Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
  • C07K7/04—Linear peptides containing only normal peptide links
  • C07K7/06—Linear peptides containing only normal peptide links having 5 to 11 amino acids
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/0005—Vertebrate antigens
  • A61K39/0011—Cancer antigens
  • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
  • A61K39/001103—Receptors for growth factors
  • A61K39/001106—Her-2/neu/ErbB2, Her-3/ErbB3 or Her 4/ErbB4
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K40/00—Cellular immunotherapy
  • A61K40/10—Cellular immunotherapy characterised by the cell type used
  • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K40/00—Cellular immunotherapy
  • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
  • A61K40/41—Vertebrate antigens
  • A61K40/42—Cancer antigens
  • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
  • A61K40/4203—Receptors for growth factors
  • A61K40/4205—Her-2/neu/ErbB2, Her-3/ErbB3 or Her 4/ ErbB4
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
  • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
  • C07K14/4702—Regulators; Modulating activity
  • C07K14/4705—Regulators; Modulating activity stimulating, promoting or activating activity
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
  • C07K14/71—Receptors; Cell surface antigens; Cell surface determinants for growth factors; for growth regulators
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N15/86—Viral vectors
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57557—Immunoassay; Biospecific binding assay; Materials therefor for cancer of other specific parts of the body, e.g. brain
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
  • G01N33/57585—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites involving compounds identifiable in body fluids
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
  • G01N2333/71—Assays involving receptors, cell surface antigens or cell surface determinants for growth factors; for growth regulators
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/82—Translation products from oncogenes
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10S530/00—Chemistry: natural resins or derivatives; peptides or proteins; lignins or reaction products thereof
  • Y10S530/806—Antigenic peptides or proteins
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10S530/00—Chemistry: natural resins or derivatives; peptides or proteins; lignins or reaction products thereof
  • Y10S530/827—Proteins from mammals or birds
  • Y10S530/828—Cancer

Definitions

• the present invention is generally directed toward polypeptides, and nucleic acid molecules encoding such polypeptides, for eliciting or enhancing an immune response to HER-2/neu protein, including for use in the treatment of malignancies in which the HER-2/neu oncogene is associated.
• cancer is the leading cause of death in women between the ages of 35 and 74.
• Breast cancer is the most common malignancy in women and the incidence for developing breast cancer is on the rise.
• Standard approaches to cure breast cancer have centered around a combination of surgery, radiation and chemotherapy. These approaches have resulted in some dramatic successes in certain malignancies.
• these approaches have not been successful for all malignancies and breast cancer is most often incurable when attempting to treat beyond a certain stage.
• Alternative approaches to prevention and therapy are necessary.
• a common characteristic of malignancies is uncontrolled cell growth. Cancer cells appear to have undergone a process of transformation from the normal phenotype to a malignant phenotype capable of autonomous growth. Amplification and overexpression of somatic cell genes is considered to be a common primary event that results in the transformation of normal cells to malignant cells. The malignant phenotypic characteristics encoded by the oncogenic genes are passed on during cell division to the progeny of the transformed cells.
• Ongoing research involving oncogenes has identified at least forty oncogenes operative in malignant cells and responsible for, or associated with, transformation. Oncogenes have been classified into different groups based on the putative function or location of their gene products (such as the protein expressed by the oncogene) .
• Oncogenes are believed to be essential for certain aspects of normal cellular physiology.
• the HER-2/neu oncogene is a member of the tyrosine protein kinase family of oncogenes and shares a high degree of homology with the epidermal growth factor receptor.
• HER-2/neu presumably plays a role in cell growth and/or differentiation.
• HER-2/neu appears to induce malignancies through quantitative mechanisms that result from increased or deregulated expression of an essentially normal gene product.
• HER-2/neu (pl85) is the protein product of the HER-2/neu oncogene.
• the HER-2/neu gene is amplified and the HER-2/neu protein is overexpressed in a variety of cancers including breast, ovarian, colon, lung and prostate cancer.
• " HER-2/neu is related to malignant transformation. It is found in 50%-60% of ductal in si tu carcinoma and 20%-40% of all breast cancers, as well as a substantial fraction of adenocarcinomas arising in the ovaries, prostate, colon and lung.
• HER-2/neu is intimately associated not only with the malignant phenotype, but also with the aggressiveness of the malignancy, being found in one-fourth of all invasive breast cancers.
• HER-2/neu overexpression is correlated with a poor prognosis in both breast and ovarian cancer.
• HER-2/neu is a transmembrane protein with a relative molecular mass of 185 kd that is approximately 1255 amino acids (aa) in length. It has an extracellular binding domain (ECD) of approximately 645 aa, with 40% homology to epidermal growth factor receptor (EGFR) , a highly hydrophobic transmembrane anchor domain (TMD) , and a carboxyterminal cytoplasmic domain (CD) of approximately 580 aa with 80% homology to EGFR.
• ECD extracellular binding domain
• the present invention fulfills this need, and further provides other related advantages .
• the present invention provides polypeptides, nucleic acid molecules (directing the expression of such polypeptides) and viral vectors
• a polypeptide or nucleic acid molecule according to this invention may be present in a composition that includes a pharmaceutically acceptable carrier or diluent.
• a polypeptide, nucleic acid molecule, viral vector or pharmaceutical composition may be used for immunization on a one-time basis (e.g., when a malignancy is suspected) or on a periodic basis (e.g., for an individual with an elevated risk of acquiring or reacquiring a malignancy) .
• a medicament for immunization may be useful in the treatment of an existing tumor or to prevent tumor occurrence or reoccurrence .
• the present invention provides a polypeptide encoded by a DNA sequence selected from: (a) nucleotides 2026 through 3765 of SEQ ID NO:l; and (b) DNA sequences that hybridize to a nucleotide sequence complementary to nucleotides 2026 through 3765 of SEQ ID NO: 1 under moderately stringent conditions, wherein the DNA sequence encodes a polypeptide that produces an immune response to HER-2/r.eu protein.
• a polypeptide has the amino acid sequence of SEQ ID NO:2 from lysine, amino acid 676, through valine, amino acid 1255, or a variant thereof that produces at least an equivalent immune response.
• a composition is provided that comprises a polypeptide of the present invention in combination with a pharmaceutically acceptable carrier or diluent.
• a polypeptide or composition of the present invention is provided for the immunization of a warm-blooded animal against a malignancy in which the HER-2/neu oncogene is associated.
• such a polypeptide or composition is used for the manufacture of a medicament for immunization of a warm-blooded animal against a malignancy in which the HER-2/neu oncogene is associated.
• a nucleic acid molecule directing the expression of a polypeptide according to the present invention is provided for immunization by transfecting the cells of a warm-blooded animal with the nucleic acid molecule.
