/or shorter treatment duration.
A combination therapy of the invention may be used prior to or following surgery to remove a tumor and may be used prior to, during or after radiation therapy.
In some embodiments, a combination therapy of the invention is administered to a patient who has not been previously treated with a biotherapeutic or chemotherapeutic agent, i.e., is treatment-naïve. In other embodiments, the combination therapy is administered to a patient who failed to achieve a sustained response after prior therapy with a biotherapeutic or chemotherapeutic agent, i.e., is treatment-experienced. In certain embodiments, a combination therapy of the invention is administered to a patient with previously treated metastatic Castration-Resistant Prostate Cancer (mCRPC).
A combination therapy of the invention is typically used to treat a tumor that is large enough to be found by palpation or by imaging techniques well known in the art, such as MRI, ultrasound, or CAT scan. In some embodiments, a combination therapy of the invention is used to treat an advanced stage tumor having dimensions of at least about 200 mm3′ 300 mm3, 400 mm3, 500 mm3, 750 mm3, or up to 1000 mm3.
A combination therapy of the invention is preferably administered to a patient diagnosted with a prostate cancer that tests positive for PD-L1 expression. In some embodiments, PD-L1 expression is detected using a diagnostic anti-human PD-L1 antibody, or antigen binding fragment thereof, in an IHC assay on an FFPE or frozen tissue section of a tumor sample removed from the patient. Typically, the patient's physician would order a diagnostic test to determine PD-L1 expression in a tumor tissue sample removed from the patient prior to initiation of treatment with the PD-1 antagonist and the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or the LmddmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, but it is envisioned that the physician could order the first or subsequent diagnostic tests at any time after initiation of treatment, such as for example after completion of a treatment cycle. Each possibility represents a separate embodiment of the methods and compositions as provided herein.
In one embodiment, the dosage regimen is tailored to the particular patient's conditions, response and associate treatments, in a manner which is conventional for any therapy, and may need to be adjusted in response to changes in conditions and/or in light of other clinical conditions.
In some embodiments, selecting a dosage regimen (also referred to herein as an administration regimen) for a combination therapy of the invention depends on several factors, including the serum or tissue turnover rate of the entity, the level of symptoms, the immunogenicity of the entity, and the accessibility of the target cells, tissue or organ in the individual being treated. Preferably, a dosage regimen maximizes the amount of each therapeutic agent delivered to the patient consistent with an acceptable level of side effects. Accordingly, the dose amount and dosing frequency of each biotherapeutic and chemotherapeutic agent in the combination depends in part on the particular therapeutic agent, the severity of the cancer being treated, and patient characteristics. Guidance in selecting appropriate doses of antibodies, cytokines, and small molecules are available. See, e.g., Wawrzynczak (1996) Antibody Therapy, Bios Scientific Pub. Ltd, Oxfordshire, UK; Kresina (ed.) (1991) Monoclonal Antibodies, Cytokines and Arthritis, Marcel Dekker, New York, N.Y.; Bach (ed.) (1993) Monoclonal Antibodies and Peptide Therapy in Autoimmune Diseases, Marcel Dekker, New York, N.Y.; Baert et al. (2003) New Engl. J. Med. 348:601-608; Milgrom et al. (1999) New Engl. J. Med. 341:1966-1973; Slamon et al. (2001) New Engl. J. Med. 344:783-792; Beniaminovitz et al. (2000) New Engl. J. Med. 342:613-619; Ghosh et al. (2003) New Engl. J. Med. 348:24-32; Lipsky et al. (2000) New Engl. J. Med. 343:1594-1602; Physicians' Desk Reference 2003 (Physicians' Desk Reference, 57th Ed); Medical Economics Company; ISBN: 1563634457; 57th edition (November 2002). Determination of the appropriate dosage regimen may be made by the clinician, e.g., using parameters or factors known or suspected in the art to affect treatment or predicted to affect treatment, and will depend, for example, the patient's clinical history (e.g., previous therapy), the type and stage of the cancer to be treated and biomarkers of response to one or more of the therapeutic agents in the combination therapy.
Biotherapeutic agents in a combination therapy of the invention may be administered by continuous infusion, or by doses at intervals of, e.g., daily, every other day, three times per week, or one time each week, two weeks, three weeks, monthly, bimonthly, etc. A total weekly dose is generally at least 0.05 μg/kg, 0.2 μg/kg, 0.5 μg/kg, 1 μg/kg, 10 μg/kg, 100 μg/kg, 0.2 mg/kg, 1.0 mg/kg, 2.0 mg/kg, 10 mg/kg, 25 mg/kg, 50 mg/kg body weight or more. See, e.g., Yang et al. (2003) New Engl. J. Med. 349:427-434; Herold et al. (2002) New Engl. J. Med. 346:1692-1698; Liu et al. (1999) J. Neurol. Neurosurg. Psych. 67:451-456; Portielji et al. (20003) Cancer Immunol. Immunother. 52:133-144.
In some embodiments that employ an anti-human PD-1 mAb as the PD-1 antagonist in the combination therapy, the dosing regimen will comprise administering the anti-human PD-1 mAb at a flat dose of 100 to 500 mg or a weight-based dose of 1 to 10 mg/kg at intervals of about 14 days (±2 days) or about 21 days (±2 days) or about 30 days (±2 days) throughout the course of treatment.
In other embodiments that employ an anti-human PD-1 mAb as the PD-1 antagonist in the combination therapy, the dosing regimen will comprise administering the anti-human PD-1 mAb at a dose of from about 0.005 mg/kg to about 10 mg/kg, with intra-patient dose escalation. In other escalating dose embodiments, the interval between doses will be progressively shortened, e.g., about 30 days (±2 days) between the first and second dose, about 14 days (±2 days) between the second and third doses. In certain embodiments, the dosing interval will be about 14 days (±2 days), for doses subsequent to the second dose.
In certain embodiments, a subject will be administered an intravenous (IV) infusion of a medicament comprising any of the PD-1 antagonists described herein.
In one embodiment of the invention, the PD-1 antagonist in the combination therapy is nivolumab, which is administered intravenously at a dose selected from the group consisting of: 1 mg/kg Q2W, 2 mg/kg Q2W, 3 mg/kg Q2W, 5 mg/kg Q2W, 10 mg Q2W, 1 mg/kg Q3W, 2 mg/kg Q3W, 3 mg/kg Q3W, 5 mg/kg Q3W, and 10 mg Q3W.
In another embodiment of the invention, the PD-1 antagonist in the combination therapy is MK-3475, which is administered in a liquid medicament at a dose selected from the group consisting of 200 mg Q3W, 1 mg/kg Q2W, 2 mg/kg Q2W, 3 mg/kg Q2W, 5 mg/kg Q2W, 10 mg Q2W, 1 mg/kg Q3W, 2 mg/kg Q3W, 3 mg/kg Q3W, 5 mg/kg Q3W, and 10 mg Q3W or equivalents of any of these doses (e.g., a PK model of MK-3475 estimates that the fixed dose of 200 mg Q3W provides exposures that are consistent with those obtained with 2 mg/kg Q3W). In some embodiments, MK-3475 is administered as a liquid medicament which comprises 25 mg/ml MK-3475, 7% (w/v) sucrose, 0.02% (w/v) polysorbate 80 in 10 mM histidine buffer pH 5.5, and the selected dose of the medicament is administered by IV infusion over a time period of 30 minutes+/−10 min.
In another embodiment of the invention, the attenuated bacterial or attenuated Listeria in the combination therapy is a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, which is administered in a liquid medicament at a dose selected from the group consisting of 0.5×109, 1×109, 5×109 and 1×1010 cfu. In some embodiments, a dose is selected from the group consisting of 1×109-3.31×1010 CFU, 5-500×108 CFU, 7-500×108 CFU, 10-500×108 CFU, 20-500×108 CFU, 30-500×108 CFU, 50-500×108 CFU, 70-500×108 CFU, 100-500×108 CFU, 150-500×108 CFU, 5-300×108 CFU, 5-200×108 CFU, 5-150×108 CFU, 5-100×108 CFU, 5-70×108 CFU, 5-50×108 CFU, 5-30×108 CFU, 5-20×108 CFU, 1-30×109 CFU, 1-20×109CFU, 2-30×109 CFU, 1-10×109 CFU, 2-10×109 CFU, 3-10×109 CFU, 2-7×109 CFU, 2-5×109 CFU, or 3-5×109 CFU. In another embodiment, the dose is 0.5×109 CFU. In another embodiment, the dose is 1×109 CFU. In another embodiment, the dose is 5×109 CFU. In another embodiment, the dose is 1×1010 CFU.
In other embodiments, a dose is selected from the group consisting of 1×109 organisms, 1.5×109 organisms, 2×109 organisms, 3×109 organisms, 4×109 organisms, 5×109 organisms, 6×109 organisms, 7×109 organisms, 8×109 organisms, 10×109 organisms, 1.5×1010 organisms, x 1010 organisms, 2.5×1010 organisms, 3×1010 organisms, 0.3×1010 organisms, 4×1010 organisms or 5×1010 organisms.
Each dose and range of doses represents a separate embodiment of the present invention.
In some embodiments, pharmaceutical compositions containing strains and compositions of the present invention area dministered to a subject by any method known to a person skilled in the art, such as parenterally, paracancerally, transmucosally, transdermally, intramuscularly, intravenously, intra-dermally, subcutaneously, intra-peritonealy, intra-ventricularly, intra-cranially, intra-vaginally or intra-tumorally.
In another embodiment of the methods and compositions provided herein, the strains or compositions are administered orally, and are thus formulated in a form suitable for oral administration, i.e. as a solid or a liquid preparation. Suitable solid oral formulations include tablets, capsules, pills, granules, pellets and the like. Suitable liquid oral formulations include solutions, suspensions, dispersions, emulsions, oils and the like. In another embodiment of the present invention, the active ingredient is formulated in a capsule. In accordance with this embodiment, the compositions of the present invention comprise, in addition to the active compound and the inert carrier or diluent, a hard gelating capsule.
In another embodiment, the strains or compositions are administered by intravenous, intra-arterial, or intra-muscular injection of a liquid preparation. Suitable liquid formulations include solutions, suspensions, dispersions, emulsions, oils and the like. In one embodiment, the pharmaceutical compositions are administered intravenously and are thus formulated in a form suitable for intravenous administration. In another embodiment, the pharmaceutical compositions are administered intra-arterially and are thus formulated in a form suitable for intra-arterial administration. In another embodiment, the pharmaceutical compositions are administered intra-muscularly and are thus formulated in a form suitable for intra-muscular administration.
In another embodiment, the vaccines or compositions are administered by intravenous, intra-arterial, or intra-muscular injection of a liquid preparation. Suitable liquid formulations include solutions, suspensions, dispersions, emulsions, oils and the like. In one embodiment, the pharmaceutical compositions are administered intravenously and are thus formulated in a form suitable for intravenous administration. In another embodiment, the pharmaceutical compositions are administered intra-arterially and are thus formulated in a form suitable for intra-arterial administration. In another embodiment, the pharmaceutical compositions are administered intra-muscularly and are thus formulated in a form suitable for intra-muscular administration.
In one embodiment, the vaccines of the methods and compositions as provided herein may be administered to a host vertebrate animal, preferably a mammal, and more preferably a human, either alone or in combination with a pharmaceutically acceptable carrier. In another embodiment, the vaccine is administered in an amount effective to induce an immune response to the Listeria strain itself or to a heterologous antigen which the Listeria species has been modified to express. In another embodiment, the amount of vaccine or immunogenic composition to be administered may be routinely determined by one of skill in the art when in possession of the present disclosure. In another embodiment, a pharmaceutically acceptable carrier may include, but is not limited to, sterile distilled water, saline, phosphate buffered solutions or bicarbonate buffered solutions. In another embodiment, the pharmaceutically acceptable carrier selected and the amount of carrier to be used will depend upon several factors including the mode of administration, the strain of Listeria and the age and disease state of the vaccinee. In another embodiment, administration of the vaccine may be by an oral route, or it may be parenteral, intranasal, intramuscular, intravascular, intrarectal, intraperitoneal, or any one of a variety of well-known routes of administration. In another embodiment, the route of administration may be selected in accordance with the type of infectious agent or tumor to be treated.
In another embodiment, the present invention provides a method of treating, suppressing, or inhibiting at least one tumor in a subject comprising administering the immunogenic composition provided herein.
In some embodiments an attenuated bacteria, or attenuated Listeria, or LmddA-142 or LmddA-143 is administered as a liquid medicament, and the selected dose of the medicament is administered by IV infusion over a time period of 30 minutes+/−10 min.
The optimal dose for MK-3475 in combination with a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain may be identified by dose escalation of one or both of these agents.
In one embodiment, the patient is treated with the combination therapy on day 1 of weeks 1, 4 and 7 in a 12 week cycle, with MK-3475 administered at a starting dose of 200 mg and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain administered at a starting dose of 1×109 cfu. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 0.5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain administered at a starting dose of 5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 1×1010 CFU.
In one embodiment, the patient is treated with the combination therapy, wherein MK-3475 is administered on Day 1 Q3W of a 12-week cycle at a starting dose of 200 mg, and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered on Day 1 of Weeks 1, 4, and 7 of the 12-week cycle at a starting dose of 1×109 cfu. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 0.5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain administered at a starting dose of 5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 1×1010 CFU. In another embodiment, administration is administered up to 3 days before or 3 days after the scheduled Day 1 of each cycle.
In one embodiment, the patient is treated with the combination therapy, wherein MK-3475 is administered on Day 1 of week 1, 4, 7 and 10 of a 12-week cycle at a starting dose of 200 mg, and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered on Day 1 of Weeks 1, 4, and 7 of the 12-week cycle at a starting dose of 1×109 cfu. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 0.5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain administered at a starting dose of 5×109 CFU. In another embodiment, the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 1×1010 CFU. In another embodiment, administration is administered up to 3 days before or 3 days after the scheduled Day 1 of each cycle.
In an embodiment, the MK-3475 infusion is administered first, followed by a NSAIDS, e.g., naproxen or ibuprofen, and oral antiemetic medication within 30 minutes prior to the live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or the live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or the LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or the LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain infusion.
In another embodiment, MK-3475 is administered at a starting dose of 200 mg Q3W and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered Q3W at a starting dose of between 1×109 and 1×1010 cfu. In another embodiment, MK-3475 is administered at a starting dose of 200 mg Q3W and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered Q3W at a starting dose of between 0.5×109 and 1×1010 cfu.
In yet another embodiment, a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is administered at a starting dose of 5×109 Q3W and MK-3475 is administered at a starting dose of 200 mg Q3W, and if the starting dose of the combination is not tolerated by the patient, then the dose of a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is reduced to 1×109 cfu Q3W.
In some embodiments, dosage levels below the lower limit of the aforesaid range may be more than adequate, while in other cases still larger doses may be employed, as determined by those skilled in the art.
In some embodiments, a treatment cycle begins with the first day of combination treatment and lasts for at least 12 weeks, 24 weeks or 48 weeks. On any day of a treatment cycle that the drugs are co-administered, the timing between the separate IV infusions of MK-3475 and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain is between about 15 minutes to about 45 minutes. The invention contemplates that MK-3475 and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain may be administered in either order or by simultaneous IV infusion.
In some embodiments, the combination therapy is administered for at least 2 to 4 weeks after the patient achieves a CR.
In some embodiments, the patient selected for treatment with the combination therapy of the invention has been diagnosed with a metastatic prostate cancer and the patient has progressed or become resistant to no more than 3 prior systemic treatment regimens.
In an embodiment, the patient selected for treatment with the combination therapy of the invention had a serum PSA level ≧5 ng/mL within 1 week prior to starting the combination therapy.
In another embodiment, the patient selected for treatment with the combination therapy of the invention had a rising PSA level within the 4 weeks prior to starting the combination therapy.
The present invention also provides a medicament which comprises a PD-1 antagonist as described above and a pharmaceutically acceptable excipient. When the PD-1 antagonist is a biotherapeutic agent, e.g., a mAb, the antagonist may be produced in CHO cells using conventional cell culture and recovery/purification technologies.
In some embodiments, a medicament comprising an anti-PD-1 antibody as the PD-1 antagonist may be provided as a liquid formulation or prepared by reconstituting a lyophilized powder with sterile water for injection prior to use. WO 2012/135408 describes the preparation of liquid and lyophilized medicaments comprising MK-3475 that are suitable for use in the present invention. In some embodiments, a medicament comprising MK-3475 is provided in a glass vial which contains about 50 mg of MK-3475.
The present invention also provides a medicament which comprises a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain and a pharmaceutically acceptable excipient. A live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain may be prepared as described in Wallecha et al. CLINICAL ANDSTRAINIMMUNOLOGY, January 2009, p. 96-103.
The PD-1 antagonist medicament and the a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain medicament may be provided as a kit which comprises a first container and a second containiner and a package insert. The first container contains at least one dose of a medicament comprising an anti-PD-1 antibody, the second container contains at least one dose of a medicament comprising a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, and the package insert, or label, which comprises instructions for treating a patient for a prostate cancer using the medicaments. The first and second containers may be comprised of the same or different shape (e.g., vials, syringes and bottles) and/or material (e.g., plastic or glass). The kit may further comprise other materials that may be useful in administering the medicaments, such as diluents, filters, IV bags and lines, needles and syringes. In some embodiments of the kit, the anti-PD-1 antagonist is an anti-PD-1 antibody and the instructions state that the medicaments are intended for use in treating a patient having a prostate cancer that tests positive for PD-L1 expression by an IHC assay.
These and other aspects of the invention, including the exemplary specific embodiments listed below, will be apparent from the teachings contained herein.
Exemplary Specific Embodiments of the Invention


