# Patent

## Title
Listeria-based and LLO-based vaccines

## Abstract

This invention provides methods of treating and vaccinating against an antigen-expressing tumor and inducing an immune response against a sub-dominant epitope of antigen, comprising a fusion of an LLO fragment to the antigen or a recombinant Listeria strain expressing the antigen. The present invention also provides recombinant peptides comprising a listeriolysin (LLO) protein fragment fused to a Her-2 protein or fragment thereof, recombinant Listeria strains expressing a Her-2 protein, vaccines and immunogenic compositions comprising same, and methods of inducing an anti-Her-2 immune response and treating and vaccinating against a Her-2-expressing tumor, comprising same.

## Background
CROSS REFERENCE TO RELATED APPLICATION
This application is a continuation-in-part of U.S. application Ser. No. 10/949,667, filed Sep. 24, 2004. This application is hereby incorporated in its entirety by reference herein.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
The invention described herein was supported in part by grants from The National Institutes of Health (Grant No. CA72108) and the Department of Defense (W81XWH-04-1-0338). The U.S. Government may have certain rights in this invention.


FIELD OF INVENTION
This invention provides methods of treating and vaccinating against an antigen-expressing tumor and inducing an immune response against a sub-dominant epitope of antigen, comprising a fusion of an LLO fragment to the antigen or a recombinant Listeria strain expressing the antigen. The present invention also provides recombinant peptides comprising a listeriolysin (LLO) protein fragment fused to a Her-2 protein or fragment thereof, recombinant Listeria strains expressing a Her-2 protein, vaccines and immunogenic compositions comprising same, and methods of inducing an anti-Her-2 immune response and treating and vaccinating against a Her-2-expressing tumor, comprising same.
BACKGROUND OF THE INVENTION
Her-2/neu (referred to henceforth as “Her-2”) is a 185 kDa glycoprotein that is a member of the epidermal growth factor receptor (EGFR) family of tyrosine kinases, and consists of an extracellular domain, a transmembrane domain, and an intracellular domain which is known to be involved in cellular signaling (Bargmann C I et al, Nature 319: 226, 1986; King C R et al, Science 229: 974, 1985). It is overexpressed in 25 to 40% of all breast cancers and is also overexpressed in many cancers of the ovaries, lung, pancreas, and gastrointestinal tract. The overexpression of Her-2 is associated with uncontrolled cell growth and signaling, both of which contribute to the development of tumors. Patients with cancers that overexpress Her-2 exhibit tolerance even with detectable humoral, CD8+ T cell, and CD4+ T cell responses directed against Her-2.
Listeria monocytogenes is an intracellular pathogen that primarily infects antigen presenting cells and has adapted for life in the cytoplasm of these cells. Host cells, such as macrophages, actively phagocytose L. monocytogenes and the majority of the bacteria are degraded in the phagolysosome. Some of the bacteria escape into the host cytosol by perforating the phagosomal membrane through the action of a hemolysin, listeriolysin O (LLO). Once in the cytosol, L. monocytogenes can polymerize the host actin and pass directly from cell to cell further evading the host immune system and resulting in a negligible antibody response to L. monocytogenes. 
SUMMARY OF THE INVENTION
This invention provides methods of treating and vaccinating against an antigen-expressing tumor and inducing an immune response against a sub-dominant epitope of antigen, comprising a fusion of an LLO fragment to the antigen or a recombinant Listeria strain expressing the antigen. The present invention also provides recombinant peptides comprising a listeriolysin (LLO) protein fragment fused to a Her-2 protein or fragment thereof, recombinant Listeria strains expressing a Her-2 protein, vaccines and immunogenic compositions comprising same, and methods of inducing an anti-Her-2 immune response and treating and vaccinating against a Her-2-expressing tumor, comprising same.
In one embodiment, the present invention provides a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a fragment of a Her-2 protein, the fragment of a Her-2 protein having a length of about 150 to about 420 amino acids.
In another embodiment, the present invention provides a recombinant polypeptide comprising an N-terminal fragment of an LLO protein fused to a Her-2 protein or fused to a fragment thereof.
In another embodiment, the present invention provides a method of inducing an anti-Her-2 immune response in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a Her-2 protein or fused to a fragment thereof, or administering a recombinant nucleotide encoding the recombinant polypeptide, thereby inducing an anti-Her-2 immune response in a subjects.
In another embodiment, the present invention provides a method of impeding a growth of a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the Her-2 protein or a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding, the growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of shrinking a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the Her-2 protein or a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of impeding a growth of a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen or a fragment thereof, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of shrinking a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen or a fragment thereof, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to an antigen-expressing tumor, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a fragment of the antigen or a recombinant nucleotide encoding the recombinant polypeptide, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking immune tolerance of a subject to an antigen-expressing tumor.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to an antigen-expressing tumor, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding a fragment of the antigen, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking immune tolerance of a subject to an antigen-expressing tumor.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Schematic representation of pGG55, used to construct the Lm-Δ-LLO-HER-2 vaccines.
FIG. 2. Recombinant Listeria monocytogenes is capable of secreting each of Her-2 fragments as a ΔLLO-fusion protein. (A) Map of rat Her-2 fragments. (B) Confirmation of secretion of the fusion peptides by Western blot. Marker (lane 1), Lm-ΔLLO-E7 (lane 2), Lm-ΔLLO-EC1 (lane 3), Lm-ΔLLO-EC2 (lane 4), Lm-ΔLLO-EC3 (lane 5), Lm-ΔLLO-IC1 (lane 6), and Lm-ΔLLO-IC2 (lane 7).
FIG. 3. Lm-ΔLLO-Her-2 vaccines each induce a halt in tumor growth of established NT-2 tumors. Each data point represents the average of shortest and longest surface tumor diameter of one mouse at a given time point. Mice were sacrificed when the average tumor diameter reached 2.0 cm; tumor measurements are only shown for the surviving mice at a given time point. Representative figures of two experiments are shown. (A) Lm-ΔLLO-EC1, Lm-ΔLLO-EC2, and Lm-ΔLLO-EC3; (B) Lm-ΔLLO-IC1, and Lm-ΔLLO-IC2.
FIG. 4. CD8+ T cells participate in Lm-LLO-Her-2 induced tumor stasis. Tumor measurements are shown only for the surviving mice at a given time point. (A) Lm-ΔLLO-EC1, Lm-ΔLLO-EC2, and Lm-ΔLLO-EC3 both depleted and undepleted for CD8+ T cells. (B) Lm-ΔLLO-IC1 and Lm-ΔLLO-IC2 both depleted and undepleted for CD8+ T cells.
FIG. 5. Lm-ΔLLO-EC2 induces a 3-fold increase in tetramer+, CD8+ T cells. FVB/N mice were immunized with Lm-ΔLLO-EC2 or PBS. Subsequently, splenocytes were stained with an H-2q Her-2 tetramer, anti-CD8, and anti-CD62L.
FIG. 6. Each of the Lm-ΔLLO-Her-2 vaccine constructs induces similar levels of anti-Her-2 CTL activity. A wildtype 3T3 (negative control). B. 3T3-neu (full length Her-2). Results are shown as the mean of triplicate cultures, and are representative of 5 experiments.
FIG. 7. Delivery by LM and fusion to ΔLLO increases the anti-tumor immune response of Her-2 vaccines. Average tumor diameter for each mouse is depicted. Tumor measurements are shown only for the surviving mice at a given time point. (A) Lm-ΔLLO-EC1 vs. pcDNA ΔLLO-EC1+GM-CSF, (B) pcDNA EC1+GM-CSF vs. pcDNA ΔLLO-EC1+GM-CSF, (C) pcDNA neu+GM-CSF vs. pcDNA ΔLLO-neu+GM-CSF, (D) pcDNA ΔLLO-neu+GM-CSF vs. pcDNA ΔLLO-EC1+GM-CSF and (E) pcDNA neu+GM-CSF vs. pcDNA EC1+GM-CSF.
FIG. 8. Lm-ΔLLO-Her-2 vaccine slow the growth of established rat Her-2 expressing tumors in rat Her-2/neu transgenic mice, in which rat Her-2 is expressed as a self-antigen.
FIG. 9. LLO-Her-2 vaccines control spontaneous tumor growth in Her-2/neu transgenic mice.
FIG. 10. Schematic representation of human Her-2 fragments used to create LLO-human Her-2 vaccines.



DETAILED DESCRIPTION OF THE INVENTION
This invention provides methods of treating and vaccinating against an antigen-expressing tumor and inducing an immune response against a sub-dominant epitope of antigen, comprising a fusion of an LLO fragment to the antigen or a recombinant Listeria strain expressing the antigen. The present invention also provides recombinant peptides comprising a listeriolysin (LLO) protein fragment fused to a Her-2 protein or fragment thereof, recombinant Listeria strains expressing a Her-2 protein, vaccines and immunogenic compositions comprising same, and methods of inducing an anti-Her-2 immune response and treating and vaccinating against a Her-2-expressing tumor, comprising same.
As provided herein, the results of the present invention demonstrate that administration of compositions of the present invention has utility for inducing formation of antigen-specific T cells (e.g. cytotoxic T cells) that recognize and kill tumor cells, thereby arresting the growth of and shrinking tumor cells and treating the resulting cancer (Examples herein).
In one embodiment, the present invention provides a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a fragment of a Her-2 protein, the fragment of a Her-2 protein having a length of about 150 to about 420 amino acids.
In another embodiment, the present invention provides a recombinant polypeptide comprising an N-terminal fragment of an LLO protein fused to a Her-2 protein or fused to a fragment thereof.
In another embodiment, the present invention provides a recombinant polypeptide comprising a fragment of a Her-2 protein. In one embodiment, the fragment consists of about AA 20-326 of the Her-2 protein. In another embodiment, the fragment consists of about AA 303-501 thereof. In another embodiment, the fragment consists of about AA 479-655 thereof. In another embodiment, the fragment consists of about AA 690-1081 thereof. In another embodiment, the fragment consists of about AA 1020-1255 thereof. In other embodiments, the fragment consists of any of the Her-2 fragments mentioned below. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the Her-2 protein of methods and compositions of the present invention is a human Her-2 protein. In another embodiment, the Her-2 protein is a mouse Her-2 protein. In another embodiment, the Her-2 protein is a rat Her-2 protein. In another embodiment, the Her-2 protein is a primate Her-2 protein. In another embodiment, the Her-2 protein is a Her-2 protein of any other animal species known in the art. In another embodiment, the Her-2 protein is a variant of a Her-2 protein. In another embodiment, the Her-2 protein is a homologue of a Her-2 protein. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the Her-2 protein is a rat Her-2 protein having the sequence:








(SEQ ID No: 40)









MIIMELAAWCRWGFLLALLPPGIAGTQVCTGTDMKLRLPASPETHLDMLR



 


HLYQGCQVVQGNLELTYVPANASLSFLQDIQEVQGYMLIAHNQVKRVPLQ


 


RLRIVRGTQLFEDKYALAVLDNRDPQDNVAASTPGRTPEGLRELQLRSLT


 


EILKGGVLIRGNPQLCYQDMVLWKDVFRKNNQLAPVDIDTNRSRACPPCA


 


PACKDNHCWGESPEDCQILTGTICTSGCARCKGRLPTDCCHEQCAAGCTG


 


PKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMHNPEGRYTFGASCV


 


TTCPYNYLSTEVGSCTLVCPPNNQEVTAEDGTQRCEKCSKPCARVCYGLG


 


MEHLRGARAITSDNVQEFDGCKKIFCSLAFLPESFDGDPSSGIAPLRPEQ


 


LQVFETLEEITGYLYISAWPDSLRDLSVFQNLRIIRGRILHDGAYSLTL


 


QGLGIHSLGLRSLRELGSGLALIHRNAHLCFVHTVPWDQLFRNPHQALLH


 


SGNRPEEDCGLEGLVCNSLCAHGHCWGPGPTQCVNCSHFLRGQECVEECR


 


VWKGLPREYVSDKRCLPCHPECQPQNSSETCFGSEADQCAACAHYKDSSS


 


CVARCPSGVKPDLSYMPIWKYPDEEGICQPCPINCTHSCVDLDERGCPAE


 


QRASPVTFIIATVEGVLLFLILVVVVGILIKRRRQKIRKYTMRRLLQETE


 


LVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGEN


 


VKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQ


 


LVTQLMPYGCLLDHVREHRGRLGSQDLLNWCVQIAKGMSYLEDVRLVHRD


 


LAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESIL


 


RRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPP


 


ICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLG


 


PSSPMDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFSPDPTPGTGSTAHR


 


RHRSSSTRSGGGELTLGLEPSEEGPPRSPLAPSEGAGSDVFDGDLAMGVT


 


KGLQSLSPHDLSPLQRYSEDPTLPLPPETDGYVAPLACSPQPEYVNQSEV


 


QPQPPLTPEGPLPPVRPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPE


 


YLVPREGTASPPHPSPAFSPAFDNLYYWDQNSSEQGPPPSNFEGTPTAEN


 


PEYLGLDVPV.






was used to create the fragments in Example 1. In another embodiment, the Her-2 protein is encoded for by the nucleic acid sequence set forth in SEQ ID No: 41.