• such a nucleic acid molecule is used for the manufacture of a medicament for immunization of a warm-blooded animal against a malignancy in which the HER-2/neu oncogene is associated.
• a viral vector directing the expression of a polypeptide according to the present invention is provided for immunization by infecting the cells of a warm-blooded animal with the vector.
• such a viral vector is used for the manufacture of a medicament for immunization of a warm ⁇ blooded animal against a malignancy in which the HER-2/neu oncogene is associated.
• Figure 1 shows the results of the priming of naive T lymphocytes to HER-2/neu polypeptide by dendritic cells.
• Bone marrow-derived DC were generated with GM-CSF and IL6 from CD34+ stem cells.
• DC pulsed with HER-2/neu polypeptide induced protein-specific proliferation of autologous CD4+/CD45RA+ T lymphocytes after 7 days of culturing T cells with DC.
• Bone marrow-derived CD34+ stem cells cultured for one week in serum-free medium containing GM-CSF and IL-6 were used as APC.
• APC were plated into 96-well round-bottomed plates (Corning, Corning, NY, USA) at various concentrations and incubated for 16-18 hours with 20-25 ⁇ g/ml of recombinant HER-2/.neu polypeptide.
• CD4+ T lymphocytes were isolated from autologous peripheral blood mononuclear cells by positive selection using immunoaffinity columns (CellPro, Inc., Bothell, WA, USA) .
• Antigen-pulsed APC were irradiated (10 Gy) , and CD4+ T lymphocytes were added at 10 5 per well. Proliferative response of T cells was measured by the uptake of ( 3 H) thy idine (l ⁇ Ci/well) added on day 7 for 16- 18 hours.
• Proliferation assays were performed in serum- and cytokine-free medium in 5 well replicates.
• the symbols represent: —•— DC + HER-2/neu polypeptide + CD4+/CD45RA+ T cells; —O— DC + CD4+/CD45RA+ T cells; and —D— DC + HER-2/neu polypeptide.
• Figure 2 shows the response of CD4+ cells to HER-2/neu polypeptide.
• CD4+ T cells from normal donors were tested for responses to recombinant human HER-2/neu polypeptide.
• the symbols represent: — ⁇ — SC+CD4; and • - ⁇ -•• SC+CD4+HER-2/neu polypeptide.
• SC is stem cells.
• Figure 3 shows that rats immunized with rat HER-2/neu polypeptide develop rat neu specific antibodies.
• Rats were immunized with recombinant rat HER-2/.neu polypeptide 25 ug in MPL or vaccel ad uvant. Three immunizations were given, each 20 days apart. Twenty days after the final immunization rats were assessed for antibody responses to rat neu . Animals immunized with rat HER-2/neu polypeptide and the vaccel adjuvant showed high titer rat neu specific responses. The control was an animal immunized with human HER-2/neu polypeptide (foreign protein) .
• MPL and “vaccel” are adjuvants (Ribi, Bozeman, MT, USA) .
• Neg is HER-2/neu protein.
• Figure 4 shows that breast cancer patients have preexistent immunity to HER-2/neu polypeptide.
• PBMC peripheral blood mononuclear cells
• HER-2/neu positive-stage II breast cancer patient has a significant response to recombinant human HER-2/neu polypeptide.
• the symbols "p” represent peptides for HER-2/neu protein, "tt” represents tetanus toxoid, and "hHNP” represents recombinant human HER-2/neu polypeptide.
• HER-2/neu polypeptide - refers to a portion of the HER-2/neu protein (the protein also known as pl85 or c-erbB2) having the amino acid sequence of SEQ ID N0:2 from lysine, amino acid 676, through valine, amino acid 1255; and may be naturally derived, synthetically produced, genetically engineered, or a functionally equivalent variant thereof, e.g., where one or more amino acids are replaced by other amino acid(s) or non-amino acid(s) which do not substantially affect elicitation or enhancement of an immune response to HER- 2 /neu protein (e.g., variant stimulates a response by helper T cells or cytotoxic T cells) .
• Proliferation of T cells includes the multiplication of T cells as well as the stimulation of T cells leading to multiplication, i.e., the initiation of events leading to mitosis and mitosis itself. Methods for detecting proliferation of T cells are discussed below.
• the present invention is directed toward compounds and compositions to elicit or enhance immunity to the protein product expressed by the HER-2/neu oncogene, including for malignancies in a warm ⁇ blooded animal wherein an amplified HER-2/neu gene is associated with the malignancies. Association of an amplified HER-2/neu gene with a malignancy does not require that the protein expression product of the gene be present on the tumor. For example, overexpression of the protein expression product may be involved with initiation of a tumor, but the protein expression may subsequently be lost.
• a use of the present invention is to elicit or enhance an effective autochthonous immune response to convert a HER-2/neu positive tumor to HER-2/neu negative.
• the disclosure of the present invention shows that a polypeptide based on a particular portion (HER-2/neu polypeptide) of the protein expression product of the HER-2/neu gene can be recognized by thymus-dependent lymphocytes (hereinafter "T cells") and, therefore, the autochthonous immune T cell response can be utilized prophylactically or to treat malignancies in which such a protein is or has been overexpressed.
• T cells thymus-dependent lymphocytes
• nucleic acid molecules directing the expression of such a peptide may be used alone or in a viral vector for immunization.
• CD4+ T cell populations are considered to function as helpers/inducers through the release of lymphokines when stimulated by a specific antigen; however, a subset of CD4 + cells can act as cytotoxic T lymphocytes (CTL) .
• CD8 + T cells are considered to function by directly lysing antigenic targets; however, under a variety of circumstances they can secrete lymphokines to provide helper or DTH function.
• the phenotypic CD4 and CD8 markers are linked to the recognition of peptides bound to class II or class I MHC antigens.
• CD4 + and CD8 + T cells respond to different antigens or the same antigen presented under different circumstances.
• the binding of immunogenic peptides to class II MHC antigens most commonly occurs for antigens ingested by antigen presenting cells. Therefore, CD4 + T cells generally recognize antigens that have been external to the tumor cells.
• binding of peptides to class I MHC occurs only for proteins present in the cytosol and synthesized by the target itself, proteins in the external environment are excluded.
• An exception to this is the binding of exogenous peptides with a precise class I binding motif which are present outside the cell in high concentration.
• CD4 + and CD8 + T cells have broadly different functions and tend to recognize different antigens as a reflection of where the antigens normally reside.
• a polypeptide portion of the protein product expressed by the HER-2/neu oncogene is recognized by T cells. Circulating HER-2/neu polypeptide is degraded to peptide fragments. Peptide fragments from the polypeptide bind to major histocompatibility complex (MHC) antigens.
• MHC major histocompatibility complex
• T cells expressing a T cell receptor with high affinity binding of the peptide-MHC complex will bind to the peptide-MHC complex and thereby become activated and induced to proliferate.
