WO2003066820A2 - Nucleic acid molecules encoding cd1-derived endosomal targeting proteins and uses thereof - Google Patents

Abstract

The present invention provides chimeric nucleic acid molecules encoding CD1 fusion proteins, comprising a leader peptide sequence, a CD1 endosomal targeting sequence, and an antigen of interest. In the CD1 fusion protein, the leader peptide sequence and CD1 endosomal targeting sequence direct production, processing, trafficking, and cell surface presentation of the antigen of interest via the MHCII antigen presenting pathway. The invention also provides methods for producing the CD1 fusion protein or the antigen of interest or fragments thereof, methods for targeting the antigen of interest to the MHCII antigen presenting pathway, and methods for presenting on a cell the antigen of interest. Additionally, the present invention provides methods for inducing in a subject an immune response mediated by a CD1 endosomal targeting sequence, methods for inducing in a subject an immune response to an antigen of interest, and methods for inducing in a subject an immune response mediated by an MHCII antigen presenting pathway.

Description

NUCLEIC ACID MOLECULES ENCODING CD1-DERIVED ENDOSOMAL TARGETING PROTEINS AND USES THEREOF

This application claims priority to provisional application, U. S. Serial No. 60/355,432, filed February 5, 2002, the contents of which are hereby incorporated by reference in their entirety into this application.

Throughout this application various publications are referenced. The disclosures of these publications are hereby incorporated by reference in their entirety into this application in order to more fully describe the state of the art to which the invention pertains.

FIELD OF INVENTION

The present invention relates to chimeric DNA molecules encoding a CDI fusion protein comprising a CDI endosomal targeting sequence and an antigen of interest. The CDI fusion protein is produced and targeted to the MHCII antigen presenting pathway thereby presenting the antigen of interest on a cell surface.

BACKGROUND OF THE INVENTION

Immune defense against microbial or viral infection and cancer depends on the successful recognition of foreign antigens by T cells. Studies of animal models of infection and cancer indicate a pivotal role for CD4+ T cells in host protection from disease (1-5). CD4+ T cells recognize antigenic peptides derived from the degradation of extracellular or endocytic proteins in the context of major histocompatibility complex II (MHC II) proteins (6).

Once activated, CD4+ T cells the release distinct subsets of cytokines (7, 8). In the context of infection, type 1 cytokines such as IFN-gamma and IL-2, promote a cellular response against intracellular pathogens such as viruses, certain bacteria, and cancer through the activation of NK cells and/or CD8+ cytotoxic T cells. In addition, the production of IFN-gamma further promotes the destruction of intracellular bacteria through activation of microbicidal activity in macrophages. Secretion of IFN-gamma also causes antibody class-switching in B cells resulting in the synthesis of distinct antibody isotype. In addition to type 1 cytokines, activated CD4+ T cells may also produce type 2 cytokines such as IL-4, IL-5, IL-10, and IL-13. These cytokines promote a humoral or antibody response against extracellular pathogens. Lastly, CD4+ T cells are also capable of both cytotoxicity as well as the direct killing of intracellular bacteria by the release of the antimicrobial protein granulysin (9).

There is worldwide interest in the use of DNA vaccines encoding various antigens to activate T cell responses in the prevention and/or therapy of infection and cancer. Of the DNA vaccines created thus far, the great majority target the MHC I antigen presentation pathway and result in efficient CD8+ T cell responses (10). Recent studies have demonstrated the possibility of targeting the MHC II antigen presentation pathway through the creation of DNA constructs that encode fusions between antigens of interest and late endosomal/lysosomal/MHC-II compartment (MIIC) targeting sequences (11). Once expressed, the resultant protein fusions enter the MHC II antigen presentation compartments including the MIIC. These constructs have utilized targeting sequences derived from invariant chain (Ii), lysosome integral membrane protein (LIMP-2) (12), and lysosome-associated membrane protein-1 (LAMP-1) (13) in experimental systems to date.

In the present study, we describe a novel method to elicit CD4+ T cell responses in vivo. We evaluate the ability of human CDI -derived endosomal targeting sequences to target three antigens, Mycobacterium leprae GRO ES, M. tuberculosis ESAT-6, and the human melanoma-derived MART-1, to vesicles involved in the MHC II antigen processing/presentation pathway. The human CDI proteins (a-d) are antigen presentation molecules that display differential tissue expression patterns (14). In addition, the different CDI isoforms survey distinct intracellular compartments such that each CDI molecule has a unique intracellular distribution, a distinct advantage over other targeting strategies in which trafficking is limited to MIIC compartments (15). For example, CD la traffics from the cell surface into early recycling endosomes. CD lb and CD Id traffic into more mature endosomal compartments such as late endosomes/lysosomes and MIIC. CDlc traffics to compartments utilized by both CD la and CD lb/CD Id.

Unlike LIMP-1 and Ii which are believed to traffic directly from the trans-Golgi network to the MIIC, the CDI proteins (b-d) enter endosomal vesicles from the cell surface similar to exogenously acquired antigens and traffic through a series of different endosomal compartments prior to their arrival in the MIIC. It has recently been demonstrated that many MHC II epitopes are processed in a MllC-independent manner in earlier endosomal compartments that contain specific proteases. More importantly, direct traffic of antigens to the MIIC may result in the destruction of potential protective MHC II epitopes.

The present invention provides nucleic acid molecules encoding CDI endosomal targeting sequence which direct or target an antigen of interest to the endosomal MHCII antigen presenting pathway. The inventive nucleic acid molecules are useful for inducing an immune response against antigens of interest which are associated with, e.g., microbial or viral infections, and antigens associated with cancers.

SUMMARY OF THE INVENTION

The present invention provides chimeric nucleic acid molecules encoding CDI fusion proteins comprising a leader peptide sequence, a CDI endosomal targeting sequence, and an antigen of interest. The objective of the invention is to present the antigen of interest on the surface of a cell via the MHCII antigen presenting pathway. In the CDI fusion protein, the antigen of interest is joined to the leader peptide sequence and the CDI endosomal targeting sequence which direct production, processing, trafficking, and cell surface presentation of the antigen of interest via the MHCII antigen presenting pathway. The presented antigen of interest can induce an immune response in the subject.

The encoded CDI fusion proteins are produced in a cell and presented on a cell via the endosomal MHCII antigen presenting pathway.

The present invention also provides vectors and host vector systems which comprise the chimeric nucleic acid molecules.

The present invention also provides pharmaceutical compositions comprising the chimeric nucleic acid molecules, vectors or host vector systems.

The present invention provides methods for producing the CDI fusion proteins, methods for targeting the antigen of interest to the MHCII antigen presenting pathway, methods for presenting on a cell the antigen of interest, methods for producing an antigen of interest bound with an MHCII complex, methods for inducing an immune response, methods for inducing an immune response via the MHCII pathway, methods for activating CD4+ T cells, and methods for preventing a variety of disorders including infectious diseases including those caused by viruses, bacteria, fungi, autoimmune disorders, including diabetes, lupus, multiple sclerosis and inhibiting tumor growth.

BRIEF DESCRIPTIONS OF THE FIGURES

Figure 1: Subcellular localization of GFP/CD1 fusion constructs in human cells. All of the cDNA constructs generated for this study contained the same DNA sequence in the leader, GFP, and transmembrane domains. However, each construct encoded a unique CDI -derived cytoplasmic tail.

Figure 2: In vitro T cell stimulation assay using THP-1 cells expressing various Gro

ES/CD1 fusion proteins as antigen presenting cells. A) IFN-gamma production by the Gro ES specific CD4+ T cell line D 103-5 stimulated with THP-1 clones expressing the

Gro ES peptide alone and with CD la and CD lb derived targeting sequences. B) THP-1 cells expressing Gro ES fusions to CDlc and CD Id are also capable of stimulating D103- 5. THP+pep=THP-l cells pulsed with lμM GRO-ES peptide. Semi-quantitative RT- PCR amplification of GRO-ES peptide sequence in b-actin-normalized cDNA preparations are depicted below each graph.

Figure 3: Frequency of ESAT-6-specific CD4+ and CD8+ splenocytes following subcutaneous immunization with rESAT-6 protein+IL-12 or various ESAT-6/CD1 fusion constructs.

Figure 4: ESAT-6-specific IFN-gamma release by splenocytes following intradermal immunization with recombinant ESAT-6+rIL-12 or DNA constructs encoding ESAT-6 alone or fused to different targeting sequences.

Figure 5: Frequency of MART-1 specific cells following DNA immunization in two independent experiments.

Figure 6: Tumor size after DNA immunization.

Figure 7: A schematic diagram showing chimeric nucleic acid constructs of GRO- ES/CD1.

Figure 8A: Nucleotide and amino acid sequence of the GroES/CDla fusion construct.

Figure 8B: Nucleotide and amino acid sequence of the GroES/CDlb fusion construct.

Figure 8C: Nucleotide and amino acid sequence of the GroES/CDlc fusion construct.

Figure 8D: Nucleotide and amino acid sequence of the GroES/CDld fusion construct.

Figure 8E: Nucleotide and amino acid sequence of human CD lb leader peptide sequence. Figure 8F: Nucleotide and amino acid sequence of Gro ES sequence from M. leprae.

Figure 8G: Nucleotide and amino acid sequence of human CDlb transmembrane sequence.

Figure 8H: Nucleotide and amino acid sequences of human CD la, b, c, and d cytoplasmic tail sequences.

Figure 9A: Nucleotide and amino acid sequence of the ESAT-6/CDla fusion construct.

Figure 9B: Nucleotide and amino acid sequence of the ESAT-6/CDlb fusion construct.

Figure 9C: Nucleotide and amino acid sequence of the ESAT-6/CDlc fusion construct.

Figure 9D: Nucleotide and amino acid sequence of the ESAT-6/CDld fusion construct.

Figure 9E: Nucleotide and amino acid sequence of human CDlb leader peptide sequence.

Figure 9F: Nucleotide and amino acid sequence of ESAT-6 sequence from M. tuberculosis.

Figure 9G: Nucleotide and amino acid sequence of human CDlb transmembrane sequence.

Figure 9H: Nucleotide and amino acid sequences of human CD la, b, c, and d cytoplasmic tail sequences.

Figure 10A: Nucleotide and amino acid sequence of the MART-1/CDla fusion construct. Figure 10B: Nucleotide and amino acid sequence of the MART-1/CDlb fusion construct.

Figure IOC: Nucleotide and amino acid sequence of the MART- 1 /CDlc fusion construct.

Figure 10D: Nucleotide and amino acid sequence of the MART- 1 /CD Id fusion construct.

Figure 10E: Nucleotide and amino acid sequence of human CDlb leader peptide sequence.

Figure 10F: Nucleotide and amino acid sequence of human MART-1 sequence.

Figure 10G: Nucleotide and amino acid sequence of human CDlb transmembrane sequence.

Figure 10H: Nucleotide and amino acid sequences of human CD la, b, c, and d cytoplasmic tail sequences.

Figure 1 IA: Nucleotide and amino acid sequence of the EGFP/CDla fusion construct.

Figure IIB: Nucleotide and amino acid sequence of the EGFP/CDlb fusion construct.

Figure 1 IC: Nucleotide and amino acid sequence of the EGFP/CDlc fusion construct.

Figure 11D: Nucleotide and amino acid sequence of the EGFP/CDld fusion construct.

Figure HE: Nucleotide and amino acid sequence of human CDlb leader peptide sequence. Figure 1 IF: Nucleotide and amino acid sequence of enhanced Green Fluorescent Protein

(EGFP).

Figure 11G: Nucleotide and amino acid sequence of human CDlb transmembrane sequence.

Figure 11H: Nucleotide and amino acid sequences of human CD la, b, c, and d cytoplasmic tail sequences.

DETAILED DESCRIPTION OF THE INVENTION

DEFINITIONS

All scientific and technical terms used in this application have meanings commonly used in the art unless otherwise specified. As used in this application, the following words or phrases have the meanings specified.

As used herein, "wild type" refers to a nucleic acid or polypeptide molecule having the same nucleotide and/or amino acid sequence as a naturally-occurring molecule, respectively. A wild type CDI polypeptide molecule has the amino acid sequence of naturally occurring CDI as shown in Figures 8-11 or in Genbank M28825, 28826, 28827 and J04142, or any fragment or portion thereof.

As used herein, the term "derivative" means any modification or alteration of a wild type molecule. Derivatives include, but are not limited to: a substitution, conservative or non- conservative, in a amino acid and/or nucleotide sequence including substitutions by other amino acids, nucleotides, amino acid analogs or nucleotide analogs; a deletion of one or more amino acids and/or nucleotides; an insertion of one or more amino acids and/or nucleotides; and pre- and/or post-translational modifications. A derivative molecule can share sequence similarity and/or activity with its parent molecule. As used herein, a first nucleotide or amino acid sequence is said to have sequence "identity" to a second nucleotide or amino acid sequence, respectively, when a comparison of the first and the second sequences shows that they are exactly alike.

As used herein, a first nucleotide or amino acid sequence is said to be "similar" to a second sequence when a comparison of the two sequences shows that they have few sequence differences (i.e., the first and second sequences are nearly identical). For example, two sequences are considered to be similar to each other when the percentage of nucleotides or amino acids that differ between the two sequences can be between about 60% to 99.99%.

As used herein, the term "complementary" refers to nucleic acid molecules having purine and pyrimidine nucleotide bases which have the capacity to associate through hydrogen bonding to form base pairs thereby mediating formation of double stranded nucleic acid molecules. The following base pairs are related by complementarity: guanine and cytosine; adenine and thymine; and adenine and uracil. Complementary applies to all base pairs comprising two single-stranded nucleic acid molecules, or to all base pairs comprising a single-stranded nucleic acid molecule folded upon itself.

As used herein, the term "conservative" refers to substituting an amino acid residue for a different amino acid residue that has similar chemical properties. A conservative amino acid substitution includes: substituting any hydrophobic (e.g., nonpolar) amino acid for any other hydrophobic amino acid; or substituting any hydrophilic (polar, uncharged) amino acid for any other hydrophilic amino acid; or substituting any positively charged amino acid for any other positively charge amino acid; or substituting any negatively charge amino acid for any other negatively charged amino acid (TE Creighton, "Proteins" WH Freeman and Company, New York). The amino acid substitutions include, but are not limited to, substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A), or glycine (G) and serine (S) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered conservative in particular environments.

As used herein, the term "nonconservative" refers to substituting an amino acid residue for a different amino acid residue that has different chemical properties. The nonconservative substitutions include, but are not limited to aspartic acid (D) being replaced with glycine (G); asparagine (N) being replaced with lysine (K); or alanine (A) being replaced with arginine (R).

The single-letter codes for amino acid residues include the following: A = alanine, R = arginine, N = asparagine, D = aspartic acid, C = cysteine, Q = Glutamine, E = Glutamic acid, G = glycine, H = histidine, I = isoleucine, L = leucine, K = lysine, M = methionine, F = phenylalanine, P = proline, S = serine, T = threonine, W = tryptophan, Y = tyrosine, V = valine.

In order that the invention herein described can be more fully understood, the following description is set forth.

MOLECULES OF THE INVENTION

The molecules of the present invention include nucleic acid molecules encoding a CDI fusion protein, or fragments or derivatives thereof. The nucleic acid molecules of the invention comprise CDI endosomal targeting sequences joined to an antigen of interest. These nucleic acid molecules are useful because they are used to produce a CDI fusion protein in a cell (which includes the antigen of interest) and direct the antigen of interest to be presented on the surface of a cell via the MHCII antigen presenting pathway.

In its various aspects, the present invention provides: CDI fusion proteins, or fragments or derivatives thereof; nucleic acid molecules encoding the CDI fusion proteins, or fragments or derivatives thereof; recombinant DNA molecules; transformed host cells; host-vector systems; methods for producing the nucleic acid an CDI fusion proteins; methods for using the compositions of the invention; and assays.

NUCLEIC ACID COMPOSITIONS

The present invention provides chimeric nucleic acid molecules encoding CDI fusion proteins. The chimeric nucleic acid molecules encode CDI fusion proteins comprising a leader peptide sequence, a CDI endosomal targeting sequence and an antigen of interest. The CDI fusion protein can also include a transmembrane domain.