    1. A method for treating a prostate cancer in a patient comprising administering to the individual a combination therapy which comprises a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain. Each possibility represents a separate embodiment as provided herein.
    2. A medicament comprising a PD-1 antagonist for use in combination with a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain for treating a prostate cancer in a patient. Each possibility represents a separate embodiment as provided herein.
    3. A medicament comprising a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (104035 dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain for use in combination with a PD-1 antagonist for treating a prostate cancer in a patient. Each possibility represents a separate embodiment as provided herein.
    4. The medicament of embodiment 3 or 4, which further comprises a pharmaceutically acceptable excipient or adjuvant, or a combination thereof.
    5. Use of a PD-1 antagonist in the manufacture of medicament for treating a prostate cancer in a patient when administered in combination with a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (104035 dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (104035 dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain. Each possibility represents a separate embodiment as provided herein.
    6. Use of a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (104035 dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (104035 dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain in the manufacture of a medicament for treating a prostate cancer in a patient when administered in combination with a PD-1 antagonist. Each possibility represents a separate embodiment as provided herein.
    7. Use of a PD-1 antagonist and a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain in the manufacture of medicaments for treating a cancer in a patient. Each possibility represents a separate embodiment as provided herein.
    8. A kit which comprises a first container, a second container and a package insert, wherein the first container comprises at least one dose of a medicament comprising an anti-PD-1 antagonist, the second container comprises at least one dose of a medicament comprising a live-attenuated bacterial strain that is used to stimulate APCs capable of driving a cellular immune response to PSA expressing cells or a live-attenuated Listeria monocytogenes strain bioengineered, by transforming it with an expression vector to express a PSA antigen fused to a tLLO or an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain or an LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, and the package insert comprises instructions for treating a patient for prostate cancer using the medicaments. Each possibility represents a separate embodiment as provided herein.
    9. The kit of embodiment 8, wherein the instructions state that the medicaments are intended for use in treating a patient having a prostate cancer that tests positive for PD-L1 expression by an immunohistochemical (IHC) assay.
    10. The method, medicament, use or kit of any of embodiments 1 to 9, wherein the PD-1 antagonist is a monoclonal antibody, or antigen binding fragment thereof.

