Classifications

• • 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

Definitions

• hormones and polypeptide growth factors are controlled by hormones and polypeptide growth factors. These diffusable molecules allow cells to communicate with each other and act in concert to form cells and organs, and to repair and regenerate damaged tissue.
• hormones and growth factors include the steroid hormones (e.g. estrogen, testosterone), parathyroid hormone, follicle stimulating hormone, the interleukins, platelet derived growth factor (PDGF), epidermal growth factor (EGF), granulocyte- macrophage colony stimulating factor (GM-CSF), erythropoietin (EPO) and calcitonin. Hormones and growth factors influence cellular metabolism by binding to proteins. Proteins may be integral membrane proteins that are linked to signaling pathways within the cell, such as second messenger systems. Other classes of proteins are soluble molecules, such as the transcription factors.
• cytokines molecules that promote the proliferation, maintenance, survival or differentiation of cells.
• examples of cytokines include erythropoietin (EPO), which stimulates the development of red blood cells; thrombopoietin (TPO), which stimulates development of cells of the megakaryocyte lineage; and granulocyte-colony stimulating factor (G-CSF), which stimulates development of neutrophils.
• EPO erythropoietin
• TPO thrombopoietin
• G-CSF granulocyte-colony stimulating factor
• the present invention fills this need by providing for a new cyclic nucleotide (cAMP, cGMP) binding protein polypeptide termed "Zlmda6".
• cAMP cyclic nucleotide
• cGMP cyclic nucleotide binding protein polypeptide
• Zlmda6 Zlmdao polynucleotides that encode Zlmdao polypeptides and Zlmdao fusion proteins.
• the present invention provides isolated polypeptides having an amino acid sequence that is at least 90% identical to an amino acid sequence selected from the group consisting of (a) amino acid residues of SEQ ID NO: 2, or (b) the amino acid sequence of SEQ ID NO: 2, wherein the isolated polypeptide either specifically binds with an antibody that specifically binds with a polypeptide having the amino acid sequence of SEQ ID NO: 2.
• examples of such polypeptides include polypeptides comprising the amino acid sequence of either SEQ ID NO: 2.
• the present invention further provides pharmaceutical compositions that comprise such polypeptides, and a pharmaceutically acceptable carrier.
• Additional variant human Zlmda ⁇ polypeptides include those in which the amino acid sequence of the variant polypeptide shares an identity with the amino acid sequence of SEQ ID NO: 2 selected from the group consisting of at least 90% identity, at least 95% identity, or greater than 95% identity, and wherein any difference between the amino acid sequence of the variant polypeptide and the amino acid sequence of SEQ ID NO: 2 is due to one or more conservative amino acid substitutions.
• the present invention further provides isolated nucleic acid molecules that encode SEQ ID NO: 2, in particular a nucleotide sequence comprising the nucleotide sequence of nucleotides 1 to 1728 of SEQ ID NO: 1.
• the present invention also provides vectors and expression vectors comprising such nucleic acid molecules, recombinant host cells comprising such vectors and expression vectors, and recombinant viruses comprising such expression vectors. These expression vectors and recombinant host cells can be used to prepare Zlmda ⁇ polypeptides.
• the present invention provides pharmaceutical compositions, comprising a pharmaceutically acceptable carrier and at least one of such an expression vector or recombinant virus.
• such pharmaceutical compositions comprise a human Zlmdao gene, or a variant thereof.
• the present invention further contemplates antibodies and antibody fragments that specifically bind with -Zlmdao polypeptides.
• Such antibodies include polyclonal antibodies, murine monoclonal antibodies, humanized antibodies derived from murine monoclonal antibodies, and human monoclonal antibodies.
• antibody fragments include F(ab') 2 , F(ab) 2 , Fab', Fab, Fv, scFv, and minimal recognition units.