In another embodiment, the Her-2 protein is a human Her-2 protein having the sequence:








(SEQ ID No: 43)









MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLY



 


QGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLR


 


IVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILK


 


GGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCK


 


GSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHS


 


DCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACP


 


YNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHL


 


REVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVF


 


ETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGI


 


SWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRP


 


EDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGL


 


PREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARC


 


PSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASP


 


LTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPL


 


TPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPV


 


AIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQL


 


MPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARN


 


VLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFT


 


HQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTID


 


VYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPL


 


DSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSS


 


STRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQS


 


LPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPP


 


SPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQ


 


GGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLG


 


LDVPV.






SEQ ID No: 43 is used to create the fragments in Example 10. In another embodiment, the Her-2 protein is encoded for by the nucleic acid sequence set forth in SEQ ID No: 44.

In other embodiments, the Her-2 protein has a sequence set forth in GenBank Accession No. NM—004448 or NM—001005862. These Her-2 proteins have transmembrane (TM) regions spanning AA 653-675 and 623-645, respectively. The human Her-2 protein set forth in SEQ ID No: 43 has a TM region spanning 653-676. Thus, in another embodiment, the generation of Her-2 fragments corresponding to those of the present invention from variations of SEQ ID No: 40 such as these requires adjustment of the residue numbers defining the fragments, as described below.
In other embodiments, a Her-2 protein is a protein referred to as “HER-2/neu,” “Erbb2,” “v-erb-b2,” “c-erb-b2,” “neu,” or “cNeu.” Each possibility represents a separate embodiment of the present invention.
In another embodiment, the fragment of a Her-2 protein of methods and compositions of the present invention consists of about amino acid (AA) 20-326 (EC1 of Example 1; SEQ ID No: 35). In another embodiment, the fragment consists of about AA 303-501 (EC2; SEQ ID No: 36) of the Her-2 protein. In another embodiment, the fragment consists of about AA 479-655 (EC3; SEQ ID No: 37) of the Her-2 protein. In another embodiment, the fragment of a Her-2 protein consists of about AA 690-1081 (IC1; SEQ ID No: 38) of the Her-2 protein. In another embodiment, the fragment consists of about AA 1020-255 (IC2; SEQ ID No: 39) of the Her-2-protein. Each possibility represents a separate embodiment of the present invention.
The AA numbers and ranges listed above are based on the rat Her-2 sequence, for which the TM domain spans residues 656-689. In another embodiment, corresponding regions of other Her-2 proteins (e.g. Her-2 proteins from other species) are determined by aligning the TM domains of the other Her-2 proteins and adjusting the AA ranges. For example, for human Her-2 transcript variant 2, GenBank Accession No. NM—001005862, the TM region spans AA 623-645. Thus, in this embodiment, the region of this protein corresponding to EC3 is about AA 446-622, determined by subtracting 33 from the AA numbers to account for the 33 AA difference in the extracellular border of the TM domain. Similarly, the region of this protein corresponding to IC 1 is 646-1037, determined by subtracting 44 from the numbers to account for the 44 AA difference in the intracellular border of the TM domain. In another embodiment, corresponding regions of other Her-2 proteins are determined by alignment with the ends of the protein. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the fragment is a fragment of the extracellular domain of the Her-2 protein. In another embodiment, the fragment consists of about one-third to one-half of the extracellular domain of the Her-2 protein. In another embodiment, the fragment consists of about one-tenth to one-fifth thereof. In another embodiment, the fragment consists of about one-fifth to one-fourth thereof. In another embodiment, the fragment consists of about one-fourth to one-third thereof. In another embodiment, the fragment consists of about one-third to one-half thereof. In another embodiment, the fragment consists of about one-half to three quarters thereof. In another embodiment, the fragment consists of about three quarters to the entire extracellular domain. In another embodiment, the fragment consists of about 5-10% thereof. In another embodiment, the fragment consists of about 10-15% thereof. In another embodiment, the fragment consists of about 15-20% thereof. In another embodiment, the fragment consists of about 20-25% thereof. In another embodiment, the fragment consists of about 25-30% thereof. In another embodiment, the fragment consists of about 30-35% thereof. In another embodiment, the fragment consists of about 35-40% thereof. In another embodiment, the fragment consists of about 45-50% thereof. In another embodiment, the fragment consists of about 50-55% thereof. In another embodiment, the fragment consists of about 55-60% thereof. In another embodiment, the fragment consists of about 5-15% thereof. In another embodiment, the fragment consists of about 10-20% thereof. In another embodiment, the fragment consists of about 15-25% thereof. In another embodiment, the fragment consists of about 20-30% thereof. In another embodiment, the fragment consists of about 25-35% thereof. In another embodiment, the fragment consists of about 30-40% thereof. In another embodiment, the fragment consists of about 35-45% thereof. In another embodiment, the fragment consists of about 45-55% thereof. In another embodiment, the fragment consists of about 50-60% thereof. In another embodiment, the fragment consists of about 55-65% thereof. In another embodiment, the fragment consists of about 60-70% thereof. In another embodiment, the fragment consists of about 65-75% thereof. In another embodiment, the fragment consists of about 70-80% thereof. In another embodiment, the fragment consists of about 5-20% thereof. In another embodiment, the fragment consists of about 10-25% thereof. In another embodiment, the fragment consists of about 15-30% thereof. In another embodiment, the fragment consists of about 20-35% thereof. In another embodiment, the fragment consists of about 25-40% thereof. In another embodiment, the fragment consists of about 30-45% thereof. In another embodiment, the fragment consists of about 35-50% thereof. In another embodiment, the fragment consists of about 45-60% thereof. In another embodiment, the fragment consists of about 50-65% thereof. In another embodiment, the fragment consists of about 55-70% thereof. In another embodiment, the fragment consists of about 60-75% thereof. In another embodiment, the fragment consists of about 65-80% thereof. In another embodiment, the fragment consists of about 70-85% thereof. In another embodiment, the fragment consists of about 75-90% thereof. In another embodiment, the fragment consists of about 80-95% thereof. In another embodiment, the fragment consists of about 85-100% thereof. In another embodiment, the fragment consists of about 5-25% thereof. In another embodiment, the fragment consists of about 10-30% thereof. In another embodiment, the fragment consists of about 15-35% thereof. In another embodiment, the fragment consists of about 20-40% thereof. In another embodiment, the fragment consists of about 30-50% thereof. In another embodiment, the fragment consists of about 40-60% thereof. In another embodiment, the fragment consists of about 50-70% thereof. In another embodiment, the fragment consists of about 60-80% thereof. In another embodiment, the fragment consists of about 70-90% thereof. In another embodiment, the fragment consists of about 80-100% thereof. In another embodiment, the fragment consists of about 5-35% thereof. In another embodiment, the fragment consists of about 10-40% thereof. In another embodiment, the fragment consists of about 15-45% thereof. In another embodiment, the fragment consists of about 20-50% thereof. In another embodiment, the fragment consists of about 30-60% thereof. In another embodiment, the fragment consists of about 40-70% thereof. In another embodiment, the fragment consists of about 50-80% thereof. In another embodiment, the fragment consists of about 60-90% thereof. In another embodiment, the fragment consists of about 70-100% thereof. In another embodiment, the fragment consists of about 5-45% thereof. In another embodiment, the fragment consists of about 10-50% thereof. In another embodiment, the fragment consists of about 20-60% thereof. In another embodiment, the fragment consists of about 30-70% thereof. In another embodiment, the fragment consists of about 40-80% thereof. In another embodiment, the fragment consists of about 50-90% thereof. In another embodiment, the fragment consists of about 60-100% thereof. In another embodiment, the fragment consists of about 5-55% thereof. In another embodiment, the fragment consists of about 10-60% thereof. In another embodiment, the fragment consists of about 20-70% thereof. In another embodiment, the fragment consists of about 30-80% thereof. In another embodiment, the fragment consists of about 40-90% thereof. In another embodiment, the fragment consists of about 50-100% thereof. In another embodiment, the fragment consists of about 5-65% thereof. In another embodiment, the fragment consists of about 10-70% thereof. In another embodiment, the fragment consists of about 20-80% thereof. In another embodiment, the fragment consists of about 30-90% thereof. In another embodiment, the fragment consists of about 40-100% thereof. In another embodiment, the fragment consists of about 5-75% thereof. In another embodiment, the fragment consists of about 10-80% thereof. In another embodiment, the fragment consists of about 20-90% thereof. In another embodiment, the fragment consists of about 30-100% thereof. In another embodiment, the fragment consists of about 10-90% thereof. In another embodiment, the fragment consists of about 20-100% thereof. In another embodiment, the fragment consists of about 10-100% thereof.
In another embodiment, the fragment consists of about 5% of the extracellular domain. In another embodiment, the fragment consists of about 6% thereof. In another embodiment, the fragment consists of about 8% thereof. In another embodiment, the fragment consists of about 10% thereof. In another embodiment, the fragment consists of about 12% thereof. In another embodiment, the fragment consists of about 15% thereof. In another embodiment, the fragment consists of about 18% thereof. In another embodiment, the fragment consists of about 20% thereof. In another embodiment, the fragment consists of about 25% thereof. In another embodiment, the fragment consists of about 30% thereof. In another embodiment, the fragment consists of about 35% thereof. In another embodiment, the fragment consists of about 40% thereof. In another embodiment, the fragment consists of about 45% thereof. In another embodiment, the fragment consists of about 50% thereof. In another embodiment, the fragment consists of about 55% thereof. In another embodiment, the fragment consists of about 60% thereof. In another embodiment, the fragment consists of about 65% thereof. In another embodiment, the fragment consists of about 70% thereof. In another embodiment, the fragment consists of about 75% thereof. In another embodiment, the fragment consists of about 80% thereof. In another embodiment, the fragment consists of about 85% thereof. In another embodiment, the fragment consists of about 90% thereof. In another embodiment, the fragment consists of about 95% thereof. In another embodiment, the fragment consists of about 100% thereof. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the fragment is a fragment of the intracellular domain of the Her-2 protein. In one embodiment, the fragment is from about one third to one-half of the intracellular domain. In another embodiment, the fragment of the intracellular domain is any of the amounts, fractions, or ranges listed above for the extracellular domain. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the fragment of a Her-2 protein of methods and compositions of the present invention does not include a signal sequence thereof. In one embodiment, omission of the signal sequence enables the Her-2 fragment to be successfully expressed in Listeria, due the high hydrophobicity of the signal sequence. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the fragment of a Her-2 protein of methods and compositions of the present invention does not include a TM domain thereof. In one embodiment, omission of the TM enables the Her-2 fragment to be successfully expressed in Listeria, due the high hydrophobicity of the TM. Each possibility represents a separate embodiment of the present invention.
The LLO utilized in methods and compositions of the present invention is, in one embodiment is a Listeria LLO. In one embodiment, the Listeria from which the LLO is derived is Listeria monocytogenes (LM). In another embodiment, the Listeria is Listeria ivanovii. In another embodiment, the Listeria is Listeria welshimeri. In another embodiment, the Listeria is Listeria seeligeri. In another embodiment, the LLO protein is a non-Listerial LLO protein.
In another embodiment, the LLO protein has the sequence:








MKKIMLVFITLILVSLPIAQQTEAKDASAFNKENSISSMAPPASPPASPK



 


TPIEKKHADEIDKYIQGLDYNKNNVLVYHGDAVTNVPPRKGYKDGNEYIV


 


VEKKKKSINQNNADIQVVNAISSLTYPGALVKANSELVENQPDVLPVKRD


 


SLTLSIDLPGMTNQDNKIVVKNATKSNVNNAVNTLVERWNEKYAQAYPNV


 


SAKIDYDDEMAYSESQLIAKFGTAFKAVNNSLNVNFGAISEGKMQEEVIS


 


FKQIYYNVNVNEPTRPSRFFGKAVTKEQLQALGVNAENPPAYISSVAYGR


 


QVYLKLSTNSHSTKVKAAFDAAVSGKSVSGDVELTNIIKNSSFKAVIYGG


 


SAKDEVQIIDGNLGDLRDILKKGATFNRETPGVPIAYTTNFLKDNELAVI


 


KNNSEYIETTSKAYTDGKINIDHSGGYVAQFNISWDEVNYDPEGNEIVQH


 


KNWSENNKSKLAHFTSSIYLPGNARNINVYAKECTGLAWEWWRTVIDDRN


 


LPLVKNRNISIWGTTLYPKYSNKVDNPIE;






GenBank Accession No. P13128; SEQ ID NO: 34; nucleic acid sequence is set forth in GenBank Accession No. X15127; SEQ ID NO: 33). The first 25 amino acids 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 other embodiments, the LLO protein has a sequence set forth in GenBank Accession No. DQ054588, DQ054589, AY878649, U25452, or U25452. In another embodiment, the LLO protein is a variant of an LLO protein. In another embodiment, the LLO protein is a homologue of an LLO protein. Each possibility represents a separate embodiment of the present invention.

