The present invention relates to peptides of the extracellular domain of a HER-2/neu protein, conjugates comprising said peptides linked to an immunogenic carrier, compositions thereof, nucleic acid molecules, vectors and transformed or transfected host cells comprising said nucleic acid molecules encoding said peptides or conjugates, and methods for producing the disclosed peptides, conjugates and compositions. The present invention also relates to diagnostic methods of detecting cancerous conditions associated with HER-2/neu or monitoring the effectiveness of treatment against cancerous conditions associated with HER-2/neu. The present invention also relates to methods of eliciting or enhancing an immune response to HER-2/neu in a subject in need thereof.

Description of the Invention

SUMMARY OF INVENTION

The present invention relates to a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the peptide of the present invention consists of between 10 to 20 contiguous amino acids of the extracellular domain of a HER-2/neu protein. Preferably, the peptides of the present invention consists of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the peptides of the present invention consist of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the peptides of the present invention consist of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

In one embodiment, the peptides of the present invention further bind antibodies that specifically bind a HER-2/neu protein. In another embodiment, the peptides of the present invention elicit or enhance an immune response. The present invention also provides compositions comprising the peptides of the present invention and a pharmaceutically acceptable carrier.

The present invention provides kits for detecting antibodies that specifically bind a HER-2/neu protein, wherein said kit comprises a first container or containers comprising any peptide of the present invention, or a functionally equivalent peptide thereof, and a second container containing buffers and factors necessary to form or detect a complex between a HER-2/neu protein and a peptide or functionally equivalent peptide thereof.

The present invention also provides functionally equivalent peptides of any of the peptides of the present invention. In one embodiment, the present invention provides functionally equivalent peptides of a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the present invention provides functionally equivalent peptides of a peptide consisting of between 10 to 20 contiguous amino acids of the extracellular domain of a HER-2/neu protein. Preferably, the present invention provides functionally equivalent peptides of a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the present invention provides functionally equivalent peptides of a peptide consisting of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the present invention provides functionally equivalent peptides of a peptide consisting of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

In one embodiment, the functionally equivalent peptides of the present invention are produced by: 1) the insertion of one or more amino acids to any peptide of the present invention; 2) the deletion of one or more amino acids to any peptide of the present invention; 3) the substitution of amino acids with non-identical amino acids or non-amino acids within any peptide of the present invention; or 4) the modification of one or more amino acids of any peptide of the present invention by adding carbohydrate, lipid, phosphate groups, acetyl groups, and the like. Preferably, the functionally equivalent peptides of the present invention are produced by the substitution of one or more amino acids of the peptides of the present invention by non-identical amino acids or non-amino acids. More preferably, the functionally equivalent peptides of the present invention are produced by the conservative substitution of one or more amino acids of the peptides of the present invention. More preferably, the functionally equivalent peptides of the present invention are produced by introducing between 1 and 5 conservative substitutions. In another preferred embodiment, the functionally equivalent peptides of the present invention are produced by introducing between 1 and 3 conservative substitutions. Most preferably, the functionally equivalent peptides of the present invention are produced by introducing one conservative substitution.

The present invention also contemplates functionally equivalent peptides wherein, in addition to the conservative substitutions disclosed herein, one or more of the amino acids of the peptide are modified by oxidation or reduction.

The present invention also contemplates functionally equivalent peptides wherein, in addition to the conservative substitutions disclosed herein, one or more of the amino acids of the peptides of the present invention are modified by the addition of one or more members selected from a group consisting of: carbohydrate, lipid, phosphate groups and acetyl groups.

The present invention also contemplates functionally equivalent peptides wherein, in addition to the insertions, deletions and substitutions disclosed herein, one or more of the amino acids of the peptides of the present invention are modified by oxidation or reduction. In a preferred embodiment, the present invention contemplates functionally equivalent peptides wherein one or more of the amino acids of any of the peptides disclosed herein are modified by oxidation or reduction.

The present invention also contemplates functionally equivalent peptides wherein, in addition to the insertions, deletions and substitutions disclosed herein, one or more of the amino acids of any of the peptides disclosed herein are modified by the addition of one or more members selected from a group consisting of: carbohydrate, lipid, phosphate groups and acetyl groups. In a preferred embodiment, the present invention also provides functionally equivalent peptides of any of the peptides disclosed herein, wherein one or more of the amino acids of the peptide are modified by the addition of one or more members selected from a group consisting of: carbohydrate, lipid, phosphate groups and acetyl groups.

In one embodiment, the functionally equivalent peptides of the present invention further bind antibodies that specifically bind a HER-2/neu protein.

In one embodiment, the functionally equivalent peptides of the present invention elicit or enhance an immune response. In a preferred embodiment, the ability of the functionally equivalent peptides of the present invention to elicit or enhance an immune response is substantially equivalent to that of the corresponding, unmodified peptide.