• small numbers of immune T cells will secrete lymphokines, proliferate and differentiate into effector and memory T cells.
• the primary immune response will occur in vivo but has been difficult to detect in vi tro .
• Subsequent encounter with the same antigen by the memory T cell will lead to a faster and more intense immune response.
• the secondary response will occur either in vivo or in vi tro .
• the in vi tro response is easily gauged by measuring the degree of proliferation, the degree of cytokine production, or the generation of cytolytic activity of the T cell population re-exposed in the antigen.
• Substantial proliferation of the T cell population in response to a particular antigen is considered to be indicative of 'prior exposure or priming to the antigen.
• the compounds of this invention generally comprise HER-2/neu polypeptides or DNA molecules that direct the expression of such peptides, wherein the DNA molecules may be present in a viral vector.
• the polypeptides of the present invention include variants of the polypeptide of SEQ ID NO:2 from amino acid 676 through amino acid 1255, that retain the ability to stimulate an immune response.
• Such variants include various structural forms of the native polypeptide. Due to the presence of ionizable amino and carboxyl groups, for example, a HER-2/neu polypeptide may be in the form of an acidic or basic salt, or may be in neutral form. Individual amino acid residues may also be modified by oxidation or reduction.
• Variants within the scope of this invention also include polypeptides in which the primary amino acid structure native HER-2/neu polypeptide is modified by forming covalent or aggregative conjugates with other peptides or polypeptides, or chemical moieties such as glycosyl groups, lipids, phosphate, acetyl groups and the like.
• Covalent derivatives may be prepared, for example, by linking particular functional groups to amino acid side chains or at the N- or C-terminus.
• the present invention also includes HER-2/neu polypeptides with or without glycosylation.
• Polypeptides expressed in yeast or mammalian expression systems may be similar to or slightly different in molecular weight and glycosylation pattern than the native molecules, depending upon the expression system.
• expression of DNA encoding polypeptides in bacteria such as E . col i typically provides non-glycosylated molecules.
• N- glycosylation sites of eukaryotic proteins are characterized by the amino acid triplet Asn-Ai-Z, where Ai is any amino acid except Pro, and Z is Ser or Thr.
• Variants of HER-2/neu polypeptides having inactivated N- glycosylation sites can be produced by techniques known to those of ordinary skill in the art, such as oligonucleotide synthesis and ligation or site-specific mutagenesis techniques, and are within the scope of this invention.
• N-linked glycosylation sites can be added to a HER-2/neu polypeptide.
• polypeptides of this invention also include variants of the SEQ ID NO:2 polypeptide (i.e., variants of a polypeptide having the amino acid sequence of SEQ ID NO:2 from amino acid 676 through amino acid 1255) that have an amino acid sequence different from this sequence because of one or more deletions, insertions, substitutions or other modifications.
• variants are substantially homologous to the native HER-2/neu polypeptide and retain the ability to stimulate an immune response.
• Substantial homology refers to amino acid sequences that may be encoded by DNA sequences that are capable of hybridizing under moderately stringent conditions to a nucleotide sequence complimentary to a naturally occurring DNA sequence encoding the specified polypeptide portion of SEQ ID NO:2 herein (i.e., nucleotides 2026 through 3765 of SEQ ID NO:l) .
• Suitable moderately stringent conditions include prewashmg in a solution of 5 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0) ; hybridizing at 50°C-65°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0.2X SSC (containing 0.1% SDS) .
• hybridizing DNA sequences are also within the scope of this invention.
• the effect of any such modifications on the ability of a HER-2/neu polypeptide to produce an immune response may be readily determined (e.g., by analyzing the ability of the mutated HER-2/neu polypeptide to induce a T cell response using, for example, the methods described herein) .
• ammo acid substitutions may be made a variety of ways to provide other embodiments of variants within the present invention.
• amino acid substitutions may be made conservatively; i.e., a substitute amino acid replaces an amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged.
• ammo acids represent conservative changes: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, lie, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his.
• An example of a non-conservative change is to replace an amino acid of one group with an amino acid from another group.
• Another way to make amino acid substitutions to produce variants of the present invention is to identify and replace amino acids in T cell motifs with potential to bind to class II MHC molecules (for CD4+ T cell response) or class I MHC molecules (for CD8+ T cell response) .
• Peptide segments (of a HER-2/neu polypeptide) with 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 Si tes, that incorporates several computer algorithms designed to distinguish potential sites for T cell recognition can be used (Feller and de la Cruz, Na t ure 349 : 120-121 , 1991) .
• HLA-A2.1 has been defined by Edman degradation of peptides stripped from HLA-A2.1 molecules of a cultured cell line
• the method identified the typical or average HLA-A2.1 binding peptide as being 9 amino acids in length with dominant anchor residues occurring at positions 2 (L) and 9 (V) . Commonly occurring strong binding residues have been identified at positions 2 (M) , 4 (E,K) , 6 (V) , and 8 (K) . The identified motif represents the average of many binding peptides .
• the derived peptide motif as currently defined is not particularly stringent. Some HLA-A2.1 binding peptides do not contain both dominant anchor residues and the amino acids flanking the dominant anchor residues play major roles in allowing or disallowing binding. Not every peptide with the current described binding motif will bind, and some peptides without the motif will Dind. However, the current motif is valid enough to allow identification of some peptides capable of binding. Of note, the current HLA-A2.1 motif places 6 ammo acids between the dominant anchor amino acids at residues 2 and 9.
• ammo acid substitutions may be made conservatively or non-conservatively. The latter type of substitutions are intended to produce an improved polypeptide that is more potent and/or more broadly cross-reactive (MHC polymorphism) .
• MHC polymorphism An example of a more potent polypeptide is one that binds with higher affinity to the same MHC molecule as natural polypeptide, without affecting recognition by T cells specific for natural polypeptide.
• An example of a polypeptide with broader cross-reactivity is one that induces more broadly cross-reactive immune responses (i.e., binds to a greater range of MHC molecules) than natural polypeptide.
• one or more amino acids residing between peptide motifs and having a spacer function may be substituted conservatively or non-conservatively. It will be evident to those of ordinary skill in the art that polypeptides containing one or more amino acid substitutions may be tested for beneficial or adverse immunological interactions by a variety of assays, including those described herein for the ability to stimulate T cell recognition.
• Variants within the scope of this invention may also, or alternatively, contain other modifications, including the deletion or addition of amino acids, that have minimal influence on the desired immunological properties of the polypeptide. It will be appreciated by those of ordinary skill in the art that truncated forms or non-native extended forms of a HER-2/neu polypeptide may be used, provided the desired immunological properties are at least roughly equivalent to that of full length, native HER-2/neu polypeptide. Cysteine residues may be deleted or replaced with other amino acids to prevent formation of incorrect intramolecular disulfide bridges upon renaturation. Other approaches to mutagenesis involve modification of adjacent dibasic amino acid residues to enhance expression in yeast systems in which KEX2 protease activity is present.
