Indian Patents
Title of Invention

MODIFIED CEA /B7 VECTORS
Abstract The present invention relates to a nucleic acid encoding a polypeptide and the use of the nucleic acid or polypeptide in preventing and/or treating cancer. In particular, the invention relates to improved vectors for the insertion and expression of foreign genes encoding tumor antigens for use in immunotherapeutic treatment of cancer.
Full Text FORM 2
THE PATENTS ACT, 1970 (39 of 1970)
COMPLETE SPECIFICATION
(See Section 10)
TITLE
"MODIFIED CEA/B7 VECTORS"
APPLICANT
SANOFI PASTEUR, INC.
of Discovery Drive, Swiftwater, PA 18370, USA;
Nationality: a US corporation
and
Therion Biologies, Inc.
of 76 Rodgers Street, Cambridge, MA 02142-1119, USA;
Nationality ; a US corporation
The following specification particularly describes
the nature of this invention and the manner in which
it is to be performed

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MODIFIED CEA /B7 VECTOR FIELD OF THE INVENTION
The present invention relates to a nucleic acid encoding a polypeptide and the use of 5 the nucleic acid or polypeptide in preventing and / or treating cancer. In particular, the invention relates to improved vectors for the insertion and expression of foreign genes encoding tumor antigens for use in immunotherapeutic treatment of cancer.
BACKGROUND OF THE INVENTION
10 There has been tremendous increase in last few years in the development of
vaccines with Tumour-associated antigens (TAAs) due to the great advances in identification of molecules based on the expression profiling on primary tumours and normal cells with the help of several techniques such as high density microarray, SEREX, imminohistochemistry (IHC), RT-PCR, in-situ hybridization (ISH) and laser capture microscopy (Rosenberg,
15 Immunity, 1999; Sgroi et al, 1999, Scheoa et aL, 1995, Offrings et al. 2000), The TAAs are antigens expressed or over-expressed by tumour cells and could be specific to one or several tumours for example CEA antigen is expressed in colorectal, breast and lung cancers. Sgroi et al (1999) identified several genes differentially expressed in invasive and metastatic carcinoma cells with combined use of laser capture microdissection and cDNA microarrays.
20 Several delivery systems like DNA or viruses could be used for therapeutic vaccination against human cancers (Bonnet et al, 2000) and can elicit immune responses and also break immune tolerance against TAAs. Tumour cells can be rendered more immunogenic by inserting transgenes encoding T cell co-stimulatory molecules such as B7.1 or cytokines IFNgamma, IL2, GM-CSF etc. Co-expression of a TAA and a cytokine or a co-stimulatory
25 molecule can develop effective therapeutic vaccine (Hodge et al, 95, Bronte et al, 1995, Chamberlain et al, 1996).
There is a need in the art for reagents and methodologies useful in stimulating an immune response to prevent or treat cancers. The present inventions provides such reagents and methodologies which overcome many of the difficulties encountered by others in
30 attempting to treat cancers such as cancer. In particular, the present invention provides a novel coding sequence for CEA This nucleotide sequence, CEA(6D)-1,2, includes sequencemodifications mat eliminate the expression of truncated forms of CEA as expressed from

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expression vectors. Such a modified sequence is desired by those of sldll in the art to improve expression and immunization protocols for CEA.
SUMMARY OF THE INVENTION
5 The present invention provides an immunogenic target for administration to a patient
to prevent and / or treat cancer. In particular, the immunogenic target is a CEA tumor antigen (“TA”) and / or an angiogenesis-associated antigen (“AA”). In one embodiment, the immungenic target is encoded by a modified CEA nucleotide sequence (CEA(6D)-1,2) that improves CEA expression in transfected cells. In certain embodiments, the TA and / or AA
10 are administered to a patient as a nucleic acid contained within a plasmid or other delivery vector, such as a recombinant virus. The TA and / or AA may also be administered in combination with an immune stimulator, such as a co-stimulatory molecule or adjuvant
BRIEF DESCRIPTION OF THE DRAWINGS
15 Figure 1. A. Illustration of plasmid p3’H6MCEA comprising the CEA coding sequence
with the 6D modification under the control of partial H6 promoter. B. Illustration of plasmid
pSE1544.9 (pUC18-mCEA repeat 1).
Figure 2. Illustration of plasmid pSE16l6.44 (pUCl 8-mCEA-modified repeat 1).
Figure 3, Illustration of plasmid pSE1658.15 (p3’H6MCEA-modified repeat 1).
20 Figure 4. Illustration of plasmid pBSmCEA.
Figure 5. Illustration of plasmid pSE1686.1 (pUCl 8 mCEA modified repeat 2.
Figure 6. Illustration of plasmid pSEl696.1 (pUC18 mCEA modified repeat 2.
Figure 7. Illustration of plasmid p3 'H6modMCEA-lst&2nd repeats.
Figure 8. Illustration of plasmid pNVQH6MCEA(6Dlst&2nd).
25 Figure 9A-D. Comparison of nucleotide sequence of CAP(6D) and CAP(6D)-1,2.
Differences between the sequences are underlined.
Figure 10. PCR analysis to confirm the presence of CAP(6D)-l,2 in NYVAC DNA.
Figure 11. Immunoblot illustrating the lack of truncated CEA in cells expressing CAP(6D>
1,2.
30 Figure 12. Human B7,1 gene in an ALVAC C6 donor plasmid under the control of the H6 promoter.
Figure 13. CAP(6D)-1,2 CEA DNA sequence in an ALVAC C3 donor plasmid under the
control of the H6 promoter.

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DETAILED DESCRIPTION
The present invention provides reagents and methodologies useful for treating and / or preventing cancer. All references cited within this application are incorporated by reference.
In one embodiment, the present invention relates to the induction or enhancement of 5 an immune response against one or more tumor antigens (“TA”) to prevent and / or treat cancer. In certain embodiments, one or more TAs may be combined. In preferred embodiments, the immune response results from expression of a TA in a host cell following administration of a nucleic acid vector encoding the tumor antigen or the tumor antigen itself in the form of a peptide or polypeptide, for example.
10 As used herein, an “antigen” is a molecule (such as a polypeptide) or a portion thereof
that produces an immune response in a host to whom the antigen has been administered, The immune response may include the production of antibodies that bind to at least one epitope of the antigen and / or the generation of a cellular immune response against cells expressing an epitope of the antigen. The response may be an enhancement of a current immune response is by, for example, causing increased antibody production, production of antibodies with increased affinity for the antigen, or an increased cellular response (i.e., increased T cells). An antigen that produces an immune response may alternatively be referred to as being immunogenic or as an immunogen. In describing the present invention, a TA may be referred to as an “immunogenic target”.
20 TA includes both tumor-associated antigens (TAAs) and tumor-specific antigens
(TSAs), where a cancerous cell is the source of the antigen. A TAA is an antigen that is expressed on the surface of a tumor cell in higher amounts than is observed on normal cells or an antigen that is expressed on normal cells during fetal development A TSA is an antigen that is unique to tumor cells and is not expressed on normal cells. TA further
25 includes TAAs or TSAs, antigenic fragments thereof; and modified versions that retain their antigenicity.
TAs are typically classified into five categories according to their expression pattern, function, or genetic origin: cancer-testis (CT) antigens (i.e., MAGE, NY-ESO-l); melanocyte differentiation antigens (i.e., Melan A/MART-1, tyrosinase, gp100); mutational antigens (i.e„
MUM-1, p53, CDK-4); overexpressed ‘self’ antigens (i.e., HER.-2/neu, p53); and, viral antigens (i.e., HPV, EBV). For the purposes of practicing the present invention, a suitable TA is any TA that induces or enhances an anti-tumor immune response in a host to whom the TA has been administered. Suitable TAs include, for example, gpl00 (Cox et al., Science,

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264:716-719 (1994)), MART-1/Melan A (Kawakami et al, / Exp. Me., 180:347-352
(1994)), gp75 (TRP-1) (Wang et al, /. Exp, Med., 186:1131-1140 (1996)), tyrosinase (Wolfel-
et al., Eur. J. Immunol., 24:759-764 (1994); WO 200175117; WO 200175016; WO
200175007), NY-ESO-I (WO 98/14464; WO 99/18206), melanoma proteoglycan (Hettstrom
5 et al., J. Immunol, 130:1467-1472 (1983)), MAGE family antigens (Le., MAGE-1,
2,3,4,6,12, 51; Van der Bruggen et al, Science, 254:1643-1647 (1991); U.S. Pat, Nos.
6,235,525; CN 1319611), BAGE family antigens (Boel et al., Immunity, 2:167-175 (1995)),
GAGE family antigens (i.e., GAGE-1,2; Van den Eynde et al, J. Exp. Med., 182:689-698
(1995); U.S. Pat. No. 6,013,765), RAGE family antigens (Le., RAGE-1; Gangler et at,
10 Immunogenetics, 44:323-330 (1996); U.S. Pat. No. 5,939,526), N-acetylghioosammyltransferase-V (Guilloux et at, J. Exp. Med., 183:1173-1183 (1996)), pl5 (Robbins et al., J. Immunol. 154:5944-5950 (1995)), B-catenin (Robbins et al„ J. Exp. Med., 183:1185-1192 (1996)), MUM-1 (Coulie et al., Proc. Natl. Acad. Sci. USA, 92:7976-7980 (1995)), cyclin dependent kinase-4 (CDK4) (Wolfel et al., Science, 269:1281-1284 (1995)),
15 p21-ras (Fossum et at., Int. J. Cancer, 56:40-45 (1994)), BCBL-abl (Boccbia et aL, Blood, 85:2680-2684 (1995)), p53 (Theobald et al., Proc, Natl, Acad Sci. USA, 92:11993-11997 (1995)), pl85 HER2/neu (erb-Bl; Fiak et al., J. Exp. Med, 181:2109-2117 (1995)), epidermal growth factor receptor (EGFR) (Harris et al, Breast Cancer Res. Treat, 29:1-2 (1994)), carcinoembryonic antigens (CEA) (Kwong et al., /. Natl. Cancer Inst., 85;982-990
20 (1995) U.S. Pat. Nos. 5,756,103; 5,274,087; 5,571,710; 6,071,716; 5,698,530; 6,045,802; EP 263933; EP 346710; and, EP 784483); carcinoma-associated mutated mucins (i.e., MUC-1 gene products; Jerome et al., J. Immunol., 151:1654-1662 (1993)); EB,NA gene products of EBV (i.e., EBNA-1; Rickinson et al., Cancer Surveys, 13:53-80 (1992)); E7, E6 proteins of human papillomavirus (Ressing et aL, J. Immunol, 154:5934-5943 (1995)); prostate specific
25 antigen (PSA; Xue et al., The Prostate, 30:73-78 (1997)); prostate specific membrane antigen (PSMA; Israeli, et al, Cancer Res., 54:1807-1811 (1994)); idiotypic epitopes or antigens, for example, immunoglobulin idiorypes or T cell receptor idiorypes (Chen et al, J. Immunol., 153:4775-4787 (1994)); KSA (U.S. Patent No. 5,348,887), kinesin 2 (Diete, et al. Bioohem Biophys Res Commun 2000 Sep 7;275(3):731-8), HIP-55, TGFβ-1 anti-apoptotic
30 factor (Toomey, et al. Br J Biomed Sci 2001;58(3):177-83), tumor protein D52 (Bryne LA., et al., Genomics, 35:523-532 (1996)), HIFT, NY-BR-1 (WO 01/47959), NY-BR-62, NV-BR-75, NY-BR-85, NY-BR-87, NY-BR-96 Scanlan, M. Serologic and Bioinformatic Approaches to the Identification of Human Tumor Antigens, in Cancer Vaccines 2000,