In another embodiment, “truncated LLO” or “ΔLLO” refers to a fragment of LLO that comprises the PEST-like domain. 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 cystine 484. In another embodiment, the LLO fragment consists of a PEST sequence. In another embodiment, the LLO fragment comprises a PEST sequence. In another embodiment, the LLO fragment consists of about the first 441 amino acids of the LLO protein. In another embodiment, the LLO fragment is a non-hemolytic form of the LLO protein.
In one embodiment, the PEST-like domain referred to above has the sequence set forth in SEQ ID NO: 42. In another embodiment, the PEST-like domain is any other PEST-like domain known in the art. Each possibility represents a separate embodiment of the present invention.
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 1-75. 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 present invention provides a vaccine comprising a recombinant polypeptide of the present invention.
In another embodiment, the present invention provides a nucleotide molecule encoding a recombinant polypeptide of the present invention. In another embodiment, the present invention provides a vaccine comprising the nucleotide molecule.
In another embodiment, the present invention provides a nucleotide molecule encoding a recombinant polypeptide of the present invention.
In another embodiment, the present invention provides a vaccine comprising a nucleotide molecule or recombinant polypeptide of the present invention.
In another embodiment, the present invention provides an immunogenic composition comprising a nucleotide molecule or recombinant polypeptide of the present invention.
In another embodiment, the present invention provides a vector comprising a nucleotide molecule or recombinant polypeptide of the present invention.
In another embodiment, the present invention provides a recombinant form of Listeria comprising a nucleotide molecule of the present invention.
In another embodiment, the present invention provides a vaccine comprising a recombinant form of Listeria of the present invention.
In another embodiment, the present invention provides a culture of a recombinant form of Listeria of the present invention.
In another embodiment, the Listeria of methods and compositions of the present invention is LM. In another embodiment, the Listeria is Listeria ivanovii. In another embodiment, the Listeria is Listeria welshimeri. In another embodiment, the Listeria is Listeria seeligeni. Each type of Listeria represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a recombinant form of Listeria comprising a nucleotide molecule encoding a Her-2 protein or a fragment thereof.
In another embodiment, the present invention provides a method of inducing an anti-Her-2 immune response in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a Her-2 protein or fused to a fragment thereof, thereby inducing an anti-Her-2 immune response in a subject.
In one embodiment, the fusion protein of methods and compositions of the present invention comprises an LLO signal sequence from LLO. In another embodiment, the two molecules of the protein (the LLO fragment and the antigen) are joined directly. In another embodiment, the two molecules are joined by a short spacer peptide, consisting of one or more amino acids. In one embodiment, the spacer has no specific biological activity other than to join the proteins or to preserve some minimum distance or other spatial relationship between them. In another embodiment, the constituent amino acids of the spacer are selected to influence some property of the molecule such as the folding, net charge, or hydrophobicity. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing an anti-Her-2 immune response in a subject, comprising administering to the subject a recombinant nucleotide encoding a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a Her-2 protein or fused to a fragment thereof, thereby inducing an anti-Her-2 immune response in a subject.
In one embodiment, the step of administering a recombinant polypeptide or recombinant nucleotide of the present invention is performed with a recombinant form of Listeria comprising the recombinant nucleotide or expressing the recombinant polypeptide. In another embodiment, the administering is performed with a different bacterial vector. In another embodiment, the administering is performed with a viral vector. In another embodiment, the administering is performed with a DNA vaccine (e.g. a naked DNA vaccine). In another embodiment, administration of a recombinant polypeptide of the present invention is performed by producing the protein recombinantly, then administering the recombinant protein to a subject. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the immune response elicited by methods and compositions of the present invention comprises a CD8+ T cell mediated response. In another embodiment, the immune response consists primarily of a CD8+ T cell-mediated response. In another embodiment, the only detectable component of the immune response is a CD8+ T cell-mediated response.
In another embodiment, the immune response elicited by methods and compositions of the present invention comprises a CD4+ T cell-mediated response. In another embodiment, the immune response consists primarily of a CD4+ T cell-mediated response. In another embodiment, the only detectable component of the immune response is a CD4+ T cell-mediated response. In another embodiment, the CD4+ T cell-mediated response is accompanied by a measurable antibody response against the antigen. In another embodiment, the CD4+ F cell-mediated response is not accompanied by a measurable antibody response against the antigen.
In another embodiment, the immune response elicited by methods and compositions of the present invention comprises an immune response to a subdominant epitope of the antigen. In another embodiment, the immune response does not comprise an immune response to a subdominant epitope. In another embodiment, the immune response consists primarily of an immune response to a subdominant epitope. In another embodiment, the only measurable component of the immune response is an immune response to a subdominant epitope.
Each type of immune response represents a separate embodiment of the present invention.
Methods of measuring immune responses are well known in the art, and include, e.g. measuring suppression of tumor growth (Examples 2, 5, 8, and 9 herein), flow cytometry (FACS; Example 3), target cell lysis assays (e.g. chromium release assay; Examples 4 and 6), the use of tetramers, and others. Each method represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of impeding a growth of a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the Her-2 protein or a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of shrinking a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the Her-2 protein or a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to a Her-2-expressing tumor, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the Her-2 protein or a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby breaking immune tolerance of a subject to a Her-2-expressing tumor.
In another embodiment, the present invention provides a method of impeding a growth of a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen or a fragment thereof, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of shrinking, a Her-2-expressing tumor in a subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen or a fragment thereof, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby impeding a growth of a Her-2-expressing tumor in a subject.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to a Her-2-expressing tumor, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen or a fragment thereof, whereby the subject mounts an immune response against the Her-2-expressing tumor, thereby breaking immune tolerance of a subject to a Her-2-expressing tumor.
In another embodiment, the present invention provides a method of improving an antigenicity of a Her-2 protein, comprising the step of fusing a nucleotide encoding an N-terminal fragment of a LLO protein to a nucleotide encoding the Her-2 protein or a fragment thereof to create a recombinant nucleotide, thereby improving an antigenicity of a Her-2 protein.
In another embodiment, a method of the present invention of improving an anti genicity of a Her-2 protein further comprising engineering a Listeria strain to express the recombinant nucleotide. In another embodiment, a different bacteria vector is used to express the recombinant nucleotide. In another embodiment, a viral vector is used to express the recombinant nucleotide. In another embodiment, a DNA vaccine (e.g. a naked DNA vaccine) is used to express the recombinant nucleotide. In another embodiment, administration of the LLO-Her-2 fusion peptide encoded by the nucleotide is performed by producing the protein recombinantly, then administering the recombinant protein to a subject. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the anti-Her-2 immune response elicted by methods and compositions of the present invention comprises a first immune response against an epitope of the Her-2 protein that is present in the fragment and a second immune response to an epitope of the Her-2 protein that is not present in the fragment, as further detailed hereinbelow.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to an antigen-expressing tumor, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a fragment of the antigen or a recombinant nucleotide encoding the recombinant polypeptide, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking immune tolerance of a subject to an antigen-expressing tumor.
In another embodiment, the present invention provides a method of breaking immune tolerance of a subject to an antigen-expressing tumor, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding a fragment of the antigen, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking immune tolerance of a subject to an antigen-expressing tumor.
In another embodiment, the present invention provides a method of identifying a CD8+ T cell epitope of an antigen, comprising the steps of (a) fusing a nucleotide molecule encoding the antigen to a nucleotide molecule encoding an N-terminal fragment of a LLO protein, thereby creating a recombinant nucleotide an LLO-antigen fusion protein; (b) administering the LLO-antigen fusion to a subject; (c) isolating a CD8+ T cell from the subject; and (d) determining the epitope recognized by the CD8+ T cell; thereby identifying a CD8+ T cell epitope of an antigen. In one embodiment, the CD8+ T cell epitope is a subdominant epitope. Each possibility represents a separate embodiment of the present invention.
“Dominant CD8+ T cell epitope,” in one embodiment, refers to an epitope that is recognized by over 30% of the antigen-specific CD8+ T cells that are elicited by vaccination, infection, or a malignant growth with a protein or a pathogen or cancer cell containing the protein. In another embodiment, the term refers to an epitope recognized by over 35% of the antigen-specific CD8+ T cells that are elicited thereby. In another embodiment, the term refers to an epitope recognized by over 40% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 45% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 50% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 55% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 60% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 65% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 70% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 75% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 80% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 85% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 90% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 95% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 96% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 97% of the antigen-specific CD8+ T cells. In another, embodiment, the term refers to an epitope recognized by over 98% of the antigen specific CD8+ T cells.
“Subdominant CD8+ T cell epitope,” in one embodiment, refers to an epitope recognized by fewer than 30% of the antigen-specific CD8+ T cells that are elicited by vaccination, infection, or a malignant growth with a protein or a pathogen or cancer cell containing the protein. In another embodiment, the term refers to an epitope recognized by fewer than 28% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 26% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 24% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 22% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 20% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 18% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 16% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 14% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 12% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 10% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 8% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 6% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 5% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by over 4% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 3% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 2% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 1% of the antigen-specific CD8+ T cells. In another embodiment, the term refers to an epitope recognized by fewer than 0.5% of the antigen-specific CD8+ T cells.
In another embodiment, the “subdominant epitope” refers to an epitope not revealed by other methods of vaccination. For example, Ercolini et al (J Immunol 2003, 170: 4273-4280) vaccinated subjects with both neu-expressing tumor cells transfected with GM-CSF and recombinant vaccinia expressing Her-2, yet found a single dominant epitope, AA 420-429. By contrast, use of the ΔLLO-Her-2 fusions in the experiments described herein revealed additional epitopes in addition to AA 420-429. Delivering the fusions with recombinant LM reveals yet more epitopes.
In another embodiment, the dominant epitope or subdominant epitope is dominant or subdominant, respectively, in the subject being treated. In another embodiment, the dominant epitope or subdominant epitope is dominant or subdominant in a population being treated.
Each type of the dominant epitope and subdominant epitope represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of breaking an immune tolerance of a subject to an antigen-expressing tumor, wherein the antigen is expressed at a detectable level on a non-tumor cell of the subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to the antigen or fused to a fragment thereof or a recombinant nucleotide encoding the recombinant polypeptide, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking an immune tolerance of a subject to an antigen-expressing tumor.
In another embodiment, the present invention provides a method of breaking an immune tolerance of a subject to an antigen-expressing tumor, wherein the antigen is expressed at a detectable level on a non-tumor cell of the subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding the antigen, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby breaking an immune tolerance of a subject to an antigen-expressing tumor.
“Detectable level” refers, in one embodiment, to a level detectable by a standard assay. In one embodiment, the assay is an immunological assay. In one embodiment, the assay is enzyme-linked immunoassay (ELISA). In another embodiment, the assay is Western blot (Example 1). In another embodiment, the assay is FACS (Example 3). In another embodiment, a detectable level is determined relative to the background level of a particular assay. Methods for performing each of these techniques are well known to those skilled in the art, and each technique represents a separate embodiment of the present invention.
The antigen in methods and compositions of the present invention is, in one embodiment, expressed at a detectable level on a non-tumor cell of the subject. In another embodiment, the antigen is expressed at a detectable level on at least a certain percentage (e.g. 0.01%, 0.03%, 0.1%, 0.3%, 1%, 2%, 3%, or 5%) of non-tumor cells of the subject. In one embodiment, “non-tumor cell” refers to a cell outside the body of the tumor. In another embodiment, “non-tumor cell” refers to a non-malignant cell. In another embodiment, “non-tumor cell” refers to a non-transformed cell. In another embodiment, the non-tumor cell is a somatic cell. In another embodiment, the non-tumor cell is a germ cell. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of inducing a CD8+ T cell-mediated immune response in a subject against a subdominant CD8+ T cell epitope of an antigen, comprising the steps of (a) fusing a nucleotide molecule encoding the antigen or a fragment thereof to a nucleotide molecule encoding an N-terminal fragment of a LLO protein, thereby creating a recombinant nucleotide encoding an LLO-antigen fusion protein; and (b) administering the recombinant nucleotide or the LLO-antigen fusion to the subject; thereby inducing a CD8+ T cell-mediated immune response against a subdominant CD8+ T cell epitope of an antigen.
In another embodiment, the present invention provides a method of inducing an immune response to a first epitope of an antigen, in an animal expressing the antigen on a tumor or an infectious agent, by vaccinating an animal with a recombinant Listeria expressing a fragment of the antigen, wherein the fragment used in vaccination does not include the first epitope. Rather, the fragment contains a second epitope of the same antigen, against which the animal mounts an immune response. A continuing immune response against the tumor or infectious agent results in recognition of the first epitope by epitope spreading, as shown herein.
In another embodiment, the present invention provides a method of inducing an immune response to a first epitope of an antigen, in an animal expressing the antigen on a tumor or an infectious agent, by vaccinating an animal with a vaccine comprising LLO fused to a fragment of the antigen, wherein the fragment used in vaccination does not include the first epitope. Rather, the fragment contains a second epitope, against which the animal mounts an immune response. A continuing immune response against the tumor or infectious agent results in recognition of the first epitope by epitope spreading, as shown herein.
In one embodiment, the immune response to the first epitope is initiated at least 2 weeks following the step of administering. In another embodiment, the immune response to the first epitope is initiated at least 2 weeks following conclusion of the step of administering. In another embodiment, the time frame is 1 week. In another embodiment, the time frame is 10 days. In another embodiment, the time frame is 17 days. In another embodiment, the time frame is 3 weeks. In another embodiment, the time frame is 4 weeks. Each possibility represents a separate embodiment of the present invention.
As provided herein, the results of the present invention further demonstrate that vaccination with recombinant antigen-expressing LM induces epitope spreading. In another embodiment, vaccination with LLO-antigen fusions, even outside the context of LM, induces epitope spreading as well. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method of impeding a growth of an antigen-expressing tumor in a subject, comprising administering to the subject a recombinant polypeptide comprising an N-terminal fragment of a LLO protein fused to a fragment of the antigen or a recombinant nucleotide encoding the recombinant polypeptide, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby impeding a growth of an antigen-expressing tumor in a subject.
In another embodiment, the present invention provides a method of impeding a growth of an antigen-expressing tumor in a subject, comprising administering to the subject a recombinant form of Listeria comprising a recombinant nucleotide, the recombinant nucleotide encoding a fragment of the antigen, wherein the antigen has one or more dominant CD8+ T cell epitopes and wherein the fragment does not contain any of the dominant CD8+ T cell epitopes, whereby the subject mounts an immune response against the antigen-expressing tumor, thereby impeding a growth of an antigen-expressing tumor in a subject.
In another embodiment, the antigen of methods of the present invention is a Her-2 protein. In another embodiment, the antigen is a HPV-16 E7 protein. In another embodiment, the antigen is bcr/abl. In another embodiment, the antigen is HPV E6 in another embodiment, the antigen is MZ2-E. In another embodiment, the antigen is MAGE-1. In another embodiment, the antigen is MUC-1. In another embodiment, the antigen is NY/ESO-1. In another embodiment, the antigen is Wilms tumor antigen. In another embodiment, the antigen is telomerase. In another embodiment, the antigen is Proteinase 3′. In another embodiment, the antigen is Tyrosinase related protein 2. In another embodiment, the antigen is HIV-1 Gag protein. In another embodiment, the antigen is SIV-1 Gag protein. In another embodiment, the antigen is HIV-1 Env protein. In another embodiment, the antigen is any other tumor antigen known in the art. In another embodiment, the antigen is any other infectious disease antigen known in the art. Each possibility represents a separate embodiment of the present invention.
In other embodiments, the antigen is derived from a tumor or an infectious organism, including, but not limited to fungal pathogens, bacteria, parasites, helminths, viruses, and the like. In other embodiments, the antigen is selected from tetanus toxoid, hemagglutinin molecules from influenza virus, diphtheria toxoid, HIV gp120, HIV gag protein, IgA protease, insulin peptide B, Spongospora subterranea antigen, vibriose antigens, Salmonella antigens, pneumococcus antigens, respiratory syncytial virus antigens, Haemophilus influenza outer membrane proteins, Helicobacter pylori urease, Neisseria meningitidis pilins, N. gonorrhoeae pilins, the melanoma-associated antigens (TRP-2, MAGE-1, MAGE-3, gp-100, tyrosinase, MART-1, HSP-70, beta-HCG), human papilloma virus antigens E1 and E2 from type HPV-16, -18, -31, -33, -35 or -45 human papilloma viruses, the tumor antigens CEA, the ras protein, mutated or otherwise, the p53 protein, mutated or otherwise, Muc1, or pSA.