• a HER-2/neu polypeptide may generally be obtained using a genomic or cDNA clone encoding the protein.
• a genomic sequence that encodes full length HER-2/neu is shown in SEQ ID NO: 1, and the deduced amino acid sequence is presented in SEQ ID NO: 2.
• Such clones may be isolated by screening an appropriate expression library for clones that express HER-2/neu protein.
• the library preparation and screen may generally be performed using methods known to those of ordinary skill in the art, such as methods described in Sambrook et al . , Molecular Cl oning: A Labora tory Manual , Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989, which is incorporated herein by reference.
• a bacteriophage expression library may be plated and transferred to filters.
• the filters may then be incubated with a detection reagent.
• a detection reagent is any compound capable of binding to HER-2/neu protein, which may then be detected by any of a variety of 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.
• the reporter group is horseradish peroxidase, which may be detected by incubation with a substrate such as tetramethylbenzidine or 2, 2 ' -az ⁇ no-d ⁇ -3-ethylbenz- thiazolme sulfonic acid.
• a substrate such as tetramethylbenzidine or 2, 2 ' -az ⁇ no-d ⁇ -3-ethylbenz- thiazolme sulfonic acid.
• Variants of the polypeptide that retain the ability to stimulate an immune response may generally be identified by modifying the sequence in one or more of the aspects described above and assaying the resulting polypeptide for the ability to stimulate an immune response, e.g., a T cell response.
• assays may generally be performed by contacting T cells with the modified polypeptide and assaying the response.
• Naturally occurring variants of the polypeptide may also be isolated by, for example, screening an appropriate cDNA or genomic library with a DNA sequence encoding the polypeptide or a variant thereof. The above-described sequence modifications may be introduced using standard recombinant techniques or by automated synthesis of the modified polypeptide.
• mutations can be introduced at particular loci by synthesizing oligonucleotides containing a mutant sequence, flanked by restriction sites enabling ligation to fragments of the native sequence. Following ligation, the resulting reconstructed sequence encodes an analogue having the desired amino acid insertion, substitution, or deletion.
• oligonucleotide-directed site- specific mutagenesis procedures can be employed to provide a gene in which particular codons are altered according to the substitution, deletion, or insertion required. Exemplary methods of making the alterations set forth above are disclosed by Walder et al .
• a mutation site may be predetermined, it is not necessary that the nature of the mutation per se be predetermined. For example, in order to select for optimum characteristics of mutants at a given site, random mutagenesis may be conducted at the target codon and the expressed HER-2/.neu polypeptide mutants screened for the desired activity.
• nucleotide sequence which encodes a HER-2/neu polypeptide will be expressed in the final product.
• nucleotide substitutions may be made to enhance expression, primarily to avoid secondary structure loops in the transcribed mRNA (see, e.g., European Patent Application 75,444A) , or to provide codons that are more readily translated by the selected host, such as the well-known E. col i preference codons for E . coli expression.
• the polypeptides of the present invention are preferably produced by recombinant DNA methods. Such methods include inserting a DNA sequence encoding a HER-2/neu polypeptide into a recombinant expression vector and expressing the DNA sequence in a recombinant microbial, mammalian or insect cell expression system under conditions promoting expression.
• DNA sequences encoding the polypeptides provided by this invention can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene which is capable of being inserted in a recombinant expression vector and expressed in a recombinant transcriptional unit.
• 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.
• suitable transcriptional or translational 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.
• DNA for a signal peptide 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.
• 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 (Pharmacia Fine Chemicals, Uppsala, Sweden) and pGEMl (Promega Biotec, Madison, WI, USA) .
• 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 . col i species (Bolivar et al .
• pBR322 contains genes for ampicillin and tetracycline resistance and thus provides simple means for identifying transformed cells.
• Promoters commonly used in recombinant microbial expression vectors include the ⁇ -lactamase (penicillinase) and lactose promoter system (Chang et al., Na t ure 275 : 615 , 1978; and Goeddel et al., Na ture 281 : 544 , 1979), the tryptophan (trp) promoter system (Goeddel et al . , Nucl . Acids Res .
• Plasmid vectors available from the American Type Culture Collection which incorporate derivatives of the ⁇ P promoter include plasmid pHUB2, resident in £. 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 . , J. Biol . Chem . 255 : 2073, 1980) or other glycolytic enzymes (Hess et al . , J. Adv. Enzyme Reg . 7:149, 1968; and Holland et al . , Biochem .
• yeast vectors can be assembled using 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 R. Hitzeman et al . , European Patent Application 73,657.
• Preferred yeast vectors can be assembled using
• DNA sequences from pBR322 for selection and replication in E . col i (Amp r gene and origin of replication) and yeast DNA sequences including a glucose-repressible ADH2 promoter and ⁇ -factor secretion leader.
• the ADH2 promoter has been described by Russell et al . (J. Biol . Chem . 258 : 2614 , 1982) and Beier et al . ( Na t ure 300 : 124 , 1982) .
• the yeast ⁇ -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 .
• 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.
• 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., Na ture 273 : 113 , 1978) . Smaller or larger SV40 fragments may also be used, provided the approximately 250 bp sequence extending from the Hind III site toward the Bgl II site located in the viral origin of replication is included.
• 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 and Berg, Mol . Cel l .
• a useful system for stable high level expression of mammalian receptor cDNAs in C127 mu ⁇ ne mammary epithelial cells can be constructed substantially as described by Cosman et al . (Mol . Immunol . 23 : 935 , 1986) .
• a preferred eukaryotic vector for expression of LbeIF4A protein DNA is pDC406 (McMahan et al., EMBO J. 1 0 : 2821 , 1991), and includes regulatory sequences derived from SV40, human immunodeficiency virus (HIV) , and Epstein-Barr virus (EBV) .
• Other preferred vectors include pDC409 and pDC410, which are derived from pDC406.
• pDC410 was derived from pDC406 by substituting the EBV origin of replication with sequences encoding the SV40 large T antigen.
• pDC409 differs from pDC406 in that a Bgl II restriction site outside of the multiple cloning site has been deleted, making the Bgl II site within the multiple cloning site unique .
• a useful cell line that allows for episomal replication of expression vectors, such as pDC406 and pDC409, which contain the EBV origin of replication, is CV-1/EBNA (ATCC CRL 10478) .
• the CV-L/EBNA cell line was derived by transfection of the CV-1 cell line with a gene encoding Epstein-Barr virus nuclear antigen-I (EBNA-1) and constitutively express EBNA-1 driven from human CMV immediate-early enhancer/promoter.