In another embodiment, the functionally equivalent peptides of the present invention elicit or enhance an immune response when the functionally equivalent peptide is conjugated to an immunogenic carrier. In a preferred embodiment, the ability of the functionally equivalent peptides of the present invention to elicit or enhance an immune response when the functionally equivalent peptide is conjugated to an immunogenic carrier is substantially equivalent to that of the corresponding, unmodified peptide.

The present invention is further directed to peptides, and functionally equivalent peptides thereof, linked to an immunogenic carrier to form a conjugate that elicits or enhances an immune response to a HER-2/neu protein in a subject in need thereof. In a preferred embodiment, the peptides of said conjugates consist of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the peptides of said conjugates consists of between 10 to 20 amino acids. Preferably, the peptides of said conjugates consist of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the peptides of the conjugates of the present invention consist of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the conjugates of the present invention comprise peptides that consist of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

The immunogenic carrier of the conjugates of the present invention is selected from a group of compounds, well known in the art, that, when linked to a peptide of the present invention, elicits or enhances an immune response to a HER-2/neu protein in a subject in need thereof. Preferably, the immunogenic carrier is selected from the group consisting of key-hole limpet hemocyanin (KLH) and tetanus toxoid (TT).

In a preferred embodiment, the conjugates of the present invention comprise between 2 and 10 peptides of the present invention linked to an immunogenic carrier. Preferably, the present invention contemplates conjugates comprising 5 peptides linked to an immunogenic carrier. More preferably, the present invention contemplates conjugates comprising 3 peptides linked to an immunogenic carrier. Most preferably, the conjugates of the claimed invention comprise 2 peptides linked to an immunogenic carrier. The present invention contemplates conjugates wherein each of the peptides may be linked directly to the immunogenic carrier. Alternatively, a peptide or peptides of the conjugates of the present invention may form links to one or more of the other peptides of the conjugate, wherein one or more of those peptides are linked to the immunogenic carrier. The peptides of the conjugates of the present invention may be either identical or non-identical.

The present invention also provides compositions comprising any of the disclosed conjugates and a pharmaceutically acceptable carrier, wherein the compositions elicit or enhance an immune response. In a preferred embodiment, the compositions of the present invention comprise conjugates wherein the peptides consist of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the compositions comprise conjugates wherein the peptides consist of between 10 to 20 amino acids. Preferably, the compositions comprise conjugates wherein the peptides consist of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the compositions of the present invention comprise conjugates wherein the peptides consist of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the compositions comprise conjugates wherein the peptides consist of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2). The present invention also contemplates methods of eliciting or enhancing an immune response comprising the administration of said compositions to a subject in need thereof.

The present invention also provides isolated nucleic acid molecules that encode the disclosed peptides of the present invention and functionally equivalent peptides thereof. In one embodiment, the present invention provides an isolated nucleic acid molecule encoding a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the isolated nucleic acid molecules of the present invention encode a peptide consisting of between 10 to 20 contiguous amino acids of the extracellular domain of a HER-2/neu protein. Preferably, the nucleic acid molecules of the present invention encode a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the nucleic acid molecules of the present invention encode a peptide consisting of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the nucleic acids of the present invention encode a peptide that consists of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

The present invention also contemplates an isolated nucleic acid molecule that, in addition to encoding one or more of the peptides and/or functionally equivalent peptides of the present invention, further encodes an immunogenic carrier. In a preferred embodiment, the isolated nucleic acid molecules encode one or more of the peptides and/or functionally equivalent peptides of the present invention and an immunogenic carrier selected from the group consisting of key-hole limpet hemocyanin (KLH) and tetanus toxoid (TT).

The present invention also provides a DNA vector comprising an isolated nucleic acid molecule of the present invention, as described, that is operably linked to one or more suitable regulatory sequences which induce expression and/or integration of the DNA sequence in a host cell. In a preferred embodiment, the vectors of the present invention comprise an isolated nucleic acid molecule encoding a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the vectors of the present invention comprise isolated nucleic acid molecules that encode a peptide consisting of between 10 to 20 contiguous amino acids of the extracellular domain of a HER-2/neu protein. Preferably, the vectors of the present invention comprise an isolated nucleic acid molecule that encodes a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the vectors of the present invention comprise an isolated nucleic acid molecule that encodes a peptide consisting of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the vectors of the present invention comprises an isolated nucleic acid molecule that encodes a peptide consisting of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

In one embodiment, the isolated nucleic acid molecules and vectors of the present invention encode peptides that further bind antibodies that specifically bind a HER-2/neu protein.