In other embodiments, the antigen is an antigen associated with one of the following diseases; cholera, diphtheria, Haemophilus, hepatitis A, hepatitis B, influenza, measles, meningitis, mumps, pertussis, small pox, pneumococcal pneumonia, polio, rabies, rubella, tetanus, tuberculosis, typhoid, Varicella-zoster, whooping cough3 yellow fever; the immunogens and antigens from Addison's disease, allergies, anaphylaxis, Bruton's syndrome, cancer, including solid and blood borne tumors, eczema, Hashimoto's thyroiditis, polymyositis, dermatomyositis, type 1 diabetes mellitus, acquired immune deficiency syndrome, transplant rejection, such as kidney, heart, pancreas, lung, bone, and liver transplants, Graves' disease, polyendocrine autoimmune disease, hepatitis, microscopic polyarteritis, polyarteritis nodosa, pemphigus, primary biliary cirrhosis, pernicious anemia, coeliac disease, antibody-mediated nephritis, glomerulonephritis, rheumatic diseases, systemic lupus erthematosus, rheumatoid arthritis, seronegative spondylarthriti des, rhinitis, sjogren's syndrome, systemic sclerosis, sclerosing cholangitis, Wegener's granulomatosis, dermatitis herpetiformis, psoriasis, vitiligo, multiple sclerosis, encephalomyelitis, Guillain-Barre syndrome, myasthienia gravis, Lambert-Eaton syndrome, sclera, episciera, uveitis, chronic m ucocutaneous candidiasis, urticaria, transient hypogammaglobulinemia of infancy, myeloma, X-linked hyper IgM syndrome, Wiskott-Aldrich syndrome, ataxia telangiectasia, autoimmune hemolytic anemia, autoimmune thrombocytopenia, autoimmune neutiopenia, Waldenstrom's macroglobulinemia, amyloidosis, chronic lymphocytic leukemia, non-Hodgkin's lymphoma, malarial circumsporozite protein, microbial antigens, viral antigens, autoantigens, and lesteriosis.
In other embodiments, the antigen is one of the following tumor antigens: a MAGE (Melanoma-Associated Antigen E) protein, e.g. MAGE 1, MAGE 2, MAGE 3, MAGE 4, a tyrosinase; a mutant ras protein; a mutant p53 protein; p97 melanoma antigen, a ras peptide or p53 peptide associated with advanced cancers: the HPV 16/18 antigens associated with cervical cancers, KLH antigen associated with breast carcinoma, CEA (carcinoembryonic antigen) associated with colorectal cancer, gp100, a MARTI antigen associated with melanoma, or the PSA antigen associated with prostate cancer.
The skilled artisan will appreciate that any of the above antigens can be fused to an LLO fragment. Each of the above antigens represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a method for, suppressing formation of tumors in a host, comprising administering to the host a composition of the present invention, thereby suppressing formation of tumors in a host.
In another embodiment, the present invention provides a method for inducing formation of tumor-infiltrating CD8+ T cells in a host having cancer, comprising administering to the host a composition of the present invention, thereby inducing formation of tumor-infiltrating CD8+ T cells in a host having cancer.
In another embodiment, the present invention provides a method for inducing formation of cytotoxic T cells in a host having cancer, comprising administering to the host a composition of the present invention, thereby inducing formation of cytotoxic T cells in a host having cancer.
In another embodiment, the present invention provides a method of reducing an incidence of cancer, comprising administering a composition of the present invention. In another embodiment, the present invention provides a method of ameliorating cancer, comprising administering a composition of the present invention. Each possibility represents a separate embodiment of the present invention.
In one embodiment of methods of the present invention, the composition is administered to the cells of the subject ex vivo, in another embodiment, the composition is administered to the cells of a donor ex vivo, in another embodiment, the composition is administered to the cells of a donor in vivo, then is transferred to the subject. Each possibility represents a separate embodiment of the present invention.
In one embodiment, the cancer treated by a method of the present invention is breast cancer. In another embodiment, the cancer is a melanoma. In another embodiment, the cancer is pancreatic cancer. In another embodiment, the cancer is ovarian cancer. In another embodiment, the cancer is gastric cancer. In another embodiment, the cancer is a carcinomatous lesion of the pancreas. In another embodiment, the cancer is pulmonary adenocarcinoma. In another embodiment, the cancer is colorectal adenocarcinoma. In another embodiment, the cancer is pulmonary squamous adenocarcinoma. In another embodiment, the cancer is gastric adenocarcinoma. In another embodiment, the cancer is an ovarian surface epithelial neoplasm (e.g. a benign, proliferative or malignant variety thereof). In another embodiment, the cancer is an oral squamous cell carcinoma. In another embodiment, the cancer is non small-cell lung carcinoma. In another embodiment, the cancer is an endometrial carcinoma. In another embodiment, the cancer is a bladder cancer. In another embodiment, the cancer is a head and neck cancer. In another embodiment, the cancer is a prostate carcinoma. Each possibility represents a separate embodiment of the present invention.
In another embodiment of the methods of the present invention, the subject mounts an immune response against the antigen-expressing tumor or target antigen, thereby mediating the anti-tumor effects.
In another embodiment, the present invention provides an immunogenic composition for treating cancer, the composition comprising a fusion of a truncated LLO to a Her-2 protein. In another embodiment, the immunogenic composition further comprises a Listeria strain expressing the fusion. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the present invention provides an immunogenic composition for treating cancer, the composition comprising a Listeria strain expressing a Her-2 protein.
In one embodiment, a treatment protocol of the present invention is therapeutic. In another embodiment, the protocol is prophylactic. In another embodiment, the vaccines of the present invention are used to protect people at risk for cancer because of familial genetics or other circumstances that predispose them to certain types of cancer, e.g., cervical cancer in women whose husbands have papilloma virus. In another embodiment, the vaccines are used as a cancer immunotherapy after debulking of tumor growth by surgery, conventional chemotherapy or radiation treatment. Following such treatments, the vaccines of the present invention are administered so that the CTL response to the tumor antigen of the vaccine, destroys remaining metastases and prolongs remission from the cancer. In another embodiment, vaccines of the present invention are used to effect the growth of previously established tumors and to kill existing tumor cells. Each possibility represents a separate embodiment of the present invention.
In other embodiments, the vaccines and immunogenic compositions utilized in any of the methods described above have any of the characteristics of vaccines and immunogenic compositions of the present invention. Each characteristic represents a separate embodiment of the present invention.
Various embodiments of dosage ranges are contemplated by this invention. In one embodiment, in the case of vaccine vectors, the dosage is in the range of 0.001 LD50/dose. In another embodiment, the dosage is 0.002 LD50/dose. In another embodiment the dosage is 0.003 LD50/dose. In another embodiment the dosage is 0.004 LD50/dose. In another embodiment the dosage is 0.006 LD50/dose. In another embodiment the dosage is 0008 LD50/dose. In another embodiment the dosage is 0.01 LD50/dose. In another embodiment the dosage is 0.02 LD50/dose. In another embodiment the dosage is 0.03 LD50/dose. In one embodiment, the dosage is 0.04 LD50/dose. In another embodiment, the dosage is 0.06 LD50/dose. In another embodiment, the dosage 0.08 LD50/dose. In another embodiment, the dosage is 0.1 LD50/dose. In another embodiment, the dosage is 0.15 LD50/dose. In another embodiment, the dosage is 0.2 LD50/dose. In another embodiment, the dosage is 0.25 LD50/dose. In another embodiment, the dosage in 0.3 LD50/dose. In another embodiment, the dosage is 0.4 LD50/dose. In another embodiment, the dosage is 0.5 LD50/dose.
In another embodiment, the dosage is 107 bacteria/dose. In another embodiment, the dosage is 1.5×107 bacteria/dose. In another embodiment, the dosage is 2×107 bacteria/dose. In another embodiment, the dosage is 3×107 bacteria/dose. In another embodiment, the dosage is 4×107 bacteria/dose. In another embodiment, the dosage is 6×107 bacteria/dose. In another embodiment, the dosage is 8×107 bacteria/dose. In another embodiment, the dosage is 1×108 bacteria/dose. In another embodiment, the dosage is 1.5×108 bacteria/dose. In another embodiment, the dosage is 2×108 bacteria/dose. In another embodiment, the dosage is 3×108 bacteria/dose. In another embodiment, the dosage is 4×108 bacteria/dose. In another embodiment, the dosage is 6×108 bacteria/dose. In another embodiment, the dosage is 8×108 bacteria/dose. In another embodiment, the dosage is 1×109 bacteria/dose. In another embodiment, the dosage is 1.5×109 bacteria/dose. In another embodiment, the dosage is 2×109 bacteria/dose. In another embodiment, the dosage is 3×109 bacteria/dose. In another embodiment, the dosage is 5×109 bacteria/dose. In another embodiment, the dosage is 6×109 bacteria/dose. In another embodiment, the dosage is 8×109 bacteria/dose. In another embodiment, the dosage is 1×1010 bacteria/dose. In another embodiment, the dosage is 1.5×1010 bacteria/dose. In another embodiment, the dosage is 2×1010 bacteria/dose. In another embodiment, the dosage is 3×1010 bacteria/dose. In another embodiment, the dosage is 5×1010 bacteria/dose. In another embodiment, the dosage is 6×1010 bacteria/dose. In another embodiment, the dosage is 8×1010 bacteria/dose. In another embodiment, the dosage is 8×109 bacteria/dose. In another embodiment, the dosage is 1×1011 bacteria/dose. In another embodiment, the dosage is 1.5×1011 bacteria/dose. In another embodiment, the dosage is 2×1011 bacteria/dose. In another embodiment, the dosage is 3×1011 bacteria/dose. In another embodiment, the dosage is 5×1011 bacteria/dose. In another embodiment, the dosage is 6×1011 bacteria/dose. In another embodiment, the dosage is 8×1011 bacteria/dose. Each possibility represents a separate embodiment of the present invention.
In another embodiment, in the case of recombinant polypeptides, the dosage is 1 mg/dose. In another embodiment, the dosage is 1.5 mg/dose. In another embodiment, the dosage is 2 mg/dose. In another embodiment, the dosage is 3 mg/dose. In another embodiment, the dosage is 4 mg/dose. In another embodiment, the dosage is 6 mg/dose. In another embodiment, the dosage is 8 mg/dose. In another embodiment, the dosage is 10 mg/dose. In another embodiment, the dosage is 15 mg/dose. In another embodiment, the dosage is 20 mg/dose. In another embodiment, the dosage is 30 mg/dose. In another embodiment, the dosage is 40 mg/dose. In another embodiment, the dosage is 60 mg/dose. In another embodiment, the dosage is 80 mg/dose. In another embodiment, the dosage is 100 mg/dose. In another embodiment, the dosage is 150 mg/dose. In another embodiment, the dosage is 200 mg/dose. In another embodiment, the dosage is 300 mg/dose. In another embodiment, the dosage is 400 mg/dose. In another embodiment, the dosage is 600 mg/dose. In another embodiment, the dosage is 800 mg/dose. In another embodiment, the dosage is 1000 mg/dose.
Each of the above doses represents a separate embodiment of the present invention.
In one embodiment, a vaccine or immunogenic composition of the present invention is administered alone to a subject. In another embodiment, the vaccine or immunogenic composition is administered together with another cancer therapy. Each possibility represents a separate embodiment of the present invention.
The recombinant Listeria of methods and compositions of the present invention is, in one embodiment, stably transformed with a construct encoding an antigen or an LLO-antigen fusion. In one embodiment, the construct contains a polylinker to facilitate further subcloning. Several techniques for producing recombinant Listeria are known.
In one embodiment, the construct or heterologous gene 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 this case, a recombinant LM strain that expresses E7 was made by chromosomal integration of the E7 gene under the control of the hly promoter and with the inclusion of the hly signal sequence to ensure secretion of the gene product, yielding the recombinant referred to as Lm-AZ/E7. 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 heterologous gene 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 heterologous gene 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 rRNA 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. Each possibility represents a separate embodiment of the present invention.
In another embodiment, the construct is carried by the Listeria strain on a plasmid. Cloning of the gene into a prfA-containing vector and using this plasmid to complement a prfA(−) Listeria mutant has been used to construct DP-L2028. DP-L2028 is the influenza NP expressing strain used in the tumor protection experiments. An LM vector that expresses an E7 fusion protein has also been constructed via this technique. Lm-GG/E7 was made by complementing a prfA-deletion mutant with a plasmid containing a copy of the prfA gene and a copy of the E7 gene fused to a form of the LLO (hly) gene truncated to eliminate the hemolytic activity of the enzyme, as described in U.S. Pat. No. 6,565,852. Functional LLO is maintained by the organism via the endogenous chromosomal copy of hly.
In other embodiments, one of several approaches is taken to express the tumor antigen in Listeria. In one embodiment, a fusion protein of the selected tumor antigen and a Listerial protein, such as PI-PLC, or a construct encoding same, is generated. In another embodiment, a signal sequence, of a secreted Listerial protein such as hemolysin or phospholipases, is fused to the antigen-encoding gene.
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. Each possibility represents a separate embodiment of the present invention.
In other embodiments, one of various promoters is used to express the antigen or fusion protein containing same. In one embodiment, an LM promoter is used, eg, promoters for the genes hly, acta, pica, plcB and mpl, which encode the Listerial proteins hemolysin, act A, phosphiotidylinositol-specific phospholipase, phospholipase C, and metal loprotease, respectively. Each possibility represents a separate embodiment of the present invention.
Panels of antigens are, in one embodiment, useful in immunotherapy against cancer to compensate for the fact that antigen-loss variants of the tumors can grow out under immune system pressure (Zhang et al, Clin Cancer Res 1998 4: 2669; Kawashima et al, Hum Immunol 1998 59: 1). Thus, in another embodiment, methods and compositions of the present invention comprise a cocktail of recombinant fusion proteins, each fusion protein comprising a different tumor associated antigen fused to a truncated LLO, or a cocktail of recombinant LM strains, each expressing a different tumor associated antigen. Each possibility represents a separate embodiment of the present invention.
In another embodiment, methods and compositions of the present invention utilize a homologue of a Her-2 or LLO sequence of the present invention (e.g. SEQ ID No: 33, 34, 40, 41, 43, and 44). The terms “homology,” “homologous,” etc, when in reference to any protein or peptide, refer in one embodiment, to a percentage of amino acid residues in the candidate sequence that are identical with the residues of a corresponding native polypeptide, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology, and not considering any conservative substitutions as part of the sequence identity. Methods and computer programs for the alignment are well known in the art.
In another embodiment, the term “homology,” when in reference to any nucleic acid sequence similarly indicates a percentage of nucleotides in a candidate sequence that are identical with the nucleotides of a corresponding native nucleic acid sequence.
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” refers to identity to a sequence selected from SEQ ID No: 33, 34, 40, 41, 43, and 44 of greater than 70%. In another embodiment, “homology” refers to identity to a sequence selected from SEQ ID No: 33, 34, 40, 41, 43, and 44 of greater than 72%. In another embodiment, the identity is greater than 75%. In another embodiment, the identity is greater than 78%. In another embodiment, the identity is greater than 80%. In another embodiment, the identity is greater than 82%. In another embodiment, the identity is greater than 83%. In another embodiment, the identity is greater than 85%. In another embodiment, the identity is greater than 87%. In another embodiment, the identity is greater than 88%. In another embodiment, the identity is greater than 90%, in another embodiment, the identity is greater than 92%. In another embodiment, the identity is greater than 93%. In another embodiment, the identity is greater than 95%. In another embodiment the identity is greater than 96%. In another embodiment, the identity is greater than 97%. In another embodiment, the identity is greater than 98%. In another embodiment, the identity is greater than 99%. In another embodiment, the identity is 100%. Each possibility represents a separate embodiment of the present invention.
In another embodiment, homology is determined is 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 of the present invention, “nucleic acids” 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 of the present invention.
Protein and/or peptide homology for any amino acid sequence listed herein is determined, in one embodiment, by methods well described in the art, including immunoblot analysis, or via computer algorithm analysis of amino acid sequences, utilizing any of a number of software packages available, via established methods. Some of these packages may include the FASTA, BLAST, MPsrch or Scanps packages, and may employ the use of the Smith and Waterman algorithms, and/or global/local or BLOCKS alignments for analysis, for example. Each method of determining homology represents a separate embodiment of the present invention.
In another embodiment, the present invention provides a kit comprising a reagent utilized in performing a method of the present invention. In another embodiment, the present invention provides a kit comprising a composition, tool, or instrument of the present invention.
The terms “contacting” or “administering,” in one embodiment, refer to directly contacting the cancer cell or tumor with a composition of the present invention. In another embodiment, the terms refer to indirectly contacting the cancer cell or tumor with a composition of the present invention. In another embodiment, methods of the present invention include methods in which the subject is contacted with a composition of the present invention after which the composition is brought in contact with the cancer cell or tumor by diffusion or any other active transport or passive transport process known in the art by which compounds circulate within the body. Each possibility represents a separate embodiment of the present invention.
Pharmaceutical Compositions
The pharmaceutical compositions containing vaccines and compositions of the present invention can be, in another embodiment, administered 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 methods and compositions of the present invention, the vaccines 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 vaccines or compositions are administered by intravenous, intra-arterial, or intramuscular 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 intramuscularly and are thus formulated in a form suitable for intramuscular administration.
In one embodiment, the term “treating” refers to curing a disease. In another embodiment, “treating” refers to preventing a disease. In another embodiment, “treating” refers to reducing the incidence of a disease. In another embodiment, “treating” refers to ameliorating symptoms of a disease. In another embodiment, “treating” refers to inducing remission. In another embodiment, “treating” refers to slowing the progression of a disease. The terms “reducing”, “suppressing” and “inhibiting” refer in another embodiment to lessening or decreasing. Each possibility represents a separate embodiment of the present invention.
EXPERIMENTAL DETAILS SECTION
Example 1
Generation of L. Monocytogenes Strains that Secrete LLO Fragments Fused to Her-2 Fragments
Materials and Experimental Methods
Subcloning
pGG-55, the backbone of the Listeria Her-2 constructs used in the Examples, was created from pAM401. pAM401, a shuttle vector able to replicate in both gram+ and gram− bacteria, contains a gram+ chloramphenicol resistance gene and a gram− tetracycline resistance gene (Wirth, R et al, J Bacteriol, 165: 831, 1986). To produce pGG-55, an hly-HPV 16 E7 fusion gene (including the hly promoter and the portion of hly encoding the first 441 amino acids of LLO; referred to below as “ΔLLO”) and the pluripotent transcription factor, prfA (positive regulatory factor of listeriolysin expression) gene were cloned into pAM401 (FIG. 1).
L. monocytogenes (LM) strains Lm-ΔLLO-EC1, Lm-ΔLLO-EC2, Lm-ΔLLO-EC3, Lm-ΔLLO-IC1, and Lm-ΔLLO-IC2 each contain a plasmid expressing a fragment of rat Her-2 fused to the Listeria hly gene. The following overlapping fragments of the extracellular and intracellular domains of Her-2 were cloned into the plasmid pGG-55: base pairs (bp) 74-994, (Lm-ΔLLO-EC1; corresponding to AA 20-326 of Her-2), 923-1519 (Lm-ΔLLO-EC2; corresponding to AA 303-501), 1451-1981 (Lm-ΔLLO-EC3; corresponding to AA 479-655), 2084-3259 (Lm-ΔLLO-IC1; corresponding to AA 690-1081), and 3073-3796 (Lm-ΔLLO-IC2; corresponding to AA 1020-1255). The fragments are depicted in FIG. 2A. The LD50 of EC1, EC2, EC3, IC1, and IC2 were 1×108, 1×109, 5×108, 1×108, and 1×108, respectively.
Each Her-2 fragment was amplified by PCR from the pNINA plasmid, which contains the full-length rat Her-2 gene, using the following primers. Restriction sites (XhoI in the case of EC1, IC1, and IC2 5′ primers; SpeI for the 3′ primers; and SalI for the EC2 and EC3 5′ primers) are underlined, and the FLAG tag sequence in the EC2 and EC3 the 3′ primers are indicated by italics:








EC1: 5′ primer:









(SEQ ID No: 1)









CACGCGGATGAAATCGATAAGCTCGAGCCCCCCGGAATCGCGGGCAC;



 


3′ primer:








(SEQ ID No: 2)









CCGGACTAGTGACCTCTTGGTTATTCGGGGGACACACC.



 


EC2: 5′ primer:








(SEQ ID No: 3)









CCGGGTCGACTGCCCCTACAACTACCTGTCTACG;



 


3′ primer:








(SEQ ID No: 4)









CCGGACTAGTTTACTTGTCATCGTCGTCCTTGTAGTCCCCACTGTGGAGC



AGGGCCTG;


 


EC3: 5′ primer:








(SEQ ID No: 5)









CCGGGTCGACTGCTTTGTACACACTGTACCTTGG;



 


3′ primer:








(SEQ ID No: 6)









CCGGACTAGTTTACTTGTCATCGTCGTCCTTGTAGTCCGGGCTGGCTCTC



TGCTCTGC;


 


IC1: 5′ primer:








(SEQ ID No: 7)









CCGGCTCGAGTATACGATGCGTAGGCTGCTGCAGG;



 


3′ primer:








(SEQ ID No: 8)









CCGGACTAGTAGCCAGTGGAGATCTGGGGGGCCC;



 


IC2: 5′ primer:








(SEQ ID No: 9)









CCGGCTCGAGGGTGACCTGGTAGACGCTGAAG



and


 


3′ primer:








(SEQ ID No: 10)









CCGGACTAGTTACAGGTACATCCAGGCCTAGG.