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Cancer Research Institute, New York, NY), including “wild-type” (i.e., normally encoded by the genome, naturally-occurring), modified, and mutated versions as well as other fragments
and derivatives thereof. Any of these TAs may be utilized alone or in combination with one
another in a co-immunization protocol.
5 In certain cases, it may be beneficial to co-immunize patients with both TA and other antigens, such as angiogenesis-associated antigens (“AA”). An AA is an immunogenic molecule (i.e„ peptide, polypeptide) associated with cells involved in the induction and / or continued development of blood vessels. For example, an AA may be expressed on an endothelial cell (“EC”), which is a primary structural component of blood vessels. Where me
10 cancer is cancer, it is preferred that that the AA be found within or near blood vessels that supply a tumor. Immunization of a patient against an AA preferably results in an anti-AA immune response whereby angiogenic processes that occur near or within tumors are prevented and / or inhibited.
Exemplary AAs include, for example, vascular endothelial growth factor (i.e., VEGF;
15 Bemardini, et al. J. Urol, 2001,166X4): 1275-9; Stames, et aL J. Thorac Cardiovasc Surg., 2001, 122(3): 518-23), the VEGF receptor (i.e., VEGF-R, flk-1/KDR; Stames, et al. J. Thorac. Cardiovasc. Surg., 2001,122(3): 518-23), EPH receptois (i.e., EPHA2; Gerety, et al. 1999, Cell, 4:403-414), epidermal growth factor receptor (Le., EGFR; Ciardeillo, et al Clin. Cancer Res., 2001, 7(10): 2958-70), basic fibroblast growth meter (i.e, bFGF; Davidson, et
20 al. Clin. Exp. Metastasis 2000,18(6): 501-7; Poon, et al. Am J. Surg., 2001,182(3):298-304), platelet-derived cell growth factor (Le., PDGF-B), platelet-derived endothelial cell growth factor (PD-ECGF; Hong, et al, J, Mol. Med., 2001, 8(2):141-8), transforming growth factors (Le., TGF-a; Hong, et al. J. Mol. Med., 2001, 8(2):141-8), endoghn (Balza, et al, Int. J. Cancer, 2001, 94: 579-585), Id proteins (Benezra, R. Trends Cardiovasc. Med., 2001,
25 11(6);237-41), proteases such as uPA, uPAR, and matrix metalloproteinases (MMP-2, MMP-9; Djonov, et al. J. Pathol., 2001,195(2): 147-55), nitric oxide synthase (Am. J. Ophthalmol., 2001, l32(4):551-6), aminopeptidase (Rouslhati, E. Nature Cancer, 2: 84-90, 2002), thrombospondins (i.e., TSP-1, TSP-2; Alvarez, et al. Gynecol. Oncol., 2001, 82(2)273-8; Selri, et al, Int. J. Oncol., 2001, 19(2):305-10), k-ras (Zhang, et al Cancer Res., 2001,
30 61(16):6050-4), Wnt (Zhang, et al. Cancer Res., 2001, 61(16):6050-4), cychn-dependent kinases (CDKs; Drug Resist Updat. 2000, 3(2):83-88), microtubules (Timar, et al 2001. Path. Oncol Res., 7(2): 85-94), heat shock proteins: (i.e., HSP90 (Timar, supra)), heparin-binding factors (i.e., heparinase; Gohji, et al. Int. J. Cancer, 2001, 95(5):295-30l), synthases

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(i.e., ATP synthase, thymidilate synthase), collagen receptors, integrins (ie., αΰβ3, αΰβ5, α1β2, α2β1, α5β1), the surface proteolglycan NG2, AAC2-1 (SEQ ID NO.:l), or AAC2-2 (SEQ ID NQ.:2), among others, including “wild-type” (i.e, normally encoded by the genome, nahnnlly-occurrmg), modified, mutated versions as well as other fragments and derivatives thereof. Any of these targets may be suitable in practicing the present invention, either alone or in combination with one another or with other agents.
In certain embodiments, a nucleic acid molecule encoding an immunogenic target is utilized- The nucleic acid molecule may comprise or consist of a nucleotide sequence encoding one or more immunogenic targets, or fragments or derivatives thereof, such as thatcontained in a DNA insert in an ATCC Deposit. The term “nucleic acid sequence” or “nucleic acid molecule” refers to a DNA or RNA sequence. The term encompasses molecules formed from any of the known base analogs of DNA and RNA such, as, but not. limited to 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinyl-cytosine, pseudoisocytosine, 5-(carboxyhydroxyhnethyl) uracil, 5-fluorouracil, 5-broraouracil, 5- caiboxvmethylaminomethyl-2-thiouracil, 5-carboxy-memylaminomethyluracil,dihydrouracil, inosine, N6-iso-pentenylademne, 1-methyladenine, l-methilpseudouracil, 1-methylguanine, l-methylinosine, 2,2-dimethyl-guamne, 2-methyladenme, 2-raethylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenuie, 7-methylguanine, 5-methylaminomethyluracil, 5-me&oxyammo-memyl-2-miouracil, beta-D-mannosylqucosine,5’ -mefhoxycarbonyl-methyluracil, 5-methoxyuracil, 2-memylmio-N6-isopentenyladenme, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudonraciL, queosine, 2-thiocytosine, 5-methyI-2-miouracil, 2-thiouracil, 4-thiouiacil, 5-methyluracil, N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine, among others.
An isolated nucleic acid molecule is one that: (1) is separated from at least about 50 percent of proteins, lipids, carbohydrates, or other materials with which it is naturally found when total nucleic acid is isolated from the source cells; (2) is not be linked to all or a portion of a polynucleotide to which me nucleic acid molecule is linked in nature; (3) is operably linked to a polynucleotide which it is not linked to in nature; and / or, (4) does not occur in nature as part of a larger polynucleotide sequence. Preferably, the isolated nucleic acid molecule of the present invention is substantially tree from any other contaminating nucleic acid molecule(s) or other contaminants that we found in its natural environment that would interfere with its use in polypeptide production of its therapeutic, diagnostic, prophylactic or

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research use. As used herein, the term “Naturally occurring” or “native” or “naturally found” when used in connection with biological materials such as nucleic acid molecules, polypeptides, host cells, and the like, refers to materials which are found in nature and are not manipulated by man. Similarly, “non-naturally occurring” or “non-native” as used herein
5 refers to a material that is not found in nature or that has been structurally modified or synthesized by man.
The identity of two or more nucleic acid or polypeptide molecules is determined by comparing the sequences. As known in the art, “identity” means the degree of sequence relatedness between nucleic acid molecules or polypeptides as deterarined by the match
10 between the units making up the molecules (i.e., nucleotides or amino acid residues). Identity measures the percent of identical matches between the smaller of two or more sequences with gap alignments (if any) addressed by a particular mathematical model or computer program (i.e., an algorithm). Identity between nucleic acid sequences may also be determined by the ability of the related sequence to hybridize to the nucleic acid sequence or isolated nucleic
I5 acid molecule. In defining such sequences, the term “highly stringent conditions” and “moderately stringent conditions” refer to procedures that permit hybridization of nucleic acid strands whose sequences are complementary, and to exclude hybridization of significantly mismatched nucleic acids. Examples of “highly stringent conditions” for hybridization and washing are 0.015 M sodium chloride, 0.0015 M sodium citrate at 65-68°C
20 or 0.015 M sodium chloride, 0.0015 M sodium citrate, and 50% formamide at 42°C. (see, for example, Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory, 1989); Anderson el al., Nucleic Add Hybridisation: A Practical Approach Ch. 4 (IRL Press Limited)). The term “moderately stringent conditions” refers to conditions under which a DNA duplex with a greater degree of base pair
25 mismatching than could occur under “highly stringent conditions” is able to form. Exemplary moderately stringent conditions are 0.015 M sodium chloride, 0.0015 M sodium citrate at 50-650C or 0.015 M sodium chloride, 0.0015 M sodium citrate, and 20% formamide at 37-50°C. By way of example, moderately stringent conditions of 50°e in 0.015 M sodium ion will allow about a 21% mismatch. During hybridization, other agents may be included in
30 the hybridization and washing buffers for the purpose of reducing non-specific and/or background hybridization, Examples are 0.1% bovine serum albumin, 0.1% polyvinylpyrrolidone, 0.1% sodium pyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO4 (SDS), ficoll, Denhardt’s solution, sonicated salmon sperm DNA (or another non-complementary

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research use. As used herein, the term “naturally occurring” or “native” or “naturally found” when used in connection with biological materials such as nucleic acid molecules, polypeptides, host cells, and the like, refers to materials which are found in nature and are not manipulated by man. Similarly, “non-naturally occurring” or “non-native” as used herein
5 refers to a material that is not found in nature or that has been structurally modified or synthesized by man.
The identity of two or more nucleic acid or polypeptide molecules is determined by comparing the sequences. As known in foe art, “identity” means the degree of sequence relatedness between nucleic acid molecules or polypeptides as determined by the match
10 between the units making up the molecules (i.e., nucleotides or amino acid residues). Identity measures the percent of identical matches between the smaller of two or more sequences with gap alignments (if any) addressed by a particular mathematical model or computer program (i.e., an algorithm). Identity between nucleic acid sequences may also be determined by the ability of the related sequence to hybridize to the nucleic acid sequence or isolated nucleic
15 acid molecule. In defining such sequences, the term “highly stringent conditions” and “moderately stringent conditions” refer to procedures that permit hybridization of nucleic acid strands whose sequences are complementary, and to exclude hybridization of significantly mismatched nucleic acids. Examples of “highly stringent conditions” for hybridization and washing are 0,015 M sodium chloride, 0.0015 M sodium citrate at 65-68°C
20 or 0.015 M sodium chloride, 0.0015 M sodium citrate, and 50% formamide at 420C. (see, for example, Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory, 1989); Anderson et al, Nucleic Add Hybridisation: A Practical Approach Ch, 4 QBL Press Limited)), The term “moderately stringent conditions” refers to conditions under which a DNA duplex with a greater degree of base pair
25 mismatching than could occur under “highly stringent conditions” is able to form. Exemplary moderately stringent conditions are 0.015 M sodium chloride, 0,0015 M sodium citrate at 50-65°C or 0.015 M sodium chloride, 0.0015 M sodium citrate, and 20% formamide at 37-50°C. By way of example, moderately stringent conditions of 500C in 0.015 M sodium ion will allow about a 21% mismatch. During hybridization, other agents may be included in
30 the hybridization and washing buffers for the purpose of reducing non-specific and/or background hybridization. Examples are 0.1% bovine serum albumin, 0.1% polyvinylpyrrolidone, 0.1% sodium pyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO4 (SDS), ficoll, Denhardt’s solution, sonicated salmon sperm DNA (or another non-complementary

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DNA), and dextran sulfate, although other suitable agents can also be used. The concentration and types of these additives can be changed without substantially affecting the stringency of the hybridization conditions. Hybridization experiments are usually earned out at pH 6,8-7.4; however, at typical ionic strength conditions, the rate of hybridization is nearly
independent of pH.
In preferred embodiments of the present invention, vectors are used to transfer a nucleic acid sequence encoding a polypeptide to a cell. A vector is any molecule used to transfer a nucleic acid sequence to a host cell. In certain cases, an expression vector is utilized. An expression vector is a nucleic acid molecule that is suitable for transformation of a host cell and contains nucleic acid sequences that direct and / or control the expression of the transferred nucleic acid sequences. Expression includes, but is not limited to, processes such as. transcription, translation, and splicing, if introns are present Expression vectors typically comprise one or more flanking sequences operably linked to a heterologous nucleic acid sequence encoding a polypeptide, Flanking sequences may be homologous (i.e., from the same species and / or strain as me host cell), heterologous (ie., from a species other than the host cell species or strain), hybrid (i.e., a combination of flanking sequences from more than one source), or synthetic, for example.
A flanking sequence is preferably capable of effecting me replication, transcription and / or translation of the coding sequence and is operably linked to a coding sequence. As used herein, the term operably linked refers to a linkage of polynucleotide elements in a functional relationship. For instance, a promoter or enhancer is Operably linked to a coding sequence if it affects the transcription of the coding sequence. However, a flanking sequence need not necessarily be contiguous with the coding sequence, so long as it functions correctly. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the coding sequence and the promoter sequence may still be considered operably linked to the coding sequence. Similarly, an enhancer sequence may be located upstream or downstream from the coding sequence and affect transcription of the sequence.
In certain embodiments, it is preferred that the flanking sequence is a trascriptionalregulatory region that drives high-level gene expression in the target cell. The transcriptional regulatory region may comprise, for example, a promoter, enhancer, silencer, repressor element, or combinations thereof, The transcriptional regulatory region may be either constitutive, tissue-specific, cell-type specifi(i.e., the region is drives higher levels of