The present invention also provides host cells transformed or transfected with a vector comprising an isolated nucleic acid molecule of the present invention operably linked to one or more suitable regulatory sequences which induce expression and/or integration of the DNA sequence in a host cell. In a preferred embodiment, the host cells of the present invention are transformed or transfected with vectors comprising an isolated nucleic acid molecule encoding a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein. In another embodiment, the host cells of the present invention are transformed or transfected with vectors comprising isolated nucleic acid molecules that encode a peptide consisting of between 10 to 20 contiguous amino acids of the extracellular domain of a HER-2/neu protein. Preferably, the host cells of the present invention are transformed or transfected with vectors comprising an isolated nucleic acid molecule that encodes a peptide consisting of between 9 to 25 contiguous amino acids of the extracellular domain of a HER-2/neu protein, wherein the extracellular domain of the HER-2/neu protein is described by amino acids corresponding to amino acid positions 1-675 of SEQ ID NO: 3. More preferably, the host cells of the present invention are transformed or transfected with vectors comprising an isolated nucleic acid molecule that encodes a peptide consisting of a sequence of amino acids corresponding to amino acid positions 544 to 560 of SEQ ID NO: 3 or a sequence of amino acids corresponding to amino acid positions 610 to 623 of SEQ ID NO: 3. Most preferably, the host cells of the present invention are transformed or transfected with vectors comprising an isolated nucleic acid molecule that encodes a peptide consisting of the amino acid sequence CRVLQGLPREYVNARHC (SEQ ID NO: 1) or the amino acid sequence YMPIWKFPDEEGAC (SEQ ID NO: 2).

The present invention also provides methods of eliciting or enhancing an immune response in a subject in need thereof comprising administering any of the compositions of the present invention wherein the composition elicits or enhances an immune response in said subject.

The present invention also provides methods of eliciting or enhancing an immune response in a subject in need thereof comprising administering a composition comprising any of the transformed or transfected host cells described above wherein the composition elicits or enhances an immune response in said subject.

The present invention also provides methods of producing a peptide of the present invention or functionally equivalent peptide thereof comprising culturing any of the host cells of the present invention. In a preferred embodiment, the method of producing a peptide of the present invention or functionally equivalent peptide thereof further comprises purification of said peptide.

The present invention also provides methods of producing a conjugate comprising culturing the host cells described above, wherein the host cells are transformed or transfected with a vector comprising an isolated nucleic acid molecule encoding any one or more of the peptides of the present invention or functionally equivalent peptides thereof, as described above, and that further encodes an immunogenic carrier. In a preferred embodiment, the method of producing a peptide of the present invention or functionally equivalent peptide thereof further comprises purification of said peptide.

The present invention also provides methods of producing a conjugate comprising linking any one or more of the peptides of the present invention or functionally equivalent peptides thereof to an immunogenic carrier.

The present invention also provides methods of detecting the presence of antibodies against the HER-2/neu protein comprising mixing a biological fluid or tissue obtained from a subject with any of the peptides of the present invention or functionally equivalent peptides thereof for a complex between said peptide and said antibody, wherein complex formation indicates the presence of antibodies against a HER-2/neu protein.

DETAILED DESCRIPTION OF INVENTION

As used herein, "biological fluids" refers to any fluid in or isolated from human or other animal, including but not limited to, whole blood, serum, plasma, ascites, cerebrospinal fluid, urine, lymph fluids, synovial fluids, bronchoalveolar lavage, pleural fluids, various external secretions of the respiratory, intestinal and genitourinary tracts, tears, saliva, milk, white blood cells, myelomas, normal and diseased cells, cell culture supernatants, fixed tissue specimens and fixed cell specimens, and the like.

As used herein, the term "conjugate" refers to a chemical compound that has been formed by the joining of two or more molecules.

As used herein, the term "elicit or enhance an immune response" refers to the ability of an agent to act as an antigen and produce antibodies specific to the agent, or the ability of an agent to cause T cells to proliferate, differentiate, produce cytolytic activity or induce cytokine production.

As used herein, the term "extracellular domain of a HER-2/neu" refers to the portion of the HER-2/neu protein that is located outside the cell, or a fragment thereof. Preferably, the "extracellular domain of a HER-2/neu" consists of amino acids 1-675 of the polypeptide described by SEQ ID NO: 3.

As used herein, the term "immunogenic" refers to the ability of a molecule or composition to induce a humoral or cellular immune response.

As used herein, the term "isolated peptide" refers to a peptide after physical, mechanical or chemical methods are employed to remove the peptide from cellular constituents that are normally associated with the recombinantly produced peptide. A skilled artisan can readily employ standard purification methods to obtain such an isolated peptide.

As used herein, the term "linked" refers to a covalent association between an immunogenic carrier and one or more peptides of the claimed invention. For example, the covalent association may be either a peptide or a non-peptide bond. Linking of a peptide or peptides to an immunogenic carrier through a peptide bond may be accomplished recombinantly by methods well known in the art. Non-peptide covalent associations may be prepared through reaction of particular functional groups of amino acid side chains or the N- and/or C-terminals of the peptide(s) or carrier to form a covalent bond. The functional groups may be either naturally present in the peptide(s) or immunogenic carrier or introduced by chemical modification of the peptide(s) and/or immunogenic carrier by methods well known in the art.