• EBNA-1 Epstein-Barr virus nuclear antigen-I
• Transformed host cells are cells which have been transformed or transfected with expression vectors constructed using recombinant DNA techniques and which contain sequences encoding a HER-2/neu polypeptide of the present invention.
• Transformed host cells may express the desired HER-2/neu polypeptide, but host cells transformed for purposes of cloning or amplifying HER-2/neu DNA do not need to express the HER-2/neu polypeptide.
• Expressed polypeptides will preferably be secreted into the culture supernatant, depending on the DNA selected, but may also be deposited in the cell membrane.
• Suitable host cells for expression of recombinant proteins include prokaryotes, yeast or higher eukaryotic cells under the control of appropriate promoters.
• Prokaryotes include gram negative or gram positive organisms, for example E . col i or Ba cil l i .
• 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.
• Prokaryotic expression hosts may be used for expression of HER-2/neu polypeptides that do not require extensive proteolytic and disulfide processing.
• Prokaryotic expression vectors generally comprise one or more phenotypic selectable markers, for example a gene encoding proteins conferring antibiotic resistance or supplying an autotrophic requirement, and an origin of replication recognized by the host to ensure amplification within the host.
• Suitable prokaryotic hosts for transformation include E . coli , Ba cill us subtil is , Salmonella typhimurium , and various species within the genera Pseudomonas , Streptomyces , and Staphylococcus, although other hosts may also be employed.
• Recombinant HER-2/neu polypeptides may also be expressed in yeast hosts, preferably from the Sa ccharomyces species, such as S. cerevisiae .
• yeast hosts preferably from the Sa ccharomyces species, such as S. cerevisiae .
• Yeast of other genera, such as Pichia or Kl uyveromyces may also be employed.
• Yeast vectors will generally contain an origin of replication from the 2 ⁇ yeast plasmid or an autonomously replicating sequence (ARS), a promoter, DNA encoding the HER-2/neu polypeptide, sequences for polyadenylation and transcription termination and a selection gene.
• yeast vectors will include an origin of replication and selectable marker permitting transformation of both yeast and E. col i , e.g., the ampicillm resistance gene of E .
• col i and the S . cerevisiae trpl gene which provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, and a promoter derived from a highly expressed yeast gene to induce transcription of a structural sequence downstream.
• the presence of the trpl lesion in the yeast host cell genome then provides an effective environment for detecting transformation by growth in the absence of tryptophan.
• Suitable yeast transformation protocols are known to those of skill in the art.
• An exemplary technique described by Hind et al . ( Proc . Na tl . Acad. Sci . USA 75:1929, 1978), involves selecting for Trp + transformants in a selective medium consisting of 0.67% yeast nitrogen base, 0.5% casammo acids, 2% glucose, 10 mg/ml adenine and 20 mg/ml uracil.
• Host strains transformed by vectors comprising the ADH2 promoter may be grown for expression in a rich medium consisting of 1% yeast extract, 2% peptone, and 1% glucose supplemented with 80 mg/ml adenine and 80 mg/ml uracil. Derepression of the ADH2 promoter occurs upon exhaustion of medium glucose. Crude yeast supernatants are harvested by filtration and held at 4°C prior to further purification.
• Various mammalian or insect (e.g., Spodoptera or Tri chopl usia ) cell culture systems can also be employed to express recombinant polypeptide.
• Baculovirus systems for production of heterologous polypeptides insect cells are reviewed, for example, by Luckow and Summers, Bio/Technology 6 : 41 , 1988.
• suitable mammalian host cell lines include the COS-7 lines of monkey kidney cells, described by Gluzman ( Cell 23 : 115 , 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.
• 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 ⁇ bosome binding sites, a polyadenylation site, splice donor and acceptor sites, and transcriptional termination sequences.
• 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 ⁇ bosome binding sites, a polyadenylation site, splice donor and acceptor sites, and transcriptional termination sequences.
• Purified HER-2/neu polypeptides may be prepared by culturmg suitable host/vector systems to express the recombinant translation products of the DNAs of the present invention, which are then purified from culture media or cell extracts.
• supernatants from systems which secrete recombinant polypeptide into culture media may be first concentrated using a commercially available protein concentration filter, such as an Amicon or Millipore Pellicon ultraflltration unit. Following the concentration step, the concentrate may be applied to a suitable purification matrix.
• a suitable affinity matrix may comprise a counter structure protein (i.e., a protein to which a HER-2/neu polypeptide binds in a specific interaction based on structure) or lect or antibody molecule bound to a suitable support.
• an anion exchange resin can be employed, for example, a matrix or substrate having pendant diethylaminoethyl (DEAE) groups.
• the matrices can be acrylamide, agarose, dextran, cellulose or other types commonly employed in protein purification.
• a cation exchange step can be employed. Suitable cation exchangers include various insoluble matrices comprising sulfopropyl or carboxymethyl groups. Sulfopropyl groups are preferred. Gel filtration chromatography also provides a means of purifying a HER-2/neu.
• Affinity chromatography is a preferred method of purifying HER-2/r.eu polypeptides.
• monoclonal antibodies against the HER-2/neu polypeptide may also be useful in affinity chromatography purification, by utilizing methods that are well-known in the art.
• RP-HPLC reverse-phase high performance liquid chromatography
• hydrophobic RP-HPLC media e.g., silica gel having pendant methyl or other aliphatic groups
• Recombinant HER-2/neu polypeptide produced in bacterial culture is preferably isolated by initial extraction from cell pellets, followed by one or more concentration, salting-out, aqueous ion exchange or size exclusion chromatography steps. High performance liquid chromatography (HPLC) may be employed for final purification steps.
• Microbial cells employed in expression of recombinant LbeIF4A protein can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents .
• Fermentation of yeast which express HER-2/neu polypeptide as a secreted protein greatly simplifies purification.
• Secreted recombinant protein resulting from a large-scale fermentation can be purified by methods analogous to those disclosed by Urdal et al . (J. Chroma tog. 296 : 111 , 1984) .
• This reference describes two sequential, reverse-phase HPLC steps for purification of recombinant human GM-CSF on a preparative HPLC column.
• Preparations of HER-2/.neu polypeptides synthesized in recombinant culture may contain non- HER-2/.neu cell components, including proteins, in amounts and of a character which depend upon the purification steps taken to recover the HER-2/neu polypeptide from the culture. These components ordinarily will be of yeast, prokaryotic or non-human eukaryotic origin. Such preparations are typically free of other proteins which may be normally associated with the HER-2/neu protein as it is found in nature in its species of origin.
• Automated synthesis provides an alternate method for preparing polypeptides of this invention.
• 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, J. Am. Chem . Soc . 85 :2149-2146, 1963.)
• Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Applied Biosystems, Inc. of Foster City, CA, and may generally be operated according to the manufacturer's instructions.