11. The method, medicament, use or kit of embodiment 9, wherein the PD-1 antagonist is MPDL3280A, BMS-936559, MEDI4736, MSB0010718C or a monoclonal antibody which comprises the heavy chain and light chain variable regions of SEQ ID NO:24 and SEQ ID NO:21, respectively, of WO2013/019906.

    12. The method, medicament, use or kit of embodiment 10, wherein the PD-1 antagonist is a monoclonal antibody, or antigen binding fragment thereof, and blocks binding of PD-L1 and PD-L2 to PD-1.
    13. The method, medicament, use or kit of embodiment 12, wherein the monoclonal antibody, or antigen binding fragment thereof, comprises: (a) light chain CDRs of SEQ ID NOs: 1, 2 and 3 and heavy chain CDRs of SEQ ID NOs: 4, 5 and 6; or (b) light chain CDRs of SEQ ID NOs: 7, 8 and 9 and heavy chain CDRs of SEQ ID NOs: 10, 11 and 12.
    14. The method, medicament, use or kit of embodiment 12, wherein the monoclonal antibody, or antigen binding fragment thereof, comprises light chain CDRs of SEQ ID NOs: 7, 8 and 9 and heavy chain CDRs of SEQ ID NOs: 10, 11 and 12.
    15. The method, medicament, use or kit of embodiment 12, wherein the PD-1 antagonist is an anti-PD-1 monoclonal antibody which comprises a heavy chain and a light chain, and wherein the heavy chain comprises SEQ ID NO:21 and the light chain comprises SEQ ID NO:22.
    16. The method, medicament, use or kit of embodiment 12, wherein the PD-1 antagonist is an anti-PD-1 monoclonal antibody which comprises a heavy chain and a light chain, and wherein the heavy chain comprises SEQ ID NO:23 and the light chain comprises SEQ ID NO:24.
    17. The method, medicament, use or kit of any of embodiments 10-16, wherein the prostate cancer is metastatic.
    18. The method, medicament, use or kit of embodiment 17, wherein the cancer is metastatic Castration-resistant Prostate Cancer (mCRPC).
    19. The method, medicament, use or kit of any of embodiments 10-18, wherein the patient has not been previously treated for prostate cancer.
    20. The method, medicament, use or kit of any of embodiments 10-18, wherein the patient has previously been treated for prostate cancer.
    21. The method, medicament, use or kit of any of embodiments 10-20, wherein the prostate cancer tests positive for PD-L1.
    22. The method, medicament, use or kit of embodiment 21, wherein the PD-L1 expression is elevated.

23. The method, medicament, use or kit of embodiment 12, wherein the PD-1 antagonist is MK-3475 or nivolumab.

    24. The method, medicament, use or kit of embodiment 25, wherein MK-3475 is formulated as a liquid medicament which comprises 25 mg/ml MK-3475, 7% (w/v) sucrose, 0.02% (w/v) polysorbate 80 in 10 mM histidine buffer pH 5.5.
    25. The method, medicament, use or kit of any of embodiments 1 to 24, wherein the attenuated Listeria is LmddA-142 or LmddA-143
    26. The method, medicament, use of kit of any of embodiments 1 to 25, wherein the PD-1 antagonist is MK-3475, the attenuated Listeria is LmddA-142 or LmddA-143, the patient is diagnosed with a metastatic prostate cancer, and doses of the PD-1 antagonist and the attenuated Listeria are selected from the group consisting of one of the combinations in the table below:

