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transcription in a one type of tissue or cell as compared to another), or regulatable (i.e., responsive to interaction with a compound such as tetracycline). The source of a transcriptional regulatory region may be any prokaiyotic or eukaryotic organism, any vertebrate or invertebrate organism, or any plant, provided that the flanking sequence functions in a cell by causing transcription of a nucleic add within that cell. A wide variety of transcriptional regulatory regions may be utilized in practicing the present invention.
Suitable transcriptional regulatory regions include the CMV promoter (i.e., the CMV-immediate early promoter); promoters from eukaryotic genes (i.e., me estogen-inducible chicken ovalbumin gene, the interferon genes, the gluco-corticoid-inducible tyrosine aminotransferase gene, and the thymidine kinase gene); and the major early and late adenovirus gene promoters; the SV40 early promoter region (Bemoist and Chambon, 1981, Nature 290:304-10); the promoter contained in the 3’ long terminal repeat (LTR) of Rous sarcoma virus (RSV) (Yamamoto, et al, 1980, Celt 22:787-97); the herpes simplex virus thymidine kinase (HSV-TK) promoter (Wagner et al, 1981, Proc Natl Acad. Sci. U.SA.
78:1444-45); the regulatory sequences of the metallothionine gene (Brinster et al, 1982, Nature 296:39-42); prokaryotic expression vectors such as the beta-lactamase promoter (Villa-Kamaroff et al, 1978, Proc. Natl Acad. Sci. U.SJL, 75:3727-31); or the tac promoter (DeBoer et al., 1983, Proc Natl Acad, Sci. U.SA., 80:21-25). Tissue- and / or cell-type specific transcriptional control regions include, for example, the elastase I gene control region which is active in pancreatic acinar cells (Swift et al., 1984, Cell 38:639-46; Ornitz et al, 1986, Cold Spring Harbor Symp. Quant. Biol. 50:399-409 (1986); MacDonald, 1987, Hepatology 7:425-515); the insulin gene control region which is active in pancreatic beta cells (Hanaham, 1985, Nature 315:115-22); the immunoglobulin gene control region which is active in lymphoid cells (Grosschedl et al, 1984, Cell 38:647-58; Adames et al, 1985,
Nature 318:533-38; Alexander et al, 1987, Mol Cell Biol, 7:1436-44); me mouse mammary tumor virus control region in testicular, breast, lymphoid and mast cells (Leder et al, 1986, Cell 45:485-95); the albumin gene control region in liver (Pinkert et al, 1987, Genes andDevel 1:268-76); the alpha-feto-protein gene control region in liver (Krumlauf et al, 1985, Mol Cell Biol, 5:1639-48; Hammer et al, 1987, Science 235:53-58); the alpha 1-antitrypsin gene control region in liver (Kelsey et al, 1987, Genes and Devel 1:161-71); the bcta-globin gene control region in myeloid cells (Mogram et al, 1985, Nature 315:338-40; Kollias et al, 1986, Cell 46:89-94); the mvelin basic protein gene control region in oligodendrocyte cells in the brain (Readhead et al., 1387, Cell 48:703-12); the myosin light

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chain-2 gene control region in skeletal muscle (Sani, 1985, Nature 314:283-86); the gonadotropic releasing hormone gene control region in the hypothalamus (Mason et al, 1986, Science 234:1372-78), and the tyrosinase promoter in melanoma ceUs (Hart, I. Semin Oncol 1996 Feb;23(l):154-8; Siders, et al. Cancer Gene Ther 1998 Sep-Oct;5(5):281-91)among others. Other suitable promoters are known in the art.
As described above, enhancers may also be suitable flanking sequences. Enhancers are cis-acting elements of DNA, usually about 10-300 bp in length, that act on the promoter to increase transcription. Enhancers are typically orientation- and position-independent, having been identified both 5’ and 3’ to controlled coding sequences. Several enhancer
sequences available from mammalian genes are known (i.e., globin, elastase, albumin, alpha-feto-protein and insulin). Similarly, the SV40 enhancer, the cytomegalovirus early promoter enhancer, the polyoma enhancer, and adenovirus enhancers are useful with eukaryotic promoter sequences. While an enhancer may be spliced into the vector at a position 5’or 3’ to nucleic acid coding sequence, it is typically located at a site 5’ from the promoter. Othersuitable enhancers are known in the art, and would be applicable to the present invention.
While preparing reagents of the present invention, cells may need to be transfected or transformed, Transfection refers to the uptake of foreign or exogenous DNA by a cell, and a cell has been transfected when the exogenous DNA has been introduced inside the cell membrane. A number of transfection techniques are well known in the art (i.e., Graham et al, 1973, Virology 52:456; Sambrook et al., Molecular Cloning. A Laboratory Manual (Cold Spring Harbor Laboratories, 1989); Davis et alt Basic Methods in Molecular Biology (Elsevier, 1986); and Chu et al, 1981, Gene 13:197). Such techniques can be used to introduce one or more exogenous DNA moieties into suitable host cells.
In certain embodiments, it is preferred that transfection of a cell results in
transformation of that cell. A cell is transformed when there is a change in a characteristic of the cell, being transformed when it has been modified to contain a new nucleic acid, Following transfection, the transfected nucleic acid may recombine with that of the cell by physically integrating into a chromosome of the cell, may be maintained transiently as an episomal element without being replicated, or may replicate independently as a plasmid. A
cell is stably transformed when the nucleic acid is replicated with the division of the cell.
The present invention further provides isolated immunogenic targets in polypeptide form. A polypeptide is considered isolated where it: (1) has been separated from at least about 50 percent of polynucleotides, lipids,carbohydrates, or other materials with which it is

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naturally found when isolated from the source cell; (2) is not linked (by covalent or noncovalent interaction) to all or a portion of a polypeptide to which the “isolated polypeptide” is linked in nature; (3) is operably linked (by covalent or noncovalent interaction) to a polypeptide with which it is not linked m nature; or, (4) does not occur m nature. Preferably, the isolated polypeptide is substantially free from- any other contaminating polypeptides or other contaminants that are found in its natural environment that would interfere with its therapeutic, diagnostic, prophylactic or research use.
Immunogenic target polypeptides may be mature polypeptides, as defined herein, and may or may not have an amino terminal methionine residue, depending on the method by which they are prepared. Further contemplated are related polypeptides such as, for example,fragments, variants (i.e., allelic, splice), orthologs, homologies, and derivatives, for example, mat possess at least one characteristic or activity (i.e., activity, antigenicity) of the immunogenic target Also related are peptides, which refers to a series of contiguous amino acid residues having a sequence corresponding to at least a portion of the polypeptide from which its sequence is derived. In preferred embodiments, die peptide comprises about 5-10 amino acids, 10-15 amino acids, 15-20 amino acids, 20-30 ammo acids, or 30-50 amino acids. In a more preferred embodiment, a peptide comprises 9-12 amino acids, suitable for presentation upon Class IMHC molecules, for example.
A fragment of a nucleic acid or polypeptide comprises a truncation of the sequence
(i.e., nucleic acid or polypeptide) at the amino terminus (with or without a leader sequence) and / or the caiboxy terminus, Fragments may also include variants (i.e., allelic, splice), orthologs, homologues, and other variants having one or more amino acid additions or substitutions or internal deletions as compared to the parental sequence. In preferred embodiments, truncations and/or deletions comprise about 10 amino acids, 20 amino acids, 30 amino acids, 40 amino acids, 50 amino acids, or more. The polypeptide fragments so produced will comprise about 10 amino acids, 25 amino acids, 30 amino acids, 40 amino acids, 50 amino acids, 60 ammo acids, 70 amino acids, or more. Such polypeptide fragments may optionally comprise an amino terminal methionine residue. It will be appreciated that such fragments can be used, for example, to generate antibodies or cellular immune responses
to immunogenic target polypeptides.
A variant is a sequence having one or more sequence substitutions, deletions, and/or additions as compared to the subject sequence. Variants may be naturally occurring or artificially constructed. Such variants may be prepared from the corresponding nucleic acid

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molecules, In preferred embodiments, the variants have from 1 to 3, or from 1 to 5, or fiom 1 to 10, or from 1 to 15, or from 1 to 20, or from 1 to 25, or from 1 to 30, or from 1 to 40, or from 1 to 50, or more man 50 amino acid substitutions, insertions, additions and/or deletions.
An allelic variant is one of several possible naturally-occurring alternate forms of a gene occupying a given locus on a chromosome, of an organism or a population of organisms. A splice variant is a polypeptide generated from one of several RNA transcript resulting from splicing of a primary transcript. An ortholog is a similar nucleic acid or polypeptide sequence from another species, For example, me mouse and human versions of an immunogenic target polypeptide may be considered orthologs of each other. A derivative of a sequence is one that is derived from a parental sequence those sequences having substitutions, additions, deletions, or chemically modified variants. Variants may also include fusion proteins, which refers to the fusion of one or more first sequences (such as a peptide) at the amino or carboxy terminus of at least one other sequence (such as a heterologous peptide).
“Similarity” is a concept related to identity, except that similarity refers to a measure
of relatedness which includes both identical matches and conservative substitution matches. If two polypeptide sequences have, for example, 10/20 identical amino acids, and the remainder are all non-conservative substitutions, men the percent identity and similarity would both be 50%. If in the same example, there are five more positions where there areconservative substitutions, then the percent identity remains 50%, but me percent similarity would be 75% (15/20). Therefore, in cases where there are conservative substitutions, the percent similarity between two polypeptides will be higher man the percent identity between those two polypeptides. '
Substitutions may be conservative, or non-conservative, or any combination thereof.
Conservative amino acid modifications to the sequence of a polypeptide (and the corresponding modifications to the encoding nucleotides) may produce polypeptides having functional and chemical characteristics similar to those of a parental polypeptide. For example, a “conservative amino acid substitution” may involve a substitution of a native amino acid residue with a non-native residue such that mere is little or no effect on the size, polarity, charge, hydrophobicity, or hydrophilicity of the amino acid residue at that position and, in particlar, does not result in decreased immunogenicity. Suitable conservative amino acid substitutions are shown in Table I.