The leader peptide sequence is any amino acid sequence, that is part of a polypeptide, that directs movement of the polypeptide through the cell. For example, the leader sequence directs secretion of the polypeptide through a cell membrane, including secreting the polypeptide to the cell surface. The leader peptide directs co-translational insertion of the nascent polypeptide into the lumen of an endoplasmic reticulum. The leader peptide sequence is from any polypeptide, including immunoglobulin, oncostatin- M, beta actin, or ompA. In one embodiment, the leader peptide sequence is a CDI leader peptide sequence.

The CDI endosomal targeting sequence is any amino acid sequence that directs the CDI fusion protein to the endosomal MHCII antigen presenting pathway in a cell (Figures 8- 11, or Genbank M28825, 28826, 28827 and J04142). The CDI endosomal targeting sequence includes the cytoplasmic tail domain of a CDI protein. In one embodiment, the CDI endosomal targeting sequence includes a tyrosine motif YXXZ, where Y is tyrosine, X is any amino acid, and Z is a bulky hydrophobic amino acid. The bulky hydrophobic amino acid is alanine, isoleucine, leucine methionine, phenylalanine, proline, trytophan or valine. For example, the tyrosine motif comprises the amino acid sequence: YQNIP (Tyr-Gln-Asn-Ile-Pro). In another embodiment, the CDI endosomal targeting sequence includes a dileucine motif having the amino acid sequence leucine-leucine, valine- valine, or isoleucine-leucine. The CDI fusion protein can include the tyrosine and/or dileucine motif (s).

The transmembrane sequence is any amino acid sequence comprising hydrophobic amino acid residues which function to anchor the CDI fusion protein to the surface of a cell, hi one embodiment, the transmembrane sequence is a CDI transmembrane sequence (e.g., Figures 8G, 9G, 10G and 11G).

The leader peptide sequence and/or the CDI endosomal targeting sequence and/or the transmembrane domain are from any one CDI isoform, or any combination of any CDI isoforms, or portion thereof, including CD la (Genbank M28825), CDlb (Genbank M28826), CDlc (Genbank M28827), and CDld (Genbank J04142).

The chimeric nucleic acid molecules of the invention comprise a leader peptide sequence and/or a CDI endosomal targeting sequence and/or a transmembrane sequence from any species, or a combination or portions thereof, including human, bovine, porcine, murine, equine, canine, feline, simian, ovine, piscine or avian.

In one embodiment, the nucleotide sequence encoding a leader sequence is shown in Figures 8E, 9E, 10E or HE.

In another embodiment, the nucleotide sequence encoding a CDI endosomal targeting sequence is shown in Figures 8H, 9H, 10H or 1 IH.

In another embodiment, the nucleotide sequence encoding the transmembrane sequence is shown in Figures 8G, 9G, 10G or 11 G. In another embodiment, the nucleotide sequence encoding a CDI fusion protein is shown in any one of Figures 8A-D, 9A-D, 10A-D and 11A-D.

The chimeric nucleic acid molecules of the invention encode CDI fusion proteins including an antigen of interest against which an elicited immune response is desired. The antigen of interest includes a whole or a portion of a protein against which an elicited immune response is desired. The antigen of interest includes any protein associated with infective organisms, such as bacterial proteins, viral proteins and fungal proteins. The antigen of interest also includes any tumor associated antigens, cell surface proteins, antigens associated with immune system diseases, or reporter proteins.

The antigen of interest is a protein from any bacterial species, including but not limited to Mycobacteria (e.g. species leprae, tuberculosis, avium, intracellulare, kansaii, gordonae); Pseudomonas; Yersinia; Salmonella; Helicobacter (e.g., species pyloris); Borelia (e.g., species burgdorferi); Legionella (e.g., species pneumophilia); Staphylococcus (e.g., species aureus); Neisseria (e.g., species gonorrhoeae, meningitides); Listeria (e.g., species monocytogenes); Streptococcus (e.g., species pyogenes, agalactiae, viridans, faecalis, bovis, pneumoniae, and sps. Anaerobic); Campylobacter; Enterococcus; Haemophilus (e.g., species influenzae); Bacillus (e.g., species antracis); Corynebacterium (e.g., species diphtheriae); Erysipelothrix (e.g., species (rhusiopathiae); Clostridium (e.g. species perfringers, tetani); Enterobacter (e.g., species aerogenes); Klebsiella (e.g., species pneumoniae); Pasturella (e.g., species multocida); Bacteroides; Fusobacterium (e.g., nucleatum); Streptobacillus (e.g., species moniliformis); Treponema (e.g., species palladium); Treponema (e.g., species pertenue); Leptospira, Actinomyces (e.g., species israelli).

In one embodiment, the antigen of interest includes bacterial proteins such as GRO ES (29), ESAT-6 (30), antigen 85 complex from M. tuberculosis (e.g., Af85A, Ag85B).

The antigen of interest is a protein from any virus, including: Retroviridae (e.g., human immunodeficiency viruses, including HIV-1, HTLV-III, LAV, HTLV-III/LAV, HIV-III and HIV-LP); Picornaviridae (e.g., polio viruses, hepatitis A virus; enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g., strains that cause gastroenteritis); Togaviridae (e.g., equine encephalitis viruses, rubella viruses); Flaviridae (e.g., dengue viruses, encephalitis viruses, yellow fever viruses); Coronaviridae (e.g., coronaviruses); Rhabdoviridae (e.g., vesicular stomatitis viruses, rabies viruses); Filoviridae (e.g., ebola viruses); Paramyxoviridae (e.g., parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (e.g., influenza viruses); Bungaviridae (e.g., Hantaan viruses, bunga viruses, phlebovϊruses and Nairo viruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g., reoviruses, orbiviurses and rotaviruses); Birnaviridae; Hepadnaviridae (Hepatitis B virus); Parvoviridae (parvo viruses); Papovaviridae (papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses); Herpesviridae (heφes simplex virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), heφes viruses); Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g., African swine fever virus); etiological agents of Spongiform encephalopathies; agents of delta hepatitis; agents of non-A, non-B hepatitis; Hepatitis C; Norwalk viruses, and astroviruses.

In one embodiment, the antigen of interest from a virus includes RSV, HIV, and hepatitis A, B, or C.

The antigen of interest is a protein from an infectious fungus include: Cryptococcus neoformans; Histoplasma capsulatum; Coccidioides immitis; Blastomvces dermatitidis; Chlamydia trachomatis; and Candida albicans.

The antigen of interest also includes other infectious organisms such as Plasmodium falciparum and Toxoplasma gondii.

The antigen of interest includes tumor associated antigens from various tumors, such as skin, pancarcinoma, breast, small cell lung, non-small cell lung, gastrointestinal, prostate, bladder, ovarian, melanoma, central nervous system tumors, leukemias, lymphomas, and sarcomas. In one embodiment, the tumor associated antigen includes MART-1 (31), Melan-A, tyrosinase, p97, beta-HCG, GalNAc, MAGE-1, MAGE-2, MAGE-4, MAGE-12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, K19, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSA, PSM, alpha-fetoprotein, thyroperoxidase, gplOO, and pl85^neu.

The antigen of interest includes cell surface proteins, such as Carcinoembryonic Antigen (CEA), and Prostate Specific Antigen (PSA).

The antigen of interest includes antigens associated with immune system diseases, where the immune system disease is any disease mediated by B cell-T cell interactions including, but not limited to, autoimmune diseases, graft related disorders and immunoproliferative diseases. Examples of immune system diseases include graft versus host disease (GVHD) (e.g., such as may result from bone marrow transplantation, or in the induction of tolerance), immune disorders associated with graft transplantation rejection, chronic rejection, and tissue or cell allo- or xenografts, including solid organs, skin, islets, muscles, hepatocytes, neurons. Examples of immunoproliferative diseases include, but are not limited to, psoriasis, T-cell lymphoma, T-cell acute lymphoblastic leukemia, testicular angiocentric T-cell lymphoma, benign lymphocytic angiitis, lupus (e.g. lupus erythematosus, lupus nephritis), Hashimoto's thyroiditis, primary myxedema, Graves' disease, pernicious anemia, autoimmune atrophic gastritis, Addison's disease, diabetes (e.g. insulin dependent diabetes mellitis, type I diabetes mellitis, type II diabetes mellitis), good pasture's syndrome, myasthenia gravis, pemphigus, Crohn's disease, sympathetic ophthalmia, autoimmune uveitis, multiple sclerosis, autoimmune hemolytic anemia, idiopathic thrombocytopenia, primary biliary cirrhosis, chronic action hepatitis, ulceratis colitis, Sjogren's syndrome, rheumatic diseases (e.g. rheumatoid arthritis), polymyositis, scleroderma, and mixed connective tissue disease.

The antigen of interest includes reporter gene products, including green fluorescent protein (GFP) (32), glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase (GUS), luciferase, luciferin, anthocyanins, or blue fluorescent protein (BFP). Other reporter gene products include HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), all available commercially from Clontech.

The antigen of interest includes, leucocyte antigens, including: CDI, CD2, CD3/TCR, CD4, CD5, CD6, CD7, CD8, CD9, CD10, CDI la, CDI lb, CDl lc, Intergrin alpha-D subunit, CDwl2, CD13, CD14, CD15, CD15s, CD16, CDwl7, CD18, CD19, CD20, CD21, CD22, CD23, CD24, CD26, CD27, CD29, CD30, CD31, CD32, CD33, CD34, CD35, CD36, CD37, CD38, CD39, CD41, CD42a,b, CD43, CD44, CD45, CD46, CD47, CD48, CD49a, CD49b, CD49c, CD49d, CD49e, CD49f, CD50, CD51, CD52, CD53, CD54, CD55, CD56, CD57, CD58, CD59, CD60, CD61, CD62E, CD62L,CD62P, CD63, CD64, CD65, CD66, CD68, CD69, CD70, CD71, CD72, CD73, CD74, CDw75, CDw76, CD77, CD79/BCR, CD81, CD82, CD83, CDw84, CD85, CD87, CD88, CD89, CD90, CD91, CDw92, CD93, CD94, CD95, CD96, CD97, CD98, CD99, CD100, CD101, CD102, CD103, CD104, CD105, CD106, CD107a, CD107b, CDwl08, CD109, CDI 17, CD120a, CD120b, CD134, CD135, CDwl37, CD138, CD147, CD148, CDwl50, CD151, CD153, CD154, CD161, CD162, CD163, CD166, 114/A10, 2B4, 4-IBBL, Aminopeptidase A, B-G, Chemokine receptors, c-kitL, CMRF35 antigen, DEC-205, DNAM-1, ESL-1, F4/80, FasL, FceRI, FLT3 ligand, FPR, Galectin 3, G-CSFR, GM- CSFR, GlyCAM-1, gp42, gp49, HTm4, IFN7R, IL-IR, IL-2R, IL-3R, IL-4R, I1-5R, IL- 6R, IL-7R, IL-8R, IL-9R, IL-10R, IL-11R, IL-12R, IL-13R, IL-14R, IL-15R, IL-17R, Integrin β7 subunit, KIR family, LI, LAG-3, LDLR, LPAP, ltk, Ly-6, Ly-9, Ly-49, Mac- 2-BP, Macrophage lectin, MAdCAM-1, Mannose receptor, MARCO, M-CSFR, MDR1, MS2, NKG2 family, OX2, OX40L, PC-1, PD-1, RT6, Sca-2, Scavenger Rl and II, Sialoadhesin, Thrombopoietin receptor, and WC1.

Isolated Nucleic Acid Molecules

The nucleic acid molecules of the invention are preferably in isolated form, where the nucleic acid molecules are substantially separated from contaminant nucleic acid molecules having sequences other than CDI fusion protein sequences. A skilled artisan can readily employ nucleic acid isolation procedures to obtain isolated, CDI fusion protein sequences (Sambrook et al., in: "Molecular Cloning" 1989). The present invention also provides for isolated nucleic acid molecules generated by recombinant DNA technology or chemical synthesis methods. The present invention also provides nucleic acid molecules isolated from various mammalian species including, bovine, porcine, murine, equine, canine, feline, simian, ovine or human, or other sources such as piscine, avian or insect.

The isolated nucleic acid molecules include DNA, RNA, DNA/RNA hybrids, and related molecules, nucleic acid molecules complementary to the nucleotide sequences encoding CDI fusion proteins, or a fragment or derivative thereof, and those which hybridize to the nucleic acid molecules that encode the CDI fusion proteins. The preferred nucleic acid molecules have nucleotide sequences identical to or similar to the nucleotide sequences disclosed herein. Specifically contemplated are genomic DNA, RNA e.g., small interfering RNA, cDNA, ribozymes and antisense molecules.

The present invention provides various isolated, and recombinant nucleic acid molecules, or fragments or derivatives thereof, comprising polynucleotide sequences encoding the CDI fusion proteins of the invention. The present invention also provides polynucleotide sequences that encode a fragment or derivative of the CDI fusion proteins. The present invention further provides related polynucleotide molecules, such as polynucleotide sequences complementary to the chimeric nucleic acid molecules of the invention, or a part thereof, and those that hybridize to the nucleic acid molecules of the invention.

The polynucleotide sequences of the invention, are preferably in isolated form, and include, but are not limited to, DNA, RNA, DNA RNA hybrids, and related molecules, and fragments thereof. Specifically contemplated are genomic DNA, cDNA, ribozymes, and antisense RNA or DNA molecules, small, interfering RNA (siRNA), as well as nucleic acids molecules based on an alternative backbone or including alternative bases, whether derived from natural sources or synthesized. The nucleic acid molecules of the invention encode the CDI fusion proteins of the invention and/or fragments or derivatives thereof, where the encoded CDI fusion proteins exhibit similar or identical functional activity of a naturally-occurring CDI protein.

In accordance with the practice of the invention, the nucleic acid molecules of the invention can be isolated full-length or partial length molecules or oligomers of the CDI fusion protein nucleotide sequences. The nucleotide sequence of the invention can encode all or portions of the CDI fusion proteins of the invention, including the leader sequence, CDI endosomal targeting sequence, and antigen of interest. The nucleotide sequence can also encode a CDI transmembrane sequence.

Identical and Similar Nucleotide Sequences

The present invention provides isolated nucleic acid molecules having polynucleotide sequences identical or similar to the CDI fusion proteins sequences disclosed herein. Accordingly, the polynucleotide sequences can be identical to a particular CDI fusion proteins sequence, as described in Figures 8A-D, 9A-D, 10A-D, and 11 A-D. Alternatively, the polynucleotide sequences can be similar to the disclosed sequences.

One embodiment of the invention provides nucleic acid molecules that exhibit sequence identity or similarity with the CDI fusion proteins nucleotide sequences, such as molecules that have at least 60%> to 99.9% sequence similarity and up to 100% sequence identity with the sequences of the invention as shown in Figures 8A-D, 9A-D, 10A-D, and 11 A-D. Another embodiment provides nucleic acid molecules that exhibit between about 75% to 99.9%o sequence similarity, and another embodiment provides molecules that have between about 86% to 99.9% sequence similarity. Yet another embodiment provides molecules that have 100% sequence identity with the CDI fusion proteins sequences of the invention as shown in Figures 8A-D, 9A-D, 10A-D, and 11A-D. Complementary Nucleotide Sequences

The present invention also provides nucleic acid molecules that are complementary to the sequences as described in Figures 8A-D, 9A-D, 10A-D, and 11 A-D. Complementarity can be full or partial. A nucleotide sequence that is fully complementary is complementary to the entire CDI fusion protein nucleotide sequence as described in any one of Figures 8A-D, 9A-D, 10A-D, and 11 A-D. A nucleotide sequence that is partially complementary is complementary to only a portion of sequences as described in any one of Figures 8A-D, 9A-D, 10A-D, and 11 A-D. The complementary molecules include anti- sense nucleic acid molecules. The anti-sense molecules are useful for RNA interference (RNAi), DNA interference, inhibiting growth of a cell or killing a cell expressing a naturally-occurring CDI molecule or expressing a CDI fusion proteins. The complementary molecules also include small interfering RNA (siRNA) (Elbashir et al, 2001, Nature 411:494-498; Hammond et al, 2001, Nature Review 2:110-119).