As used herein, the term "recombinantly produced" refers to material produced by genetic engineering. As used herein, the term "recombinant DNA" refers to genetically engineered DNA prepared by transplanting or splicing genes from one species into the cells of a host organism of the same or a different species for purposes of replication, amplification, integration, or expression.

As used herein, the term "functionally equivalent peptide" refers to a peptide of between 9 and 25 amino acids, wherein any one or more of the following modifications have been made: 1) one or more amino acids of a peptide are replaced by other non-identical amino acids or non-amino acids; 2) amino acids are deleted; 3) amino acids are added to the peptide; or 4) amino acids are chemically or post-translationally modified by oxidation, reduction, condensation, and the addition of chemical groups such as carbohydrates, lipids, phosphates, acetyl groups, and the like.

Amino acid substitutions may be made in a variety of ways to provide the functionally equivalent peptides of the present invention. First, an amino acid may be conservatively substituted by replacing an amino acid with one that has similar charge, steric, hydropathic or chemical properties. The following groups contain amino acids that share similar charge, steric, hydropathic or chemical properties: (1) Ala (A), Gly (G), Glu (E), Asp (D), Gln (Q), Asn (N), Ser (S), Thr (T); (2) Cys (C), Ser (S), Tyr (Y), Thr (T); (3) Val (V), Ile (I), Leu (L), Met (M), Ala (A), Phe (F); (4) Lys (K), Arg (R), His (H); and (5) Phe (F), Tyr (Y), Trp (W), His (H). Substitution of an amino acid with a member of the same group would represent a conservative substitution. Substitution of an amino acid of one group with an amino acid from another group represents a non-conservative substitution.

The above-described sequence modifications may be introduced using standard recombinant techniques or by automated synthesis of the modified peptide. Oligonucleotide-directed site-specific mutagenesis procedures can be employed to provide a gene in which particular codons are altered to produce the desired substitution, deletion, or insertion. Exemplary methods of making the alterations set forth above are disclosed by Walder et al. (1986) Gene 42: 133; Bauer et al. (1985) Gene 37: 73; Craik (1985) BioTechniques January, 1985: 12-19; Smith et al. (1981) Genetic Engineering: Principles and Methods, Plenum Press; and U.S. Pat. Nos. 4,518,584 and 4,737,462.

Functionally equivalent peptides of the present invention may be produced by identifying and replacing amino acids in T-cell motifs that have the potential to bind to class II MHC molecules (for CD4.sup.+ T-cell response) or class I MHC molecules (for CD8.sup.+ T-cell response). Peptides of the extracellular domain of a HER-2/neu protein containing a motif with theoretical potential to bind to class II MHC molecules may be identified by computer analysis. For example, a protein sequence analysis package, "T Sites", incorporates several computer algorithms designed to distinguish potential sites for T-cell recognition. (Feller et al. (1991) Nature 349: 720-721). Two searching algorithms--AMPHI (Feller et al. (1991) Nature 349: 720-721; Margalit et al. (1987) J. Immunol. 138: 2213-2229) and the Rothbard and Taylor algorithm (Rothbard et al. (1988) EMBO 7: 93-100)--identify epitope motifs according to alpha-helical periodicity and amphipathicity and epitope motifs according to charge and polarity, respectively. Peptides with both motifs are most appropriate for binding to class II MHC molecules. CD8.sup.+-T cells recognize peptide bound to class I MHC molecules. Falk et al. have determined that peptides binding to particular MHC molecules share discernible sequence motifs (Falk et al. (1991) Nature 351: 290-296).

Functionally equivalent peptides of the present invention can be produced, for example, by using bacteriophage peptide-expression libraries of structural variants of the peptides of present invention. The libraries are initially screened to identify those peptides that bind an antibody that specifically binds either the corresponding unmodified peptide or a HER-2/neu protein. Peptides identified in this initial screening are then screened to determine whether they elicit or enhance an immune response. A similar procedure for producing such functionally equivalent peptides is described in European Patent Application EP 100 41 342.0, the disclosure of which is incorporated herein by reference.

Functionally equivalent peptides may be assayed to determine whether they retain the ability to elicit or enhance an immune response by contacting T cells with the structurally-modified peptide and assaying the response. It will be evident to those of ordinary skill in the art that peptides and functionally equivalent peptides may be tested for the ability to elicit or enhance an immune response by a variety of assays that are well known in the art, including detection of: 1) T-cell proliferation; 2) T-cell differentiation; 3) cytokine production; and 4) cytolytic activity.