Fragments were amplified by PCR and cloned into the pCR 2.1 expression system (Invitrogen, Carlsbad, Calif.), then excised with the delineated enzymes. The E7 gene was excised from the pGG-55 plasmid using Xho I and Spe I, then the Her-2 fragment was fusion was ligated into E7 site (ends digested with Sal I are compatible with X7101 ends). XFL-7, a prfA negative strain of LM, (Gunn G R et al, J Immunol 167: 647, 2001) was transfected with the plasmids by electroporation.
Bacteria
Bacteria were grown in brain heart infusion medium (BD, Sparks, Md.) with 50 μg/ml chloramphenicol and were frozen in 1 ml aliquots at −80° C.
Western Blots
ΔLLO-Her-2 expressing strains were grown overnight at 37° C. in Luria-Bertani (LB) medium with 50 microgram per milliliter (μg/ml) chloramphenicol. Supernatants were TCA precipitated and resuspended in 1×LDS sample buffer (Invitrogen, San Diego, Calif.). 15 microliter (μl) of each sample was loaded on a 4-12% Bis-Tris SDS-PAGE gel (Invitrogen, San Diego, Calif.). Gels were transferred to a Immobilon-P polyvinylidene fluoride membrane (Millipore, Billerica, Mass.) and blotted with a polyclonal rabbit serum recognizing residues 1-30 of LLO, followed by HRP-conjugated anti-rabbit antibody (Amersham Pharmacia Biotech, UK).
Statistical Analyses
Statistical analyses were performed using Student's t-test throughout the Examples.
Results
Five recombinant LM strains were constructed that express and secrete overlapping fragments of the rat Her-2 gene fused to the N-terminal portion of L. monocytogenes LLO protein (FIG. 2A). The signal sequence and transmembrane domain of Her-2 were not included among the fragments due to their hydrophobicity and the inability of LM to secrete extremely hydrophobic domains. Secretion of each Her-2 fragment was confirmed by Western blot (FIG. 2B). Molecular weights of the proteins Lm-ΔLLO-EC1 Lm-ΔLLO-EC2 Lm-ΔLLO-EC3, Lm-ΔLLO-IC1, and Lm-ΔLLO-IC2 were 83, 70, 68, 92.5, and 74-kDa (kilodalton), respectively. The strains were attenuated relative to the wild-type 10403S strain, exhibiting virulences comparable to Lm-ΔLLO-E7; namely 1×108, 5×108, 1×109, 1×108, and 1×108 colony forming units (CFU), respectively.
Example 2
Vaccination with LLO-Her-2 Constructs Halts and Reverses Growth of Her-2-Expressing Tumors
Materials and Experimental Methods
Mice
Six to eight week old female FVB/N mice were purchased from Charles River Laboratories (Wilmington, Mass.).
Cell Lines
The FVB/N syngeneic NT-2 tumor cell line, derived from a spontaneously occurring mammary tumor in an FVB/N Her-2 transgenic mouse (Reilly R T et al, Canc Res 60: 3569, 2000), constitutively expresses low levels of rat Her-2 and is tumorigenic in wild type syngeneic mice. NT-2 cells were grown in RPMI 1640 medium with 20% FCS, 10.2 mM HEPES, 2 millimolar (mM) L-glutamine, 100 micromolar (μM) nonessential amino acids, 1 mM sodium pyruvate, 50 U (units)/ml penicillin G, 50 μg/ml streptomycin, 20 μg/ml insulin, and 2 μg/ml gentamycin at 37° C. with 5% CO2.
Experimental Setup
6-8 week-old FVB/N mice (n=8) were injected subcutaneously in the right flank with 2×106NT-2 tumor-cells in 200 μl PBS. Seven days post-tumor inoculation, palpable tumors of 4-5 mm were observed, after which mice were injected intraperitoneally with recombinant LM or PBS on days 7, 14, and 21. The shortest and longest surface diameters of the tumors were measured every 2 days with calipers. Mice were sacrificed if they reached a point at which mean tumor diameter reached 20 mm.
Results
LM strains expressing ΔLLO-Her-2 fusions were compared to PBS and Lm-ΔLLO-E7 (negative controls) for their ability to induce immunity against and reduction oftumors composed of the rat Her-2 expressing tumor line, NT-2. FVB/N mice were injected with NT-2 tumors, then, on days 7, 14, and 21 following tumor inoculation, were administered 0.1 LD50 of recombinant LM or PBS. Injection of LM expressing the ΔLLO-Her-2 fusions halted tumor growth after the first injection (FIGS. 2A and B); the cessation in tumor growth continued through the last timepoint, more than nine weeks after the last Her-2 vaccination. Moreover, a complete regression of tumors was subsequently observed in three out of 8 of the Lm-ΔLLO-EC2 and Lm-ΔLLO-EC3 mice and 1 of 8 of the Lm-ΔLLO-EC1 and Lm-ΔLLO-IC1 mice. Additional mice from all five of the ΔLLO-Her-2 groups exhibited a reduction in tumor size. As expected, tumors grew continually in mice injected with PBS and Lm-ΔLLO-E7.
These findings demonstrate that fusions of a LLO fragment to Her-2 are capable of eliciting immunity against Her-2-expressing tumors. These findings further indicate that the elicited immunity (a) is strong enough to induces the complete regression of greater than 75% of established Her-2-expressing tumors; and (b) lasts over the course of over at least several months.
Example 3
Immune Responses Induced by the Lm-LLO-Her-2 Vaccine Include CD8+ T Cells
Materials and Experimental Methods
CD8+ T Cell Depletion
CD8+ T cells were depleted by injection with 0.5 mg of the anti-CD8 antibody 2.43 (Sarmiento M et al, J Immunol 125(6): 2665-72, 1980) on days 6, 7, 8, 11, 14, 17, 20, and 23 post-tumor injection. CD8+ T cell populations were reduced by greater than 95% as measured by flow cytometric analysis on day 24.
Flow Cytometric Analysis
Three color flow cytometry for CD8 (53-6.7, FITC conjugated), CD62 ligand (MeI-14, APC conjugated) (BD Biosciences Pharmingen, San Diego, Calif.), and Her-2H-2q tetramer (PE conjugated) was performed using a FACSCalibur flow cytometer with CellQuest software (Becton Dickinson, San Jose, Calif.). Tetramers, provided by the NIAID Tetramer Core Facility of Emory University and the NIH AIDS Research and Reference Reagent Program, were loaded with an H-2q specific PDSLRDLSVF peptide. Splenocytes were stained at room temperature (rt) with the tetramer for one hour (hr) at 1:200 dilution, then at 4° C. with anti-CD8 and anti-CD62L antibodies for 30 minutes (min). The CD8+, CD62Llow subset was selected (“gated on”), and percentages of tetramer+ cells were compared using FlowJo software (Tree Star, Inc, Ashland, Oreg.).
Results
In order to determine the type of T cells that were mediating the observed anti-Her-2 immune responses, FVB/N mice with NT-2 tumors were depleted of CD8+ T cells, beginning 1 day prior to vaccination with Lm-ΔLLO-Her-2 vaccines, then vaccinated as described in Example 2. In the CD8+-injected mice, each of the Lm-ΔLLO-Her-2 vaccines lost effectiveness (FIGS. 3A and B); while in the non-depleted mice, tumor growth was controlled, as observed in Example 2.
Tetramer analysis was next used to confirm the above results. Non-tumor bearing 6-8 week-old FVB/N mice were immunized with either PBS or 0.1 LD50 Lm-ΔLLO-EC2 and boosted 21 days later. Splenocytes were harvested 5 day's after the boost and were stained with an H-2q tetramer specific for the epitope defined by amino acids 420-429 (PDSLRDLVF), A three-fold increase in tetramer, positive cells was observed in the Lm-ΔLLO-EC2-vaccinated mice (FIG. 5).
These results show that CD8+ T cells are featured in the immunity elicited by the LLO-Her-2 fusion vaccines.
Example 4
LLO-Her-2 Fusion Vaccines Induce Immune Responses to Sub-Dominant CD8+ T Cell Epitopes
Materials and Experimental Methods
Cells
NIH 3T3 cells, a mouse fibroblast line, were obtained from the American Type Culture Collection (ATCC). The NIH 3T3 and all the derived cells were cultured in DMEM supplemented with 10% FCS, 2 mM L-glutamine, 100 μM nonessential amino acids, 1 mM sodium pyruvate, 50 U/ml penicillin G, and 50 μg/ml streptomycin. Culture media for the 3T3-neu cell lines was supplemented with 1 mg/ml G418. Cells were grown at 37° C. with 5% CO2.
3T3-Her-2 Lines
Briefly, wild type 3T3 cells were transduced with overlapping fragments of the rat Her-2 gene, creating nine 3T3 Her-2 fragment lines, and one 3T3 line expressing the full-length rat Her-2. Her-2 fragments were created using the following PCR primers:










Fragment 1 (bp 1-508):









(SEQ ID No: 11)











5′-CCGGGCCGAATTCGCAATGATC




and



 








(SEQ ID No: 12)











3′-CCCCGAATTCCTACTGAGGGTTCCCACGGATCAA.




 



Fragment 2 (bp 458-886):








(SEQ ID No: 13)











5′-GACATGAAGTTGCGGCTCCCTAGTCTCACAGAGATCCTGAAG




and



 








(SEQ ID No: 14)











3′-CCCCGAATTCCTACTCAGGGTTGTGCATGGACTC.




 



Fragment 3 (bp 836-1294):








(SEQ ID No: 15)











5′-GACATGAAGTTGCGGCTCCCTGCCCTCGTCACCTACAACACA




and



 








(SEQ ID No: 16)











3′-CCCCGAATTCCTAGAGGTCACGGAGACTGTCTGG.




 



Fragment 4 (bp 1244-1675):








(SEQ ID No: 17)











5′-GACATGAAGTTGCGGCTCCCTATCACAGGTTACCTGTACATC




and



 








(SEQ ID No: 18)











3′-CCCCGAATTCCTACTTCCATACTCGGCACTCCTC.




 



Fragment 5 (bp 1607-2077):








(SEQ ID No: 19)











5′-GACATGAAGTTGCGGCTCCCTACCCAGTGTGTCAACTGCAGT




and



 








(SEQ ID No: 20)











3′-CCCCGGTACCCTAGATCTTCTGTCTCCTTCGTTT.




 



Fragment 6 (bp 2009-2476):








(SEQ ID No: 21)











5′-GACATGAAGTTGCGGCTCCCTGGCGTCCTGCTGTTCCTGATC




and



 








(SEQ ID No: 22)











3′-CCCCGGTACCCTAACCTCGGTGTTCTCGGACATG.




 



Fragment 7 (bp 2405-2872),








(SEQ ID No: 23)











5′-GACATGAAGTTGCGGCTCCCTTCCACAGTACAGCTGGTGACA




and



 








(SEQ ID No: 24)











3′-CCCCGGTACCCTAGCAGATTGGAGGCTGAGGTAG.




 



Fragment 8 (bp 2801-3271),








(SEQ ID No: 25)











5′-GACATGAAGTTGCGGCTCCCTGATGGAATCCCAGCCCGGGAG




and



 








(SEQ ID No: 26)











3′-CCCCGGTACCCTACCCTTCCGAGGGAGCCAGTGG.




 



Fragment 9 (bp 3203-3796),








(SEQ ID No: 27)











5′-GACATGAAGTTGCGGCTCCCTGAGCTGACACTGGGCCTGGAG




and



 








(SEQ ID No: 28)











3′-CCCCGGTACCCTATACAGGTACATCCAGGCCTAG.







Fragments 1-9 span amino acids 1-165, 148-291, 274-426, 410-553, 531-687, 655-820, 797-952, 929-1085, 1063-1255 of Her-2, respectively. Each fragment was ligated into the pcDNA3.1 mammalian transfection vector, which contains a cytomegalovirus (CMV) promoter (Invitrogen, Carlsbad, Calif.), at the multicloning site. Constructs were transfected into 3T3 cells using electroporation (20 μg/l×107 cells) or Lipofectamine (1.5 μg/3×105 cells; Life Technologies). Several clones of each fragment were isolated by limiting dilution. Expression of Her-2 fragments in the clones was determined by RT-PCR.
Chromium Release Assay
FVB/N mice were immunized with 0.1 LD50 of each of the Lm-ΔLLO-Her-2 vaccines. Splenocytes were harvested 9 days later and cultured for four days with irradiated (20,000 rads) NT-2 tumor cells at a 100:1 ratio of splenocytes to tumor cells with 20 U/ml IL-2 (Roche, Indianapolis, Ind.). Splenocytes were then used as effector cells in a standard 51Cr release assay. Target cells were labeled with chromium-51 (53Cr) and cultured for four hours with splenocytes at effector:target ratios of 200:1, 100:1, 50:1, and 25:1 in triplicate. Following the incubation, 100 μl of supernatant was assayed for 51Cr release. The percent specific lysis was determined as [(experimental counts per minute−spontaneous counts per minute)/(total counts per minute−spontaneous counts per minute)]×100. “Total counts per minute” refers to the total number of counts in the target cell population, measured by lysing the cells after labeling and counting the label. In other words, this is the maximum amount of 51Cr that could be released.
Results
CTL assays were performed in order to confirm that each of the Lm-ΔLLO-Her-2 vaccines elicit anti-Her-2 CD8+ T cell immune responses. Mice were vaccinated with each of the ΔLLO-Her-2 fusion vaccines, and splenocytes were isolated and tested for ability to induce lysis, as measured by 51Cr release assay, of 3T3 cells transduced with full length rat Her-2 (B), using wild-type 3T3 cells as a negative control (A). Each vaccine induced an anti-Her-2 CTL response, as evidenced by significant levels of lysis at E:T ratios of 200:1 or 100:1. Splenocytes from PBS-vaccinated mice, an additional negative control, induced only background levels of lysis (FIG. 6). These findings provide further evidence that each of the ΔLLO-Her-2 fusion vaccines induces anti-Her-2 CTL immune responses.
To delineate the epitopes recognized by the CTL, elicited by each vaccine, a panel of 3T3 cells expressing each of 9 Her-2 fragments were used as target cells in the above-described lysis assay, following vaccination with the corresponding ΔLLO-Her-2 fusion vaccine. Each vaccine elicited a CTL response to at least one Her-2 fragment. For several of the Her-2 fragments, levels of lysis over background reached statistical significance (p<0.05). Based on a combination of the negative and positive results, regions of Her-2 containing sub-dominant epitopes were delineated (Table 1). Thus, vaccination with the Lm-ΔLLO-Her-2 fragment vaccines revealed sub-dominant epitopes within Her-2 protein.







TABLE 1







Regions of Her-2/neu with potential H-2q epitopes, based on percent


specific lysis in the CTL assay. Percent (specific lysis - background


lysis by splenocytes from PBS-vaccinated mice) is depicted for the


E:T ratios of 200:1 and 100:1. Assays were performed in triplicate;


results of a representative experiment are shown.