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Table I
Original Residues Exemplary Substitutions Preferred Substitutions
Ala Val Lai, Ile Val
Arg Lys, Gin, Asn Lys
Asn Gin Gin
Asp Glu Glu
Cys Ser, Ala Ser
G1n Asn Asn
Glu Asp Asp
Gly Pro, Ala Ala
His Asn, Gin, Lys, Arg Arg
Ile Leu, Val, Met, Ala, Phe, Norleucine Leu
Leu Norleucine, lie, Val, Met, Ala, Phe He
Lys Arg, 1,4 Diamino hutyric Acid, Gln, Asn Arg
Met Leu, Phe, lie Leu
Phe Leu, VaL He, Ala, Tyr Leu
Pro Ala Gly
Ser Thr, Ala, Cys Thr
Thr Ser Ser
Trp Tyr, Phe Tyr
Tyr Trp, Phe, Thr, Ser Phe
Val Ile, Met, Leu, Phe, Ala, Norleucine Leu
























A skilled artisan will be able to determine suitable variants of polypeptide using well-known techniques. For identifying suitable areas of the molecule that may be changed without destroying biological activity (i.e., MHC binding, immunogenicity), one skilled in the art may target areas not believed to be important for that activity. For example, when similar polypeptides with similar activities from the same species or from other species are known, one skilled in the art may compare the amino acid sequence of a polypeptide to such similar polypeptides. By performing such analyses, one can identify residues and portions of the molecules that are conserved among similar polypeptides. It will be appreciated that changes in areas of the molecule that are not conserved relative to such similar polypeptides would be less likely to adversely affect the biological activity and/or structure of a polypeptide. Similarly, the residues required for binding to MHC are known, and may be modified to improve binding. However, modifications resulting in decreased binding to MHC will not be appropriate in most situations. One skilled in the art would also know that, even in relatively conserved regions, one may substitute chemically similar amino acids for the naturally occurring residues while retaining activity. Therefore, even areas that may be important for biological activity or for structure maybe subject to conservative amino acid

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substitutions without destroying the biological activity or without adversely affecting me polypeptide structure.
Other preferred polypeptide variants include glycosylation variants wherein the number and/or type of glycosylation sites have been altered compared to the subject amino acid sequence. In one embodiment, polypeptide variants comprise a greater or a lesser number of N-linked glycosylation sites than the subject amino acid sequence. An N-linked glycosylation site is characterized by rae sequence Asn-X-Ser or Asn-X-Thr, wherein the amino acid residue designated as X may be any amino acid residue except proline. The substitution of amino acid residues to create this sequence provides a potential new site for me addition of an N-linked carbohydrate chain. Alternatively, substitutions that eliminate this sequence will remove an existing N-linked carbohydrate chain. Also provided is a rearrangement of N-linked carbohydrate chains wherein one or more N-linked glycosylation sites (typically those that are naturally occurring) are eliminated and one or more new N-linked sites are created. To affect O-linked glycosylation of a polypeptide, one would modify serine and / or threonine residues.
Additional preferred variants include cysteine variants, wherein one or more cysteine residues are deleted or substituted with another amino acid (e.g., serine) as compared to the subject amino acid sequence set. Cysteine variants arc useful when polypeptides must be refolded into a biologically active conformation such as after the isolation of insoluble inclusion bodies. Cysteine variants generally have fewer cysteine residues man the native protein, and typically have an even number to minimize interactions resulting from unpaired cysteines.
In other embodiments, the isolated polypeptides of the current invention include fusion polypeptide segments that assist in purification of the polypeptides. Fusions can be made either at the amino terminus or at the carboxy terminus of the subject polypeptide variant thereof. Fusions may be direct with no linker or adapter molecule or may be through a linker or adapter molecule, A linker or adapter molecule may be one or more amino add residues, typically from about 20 to about SO amino acid residues. A linker or adapter molecule may also be designed with a cleavage site for a DNA restriction endonuclease or for a protease to allow for the separation of the fused moieties. It will be appreciated that once constructed, the fusion polypeptides can be derivatized according to the methods described herein. Suitable fusion segments include, among others, metal binding domains (e.g., a poly-histidine segment), immunoglobulin binding domains (i.e., Protein A, Protein G, T cell,

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B cell, Fc receptor, or complement protein antibody-binding domains), sugar binding domains (e.g., a maltose binding domain), and/or a “tag”domain (i.e., at least a portion of a-galactosidase, a strep tag peptide, a T7 tag peptide, a FLAG peptide, or other domains that can be purified using compounds that bind to the domain, such as monoclonal antibodies).This tag is typically fused-to the polypeptide upon expression of the polypeptide, and can serve as a means for affinity purification of the sequence of interest polypeptide from the host cell. Affinity purification can be accomplished, for example, by column chromatography using antibodies against the tag as an affinity matrix. Optionally, the tag can subsequently be removed from the purified sequence of interest polypeptide by various means such as using
certain peptidases for cleavage. As described below, fusions may also be made between a TA and a co-stimulatory components such as the chemokines CXC10 (P-10), CCL7 (MCP-3), or CCL5 (RANTES), for example.
A fusion motif may enhance transport of an immunogenic target to an MHC processing compartment, such as the endoplasmic reticulum, These sequences, referred to as traduction or transcytosis sequences, include sequences derived from HIV tat (see Kim et al. 1997 J- Immunol. 159:1666), Drosophito antennapedia (see Schutze-Redelmeier et al. 1996 J. Immunol. 157:650), or human period-1 protein (hPERl; in particular, SRRHHCRSKAKRSRHH).
In addition, the polypeptide or variant thereof may be fused to a homologous
polypeptide to form a homodimer or to a heterologous polypeptide to form a heterodimer.Heterologous peptides and polypeptides include, but are not limited to: an epitope to allowfor the detection and/of isolation of a fusion polypeptide; a transmembrane1 receptor protein. or a portion thereof, such as an extracellular domain or a transmembrane and intracellulardomain; a ligand or a portion thereof which binds to a transmembrane receptor protein; an enzyme or portion thereof which is catalytically active; a polypeptide or peptide which promotes oligomerization, such as a leucine zipper domain; a polypeptide or peptide which increases stability, such as an immunoglobulin constant region; and a polypeptide which has a therapeutic activity different from the polypeptide or variant thereof.
In certain embodiments, it may be advantageous to combine a nucleic acid sequence
30 encoding an immunogenic target, polypeptide, or derivative thereof with one or more co-stimulatory components) such as cell surface proteins, cytokines or chemokines in a composition of the present invention. The co-stimulatory component may be included in the composition as a polypeptide or as a nucleic acid encoding the polypeptide, for example.

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Suitable co-stimulatory molecules include, for instance, polypeptides that bind members of the CD28 family (i.e., CD28, ICOS; Hutloff, et al. Nature 1999, 397:263-265; teach, et al. J Exp Med 1994, 180: 2049-2058) such as the CD28 binding polypeptides B7.1 (CD80; Schwartz, 1992; Chen et al, 1992; Ellis, et al. J, Immunol, 156(8): 2700-9) and &12 (CD86; Ellis, et al. J. Immunol, 156(8): 2700-9); polypeptides which bind members of the integrin family (i.e., LFA-1 (CDlla / CD18); Sedwick, et al. J Immunol 1999, 162: 1367-1375; Wtilfmg, et al. Science 1998, 282: 2266-2269; Lub, et al. Immunol Today 1995,16: 479-483) including members of the ICAM family (i.e., ICAM-1, -2 or -3); polypeptides which bind CD2 family members (i.e., CD2, signalling lymphocyte activation molecule (CDwl50or "SLAM"; Aversa, et al. J Immunol 1997, 158: 4036-4044)) such as CD58 (LFA-3; CD2 ligand; Davis, et al. Immunol Today 1996, 17: 177-187) or SLAM ligands (Sayos; et al Nature 1998,395:462-469); polypeptides which bind heat stable antigen (HSA or CD24; Zhou, ct al. Eur J Immunol 1997, 27: 2524-2528); polypeptides which bind to members of the TNF receptor (TNFR) family (i.e., 4-1BB (CD137; Vinay, et al. Semin Immunol 1998, 10: 481-489), OX40 (CD134; Weinberg, et al, Semin Immunol 1998, 10: 471-480; Higgins, et al. J Immunol 1999, 162: 486-493), and CD27 (Lens, et al. Semin Immunol 1998, 10: 491-499)) such as 4-1BBL (4-1BB Hgand;. Vinay, et al. Semm Immunol 1998, 10: 481-48; DeBenedette, et al. J Immunol 1997,158: 551-559), TNFR associated fector-1 (TRAF-1; 4- IBB ligand; Saoulli, et al. J Exp Med 1998, 187: 1849-1862, Arch, et al. Mol CellBiol1998,18: 558-565), TRAF-2 (4-1BB and OX40 ligand; Saoulli, et al. J Exp Med 1998,187: 1849-1862; Oshima, et al. Int Immunol 1998, 10: 517-526, Kawamata, etal J Biol Ckem . 1998, 273: 5808-5814), TRAF-3 (4-IBB and OX40 ligand; Arch, et al. Mol Cell Biol 1998, 18: 558-565; Jang, et al. Biochem Biophys Res Commun 1998, 242: 613-620: Kawamata Set al. J Biol Chem 1998, 273: 5808-5814), OX40L (OX40 ligand; Gramaglia, et aL J Immunol 1998,161: 6510-6517), TRAF-5 (OX40 ligand; Arch, et al Mol Cell Biol 1998, 18: 558-565; Kawamata, et al. J Biol Chem 1998, 273: 5808-5814), and CD70 (CD27 ligand; Couderc, et al. Cancer Gene Ther., 5(3): 163-75). CD154 (CD40 hgand or “CD40L”; Gurunathan, et al. J. Immunol, 1998, 161: 4563-4571; Sine, et al. Hum. Gene
Ther, 2001,12:1091-1102) may also be suitable.
One or more cytokines may also be suitable re-stimulatory components or “adjuvants”, either as polypeptides or being encoded by nucleic acids contained within the compositions of the present invention (Parmiani, et al Immunol Lett 2000 Sep 15; 74(1): 41-

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4; Berzofsky, et al. Nature Immunol. 1:209-219). Suitable cytokines include, for example, interieukin-2 (IL-2) (Rosenberg, et al. Nature Med. 4: 321-327 (1998)), BL-4, IL-7, IL-12 (reviewed by Pardoll, 1992; Harries, et at J, Gene Med. 2000 M-Aug;2(4):243-9; Rao, et al. /. Immunol. 156: 3357-3365 (1996)), IL-15 (Xiu, et al. Vaccine, 17:858-866,1999), EL-16 (Cruikshank, et al. J. Leuk Biol, 67(6): 757-66, 2000), IL-18 (J. Cancer Res. Clin. Oncol. 2001. 127(12): 718-726), GM-CSF (CSF (Disis, et al. Blood, 88: 202-210 (1996)), tumor necrosis factor-alpha (TNF-a), or interferon-gamma (ENF-y). Other cytokines may also be suitable for practicing the present invention, as is known in the art.
Chemokines may also be utilized. For example, fusion proteins comprising CXCL10
(DP-10) and CCL7 (MCP-3) fused to a tumor self-antigen have been shown to induce antitumor immunity (Biragyn, et al. Nature Biotech. 1999, 17: 253-258). The chemokines CCL3 (MlP-la) and CCL5 (RANTES) (Boyer, et al. Vaccine, 1999,17 (Supp. 2): S53-S64) may also be of use in practicing the present invention. Other suitable chemokines are known in the art.
It is also known in the art that suppressive or negative regulatory immune
mechanisms may be blocked, resulting in enhanced immune responses. For instance, treatment with anti-CTLA-4 (Shrikant, et al, Immunity, 1996,14: 145-155; Sutmuller, et al. J. Exp. Med., 2001,194: 823-832), anti-CD25 (Sutmuller, supra), anti-CD4 (Matsui, et al. J. Immunol., 1999, 163: 184-193), the fusion protein ILl3Ra2-Fc (Terabe, et al. Nature Immunol., 2000, 1: 515-520), and combinations thereof (i.e., anti-CTLA-4 and anti-CD25, Sutmuller, supra) have been shown to upregulate anti-tumor immune responses and would be suitable in practicing the present invention.
Any of these components may be used alone or in combination with other agents. For instance, it has been shown that a combination of CD80, ICAM-1 and LFA-3 (“TRICOM”) may potentiate anti-cancer immune responses (Hodge, et al Cancer Res, 59: 5800-5807 (1999)., Other effective combinations include, for example, IL-12 + GM-CSF (Ahlers, et al J. Immunol, 158: 3947-3958 (1997); Iwasaki, et al, J. Immunol. 158:4591-4601 (1997)), IL-12 + GM-CSF + TNF-α (Ahlers, et al. Int. Immunol 13: 897-908 (2001)), CD80 + IL-12 (Fruend, et al. Int, J. Cancer, 85:508-517 (2000); Rao, et aL supra), and CD86 + GM-CSF + IL-12 (Iwasaki, supra). One of skill in the art would be aware of additional combinations useful in carrying out the present invention.In addition, the skilled artisan would be aware of additional reagents or methods that may be used to modulate such mechanisms. These