Hybridizing Nucleic Acid Molecules

The present invention further provides nucleic acid molecules having polynucleotide sequences that selectively hybridize to the CDI fusion protein nucleotide sequences of the invention as shown in any one of Figures 8A-D, 9A-D, 10A-D, and 11 A-D. The nucleic acid molecules that hybridize can hybridize under high stringency hybridization conditions. Typically, hybridization under standard high stringency conditions will occur between two complementary nucleic acid molecules that differ in sequence complementarity by about 70% to about 100%. It is readily apparent to one skilled in the art that the high stringency hybridization between nucleic acid molecules depends upon, for example, the degree of identity, the stringency of hybridization, and the length of hybridizing strands. The methods and formulas for conducting high stringency hybridizations are well known in the art, and can be found in, for example, Sambrook, et al., in: "Molecular Cloning" (1989). h general, stringent hybridization conditions are those that: (1) employ low ionic strength and high temperature for washing, for example, 0.015M NaCl/0.0015M sodium titrate/0.1%) SDS at 50 degrees C; or (2) employ during hybridization a denaturing agent such as formamide, for example, 50% (vol/vol) formamide with 0.1%> bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42 degrees C.

Another example of stringent conditions include the use of 50% formamide, 5 x SSC (0.75M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 mg/ml), 0.1%> SDS, and 10% dextran sulfate at 42 degrees C, with washes at 42 degrees C in 0.2 x SSC and 0.1% SDS. A skilled artisan can readily determine and vary the stringency conditions appropriately to obtain a clear and detectable hybridization signal.

Nucleic Acid Fragments

The present invention further provides nucleic acid molecules encoding fragments of the CDI fusion proteins of the invention, such as a portion of the CDI fusion proteins sequences disclosed herein and as shown in any one of Figures 8 A-D, 9 A-D, 10A-D, and 11 A-D. The size of the fragment will be determined by its intended use. For example, if the fragment is chosen to encode a CDI fusion protein comprising the endosomal targeting sequence or domain of a naturally-occurring, wild-type CDI molecule, then the skilled artisan shall select the polynucleotide fragment that is large enough to encode this domain(s). If the fragment is to be used as a nucleic acid probe or PCR primer, then the fragment length is chosen to obtain a relatively small number of false positives during a probing or priming procedure.

The nucleic acid molecules, fragments thereof, and probes and primers of the present invention are useful for a variety of molecular biology techniques including, for example, hybridization screens of libraries, or detection and quantification of mRNA transcripts as a means for analysis of gene transcription and/or expression. The probes and primers can be DNA, RNA or derivatives of DNA or RNA molecules. A probe or primer length of at least 15 base pairs is suggested by theoretical and practical considerations (Wallace, B. and Miyada, G. 1987 in: "Oligonucleotide Probes for the Screening of Recombinant DNA Libraries" in: Methods in Enzymolo y, 152:432-442, Academic Press).

Fragments of the CDI fusion protein nucleotide sequences that are particularly useful as selective hybridization probes or PCR primers can be readily identified from the CDI fusion protein nucleotide sequences, using art-known methods. For example, sets of PCR primers that bind and/or detect a portion of CDI fusion protein transcripts can be made by the PCR method described in U.S. Patent No. 4,965,188. The probes and primers of this invention can be prepared by methods well known to those skilled in the art (Sambrook, et al. supra). The probes and primers can be synthesized by chemical synthesis methods (ed: Gait, M. J. 1984 in: "Oligonucleotide Synthesis", IRL Press, Oxford, England).

One embodiment of the present invention provides nucleic acid primers that are complementary to the CDI fusion protein sequences, which allow specific amplification of nucleic acid molecules of the invention or of any specific portions thereof. Another embodiment provides nucleic acid probes that are complementary for selectively or specifically hybridizing to the CDI fusion protein sequences or to any portion thereof.

Fusion Gene Sequences

The present invention provides fusion gene sequences, which include a CDI fusion protein sequence fused (e.g., linked or joined) to a non-CD 1 fusion sequence. The CDI fusion proteins sequence is operatively fused, in-frame, to a non-CD 1 fusion sequence.

The fusion gene sequences of the invention include a nucleotide sequence encoding CDI fusion proteins fused to an epitope tag, including but not limited to, histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags. The fusion gene sequences of the invention include a nucleotide sequence encoding CDI fusion proteins fused to a full-length or partial-length reporter gene sequence, including but not limited to glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), and autofluorescent proteins including blue fluorescent protein (BFP). Reporter sequences also include HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP)

The fusion gene sequences of the invention include a nucleotide sequence encoding CDI fusion proteins fused to a gene sequence encoding a protein or a fragment of a protein that bind DNA molecules or bind other cellular molecules, including but not limited to maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and heφes simplex virus (HSV) BP16 protein fusions.

The fusion gene sequences of the invention include a nucleotide sequence encoding CDI fusion proteins fused to a gene sequence encoding a cleavage site moiety. The cleavage site can be located between the CDI fusion proteins-encoding sequence and the cleavage sequence. The cleavage site moiety includes, but is not limited to thrombin, and factor Xa recognition sequences.

Chimeric Nucleotide Sequences

The present invention provides chimeric gene sequences encoding recombinant, chimeric CDI fusion proteins. The chimeric molecules encode chimeric polypeptides operatively fused, in-frame. The chimeric nucleotide molecules encode a portion of a CDI protein isolated from a first source fused to a portion of a CDI protein isolated from a second, different source.

In one example, a chimeric nucleotide molecule encodes the CDI leader peptide sequence of a CDI molecule from a first source, fused to the CDI endosomal targeting sequence or domain of a CDI molecule from a second source. In another example, a chimeric nucleotide molecule encodes a portion of the leader peptide sequence of a CDI molecule from a first source, fused to the remaining portion of the leader peptide sequence of a CDI molecule from a second source.

Codon Usage Variants

The present invention provides isolated codon-usage variants that differ from the disclosed CDI fusion protein nucleotide sequences, yet do not alter the predicted polypeptide sequence or biological activity of the encoded CDI fusion proteins. For example, a number of amino acids are designated by more than one triplet codon. Codons that specify the same amino acid can occur due to degeneracy in the genetic code. Examples include nucleotide codons CGT, CGG, CGC, and CGA encoding the amino acid, arginine (R); or codons GAT, and GAC encoding the amino acid, aspartic acid (D). Thus, a protein can be encoded by one or more nucleic acid molecules that differ in their specific nucleotide sequence, but still encode protein molecules having identical sequences. The amino acid coding sequence is as follows:

Amino Acid Symbol One Letter Codons Symbol

Alanine Ala A GCU, GCC, GCA, GCG

Cysteine Cys C UGU, UGC

Aspartic Acid Asp D GAU, GAC

Glutamic Acid Glu E GAA, GAG

Phenylalanine Phe F UUU, UUC

Glycine Gly G GGU, GGC, GGA, GGG

Histidine His H CAU, CAC

Isoleucine Ile I AUU, AUC, AUA

Lysine Lys K AAA, AAG

Leucine Leu L UUA, UUG, CUU, CUC, CUA, CUG

Methionine Met M AUG

Asparagine Asn N AAU, AAC Amino Acid Symbol One Letter Codons Symbol

Proline Pro P CCU, CCC, CCA, CCG

Glutamine Gin Q CAA, CAG

Arginine Arg R CGU, CGC, CGA, CGG, AGA, AGG

Serine Ser S UCU, UCC, UCA, UCG, AGU, AGC

Threonine Thr T ACU, ACC, ACA, ACG

Valine Val V GUU, GUC, GUA, GUG

Tryptophan Tφ w UGG

Tyrosine Tyr Y UAU, UAC

The codon-usage variants can be generated by recombinant DNA technology. Codons can be selected to optimize the level of production of the CDI fusion protein transcript or the CDI fusion proteins in a particular prokaryotic or eukaryotic expression host, in accordance with the frequency of codon utilized by the host cell. Alternative reasons for altering the nucleotide sequences encoding a CDI fusion proteins include the production of RNA transcripts having more desirable properties, such as an extended half-life or increased stability. A multitude of variant CDI fusion protein nucleotide sequences that encode the respective CDI fusion proteins can be isolated, as a result of the degeneracy of the genetic code. Accordingly, the present invention provides selecting every possible triplet codon to generate every possible combination of nucleotide sequences that encode the disclosed CDI fusion proteins, or that encode molecules having the biological activity of the CDI fusion proteins. This particular embodiment provides isolated nucleotide sequences that vary from the sequences as described in described in any one of Figures 8A-D, 9A-D, 10A-D, and 11 A-D, such that each variant nucleotide sequence encodes a molecule having sequence identity with the amino acid sequence described in Figures 8A-D, 9A-D, 10A-D, and 11 A-D.

Variant Nucleotide Sequences

The present invention provides nucleic acid molecules comprising polynucleotide sequences encoding variant forms of any of the CDI fusion proteins of the invention. The variant nucleotide sequences encode variant forms of the leader peptide sequence of the CDI fusion proteins. The variant nucleotide sequences encode variant forms of the endosomal targeting domain of the CDI fusion proteins of the invention. The variant nucleotide sequences encode variant forms of the transmembrane domain of the CDI fusion proteins. In one embodiment, the variant nucleotide sequences encode variant CDI fusion proteins having the same or similar functional activity of a naturally- occurring, wild-type CDI molecule.

The variant nucleotide sequences of the present invention include conservative or non- conservative amino acid substitutions. The variant nucleotide sequences include mutations such as amino acid substitutions, deletions, insertions, additions, truncations, or processing or cleavage enors of the protein. The variant nucleotide sequences include allelic, homolog, or ortholog variants of the naturally-occurring CDI sequence.

Derivative Nucleic Acid Molecules

The nucleic acid molecules of the invention also include derivative nucleic acid molecules which differ from DNA or RNA molecules, and anti-sense molecules. Derivative molecules include peptide nucleic acids (PNAs), and non-nucleic acid molecules including phosphorothioate, phosphotriester, phosphoramidate, and methylphosphonate molecules, that bind to single-stranded DNA or RNA in a base pair- dependent manner (PC Zamecnik, et al, 1978 Proc. Natl. Acad. Sci. 75:280284; PC Goodchild, et al., 1986 Proc. Natl. Acad. Sci. 83:4143-4146). Peptide nucleic acid molecules comprise a nucleic acid oligomer to which an amino acid residue, such as lysine, and an amino group have been added. These small molecules, also designated anti-gene agents, stop transcript elongation by binding to their complementary (template) strand of nucleic acid (PE Nielsen, et al., 1993 Anticancer Drug Des 8:53-63). Reviews of methods for synthesis of DNA, RNA, and their analogues can be found in: Oligonucleotides and Analogues, eds. F Eckstein, 1991, IRL Press, New York; Oligonucleotide Synthesis, ed. MJ Gait, 1984, IRL Press, Oxford, England. Additionally, methods for antisense RNA technology are described in U. S. patents 5,194,428 and 5,110,802. A skilled artisan can readily obtain these classes of derivative nucleic acid molecules using the herein described CDI fusion proteins polynucleotide sequences, see for example "Innovative and Perspectives in Solid Phase Synthesis" (1992) Egholm, et al. pp 325-328 orU. S. Patent No. 5,539,082.

Labeled Nucleic Acid Molecules

The present invention provides nucleic acid molecules of the invention linked or labeled with a detectable marker. Examples of a detectable marker include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator or an enzyme. Technologies for generating labeled nucleic acid molecules are well known, see, for example, Sambrook et al., in Molecular Cloning (1989).

VECTORS

The present invention provides recombinant, chimeric nucleic acid molecules that include nucleotide sequences encoding the CDI fusion protein, or a fragment or a derivative thereof, as described herein. The chimeric nucleic acid molecule is a DNA molecule that has been subjected to molecular manipulation in vitro. Methods for generating chimeric DNA molecules are well known in the art, for example, see Sambrook et al., Molecular Cloning (1989). In one embodiment, the chimeric DNA molecules of the present invention are operably linked to one or more expression control sequences and/or vector sequences.

The chimeric nucleic acid molecules of the invention each comprise the polynucleotide sequence, or fragments or derivatives thereof, encoding a CDI fusion protein linked to a vector to generate a recombinant vector molecule.

The term vector includes, but is not limited to, plasmids, cosmids, BACs, YACs PACs and phagemids. The vector can be an autonomously replicating vector comprising a replicon that directs the replication of the vector within the appropriate host cell. Alternatively, the vector directs integration of the recombinant vector into the host cell. Various viral vectors can also be used, such as, for example, a number of well known retroviral and adenoviral vectors (Berkner 1988 Biotechniques 6:616-629).

The vectors of the invention permit expression of the CDI fusion protein, or fragments or derivatives thereof, in prokaryotic or eukaryotic host cells. The vectors can be expression vectors, comprising an expression control element, such as a promoter sequence, which enables transcription of the CDI fusion protein nucleotide sequence and can be used for regulating the expression (e.g., transcription and/or translation) of a linked CDI fusion protein sequence in an appropriate host cell.

The expression control elements can be of various origins, including naturally-occurring and synthetic. The naturally-occurring elements can be cellular or viral in origin. Expression control elements are known in the art and include, but are not limited to, inducible promoters, constitutive promoters, secretion signals, enhancers, transcription terminators, and other transcriptional regulatory elements.

Other expression control elements that are involved in translation are known in the art, and include the Shine-Dalgamo sequence (e.g., prokaryotic host cells), and initiation and termination codons. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic.

The promoters can be inducible which are regulated by environmental stimuli or the growth medium of the cells, including those from the genes for heat shock proteins, alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, enzymes associated with nitrogen catabolism, and enzymes responsible for maltose and galactose utilization.

The promoters can be constitutive including yeast beta-factor, alcohol oxidase, cytomegalovirus, and PGH. For reviews, see Ausubel et al (1987 Cunent Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.) and Grant et al (1987 Methods in Enzymology 153:516-544).

The efficiency of transcription can be augmented by the inclusion of enhancers appropriate to the cell system in use (Scharf, D., et al, 1994 Results Probl. Cell. Differ. 20:125-62; Bittner, et al., 1987 Methods in Enzymol. 153:516-544). Viral promoters include SV40 early promoter or the promoter included within the LTR of a retroviral vector. Other viral promoters include the cytomegalovirus promoter (M Boshart, et al., 1985 Cell 41:521-530).

Commonly used eukaryotic control sequences for use in expression vectors include promoters and control sequences compatible with mammalian cells such as, for example, CMV promoter and avian sarcoma virus (ASV) (πLN vector). Other commonly used promoters include the early and late promoters from Simian Virus 40 (SV40) (Fiers, et al., 1973 Nature 273:113), or other viral promoters such as those derived from polyoma, Adenovirus 2, and bovine papilloma virus. An inducible promoter, such as hMTII (Karin, et al., 1982 Nature 299:797-802) can also be used.

Transcriptional control sequences for yeast vectors include promoters for the synthesis of glycolytic enzymes (Hess et al., 1968) J Adv Enzyme Reg. 7:149; Holland et al., 1978 Biochemistry 17:4900). Additional promoters known in the art include the CMV promoter provided in the CDM8 vector (Toyama and Okayama 1990 FEBS 268:217- 221); the promoter for 3-phosphoglycerate kinase (Hitzeman et al., 1980 J Biol Chem 255:2073), and those for other glycolytic enzymes.

Specific translation initiation signals can also be required for efficient translation of a CDI fusion protein sequence. These signals include the ATG-initiation codon and adjacent sequences. The ATG-initiation sequences or upstream sequences of a naturally- occurring CDI molecule can be inserted into the appropriate expression vector. Alternatively, a synthetic ATG-initiation codon and other sequences can be used. The ATG-initiation codon must be in the conect reading-frame to ensure translation of the insert sequence.

The expression control elements can be placed at the 3' end of the coding sequences. These sequences can act to stabilize messenger RNA. Such terminators are found in the 3' untranslated region following the coding sequences in several yeast-derived and mammalian genes.

The expression vector can include at least one selectable marker gene encoding a gene product that confers drug resistance such as resistance to kanamycin, ampicillin or tetracyline.