MK-3475
LmddA-142
LmddA-143









200 mg Q3W
1 × 109 cfu
1 × 109 cfu



200 mg Q3W
2 × 109 cfu
2 × 109 cfu



200 mg Q3W
5 × 109 cfu
5 × 109 cfu



200 mg Q3W
 1 × 1010 cfu
 1 × 1010 cfu










General Methods

Standard methods in molecular biology are described Sambrook, Fritsch and Maniatis (1982 & 1989 2nd Edition, 2001 3rd Edition) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Sambrook and Russell (2001) Molecular Cloning, 3rd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Wu (1993) Recombinant DNA, Vol. 217, Academic Press, San Diego, Calif.). Standard methods also appear in Ausbel, et al. (2001) Current Protocols in Molecular Biology, Vols. 1-4, John Wiley and Sons, Inc. New York, N.Y., which describes cloning in bacterial cells and DNA mutagenesis (Vol. 1), cloning in mammalian cells and yeast (Vol. 2), glycoconjugates and protein expression (Vol. 3), and bioinformatics (Vol. 4).
Methods for protein purification including immunoprecipitation, chromatography, electrophoresis, centrifugation, and crystallization are described (Coligan, et al. (2000) Current Protocols in Protein Science, Vol. 1, John Wiley and Sons, Inc., New York). Chemical analysis, chemical modification, post-translational modification, production of fusion proteins, glycosylation of proteins are described (see, e.g., Coligan, et al. (2000) Current Protocols in Protein Science, Vol. 2, John Wiley and Sons, Inc., New York; Ausubel, et al. (2001) Current Protocols in Molecular Biology, Vol. 3, John Wiley and Sons, Inc., NY, NY, pp. 16.0.5-16.22.17; Sigma-Aldrich, Co. (2001) Products for Life Science Research, St. Louis, Mo.; pp. 45-89; Amersham Pharmacia Biotech (2001) BioDirectory, Piscataway, N.J., pp. 384-391). Production, purification, and fragmentation of polyclonal and monoclonal antibodies are described (Coligan, et al. (2001) Current Protcols in Immunology, Vol. 1, John Wiley and Sons, Inc., New York; Harlow and Lane (1999) Using Antibodies, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Harlow and Lane, supra). Standard techniques for characterizing ligand/receptor interactions are available (see, e.g., Coligan, et al. (2001) Current Protocols in Immunology, Vol. 4, John Wiley, Inc., New York).
Monoclonal, polyclonal, and humanized antibodies can be prepared (see, e.g., Sheperd and Dean (eds.) (2000) Monoclonal Antibodies, Oxford Univ. Press, New York, N.Y.; Kontermann and Dubel (eds.) (2001) Antibody Engineering, Springer-Verlag, New York; Harlow and Lane (1988) Antibodies A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., pp. 139-243; Carpenter, et al. (2000) J. Immunol. 165:6205; He, et al. (1998) J. Immunol. 160:1029; Tang et al. (1999) J. Biol. Chem. 274:27371-27378; Baca et al. (1997) J. Biol. Chem. 272:10678-10684; Chothia et al. (1989) Nature 342:877-883; Foote and Winter (1992) J. Mol. Biol. 224:487-499; U.S. Pat. No. 6,329,511).
An alternative to humanization is to use human antibody libraries displayed on phage or human antibody libraries in transgenic mice (Vaughan et al. (1996) Nature Biotechnol. 14:309-314; Barbas (1995) Nature Medicine 1:837-839; Mendez et al. (1997) Nature Genetics 15:146-156; Hoogenboom and Chames (2000) Immunol. Today 21:371-377; Barbas et al. (2001) Phage Display: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; Kay et al. (1996) Phage Display of Peptides and Proteins: A Laboratory Manual, Academic Press, San Diego, Calif.; de Bruin et al. (1999) Nature Biotechnol. 17:397-399).
Purification of antigen is not necessary for the generation of antibodies. Animals can be immunized with cells bearing the antigen of interest. Splenocytes can then be isolated from the immunized animals, and the splenocytes can fused with a myeloma cell line to produce a hybridoma (see, e.g., Meyaard et al. (1997) Immunity 7:283-290; Wright et al. (2000) Immunity 13:233-242; Preston et al., supra; Kaithamana et al. (1999) J. Immunol. 163:5157-5164).
Antibodies can be conjugated, e.g., to small drug molecules, enzymes, liposomes, polyethylene glycol (PEG). Antibodies are useful for therapeutic, diagnostic, kit or other purposes, and include antibodies coupled, e.g., to dyes, radioisotopes, enzymes, or metals, e.g., colloidal gold (see, e.g., Le Doussal et al. (1991) J. Immunol. 146:169-175; Gibellini et al. (1998) J. Immunol. 160:3891-3898; Hsing and Bishop (1999) J. Immunol. 162:2804-2811; Everts et al. (2002) J. Immunol. 168:883-889).
Methods for flow cytometry, including fluorescence activated cell sorting (FACS), are available (see, e.g., Owens, et al. (1994) Flow Cytometry Principles for Clinical Laboratory Practice, John Wiley and Sons, Hoboken, N.J.; Givan (2001) Flow Cytometry, 2nd ed.; Wiley-Liss, Hoboken, N.J.; Shapiro (2003) Practical Flow Cytometry, John Wiley and Sons, Hoboken, N.J.). Fluorescent reagents suitable for modifying nucleic acids, including nucleic acid primers and probes, polypeptides, and antibodies, for use, e.g., as diagnostic reagents, are available (Molecular Probesy (2003) Catalogue, Molecular Probes, Inc., Eugene, Oreg.; Sigma-Aldrich (2003) Catalogue, St. Louis, Mo.).
Standard methods of histology of the immune system are described (see, e.g., Muller-Harmelink (ed.) (1986) Human Thymus: Histopathology and Pathology, Springer Verlag, New York, N.Y.; Hiatt, et al. (2000) Color Atlas of Histology, Lippincott, Williams, and Wilkins, Phila, Pa.; Louis, et al. (2002) Basic Histology: Text and Atlas, McGraw-Hill, New York, N.Y.).
Software packages and databases for determining, e.g., antigenic fragments, leader sequences, protein folding, functional domains, glycosylation sites, and sequence alignments, are available (see, e.g., GenBank, Vector NTI® Suite (Informax, Inc, Bethesda, Md.); GCG Wisconsin Package (Accelrys, Inc., San Diego, Calif.); DeCypher® (TimeLogic Corp., Crystal Bay, Nev.); Menne, et al. (2000) Bioinformatics 16: 741-742; Menne, et al. (2000) Bioinformatics Applications Note 16:741-742; Wren, et al. (2002) Comput. Methods Programs Biomed. 68:177-181; von Heijne (1983) Eur. J. Biochem. 133:17-21; von Heijne (1986) Nucleic Acids Res. 14:4683-4690).







TABLE 3







provides a brief description of the sequences in the sequence listing.








SEQ ID NO:
Description











1
hPD-1.08A light chain CDR1


2
hPD-1.08A light chain CDR2


3
hPD-1-08A light chain CDR3


4
hPD-1.08A heavy chain CDR1


5
hPD-1.08A heavy chain CDR2


6
hPD-1.08A heavy chain CDR3


7
hPD-1.09A light chain CDR1


8
hPD-1.09A light chain CDR2


9
hPD-1.09A light chain CDR3


10
hPD-1.09A heavy chain CDR1


11
hPD-1.09A heavy chain CDR2


12
hPD-1.09A heavy chain CDR3


13
109A-H heavy chain variable region


14
409A-H heavy chain full length


15
K09A-L-11 light chain variable region


16
K09A-L-16 light chain variable region


17
K09A-L-17 light chain variable region


18
K09A-L-11 light chain full length


19
K09A-L-16 light chain full length


20
K09A-L-17 light chain full length


21
MK-3475 Heavy chain


22
MK-3475 Light chain


23
Nivolumab Heavy chain


24
Nivolumab light chain


25
KLK3 protein


26
KLK3 protein


27
KLK3 protein


28
Nucleotide encoding KLK3 protein


29
KLK3 protein


30
Nucleotide encoding KLK3 protein


31
KLK3 protein


32
Nucleotide encoding KLK3 protein


33
KLK3 protein


34
Nucleotide encoding KLK3 protein


35
KLK3 protein


36
Nucleotide encoding KLK3 protein


37
KLK3 protein


38
Nucleotide encoding KLK3 protein


39
KLK3 protein


40
Nucleotide encoding KLK3 protein


41
KLK3 protein


42
KLK3 protein


43
KLK3 protein


44
KLK3 protein


45
Nucleotide encoding KLK3 protein


46
Primer Adv60-PSA


47
Primer Adv61-PSA


48
tLLO-PSA fusion polypeptide


49
LLO PEST seqeunce


50
KLK3 protein


51
KLK3 protein


52
KLK3 protein


53
LLO polypeptide


54
LLO polypeptide


55
LLO polypeptide


56
ActA PEST sequence


57
ActA PEST sequence


58
ActA PEST sequence


59
ActA PEST sequence


60
Streptococcus pyogenes Streptolysin O PEST sequence


61
Streptococcus equisimilis Streptolysin O PEST-like



sequence


62
pADV142 nucleic acid sequence


63
KLK3 protein


64
KLK3 protein


65
KLK3 protein


66
KLK3 protein









A recombinant Lm of this invention secretes PSA fused to tLLO (Lm-LLO-PSA), which elicits a potent PSA-specific immune response associated with regression of tumors in a mouse model for prostate cancer. Details for the vectors used to create the LmddA-142 strain and the LmddA-143 strain are provided in Table 4 below. The pADV142 plasmid, which has no antibiotic resistance markers, was used to create the LmddA-142 strain. This new strain is 10 times more attenuated than Lm-LLO-PSA. In addition, LmddA-142 is slightly more immunogenic and significantly more efficacious in regressing PSA expressing tumors than the Lm-LLO-PSA.