Bacteriophage peptide-expression libraries may generally be produced and screened using methods known to those of ordinary skill in the art, such as methods described in Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., which is incorporated herein by reference. In the context of this invention, a "detection reagent" is any compound capable of binding to HER-2/neu protein, which may then be detected by any means known to those of ordinary skill in the art. Typical detection reagents contain a "binding agent," such as Protein A, Protein G, IgG or a lectin, coupled to a reporter group. Preferred reporter groups include enzymes, substrates, cofactors, inhibitors, dyes, radionuclides, luminescent groups, fluorescent groups and biotin. More preferably, the reporter group is horseradish peroxidase, which may be detected by incubation with a substrate such as tetramethylbenzidine or 2,2'-azino-di-3-ethylbenz-thiazoline sulfonic acid. Plaques containing nucleic acid sequences that express functionally equivalent peptides of the present invention are isolated and purified by techniques known to those of ordinary skill in the art. Appropriate methods may be found, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989.

In one embodiment, the peptide libraries used in the present invention may be libraries that are chemically synthesized in vitro. Examples of such libraries are given in Houghten et al. (1991) Nature 354: 84-86, which describes mixtures of free hexapeptides in which the first and second residues in each peptide were individually and specifically defined; Lam et al. (1991) Nature 354: 82-84, which describes a "one bead, one peptide" approach in which a solid phase split synthesis scheme produced a library of peptides in which each bead in the collection had immobilized thereon a single, random sequence of amino acid residues; Medynski (1994) Bio/Technology 12: 709-710, which describes split synthesis and T-bag synthesis methods; and Gallop et al. (1994) J. Medicinal Chemistry 37(9):1233-1251. Simply by way of other examples, a combinatorial library may be prepared, according to the methods of Ohlmeyer et al. (1993) Proc. Natl. Acad. Sci. USA 90: 10922-10926; Erb et al. (1994) Proc. Natl. Acad. Sci. USA 91: 11422-11426; Houghten et al. (1992) Biotechniques 13: 412; Jayawickreme et al. (1994) Proc. Natl. Acad. Sci. USA 91: 1614-1618; or Salmon et al. (1993) Proc. Natl. Acad. Sci. USA 90: 11708-11712. PCT Publication No. WO 93/20242 and Brenner et al. (1992) Proc. Natl. Acad. Sci. USA 89: 5381-5383 describe "encoded combinatorial chemical libraries," that contain oligonucleotide identifiers for each chemical polymer library member. Compounds synthesized so as to be immobilized on a substrate are released from the substrate prior to use in the inhibition assay.

Libraries of non-peptides, e.g., peptide derivatives (for example, that contain one or more non-naturally occurring amino acids) can also be used. One example of these are peptoid libraries (Simon et al. (1992) Proc. Natl. Acad. Sci. USA 89: 9367-9371). Peptoids are polymers of non-natural amino acids that have naturally occurring side chains attached not to the alpha carbon but to the backbone amino nitrogen. Since peptoids are not easily degraded by human digestive enzymes, they are advantageously more easily adaptable to drug use. Another example of a library that can be used, in which the amide functionalities in peptides have been permethylated to generate a chemically transformed combinatorial library, is described by Ostresh et al. (1994) Proc. Natl. Acad. Sci. USA 91: 11138-11142).

The members of the libraries that can be screened according to the invention are not limited to the 20 naturally occurring amino acids. In particular, chemically synthesized libraries and polysome-based libraries allow the use of amino acids in addition to the 20 naturally occurring amino acids (by their inclusion in the precursor pool of amino acids used in library production). In specific embodiments, the library members contain one or more non-natural or non-classical amino acids or cyclic peptides. Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, .alpha.-amino isobutyric acid; 4-aminobutyric acid; 2-amino butyric acid; .gamma.-Abu; .epsilon.-Ahx; 6-amino hexanoic acid; 2-amino isobutyric acid; 3-amino propionic acid; ornithine; norleucine; norvaline; hydroxyproline; sarcosine; citrulline; cysteic acid; t-butylglycine; t-butylalanine; phenylglycine; cyclohexylalanine; .beta.-alanine; designer amino acids such as .beta.-methyl amino acids; C.alpha.-methyl amino acids; N.alpha.-methyl amino acids; fluoro-amino acids; and the like. Furthermore, the natural and non-natural amino acids can be either D (dextrorotary) or L (levorotary).

The present invention also contemplates isolated nucleic acid molecules that encode the functionally equivalent peptides described herein, vectors, transformed or transfected host cells and methods of producing functionally equivalent peptides.

The peptides or the functionally equivalent peptides of the present invention are preferably conjugated to the carrier by chemical means. The peptides or the functionally equivalent peptides of the present invention can be conjugated to the carrier as a monomer, dimer, trimer or oligomer. The conjugation of peptides or the functionally equivalent peptides to an immunogenic carrier is described, for example, in Turpen et al. (1995) Bio/Technology 13: 53-57, which is incorporated herein by reference.