The expression vector can include any marker gene. These include, but are not limited to, the heφes simplex virus thymidine kinase (M Wigler et al., 1977 Cell 11:223-32) and adenine phosphoribosyltransferase (I Lowy et al., 1980 Cell 22:817-23) genes which can be employed in tk-minus or aprt-minus cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (M Wigler et al., 1980 Proc Natl Acad Sci 77:3567-70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (F Colbere-Garapin et al., 1981 J. Mol. Biol. 150:1-14) and ais or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (LE Muny, in: McGraw Yearbook of Science and Technology (1992) McGraw Hill New York N.Y., pp 191-196). Additional selectable genes have been described, for example, tφB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman, and Mulligan 1988 Proc. Natl. Acad. Sci. 85:8047-51). Recently, the use of visible markers has gained popularity with such markers as anthocyanins, β-glucuronidase and its substrate, GUS, and luciferase and its substrate, luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (CA Rhodes et al., 1995 Methods Mol. Biol. 55:121-131).

The vector also comprises multiple endonuclease restriction sites that enable convenient insertion of exogenous DNA sequences. Methods for generating a recombinant expression vector encoding the CDI fusion proteins of the invention are well known in the art (T Maniatis, et al., 1989 Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; F Ausubel, et al. 1989 Cunent Protocols in Molecular Biology, John Wiley & Sons, New York N.Y.).

The expression vectors used for generating CDI fusion proteins are compatible with eukaryotic host cells. The vectors can be compatible with vertebrate cells. These vectors can include expression control elements such as promoters and/or enhancers from mammalian genes or mammalian viruses. Other expression vectors can include tissue- or cell-specific promoters and/or enhancers from mammalian genes or mammalian viruses.

The expression vectors can be compatible with other eukaryotic host cells, including insect, plant, or yeast cells. The expression vectors can include expression control elements, such as the baculovirus polyhedrin promoter for expression in insect cells. The promoters and/or enhancers derived from plant cells (e. g., heat shock, RUBISCO, storage protein genes), viral promoters or leader sequences or from plant viruses can also be used.

Eukaryotic cell expression vectors are well known in the art and are available from several commercial sources, including PSVL and pKSV-10 (Pharmacia), pBPV-l/pML2d

(International Biotechnologies, Inc.), pTDTl (ATCC, #31255), and similar eukaryotic expression vectors. Examples of expression vectors for eukaryotic host cells include, but are not limited to, vectors for mammalian host cells including: BPV-1; pHyg; pRSV; pSV2; pTK2 (Maniatis); pIRES (Clontech); pRc/CMV2; pRc/RSV; pSFVl (Life Technologies); pVPakc Vectors; pCMV vectors; pSG5 vectors (Stratagene); retroviral vectors (e.g., pFB vectors (Stratagene)); pCDNA-3 (Invitrogen) or modified forms thereof; adenoviral vectors; Adeno-associated virus vectors; baculovirus vectors. Other expression vectors for eukaryotic host cells include pESC vectors (Stratagene) for yeast and pFastBac for expression in insect cells (Gibco/BRL, Rockville, MD). In one embodiment, the expression vector can be pSR-alpha-neo (M Sugita, et al., 1996 Science

273:349). The expression vectors can include expression control elements for expression in bacterial host cells. These expression control elements can be induced by environmental conditions such as heat-shock, or by addition of agents such as isopropyl-jδ-D-thiogalactopyranoside (e.g., IPTG) (N Yamaguchi, et al. 2002 The J of Biol Chem 277:6806-6812). Prokaryotic cell expression vectors are well known in the art and are available from several commercial sources. For example, pGEX vector (Promega, Madison, WI), pTrcHisB vector (Invitrogen), pET vector (e.g., pET-21, Novagen Coφ.), BLUESCRIPT phagemid (Stratagene, LaJolla, CA), pSPORT (Gibco BRL, Rockville, MD), or pfrp-lac hybrids can be used to express the CD 1 fusion proteins in bacterial host cells.

HOST-VECTOR SYSTEMS

The present invention further provides a host- vector system comprising a vector, plasmid, phagemid, BAC, PAC, YAC or cosmid comprising a CDI fusion protein nucleotide sequence, or a fragment or derivative thereof, introduced into a suitable host cell.

The host-vector system can be used to transcribe and/or produce the CDI fusion proteins of the invention. A variety of expression vector/host systems can be utilized to carry and produce the CDI fusion protein sequences. The host cell can be either prokaryotic or eukaryotic.

Eukaryotic Host Cells

Examples of suitable eukaryotic host cells include animal cells such as mammalian cells, and also insect cells, yeast cells, or plant cells.

In mammalian host cells, a number of viral-based expression systems can be utilized. In cases where an adenovirus is used as an expression vector, a CDI fusion protein nucleotide sequence can be ligated into an adenovirus transcription/translation vector having the late promoter and tripartite leader sequence. Insertion in a nonessential El or E3 region of the viral genome results in a viable virus capable of expressing a CDI fusion protein in infected host cells (Logan and Shenk 1984 Proc Natl Acad Sci 81:3655-59). In addition, transcription enhancers, such as the rous sarcoma virus (RSV) enhancer, can be used to increase expression in mammalian host cells.

An expression system that can be used to express CDI fusion protein is an insect system. In one such system, Auto rapha californica nuclear polyhedrosis virus (AcNPV) can be used as a vector to express foreign genes in Spodoptera frugiperda insect cells or in Trichoplusia larvae. The sequence encoding a CDI fusion protein can be cloned into a nonessential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of a CDI fusion protein nucleotide sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses can then used to infect S frugiperda cells or Trichoplusia larvae in which the CDI fusion protein can be expressed (Smith et al 1983 J Virol 46:584; EK Engelhard, et al, 1994 Proc Nat Acad Sci 91:3224-3227).

In yeast, Saccharomyces cerevisiae, a number of vectors including constitutive or inducible promoters such as beta-factor, alcohol oxidase and PGH can be used. For reviews, see Ausubel et al (Cunent Protocols in Molecular Biology, John Wiley & Sons, New YorkN.Y.) and Grant et al (1987 Methods in Enzymology 153:516-544).

In cases where plant expression vectors are used, the expression of a sequence encoding a CDI fusion protein can be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV (Brisson, et al., 1984 Nature 310:511-514) can be used alone or in combination with the omega leader sequence from TMV (Takamatsu, et al., 1987 EMBO J 6:307-311). Alternatively, plant promoters such as the small subunit of RUBISCO (Coruzzi et al 1984 EMBO J 3:1671-1680; Broglie et al 1984 Science 224:838-843); or heat shock promoters (J Winter and RM Sinibaldi 1991 Results Probl Cell Differ 17:85-105) can be used.

In addition, a host cell strain can be chosen for its ability to modulate the expression of the inserted CDI fusion protein nucleotide sequences or to process the expressed protein in the desired fashion. Such modifications of the expressed CDI fusion protein include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation. Post-translational processing which cleaves a precursor form of the protein (e.g., a prepro protein) can also be important for conect insertion, folding and/or function. Different host cells such as THP-1, D 103-5 T cells, HeLa, EL-4, CHO, MDCK, 293, WI38, etc. have specific cellular machinery and characteristic mechanisms for such post-translational activities and can be chosen to ensure the conect modification and processing of the introduced, foreign protein. In one embodiment, the host-vector system comprises THP-1 cells and plasmid pSR-alpha-neo (M Sugita, et al., 1996 Science 273:349) including the chimeric nucleic acid molecule of the invention.

Prokaryotic Host Cells

Examples of suitable prokaryotic host cells include bacteria strains from genera such as Escherichia, Bacillus, Pseudomonas, Streptococcus, and Streptomyces.

In bacterial systems, a number of expression vectors can be selected depending upon the use intended for the CDI fusion proteins. For example, when large quantities of the CDI fusion proteins are needed for the induction of antibodies, vectors that direct high level expression of fusion proteins that are soluble and readily purified can be desirable. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the CDI fusion protein nucleotide sequence can be ligated into the vector in-frame with sequences for the amino-terminal Met and the subsequent 7 residues of galactosidase so that a hybrid protein is produced. Other vectors include the pIN vectors (Van Heeke & Schuster 1989 J Biol Chem 264:5503-5509), and the like. The pGEX vectors (Promega, Madison Wis.) can also be used to express foreign proteins as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsoφtion to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems are designed to include heparin, thrombin or factor Xa protease cleavage sites so that the cloned protein of interest can be released from the GST moiety at will.

The methods for introducing the CDI fusion protein nucleotide sequences into the host cells are well-known methods that depend on the type of vector used and host system employed.

For example, in vertebrate cells, the nucleic acid sequences are introduced with vectors using various methods, including calcium phosphate-mediated DNA transfection (Graham and Van der Eb 1973 Virology 52:456-467; M Wigler, et al 1977 Cell 11:223-232) or other cationic-mediated transfection methods, electroporation (E Neuman, et al 1982 EMBO J 1:841-845), microinjection (WF Anderson, et al 1980 Proc Natl Acad Sci USA 77:5399-5403; MR Cappechi 1980 Cell 22:479-488; A Graessman, et al 1979 J Virology 32:989-994), or lipid methods including encapsulation of DNA in lipid vesicles (M Schaefer-Ridder 1982 Science 215:166-168). Other methods include the particle gun method. Still other methods include using an adenovirus transcription translation vector comprising the late promoter and tripartite leader sequence. A nucleic acid sequence can be inserted in a nonessential El or E3 region of the adenoviral genome to create a viable virus capable of expressing the protein encoded by the nucleic acid sequence (Logan and Shenk 1984 Proc Natl Acad Sci 81:3655-59). Alternatively, retroviral transfer methods can be used (E Gibloa, et al 1986 BioTechniques 4:504-512).

Plant cells can be introduced by direct DNA transformation or pathogen-mediated transfection. For reviews of such techniques, see Hobbs, S. in: "McGraw Yearbook of Science and Technology" (1992) McGraw Hill New York N.Y., pp 191-196; or Weissbach and Weissbach (1988) in: "Methods for Plant Molecular Biology", Academic Press, New York N.Y., pp 421-463. Alternatively, plant cells can be introduced via a particle-gun method using metal particles.

Prokaryotic host cells are introduced (e.g., transformed) with nucleic acid molecules by electroporation or salt treatment methods (Cohen et al., 1972 Proc Acad Sci USA 69:2110; Maniatis, T., et al., 1989 in: Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.

Selection of Transformed Cells

The cells introduced with the CDI fusion protein nucleotide sequences can be identified by techniques well known in the art. The cells can be selected, lysed and their DNA content examined for the presence of the introduced sequences using a DNA gel blot method or similar method (Southern 1975 J Mol Biol 98:503; Berent et al., 1985 Biotech 3:208). Alternatively, the proteins produced from the cells of the invention can be assayed via a biochemical assay or immunological method.

Any number of selection systems can be used to recover the introduced (e.g, transformed or transfected) cells. The introduced cells can be selected based on expression of heφes simplex virus thymidine kinase (Wigler, M., et al., 1977 Cell 11:223-32), or adenine phosphoribosyltransferase (Lowy, I. et al., 1980 Cell 22:817-23) genes which can be employed in tk-minus or aprt-minus cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as a basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler, M., et al., 1980 Proc Natl Acad Sci 77:3567- 70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere- Garapin, F., et al., 1981 J. Mol. Biol. 150:1-14) and ais or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. Additional selectable genes have been described, for example, frpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (SC Hartman and RC Mulligan 1988 Proc. Natl. Acad. Sci. 85:8047-51). Recently, the use of visible markers has gained popularity with such markers as anthocyanins, beta- glucuronidase and its substrate, GUS, and luciferase and its substrate, luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (C Rhodes, et al., 1995 Methods Mol. Biol. 55:121-131). PROTEINS OF THE INVENTION

The present invention provides CDI fusion proteins comprising a leader peptide sequence, a CDI endosomal targeting sequence, and an antigen of interest. The CDI fusion protein can also include a transmembrane sequence.

The leader peptide sequence and CDI endosomal targeting sequence have the same functional activity in the CDI fusion protein as a naturally-occurring, wild-type CDI protein. The functional activity of a wild-type CDI protein includes trafficking to and in the MHCII antigen presenting pathway of a cell, which includes: co-translational insertion of the CDI protein into the lumen of the endoplasmic reticulum; post- translational processing of the CDI protein in the endoplasmic reticulum and/or Golgi; packaging the CDI protein in an intracellular vesicle (e.g., endosome, early endosome, late endosome, or lysosome); trafficking the packaged vesicle to the cell membrane; and mediating antigen presentation on the cell surface (e.g., presenting a lipid, or fragments thereof, with an MHCII complex). Other functional activities includes, recycling the vesicles which are packaged with the CDI protein from the cell membrane to the endoplasmic reticulum and/or Golgi. The functional activity of the wild-type CDI protein also includes antigen presentation at the cell surface via a non-endosomal MHCII pathway.

In the CDI fusion protein, the leader peptide sequence and the CDI endosomal targeting sequence direct the antigen of interest, or a fragment thereof, to be presented on a cell surface via the MHCII antigen presenting pathway.

The presented antigen of interest, or a fragment thereof, can induce an immune response against the antigen of interest.

In the CDI fusion protein, the antigen of interest is any protein sequence, or a fragment thereof, against which an elicited immune response is desired. The antigen of interest includes any protein associated with infective organisms, such as bacterial proteins, viral proteins and fungal proteins, as well as any tumor associated antigens, cell surface proteins, or reporter proteins.

The CDI fusion proteins of the invention may be embodied in many forms, preferably in isolated form or in purified form.

The CDI fusion proteins may be isolated from mammalian species including, bovine, ovine, porcine, murine, equine, and preferably human. Alternatively, the CDI fusion proteins may be generated by synthetic, semi-synthetic, or recombinant methods.

A skilled artisan can readily employ standard isolation and purification methods to obtain isolated CDI fusion proteins (Marchak, D. R., et al., 1996 in: "Strategies for Protein Purification and Characterization", Cold Spring Harbor Press, Plainview, N. Y.). The nature and degree of isolation and purification will depend on the intended use. For example, purified CDI fusion protein molecules will be substantially free of other proteins or molecules that impair the binding of CDI fusion to antibodies or other ligands. Embodiments of the CDI fusion proteins include a purified CDI fusion protein or fragments thereof, having the biological activity of a CDI fusion protein. In one form, such purified CDI fusion proteins, or fragments thereof, retain the ability to bind antibody or other ligand.

In a cell, the nucleotide sequences encoding the CDI fusion protein are predicted to include signal peptide sequences and introns, therefore it is expected that the cell will produce various forms of a particular CDI fusion protein as a result of post-translational modification. For example, various forms of isolated, CDI fusion proteins may include: precursor forms that include the signal peptide, mature forms that lack the signal peptide, and different mature forms of a CDI fusion protein that result from post-translational modification such as acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation. Post-translational modification also includes cleavage of a precursor form of the protein. The present invention provides isolated and purified proteins, polypeptides, and fragments thereof, having an amino acid sequence identical to the predicted amino acid sequence of the CDI fusion proteins disclosed herein. Accordingly, the amino acid sequences may be identical to a particular CDI fusion proteins, as shown in Figures 8A- D, 9A-D, 1 OA-D, and 11 A-D.

The present invention also includes proteins having sequence variations from the predicted CDI fusion protein sequences disclosed herein (Figures 8 A-D, 9A-D, 10A-D, and 11 A-D). For example, the proteins having the variant sequences includes allelic variants, mutant variants, conservative substitution variants, and CDI fusion proteins isolated from other mammalian organisms. The amino acid sequences may be similar to the disclosed sequences. For example, two protein sequences are considered to be similar to each other when the percentage of amino acid residues that differ between the two sequences is between about 60% to 99.99%.

The present invention encompasses mutant alleles of CDI fusion that encode mutant forms of CDI fusion proteins having one or more amino acid substitutions, insertions, deletions, truncations, or frame shifts. Such mutant forms of proteins typically do not exhibit the same biological activity as wild-type proteins. The mutant alleles of the CDI fusion proteins may or may not encode CDI fusion proteins having the same biological activity as wild-type CDI proteins.

Another variant of CDI fusion proteins may have amino acid sequences that differ by one or more amino acid substitutions. The variant may have conservative amino acid changes, where a substituted amino acid has similar structural or chemical properties, such as replacement of leucine with isoleucine. Alternatively, a variant may have nonconservative amino acid changes, such as replacement, of a glycine with a tryptophan.