TABLE 4





Plasmids and strains
















Plasmids 
Features





pADV119
Derived from pTV3 by deleting the prfA gene


pADV134
Derived from pADV119 by replacing the Lm dal gene 



by the Bacillus dal gene


pADV142
Derived from pADV134 by replacing HPV16 e7 with 



klk3 (Map at FIG. 9B; sequence FIG. 9C)





Strains
Genotype





10403S
Wild-type Listeria monocytogenes:: str


XFL-7
10403S prfA(−)


Lmdd
10403S dal(−) dat(−)


LmddA
10403S dal(−) dat(−) actA(−)


LmddA-142
10403S dal(−) dat(−) actA(−) pADV142


Lmdd-143 
10403S dal(−) dat(−) with klk3 fused to the hly gene in the



chromosome


LmddA-143
10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene 



in the chromosome (FIG. 8 shows the chromosomal 



structure and FIG. 9A shows a map of the pADV143 



plasmid)









The sequence of the plasmid pAdv142 (6523 bp) was as follows:







(SEQ ID NO: 62)


cggagtgtatactggcttactatgaggcactgatgagggtgtcagtgaa


 


gtgcttcatgtggcaggagaaaaaaggctgcaccggtgcgtcagcagaa


 


tatgtgatacaggatatattccgcacctcgctcactgactcgctacgct


 


cggtcgttcgactgcggcgagcggaaatggcttacgaacggggcggaga


 


tacctggaagatgccaggaagatacttaacagggaagtgagagggccgc


 


ggcaaagccgtattccataggctccgcccccctgacaagcatcacgaaa


 


tctgacgctcaaatcagtggtggcgaaacccgacaggactataaagata


 


ccaggcgtaccccctggcggctccctcgtgcgctctcctgacctgccat


 


cggataccggtgtcattccgctgttatggccgcgtttgtctcattccac


 


gcctgacactcagttccgggtaggcagttcgctccaagctggactgtat


 


gcacgaaccccccgttcagtccgaccgctgcgccttatccggtaactat


 


cgtcttgagtccaacccggaaagacatgcaaaagcaccactggcagcag


 


ccactggtaattgatttagaggagttagtcttgaagtcatgcgccggtt


 


aaggctaaactgaaaggacaagattggtgactgcgctcctccaagccag


 


ttacctcggttcaaagagttggtagctcagagaaccttcgaaaaaccgc


 


cctgcaaggcggttttttcgttttcagagcaagagattacgcgcagacc


 


aaaacgatctcaagaagatcatcttattaatcagataaaatatactagc


 


cctcattgattagtatattcctatcttaaagttactatatgtggaggca


 


ttaacatagttaatgacgtcaaaaggatagcaagactagaataaagcta


 


taaagcaagcatataatattgcgatcatattagaagcgaatttcgcca


 


atattataattatcaaaagagaggggtggcaaacggtataggcattatt


 


aggttaaaaaatgtagaaggagagtgaaacccatgaaaaaaataatgct


 


agtattattacacttatattagttagtctaccaattgcgcaacaaactg


 


aagcaaaggatgcatctgcattcaataaagaaaattcaatttcatccat


 


ggcaccaccagcatctccgcctgcaagtcctaagacgccaatcgaaaag


 


aaacacgcggatgaaatcgataagtatatacaaggattggattacaata


 


aaaacaatgtattagtataccacggagatgcagtgacaaatgtgccgcc


 


aagaaaaggttacaaagatggaaatgaatatattgagtggagaaaaaga


 


agaaatccatcaatcaaaataatgcagacattcaagagtgaatgcaatt


 


tcgagcctaacctatccaggtgctctcgtaaaagcgaattcggaattag


 


tagaaaatcaaccagatgactccctgtaaaacgtgattcattaacactc


 


agcattgatttgccaggtatgactaatcaagacaataaaatagttgtaa


 


aaaatgccactaaatcaaacgttaacaacgcagtaaatacattagtgga


 


aagatggaatgaaaaatatgctcaagcttatccaaatgtaagtgcaaaa


 


attgattatgatgacgaaatggcttacagtgaatcacaattaattgcga


 


aatttggtacagcatttaaagctgtaaataatagcttgaatgtaaactt


 


cggcgcaatcagtgaagggaaaatgcaagaagaagtcattagttttaaa


 


caaatttactataacgtgaatgttaatgaacctacaagaccttccagat


 


ttttcggcaaagctgttactaaagagcagagcaagcgcttggagtgaat


 


gcagaaaatcctcctgcatatatctcaagtgtggcgtatggccgtcaag


 


tttatttgaaattatcaactaattcccatagtactaaagtaaaagctgc


 


ttttgatgctgccgtaagcggaaaatctgtctcaggtgatgtagaacta


 


acaaatatcatcaaaaattcaccacaaagccgtaatttacggaggaccg


 


caaaagatgaagttcaaatcatcgacggcaacctcggagacttacgcga


 


tattttgaaaaaaggcgctacttttaatcgagaaacaccaggagttccc


 


attgcttatacaacaaacttcctaaaagacaatgaattagctgttatta


 


aaaacaactcagaatatattgaaacaacttcaaaagcttatacagatgg


 


aaaaattaacatcgatcactctggaggatacgttgctcaattcaacatt


 


tcagggatgaagtaaattatgatctcgagattgtgggaggctgggagtg


 


cgagaagcattcccaaccctggcaggtgcttgtggcctctcgtggcagg


 


gcagtctgcggcggtgttctggtgcacccccagtgggtcctcacagctg


 


cccactgcatcaggaacaaaagcgtgatcttgctgggtcggcacagcct


 


gatcatcctgaagacacaggccaggtatttcaggtcagccacagcaccc


 


acacccgctctacgatatgagcctcctgaagaatcgattcctcaggcca


 


ggtgatgactccagccacgacctcatgctgctccgcctgtcagagcctg


 


ccgagctcacggatgctgtgaaggtcatggacctgcccacccaggagcc


 


agcactggggaccacctgctacgcctcaggctggggcagcattgaacca


 


gaggagttcttgaccccaaagaaacttcagtgtgtggacctccatgtta


 


tttccaatgacgtgtgtgcgcaagttcaccctcagaaggtgaccaagtt


 


catgctgtgtgctggacgctggacagggggcaaaagcacctgctcgggt


 


gattctgggggcccacttgtctgttatggtgtgcttcaaggtatcacgt


 


catggggcagtgaaccatgtgccctgcccgaaaggccttccctgtacac


 


caaggtggtgcattaccggaagtggatcaaggacaccatcgtggccaac


 


cccTAAcccgggccactaactcaacgctagtagtggatttaatcccaaa


 


tgagccaacagaaccagaaccagaaacagaacaagtaacattggagtta


 


gaaatggaagaagaaaaaagcaatgatttcgtgtgaataatgcacgaaa


 


tcattgcttattatttaaaaagcgatatactagatataacgaaacaacg


 


aactgaataaagaatacaaaaaaagagccacgaccagttaaagcctgag


 


aaactttaactgcgagccttaattgattaccaccaatcaattaaagaag


 


tcgagacccaaaataggtaaagtatttaattactttattaatcagatac


 


ttaaatatctgtaaacccattatatcgggatttgaggggatttcaagtc


 


ataagaagataccaggcaatcaattaagaaaaacttagttgattgccat


 