Percent Specific
Neu regions



Neu region
Lysis of Target Cells
containing an












LM strain
spanned

200:1
100:1
epitope















Lm-ΔLLO-
 20-326
3T3-neu-1
14.3*
0.7
 20-148


EC1

3T3-neu-2
0
0  




3T3-neu-3
6.5*
3.5
291-326


Lm-ΔLLO-
303-501
3T3-neu-3
10.9*
7.4
303-426


EC2

3T3-neu-4
23.8*
 8.4*
410-501


Lm-ΔLLO-
479-655
3T3-neu-4
1
0  


EC3

3T3-neu-5
34.4*
25.3*
531-655


Lm-ΔLLO-
 690-1081
3T3-neu-6
6.9*
9* 
690-797


IC1

3T3-neu-7
0
2.3




3T3-neu-8
18.2*
6.4
 952-1081


Lm-ΔLLO-
1020-1255
3T3-neu-8
10.3*
 8.2*
1020-1085


IC2

3T3-neu-9
16.5
0  
1063-1255





*Denotes statistically significant lysis above background (p < 0.05).






Example 5
Fusion to LLO and Delivery by LM Enhances the Immunogenicity of Her-2
Materials and Experimental Methods
DNA Vaccines
DNA vaccines were constructed using pcDNA 3.1. Her-2 and the EC1 fragment were amplified by PCR using the following primers:
Full length, unfused Her-2: 5′ CCGGGCTAGCATGGTCATCATGGAGCTGGCCGG (Nhe I site underlined; SEQ ID No: 29) and 3′ CCGGGATATCTTACTGTCATCGTCGTCCTTGTAGTCTCATACAGGTACATCCA GGCC (EcoRV site underlined, FLAG tag in italics, stop codon in bold; SEQ ID No: 30). The above 5′ primer was also used for amplifying unfused EC1, and the 3′ primer for amplifying ΔLLO-full length Her-2.
ΔLLO-full length Her-2: 5′ CCGGGTCGACATGGTCATCATGGAGCTGGCCGG (Sal I site underlined; SEQ ID No: 31). This primer was also used for amplifying ΔLLO-EC1.
Unfused EC1: 3′ CCGGGATATCTTACTTGTCATCGTCGTCCTTGTAGTCTCAGACCTCTTGGTTATTCGGGGG (EcoRV site underlined, FLAG tag in italics, stop codon in bold; SEQ ID No: 32). This primer was also used for amplifying unfused EC1 fused to ΔLLO.
Fragments were cloned into the multicloning site of pcDNA3.1, and used to transform Escherichia coli. Bacteria were grown in Luria-Bertani media (BD, Sparks, Md.) with 50 micrograms per milliliter (μg/ml) ampicillin.
Tumor Regression Experiments
Tumor regression experiments were performed as described in Example 2, except that 7×105 NT-2 cells were utilized, and vaccinations were administered on days 3, 10, and 18. DNA vaccines (50 μg each of the pcDNA plasmid+ and the GM-CSF plasmid or GM-CSF alone) were administered intra-muscularly and Lm administered intraperitoneally.
Results
Several factors were present in the Lm-ΔLLO-Her-2 vaccines that may have contributed to the recognition of sub-dominant epitopes: (a) delivery by LM; (b) fusion of the target antigen to ΔLLO; (c) breaking Her-2 into fragments. To determine which one or more of these factors contributed to the recognition of sub-dominant epitopes, as evidence by enhanced anti-Her-2 immune responses, mice were vaccinated with (a) pcDNA 3.1-full length Her-2 (a. DNA vaccine; “pcDNA neu”); (b) pcDNA 3.1 ΔLLO-full length Her-2 (pcDNA LLO-neu); (c) pcDNA 3.1-EC1 (pcDNA EC1); (d) pcDNA 31-ΔLLO-EC1 (pcDNA LLO-EC1); or (e) Lm-ΔLLO-EC1, and a tumor regression experiment was performed GM-CSF was included with the DNA vaccines because of its ability to enhance the efficacy of DNA vaccines (McKay P F, Barouch D H et al, Eur J Immunol 2004 April; 34(4): 1011-20).
As depicted in FIG. 7A, the best control of tumor growth was observed with Lm-ΔLLO-EC1; 2/8 of the mice never developed palpable tumors; the tumor completely regressed in another two; and the other 4 mice exhibited slower (retarded) tumor growth than the mock-vaccinated controls. In the case of pcDNA ΔLLO-EC1, one mouse never developed a tumor, and several of the other mice exhibited retarded tumor growth. Fusion to ΔLLO enhanced immunogenicity of EC1, as seen by comparison of pcDNA EC1 vs. pcDNA ΔLLO-EC1 and pcDNA neu vs. pcDNA ΔLLO-neu (FIGS. 6B-C); vaccines in which the antigen was unfused exhibited tumors that grew at the same rate as mock-vaccinated controls. An enhancing effect of dividing Her-2 into smaller fragments, in the case of the ΔLLO fusions, is seen from a comparison of pcDNA ΔLLO-neu vs. pcDNA ΔLLO-EC1, in which the latter group exhibited superior tumor control (FIG. 7D). No effect was seen for the unfused antigens, as seen from a comparison of pcDNA neu vs. pcDNA EC1 (FIG. 7E).
Example 6
LLO-Her-2 DNA Vaccines Induce Immune Responses to Sub-Dominant CD8+ T Cell Epitopes
Immune responses to the DNA vaccines were further analyzed by measuring lysis of 3T3 cells transduced with Her-2 fragments, as described in Example 4. T cells from mice vaccinated with pcDNA 3.1-ΔLLO-Her-2 or pcDNA 3.1-ΔLLO-EC1 lysed cells from more 3T3-Her-2 target cell groups than did the corresponding non-fused DNA vaccines (Table 2).







TABLE 2







Regions of Her-2/neu with potential epitopes based on


DNA vaccinations of wt FVB mice.











Neu
Percent Specific
Neu regions



region
Lysis of Target Cells
containing












LM strain
spanned

200:1 
100:1
an epitope















pcDNA neu + GM-
1-1255
3T3-neu-1
17.4*
12.4*
 20-148


CSF

3T3-neu-2
0  
0.1




3T3-neu-3
0  
1.6




3T3-neu-4
23.4*
19.5*
410-479




3T3-neu-5
0  
0.3




3T3-neu-6
2.6
0




3T3-neu-7
0  
0.6




3T3-neu-8
0  
1.2




3T3-neu-9
0  
0.1


pcDNA ΔLLO-
1-1255
3T3-neu-1
30.9*
20.5*
 20-148


neu + GM-CSF

3T3-neu-2
0.4
0




3T3-neu-3
1.9
1.7




3T3-neu-4
31.2*
25.5*
410-501




3T3-neu-5
 6.4*
6.4
479-531




3T3-neu-6
0  
0




3T3-neu-7
0  
2.5




3T3-neu-8
0  
4




3T3-neu-9
21*  
15.8*
1085-1255


pcDNA EC1 + GM-
1-326 
3T3-neu-1
7.8
1.9


CSF

3T3-neu-2
0  
2.1




3T3-neu-3
 8.5*
0
291-326


pcDNA ΔLLO-
1-326 
3T3-neu-1
14.6*
8.5*
 20-148


EC1 + GM-CSF

3T3-neu-2
0  
0.5




3T3-neu-3
 9.9*
5.1
291-326





*denotes statistically significant lysis above background (p < 0.05). Percent specific lysis was calculated as % = 100 × ((experimental lysis − spontaneous lysis)/(total lysis − spontaneous lysis)).






Thus, fusion of an LLO fragment to full length Her-2 or a Her-2 fragment resulted in a broadening of the regions recognized by CTLs. Accordingly, based on the results of Examples 5-6, subdominant CD8+ antigen epitopes can be revealed by either (a) expression by LM; (b) fusion of the antigen to an LLO fragment; or (c) dividing the antigen into smaller fragments.
Example 7
Vaccination with LLO-Her-2 Induces Epitope Spreading Materials and Experimental Methods
FVB/N are injected with NT-2 tumors, then vaccinated with each of the LM-ΔLLO-Her-2 fragment strains, as described in Example 2, or with DNA ΔLLO-Her-2 fragment vaccines, as described in Example 5. Lymphocytes are isolated from the draining lymph nodes of the tumor site at various time points following vaccination. Epitopes recognized by the lymphocytes are determined by a lysis assay, using 3T3 cells expressing each of 9H er-2 fragments, as described in Example 4.
Results
The induction of tumor regression at more than one month after the final boost is in contrast with observations using other types of vaccines, and suggests that the number of T cell subsets is being expanded by epitope spreading. For example, antigen presenting cells such as dendridic cells may be acquiring pieces of the dying cells, traveling to the draining lymph nodes, and presenting Her-2 epitopes not present in the vaccine fragment, resulting in a broadening of the and Her-2 CD8+ T cell response. To confirm this conclusion, mice are injected with NT-2 tumors, then vaccinated with each of the LM-ΔLLO-Her-2 fragment strains or DNA ΔLLO-Her-2 fragment vaccines. Lymphocytes are isolated tumor draining lymph nodes at various time points, and the epitopes recognized by the lymphocytes are determined. Emergence is observed of reactivity to epitopes not present in the vaccine fragment. This broadening of the T cell response approximately correlates with temporally tumor regression.
This result demonstrates that vaccination with recombinant antigen-expressing LM induces epitope spreading. In addition, vaccination with LLO-antigen fusions, even outside the context of LM, induces epitope spreading as well.
Example 8
Vaccination with LLO-Her-2 Overcomes Immune Tolerance to a Self Antigen
Materials and Experimental Methods
Rat Her-2/neu transgenic mice were provided by Dr. William Muller. Young, virgin HER-2/neu transgenic mice that had not spontaneously developed tumors were injected with 5×104 NT-2 cells. Because the transgenic mouse is profoundly tolerant to HER-2/neu, the minimum dose required for tumor growth in 100% of animals is much lower than wild-type mice (Reilly R T, Gottlieb M B et al, Cancer Res. 2000 Jul. 1; 60(13): 3569-76) NT-2 cells were injected into the subcutaneous space of the flank. Mice received 0.1 LD50 of the Listeria vaccine when 4-5 mm palpable tumors were detected (typically on day 7 after tumor implantation) and weekly thereafter, for an additional 4 weeks.
Results
The rat Her-2/neu gene differs from the rat neu by 5-6% of amino acid residues, and thus is immunogenic in the mouse (Nagata Y, Furugen R et al, J Immunol 159:1336-43). A transgenic mouse that over expresses rat Her-2/neu under the transcriptional control of the Mouse Mammary Tumor Virus (MMTV) promoter and enhancer is immunologically tolerant to rat Her-2/neu. These mice spontaneously develop breast cancer. The MMTV promoter also operates in hematopoietic cells, rendering the mice profoundly tolerant to HER-2/neu. This, this mouse is considered to be stringent model for human breast cancer and in general for tumors expressing antigens, such as Her-2/neu, that are expressed at low levels in normal tissue (Muller W. J. (1991) Expression of activated oncogenes in the murine mammary gland: transgenic models for human breast cancer. Canc Metastasis Rev 10: 217-27).
6-8 week-old HER-2/neu transgenic mice were injected with NT-2 cells, then immunized with each of the LM-ΔLLO-Her-2 vaccines, or with PBS or ΔLLO-E7 (negative controls). While most control mice had to be sacrificed by day 42 because of their tumor burden, tumor growth was controlled in all of the vaccinated mice (FIG. 8).
Thus, the ΔLM-LLO-Her-2 and Listeria-based Her-2 vaccines are able to break tolerance to self antigen expressed on a tumor cell, as evidenced by their ability to induce the regression of established NT-2 tumors.
Example 9
LLO-HER-2 Vaccines Control Spontaneous Tumor Growth in HER-2/NEU Transgenic Mice
Materials and Experimental Methods
ΔLM-LLO-Her-2 vaccines were administered in the following amounts: Lm-LLO-EC1: 1×10^7 cfu; Lm-Lm-LLO-IC2: 5×10^7 cfu; LLO-EC3: 1×10^8 cfu; Lm-LLO-IC2: 1×10^7 cfu; Lm-LLO-IC1: 1×10^7.
Results
The ΔLM-LLO-Her-2 vaccines were also evaluated for ability to prevent spontaneous tumor growth in the Her-2/neu transgenic mice. The transgenic mice (n=12 per vaccine group) were immunized 5 times with 0.1 LD50 of one of the vaccine strains, beginning at age 6 weeks and continuing once every three weeks. Mice were monitored for tumor formation in the mammary glands. By week 35, all of the control mice (PBS or Lm-LLO-NY-ESO-1-immunized) had developed tumors. By contrast, 92% of the Lm-LLO-IC1 group were tumor free, as were 50% of the mice Lm-LLO-EC2, Lm-LLO-EC1, and Lm-LLO-IC2, and 25% of the mice immunized with Lm-LLO-EC3 (FIG. 9).
This finding confirm the results of the previous Example, showing that ΔLM-LLO-Her-2 and Listeria-based Her-2 vaccines are able to break tolerance to self antigens.
Example 10
Generation of LLO-HER-2 Vaccines Containing Fragments of Human HER-2 Protein
A similar strategy was used to express human Her-2/neu as was used for rat Her-2 (Example 1). The full-length HER-2 gene was split into five fragments, constituting overlapping fragments of the extracellular domain, (EC-1, EC-2 and EC-3) and the cytoplasmic domain (IC-1 and IC-2) (FIG. 10). Hydrophobic regions were not included in the constructs. These sequences differed from the rat sequences slightly due to the small disimilarities between the two sequences. The human fragments corresponding to the rat fragments were 22-326, 303-501, 479-652, 677-1081, and 1020-1255.
The human HER-2 sequences are isolated from a human breast cell cancer line erg. SK-BR3 (ATCC) by reverse transcription PCR (RT-PCR) using standard molecular biology methods. For example, total cellular RNA is isolated using the RNeasy Minipreparation® kit (Qiagen) and a cDNA pool is generated (Titan-One-Tube PCR system®, Roche) using an oligo-dT primer. The HER-2 sequences of interest are specifically amplified by the second step PCR using the following primers:












Construct
5′ Primer
3′ Primer




















EC1
ctcgaggccgcgagcacccaagtg
(SEQ ID No: 45)
actagtttaatcctctgctgtcacctc
(SEQ ID No: 46)



 


EC2
ctcgagtacctttctacggacgtg
(SEQ ID No: 47)
actagtttactctggccggttggcag
(SEQ ID No: 48)


 


EC3
ctcgagacggtgccctgggaccag
(SEQ ID No: 49)
actagtttagacgatggacgtcagag
(SEQ ID No: 50)


 


IC1
ctcgagctgctgcaggaaacggag
(SEQ ID No: 51)
actagtttaagccccttcggagggtg
(SEQ ID No: 52)


 


IC2
ctcgaggctgaggagtatctg
(SEQ ID No: 53)
actagtttacactggcacgtccagac
(SEQ ID No: 54)









Restriction sites XhoI (5′) and SpeI (3′) are added to allow for subsequent cloning into the Listeria vaccine vector, and an ochre stop codon is included in the reverse primers to terminate translation of the fusion protein. There are no XhoI or SpeI sequences located in these fragments of the human HER-2 gene. The PCR products are purified (Qiaquick® PCR Purification Kit, Qiagen) and cloned into intermediate E. coli vector pCR2.1 TOPO® (Invitrogen) After transformation of TOP10 cells (Invitrogen), plasmid containing colonies are identified by PCR using primers M13 forward and M13 reverse (Invitrogen). One positive clone for each construct is grown up, plasmid DNA will be prepared (Qiafilter Midipreparation®, Qiagen) and the sequence of the HER-2/neu insert is verified by sequencing.
In order to introduce the HER-2/neu antigen sequences into the Listeria vector, pLLO-E7 is digested completely with XhoI and partially with SpeI, thereby removing the E7 gene. The HER-electrophoresis, and the pLLO-E7 vector and the HER-2/neu insert sequences are purified (Qiaquick). The HER-2/neu antigen sequences are ligated into pLLO-E7, and the ligation mix is transformed into d-alanine racemase-deficient E. coli strain MB2159 by electroporation. Colonies are tested by PCR for the presence of the HER-2/neu sequence and expanded in Luria Broth (LB) media, and plasmid DNA is prepared, then the sequence verified by restriction digestion with EcoRI, SmaI, NcoI or with HindIII which yields a specific band pattern for each construct. Plasmids are transformed into Listeria strain Lm(DA-) by electroporation, and individual clones are grown up in LB media containing 50 μg/ml streptomycin. The presence and sequence of the plasmid is again verified by restriction analysis. Expression and secretion of LLO-HER-2/neu fusion proteins is verified by Western blot of TCA-precipitated culture media, using a polyclonal PEST sequence-specific antibody.
Example 11
Testing OF LLO-HER-2 Vaccines Containing Fragments of Human HER-2 Protein
The LLO-human Her-2 strains are tested for immunogenicity in mice and in human volunteers. Next, the vaccine strains are tested for their ability to protect mice against a challenge with tumor cells expressing human Her-2, as described in the above Examples Successful strains are administered to humans having Her-2-expressing tumors, and tested for their ability to induce tumor regression. In addition, the strains are tested for their ability to protect human subjects at risk for developing Her-2-expressing cancer, due to genetic or environmental factors. The vaccine strains are found to be immunogenic and to exhibit substantial anti-tumor activity.

## Claims

1. A recombinant form of Listeria comprising a nucleotide molecule encoding a recombinant polypeptide comprising an N-terminal fragment of a listeriolysin (LLO) protein fused to a fragment of a Her-2 protein, wherein said fragment of a Her-2 protein consists of amino acids 303-501, 479-655, or 1020-1255 of SEQ ID NO: 40 or amino acids 303-501, 479-652, or 1020-1255 of SEQ ID NO: 43.

2. The recombinant form of Listeria of claim 1, wherein said N-terminal fragment of a listeriolysin (LLO) protein is non-hemolytic.

3. An immunogenic composition comprising the recombinant form of Listeria of claim 1.

4. A recombinant form of Listeria comprising a nucleotide molecule encoding a fragment of a Her-2 protein wherein said fragment of a Her-2 protein consists of amino acids 303-501, 479-655, or 1020-1255 of SEQ ID NO: 40 or amino acids 303-501, 479-652, or 1020-1255 of SEQ ID NO: 43.

5. The recombinant form of Listeria of claim 4, wherein said Her-2 protein is a human Her-2 protein.

6. An immunogenic composition comprising the recombinant form of Listeria of claim 4.

7. A recombinant L. monocytogenes strain expressing a recombinant fusion polypeptide comprising an N-terminal listeriolysin (LLO) fragment fused to a fragment of a Her-2 protein, wherein said fragment consists of amino acids 303-501 or 479-655 of SEQ ID NO: 40 or amino acids 303-501 or 479-652 of SEQ ID NO: 43.

8. A recombinant L. monocytogenes strain expressing a recombinant fusion polypeptide comprising an N-terminal listeriolysin (LLO) fragment fused to a fragment of a Her-2 protein, wherein said fragment consists of amino acids 1020-1255 of SEQ ID NO: 40 or amino acids 1020-1255 of SEQ ID NO: 43.

9. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 303-501 of SEQ ID NO: 40.

10. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 303-501 of SEQ ID NO: 43.

11. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 479-655 of SEQ ID NO: 40.

12. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 479-652 of SEQ ID NO: 43.

13. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 1020-1255 of SEQ ID NO: 40.

14. The recombinant form of Listeria of claim 1, wherein said fragment of a Her-2 protein consists of amino acids 1020-1255 of SEQ ID NO: 43.

15. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 303-501 of SEQ ID NO: 40.

16. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 303-501 of SEQ ID NO: 43.

17. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 479-655 of SEQ ID NO: 40.

18. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 479-652 of SEQ ID NO: 43.

19. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 1020-1255 of SEQ ID NO: 40.

20. The recombinant form of Listeria of claim 4, wherein said fragment of a Her-2 protein consists of amino acids 1020-1255 of SEQ ID NO: 43.

21. A method of inducing an anti-Her-2 immune response in a subject, comprising administering to said subject the recombinant form of Listeria of claim 1, thereby inducing an anti-Her-2 immune response in said subject.

22. The method of claim 21, wherein said immune response comprises a CD8+ T cell-mediated response.

23. The method of claim 21, whereby said immune response comprises an immune response to a subdominant epitope of said Her-2 protein.

24. A method of impeding the growth of a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 1, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby impeding the growth of said Her-2-expressing tumor in said subject.

25. The method of claim 24, wherein said immune response comprises a CD8+ T cell-mediated response.

26. The method of claim 24, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

27. A method of shrinking a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 1, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby shrinking said Her-2-expressing tumor in said subject.

28. The method of claim 27, wherein said immune response comprises a CD8+ T cell-mediated response.

29. The method of claim 27, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

30. A method of breaking an immune tolerance of a subject to an antigen-expressing tumor, comprising administering to said subject the recombinant form of Listeria of claim 1, wherein said Her-2 protein has one or more dominant CD8+ T cell epitopes and wherein said fragment does not contain said any of said dominant CD8+ T cell epitopes, whereby said subject mounts an immune response against said antigen-expressing tumor, thereby breaking an immune tolerance of a subject to an antigen-expressing tumor.

31. The method of claim 30, wherein said Her-2 protein is expressed at a detectable level on a non-tumor cell of said subject.

32. The method of claim 30, wherein at least part of said immune response is a CD8+ T cell response directed against an epitope of said Her-2 protein that is not any of said dominant CD8+ T cell epitopes.

33. A method of inducing a CD8+ T cell-mediated immune response in a subject against a subdominant CD8+ T cell epitope of an antigen, comprising administering to said subject the recombinant form of Listeria of claim 1, thereby inducing a CD8+ T cell-mediated immune response against a subdominant CD8+ T cell epitope of an antigen.

34. A method of inducing an anti-Her-2 immune response in a subject, comprising administering to said subject the recombinant form of Listeria of claim 4, thereby inducing an anti-Her-2 immune response in said subject.

35. The method of claim 34, wherein said immune response comprises a CD8+ T cell-mediated response.

36. The method of claim 34, whereby said immune response comprises an immune response to a subdominant epitope of said Her-2 protein.

37. A method of impeding the growth of a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 4, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby impeding the growth of said Her-2-expressing tumor in said subject.

38. The method of claim 37, wherein said immune response comprises a CD8+ T cell-mediated response.

39. The method of claim 37, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

40. A method of shrinking a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 4, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby shrinking said Her-2-expressing tumor in said subject.

41. The method of claim 40, wherein said immune response comprises a CD8+ T cell-mediated response.

42. The method of claim 40, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

43. A method of breaking an immune tolerance of a subject to an antigen-expressing tumor, comprising administering to said subject the recombinant form of Listeria of claim 4, wherein said Her-2 protein has one or more dominant CD8+ T cell epitopes and wherein said fragment does not contain said any of said dominant CD8+ T cell epitopes, whereby said subject mounts an immune response against said antigen-expressing tumor, thereby breaking an immune tolerance of a subject to an antigen-expressing tumor.

44. The method of claim 43, wherein said Her-2 protein is expressed at a detectable level on a non-tumor cell of said subject.

45. The method of claim 43, wherein at least part of said immune response is a CD8+ T cell response directed against an epitope of said Her-2 protein that is not any of said dominant CD8+ T cell epitopes.

46. A method of inducing a CD8+ T cell-mediated immune response in a subject against a subdominant CD8+ T cell epitope of an antigen, comprising administering to said subject the recombinant form of Listeria of claim 4, thereby inducing a CD8+ T cell-mediated immune response against a subdominant CD8+ T cell epitope of an antigen.

47. A method of inducing an anti-Her-2 immune response in a subject, comprising administering to said subject the recombinant form of Listeria of claim 7, thereby inducing an anti-Her-2 immune response in said subject.

48. The method of claim 47, wherein said immune response comprises a CD8+ T cell-mediated response.

49. The method of claim 47, whereby said immune response comprises an immune response to a subdominant epitope of said Her-2 protein.

50. A method of impeding the growth of a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 7, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby impeding the growth of said Her-2-expressing tumor in said subject.

51. The method of claim 50, wherein said immune response comprises a CD8+ T cell-mediated response.

52. The method of claim 50, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

53. A method of shrinking a Her-2-expressing tumor in a subject, comprising administering to said subject the recombinant form of Listeria of claim 7, whereby said subject mounts an immune response against said Her-2-expressing tumor, thereby shrinking said Her-2-expressing tumor in said subject.

54. The method of claim 53, wherein said immune response comprises a CD8+ T cell-mediated response.

55. The method of claim 53, whereby said immune response against said Her-2-expressing tumor comprises an immune response to a subdominant epitope of said Her-2 protein.

56. A method of breaking an immune tolerance of a subject to an antigen-expressing tumor, comprising administering to said subject the recombinant form of Listeria of claim 7, wherein said Her-2 protein has one or more dominant CD8+ T cell epitopes and wherein said fragment does not contain said any of said dominant CD8+ T cell epitopes, whereby said subject mounts an immune response against said antigen-expressing tumor, thereby breaking an immune tolerance of a subject to an antigen-expressing tumor.

57. The method of claim 56, wherein said Her-2 protein is expressed at a detectable level on a non-tumor cell of said subject.

58. The method of claim 56, wherein at least part of said immune response is a CD8+ T cell response directed against an epitope of said Her-2 protein that is not any of said dominant CD8+ T cell epitopes.

59. A method of inducing a CD8+ T cell-mediated immune response in a subject against a subdominant CD8+ T cell epitope of an antigen, comprising administering to said subject the recombinant form of Listeria of claim 7, thereby inducing a CD8+ T cell-mediated immune response against a subdominant CD8+ T cell epitope of an antigen.

60. A recombinant amino acid sequence consisting of the amino acid sequence of SEQ ID NO: 36.

61. A recombinant amino acid sequence consisting of the amino acid sequence of SEQ ID NO: 37.

62. A recombinant amino acid sequence consisting of the amino acid sequence of SEQ ID NO: 39.