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reagents and methods, as -well as others known by those of skill in the art, may be utilized in practicing the present invention.
Additional strategies for improving the efficiency of nucleic acid-based immunization may also be used including, for example, the use of self-replicating viral replicons (Caley, et al. 1999. Vaccine, 17: 3124-2135; Dubensky, et al. 2000. Mol. Med.- 6: 723-732; Leitner, et al. 2000. Cancer Res. 60; 51-55), codon optimization (Liu, et al 2000. Mol. Uter., 1:497-500; Dubensky, supra; Huang, et al. 2001. J. Virol 75: 4947-4951), in vivo eleclroporation (Widera, et al. 2000. /. Immunol. 164:4635-3640), incorporation of CpG stimulatory motifs (Gurunathan, et al. Ann. Rev. Immunol., 2000, 18: 927-974; Leitner, supra), sequences for targeting of the endocytic or ubiquitin-processing pathways (Thomson, et al. 1998. J. Virol. 72: 2246-2252; Velders, et al. 2001. J. Immunol 166: 5366-5373), prime-boost regimens (Gumnathan, supra; Sullivan, et al. 2000. Nature, 408: 605-609: Hanke, et al. 1998. Vaccine, 16: 439-445; Amara, et al. 2001. Science, 292: 69-74), and the use of mucosal delivery vectors such as Salmonella (Darji, et al 1997. Cell, 91: 765-775; Woo, et al. 2001 Vaccine, 19:2945-2954). Other methods are known in the art, some of which are described below.
Chemotherapeutic agents, radiation, anti-angiogenic compounds, or other agents may also be utilized in treating and / or preventing cancer using immunogenic targets (Sebti, et al. Oncogene 2000 Dec 27;19(56):6566-73). For example, in treating metastatic breast cancer,useful chemotherapeutic agents include cyclophosphamide, doxorubicin, paclitaxel, docetaxel, navelbme, capeedtabine, and mitomycin C, among others. Combination chemotherapeutic regimens have also proven effective including cyclophosphamide + methotrexate + 5-fluorouracil; cyclophosphamide + doxorubicin + 5-fluorouca«l; or, cyclophosphamide + doxorubicin, for example. Other compounds such as prednisone, a taxane, navelbine, mitomycin C, or vinblastine have been utlized for various reasons. A majority of breast cancer patients have estrogen-receptor positive (ER+) tumors and in these patients, endocrine therapy (i.e., tamoxifen) is preferred over chemotherapy. For such patients, tamoxifen or, as a second line therapy, progestins (medroxyprogesterone acetate or megestrol acetate) axe preferred. Aromatase inhibitors (i.e., aniMoglutelhimide and analogs thereof such as letrozole) decrease the availability of estrogen needed to maintain tumor growth and may be used as second or third line endocrine therapy in certain patients.
Other cancers may require different chemotherapeutic regimens. For example, metastatic colorectal cancer is typically treated with Camptosar (irinotecan or CPT-11), 5-

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fluorouracil or leucovorin, alone or in combination with one another. Proteinase and integrin inhibitors such as as the MMP inhibitors marimastate (British Biotech), COL-3 (Collagenex), Neovastat (Aetema), AG3340 (Agouran), BMS-275291 (Bristol Myers Squibb), CGS 27023A (Novartis) or lie integrin inhibitors Vitaxin (Medimmune), or MED1522 (Merck KgaA) may also be suitable for use. As such, immunological targeting of immunogenic targets associated with colorectal cancer could be performed in combination with a treatment using those chemotherapeutic agents. Similarly, chemotherapeutic agents used to treat other types of cancers are well-known in the art and may be combined with the immunogenic targets described herein,
Many anti-angiogenic agents are known in the art and would be suitable for co-
administration with the immunogenic target vaccines (sec, for example, Timar, et al 2001. Pathology Oncol. Res., 7(2): 85-94). Such agents include, for example, physiological agents such as growth factors (i.e., ANG-2, NK1,2,4 (HGF), transforming growth factor beta (TGF-β)), cytokines (i.e., interferons such as IFN-α, -β, γ, platelet factor 4 (PF-4), PR-39),proteases (i.e., cleaved AT-III, collagen XVIII fragment (Endostatin)), HmwKallikrien-d5 plasmin fragment (Angiostatin), prothrorabm-Fl-2, TSP-1), protease inhibitors (i.e., tissue inhibitor of metalloproteases such as TIMP-1, -2, or -3; maspin; plasminogen activator-inhibitors such as PAI-1; pigment epithelium derived factor (PEDF)), Tumstatin (available through ILEX, Inc.), antibody products (i.e., me collagen-binding antibodies HUIV26,HUI77, XL313; anti-VEGF; anti-integrin (i.e., Vitaxin, (Lxsys))), and glycosidases (i.e., heparinase-I, -ID). “Chemical” or modified physiological agents known or believed to have anti-angiogenic potential include, for example, vinblastine, taxol, ketoconazole, thalidomide, dolestatm, combrestatin A, rapamycin (Guba, et al. 2002, Nature Med, 8: 128-135), CEP-7055 (available from Cephalon, Inc.), flavone acetic acid, Bay 12-9566 (Bayer Corp,) AG3340 (Agouron, Inc.), CGS 27023A (Novartis), tetracylcme derivatives (i.e., COL-3 (Collagenix, Inc.)), Neovastat (Aeterna), BMS-275291 (Bristol-Myers Squibb), low dose 5-FU, low dose methotrexate (MTX), irsofladine, radicicol, cyclosporine, captopril, celecoxib, D45152-sulphated polysaccharide, canonic protein (Protamine), cationic peptide-VEGF, Suramin (polysulphonated napthyl urea), compounds that interfere with the function or production of VEGF (i.e., SU5416 or SU6668 (Sugen), PTK787/ZK22584 (Novartis)), Distamycin A, Angiozyme (ribozyme), isoflavinoids, staurosporine derivatives, genistein, EMD121974 (Merck KcgaA), ryrphostins. isoqwaolones, retinoic acid, carboxyanridotriazole, TNP-470, octreotide, 2-methoxyestradiol, anrinosterols (i.e.,

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squalamine), glutathione analogues (i.e., N-acteyl-L-cysteine), combretastatin A-4 (Oxigene) Eph receptor blocking agents (Nature, 414:933-938, 2001), Rh-Angiostatm, Rh-Endostatin.(WO 01/93897), cyclic-RGD peptide, accutin-disrategriii, benzodiazepenes, humanized anti- avb3 Ab, Rh-PAI-2, amiloride, p-amidobenzaamidine, anti-uPA ab, anti-uPAR Ab, L-phanylalanin-N-methylamides (i.e., Batimistat, Marimastat), AG3340, and miaooycline. Many other suitable agents are known in the art and would suffice in practicing the present invention.
The present invention may also be utilized in combination with, “non-traditional” methods of treating cancer. For example, it has recently been demonstrated that administration of certain anaerobic bacteria may assist in slowing tumor growth. In one study, Clostridium novyi was modified to eliminate a toxin gene carried on a phage episome and administered to mice with colorectal tumors (Dang, et al. P.N.A.S, USA, 98(26): 15155-15160, 2001). In combination with chemotherapy, the treatment was shown to cause tumor necrosis in the animals. The reagents and methodologies described m this application may be
combined with such treatment methodologies.
Nucleic acids encoding immunogenic targets may be administered to patients by any of several available techniques. Various viral vectors that have been successfully utilized for introducing a nucleic acid to a host include retrovirus, adenovirus, adeno-associated virus (AAV), herpes virus, and poxvirus, among others. It is understood in the art that many such viral vectors are available in the art. The vectors of the present invention may be constructed using standard recombinant techniques widely available to one skilled in the art. Such techniques may be found in common molecular biology references such as Molecular Cloning: A Laboratory Manual (Sambrook, et al., 1989, Cold Spring Harbor Laboratory Press), Gene Expression Technology (Methods in Eazymology, VoL 185, edited by D.Goeddel, 1991. Academic Press, San Diego, CA), and PCR Protocols; A Guide to Methods and Applications (Innis, et al. 1990. Academic Press, San Diego, CA).
Preferred retroviral vectors are derivatives of lentivirus as well as derivatives of murine or avian retroviruses. Examples of suitable retroviral vectors include, for example, Moloney murine leukemia vims (MoMuLV), Harvey murine sarcoma virus (HaMuSV) murine mammary tumor virus (MuMTV), SIV, BIV, HIV and Rous Sarcoma Virus (RSV). A number of retroviral vectors can incorporate multiple exogenous nucleic acid sequences. As recombinant retroviruses are defective, thev require assistance in order to produce infectious vector particles. This assistance can be provided by, for example, helper cell lines

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encoding retrovirus structural genes. Suitable helper cell lines include W2, PA317 and PA12,among others. The vector virions produced using such cell lines may then be used to infect a tissue cell line, such as NIH 3T3 cells, to produce large quantities of chimeric retroviral virions, Retroviral vectors may be administered by traditional methods (i.e., injection) or by implantation of a “produceccell line” in proximity to the target cell population (Culver, K., et al, 1994, Hum. Gene Ther., 5 (3): 343-79; Culver, K., et al, Cold Spring Barb. Symp. Quant Biol. 59: 685-90); Oldfield, E., 1993, Hum, Gene Ther., 4 (1): 39-69). The producer cell line is engineered to produce a viral vector and releases viral particles in the vicinity of the target cell. A portion of thre leased viral particles contact the target cells and infect thosecells, thus delivering a nucleic acid of the present invention to the target cell Following infection of the target cell, expression of the nucleic acid of the vector occurs.
Adenoviral vectors have proven especially useful for genetransfer into eukaryotic cells (Rosenfeld, M., et al, 1991, Science, 252 (5004): 431-4; Crystal, R., et al., 1994, Nat: Genet., 8 (1): 42-51), the study eukaryotic gene expression (Levrero, M., et ai, 1991, Gene,Biotechnology, 20: 363-90), and in animal models (Stratford-Perricaudet, L.s et al, 1992, Bone Marrow Transplant., 9 (Suppl. 1): 151-2 ; Rich, D., et al., 1993, Hum, Gene Ther., 4 (4): 461-76). Experimental routes for administrating recombinant Ad to different tissues in vivo have included intratracheal instillation (Rosenfeld, M., et al, 1992, Cell, 68 (1): 143-55) injection into muscle (Quantin, B., et al, 1992, Proc. Natl. Acad. Sci. U.SJL, 89 (7): 2581-4), peripheral intravenous injection (Hers, J., and Gerard, R-, 1993, Proc. Natl Acad. Sci. U.S.A., 90 (7): 2812-6) and stereotactic inoculation to brain (Le Gal La Salle, G.3 et al., 1993, Science, 259 (5097): 988-90), among others.
Adeno-associated virus (AAV) demonstrates high-level infectivity, broad host range and specificity in integrating into the host cell genome (Hermonat, P., et al, 1984, Proc Natl. Acad, Sci. U.SA., 81 (20); 6466-70). And Herpes Simplex Virus type-1 (HSV-1) is yet another attractive vector system, especially for use in the nervous system because of its neurotropic property (Geller, A., et al, 1991, Trends NeuroscL, 14 (10): 428-32; Glorioso, et al, 1995, Mol. Biotechnol, 4 (1): 87-99; Glorioso, et al., 1995, Amu. Rev. Microbiol, 49:
675-710).
Poxvirus is another useful expression vector (Smith, et al. 1983,Gene, 25 (1): 21-8; Moss, et al, 1992, Biotechnology, 20: 345-G2; Moss, et al, 1992, Curr. Top. Microbiol Immunol, 158:25-38; Moss, et al 1991. .Science, 252:1662-1667). Poxviruses shown to be