tagagtgattcaactagatcgtagcttctaactaattaattacgtaaga


 


aaggagaacagctgaatgaatatcccattgagtagaaactgtgcttcat


 


gacggcagttaaagtacaaatttaaaaatagtaaaattcgctcaatcac


 


taccaagccaggtaaaagtaaaggggctatattgcgtatcgctcaaaaa


 


aaagcatgattggcggacgtggcgagactgacttccgaagaagcgattc


 


acgaaaatcaagatacatttacgcattggacaccaaacgatatcgttat


 


ggtacgtatgcagacgaaaaccgttcatacactaaaggacattctgaaa


 


acaatttaagacaaatcaataccactttattgattagatattcacacgg


 


aaaaagaaactatttcagcaagcgatattttaacaacagctattgattt


 


aggttttatgcctacgttaattatcaaatctgataaaggttatcaagca


 


tattttgttttagaaacgccagtctatgtgacttcaaaatcagaattta


 


aatctgtcaaagcagccaaaataatctcgcaaaatatccgagaatatta


 


ggaaagtattgccagttgatctaacgtgcaatcattagggattgctcgt


 


ataccaagaacggacaatgtagaattattgatcccaattaccgttattc


 


tttcaaagaatggcaagattggtctttcaaacaaacagataataagggc


 


tttactcgttcaagtctaacggttttaagcggtacagaaggcaaaaaac


 


aagtagatgaaccctggataatctcttattgcacgaaacgaaattacag


 


gagaaaagggatagtagggcgcaatagcgttatgataccctctcatagc


 


ctactttagttcaggctattcaatcgaaacgtgcgaatataatatgatg


 


agataataatcgattagatcaacccttagaagaaaaagaagtaatcaaa


 


attgttagaagtgcctattcagaaaactatcaaggggctaatagggaat


 


acattaccattattgcaaagcttgggtatcaagtgatttaaccagtaaa


 


gatttatttgtccgtcaagggtggtttaaattcaagaaaaaaagaagcg


 


aacgtcaacgtgttcatttgtcagaatggaaagaagatttaatggctta


 


tattagcgaaaaaagcgatgtatacaagccttatttagcgacgaccaaa


 


aaagagattagagaagtgctaggcattcctgaacggacattagataaat


 


tgctgaaggtactgaaggcgaatcaggaaattactttaagattaaacca


 


ggaagaaatggtggcattcaacttgctagtgttaaatcattgagctatc


 


gatcattaaattaaaaaaagaagaacgagaaagctatataaaggcgctg


 


acagcttcgataatttagaacgtacatttattcaagaaactctaaacaa


 


attggcagaacgccccaaaacggacccacaactcgatttgatagctacg


 


atacaggctgaaaataaaacccgcactatgccattacatttatatctat


 


gatacgtgatgatactagctggctagcttaattgcttatatttacctgc


 


aataaaggatacttacttccattatactcccattaccaaaaacatacgg


 


ggaacacgggaacttattgtacaggccacctcatagttaatggatcgag


 


ccacctgcaatctcatccatggaaatatattcatccccctgccggccta


 


ttaatgtgacttagtgcccggcggatattcctgatccagctccaccata


 


aattggtccatgcaaattcggccggcaattacaggcgattcccttcaca


 


aggatgtcggtccattcaattacggagccagccgtccgcatagcctaca


 


ggcaccgtcccgatccatgtgtattaccgctgtgtactcggctccgtag


 


ctgacgctctcgccattctgatcagatgacatgtgacagtgtcgaatgc


 


agggtaaatgccggacgcagctgaaacggtatctcgtccgacatgtcag


 


cagacgggcgaaggccatacatgccgatgccgaatctgactgcattaaa


 


aaagccattacagccggagtccagcggcgctgacgcgcagtggaccatt


 


agattattaacggcagcggagcaatcagctattaaagcgctcaaactgc


 


attaagaaatagcctctactattcatccgctgtcgcaaaatgggtaaat


 


acccattgcactttaaacgagggagcggtcaagaattgccatcacgact


 


gaacttcacctctgatttacaccaagtctgacatccccgtatcgaccac


 


agatgaaaatgaagagaaccattacgtgtggcgggctgcctcctgaagc


 


cattcaacagaataacctgttaaggtcacgtcatactcagcagcgattg


 


ccacatactccgggggaaccgcgccaagcaccaatataggcgcatcaat


 


ccattagcgcagtgaaatcgcttcatccaaaatggccacggccaagcat


 


gaagcacctgcgtcaagagcagccatgctgatctgcatcaccatgcccg


 


taggcgatgattcacaactgccatcaagtggacatgacaccgatatgat


 


tacatattgctgacattaccatatcgcggacaagtcaataccgcccacg


 


tatctctgtaaaaaggattgtgctcatggaaaactcctctcattacaga


 


aaatcccagtacgtaattaagtatttgagaattaatatatattgattaa


 


tactaagatacccagattcacctaaaaaacaaatgatgagataatagct


 


ccaaaggctaaagaggactataccaactatttgttaattaa.






(FIG. 9C) This plasmid was sequenced at Genewiz facility from the E. coli strain on Feb.20, 2008. A map of the plasmid is presented as FIG. 9B.

REFERENCES


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All references cited herein are incorporated by reference to the same extent as if each individual publication, database entry (e.g. Genbank sequences or GeneID entries), patent application, or patent, was specifically and individually indicated to be incorporated by reference. This statement of incorporation by reference is intended by Applicants, pursuant to 37 C.F.R. §1.57(b)(1), to relate to each and every individual publication, database entry (e.g. Genbank sequences or GeneID entries), patent application, or patent, each of which is clearly identified in compliance with 37 C.F.R. §1.57(b)(2), even if such citation is not immediately adjacent to a dedicated statement of incorporation by reference. The inclusion of dedicated statements of incorporation by reference, if any, within the specification does not in any way weaken this general statement of incorporation by reference. Citation of the references herein is not intended as an admission that the reference is pertinent prior art, nor does it constitute any admission as to the contents or date of these publications or documents.
In the following example, numerous specific details are set forth in order to provide a thorough understanding of the invention. However, it will be understood by those skilled in the art that the present invention may be practiced without these specific details. In other instances, well-known methods, procedures, and components have not been described in detail so as not to obscure the present invention.
EXAMPLE
A Phase 1-2 Dose-Escalation and Safety Study of ADXS31-142 Alone and in Combination with Pembrolizumab (MK-3475) in Patients with Previously Treated Metastatic Castration-Resistant Prostate Cancer (mCRPC)
This is a phase 1-2, open-label, multicenter, nonrandomized, 2-part study in patients with metastatic Castration-Resistant Prostate Cancer (mCRPC). Part A of the study will be an open-label, Phase 1, multicenter, non-randomized, dose-determining trial of ADX31-142 monotherapy in subjects with metastatic castration-resistant prostate cancer (mCRPC). Part B of the study will be an open-label, Phase 1-2, multicenter, non-randomized dose-determining trial of ADXS31-142 in combination with pembrolizumab (MK-3475) in subjects with mCRPC. FIG. 10 presents a diagram of the monotherapy and combination portions of this study.
Objectives:
Part A: to evaluate safety and tolerability of ADXS31-142 monotherapy and select the recommended phase 2 dose (RP2D) in subjects with mCRPC
Part B: to evaluate safety and tolerability of ADXS31-142 in combination with pembrolizumab (MK-3475) and to establish the RP2D for this combination in subjects with mCRPC
In addition, objectives of the Study include evaluating anti-tumor activity and progression free survival (PFS) signal of ADXS31-142 monotherapy and ADXS31-142+ pembrolizumab (MK-3475) combination therapy using RECIST 1.1, immune-related Response Evaluation Criteria in Solid Tumors (irRECIST) and Prostate Cancer Working Group 2 (PCWG2) criteria to inform design of a subsequent randomized Phase 2 trial. The effects on serum prostate specific antigen (PSA) and periphaeral immunologic measures of ADXS31-142 montherapy and ADXS31-142+pembrolizumab (MK-3475) combination therapy will be determined.
Product Description
Each of these products is described in detail above.
ADXS31-142 will be provided as a concentrated suspension for injection, at a concentration of 2.7×109 cfu/mL; 1.2 mL/vial.
Pembrolizumab (MK-3475) may be provided in two different forms: (1) as a lyophilized powder for injection (50 mg); and (2) as a solution for infusion at a concentration of 25 mg/mL.
Part A—ADXS31-124 Monotherapy
Materials and Methods
Subjects:
The study will be conducted in male subjects (≧18 years) with histologically confirmed mCRPC who have progressed or become resistant to no more than 3 prior systemic treatment regimens with chemotherapy, hormonal, or immunotherapy in the metastatic setting; and wuth an Eastern Cooperative Oncology Group (ECOG) performance status of 0-1 are eligble. However, subjects can not have had more than 1 prior chemotherapeutic regimen in the metastatic setting. Subjects with evidence of progressive bone or other metastases are acceptable. Subjects may remain on castration therapy (luteinizing-hormone-releasing 15 hormone [LHRH] agonist or antagonist) during the trial.
Dose:
The dose determining phase is intended to select a recommended Phase 2 dose (RP2D) for Part B. The starting dose level (DL) of ADSX31-142 monotherapy will be 1×109 colony forming units (cfu) (DL 1). The dose will be escalated (5×109 cfu, 1×1010 cfu), remain the same or be de-escalated according to pre-defined dose-limiting toxicity (DLT) criteria associated with a DLT rate ≦0.25 by applying the modified toxicity probability interval (mTPI) design. Table 5 summarizes ADXS31-142 Monotherapy Doses to be used.