• the present invention also provides methods for detecting the presence of Zlmdao RNA in a biological sample, comprising the steps of : (a) contacting an Zlmdao nucleic acid probe under hybridizing conditions with either (i) test RNA molecules isolated from the biological sample, or (ii) nucleic acid molecules synthesized from the isolated RNA molecules, wherein the probe has a nucleotide sequence comprising a portion of the nucleotide sequence selected from the group consisting of SEQ ID NO: 1 , the complement of SEQ ID NO: 1 , and
• the presence of Zlmdao polypeptide in a biological sample can be detected by methods that comprise the steps of (a) contacting the biological sample with an antibody, or an antibody fragment, that specifically binds with a polypeptide having the amino acid sequence of SEQ ID NO: 2, wherein the contacting is performed under conditions that allow the binding of the antibody or antibody fragment to the biological sample, and (b) detecting any of the bound antibody or bound antibody fragment.
• kits for detecting Zlmdao nucleic acid molecules or Zlmda ⁇ polypeptides may comprise a container that comprises a nucleic acid molecule, wherein the nucleic acid molecule is selected from the group consisting of (a) a nucleic acid molecule comprising the nucleotide sequence of nucleotides 1 to 1728 of SEQ ID NO: 1, (b) a nucleic acid molecule comprising the complement of the nucleotide sequence of SEQ ID NO: 1, (c) a nucleic acid molecule that is a fragment of (a) consisting of at least eight nucleotides, (d) a nucleic acid molecule that is a fragment of (b) consisting of at least eight nucleotides, (e) a nucleic acid molecule comprising the nucleotide sequence of nucleotides 1 to 1728 of SEQ ID NO: 1, (
• kits may further comprise a second container that comprises one or more reagents capable of indicating the presence of the nucleic acid molecule.
• a kit for detection of Zlmda ⁇ polypeptide may comprise a container that comprises an antibody, or an antibody fragment, that specifically binds with a polypeptide having the amino acid sequence of SEQ ID NO: 2.
• the present invention also contemplates anti-idiotype antibodies, or anti- idiotype antibody fragments, that specifically bind with an anti-Zlmda ⁇ antibody or antibody fragment.
• the present invention further includes methods for detecting an alteration in chromosome 20.
• human ZZr ⁇ -f ⁇ 5nucleotide sequences can be used to examine chromosome 20, for example, in the 20 region.
• Illustrative chromosomal aberrations at the Zlmdao gene locus include aneuploidy, gene copy number changes, insertions, deletions, restriction site changes and rearrangements. These aberrations can occur within flanking sequences, including upstream promoter and regulatory regions, and can be manifested as physical alterations within a coding sequence or changes in gene expression level.
• suitable assay methods include molecular genetic techniques known to those in the art, such as restriction fragment length polymorphism analysis, short tandem repeat analysis employing polymerase chain reaction techniques, ligation chain reaction, ribonuclease protection assays, use of single-nucleotide polymorphisms, protein truncation assays, and other genetic linkage techniques known in the art.
• the present invention provides methods for diagnosing an alteration in the Zlmda ⁇ gene, of an individual, comprising: (a) amplifying nucleic acid molecules that encode Zlmdao from RNA isolated from a biological sample of the individual, and (b) detecting a mutation in the amplified nucleic acid molecules, wherein the presence of a mutation indicates an alteration in the Zlmdao gene.
• methods of detecting a chromosome 20 abnormality in a subject comprise: (a) amplifying nucleic acid molecules that encode Zlmdao from RNA isolated from a biological sample of the subject, and (b) detecting a mutation in the amplified nucleic acid molecules, wherein the presence of a mutation indicates a chromosome 20 abnormality.
• the detecting step is performed by comparing the nucleotide sequence of the amplified nucleic acid molecules to the nucleotide sequence of SEQ ID NO: 1.
• the detecting step can be performed by fractionating the amplified nucleic acid molecules and control nucleic acid molecules that encode the amino acid sequence of SEQ ID NOs: 2, and comparing the lengths of the fractionated amplified and control nucleic acid molecules.
• Exemplary methods for amplification include polymerase chain reaction or reverse transcriptase- polymerase chain reaction.