• a HER-2/neu polypeptide or a DNA molecule that directs the expression of such a peptide to generate an immune response to the HER-2/neu protein (including that expressed on a malignancy in which a HER-2/neu oncogene is associated) may be detected.
• malignancies include breast, ovarian, colon, lung and prostate cancers.
• An immune response to the HER-2/neu protein, once generated by a HER-2/ ⁇ eu polypeptide can be long-lived and can be detected long after immunization, regardless of whether the protein is present or absent in the body at the time of testing.
• An immune response to the HER-2/neu protein generated by reaction to a HER-2/neu polypeptide can be detected by examining for the presence or absence, or enhancement, of specific activation of CD4 + or CD8 + T cells. More specifically, T cells isolated from an immunized individual by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes) are incubated with HER-2/neu protein. For example, T cells may be incubated m vi tro for 2-9 days (typically 4 days) at 37°C with HER-2/neu protein (typically, 5 ⁇ g/ml of whole protein or graded numbers of cells synthesizing HER-2/neu protein) .
• T cell sample It may be desirable to incubate another aliquot of a T cell sample in the absence of HER-2/neu protein to serve as a control .
• Specific activation of CD4 + or CD8+ T cells may be detected in a variety of ways. Methods for detecting specific T cell activation include detecting the proliferation of T cells, the production of cytokines
• cytolytic activity i.e., generation of cytotoxic T cells specific for HER-2/neu protein
• CD4+ T cells a preferred method for detecting specific T cell activation is the detection of the proliferation of T cells.
• CD8 + T cells a preferred method for detecting specific T cell activation is the detection of the generation of cytolytic activity.
• T cell proliferation can be detected by measuring the rate of DNA synthesis.
• T cells which have been stimulated to proliferate exhibit an increased rate of DNA synthesis.
• a typical way to measure the rate of DNA synthesis is, for example, by pulse-labeling cultures of T cells with tritiated thymidine, a nucleoside precursor which is incorporated into newly synthesized DNA. The amount of tritiated thymidine incorporated can be determined using a liquid scintillation spectrophotomete .
• T cell proliferation examples include measuring increases in interleukin-2 (IL-2) production, Ca 2+ flux, or dye uptake, such as 3- (4, 5-dimethylthiazol-2- yl) -2, 5-diphenyl-tetrazolium.
• IL-2 interleukin-2
• dye uptake such as 3- (4, 5-dimethylthiazol-2- yl) -2, 5-diphenyl-tetrazolium.
• lymphokines such as interferon-gamma
• the relative number of T cells that can respond to intact pl85 HER" neu protein may be quantified.
• T cells which recognize the HER-2/neu protein can be proliferated in vivo .
• a medicament for immunization with a HER-2/neu peptide i.e., as a vaccine
• about 0.01 ⁇ g/kg to about 100 mg/kg body weight will be administered by the intradermal, subcutaneous or intravenous route.
• a preferred dosage is about 1 ⁇ g/kg to about 1 mg/kg, with about 5 ⁇ g/kg to about 200 ⁇ g/kg particularly preferred.
• Preferred peptides for use in a medicament for immunization are those that include the ammo acid sequence of SEQ ID NO:2 beginning at about the lysine residue at ammo acid position 676 and extending to about the valine residue at amino acid position 1255.
• HER-2/neu polypeptide As well as division of such a polypeptide into a plurality of peptides. Neither intact pl85 HER"2/neu protein nor a peptide having the amino acid sequence of its entire extracellular domain (i.e., a peptide having an amino acid sequence of SEQ ID NO:2 from amino acid position 1 up to ammo acid position 650, plus or minus about one to five positions, and with or without the first 21 ammo acid positions) are used alone for immunization.
• a HER-2/neu polypeptide (or nucleic acid) is preferably formulated for use in the above methods as a pharmaceutical composition (e.g., vaccine) .
• compositions generally comprise one or more polypeptides in combination with a pharmaceutically acceptable carrier, excipient or diluent. Such carriers will be nontoxic to recipients at the dosages and concentrations employed.
• a pharmaceutically acceptable carrier excipient or diluent.
• Such carriers will be nontoxic to recipients at the dosages and concentrations employed.
• the use of a HER-2/neu polypeptide in conjunction with chemotherapeutic agents is also contemplated.
• 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-aianine-D- isoglutamine (MDP) , lipopoly-saccharides (LPS) , glucan, IL-12, GM-CSF, gamma interferon and IL-15. It will be evident to those of ordinary skill in this art that a HER- 2 /neu polypeptide for a vaccine may be prepared synthetically or be naturally derived.
• the type of carrier will vary depending on the mode of administration and whether a sustained release is desired.
• the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer.
• 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
• Suitable biodegradable microspheres are disclosed, for example, in U.S. Patent Nos. 4,897,268 and 5,075,109.
• a HER-2/neu polypeptide may be encapsulated within the biodegradable microsphere or associated with the surface of the microsphere.
• a polypeptide having the amino acid sequence of SEQ ID NO:2 from amino acid 676 through amino acid 1255 is encapsulated within a biodegradable microsphere.
• the microsphere be larger than approximately 25 microns.
• compositions may also contain 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.
• 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.
• product is formulated as a lyophilizate using appropriate excipient solutions (e.g., sucrose) as diluents.
• compositions capable of delivering nucleic acid molecules encoding a HER-2/neu polypeptide.
• compositions include recombinant viral vectors (e.g., retroviruses (see WO 90/07936, WO 91/02805, WO 93/25234, WO 93/25698, and WO 94/03622), adenovirus (see Berkner, Biotechniques 6:616- 627, 1988; Li et al . , Hum. Gene Ther. 4:403-409, 1993; Vincent et al . , Nat. Genet.
• retroviruses see WO 90/07936, WO 91/02805, WO 93/25234, WO 93/25698, and WO 94/03622
• adenovirus see Berkner, Biotechniques 6:616- 627, 1988; Li et al . , Hum. Gene Ther. 4:403-409, 1993; Vincent e
• the DNA may be linked to killed or inactivated adenovirus (see Curiel et al., Hum. Gene Ther. 3:147-154, 1992; Cotton et al., Proc. Natl. Acad. Sci. USA 89:6094, 1992) .
• Other suitable compositions include DNA-ligand (see Wu et al . , J. Biol. Chem. 264:16985-16981, 1989) and lipid-DNA combinations (see Feigner et al . , Proc. Natl. Acad. Sci. USA 84:1413- 7417, 1989) .
• the efficiency of naked DNA uptake into cells may be increased by coating the DNA onto biodegradable beads.
• ex vivo procedures may be used in which cells are removed from an animal, modified, and placed into the same or another animal. It will be evident that one can utilize any of the compositions noted above for introduction of HER-2/neu nucleic acid molecules into tissue cells in an ex vivo context. Protocols for viral, physical and chemical methods of uptake are well known in the art.