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useful include vaccinia, NYVAC, avipox, fowlpox, caoatypox, ALVAC, and ALVAC(2), among others.
Vaccinia virus is the prototvpic virus of the pox virus family and, like other members of the pox virus group, is distinguished by its large size and complexity. The DNA of vaccinia virus is similarly large and complex. Several types of vaccinia are suitable for use in practicing the present invention. One such vaccinia-related virus is the Modified Vaccinia Virus Ankara (MVA), as described in, for example, U.S. Pat Nos. 5,185,146 and 6,440,422.
Another suitable vaccinia-related virus is NYVAC. NYVAC was derived from the Copenhagen vaccine strain of vaccinia virus by deleting six nonessential regions of the genome encoding known or potential virulence factors (see, for example, U.S. Pat Nos. 5,364,773 and 5,494,807). The deletion loci were also engineered as recipient loci for the insertion of foreign genes. The deleted regions are: thymidine hemagglutinin gene (TK; J2R); hemorrhagic region (u; B13R+B14R); A type inclusion body region (ATI; A26X); hemagglutinin gene (HA; A56R); host range gene region (C7L-K1L); and, large summit, ribonucleotide reductase (I4L). NYVAC is a genetically engineered vaccinia virus strain mat was generated by the specific deletion of eighteen open reading frames encoding gene products associated with virulence and host range. NYVAC has been show to be useful for expressing TAs (see, for example, U.S. Pat No. 6,265,189). NYVAC (vP866), vP994, vCP205, vCP1433, placZH6H4Lreverse, pMPC6H6K3E3 and pC3H6FHVB were also deposited with the ATCC under the terms of the Budapest Treaty, accession numbers VR-2559, VR-2558, VR-2557, VR-2556, ATCC-97913, ATCC-97912, and ATCC-97914, respectively.
ALVAC-based recombinant viruses (i.e., ALVAC-1 and ALVAC-2) are also suitable for use in practicing the present invention (see, for example, U.S. Pat No. 5,756,103). ALVAC(2) is identical to ALVAC(l) except that ALVAC(2) genome comprises the vaccinia E3L and K3L genes under the control of vaccinia promoters (U.S. Pat No. 6,130,066; Beattie et al, 1995a, 1995b, 1991; Chang et al., 1992; Davies et als 1993). Both ALVAC(l) and ALVAC(2) have been demonstrated to be useful in expressing foreign DNA sequences, such as TAs (Tartaglia et al., 1993 a,b; U.S. Pat No. 5,833,975). ALVAC was deposited under the 3o terms of the Budapest Treaty with the American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110-2209, USA, ATCC accession number VR-2547.
Another useful poxvirus vector is TROVAC. TROVAC refers to an attenuated fowlpox that was a plaque-cloned isolate derived from the FP-1 vaccine strain of


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fowlpoxvirus which is licensed for vaccination of 1 day old chicks. TROVAC was likewise deposited under the terms of the Budapest Treaty with the ATCC, accession number 2553.
“Non-viral” plasmid vectors may also be suitable in practicing the present invention, Preferred plasmid vectors are compatible with bacterial, insect, and / or mammalian host cells. Such vectors include, for example, PCR-n, pCR3, and pcDNA3.1 (Xnvitrogen, San Diego, CA), pBSII (Stratagene, La Jolla, CA), pET15 (Nbvagen, Madison, WQ, pGEX (Pharmacia Biotech, Piscataway, NJ), pEGFP-N2 (Clontech, Palo Alto, CA), pETL (BlueBacH, Invitrogen), pDSR-alpha (PCT pub. No. WO 90/14363) and pFaarBacDual (Gibco-BRL, Grand Island, NY) as well as Bluescript plasmid derivatives (a high copy number COLEI-based phagemid, Stratagene Cloning Systems, La Jolla, CA), PCR cloning plasmids designed for cloning Taq-amplified PCR products (e.g., TOPO™ TA cloning® kit, PCR2.1 plasmid derivatives, Invitrogen, Carlsbad, CA). Bacterial vectors may also be used with the current invention. These vectors include, for example, Shigella, Salmonella, Vibrioi ckolerae, Lactobacillus, Bacilte calmette guirin (BCG), and Streptococcus (see for example, WO 88/6626; WO 90/0594; WO 91/13157; WO 92/1796; and WO 92/21376), Many other non-viral plasmid expression vectors and systems a-e known in the art and could be used with the current invention.
Suitable nucleic acid delivery techniques include DNA-ligand complexes, adenovirus-ligand-DNA complexes, direct injection of DNA, CaP04 precipitation, gene gun techniques, electraporation, and colloidal dispersion systems, among others. Colloidal dispersion systems include macromolecule complexes, nanocapsules microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. The preferred colloidal system of this invention is a liposome, which are artificial membrane vesicles useful as delivery vehicles in vitro and in vivo. RNA, DNA and intact virions can be encapsulated within the aqueous interior and be delivered to cells in a biologically active form (Fraley, R., et al, 1981, Trends Bioehem. Set, 6; 77). The composition of the liposome is usually a combination of phospholipids, particuariy Mgh-phase-tranation4emperature phospholipids, usually in combination with step wis, especially cholesterol. Other phospholipids or other lipids may also be used. The physical characteristics of liposomes depend on pH, ionic strength, and the presence of divalent cations. Examples of lipids useful in liposome production include phosphatidyl compounds, such as phosphatidylglycerol, phosphatidylcholine, phospharldylserine, pnosphatidylethanolamine, sphingohpids, cerebrosides, and gangUosides. Particularly useful are diacylphosphatidylglycerols, where


Typeof Adjuvant General Examples Specific Examples/References
1 Gel-type AhiTnimim hydroxide/phosphate (“alum adjuvants”) (Aggerbecfc and Heron, 1995) adjuvants")
Calcium phosphate (Relyveld, 1986) 2 Microbial Muramyl dipeptide (MDP) (Chedid et aL. 1986)
Bacterial exotoxins Cholera toxin (Ox), #.«>/f labile toxin(LT)(Freytae and dements, 1999)
Endotoxin-based adjuvants Monophosphoryl lipid A (MPL)(Ulrick and Myers, 1995)
Other bacterial CpG oligonucleotides (Corral andPetray, 2000), BCG sequences (Krieg, et at Nature, 374:576), tetanus toxoid (Rice, et aL J. Immunol, 2001,167: 1558-1565)
3 Particulate Biodegradable (Gupta etaL, 1998) polymer microspheres
Immunostinmlatory complexes (Moretn and Bcngtsson, 1999) (ISCOMs)
Liposomes (Wassef etal,, 1994)
4 Oil-emulsion Freund's incomplete adjuvant (Jensen etaL, 1998) andsurfactant-based adjuvants
Microfluidized emulsions MF59 fOtt et aL. 1995}
SAF (Allison and Byars, 1992) (Allison. 1999)
Saponins QS-21 (Kcnsu, 1996)
5 Synthetic Muramyl peptide derivatives Murabutide (Ledexer, 1986)Tkeony-MDP (Allison, 1997)
Nonionic block copolymers L121 (Allison, 1999)
Polyphosphazme (PCPP) (Payne etaL, 1995)
Synthetic polynucleotides Poly A:U, Poly LC (Johnson, 1994)

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the lipid moiety contains from 14-18 carbon atoms, particularly from 16-18 carbon atoms,and is saturated. Illustrative phospholipids include egg phosphatidylcholine, dipahnitoylphosphatidylcholine and distearoylphosphatidylchoKne.
An immunogenic target may also he administered in combination with one or more adjuvants to boost the immune response. Exemplary adjuvants are shown in Table I below:
Table I

Types of Immunologic Adjuvants

The immunogenic targets of the present invention may also be used to generate antibodies for use in screening assays or for raunimomerapy. Other uses would be apparent to one of skill in the art The term “antibody” includes antibody fragments, as are known in the art, including Fab, Fab2, single chain antibodies (Fv for example), humanized antibodies, chimeric antibodies, human antibodies, produced by several methods as are known in the art



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Methods of preparing and utilizing various types of antibodies are well-known to those of skill in the art and would be suitable in practicing the present invention (see, for example, Harlow, et al. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988; Harlow, et al. Using Antibodies: A Laboratory Manual, Portable Protocol No. 1, 1998; Kohler and Milstein, Nature, 256:495 (1975)); Jones et al. Nature, 321:522-525 (1986); Riechmann et al. Nature, 332:323-329 (1988); Presta (Curr. Op. Struct Biol., 2:593-596 (1992); Verhoeyen et al. (Science, 239:1534-1536 (1988); Hoogenboom et al., J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991); Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R, Liss, p. 77 (1985); Boeroer et al., J. Immunol.,
147(l):86-95 (1991); Marks et al., Bio/Technology 10, 779-783 (1992); Lonberg et al., Nature 368 856-859 (1994); Morrison, Nature 368 812-13 (1994); Fishwild et al, Nature Biotechnology 14, 845-51 (1996); Neuberger, Nature Biotechnology 14, 826 (1996); Lonberg and Huszar, Intern. Rev. Immunol. 13 65-93 (1995); as well as U.S. Pat Nos. 4,816,567; 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; and, 5,661,016). The antibodies or derivatives therefrom may also be conjugated to therapeutic moieties such as cytotoxic drugs or toxins, or active fragments thereof such as dipmeria A chain, exotoxin A chain, ricin A chain, abrin A chain, curcin, erotic, phenomycin, enomycin, among others. Cytotoxic agents may also include radiochemicals. Antibodies and their derivatives may be incorporated into compositions of die invention for use in vitro or in vivo,
Nucleic acids, proteins, or derivatives thereof representing an immunogenic target may be used in assays to determine the presence of a disease state in a patient, to predict prognosis, or to determine the effectiveness of a chemotherapeutic or other treatment regimen. Expression profiles, performed as is known in the art, may be used to determine the relative level of expression of the immunogenic target The level of expression may then be correlated with base levels to determine whether a particular disease is present within me patient, the patient's prognosis, or whether a particular treatment regimen is effective. For example, if the patient is being treated with a particular chemomerapeutic regimen, an decreased level of expression of an immunogenic target in the patient's tissues (i.e., in peripheral blood) may indicate the regimen is decreasing the cancer load in that host Similarly, if the level of expression is increasing, another therapeutic modality may need to be utilized. In one embodiment, nucleic acid probeprobes corresponding to a nucleic acid encoding an immunogenic target may be attached to a biochio. as is known in the art, for the detection and quantification of expression in the host.


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It is also possible to use nucleic acids, proteins, derivatives therefrom, or antibodies
thereto as reagents in drug screening assays. The reagents may be used to ascertain the effect of a drug candidate on the expression of the immunogenic target in a cell line, or a cell or tissue of patient. The expression profiling technique may be combined with high throughput screening techniques to- allow rapid identification of useful compounds and monitor the effectiveness of treatment with a drug candidate (see, for example, Zlokamik, et al, Science 279, 84-8 (1998)). Drug candidates may be chemical compounds, nucleic acids, proteins, antibodies, or derivatives therefrom, whether naturally occurring or synthetically derived. Drug candidates thus identified may be utilized, among other uses, as pharmaceutical compositions for administration to patients or for use in further screening assays.
Administration of a composition of, the present invention to a host may be accomplished using any of a variety of techniques known to those of skill in the art. The composition(s) may be processed in accordance with conventional methods of pharmacy to produce medicinal agents for administration to patients, including humans and other mammals (i.e., a “pharmaceutical composition”). The pharmaceutical composition is preferably made in the form of a dosage unit containing a given amount of DNA, viral vector particles, polypeptide or peptide, for example. A suitable daily dose for a human or other mammal may vary widely depending on the condition of the patient and other factors, but, once again, can be determined using routine methods.
The pharmaceutical composition may be administered orally, parentally, by inhalation spray, rectally, mtranodally, or topically in dosage unit formulations containing conventional pharmaceutically acceptable carriers, adjuvants, and vehicles. The term “pharmaceutically acceptable carrier” or “physiologically acceptable carrier” as used herein refers to one or more formulation materials suitable, for accomplishing or enhancing the delivery of a nucleic acid, polypeptide, or peptide as a pharmaceutical composition. A “pharmaceutical composition” is a composition comprising a therapeutically effective amount of a nucleic acid or polypeptide. The terms “effective amount” and “therapeutically effective amount” each refer to the amount of a nucleic acid or polypeptide used to induce or enhance an effective immune response. It is preferred mat compositions of the present invention provide for the induction or enhancement of an anti-tumor immune response in a host which protects the host from the development of a tumor and / or.allows the host to eliminate an existing tumor from the body.