Similar minor variations may also include amino acid deletions or insertions, or both.

Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted may be found using computer programs well known in the art, for example, DNASTAR software. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the biological activity of the protein. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids; aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered conservative in particular environments .

Producing CDI Fusion Proteins

The CDI fusion proteins of the invention may be generated by recombinant methods. Recombinant methods are prefened if a high yield is desired. Recombinant methods involve expressing the cloned gene in a suitable host cell. For example, a host cell is introduced with an expression vector having a CDI fusion protein sequence, the host cell is grown or cultured under conditions that permit in vivo production of the CDI fusion protein encoded by the nucleotide sequence.

For example, in general terms, the production of recombinant CDI fusion proteins will involve using a host/vector system employing the following steps. A nucleic acid molecule is obtained that encodes a CDI fusion protein or a fragment thereof, such as any one of the polynucleotides shown in Figures 8A-D, 9A-D, Ϊ0A-D, and 11 A-D. The CDI fusion protein-encoding nucleic acid molecule is preferably inserted into an expression vector in operable linkage with suitable expression control sequences, as described herein, to generate an expression vector containing the CDI fusion protein-encoding sequence. The expression vector is introduced into a suitable host, by standard transformation methods, and the resulting transformed host is grown or cultured under conditions that allow the production and retrieval of the CDI fusion protein. For example, if expression of the CDI fusion gene is under the control of an inducible promoter, then suitable growth conditions include the appropriate inducer. The CDI fusion protein, so produced, is isolated from the growth medium or directly from the cells; recovery and purification of the protein may not be necessary in some instances where some impurities may be tolerated. A skilled artisan can readily adapt an appropriate host/expression system known in the art (Cohen, et al., supra; Maniatis et al., supra) for use with CDI fusion protein-encoding sequences to produce a CDI fusion protein.

The CDI fusion protein is produced by, introducing a host cell with the vector of the invention to generate a host vector system, growing or culturing the host vector system under suitable culture conditions so as to produce the CDI fusion protein in the host, and recovering the CDI fusion protein so produced.

The CDI fusion proteins of the invention, and fragments thereof, can be generated by chemical synthesis methods. The principles of solid phase chemical synthesis of polypeptides are well known in the art and may be found in general texts relating to this area (Dugas, H. and Penney, C. 1981 Bioorganic Chemistry, pp 54-92, Springer- Verlag, New York). CDI fusion polypeptides may be synthesized by solid-phase methodology utilizing an Applied Biosystems 430A peptide synthesizer (Applied Biosystems, Foster City, Calif.) and synthesis cycles supplied by Applied Biosystems. Protected amino acids, such as t-butoxycarbonyl-protected amino acids, and other reagents are commercially available from many chemical supply houses.

The present invention provides derivative protein molecules, such as chemically modified proteins. Illustrative of such modifications would be replacement of hydrogen by an alkyl, acyl, or amino group. The CDI fusion protein derivatives retain the biological activities of natural CDI fusion proteins. Producing CDI Fusion Proteins in a Cell

The present invention provides methods for producing the CDI fusion protein in a cell, comprising contacting a cell with the vector, under suitable conditions so that the cell so contacted produces the CDI fusion protein.

The cell produces the CDI fusion protein by transcribing and translating the chimeric nucleic acid molecule encoding the CDI fusion protein carried on the vector. The produced CDI fusion protein occurs in any form in or on the cell, including processed (e.g., in endoplasmic reticulum or Golgi), packaged in a vesicle, trafficked, recycled, intact, degraded, bound by MHCII complex, or presented on the cell surface. For example, the produced CDI fusion protein is processed by the endoplasmic reticulum and/or Golgi. The produced CDI fusion protein is packaged in an intracellular vesicle such as an endosome or lysosome, including early and late endosomes. The produced CDI fusion protein is trafficked to the cell membrane, or trafficked back to the endoplasmic reticulum or Golgi (e.g., recycled). The produced CDI fusion protein is intact, or degraded to release fragments of the antigen of interest. The produced CDI fusion protein, or fragments thereof (e.g., antigen of interest or fragments thereof), is presented on a cell surface. The produced CDI fusion protein, or the antigen of interest, is bound or not bound to an MHCII complex. The produced CDI fusion protein is processed via an endosomal/lysosomal or non-endosomal pathway. The produced CDI fusion protein is processed via an MHCII antigen presenting pathway.

ANTIBODIES OF THE INVENTION

The present invention further provides antibodies, such as polyclonal, monoclonal, chimeric, humanized, human, internalizing, anti-idiotypic antibodies, immunologically-active fragments or derivatives thereof, recombinant proteins having immunologically-activity, and immunoconjugates which bind the CDI fusion protein or any fragment thereof. The antibodies of the invention can bind selectively to the CDI fusion protein or protein fragments and will not bind (or will bind weakly) to a non-CD 1 fusion protein. The antibodies of the invention can bind to a naturally-occurring CDI fusion protein or to a recombinant CDI fusion protein. The antibodies of the invention can bind a CDI fusion protein expressed by a cell, including precursor, mature, post-translationally processed, intact, degraded, bound with an antigen or lipid antigen, or presented on the cell surface. The antibodies of the invention can bind one or more domains on the CDI fusion protein.

The antibodies of the invention can bind a cell or a tissue sample, from a subject, expressing or producing the CDI fusion protein. Such cells or tissues include skin, breast, lung, prostate, liver, kidney, intestinal, bladder, pancreatic, stomach, thyroid, testicular, ovarian, central nervous system cells or tissues, respectively. The cell is a normal cell, cancer cell or metastasized cancer cell thereof.

It is understood by those skilled in the art, that the regions or epitopes of the CDI fusion protein to which an antibody is directed can vary with the intended application. For example, antibodies used for detecting a cell-surface CDI fusion protein as expressed on a cell should be directed to an accessible epitope on cell-surface CDI fusion protein. Such antibodies can also be useful for detecting a secreted form of the CDI fusion protein, including CDI fusion proteins that occur in blood serum of a subject. Antibodies that recognize other epitopes, such as the cytoplasmic domain, can be useful for detecting the CDI fusion protein within a cell.

The antibody of the invention can recognize and bind any portion of the CDI fusion protein, including the leader peptide sequence, endosomal targeting sequence domain, cytoplasmic domain, and/or transmembrane domain, or any portion thereof.

The present invention provides isolated antibodies. The isolated antibodies are separated from contaminant components that would interfere with bind, detecting, diagnosing, imaging and/or monitoring methodologies. A preferred antibody is purified using any method known in the art. The antibodies can be from any source, including rabbit, sheep, goat, rat, mouse, dog, cat, pig, horse, monkey, ape and human.

Polyclonal Antibodies

The antibodies of the invention can be polyclonal preparations which include a population of different antibodies directed against a different epitope on the immunogen, such as a CDI fusion protein used as an immunogen.

Polyclonal antibodies can be produced by methods well-known in the art. Polyclonal antibodies can be produced by immunizing animals, usually a mammal, by multiple injections of an immunogen (antigen) and an adjuvant as appropriate (Harlow and Lane, 1988, in: "Antibodies: A Laboratory Manual." Cold Spring Harbor Press). The injections can be intradermal, subcutaneous or intraperitoneal. Administration of the immunogen is conducted generally by injection into an animal over a suitable time period and with use of a suitable adjuvant, as is generally understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation. The methods of Dunbar can be used to produce polyclonal antibodies (BS Dunbar and ED Schwoebel 1990 Methods Enzymol 182:663-670).

In general, any antibody (e.g., monoclonal, polyclonal, and the like) can be raised using an isolated CDI fusion protein, or a fragment as the immunogen. In addition, the immunogen can be a fusion protein including all or a portion of the CDI fusion proteins fused to V5, His, maltose-binding protein, GST, or human Ig. Cells expressing or overexpressing the CDI fusion protein can also be used for immunizations. Similarly, any cell engineered to express a CDI fusion protein can be used.

The full-length CDI fusion protein can be used as an immunogen to produce the polyclonal antibodies. Alternatively, the amino acid sequence of any of the CDI fusion proteins can be used to select specific regions of these polypeptides for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of these amino acid sequences can be used to identify hydrophilic regions. These amino acid sequences that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art (Rost, B., and Sander, C. 1994 Protein 19:55-72), such as Chou- Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg, Kaφlus-Schultz or Jameson-Wolf analysis. Fragments including these residues are particularly suited in generating antibodies that bind a CDI fusion protein. Polyclonal antibodies can be produced using one or more synthetic peptides having the sequence of the signal peptide sequence, endosomal targeting sequence, cytoplasmic domain, and/or transmembrane domain of the CDI fusion protein.

Methods for preparing an immunogen and for preparing immunogenic conjugates of a protein with a carrier such as BSA, KLH, or other carrier proteins are well known in the art.

The animals are typically immunized with about 1 micro gram to about 1 mg immunogen capable of eliciting an immune response, along with an enhancing carrier preparation, such as Freund's complete adjuvant, or an aggregating agent such as alum to produce an immunogen mixture. The immunogen mixture can be injected into the animal at multiple sites. The animals can be boosted with at least one subsequent administration of a lower amount of the immunogen mixture which include about 1/5 to 1/10 the original amount of the immunogen in Freund's complete adjuvant (or other suitable adjuvant). Typically, the animals are bled, the serum is assayed to determine the specific antibody titer, and the animals can be boosted again and assayed until the titer of antibody no longer increases.

The animal can include, but is not limited to any of the following: rabbit, sheep, goat, rat, mouse, dog, cat, pig, horse, monkey, ape or human.

The polyclonal antibody serum can be collected using well known methods or the antibody fraction can be enriched by chromatography with an affinity matrix that selectively binds immunoglobulin molecules such as protein A, to obtain the IgG fraction. The enriched polyclonal antibody can be further enriched using immunoaffinity chromatography such as solid phase-affixed immunogen. For example, the enriched polyclonal antibody fraction is contacted with the solid phase-affixed immunogen for a period of time sufficient for the immunogen to immunoreact with the antibody molecules to form a solid phase-affixed immunocomplex. The bound antibodies are eluted from the solid phase by standard techniques, using of buffers of decreasing pH or increasing ionic strength. The eluted fractions are assayed, and those including the specific antibodies are combined.

Monoclonal Antibodies

The antibodies of the invention can be monoclonal antibodies that bind a specific antigenic site of the CD 1 fusion protein.

Methods for preparing an immunogen and immunizing an animal are described above. The animal can include, but is not limited to any of the following: rabbit, sheep, goat, rat, mouse, dog, cat, pig, horse, monkey, ape or human.

The monoclonal antibodies can be produced by hybridoma technology first described by Kohler and Milstein (1975 Nature 256:495-497; Brown et al. 1981 J Immunol 127:539-46; Brown et al., 1980 J Biol Chem 255:4980-83; Yeh et al, 1976 Proc Natl Acad Sci USA 76:2927-31; Yeh et al, 1982 Int J Cancer 29:269-75), or human B cell hybridoma techniques (Kozbor et al., 1983 Immunol Today 4:72), or EBV-hybridoma techniques (Cole et al., 1985 Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77- 96), or recombinant DNA methods in bacteria, animal cells or plant cells (U.S. Patent No. 4,816,567), or phage antibody libraries (Clackson, et al., 1991 Nature 352:624-628; Marks, et al., 1991 J Mol Biol 222:581-597). The monoclonal antibodies can be made using a repetitive, multiple site immmunization strategy termed RIMMS (KE Kilpatrick, et al., 1997 Hybridoma 16:381-389). An alternative method includes producing affinity matured monoclonal antibodies by fusing a myloma cell line stably transfected with Bcl-2 and immune lymphocytes (KE Kilpatrick, et al., 1997 Hybridoma 16:381-389).

The hybridoma cell secreting the desired antibodies can be screened by immunoassay in which the antigen is the CDI fusion protein. When the appropriate hybridoma cells secreting the desired antibody are identified, the cells can be cultured either in vitro or by production in ascites fluid. The desired monoclonal antibodies are then recovered from the culture supernatant or from the ascites supernatant.

Chimeric Antibodies

The chimeric antibodies of the invention comprise an antibody portion (e.g, immunoglobulin portion) from one species or a particular antibody class or subclass, joined to an antibody portion from a different species or antibody class or subclass. The chimeric antibodies can be produced as CDR grafted antibodies of multiple species origin. The portions of the chimeric antibodies can be from any source, including bovine, porcine, murine, equine, canine, feline, monkey, ape, piscine, ovine, avian or human. In particular, the portions of the chimeric antibodies can be from rabbit, sheep, goat, rat, mouse, dog, cat, pig, horse, monkey, ape and human.

For example, one portion of the chimeric antibody can include a constant immunoglobulin portion from one species, and another portion includes a variable region (e.g., antigen combining region). The chimeric antibody comprises a human portion and a non-human portion. The constant region can be derived from human and the variable region can be derived from a non-human species, such as a murine species. The chimeric antibodies can be produced by methods known in the art (Morrison et al., 1985 Proc Natl Acad Sci USA 81:6851; Takeda et al., 1985 Nature 314:452; Cabilly et al., US Patent. No. 4,816,567; Boss et al., US Patent No. 4,816,397). The chimeric antibody comprises hypervariable loop regions from one species and invariant framework regions from another species. Chimeric antibodies comprising human regions are useful, as they are less likely to be antigenic to a human subject than antibodies with non-human constant regions and variable regions.

The chimeric antibodies of the present invention also comprise antibodies which are chimeric proteins, having several distinct antigen binding specificities (e.g. anti-TNP:

Boulianne et al., 1984 Nature 312:643; and anti-tumor antigens: Sahagan et al., 1986 J Immunol 137:1066). The invention also provides chimeric proteins having different effector functions (Neuberger et al., 1984 Nature 312:604), immunoglobulin constant regions from another species and constant regions of another immunoglobulin chain (Sharon et al., 1984 Nature 309:364); Tan et al, 1985 J Immunol 135:3565-3567). Additional procedures for modifying antibody molecules and for producing chimeric antibody molecules using homologous recombination to target gene modification have been described (Fell et al, 1989 Proc Natl Acad Sci USA 86:8507-8511).

In general, the procedures used to produce chimeric antibodies can involve the following steps: a) identifying and cloning the conect gene segment encoding the antigen binding portion of the antibody molecule; this gene segment (known as the VDJ, variable, diversity and joining regions for heavy chains or VJ, variable, joining regions for light chains or simply as the V or variable region) can be in either the cDNA or genomic form; b) cloning the gene segments encoding the constant region or desired part thereof; c) ligating the variable region with the constant region so that the complete chimeric antibody is encoded in a form that can be transcribed and translated; d) ligating this construct into a vector comprising a selectable marker and gene control regions such as promoters, enhancers and poly(A) addition signals; e) amplifying this construct in bacteria; f) introducing this DNA into eukaryotic cells (transfection) most often mammalian lymphocytes; g) selecting for cells expressing the selectable marker; h) screening for cells expressing the desired chimeric antibody; and k) testing the antibody for appropriate binding specificity and effector functions.

Humanized Antibodies

The antibodies of the invention include humanized antibodies, which comprise antibody portions from a human immunoglobulin. In one embodiment, a humanized antibody comprises hypervariable loop regions and/or invariant framework regions from human. In one embodiment, a humanized antibody comprises hypervariable loop regions from non- human species and invariant framework regions from human. A humanized antibody can comprise at least a portion of an immunoglobulin constant region from human. Humanized antibodies can be made according to any known method, including substituting one or more of the non-human antibody CDRs for conesponding human antibody sequences (Teng et al., 1983 Proc Natl Acad Sci USA 80:7308-7312; Kozbor et al., 1983 Immunology Today 4:7279; Olsson et al., 1982 Meth Enzymol 92:3-16; Jones 1986 Nature 321-522-525; Riechmann, et al., 1988 Nature 332:323-329; Verhoeyen et al., 1988 Science 239: 1534- 1536; Presta 1992 Cun Op Struct Biol 2:593-596; Carter et al, 1993 Proc Natl Acad Sci USA 89: 4285; Sims et al., 1993 J Immunol 151: 2296).