• the present invention is useful for enhancing or eliciting, in a patient or cell culture, a cellular immune response (e.g., the generation of antigen- specific cytolytic T cells) .
• a cellular immune response e.g., the generation of antigen- specific cytolytic T cells
• the term "patient” refers to any warm-blooded animal, preferably a human.
• a patient may be afflicted with cancer, such as breast cancer, or may be normal (i.e., free of detectable disease and infection) .
• a "cell culture” is any preparation of T cells or isolated component cells (including, but not limited to, macrophages, monocytes, B cells and dendritic cells) .
• Such cells may be isolated by any of a variety of techniques well known to those of ordinary skill in the art (such as Ficoll-hypaque density centrifugation) .
• the cells may (but need not) have been isolated from a patient afflicted with a HER-2/neu associated malignancy, and may be reintroduced into a patient after treatment.
• the present invention also discloses that HER- 2 /neu polypeptide, in addition to being immunogenic to T cells, appears to stimulate B-cells to produce antibodies capable of recognizing HER-2/neu polypeptide.
• Antibodies specific i.e., which exhibit a binding affinity of about 10 7 liters/mole or better
• HER-2/neu protein may be found in a variety of body fluids including sera and ascites. Briefly, a body fluid sample is isolated from a warm-blooded animal, such as a human, for whom it is desired to determine whether antibodies specific for HER-2/.neu polypeptide are present.
• the body fluid is incubated with HER-2/neu polypeptide under conditions and for a time sufficient to permit immunocomplexes to form between the polypeptide and antibodies specific for the protein.
• a body fluid and HER-2/neu polypeptide may be incubated at 4°C for 24-48 hours.
• the reaction mixture is tested for the presence of immunocomplexes. Detection of one or more immunocomplexes formed between HER-2/neu polypeptide 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) .
• RIA radioimmunoassays
• ELISA enzyme linked immunosorbent assays
• Suitable immunoassays include the double monoclonal antibody sandwich immunoassay technique of David et al . (U.S. Patent 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. Patent 4,452,901); immunoprecipitation of labeled ligand (Brown et al., J. Biol . Chem .
• HER-2/neu polypeptide may either be labeled or unlabeled.
• the antigen finds use in agglutination assays.
• 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 HER-2/neu polypeptide, such as antibodies specific for immunoglobulin.
• the antigen can be directly labeled.
• the reporter group can include radioisotopes, fluorophores, enzymes, luminescers, or dye particles.
• 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) .
• BSA bovine serum albumin
• NGS heat-inactivated normal goat serum
• BLOTTO buffered solution of nonfat dry milk which also contains a preservative, salts, and an antifoaming agent
• the well 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 conjugate, 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.
• a reporter group is bound to HER- 2 /neu protein.
• the step of detecting immunocomplexes involves removing substantially any unbound HER-2/neu protein and then detecting the presence or absence of the reporter group.
• a reporter group is bound to a second antibody capable of binding to the antibodies specific for HER-2/neu protein.
• the step of detecting immunocomplexes involves (a) removing substantially any unbound antibody, (b) adding the second antibody, (c) removing substantially any unbound second antibody and then (d) detecting the presence or absence of the reporter group.
• the second antibody is an anti-human antibody.
• a reporter group is bound to a molecule capable of binding to the immunocomplexes.
• the step of detecting involves (a) adding the molecule, (b) removing substantially any unbound molecule, and then (c) detecting the presence or absence of the reporter group.
• An example of a molecule capable of binding to the immunocomplexes is protein A.
• a variety of methods for detecting the immunocomplexes may be employed within the present invention.
• Reporter groups suitable for use in any of the methods include radioisotopes, fluorophores, enzymes, luminescers, and dye particles.
• detection of immunocomplexes formed between HER-2/.neu polypeptide and antibodies in body fluid which are specific for HER-2/neu polypeptide may be used to monitor the effectiveness of cancer therapy, which involves a HER-2/neu polypeptide, for a malignancy in which the HER- 2 /neu oncogene is associated.
• Samples of body fluid 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.
• the human HER-2/neu polypeptide was recovered by the PCR method (e.g., U.S. Patent Nos. 4,683,195; 4,683,202; 4,800,159) from a plasmid prepared according to Di Fiore et al. (King et al . , Science 229 : 914 - 916 , 1985; Di Fiore et al . , Science 237:178-182, 1987) using oligonucleotide primers that additionally introduced a BssHII restriction site and an enterokinase protease site on the 5' end and an EcoRI site on the 3' end.
• the primer for the 5 '-end was 5 ' -TCTGGCGCGCTGGATGACGATGACAAGAAACGACGGCAGCAGAAGATC-3 '
• thioredoxin reductase has been reported to stabilize and solubilize other heterologous proteins expressed in E . coli , it did not appear to offer any significant advantage for human HER-2/neu polypeptide expression in E . col i . While a significant proportion of the trxA-HER-2/neu polypeptide fusion protein was soluble, a majority was expressed in inclusion bodies. The fusion protein was also subjected to degradation during expression in E . col i . The presence of the thioredoxin reductase fusion partner may, however, stabilize the protein during purification. The availability of monoclonal antibodies to thioredoxin reductase provides a convenient marker to follow during purification.
• the E. col i pellet was resuspended with protease inhibitors and lysozyme and sonicated.
• the inclusion bodies were isolated by centrifugation, and are washed 3X with deoxycholate, the last wash being overnight to remove LPS .
• the washed inclusion bodies are solubilized in GuHCl for Ni purification.
• the Ni column was eluted with Imidazole in urea and dialyzed against 10 mM Tris pH8.
• HER-2/neu polypeptide The recovery of HER-2/neu polypeptide using this protocol was from 80%-95% pure full length protein with the main contaminant being degraded protein. From 500 ml of fermentation, 20 mg were recovered. It was >98% HER-2/neu polypeptide.
• the techniques used herein are well known to those in the art and have been described, for example, in J. Sambrook et al., Molecular Cloning: A Labora tory Manual , 2nd Ed., Cold Spring Harbor Laboratory Press, 1989, Cold Spring Harbor, New York, USA.
• CD34+ hematopoietic progenitor cells HPC
• CD34+ cells were purified from bone marrow of normal donors using the cell separation system Ceprate LC Kit (CellPro, Bothell, WA, USA) . Purity of recovered CD34+ cells was determined by flow cytometric analysis to be 80% to 95%.