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For oral administration, the pharmac






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30 For oral administration, pharaceutical composition may be of any of several forms including, for example, a capsule, a tablet, a suspension, or liquid, among others,. Liquids may be administered by injection as a composition with suitable camera including saline, dextrose, or water. The term parenteral as used herein includes subcutaneous, intravenous, intramuscular, intrasternal, infusion, or intraperitoneal. administration. Suppositories for rectal administration of me drug can be prepared by mixing the drug with a suitable non-irritating excipient such as cocoa butter and polyethylene glycols that are solid at ordinary temperatures but liquid at the rectal temperature,
The dosage regimen for immunizing a host or otherwise treating a disorder or a disease with a composition of this invention is based on a variety of factors, including the type of disease, the age, weight, sex, medical condition of the patient; the severity of the condition, the route of administration, and the particular compound employed. For example, a poxviral vector may be administered as a composition comprising 1 x 106 infectious particles per dose. Thus, the dosage regimen may vary widely, but can be determined routinely using standard methods.
A prime-boost regimen may also be utilized (WO 01/30382 Al) in which the targeted immunogen is initially administered in a rrfimnuj step in one fbim followed by a boosting step in which me targeted immunogen is administered in another form. The form of the targeted immunogen in the priming and boosting steps are different For instance, if the priming step utilized a nucleic acid, the boost may be administered as a peptide. Simmilarly, where a priming step utilized one type of recombinant virus (i.e., ALVAC), the boost step may utilize another type of virus (i.e., NYVAC). This prime-boost method of administration has been shown to induce strong immunological responses.
While the compositions of me invention can be administered as the sole active pharmaceutical agent, they can also be used in combination with one or more othercompositions or agents (i.e., other immunogenic targets, co-stimulatory molecules,adjuvants). When administered as a combination, the individual components can be formulated as separate compositions administered at the same time or different times, or the components can be combined as a single composition. Injectable preparations, such as sterile injectable aqueous or oleaginous suspensions, may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents. The injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable dilnent or solvent Suitable vehicles and


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solvents mat may be employed are watsolvents that may be employed are water, Ringer’s solution, and isotonic sodium chloride solution, among others. For instance, a viral vector such as a poxvirus may be prepared in 0.4% NaCl. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil may be employed, including synthetic mono- or diglycerides. In addition, fetty acids such as oleic acid find use in the preparation of injectables.
For topical administration, a suitable topical dose of a composition may be administered one to four, and preferably two or three times daily. The dose may also be administered with intervening days during which no does is applied. Suitable compositions may comprise from 0.001% to 10% w/w, for example, from 1% to 2% by weight of the formulation, although it may comprise as much as 10% w/w, but preferably not more than 5% w/w, and more preferably from 0.1% to 1% of the formulation. Formulations suitable for topical administration include liquid or semi-liquid preparations suitable for penetration through the skin {e.g., liniments, lotions, ointments, creams, or pastes) and drops suitable for administration to the eye, ear, or nose.
The pharmaceutical compositions may also be prepared in a solid form (includinggranules,powders or suppositories). The pharmaceutical compositions may be subjected toconventional pharmaceutical operations such as sterilization and/or may contain conventional adjuvants, such as preservatives, stabilizers, wetting agents, emulsifiers, buffers etc. Solid dosage forms for oral administration may include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound may be admixed with at least one inert diluent such as sucrose, lactose, or starch. Such dosage forms may also comprise, as in normal practice, additional substances other than inert diluents, e.g., lubricating agents suchas magnesium stearate. In me case of capsules, tablets, and pills, the dosage forms may also comprise buffering agents. Tablets and pills can additionally be prepared with entericcoatings. Liquid dosage forms for oral administration may include pharmaceutically acceptable emulsions, solutions, suspensions, syrups, and elixirs containing inert diluents commonly used in the art, such as water. Such compositions may also comprise adjuvants, such as wetting sweetening, flavoring, and perfuming agents.
Pharmaceutical compositions comprising a nucleic acid or polypeptide of the present invention may take any of several forms and may be administered by any of several routes. In preferred embodiments, the compositions are administered via a parenteral route (intradermal, intramuscular or subcutaneous) to induce an immune response in the host


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Alternatively, the composition mayAlternatively, the comoposition may be administered directly into a lymph node (intranodal) or tumor mass (i.e., intratumoral administration). For example, me dose could be administered subcutaneously at days 0,7, and 14, Suitable methods far immunization using compositions comprising TAs are known in the art, as shown for p53 (Hollstein et al. 1991), 5 p2l-ras (Almoguera et al, 1988), HER-2 (Fendly et al., 1990), the melanoma-associated antigens (MAGE-1; MAGE-2) (van der Bruggen et al„ 1991), p97 (Hu et al, 1988), and carcinoembryonic antigen (CEA) (Kantor et al, 1993; Fishbein et al., 1992; Kaufman et al., 1991), among others.
Preferred embodiments of administratable compositions include, for example, nucleic acids or polypeptides in liquid preparations such as suspensions, syrups, or elixirs. Preferred injectable preparations include, for example, nucleic adds or polypeptides suitable for parental, subcutaneous, intradermal, intramuscular or intravenous administration such assterile suspensions or emulsions. For example, a recombinant poxvirus may be in admixturewith a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose15 or the like, The composition may also be provided in lyophilized form for reconstituting, for instance, in isotonic aqueous, saline buffer. In addition, the compositions can be co administered or sequentially administered with other antineoplastic, anti-tumor or anti-canceragents and/or with agents which reduce or alleviate ill effects of antineoplastic, anti-tumor oranti-cancer agents.
A kit comprising a composition of the present invention is also provided. The kit can include a separate container containing a suitable carrier, diluent or excipient The kit can also include an additional anti-cancer, anti-tumor or antineoplastic agent and/or an agent that reduces or alleviates ill effects of antineoplastic, anti-tumor or anti-cancer agents for co- or sequentid-administration. Additionally, the kit can include instructions for mixing or combining ingredients and/or administration.
A better understanding of the present invention and of its many advantages will be had from the following examples, given by way of illustration.
EXAMPLES
Example1
A. Modification of mCEA (6D) repeat 1


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The presence of truncated forms of The presence of truncated CEA in cells following expression of recombinantCEA has been documented. This study set forth to generate CEA-encoding nucleic acidsequences that do not result in the expression of truncated CEA following expression in cells.Generation and expression of a new CEA-encoding nucleic acid sequence CAP(6D)-1,2, is described below.
The plasmid p3’H6MCEA was obtained from Virogenetics, Inc. This plasmid contains the MCEA gene with 6D modification under the control of partial H6 promoter (Fig. 1A; SEQ ID NO.; 1). The 912 bp Nrul - BamHI fragment fiom p3’H6MCEA was cloned into pUC18 to form plasmid pSEl544.9 (pUC18-mCEA repeat}; Fig. IB).
OPC purified Oligos 7524-7526, 7528-7533,753 5-7537, and 7567-7568 were kinased and annealed to create two fragments which were ligated to result in a 464 bp synthetic modified mCEA repeat 1 flanked by AccI and BamHI sites. This synthetic modified repeat 1. fragment was cloned into pSE1544.9 AccI-BamHI to create pSEl6l6.44 (pUC18-mCEA-modified repeat 1; Fig. 2). The 904 bp EcoRV - BamHI fragment of pSE1616-44 was cloned back into p3’H6MCEA EcoRV-BaroHI to form pSEl65S.l5 (p3’H6MCEA-modified repeat l;Fig.3).
B. Modification of mCEA(6D) repeat 2
A synthetic modified repeat 2 fragment was created by using a method called gene 20 splicing by overlap extension (SQE) and cloned into pBluescript-SK+, generating pBSmCEA (Fig. 4). The oligos used for the repeat 2 modification are shown below (section IV, B). The two different clones (pBS-mCEA-3 and pBS-mCEA-8) contained various point mutations.The 697 bp BamHI - EcoRI fragment of pBS-mCEA-3 was cloned into pUC18BamHI - EcoRI to create pSE1671,8, The 591 bp Spel - Bsu36I fragment of pBS mCEA-8 was cloned into pSE1671.8 SpeI-Bsu36I, generating plasmid designated pSEl68l.l. Two sitePCR mutagenesis, using the Quikchange site directed mutagenesis kit from Stratagene with
oligos 7751 (SEQ ID NO.:2;
GGACGGTAGTAGGTGTATGATGGAGATATAGTTGGGTCGTCTCSGGCC) and 7760 (SEQ ID NO.:3; CAGAATGAATTATCCGTTGATCACTCC), was performed to correct the two remaining point mutations pSE1681.1. The corrected clone was designated pSE1686.1 (pUCl 8 mCEA modified repeat 2; Fig. 5).
As noted recently, an Alanine codon was absent from 5’ terminus of the second repeat in plasmid p3’H6MCEA which contained CEA. To preserve the consistency of the amino


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acid sequence of CEA, me Alanine codon present in plasmid pSE1686.1contaimng the modified second repeat of CEA was knocked out This was accomplished using oligos 7802
(SEQ ID) NO:4;
CGTGACGACQATTACCGTGTATGAGCCACCAAAACCATTCATAAC) and 7803 (SEQ
ID NO.:5; GTTATGAATGGnTTGGTGGCTCATACACGGTAATCGTCGTCACG) and the Quikchange site-directed mutagenesis kit from Stratagene. The resulting plasmid, pSEl696.1 (pUCl 8 mCEA modified repeat 2; Fig. 6) was confirmed by sequencing.
The 694 bp Bsu36I-BamHI fragment from pSE1696.l was cloned into Bsu36l-BamHI site of Psel6~58.15 to combine modified repeats 1 and 2. The generated plasmid was designated p3’H6modMCEA-lst&2nd repeats (Fig. 7).
C Construction of ALVAC donor plasmid pNVQH6MCEA(6Dlst&2nd)
The 2.2 kb Nrul/Xhol fragment from p3’H6modMCEA-lst&2ndrepeats was cloned into Nrul/Xhol site of pNVQH6LSP-18, generating pNVQH6MCEA(6Dlst&2nd; Fig. 8). 15 The modified CEA sequence (“CAP(6D)-1,2”; SEQ ED NO. 6) contained within pNVQH6MCEA is shown in Fig. 9.
D. Expression of modified CEA
To test the stability of the CAP(6D)-1,2 sequence upon expression in a cell, the gene together with flanking H6 promoter was PCR amplified using pNVQH6MCEA(6DlST&2ND) as template and two oligos (8034LZ, SEQ ID NO.:7; CTGGCGCGCCTTCTTTATTCTATACTTAAAAAGTG; and 8035LZ, SEQ ID NO.:8:.
CTGGTACCAGAAAAACTATATCAGAGCAACCCCAAC). The PCR product was then cloned into an NYVAC TK donor plasmid designated pLZTKl containing the LacZ and KIL marker genes. This vector was specifically made for me generation of recombinant virus in NYVAC by using blue/white screening method. After in vitro recombination between donor plasmid pLZTKlmCEA(6Dlst&2nd) and NYVAC, the foreign CAP(6D)-1,2 sequence and marker genes are integrated into the NYVAC genome. The plaques containing intermediate recombinant NYVAC with both LacZ and mCEA appeared blue. Several rounds of plaque purification, were then performed. The second recombination event kicked out the marker genes resulting in the final white plaques containing recombinants with only the CAP(6D)-1,2 sequence but no marker genes (Fig.10).