The peptides and conjugates of the present invention may be produced from an isolated HER-2/neu protein, synthetically produced, or genetically engineered and recombinantly produced. Automated synthetic production of peptides provides an alternate method for preparing the peptides and conjugates of the present invention. For example, any of the commercially available solid-phase techniques may be employed, such as the Merrifield solid phase synthesis method, in which amino acids are sequentially added to a growing amino acid chain. (See, Merrifield (1963) J. Am. Chem. Soc. 85: 2149-2146).

The transformed host cells of the present invention are cells which have been transformed or transfected with expression vectors constructed using recombinant DNA techniques and which contain isolated nucleic acid molecules encoding any peptide or conjugate of the present invention, as disclosed herein. Transformed host cells may express the desired peptide or conjugate but host cells transformed for purposes of cloning or amplifying the nucleic acid molecules of the present invention do not need to express the desired peptide or conjugate. Expressed peptides and conjugates will preferably be secreted into the culture supernatant.

Suitable host cells for expression of recombinant proteins include prokaryotes, yeast (members of Saccharomyces, such as S. cerevisiae, Pichia or Kluyveromyces or the like) or higher eukaryotic cells under the control of appropriate promoters. Prokaryotes include gram negative or gram positive organisms, for example E. coli or Bacilli. Suitable prokaryotic hosts for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium, and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus, although other hosts may also be employed. Higher eukaryotic cells include established cell lines of insect or mammalian origin as described below. Cell-free translation systems could also be employed to produce HER-2/neu polypeptides using RNAs derived from DNA constructs. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described, for example, by Pouwels et al. (1985) Cloning Vectors: A Laboratory Manual, Elsevier, N.Y.

Various mammalian or insect (e.g., Spodoptera or Trichoplusia) cell culture systems can also be employed to express the recombinant peptides and conjugates of the present invention. Baculovirus systems for production of heterologous polypeptides in insect cells are disclosed by Luckow et al. (1988) Bio/Technology 6: 47. Examples of suitable mammalian host cell lines include the COS-7 lines of monkey kidney cells, described by Gluzman (Cell 23: 175 (1981)), and other cell lines capable of expressing an appropriate vector including, for example, CV-1/EBNA (ATCC CRL 10478), L cells, C127, 3T3, Chinese hamster ovary (CHO), COS, NS-1, HeLa and BHK cell lines.

The peptides and conjugates of the present invention, as described herein, may be isolated by physical, mechanical or chemical methods. The peptide or conjugate may be further purified by any number of techniques known in the art. For example, the peptides and conjugates may be prepared by culturing transformed or transfected host cells of the present invention and then purified from culture media or cell extracts by extraction, salting out, filtration or ultrafiltration, chromatography, including size exclusion, ion-exchange, normal-phase, reverse-phase, or affinity chromatography, or a combination thereof.

Recombinant expression vectors contain a DNA sequence encoding a HER-2/neu polypeptide operably linked to suitable transcriptional or translational regulatory elements derived from mammalian, microbial, viral or insect genes. Such regulatory elements include a transcriptional promoter, an optional operator sequence to control transcription, a sequence encoding suitable mRNA ribosomal binding sites, and sequences which control the termination of transcription and translation. An origin of replication and a selectable marker to facilitate recognition of transformants may additionally be incorporated.

DNA regions are operably linked when they are functionally related to each other. For example, DNA for a signal peptide (secretory leader) is operably linked to DNA for a polypeptide if it is expressed as a precursor which participates in the secretion of the polypeptide; a promoter is operably linked to a coding sequence if it controls the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to permit translation. Generally, operably linked means contiguous and, in the case of secretory leaders, in reading frame. DNA sequences encoding HER-2/neu polypeptides which are to be expressed in a microorganism will preferably contain no introns that could prematurely terminate transcription of DNA into mRNA.

Expression vectors for bacterial use may comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3. These pBR322 "backbone" sections are combined with an appropriate promoter and the structural sequence to be expressed. E. coli is typically transformed using derivatives of pBR322, a plasmid derived from an E. coli species (Bolivar et al. (1977) Gene 2: 95). pBR322 contains genes for ampicillin and tetracycline resistance and thus provides simple means for identifying transformed cells.