• CD34+ cells were cultured in serum-free medium (X-VIVO 10, Biowhittaker, Inc., Walkersville, MD, USA) supplemented with L-glutamine (584 ⁇ g/1), penicillin (10 IU/ml), streptomycin (100 ⁇ g/ml), 100 ng/ml human rGM-CSF and 50 ng/ml human rIL-6 (Immunex, Seattle, WA, USA) . After 0 to 17 days of culture time, cells were harvested and used for phenotyping and T cell stimulation assays. GM-CSF alone and in combination with IL-4 or TNF ⁇ have been described to induce the in vi tro growth of DC.
• GM-CSF plus IL-6 consistently gave a comparable total stimulation, but with a lower background and thus a higher stimulation index as compared to GM-CSF plus IL-4 or TNF ⁇ .
• Bone marrow derived CD34+ HPC cultured in serum- free medium containing GM-CSF and IL-6 were used as APC after a culture period of 0-17 days. Priming ability of DC was determined by culturing them with autologous, naive T lymphocytes in the presence or absence of the protein antigen recombinant human HER-2/neu polypeptide (hHNP) (10 ⁇ g/ml) .
• hHNP human HER-2/neu polypeptide
• CD4+ CD45RA+ (naive) T lymphocytes were selected from CD4+ T lymphocytes using an anti-CD45RA mAb directly conjugated to FITC (Immunotech, Westbrook, ME, USA) by flow cytometric sorting.
• the CD4+ CD45RA+ T cells obtained were 99% pure.
• DC cultures were plated into 96-well round-bottomed plates (Corning, Corning, NY, USA) at various concentrations and incubated for 16-18 hours with hHNP 10 ⁇ g/ml final concentration.
• Antigen-pulsed DC were irradiated (10 Gy) , and autologous CD4+ CD45RA+ T lymphocytes were added (5 x lOVwell) .
• Proliferative response of T cells was measured by the uptake of ( 3 H) thymidine (1 ⁇ Ci/well) added on day 6 for 16-18 hours. Proliferation assays were performed in serum-free and cytokine-free medium. The results are shown in Figure 1.
• Figure 2 shows the results of testing CD4+ T cells, from a normal donor, for responses to hHNP. Similar data was obtained with T cells from nine out of ten normal individuals.
• a standard proliferation assay a screening method for low frequency events
• a limiting dilution assay LDA
• Conventional proliferative assays are capable of readily detecting primed responses.
• the proliferative response stimulation index provides a rough correlation with precursor frequency of antigen-reactive T cells. Any specific proliferative response detected from PBL is considered to be a primed response.
• the assay system developed for detecting low lymphocyte precursor frequency responses (described below) is used. This assay is simple and cost- effective. In circumstances m which more precision is needed, the precursor frequency is validated by limiting dilution assays (Bishop and Orosz, Transplanta tion 47: 611 - 677, 1989) .
• primed CD4 + T cell responses can be detected in conventional proliferative assays, whereas unprimed responses are not detectable m the same assays. Detection of small numbers of unprimed T cells is limited by confounding background thymidine uptake including the autologous mixed lymphocyte response (AMLR) to self MHC antigen plus responses to processed self serum proteins and exogenously added serum proteins .
• AMLR autologous mixed lymphocyte response
• an assay system for low frequency responses based on Poisson sampling statistics was used (In: Pinna cles, Chiron Corporation, 1 : 1-2 , 1991) .
• This type of analysis applies specifically to low frequency events in that, if the precursor frequency is less than the number of cells in one replicate culture, many replicates are required to detect a statistically significant number of positives.
• the analysis will correct for autologous responses by setting up a known positive control (such as PHA or tetanus toxoid) and known negative control (no antigen) and evaluating all data points from lowest to highest irrespective of the experimental group to which they belong.
• M arithmetic mean
• F 3.29
• SD standard deviation
• Rats used in this study were Fischer strain 344
• HER-2/neu polypeptide in a variety of adjuvants (MPL, Vaccel; Ribi, Bozeman, MT, USA) .
• Animals received 50 ⁇ g of rHNP mixed with adjuvant subcutaneously. Twenty days later the animals were boosted with a second immunization of 50 ⁇ g of rHNP administered in the same fashion. Twenty days after the booster immunization animals were tested for the presence of antibodies directed against rat HER-2/neu protein ( neu ) .
• SKBR3 a human breast cancer cell line that is a marked overexpressor of HER-2/neu (American Type Culture Collection, Rockville, MD) , was maintained culture in 10% fetal bovine serum (FBS) (Gemini Bioproducts, Inc., Calabasas, CA) and RPMI .
• FBS fetal bovine serum
• DHFR-G8 an NIH/3T3 cell line cotransfected with cneu-p and pSV2-DHFR (American Type Culture Collection, Rockville, MD) , was used as a source of non-transforming rat neu protein (Bernards et al . , Proc . Na tl . Acad . Sci .
• This cell line was maintained in 10% FBS and Dulbecco's modified Eagle's medium with 4.5g/L glucose.
• DHFR-G8 cells were passaged through the same medium supplemented with 0.3 ⁇ M methotrexate at every third passage to maintain the neu transfectant .
• Lysates of both SKBR3 and DHFR-G8 were prepared and used as a source of neu protein. Briefly, a lysis buffer consisting of tris base, sodium chloride and
• Triton-X (1%) pH 7.5 was prepared. Protease inhibitors were added; aprotimn (l ⁇ g/ml), benzamidme (lmM) and PMSF
• the plate was washed with PBS-0.5% Tween and lysates of DHFRG8, a murine cell line transfected with rat neu DNA (American Type Culture Collection, Rockville, MD, USA) ; a source of rat neu protein, were added to alternating rows.
• the plate was incubated overnight at 4°C.
• the plate was then washed with PBS-0.5% Tween and experimental sera was added at the following dilutions: 1:25 to 1:200.
• the sera was diluted in PBS-1% BSA-1% FBS-25 ⁇ g/ml mouse IgG-0.01% NaN 3 and then serially into PBS-1% BSA. 50 ⁇ l of diluted sera was added/well and incubated 1 hour at room temperature.
• Fresh spleen or lymph node cells are harvested by mechanical disruption and passage through wire mesh and washed. 2 x 10 5 spleen cells/well and 1 x 10 5 lymph node cells/well are plated into 96-well round bottom microtiter plates (Corning, Corning, NY) with 6 replicates per experimental group.
• the media consists of EHAA 120
• HER-2/neu protein specific responses Spleen or lymph node cells are cultured for 3 in vitro stimulations. At the time of analysis 1 x 10 5 cultured spleen or lymph node T cells are plated into 96 well microtiter plates as described above.
• PBMC Peripheral blood mononuclear cells
• ADDRESSEE SEED and BERRY LLP
• GGC ATC TGG ATC CCT GAT GGG GAG AAT GTG AAA ATT CCA GTG GCC ATC 2256 Gly He Trp He Pro Asp Gly Glu Asn Val Lys He Pro Val Ala He 740 745 750

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