TABLE 5





Dose Level
Dose
Route of Administration
Regimen


















1
1 × 109 cfu
IV infusion
Day 1 of Weeks 1, 4 and 7 of 12-week cycle


2
5 × 109 cfu
IV infusion
Day 1 of Weeks 1, 4 and 7 of 12-week cycle


3
 1 × 1010 cfu
IV infusion
Day 1 of Weeks 1, 4 and 7 of 12-week cycle


−1
.5 × 109 cfu 
IV infusion
Day 1 of Weeks 1, 4 and 7 of 12-week cycle









Up to 21 subjects will be entered (with a minimum of 6 subjects treated at the recommended dose before proceeding to the next phase). A minimum of 3 subjects will be evaluated in each cohort before dose-escalation decisions are made.
FIG. 11 below presents Dose Decisions for ADSX31-142- Monotherapy.
FIG. 11 is based on a sample size of 21 subjects. Two parameters epsilon1 and epsilon2 are set at default values of 0.05. x-axis is number of subjects treated at current dose; yaxis is number of toxicities.
The Targeted dose limiting toxicity (DLT) Rate will increase to 30% for the combination regimen (Part B) in the event that a 25% DLT rate is observed at the recommended ADXS31-142 monotherapy dose.
The same DLT criteria will be utilized for study Part A and Part B. All 10 toxicities will be graded using CTCAE Version 4.0. The DLT window of observation will be 4 weeks (after 2 doses of each drug). The occurrence of any of the following toxicities will be considered a DLT, if judged by the investigator to be possibly, probably or definitely related to study treatment administration.
Endpoints
Efficacy Endpoints—The efficacy endpoints to be used in this study (PSA/PAP, other serum markers for prostate cancer, scans, and measureable and evaluable disease assessments) are those typically used to assess anti-tumor activity of mCRPC.
Safety Endpoint—The primary safety objective of this trial is to characterize the safety and tolerability of ADXS31-142 alone. The primary safety analysis will be based on subjects who experienced toxicities as defined by CTCAE criteria. Safety will be assessed by quantifying the toxicities and grades experienced by subjects who have received ADXS31-142 alone, including serious adverse events (SAEs) and events of clinical interest (ECIs).
Biomarkers
T-cells will be assessed for their specific response to PSA and other prostate cancer antigens which may include PSMA, PAP, and prostate stem cell antigen (PSCA). T-cell responses will be determined by enzyme-linked immunosorbent assay (ELISA) and/or ELISpot. PBMC immunologic gene expression analysis may also be conducted.
Serum cytokine and chemokine changes will be determined to assess immune stimulation as a result of treatment. Serum cytokine levels will include IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-15, IL-18, transforming growth factor beta (TGFβ), and tumor necrosis factor alpha (TNFα). Serum chemokines will include CXCL 9, 10, and 11.
Route of Administration
ADSX31-142 monotherapy will be administered by IV infusion by medically trained personnel.
Regimen
ADSX31-142 monotherapy will be administered on Day 1 of weeks 1, 4, and 7, of a once every 3 weeks in a 12-week treatment cycle. Trial treatment may be administered up to 3 days before or after the scheduled Day 1 of each cycle due to administrative reasons.
All trial treatments will be administered as a 30 minute IV infusion (treatment cycle intervals may be increased due to toxicity). In Part A, NSAIDs (naproxen or ibuprofen) and antiemetic medication should be administered within 30 minutes prior to the ADXS31-142 infusion.
Tumor Imaging and Assessment of Disease
Computed tomography (CT), magnetic resonance imaging (MRI) or bone scan will be considered the best currently available and reproducible methods to measure target lesions selected for response assessment. Conventional CT and MRI of the abdomen/pelvis should be performed with contiguous cuts of 10 mm or less. Spiral CT scan should be performed using a 5 mm contiguous reconstruction algorithm (as a general rule, lesion diameter should be no less than double the slice thickness). Lesions on chest x-rays will be acceptable as measurable lesions when they are clearly defined and surrounded by aerated lung; however, CT is preferable. Ultrasound will not be an acceptable method to measure disease.
Measurable and Non-Measurable Lesions and Disease
Measurable lesions will be those that can be accurately measured in at least one dimension with the longest diameter ≧2.0 cm (for spiral CT scan or MRI scan, ≧1.0 cm). Measurable disease will be present if the subject has 1 or more measurable lesions.
Non-measurable lesions/disease will be all other lesions (or sites of disease), including small lesions (those with all measurements <2.0 cm with spiral CT or <1.0 cm with MRI), or any of the following: bone lesions, leptomeningeal disease, ascites, pleural or pericardial effusion, lymphangitis, cutis/pulmonis, abdominal masses that are not confirmed and followed by imaging techniques, cystic lesions, and lesions occurring within a previously irradiated area unless they are documented as new lesions since the completion of radiation therapy.
Target/Non-Target Lesions
All measurable lesions, up to a maximum of 2 per organ and 5 in total, should be identified as target lesions to be measured and recorded at baseline. The target lesions should be representative of all involved organs. Target lesions will be selected based on their size (the lesion with the longest diameter) and suitability for accurate repeated measurements. At baseline, a sum of the longest diameters for all target lesions will be calculated and recorded as the baseline tumor burden. The baseline sum will be used as the reference point to determine the objective tumor response of the target lesions.
Measurable lesions other than the target lesions and all sites of non-measurable disease will be identified as non-target lesions and will be recorded at baseline. Non-target lesions will be evaluated at the same timepoints as target lesions.
Response in Measureable Lesions (RECIST 1.1)
At baseline, the sum of the longest diameters (SumD) of all target lesions (up to 2 lesions per organ, up to total 5 lesions) is measured. At each subsequent tumor assessment (TA), the SumD of the target lesions and of new, measurable lesions are added together to provide the total measurable tumor burden (TMTB):

TMTB=SumD Target Lesions+SumD New, Measurable Lesions

Percentage changes in TMTB per assessment time point describe the size and growth kinetics of both old and new measurable lesions as they appear. At each TA, the response in target and new measurable lesions is defined based on the change in TMTB (after ruling out irPD) as follows:
Complete Response (CR): disappearance of all target lesions. Any pathological lymph nodes (whether target or non-target) must have reduction in short axis to ≦10 mm.
Partial Response (PR): At least a 30% decrease in sum of diameter of target lesions, taking as reference the baseline sum diameter.
Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient increase
Progressive Disease (PD): At least a 20% increase in the sum of diameters of target lesions, taking as reference the smallest sum on study (this includes the baseline sum if that is the smallest on study). In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm (Note: the appearance of one or more new lesions is also considered progression).
Response in non-measurable lesions will also be assessed.
Part B—ADSX31-142+Pembrolizumab (MK-3475) Combination Therapy
Materials and Methods
Subjects
Subjects have been described above in Part A of the study. The subjects for Part B will be included in the study based on the same population criteria. The plan is to treat a total of 30 subject at RP2D.
Dose
Part B will consist of a dose-determination phase followed by an expansion cohort phase. The dose-determining phase is intended to select a RP2D for the combination. Dose escalation/de-escalation will be explored by applying the mTPI design.
During the dose-determining stage, up to 21 subjects will be entered at escalating doses of ADXS31-142 (see Table 7) in combination with pembrolizumab (MK-3475) at 200 mg (with a minimum of 6 subjects treated at the RP2D before proceeding to expansion). Dose-determination will continue until identification of a preliminary maximum tolerated dose/maximum allowable dose (MTD/MAD), up to a maximum dose of 1×1010 cfu of ADXS31-142. The MTD/MAD will be the RP2D for the dose expansion portion. If a MTD is not identified, then the highest planned dose level of ADXS31-142 in combination with pembrolizumab (MK-3475) will be considered the RP2D. The pembrolizumab (MK-3475) will remain constant at 200 mg.