The present invention also provides antibodies that are more fully-humanized or are fully humanized. These antibodies can be produced using methods known in the art (Vaughan et al., 1998 Nature Biotechnology 16: 535-539; Griffiths and Hoogenboom, "Building an in vitro immune system: human antibodies from phage display libraries", in: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man. Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from Combinatorial Libraries Id., pp 65-82; PCT Patent Application WO98/24893, Jakobovits et al., published December 3, 1997; Jakobovits, 1998, Exp. Opin. Invest. Drugs 7(4): 607-614).

Other methods for producing human antibodies include using the CDI fusion protein, or a fragment or derivative thereof, as an antigen to sensitize human lymphocytes to the antigen in vitro, followed by EBV-transformation or hybridization of the antigen-sensitized lymphocytes with mouse or human lymphocytes (Bonebaeck et al., 1988 Proc Natl Acad Sci USA 85:3995-99).

Alternatively, human antibodies can be produced using transgenic animals such as mice which are incapable of expressing endogenous immunoglobulin heavy and light chain genes, but which can express human heavy and light chain genes. The transgenic mice are immunized in the normal fashion with a selected antigen, such as the CDI fusion protein, or a fragment or derivative thereof. The human immunoglobulin transgenes harbored by the transgenic mice reanange during B cell differentiation, and subsequently undergo class switching and somatic mutations. Thus, using this technology, it is possible to produce therapeutically useful IgG, IgA, and IgB antibodies. For an overview of this technology to produce human antibodies, see Lonberg and Haszar (1995 Int Rev Immunol 13:65-93). A detailed discussion of this technology for producing human antibodies and human monoclonal antibodies can be found in U.S. Patents 5,625,126; 5,633,425; 5,569,825; 5,661,016; and 5,545,806.

Internalizing Antibodies

The antibodies of the invention can be internalizing antibodies which enter (e.g., internalize) a cell upon bind to the CDI fusion protein on the cell. An internalizing antibody that enters into a cell can inhibit growth of the cell or kill the cell. Thus, internalizing antibodies are useful for therapeutic methods such as inhibiting cell growth and/or inducing cell death. The internalization of the antibody can be analyzed using I¹²⁵ labeled antibodies (Wolff et al., 1993 Cancer Res. 53: 2560-2565).

The internalizing antibodies of the invention exhibit a rate of entering the cell. The rate can be measured starting from the time the cell is contacted with the internalizing antibody, or starting from the time a subject is administered the internalizing antibody. In one embodiment, the internalizing antibodies exhibit a rate of entering the cell within about 24 hours, or within about 12 hours, or within about 1 hour. A prefened internalizing antibody enters a cell, after contacting the cell, within about 30 to 60 minutes, or more preferably in less than about 30 minutes. In these embodiment, the rate of internalizing can be measured from the time the cell is contacted with the internalizing antibody, or from the time a subject is administered the internalizing antibody. Neutralizing Antibodies

The invention provides neutalizing antibodies, or fragments or derivatives thereof, to target specific antigens. Administration of neutralizing antibodies, or fragments or derivatives thereof, to a substrate or sample having the target antigen can render the target antigen ineffective in its actions, processes and/or potentials. Neutralizing antibodies, or fragments or derivatives thereof, can render ineffective molecules, actions, processes and/or potentials associated with the target antigen. Neutralizing antibodies, or fragments or derivatives thereof, can inhibit cellular actions, processes and/or potentials, such as cell cycling, cell differentiation, cell growth.

Recombinant Proteins

Further, the invention provides recombinant proteins which exhibit the functional activity of an antibody of the invention (e.g, binds a CDI fusion protein, or fragments or derivatives thereof). The recombinant proteins of the invention can be produced by a cell engineered to express the recombinant protein. The recombinant protean be produced by methods used to produce conventional antibodies, such as polyclonal technology, hybridoma technology, and/or phage library technologies (RD Mayforth and J Quintans 1990 New Eng J Med 323:173-178; TA Waldmann 1991 Science 252:1657-1662; G Winter and C Milstein 1991 Nature 349:293-299; SL Morrison 1992 Ann Rev Immunol 10:239-266).

The recombinant proteins of the invention can be a single chain polypeptide molecule that bind the CDI fusion proteins. The heavy (H) and light (L) chains of an Fv portion of an antibody can be encoded by a single nucleotide sequence and include a linker sequence (Bird et al. 1988 Science 242:423-426; Huston et al. 1988 Proc Natl Acad Sci USA 85:5879-5883). The recombinant proteins can be mono-specific or bispecific. The bi-specific proteins will have one portion that binds the CDI fusion protein and another portion will bind a different protein. The mono-specific proteins have one portion that binds the CDI fusion protein.

Antibodies That Competitively Inhibit

The invention provides antibodies which competitively inhibit the immunospecific binding of any of the antibodies of the invention to the CDI fusion protein. The competitive inhibiting antibody can bind to the same epitope as the epitope bound by the antibodies of the invention. These antibodies can be identified by routine competition assays using, for example, any of the antibodies of the invention (Harlow, E. and Lane, D. 1988 in: "Antibodies, A Laboratory Manual", Cold Spring Harbor Laboratory, Cold Spring Harbor, NY).

As an example, the competition assays can be a competitive ELISA assay. The competitive ELISA assay can include coating the wells of a microtiter plate with a CDI fusion protein (e.g, a wildtype or modified CDI protein, or fragments or derivatives thereof), an optional step includes pre-incubating with a candidate antibody, contacting the microtiter plate with a labeled antibody of the invention. The labeled antibody can be, for example, an antibody of the invention labeled with a detectable and/or measurable label, such as biotin. The amount of labeled antibody of the invention which is bound to the CD 1 fusion protein is indirectly conelated with the ability of the candidate antibody to compete for binding to the same epitope (e.g., to block the labeled antibody of the invention from binding the same epitope). The amount of bound labeled antibody of the invention can be measured. The candidate antibody is considered to be a competitive inhibiting antibody if it can block binding of at least about 20%, or at least about 20 to 50%, or at least 50% or more of the labeled antibody of the invention. It is appreciated by those in the art that other competition assays can be performed. Anti-Idiotypic Antibodies

The present invention provides anti-idiotypic antibodies that mimic the CDI fusion proteins. The anti-idiotypic antibodies bind an idiotype on any of the antibodies of the invention.

Methods for producing anti-idiotypic antibodies are well known in the art (Wagner et al., 1997 Hybridoma 16: 33-40; Foon et al., 1995 J Clin Invest 96: 334-342; Herlyn et al., 1996, Cancer Immunol Immunother 43: 65-76). Such anti-idiotypic antibodies can be used in anti-idiotypic therapy as presently practiced with other anti-idiotypic antibodies directed against tumor antigens.

Antibody Fragments

The invention also encompasses antibody fragments that recognize and bind a CDI fusion protein. Use of immunologically reactive fragments, such as the Fv, Fab, Fab', or F(ab')₂ fragments is often preferable, especially in a therapeutic context, as these fragments are generally less immunogenic than the whole immunoglobulin. An antibody fragment comprises a portion of an intact antibody, such as, for example, the antigen-binding or variable region of the intact antibody. The antibody fragment can comprise the constant region of the intact antibody. Antibody fragments can include Fab, F(ab')₂, or Fv fragments (U.S. Patent 5,641,870; Zapata, et al. 1995 Protein Eng 8:1057-1062), also single-chain antibodies and recombinant proteins which bind the CDI fusion proteins. The antibody fragments can be generated by papain digestion of intact antibodies to produce Fab and Fc fragments, or by pepsin digestion to produce F(ab')2 fragments.

Further, antibody effector functions can be modified so as to enhance the therapeutic effect of the antibody on cancers. For example, cysteine residues can be engineered into the Fc region, permitting the formation of interchain disulfide bonds and the generation of homodimers which can have enhanced capacities for intemalization, ADCC and/or complement-mediated cell killing (Caron et al., 1992 J Exp Med 176: 1191-1195; Shopes, 1992, J. Immunol. 148: 2918-2922). Homodimeric antibodies can also be generated by cross-linking techniques known in the art (Wolff et al, 1993 Cancer Res. 53: 2560-2565).

Labeled Antibodies

The present invention provides antibodies, such as polyclonal, monoclonal, chimeric, humanized, internalizing, anti-idiotypic antibodies, immunologically-active fragments thereof, recombinant proteins having immunologically-activity, and immunoconjugates, which are labeled with a detectable marker. The detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a chromophore, a metal chelator, biotin, or an enzyme.

The labeled antibodies of the invention can be particularly useful in various immunological assays for detecting the CDI fusion proteins in a biological sample and/or in diagnostic imaging methodologies. Such assays generally comprise one or more labeled antibodies that recognize and bind the CDI fusion proteins, and include various immunological assay formats well known in the art, including but not limited to various types of precipitation, agglutination, complement fixation, competition, inhibition, radioimmunoassays (RIA), enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA) (H Liu et al. 1998 Cancer Research 58: 4055-4060), immunohistochemical analyses and the like.

In addition, immunological imaging methods that detect cells expressing the CDI fusion proteins are also provided, including but not limited to radioscintigraphic imaging methods using the labeled antibodies of the invention. Such assays can be clinically useful in the detection and monitoring the number and/or location of cells expressing the CDI fusion proteins. Conjugated Antibodies

The antibodies of the invention, such as polyclonal, monoclonal, chimeric, humanized, internalizing, anti-idiotypic antibodies, immunologically-active fragments thereof, recombinant proteins having immunologically-activity or fragment thereof can be conjugated to therapeutic agent, such as a cytotoxic agent, thereby resulting in an immunoconjugate. For example, the therapeutic agent includes, but is not limited to, an anti-tumor drug, a toxin, a radioactive agent, a cytokine, a lymphokine, oncostatin, a second antibody or an enzyme. Further, the invention provides an embodiment wherein the antibody of the invention is linked to an enzyme that converts a prodrug into a cytotoxic drug.

Examples of cytotoxic agents include, but are not limited to ricin, ricin A-chain, doxorubicin, daunorubicin, taxol, ethiduim bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin D, diphteria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, arbrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, sapaonaria officinalis inhibitor, maytansinoids, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as Bi²¹², 1¹³¹, 1¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, P³², and At²¹¹, and radioisotopes of Lu. Antibodies can also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.

Techniques for conjugating or joining therapeutic agents to antibodies are well known (Arnon et al., in: "Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy", in: Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds), pp 243-56 (Alan R Liss, e 1985); Hellstrom et al., "Antibodies For Drug Delivery", in: Controlled Drug Delivery (2nd Ed), Robinson et al. (eds), pp 623-53 (Marcel Dekker, Inc. 1987); Thoφe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", in: Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds), pp. 475-506 (1985); and Thoφe et al., "The Preparation And Cytotoxic Properties Of Antibody- Toxin Conjugates", Immune. Rev, 62:119-58 (1982); Sodee et al., 1997, Clin Nuc Med 21: 759-766). h some circumstances, direct conjugation using, for example, carbodiimide reagents can be used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, IL, can be effective.

The immunoconjugate can be used for targeting the therapeutic agent to a cell expressing the CDI fusion proteins (ES Vitetta, et al., 1993 Immunotoxin Therapy, in: DeVita, Jr., V.T. et al., eds, Cancer: Principles and Practice of Oncology, 4th ed., JB Lippincott Co., Philadelphia, 2624-2636).

PHARMACEUTICAL COMPOSITIONS AND KITS

The present invention provides pharmaceutical compositions comprising the nucleic acid or protein molecules of the invention admixed with an acceptable carrier or adjuvant which is known to those of skill of the art. The pharmaceutical compositions preferably include suitable caniers and adjuvants which include any material which when combined with a molecule of the invention retains the molecule's activity and is non-reactive with the subject's immune system. These carriers and adjuvants include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, phosphate buffered saline solution, water, emulsions (e.g. oil/water emulsion), salts or electrolytes such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pynolidone, cellulose-based substances and polyethylene glycol. Other carriers can also include sterile solutions; tablets, including coated tablets and capsules. Typically such carriers include excipients such as starch, milk, sugar (e.g. sucrose, glucose, maltose), certain types of clay, gelatin, stearic acid or salts thereof, magnesium or calcium stearate, talc, vegetable fats or oils, gums, glycols, or other known excipients. Such carriers can also include flavor and color additives or other ingredients. Compositions comprising such carriers are formulated by well-known conventional methods. Such compositions can also be formulated within various lipid compositions, such as, for example, liposomes as well as in various polymeric compositions, such as polymer microspheres.

The preferred form depends upon the mode of administration and the therapeutic application. The most effective mode of administration and dosage regimen for the compositions of this invention depends upon the severity and course of the infection or disease, the patient's health and response to treatment and the judgment of the treating physician. Accordingly, the dosages of the compositions should be titrated to the individual patient.

Further provided are kits comprising compositions of the invention, in free form or in pharmaceutically acceptable form. The kit can comprise instructions for its administration. The kits of the invention can be used in any method of the present invention.

ADMINISTERING TO A SUBJECT

The present invention provides methods for administering the chimeric nucleic acid molecules of the invention to a subject. A single construct of a chimeric nucleic acid molecule can be administered or in combination with any of the chimeric nucleic acid molecules. The present invention contemplates that a combination of chimeric nucleic acid molecules of the invention can each be administered by different modes. The chimeric nucleic acid molecules can be administered to the subject by standard routes, such as intravenous (i.v.), intraperitoneal (i.p.), intramuscular (i.m.), subcutaneous, intradermally, and also oral administration, administration by injection, as a suppository, or the implantation of a slow-release device such as a miniosmotic pump. Administration can be performed daily as a single dose, multiple dose, or in continuous dose form. Administration can be at a tumor site. As is standard practice in the art, chimeric nucleic acid molecules of the invention can be administered with an appropriate carrier.

The present invention involves direct administration of the combination of chimeric nucleic acid molecules of the invention to a subject. Alternative methods for administration include, but are not limited to, localized injection at a specific site, administration by implantable pump or continuous infusion, or liposomes.

The subject, so administered, is human, bovine, porcine, murine, equine, canine, feline, simian, ovine, piscine or avian. METHODS OF THE INVENTION

The present invention also provides methods using the compositions described herein. The CDI fusion proteins of the invention have the same functional activity in a cell as a naturally-occurring, wild-type CDI protein. The functional activity of the CDI fusion protein is due to the leader peptide sequence and the CDI endosomal targeting sequence which direct the CDI fusion protein to the MHCII antigen presenting pathway.

Accordingly, the functional activity of the CDI fusion proteins of the invention include trafficking to and along the MHCII antigen presenting pathway of a cell, which includes any of the following steps of the pathway: co-translational insertion into the endoplasmic reticulum; post-translational processing in the endoplasmic reticulum and/or Golgi; packaging the CDI fusion protein in an intracellular vesicle (e.g., endosome, early endosome, late endosome, or lysosome); trafficking the packaged vesicle to the cell membrane; recycling the vesicles to the reticulum and/or Golgi; and mediating antigen presentation on the cell surface (e.g., presenting the antigen of interest, or fragments thereof, with an MHCII complex).

The CDI fusion proteins of the invention mediate presentation of the antigen of interest, or a fragment thereof, on a cell surface. The antigen presentation can induce an immune response against the presented antigen of interest.

Targeting To The MHCII Antigen Presenting Pathway

The present invention provides methods for targeting the antigen of interest or a fragment thereof, to the MHCII antigen presenting pathway: comprising contacting a cell with the vector of the invention under suitable conditions so that the cell so contacted produces the CDI fusion protein or a fragment thereof. The CDI fusion protein, so produced, includes the antigen of interest. Thus, the CDI fusion protein, so produced targets to the MHCII antigen presenting pathway thereby targeting the antigen of interest to the MHCII antigen presenting pathway. Presenting On A Cell Surface

The present invention provides methods for presenting the antigen of interest or a fragment thereof, on a cell surface, comprising: contacting a cell with the vector of the invention, under suitable conditions so that the cell so contacted presents the antigen of interest or a fragment thereof on the cell surface. The vector of the invention comprises the CDI fusion protein which includes the antigen of interest. The cell contacted with the vector produces the CDI fusion protein which mediates presentation of the antigen of interest on the cell surface. The antigen of interest presented on a cell surface is expressed on a cell.