• the present invention also includes methods for detecting a chromosome 20 abnormality in a subject comprising: (a) amplifying nucleic acid molecules that encode Zlmdao from RNA isolated from a biological sample of the subject, (b) transcribing the amplified nucleic acid molecules to express Zlmdao mRNA, (c) translating Zlmdao m-RNA to produce Zlmdao polypeptides, and (d) detecting a mutation in the Zlmda ⁇ polypeptides, wherein the presence of a mutation indicates a chromosome 20 abnormality.
• the detection step can be performed by fractionating, under denaturing conditions, the Zlmdao polypeptides and control polypeptides that encode the amino acid sequence of SEQ ID NO: 2 or 3, and comparing the sizes of the fractionated amplified and control polypeptides. Similar methods can be used to detect a mutation of a Zlmdao gene in an individual.
• nucleic acid or “nucleic acid molecule” refers to polynucleotides, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), oligonucleotides, fragments generated by the polymerase chain reaction (PCR), and fragments generated by any of ligation, scission, endonuclease action, and exonuclease action.
• Nucleic acid molecules can be composed of monomers that are naturally- occurring nucleotides (such as DNA and RNA), or analogs of naturally-occurring nucleotides (e.g., ⁇ -enantiomeric forms of naturally-occurring nucleotides), or a combination of both.
• Modified nucleotides can have alterations in sugar moieties and/or in pyrimidine or purine base moieties.
• Sugar modifications include, for example, replacement of one or more hydroxyl groups with halogens, alkyl groups, amines, and azido groups, or sugars can be functionalized as ethers or esters.
• fhe entire sugar moiety can be replaced with sterically and electronically similar structures, such as aza-sugars and carbocyclic sugar analogs.
• Examples of modifications in a base moiety include alkylated purines and pyrimidines, acylated purines or pyrimidines, or other well-known heterocyclic substitutes.
• Nucleic acid monomers can be linked by phosphodiester bonds or analogs of such linkages. Analogs of phosphodiester linkages include phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoranilidate, phosphoramidate, and the like.
• the term "nucleic acid molecule” also includes so- called “peptide nucleic acids,” which comprise naturally-occurring or modified nucleic acid bases attached to a polyamide backbone. Nucleic acids can be either single stranded or double stranded.
• nucleic acid molecule refers to a nucleic acid molecule having a complementary nucleotide sequence and reverse orientation as compared to a reference nucleotide sequence.
• sequence 5' ATGCACGGG 3' is complementary to 5' CCCGTGCAT 3'.
• contig denotes a nucleic acid molecule that has a contiguous stretch of identical or complementary sequence to another nucleic acid molecule. Contiguous sequences are said to "overlap" a given stretch of a nucleic acid molecule either in their entirety or along a partial stretch of the nucleic acid molecule.
• degenerate nucleotide sequence denotes a sequence of nucleotides that includes one or more degenerate codons as compared to a reference nucleic acid molecule that encodes a polypeptide.
• Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (i.e., GAU and GAC triplets each encode Asp).
• structural gene refers to a nucleic acid molecule that is transcribed into messenger RNA (mRNA), which is then translated into a sequence of amino acids characteristic of a specific polypeptide.
• an "isolated nucleic acid molecule” is a nucleic acid molecule that is not integrated in the genomic DNA of an organism.
• a DNA molecule that encodes a growth factor that has been separated from the genomic DNA of a cell is an isolated DNA molecule.
• Another example of an isolated nucleic acid molecule is a chemically-synthesized nucleic acid molecule that is not integrated in the genome of an organism.
• a nucleic acid molecule that has been isolated from a particular species is smaller than the complete DNA molecule of a chromosome from that species.
• nucleic acid molecule construct is a nucleic acid molecule, either single- or double-stranded, that has been modified through human intervention to contain segments of nucleic acid combined and juxtaposed in an arrangement not existing in nature.
• Linear DNA denotes non-circular DNA molecules having free 5' and
• Linear DNA can be prepared from closed circular DNA molecules, such as plasmids, by enzymatic digestion or physical disruption.