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The recombinant white plaques and blue plaques were picked for confirmation of CAP(6D)-1,2 sequence expression. Infection was performed using the virus from the respective plaques and the cells were harvested three days after infection for preparing either cellular DNA or cell lysate. For isolation of recombinant NYVAC DNA, DNAzol® reagent
ibcGibcoBRL) was used. PCR (PCR Condition: 95"C (5min) -> [95°C(30sec) -> 49°C(30sec) -> 7272oC(1min)] 30 cycles->72°C (7min)-> 4°C) was run to confirm the existence of CAP(6D)-I,2 sequence in the recombinant NYVAC genome. The primers used were 7569LZ (5’ ttggatccatggagtctccctcggcc 3’ forward primer, SEQ ID NO.:9) and 7570LZ (5’’ ttggaiccctatatcagagcaaeccc 3’ reverse primer; SEQ ID NO.:10), which, could amplify the full
length 2106 bp CAP(6D)-1,2.
The final recombinant white plaques PRBC-III- 2, 3, 6, 8, 9,10 all demonstrated the 2-1 kb CAP(6D)-1,2 sequence band in PCR. PRBC-m-Nl' was a blue plaque with both marker genes and CAP(6D)-1,2 sequence still in the viral genome and the CAP(6D)-1,2 sequence band was also amplified in the PCR. The prominent PCR band amplified from vCP
307 DNA (containing native CEA integrated into the ALVAC genome) was truncated CEA at 1.2 kb with a very faint full-length CEA band. The cell-only sample (no viral infection) was used as a negative control and the plasmid pLZTKlMCEA(6DlST&2ND) was a positive control used in the PCR reaction. The PCR results clearly showed the full-length CAP(6D)-1,2 in the recombinant viral genome with no other truncated form of CEA visible. This result
indicated that CAP(6D)-1,2 has increased stability relative to the native CEA in the ALVAC genome.
Protein expression was also assayed by immunoblot to confirm me absence of truncated CEA protein in cells expressing CAP(6D)-1,2 (Fig. 11). For isolation of cell lysate, cells were first washed with PBS followed by the addition of Lysis Buffer (Reporter Gene .
Assay; Boehringer Mannheim) and shaking for 15 minutes. Cell lysate was spun.down at 13,000 rpm and the supernatant was collected for Western blot analysis. Samples were loaded onto a 10% polyacrylamide gel and run at 125 volts, The protein was then transferred to a PVDF filter- membrane (Inrmobilon-P, Millipore). An HRP-linkcd mouse CEA monoclonal antibody (1:1000; Fitzgerald) was used to detect the expression of mCEA with
the enhancement from a c&emilwninescence reagent (DNA Thunder™; NEN™ Life Science Products).
All six final CAP(6D)-1,2 recombinant white plaques (PRBC-III-2,3,6,8,9,10) and one intermediate blue plaque (pRBC-III-Nl) showed only one CEA band with no other


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truncated form (Fig. 11). In contrast, protein from VCP307 plaques (recombinant ALVAC expressing native CEA) showed a clear truncated CBA product at ~60 kDa in addition to the fall length CEA. Prolonged exposure of the film verified the absence of any truncated CEA polypeptides in the CAP(6D)-1,2 recombinants. CEF was used as the negative control 5
In conclusion, the CAP(6D)-l,2 recombinants were generated with the mCEA instead
of the native CEA to prevent the expression of multiple versions of CEA. CAP(6D)-1,2 expressed from recombinant NYVAC was proven effective in eliminating truncated version of CEA by both PCR and Western blot
10 E. Recombinant ALVAC Vector forExpressfog B7.1 and CAPffiDVU CEA
The human B7.1 gene was inserted into an ALVAC C6 donor plasmid under the control of the H6 promoter as shown in Fig. 12. This donor plasmid was then used with ALVAC to generate the ALVAC recombinant vCP306 using standard techniques. The donor plasmid inserts into the Co" site of the ALVAC genome. The CAP(6D)-1,2 CEA DNA
sequence was inserted into an ALVAC C3 donor plasmid undo: the control of the H6 promoter as shown in Fig. 13, This donor plasmid was men used with vCP306 to generate the ALVAC recombinant vCP2140 (ALVAC-CAP(6D)-1,2 CEA-B7.1) expressing these genes using standard techniques. The donor plasmid inserts into the C3 site of the ALVAC genome. This vector may be used, for example, to express B7.1 and / or CEA in vitro (i.e., in cell
culture) or in vivo (for immunization purposes).
While the present invention has been described in terms of the preferred embodiments, it is understood that variations and modifications will occur to those skilled in the art. Therefore, it is intended that the appended claims cover all such equivalent variations that come within the scope of the invention as claimed.







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CLAIMS
What is claimed is:
I. An expression vector comprising the nucleic acid sequence CEA(6D)-1,2 as illustrated in SEQ ID NO.: 24 and Figure 9 or a fragment thereof.
2. The expression vector of claim 1 wherein me vector is a plasmid or a viral vector.
3. The expression vector of claim 2 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus.
4. The expression vector of claim 3 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, NYVAC, avipox, canarypox, ALVAC, ALVAC(2),
fowlpox, and TROVAC.
5. The expression vector of claim 4 wherein the viral vector is a poxvirus selected from me group consisting of NYVAC, ALVAC, and ALVAC(2).
6. The expression vector of claim 1 further comprising at least one additional tumor-associated antigen.
7. The expression vector of claim 6 wherein the vector is a plasmid or a viral vector.
8. The expression vector of claim 7 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus.
9. The expression vector of claim 8 wherein the viral vector is a poxvirus selected from the, group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2),
20 fowlpox, and TROVAC.
10.The expression vector of claim 9 wherein the viral vector is a poxvirus selected from the
group consisting of NYVAC, ALVAC, and ALVAC(2).
11.The expression vector of claim 1 further comprising at least one nucleic sequence
encoding an angiogenesis-associated antigen.
12. The expression yector of claim 11 wherein the vector is a plasmid of a viral vector.
13. The expression vector of claim 12 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus.
14. The expression vector of claim 13 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2), fowlpox, and TROVAC.
15. The expression vector of claim 14 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAC(2).


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16. The expression vector of claim 6 further comprising at least one. nucleic sequence
encoding an angiogenesis-associated antigen,
17. The expression vector of claim 16 wherein the vector is a plasmid or a viral vector.
18. The expression vector of claim 17 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus.
1 The expression vector of claim 17 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canaiypox, ALVAC, ALVAC(2), fowlpox, and TROVAC.
20.The poxvirus of claim 18 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAC(2).
21. The expression vector of claim 1,6,11 or 16 further comprising at least one nucleic acid sequence encoding a co-stimulatory, component
22. The expression vector of claim 22 wherein the vector is a plasmid or a viral vector.
23.The expression vector of claim 23 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesviitts, and adeiw-associated viurus.
24. The expression vector of claim 24 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2), fowlpox, and TROVAC.
25.The poxvirus of claim 18 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAQ2).
26. A composition comprising an expression vector in a pharmaceutically acceptable carrier, said vector comprising the nucleic acid sequence CEA(6D)-1,2 as illustrated in SEQ ID
NO.: 24 and Figure 9 or a fragment thereof.
27.The expression vector of claim 26 wherein the vector is a plasmid or a viral vector.
28. The expression vector of claim 27 wherein the viral vector is selected from the group
consisting of poxvirus, adenovirus, retrovirus, herpesvirus and adeno-associated virus. 29. The expression vector of claim 28 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2),fowlpox, and TROVAC.
30. The poxvirus of claim 29 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAC(2).


v
16. The expression vector of claim 6 further comprising at least one. nucleic sequence
encoding an angiogenesis-associated antigen,
19. The expression vector of claim 16 wherein the vector is a plasmid or a viral vector.
20. The expression vector of claim 17 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus.
1 The expression vector of claim 17 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canaiypox, ALVAC, ALVAC(2), fowlpox, and TROVAC.
20.The poxvirus of claim 18 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAC(2).
23. The expression vector of claim 1,6,11 or 16 further comprising at least one nucleic acid sequence encoding a co-stimulatory, component
24. The expression vector of claim 22 wherein the vector is a plasmid or a viral vector.
23.The expression vector of claim 23 wherein the viral vector is selected from the group consisting of poxvirus, adenovirus, retrovirus, herpesviitts, and adeiw-associated viurus.
24. The expression vector of claim 24 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2), fowlpox, and TROVAC.
25.The poxvirus of claim 18 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAQ2).
26. A composition comprising an expression vector in a pharmaceutically acceptable carrier, said vector comprising the nucleic acid sequence CEA(6D)-1,2 as illustrated in SEQ ID
NO.: 24 and Figure 9 or a fragment thereof.
27.The expression vector of claim 26 wherein the vector is a plasmid or a viral vector.
28. The expression vector of claim 27 wherein the viral vector is selected from the group
consisting of poxvirus, adenovirus, retrovirus, herpesvirus and adeno-associated virus. 29. The expression vector of claim 28 wherein the viral vector is a poxvirus selected from the group consisting of vaccinia, MVA, NYVAC, avipox, canarypox, ALVAC, ALVAC(2),fowlpox, and TROVAC.
30. The poxvirus of claim 29 wherein the viral vector is a poxvirus selected from the group consisting of NYVAC, ALVAC, and ALVAC(2).


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31.A method for preventing or treating cancer comprising administering to a host an expression vector comprising the nucleic acid sequence CEA(6D)-1,2 as illustrated inSEQ ID NO.: 24 and Figure 9 or a fragment thereof.
32. The expression vector of claim 31 wherein the vector is a plasmid or a viral vector. .
33. The expression vector of claim 32 wherein the viral vector is selected from the group
consisting of poxvirus, adenovirus, retrovirus, herpesvirus, and adeno-associated virus. 34. The expression vector of claim 33 wherein the viral vector is a poxvirus selected from the
group consisting of vaccinia, MVA, NYVAC, avipbx, cattarypox, ALVAC, ALVAC(2),
fowlpox, andTROVAC. 35. The poxvirus of claim 34 wherein the viral vector is a poxvirus selected from the group
consisting of NYVAC, ALVAC, and ALVAC(2).
36.An isolated DNA molecule comprising me CEA(6D)-1,2 sequence illustrated in SEQ ID NO.: 24 and Figure 9.
37.An isolated DNA molecule comprising a fragment of the CEA(6D)-1,2 sequence illustrated in SEQ ID NO.: 24 and Figure 9.





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1185-chenp-2006-description (complete).pdf

1185-chenp-2006-drawings.pdf

1185-chenp-2006-form 1.pdf

1185-chenp-2006-form 3.pdf

1185-chenp-2006-form 5.pdf

1185-chenp-2006-pct.pdf

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Patent Number 234869
Indian Patent Application Number 1185/CHENP/2006
PG Journal Number 29/2009
Publication Date 17-Jul-2009
Grant Date 18-Jun-2009
Date of Filing 05-Apr-2006
Name of Patentee SANOFI PASTEUR INC.
Applicant Address Discovery Drive, Swiftwater, PA 18370
Inventors:
# Inventor's Name Inventor's Address
1 PARRINGTON, Mark 1755 Steeles Avenue, Toronto, Ontario M2R 3T4
2 ZHANG, Linong 1755 Seeles Avenue, Toronto, Ontario
3 ROVINSKI, Benjamin 1755 Steeles Avenue, Toronto, Ontario
4 GRITZ, Linda 76 Rogers Street, Cambridge, MA 02142-1119
5 GREENHALGH, Patricia 76 Rogers Street, Cambridge, MA 02142-1119
PCT International Classification Number C12N15/86
PCT International Application Number PCT/US2004/33145
PCT International Filing date 2004-10-06
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/509,593 2003-10-08 U.S.A.