Producing An Antigen Of Interest Bound With An MHCII Complex

The present invention provides methods for producing a antigen of interest, or a fragment thereof, bound with an MHCII complex, comprising: contacting a cell with the vector of the invention under suitable conditions so that the cell so contacted produces the antigen of interest or a fragment thereof bound with an MHCII complex. The vector of the invention comprises the CDI fusion protein which includes the antigen of interest. The cell contacted with the vector produces the CDI fusion protein which mediates binding the antigen of interest with the MHCII complex.

Methods For Inducing An Immune Response

The present invention provides methods for inducing an immune response to the antigen of interest or a fragment thereof, comprising: contacting a cell in the subject with the vector of the invention, under suitable conditions so that the cell in the subject so contacted presents the antigen of interest or a fragment thereof on a cell thereby inducing an immune response in the subject. The vector of the invention comprises the CDI fusion protein which includes the antigen of interest. The cell contacted with the vector produces the CDI fusion protein which mediates presentation of the antigen of interest on the cell surface. The antigen of interest presented on a cell surface induces an immune response in a subject.

Methods for Inducing An Immune Response Mediated by an MHCII Pathway

The present invention provides methods for inducing an immune response to the antigen of interest or a fragment thereof, where the immune response is mediated by an MHCII antigen presenting pathway, the method comprising: contacting a cell in a subject with the vector of the invention, under suitable conditions so that the cell so contacted targets the CDI fusion protein to the MHCII pathway and the cell presents the antigen of interest or a fragment thereof on the cell surface thereby inducing an immune response to the antigen of interest. The vector of the invention comprises the CDI fusion protein which includes the antigen of interest. The cell contacted with the vector produces the CDI fusion protein which mediates presentation of the antigen of interest via the MHCII pathway. The antigen of interest presented on a cell surface in the context of MHCII complex. The complex of MHCII and the antigen of interest is recognized by T cell receptor and serve as a target for CD4+ T-cell mediated immune response and induces an immune response in a subject.

Methods for Activating CD4+ T Cells

The present invention provides methods for activating CD4+ T cells, comprising: contacting a cell with the vector of the invention, under suitable conditions so that the cell so contacted presents the antigen of interest or a fragment thereof on the cell surface as a complex with MHCII complex which is then presented to and stimulates activation of CD4+ cells and the presenting cell activates the CD4+ T cell. The activated CD4+ T cell produces cytokines, including IFN-gamma and IL-2. Additionally, the activated CD4+ T cells can provide help to B cells to produce antibodies that activate macrophages to kill intracellular organisms. The presence of activated CD4+ T cell can be detected by performing assays that detect the presence of IFN-gamma and/or IL-2. The assays may be performed using antibodies reactive with IFN-gamma or IL-2. Methods for Evaluating Immune Response

The immune response illicited by the antigen of interest is evaluated by methods that detect antibody production and methods that detect cell mediated immune response. For antibody detection methods, serum from immunized animals is tested for the presence of antibodies produced in response to the antigen of interest, where the serum can be tested at various times after immunization. The serum is screened by various methods, including immunofluorescence and/or ELISA assays, and the specificity is established by assaying the serum by Western blot analysis.

To evaluate cell mediated immune responses induced by the chimeric nucleic acid molecules of the invention, pooled splenocyte preparations from immunized animals are re-stimulated with the antigen of interest in vitro and then analyzed for lymphocyte proliferation using well-known H-Thymidine incoφoration assays. Additionally, spleen cells from immunized animals are evaluated for secretion of type I cytokines such as IL-2 and IFN-gamma, and type II cytokines such as IL-4, IL-5, IL-10, and IL-13, using standard procedures. The immune splenocytes are also evaluated for the ability to specifically lyse target cells that present appropriate peptides derived from the antigen of interest (e.g., a bacterial, viral antigen, or tumor associated antigen). To evaluate anti- tumor responses, the immunized animals are further analyzed for inhibition of tumor growth.

Methods For Inhibiting Tumor Growth

The present invention provides methods for inhibiting the growth of a tumor cell expressing an antigen of interest, comprising: contacting a cell with the vector of the invention which comprises the antigen of interest, under suitable conditions so that the cell so contacted presents the antigen of interest or a fragment thereof on the cell and induces an immune response to the presented antigen thereby inhibiting the growth of the tumor cell expressing the antigen of interest. An inhibition of tumor growth is assayed by measuring the size and/or volume of the test tumor in a subject administered the vector of the invention, and comparing the size and/or volume of the test tumor with the size and/or volume of a control tumor. The control tumor is from a different subject which is not administered the vector of the invention. The growth of the test tumor is inhibited by administration of the vector of the invention, when there is a measurable difference in size, volume, or growth rate between the test tumor and control tumor.

Methods for Inducting an Antiviral. Antimicrobial, or Antifungal Immune Response

The present invention provides methods for inducing an antiviral, antimicrobial, or antifungal immune response, comprising: contacting a cell with the vector of the invention which comprises the antigen of interest, under suitable conditions so that the cell so contacted presents the antigen of interest or a fragment thereof on the cell and induces an immune response so as to lyse a viral -infected, microbial-infected or fungal- infected cell. The induced immune response includes humoral and cell mediated immune responses. The vector of interest encodes the antigen of interest which is a viral, microbial or fungal protein or a fragment thereof.

ADVANTAGES OF THE INVENTION

One of the advantages of the present invention is that it provides chimeric nucleic acid molecules useful as nucleic acid vaccines which are relatively less expensive than protein-based vaccines. Another advantage is that the chimeric nucleic acid molecules of the invention can be used to present on a cell a wide variety of antigens of interest. Thus, the chimeric nucleic acid molecules can be used as the basis for designing a wide variety of nucleic acid-based vaccines. Additionally, the chimeric nucleic acid molecules of the invention are more efficient at antigen presenting than existing nucleic acid molecules having other targeting sequences, such as Invariant Chain (li), LAMP-1 and LIMP-2, because the chimeric nucleic acid molecules of the invention comprise CDI endosomal targeting sequences which targets the antigen of interest through intracellular compartments (e.g., late endosomes) which more effectively process antigens for antigen presentation.

The following examples are presented to illustrate the present invention and to assist one of ordinary skill in making and using the same. The examples are not intended in any way to otherwise limit the scope of the invention.

EXAMPLES

EXAMPLE 1:

The following provides a description of methods for generating various chimeric nucleic acid molecules which encode CDI fusion proteins, and methods of use.

Generating the Chimeric Nucleic Acid Molecules

The DNA constructs (e.g., chimeric nucleic acid molecules) were amplified by polymerase chain reaction (PCR) using Pfx polymerase (Invitrogen, Carlsbad CA).

The GroES constructs (Figures 8 A-D) were generated as follows. The predicted leader peptide sequence of CDlb (Figure 8A and 8E) was amplified with a 5' oligonucleotide encoding an Xba I restriction site upstream of the first eight codons of human CDlb and a 3' oligonucleotide encoding the last eight amino acids of the CDlb leader sequence fused to the first eight amino acids of the GRO ES peptide. The GRO ES sequence was modified for optimal expression in a mammalian cell using oligonucleotides (Figure 8A and 8B). The GRO ES peptide (28-39) cDNA was created through the use of overlapping oligonucleotides with the 5' and 3' oligonucleotides creating complementary sequences to the CDlb leader and transmembrane domains. The CDlb leader fragment and GRO ES cDNA fragments were combined and amplified using the oligonucleotides which recognize the CDlb leader and transmembrane sequences to generate a cDNA fragment encoding the CDlb leader, the GRO ES peptide, and the CDlb transmembrane regions (Figure 8 A).

The CDI cytoplasmic tail sequences from CDla, CDlb, CDlc, and CDld (Figure 8A and 8H) were added as follows using the CDlb cDNA as a template. A 5' oligonucleotide encoding the first eight codons of the CDlb transmembrane domain and 3' oligonucleotides encoding the last eight codons of the transmembrane domain followed by the CDla, CDlb, CDlc, and CDld cytoplasmic sequences were used to amplify cDNA fragments encoding the CDlb transmembrane region fused to the different CDI tails. These fragments were combined with the CDlb leader/GRO ES/CDlb transmembrane fragment described above and amplified using the 5' CDlb leader oligonucleotide and 3' complementary oligonucleotides recognizing the different CDI cytoplasmic tail sequences followed by an Xba I site. The resultant PCR products were digested with Xbal and ligated into the Xbal site of the pSR-alpha-neo plasmid (16). The GRO ES constructs are shown schematically in Figure 7.

The GFP constructs (Figures 11 A-D) were created using a similar strategy. The pIRES- EGFP2 vector was used as a template to amplify the GFP cDNA in a similar strategy as the one described for Gro ES. Briefly, the EGFP cDNA was amplified with oligonucleotides facilitating cloning into the adenovirus expression system pShuttle vector (Clontech, Palo Alto CA). The pShuttle/EGFP construct was verified by DNA sequencing. The CDI leader sequence, transmembrane domain, and cytoplasmic tails were added to the EGFP cDNA in a similar manner as described for the Gro ES peptide.

The ESAT-6 constructs (Figures 9A-D) were also created using a similar strategy. Since ESAT-6 is derived from M. tuberculosis, it displays codon usage bias which would make its expression in mammalian systems unfavorable. Using a similar overlapping oligonucleotide scheme as described for GRO ES, the entire ESAT-6 cDNA was recreated using oligonucleotides which encode codons more typically found in mammalian mRNAs. The resultant ESAT-6 cDNA was cloned into the Xbal site of pcDNA3.1 (Invitrogen) and sequenced for verification. Plasmid DNA from a confirmed clone was used as template to add on the CDlb leader and transmembrane domains as well as the CDla, CDlb, CDlc, CDld, mouse CDldl, and LAMP-1 cytoplasmic tail sequences as described for GRO ES above.

Similarly, the MART-1 constructs (Figures 10 A-D) were created using the p VAX- MART- 1 (kindly provided by Lisa Butterfield) as a template. Briefly, the predicted leader sequence of CDlb was amplified with the 5' oligonucleotide described above and a 3' oligonucleotide encoding the last eight amino acids of the CDlb leader sequence fused to the first eight amino acids of the MART-1. The full-length MART-1 cDNA was amplified using a 5' oligonucleotide which encoded the last eight codons of the CDlb leader peptide sequence followed by the first eight codons of MART-1 and a 3' oligonucleotide which encoded complementary sequence of the CDlb transmembrane domain followed by the last eight codons of MART-1. The resultant reaction product was combined with the CDlb transmembrane domain CD 1 cytoplasmic tail cDNA construct described above and amplified with the 5' CDlb leader oligonucleotide described above and the 3' oligonucleotides encoding various cytoplasmic tails followed by Xbal restriction sites. The new chimeric cDNAs were digested with Xbal and ligated into the Xbal site of pVAX. All of the clones described in this section were confirmed by PCR and DNA sequencing.

Transfection of HeLa cells with GFP/CD1 constructs:

HeLa cells (600,000) were plated onto 60 mm plates in DMEM (Gibco BRL, Rockville MD) supplemented with 10% FBS (Omega) and allowed to adhere overnight. On the following day, each plate received 5 micro grams of purified super-coiled plasmid DNA using Superfect per manufacturer's suggestions (Qiagen, Valencia CA). After 4 hours, the cells were washed once with growth media and then cultured in DMEM/10%FBS overnight. Subcellular localization studies:

One day after transfection, the HeLa cells were harvested using PBS/EDTA, washed in PBS, and counted. Fifty thousand cells were placed in each well of an eight-well chamber slide (Nunc) in growth media and allowed to adhere overnight. On the following day, the cells were fixed using 4% paraformaldehyde and permeabalized with 0.1% saponin. The cells were subsequently incubated with biotinylated mouse anti- human LAMP-1 antibody (BD Pharmingen) or a nonspecific isotype control overnight at 4 degrees C, washed, and incubated with streptavidin-Tritc secondary reagent. The cells were subsequently fixed in 4% paraformaldehyde and analyzed by confocal microscopy as previously described (9).

THP-1 cell culture and transfection with GRO-ES plasmids:

THP-1 cells were maintained in RPMI 1640 media (Gibco) supplemented with 10% FCS (Omega). Logarithmic phase cells were collected by centrifugation and resuspended to a final concentration of 1x10 cells/ml. 700 micro liters aliquots of this cell suspension were combined individually with 10 micro grams of linearized plasmid DNA representing each of the GRO-ES constructs described above in 0.4 cm electroporation cuvettes (Biorad) and transfected at 960 micro F, 200 V. Forty-eight hours after electroporation, the cells from each transfection were centrifuged and resuspended in RPMI 1640/10 % FCS/1 mg/ml G418 and transfened to 96-well plates to initiate cloning. On average, each transfection resulted in 1-4 clones per construct.

RT-PCR of mRNA of GRO-ES transfected THP-1 clones:

The clones generated by this method were expanded and analyzed for mRNA expression levels by RT-PCR as previously described (17). Briefly, cells were harvested by centrifugation and lysed in Tri-Zol buffer (Gibco). Supernatants containing mRNA were precipitated and digested with DNasel to remove contaminating genomic DNA. The purified RNAs from each clone were then reverse-transcribed using the Superscript II reverse transcription kit (Invitrogen) and resulting cDNAs were amplified with oligonucleotides recognizing beta-actin or the GRO-ES peptide sequence and Amplitaq (Invitrogen).

D103-5 T cell assays:

T cell assays were carried out as follows. D 103-5 cells and their culture conditions have been previously described (18). 2xl0⁴ D103-5 cells were combined with 3xl0⁴ THP-1 transfectants in 200 micro liters total volume of RPMI 1640/8% FCS/2% HS in 96-well plates. Unfransfected THP-1 pulsed with ImM GRO ES peptide served as positive controls. The cultures were incubated at 37 degrees C, 5% CO₂ for eighteen hours and supernatants were assayed for IFN-gamma secretion per manufacturer's suggestions (Endogen).

ESAT-6 immunizations and T cell assays:

Plasmid DNA for immunization was purified using the Endotoxin-Free Plasmid Mega Prep kit (Qiagen). C57BL/6 mice (in groups of three) were immunized with 100 micro grams of plasmid DNA in lxPBS three times over four weeks at two week intervals subcutaneously and intradermally with the various ESAT-6 constructs described above. In addition, a positive control group of mice received three injections of 10 micro grams of purified ESAT-6 protein (kindly provided by J. Belisle) + 2 micro grams rIL-12 while a negative control group received three injections of lxPBS. Upon completion of immunizations, pooled splenocyte preparations from each group of mice were re- stimulated with recombinant ESAT-6 protein for 6 hours and then analyzed by intracellular flow cytometry using antibodies against IFN-gamma, CD3, CD4, and CD8.

MART-1 immunizations and T cell assays:

Plasmid DNAs encoding the various MART-1 constructs described above were purified in a similar manner as the ESAT-6 constructs with the exception that they were resuspended in 0.9% sterile saline buffer. Groups of 5-6 C57BL/6 mice were injected with either 100 micro grams of plasmid DNA or buffer only intradermally three times at two week intervals. The positive control group received 1x10 DC transduced with adenovirus expressing MART-1 on the second and final injection days only. Upon completion of immunization protocol, splenocytes from one mouse in each group were harvested and restimulated with EL-4 cells stably expressing MART-1 for 24 hours in elispot plates coated with anti-IFN-gamma antibody. The resultant elispots were enumerated and recorded. The remaining mice in each group received 7xl0⁴ B16 melanoma cells in the left flank and monitored for tumor growth over the next twenty days.

Results:

The CDlb, c, and d proteins traffic to distinct intracellular locations including the MIIC as their cytoplasmic tails encode YXXZ motifs. In contrast, CDla is generally found within earlier endosomal compartments as it does not encode a cytoplasmic YXXZ motif. Previously, it was demonstrated that chimeric MHC I molecules possessing the extracellular and transmembrane domains of MHC I fused to the cytoplasmic domain of CDlb traffic in a similar manner to wild-type CDlb (19). To determine whether the fusion of CDI targeting sequences to any generic protein can result in traffic to the late endosomal/lysosomal compartments, GFP constructs fused to targeting sequences derived from the different human CDI isoforms were transfected into HeLa cells and resultant transfectants were analyzed by confocal microscopy. Our results demonstrate that the GFP-CD1 fusion proteins traffic in a similar manner as their wild-type CDI counteφarts. Thus,. the GFP/CDla fusion construct does not co-localize very extensively with LAMP-1 (Figure 1). In contrast, the GFP/CD1 constructs encoding YXXZ motifs all trafficked to late endosomes/lysosomes to similar degrees as their wild-type CDlb, -c, and -d.