TABLE 7







ADXS31-142 and Pembrolizumab (MK-3475) Combination Therapy


Doses to be used in Trial Part B












Dose

Route of



Drug
Level
Dose
Administration
Regimen














ADXS31-142
1
One level below RP2D in Part
IV infusion
Day 1 of Weeks 1, 4 and 7 of




A

12-week cycle



2
RP2D in Part A
IV infusion
Day 1 of Weeks 1, 4 and 7 of






12-week cycle



−1
Two dose levels below RP2D
IV infusion
Day 1 of Weeks 1, 4 and 7 of




in Part A

12-week cycle


Pembrolizumab

200 mg
IV infusion
Day 1 Q3W of 12-week cycle


(MK-3475)









As for Part A of this study, the expected doses for ADXS31-142 will be 0.5×109, 1×109, 5×109, and 1×1010.
The expansion cohort will be open for enrollment once the RP2D of ADXS31-142 in combination with pembrolizumab (MK-3475) is selected in the Part B dose determination phase. Further assessment of the RP2D will be explored in up to 30 patients 15 with mCRPC to evaluate the safety and clinical activity of ADXS31-142 in combination with pembrolizumab (MK-3475).
FIG. 12 below presents Dose Decisions for Combination Therapy
Adverse events will be monitored from the time informed consent is obtained and graded in severity according to the guidelines outlined in the National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE) Version 4.0.
Treatment with ADXS31-142 in combination with pembrolizumab (MK3475) will continue until documented disease progression, unacceptable adverse event(s), intercurrent illness that prevents further administration of treatment, investigator's decision to withdraw the subject, subject withdraws consent, subject experiences a complete response (irCR) and receives one additional cycle of treatment, noncompliance with trial treatment or procedure requirements, completion of 24 months of treatment with ADXS31142 and pembrolizumab (MK-3475), or administrative reasons. Subjects who attain an investigator confirmed irCR, after receiving at least 2 cycles of therapy, may consider stopping pembrolizumab (MK-3475) and continue treatment with ADX S31-142 only. After the end of treatment, each subject will be followed for 30 days after the last study drug administration for adverse event and 90 days for serious adverse events or events of clinical interest monitoring. Subjects who discontinue treatment for reasons other than disease progression will have post-treatment follow-up for disease status until disease progression, initiating a non-study cancer treatment, withdrawing consent, becoming lost to follow-up, or until the sponsor ends the study. The primary objectives of the trial are to establish a MTD or MAD and to determine safety and tolerability of ADXS31-142 in combination with pembrolizumab (MK-3475) in subjects with mCRPC.
Efficacy and Safety Endpoints will be as described for Part A of this Study.
Biomarker Research will be as described for Part A of this Study.
Route of Administration
ADSX31-142 and Pembrolizumab (MK-3475 will each be administered by IV infusion by medically trained personnel.
Regimen
Trial treatment should be administered on Day 1 of Week 1, 4 and 7 (for ADXS31-142) or Q3W (for pembrolizumab [MK-3475]) in each 12-week cycle after all procedures/assessments have been completed. Trial treatment may be administered up to 3 days before or after the scheduled Day 1 of each cycle due to administrative reasons.
All trial treatments will be administered as a 30 minute IV infusion (treatment cycle intervals may be increased due to toxicity. there should be approximately 60 minutes between the end of the first infusion and the start of the second infusion. Pembrolizumab (MK-3475) infusion will be administered first.
Assessment in target and non-target lesions is as described above for Part A.

## Claims

1. A method for treating prostate cancer in a patient comprising administering to the patient a combination therapy which comprises an antagonist of a Programmed Death 1 protein (PD-1) and a bioengineered live-attenuated Listeria monocytogenes strain transformed with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO), and wherein the live-attenuated Listeria monocytogenes strain stimulates Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells.

2. A method for treating prostate cancer in a patient comprising administering to the patient a combination therapy which comprises an anti-PD-1 monoclonal antibody, comprising a heavy chain and a light chain, wherein the heavy and light chains comprise SEQ ID NO:21 and SEQ ID NO:22, respectively, and a bioengineered live-attenuated Listeria monocytogenes strain transformed with an expression vector to express a PSA antigen fused to a truncated Listeriolysin O (tLLO), wherein the live-attenuated Listeria monocytogenes strain stimulates Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells.

3. The method of claim 1, wherein the PD-1 antagonist and the live-attenuated Listeria monocytogenes strain are administered simultaneously.

4. The method of claim 1 or 2, wherein said tLLO-PSA fusion polypeptide consists of the sequence of SEQ ID NO: 54 or a sequence at least 99% homologous thereto, wherein said tLLO enhances the immunogenicity of the fusion polypeptide.

5. The method of claim 1 or 2, wherein the live-attenuated Listeria monocytogenes strain comprises an LmddA-142 (10403S dal(−) dat(−) actA(−) pADV142) strain.

6. A method for treating prostate cancer in a patient comprising administering to the patient a combination therapy which comprises, an anti-PD-1 monoclonal antibody comprising a heavy chain and a light chain, wherein the heavy and light chains comprise SEQ ID NO:21 and SEQ ID NO:22, respectively, and a live-attenuated Listeria monocytogenes strain comprising a LmddA-143 (10403S dal(−) dat(−) actA(−) with klk3 fused to the hly gene in the chromosome) strain, wherein the live-attenuated Listeria monocytogenes strain stimulates Antigen Presenting Cells (APCs) capable of driving a cellular immune response to PSA expressing cells.

7. The method of claim 2 or 6, wherein the anti-PD-1 monoclonal antibody and the live-attenuated Listeria monocytogenes strain are administered simultaneously.

8. The method of claim 1, 2 or 6, wherein the prostate cancer is metastatic Castration-Resistant Prostate Cancer (mCRPC).

9. The method of claim 1, 2 or 6, wherein said live attenuated Listeria monocytogenes strain is administered with an adjuvant, wherein said adjuvant comprises Montanide ISA 51, GM-CSF, KLH, a cytokine, a growth factor, a cell population, QS21, Freund's incomplete adjuvant, aluminum phosphate, aluminum hydroxide, BCG, alum, an interleukin, an unmethylated CpG oligonucleotide, quill glycosides, monophosphoryl lipid A, a liposomes, a bacterial mitogen, a bacterial toxin, or a chemokine, or any combination thereof.

10. The method of claim 2 or 6, wherein the antibody is formulated as a liquid medicament which comprises 7% (w/v) sucrose, 0.02% (w/v) polysorbate 80 in 10 mM histidine buffer pH 5.5.

11. The method of claims 1, 2 or 6, wherein the prostate cancer tests positive for PD-L1 expression.

12. The method of claims 1, wherein the PD-1 antagonist is pembrolizumab.

13. The method of claim 2 or 6, wherein the anti-PD 1 monoclonal antibody is pembrolizumab.

14. The method of claim 1, wherein the PD-1 antagonist and the live-attenuated Listeria monocytogenes strain are administered sequentially.

15. The method of claim 2 or 6, wherein the anti-PD-1 monoclonal antibody and the live-attenuated Listeria monocytogenes strain are administered sequentially.