Preferred yeast vectors can be assembled using DNA sequences from pBR322 for selection and replication in E. coli (Amp.sup.r gene and origin of replication) and yeast DNA sequences including a glucose-repressible ADH2 promoter and .alpha.-factor secretion leader. The ADH2 promoter has been described by Russell et al. (J. Biol. Chem. 258: 2674 (1982)) and Beier et al. (Nature 300: 724 (1982)). The yeast .alpha.-factor leader, which directs secretion of heterologous proteins, can be inserted between the promoter and the structural gene to be expressed (See, e.g., Kurjan et al. (1982) Cell 30: 933; and Bitter et al. (1984) Proc. Natl. Acad. Sci. USA 81: 5330). The leader sequence may be modified to contain, near its 3' end, one or more useful restriction sites to facilitate fusion of the leader sequence to foreign genes. The transcriptional and translational control sequences in expression vectors to be used in transforming vertebrate cells may be provided by viral sources. For example, commonly used promoters and enhancers are derived from polyoma, adenovirus 2, simian virus 40 (SV40), and human cytomegalovirus. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early and late promoter, enhancer, splice, and polyadenylation sites may be used to provide the other genetic elements required for expression of a heterologous DNA sequence. The early and late promoters are particularly useful because both are obtained easily from the virus as a fragment which also contains the SV40 viral origin of replication (Fiers et al. (1978) Nature 273: 113). Smaller or larger SV40 fragments may also be used, provided the approximately 250 bp sequence extending from the Hind III site toward the Bg1 II site located in the viral origin of replication is included. Further, viral genomic promoter, control and/or signal sequences may be utilized, provided such control sequences are compatible with the host cell chosen. Exemplary vectors can be constructed as disclosed by Okayama et al. (1983) Mol. Cell. Biol. 3: 280.

Mammalian expression vectors may comprise nontranscribed elements such as an origin of replication, a suitable promoter and enhancer linked to the gene to be expressed, and other 5' or 3' flanking nontranscribed sequences, and 5' or 3' nontranslated sequences, such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and transcriptional termination sequences.

Promoters commonly used in recombinant microbial expression vectors include the .beta.-lactamase (penicillinase) and lactose promoter system (Chang et al. (1978) Nature 275: 615; and Goeddel et al. (1979) Nature 281: 544), the tryptophan (trp) promoter system (Goeddel et al. (1980) Nucl. Acids Res. 8: 4057; and European Patent Application 36,776) and the tac promoter (Maniatis (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, p. 412). A particularly useful bacterial expression system employs the phage .lamda.P.sub.L promoter and cI857ts thermolabile repressor. Plasmid vectors available from the American Type Culture Collection which incorporate derivatives of the .lamda.P.sub.L promoter include plasmid pHUB2, resident in E. coli strain JMB9 (ATCC 37092) and pPLc28, resident in E. coli RR1 (ATCC 53082).

Suitable promoter sequences in yeast vectors include the promoters for metallothionein, 3-phosphoglycerate kinase (Hitzeman et al. (1980) J. Biol. Chem. 255: 2073) or other glycolytic enzymes (Hess et al. (1968) J. Adv. Enzyme Reg. 7: 149; and Holland et al. (1978) Biochem. 17: 4900), such as enolase, glyceraldehyde 3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase. Suitable vectors and promoters for use in yeast expression are further described in European Patent Application 73,657.

Administration of any of the compositions of the present invention, as described herein, can induce continued expansion in the number of T cells necessary for therapeutic attack against cells in which the HER-2/neu oncogene is associated. The compositions of the present invention can be administered intravenously, subcutaneously, intraperitoneally, intramuscularly, or orally in capsule or pill form. Typically, about 0.01 .mu.g/kg to about 100 mg/kg body weight will be administered by the intradermally, subcutaneously, intraperitoneally, intramuscularly, or intravenously. A preferred dosage is about 1 .mu.g/kg to about 1 mg/kg, with about 5 .mu.g/kg to about 200 .mu.g/kg particularly preferred. It will be evident to those skilled in the art that the number and frequency of administration will be dependent upon the response of the patient. It may be desirable to administer the compositions of the present invention repetitively. It will be evident to those skilled in this art that more than one conjugate of the present invention, as described herein, may be administered either simultaneously or sequentially.

The conjugates of the present invention, as disclosed herein, are preferably formulated for use in the above methods as a pharmaceutical composition (e.g., vaccine). Compositions of the present invention comprise one or more conjugates in combination with a pharmaceutically acceptable carrier. As used herein, the term "pharmaceutically acceptable carrier" includes excipients, diluents, adjuvants and the like. Such carriers will be nontoxic to recipients at the dosages and concentrations employed. The present invention also contemplates compositions further comprising chemotherapeutic and/or other therapeutic agents.

Pharmaceutically acceptable carriers include delivery and immunostimulatory substances designed to enhance conjugate immunogenicity. Examples of vehicles for antigen delivery include aluminum salts, water-in-oil emulsions, biodegradable oil vehicles, oil-in-water emulsions, biodegradable microcapsules, and liposomes. Examples of immunostimulatory substances (adjuvants) include N-acetylmuramyl-L-alanine-D-isoglutamine (MDP), lipopoly-saccharides (LPS), glucan, IL-12, GM-CSF, gamma interferon and IL-15.

While any pharmaceutically acceptable carrier known to those of ordinary skill in the art may be employed in the compositions of this invention, the type of carrier will vary depending on the mode of administration and whether a sustained release is desired. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactic galactide) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268 and 5,075,109. The conjugates of the present invention may be encapsulated within the biodegradable microsphere or associated with the surface of the microsphere.