To determine whether CDI -mediated traffic to the late endosomal/lysosomal compartments is relevant to antigen presentation, we created chimeric DNA constructs encoding a GroES peptide antigen (derived from Mycobacterium leprae Gro ES) fused to the cytoplasmic tails of CDla, -b, -c, and -d. As a negative control, we also created a construct encoding the Gro ES peptide alone. These constructs were then transfected into the promonocytic THP-1 cell line. THP-1 cells express HLA-DRB5*0101 and are capable of presenting the M. leprae GRO-ES peptide 28-39. Only transfectants expressing Gro ES fused to the CDI targeting sequences, and not the transfectants expressing the peptide alone, stimulated the CD4+, MHC Il-restricted T cell line, D103- 5, which specifically recognizes the GroES peptide to secrete IFN-gamma (Figure 2A, B). These results indicate that antigens can be targeted to the MHC II antigen presentation pathway through fusion with CDI targeting sequences.

Based on these in vitro results, we created constructs encoding wild-type ESAT-6 or ESAT-6 fused to cytoplasmic tail sequences derived from the CDI proteins to be used as DNA vaccines in mouse models. ESAT-6 is a secretory protein derived from L tuberculosis that provides protection against challenge by M. tuberculosis in the mouse system at levels similar to the BCG vaccine when injected as recombinant protein or a cDNA expression construct (20-21). In addition, ESAT-6 has been proposed to provide protective immunity in humans (22). Of the different ESAT-6/CD1 fusion constructs, mice immunized subcutaneously with recombinant DNA encoding ESAT-6 fused to the CDlc demonstrated the greatest number of ESAT-6 specific CD4+ and CD8+ T cells. Interestingly, these mice demonstrated frequencies of ESAT-6 specific CD4+ and CD8+ T cells at levels similar to or greater than mice immunized with a DNA construct encoding wild-type ESAT-6 or purified recombinant ESAT-6 protein and IL-12 (Figure 3). In a second experiment, mice were immunized intradermally with constructs encoding ESAT-6 fused to all four human CDI targeting sequences as well as targeting sequences derived from mouse CDldl and the lysosomal protein LAMP-1. Analysis of splenocytes from mice immunized with ESAT-6 fusions to CDla, CDlc, and LAMP-1 demonstrated the greatest amount of IFN-gamma release (Figure 4). Our results indicate that fusion of pathogen-derived antigens to CDI targeting sequences can stimulate a strong immune response in vivo. In addition to ESAT-6, we evaluated the potential of immunization with antigen/CD 1 fusions to augment anti-tumor responses through fusion of MART-1 to CDI cytoplasmic tail sequences. MART-1 is a protein synthesized by melanocytes and melanomas in humans. In a previous study by Ribas, et al., mice inoculated with adenoviruses expressing MART-1 responded with increased numbers of MART-1 specific T cells and exhibited decreased melanoma growth progression (23).

In this study, to determine if the CDI fusion system is effective in inducing anti-MART-1 specific immune responses in vivo, mice were immunized with plasmid DNA encoding wild-type MART-1, MART-1 fused to the CDla, -b, and -c cytoplasmic tails, and MART-1 fused to the cytoplasmic tail of H2-M. In addition, mice were immunized with dendritic cells (DC) transduced to express MART-1 by adenovirus infection, which is a potent stimulus for MART-1 -specific immune responses. After immunization, splenocytes from one mouse from each experimental group were assayed in the frequency of MART-1 -specific IFN-gamma secreting cells in response to MART-1 expressing transfectants. Our data indicate that the MART-1/CDlb fusion construct is capable of stimulating greater numbers of IFN-gamma secreting splenocytes than either the wild-type MART-1 or any of the other MART-1 cytoplasmic tail fusion constructs (Figure 5).

To determine the biological relevance of the resultant MART-1 specific responses induced through DNA vaccination with respect to tumor growth progression, mice were challenged with an aggressive melanoma cell line. Briefly, 9-10 mice immunized with buffer alone, the wild-type MART-1 construct, the MART-1 /CD lb fusion construct, and the adenovirus transduced DC were inoculated with 7xl0⁴ B16 melanoma cells upon completion of the immunization protocol. Tumor sizes were recorded over twenty days and the results are shown in Figure 6. Our preliminary results indicate that immunization of mice with the MART-1/CDlb fusion construct decreases melanoma growth rate with significant decreases apparent on days 13 and 16. Together with the elispot data described above, our data indicate that immunization with CDI fusion constructs encoding "self or tumor antigens can stimulate rumor specific immune responses. Discussion:

Although MHC-targeted DNA vaccines have been described in the past, the CDI targeting sequences have unique properties in terms of subcellular and anatomic localization. This represents a distinct advantage over other targeting strategies in which trafficking is limited to MIIC compartments. In this study, we demonstrate that the fusion of different CDI targeting sequences to the generic protein GFP results in distinct trafficking patterns for each isoform. In addition, we found that GroES/CDl fusions are capable of entering the MHC II antigen presentation pathway resulting in CD4+ T cell stimulation in vitro. The efficacy of the antigen/CD 1 fusion to stimulate CD4+ T cell responses was also evaluated in vivo.

The striking finding of the present study was that CDla and CDlc but not CDlb, CDld, or mCDldl fusions were able to engender T cell responses against ESAT-6, whereas CDlb- but not other CDI fusions were able to engender T cell responses against MART- 1. These data confirm that it is required to traffic antigen to distinct compartments to optimize antigen presentation by MHC II and subsequent T cell recognition.

The present invention provides a novel alternative to the existing antigen-targeting systems and in future side-by-side comparisons may prove more effective in eliciting a protective CD4+ T cell response than those offered by chimeric constructs utilizing Ii- or LIMP-2- derived sequences. In previous studies, immunization of mice with a construct encoding fusion of the LAMP-1 targeting sequence to the papilloma virus E7 successfully protected mice against subsequent tumor challenge. In our analyses described herein, mice immunized with an ESAT-6/CDlc fusion construct vs. an ESAT- 6/LAMP-l fusion construct indicate that the ESAT-6/CDlc construct elicits comparable levels of IFN-gamma release as the ESAT-6/LAMP-1 construct.

CD4+ T cell activation requires the presentation of antigenic peptides by MHC II expressed on the cell-surface of professional APCs such as B cells, monocytes/macrophages, and dendritic cells. Of these three cell types, dendritic cells are the most potent APC and are believed to provide the initial instructions that define the functional identity of antigen-specific CD4+ T cells (24). In vivo, DCs are found in both primary (e.g. the thymus) and secondary lymphoid organs (such as the spleen and lymph nodes), in peripheral blood, at sites of inflammation, and in the skin. Administration of GM-CSF in vivo within or near tumors can increase the local number of DC through the differentiation of CD 14+ progenitor cells thereby increasing the frequency of antigen- specific CD4+ T cells and thus inhibiting tumor progression (25,26). By injecting the DNA vaccine intradermally or subcutaneously we are likely targeting this potent antigen presenting cell population.

Previous studies have increased the efficiency of MHC II antigen presentation by various means. Recombinant fusion proteins containing the antigen of interest fused to either the complement protein C3d (27) or the Fc portion of immunoglobulin (28) have both successfully augmented antigen uptake by professional APCs by receptor-mediated endocytosis. Although this strategy results in efficient MHC II antigen presentation, it preferentially targets cells of the monocytic lineage which may alter the identity of MHC Il-presented epitopes through the destruction of potential epitopes by these aggressive antigen presenting cells. An additional drawback to this approach is cost, because recombinant protein antigens are both expensive to produce and unstable in nature making them expensive to produce and maintain. As discussed previously, a second strategy to increase the efficiency of MHC II antigen presentation is the injection or administration of cDNA constructs encoding antigens of interest fused to endosomal targeting sequences derived from MIIC resident proteins such as LAMP-1, LIMP-2, and Invariant Chain (Ii). This strategy, although less expensive than its recombinant protein counteφart, may target antigens directly to the MIIC from the trans-Golgi network when using the LIMP-2 and Ii targeting sequences. Although this strategy successfully traffics antigens to the MIIC and is inexpensive to achieve, it differs from the natural MHC II antigen presentation pathway which traffics antigens through distinct intracellular compartments containing additional antigen processing enzymes which may be critical to the successful presentation of antigenic epitopes by MHC II. By utilizing the CDI -derived endosomal targeting system, we believe that we have taken a step towards the creation of a vaccine design strategy that is both efficient and cost- effective. The technology we have developed is marketable as a novel vaccine approach and is extremely versatile. The CDl/antigen fusion system has great potential in combating a variety of different disorders including infectious diseases caused by viruses, bacteria, and fungi, as well as cancer and autoimmune disorders, including diabetes, lupus myelitis, and multiple sclerosis.

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Claims

What is claimed:

1. A chimeric nucleic acid molecule, comprising a. a nucleotide sequence encoding a CDI fusion protein comprising a CDI endosomal targeting sequence or a fragment thereof, and b. an antigen of interest.

2. The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence comprises a leader sequence.

3. The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence comprises a transmembrane sequence.

4. The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence comprises a CDI cytoplasmic tail sequence.

5. The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence comprises an amino acid sequence YXXZ, wherein the Y is tyrosine, X is any amino acid, and Z is a bulky hydrophobic amino acid.

The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence comprises a nucleotide sequence encoding a leader peptide sequence, an antigen of interest, a transmembrane domain, and a CDI cytoplasmic tail domain.

The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence is a CDla, CDlb, CDlc, or CDld polypeptide or a fragment thereof.

8. The chimeric nucleic acid molecule of claim 1, wherein the CDI endosomal targeting sequence is a human, bovine, porcine, murine, equine, canine, feline, simian, ovine, piscine or avian CDI endosomal targeting sequence.

9. The chimeric nucleic acid molecule of claim 1 , wherein the antigen of interest is a bacterial protein, a viral protein, a fungal protein, a tumor associated antigen, a cell surface protein, or a reporter protein.

10. The chimeric nucleic acid molecule of claim 9, wherein the bacterial protein is GRO ES, ESAT, Ag85A, or Ag85B.

11. The chimeric nucleic acid molecule of claim 9, wherein the viral protein is CMV, EBV, HPV, HSV, papillovirus, RSV, HIV, hepatitis A, hepatitis B, or hepatitis C

12. The chimeric nucleic acid molecule of claim 9, wherein the tumor associated antigen is from skin, pancarcinoma, breast, small cell lung, non-small cell lung, gastrointestinal, prostate, bladder, ovarian, melanoma, central nervous system tumors, leukemias, lymphomas, or sarcomas.

13. The chimeric nucleic acid molecule of claim 9, wherein the tumor associated antigen is a MART-1, Melan-A, tyrosinase, p97, beta-HCG, GalNAc, MAGE-1, MAGE-2, MAGE-4, MAGE-12, MUC1, MUC2, MUC3, MUC4, MUC18, CEA, DDC, melanoma antigen gp75, Hker 8, high molecular weight melanoma antigen, K19, Tyrl, Tyr2, members of the pMel 17 gene family, c-Met, PSA, PSM, alpha- fetoprotein, thyroperoxidase, gplOO, or pl85^neu.

14. The chimeric nucleic acid molecule of claim 9, wherein the cell surface protein is CEA or PSA.

15. The chimeric nucleic acid molecule of claim 8, wherein the reporter protein is a green fluorescent protein (GFP), glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase (GUS), luciferase, luciferin, anthocyanins, or blue fluorescent protein (BFP), HcRed, DsRed, Cyan fluorescent protein (CFP), or yellow fluorescent protein (YFP).

16. The chimeric nucleic acid molecule of claim 1, comprising nucleotide sequences as shown in Figure 8 A, 9 A, 10A or 11 A.

17. A vector, comprising the chimeric nucleic acid molecule of claim 1.

18. The vector of claim 17 which is a plasmid, cosmid or phagemid.

19. A host vector system, comprising the chimeric nucleic acid molecule of claim 1 and a host cell.

20. The host vector system of claim 19, wherein the host cell is a prokaryote or eukaryote.

21. A pharmaceutical composition, comprising the chimeric nucleic acid molecule of claim 1 and a pharmaceutical carrier.

22. A CD 1 fusion protein encoded by the nucleic acid molecule of claim 1.

23. A CDI fusion protein, comprising a CDI endosomal targeting sequence or a fragment thereof and an antigen of interest.

24. The CDI fusion protein of claim 23, wherein the CDI endosomal targeting sequence comprises a leader peptide sequence, an antigen of interest, a transmembrane domain, and a CDI cytoplasmic tail domain.

25. The CDI fusion protein of claim 23, wherein the CDI endosomal targeting sequence comprises an amino acid sequence YXXZ, wherein the Y is tyrosine, X is any amino acid, and Z is a bulky hydrophobic amino acid.

26. The CDI fusion protein of claim 23, comprising an amino acid sequence as shown in Figure 8A, 9A, 10A or 1 IA.

27. A method for producing a CD 1 fusion protein comprising: a. introducing the vector of claim 17 into a cell; and b. growing the cell into which the vector has been introduced under sufficient conditions so that the protein is produced.

28. A method for producing a CDI fusion protein or a fragment thereof, comprising contacting a cell with the vector of claim 17 under suitable conditions so that the cell produces the CDI fusion protein.

29. A method for producing a protein comprising growing the host vector system of claim 19 so as to produce the protein in the host and recovering the protein so produced.

30. The CDI fusion protein produced by the method of claim 27 or 28.

31. A method for targeting in a cell a CDI fusion protein or fragment thereof comprising a CDI molecule and an antigen of interest to an MHCII antigen presenting pathway, comprising: a. contacting the cell with the vector of claim 17 under conditions so the cell produces the CDI fusion protein or fragment thereof and targets the CDI fusion protein or fragment thereof so produced to the MHCII antigen presenting pathway.

32. A method for targeting in a cell an antigen of interest or a fragment thereof to an MHCII antigen presenting pathway comprising: a. contacting the cell with a vector comprising a CDI endosomal targeting sequence and an antigen of interest, under conditions so the cell i. produces the antigen of interest or a fragment thereof encoded by the vector and ii. targets the antigen of interest or fragment thereof so produced to the MHCII antigen presenting pathway.

33. A method for expressing an antigen of interest or fragment thereof on the surface of a cell by targeting in the cell the antigen or fragment thereof to an MHCII antigen presenting pathway by the method of claim 32 and expressing the antigen or fragment thereof on the surface of the cell.

34. A method for expressing on a cell an antigen of interest or fragment thereof, comprising contacting the cell with the vector of claim 17 under conditions so the cell produces the CDI fusion protein or fragment thereof and expresses the antigen or fragment thereof of the CDI fusion protein so produced on the cell.

35. A method for producing an antigen of interest or fragment thereof bound with an MHCII protein complex, comprising contacting a cell with the vector of claim 17 under conditions so the cell produces the antigen of interest or fragment thereof encoded by the vector and binds the antigen of interest or fragment thereof so produced with an MHCII protein complex.

36. A method for inducing in a subject an immune response to an antigen of interest or a fragment thereof, comprising: a. contacting a cell in the subject with the vector of claim 17 so that the cell produces the antigen of interest encoded by the vector, wherein the antigen of interest or a fragment thereof so produced is immunogenic to the subject.

37. The method of claim 37, wherein the antigen of interest or fragment thereof so produced is targeted to an MHCII antigen presenting pathway.

38. The method of claim 37, wherein the antigen of interest or fragment thereof so produced is expressed on a cell in the subject.

39. The method of claim 37, wherein the antigen of interest or fragment thereof so produced is bound with an MHCII protein complex.

40. A method for inducing in a subject an immune response mediated by an MHCII antigen presentation pathway, comprising: a. contacting a cell with the vector claim 17 so that the cell produces the CDI fusion protein or fragment thereof and targets the CDI fusion protein or fragment thereof so produced to the MHCII antigen presenting pathway thereby inducing an immune response in the subject.