Pharmaceutically acceptable carriers include diluents such as buffers, antioxidants such as ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, amino acids, carbohydrates including glucose, sucrose or dextrins, chelating agents such as EDTA, glutathione and other stabilizers and excipients. Neutral buffered saline or saline mixed with nonspecific serum albumin are exemplary appropriate diluents.

Antibodies specific for HER-2/neu protein may be detected in a variety of biological fluids or tissues including sera and ascites using the peptides, or functionally equivalent peptides thereof, of the present invention. Briefly, a biological fluid or tissue sample is isolated from a warm-blooded animal, such as a human, for whom it is desired to determine whether antibodies specific for a HER-2/neu protein are present. The biological fluid or tissue is incubated with a peptide, or functionally equivalent peptides thereof, of the present invention under conditions sufficient to permit immunocomplexes to form between the polypeptide and antibodies specific for the protein. For example, a biological fluid or tissue and peptide or functionally equivalent peptides thereof, may be incubated at 4.degree. C. for 24-48 hours. Following the incubation, the reaction mixture is tested for the presence of immunocomplexes. Detection of one or more immunocomplexes formed between a peptide and antibodies specific for HER-2/neu polypeptide may be accomplished by a variety of known techniques, such as radioimmunoassays (RIA) and enzyme-linked immunosorbent assays (ELISA).

Suitable immunoassays include the double-monoclonal-antibody sandwich-immunoassay technique of David et al. (U.S. Pat. No. 4,376,110); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh, 1970); the "Western blot" method of Gordon et al. (U.S. Pat. No. 4,452,901); immunoprecipitation of labeled ligand (Brown et al. (1980) J. Biol. Chem. 255: 4980-4983); enzyme-linked immunosorbent assays as described by, for example, Raines and Ross (J. Biol. Chem. 257: 5154-5160 (1982)); immunocytochemical techniques, including the use of fluorochromes (Brooks et al. (1980) Clin. Exp. Immunol. 39: 477); and neutralization of activity (Bowen-Pope et al. (1984) Proc. Natl. Acad. Sci. USA 81: 2396-2400), all of which are hereby incorporated by reference. In addition to the immunoassays described above, a number of other immunoassays are available, including those described in U.S. Pat. Nos.: 3,817,827; 3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876, all of which are herein incorporated by reference.

For detection purposes, a peptide ("antigen") of the present invention, as described herein, may either be labeled or unlabeled. When unlabeled, the antigen finds use in agglutination assays. In addition, unlabeled antigen can be used in combination with labeled molecules that are reactive with immunocomplexes, or in combination with labeled antibodies (second antibodies) that are reactive with the antibody directed against the peptide of the present invention. Alternatively, the antigen can be directly labeled. Where it is labeled, the reporter group can include radioisotopes, fluorophores, enzymes, luminescers, or dye particles. These and other labels are well known in the art and are described, for example, in the following U.S. Pat Nos.: 3,766,162; 3,791,932; 3,817,837; 3,996,345; and 4,233,402.

Typically in an ELISA assay, antigen is adsorbed to the surface of a microtiter well. Residual protein-binding sites on the surface are then blocked with an appropriate agent, such as bovine serum albumin (BSA), heat-inactivated normal goat serum (NGS), or BLOTTO (buffered solution of nonfat dry milk which also contains a preservative, salts, and an antifoaming agent). The well is then incubated with a sample suspected of containing specific antibody. The sample can be applied neat, or, more often, it can be diluted, usually in a buffered solution which contains a small amount (0.1%-5.0% by weight) of protein, such as BSA, NGS, or BLOTTO. After incubating for a sufficient length of time to allow specific binding to occur, the well is washed to remove unbound protein and then incubated with an anti-species specific immunoglobulin antibody labeled with a reporter group. The reporter group can be chosen from a variety of enzymes, including horseradish peroxidase, beta-galactosidase, alkaline phosphatase, and glucose oxidase. Sufficient time is allowed for specific binding to occur, then the well is again washed to remove unbound antibody, and the substrate for the enzyme is added. Color is allowed to develop and the optical density of the contents of the well is determined visually or instrumentally.

In a related aspect of the invention, the detection of immunocomplexes formed between peptides of the present invention and antibodies in biological fluid or tissue which are specific for a HER-2/neu protein may be used to monitor the effectiveness of cancer therapy for a malignancy in which the HER-2/neu oncogene is associated. Samples of biological fluid or tissue taken from an individual prior to and subsequent to initiation of therapy may be analyzed for the immunocomplexes by the methodologies described above. Briefly, the number of immunocomplexes detected in both samples are compared. A substantial change in the number of immunocomplexes in the second sample (post-therapy initiation) relative to the first sample (pre-therapy) reflects successful therapy.
 

Claim 1 of 10 Claims

1. An isolated peptide as set forth in SEQ ID NO:1 or SEQ ID NO:2.

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