• Codon DNA is a single-stranded DNA molecule that is formed from an mRNA template by the enzyme reverse transcriptase. Typically, a primer complementary to portions of mRNA is employed for the initiation of reverse transcription.
• cDNA refers to a double- stranded DNA molecule consisting of such a single-stranded DNA molecule and its complementary DNA strand.
• cDNA also refers to a clone of a cDNA molecule synthesized from an RNA template.
• a “promoter” is a nucleotide sequence that directs the transcription of a structural gene.
• a promoter is located in the 5' non-coding region of a gene, proximal to the transcriptional start site of a structural gene. Sequence elements within promoters that function in the initiation of transcription are often characterized by consensus nucleotide sequences. These promoter elements include RNA polymerase binding sites, TATA sequences, CAAT sequences, differentiation-specific elements (DSEs; McGehee et al, Mol. Endocrinol. 7:551 (1993)), cyclic AMP response elements (CREs), serum response elements (SREs; Treisman, Seminars in Cancer Biol.
• DSEs differentiation-specific elements
• CREs cyclic AMP response elements
• SREs serum response elements
• GREs glucocorticoid response elements
• binding sites for other transcription factors such as CRE/ATF [O'Reilly et al, J. Biol. Chem. 257:19938 (1992)), AP2 (Ye et al, J. Biol. Chem. 269:2512% (1994)], SP1, cAMP response element binding protein [CREB; Loeken, Gene Expr. 3:253 (1993)] and octamer factors [see, in general, Watson et al, eds., Molecular Biology ofthe Gene, 4th ed. (The
• a promoter is an inducible promoter, then the rate of transcription increases in response to an inducing agent. In contrast, the rate of transcription is not regulated by an inducing agent if the promoter is a constitutive promoter. Repressible promoters are also known.
• a “core promoter” contains essential nucleotide sequences for promoter function, including the TATA box and start of transcription. By this definition, a core promoter may or may not have detectable activity in the absence of specific sequences that may enhance the activity or confer tissue specific activity.
• a “regulatory element” is a nucleotide sequence that modulates the activity of a core promoter. For example, a regulatory element may contain a nucleotide sequence that binds with cellular factors enabling transcription exclusively or preferentially in particular cells, tissues, or organelles. These types of regulatory elements are normally associated with genes that are expressed in a "cell-specific,” “tissue-specific,” or “organelle-specific” manner.
• the Zlmda6 regulatory element preferentially induces gene expression in placental, tracheal, and uterine tissues, as opposed to lung, brain, liver, kidney, spleen, thymus, prostate, testis, ovary, small intestine, and pancreas tissues.
• Heterologous DNA refers to a DNA molecule, or a population of DNA molecules, that does not exist naturally within a given host cell. DNA molecules heterologous to a particular host cell may contain DNA derived from the host cell species (i.e., endogenous DNA) so long as that host DNA is combined with non-host DNA (i.e., exogenous DNA). For example, a DNA molecule containing a non-host DNA segment encoding a polypeptide operably linked to a host DNA segment comprising a transcription promoter is considered to be a heterologous DNA molecule.
• a heterologous DNA molecule can comprise an endogenous gene operably linked with an exogenous promoter.
• a DNA molecule comprising a gene derived from a wild-type cell is considered to be heterologous DNA if that DNA molecule is introduced into a mutant cell that lacks the wild-type gene.
• a “polypeptide” is a polymer of amino acid residues joined by peptide bonds, whether produced naturally or synthetically. Polypeptides of less than about 10 amino acid residues are commonly referred to as “peptides.”
• a “protein” is a macromolecule comprising one or more polypeptide chains. A protein may also comprise non-peptidic components, such as carbohydrate groups. Carbohydrates and other non-peptidic substituents may be added to a protein by the cell in which the protein is produced, and will vary with the type of cell. Proteins are defined herein in terms of their amino acid backbone structures; substituents such as carbohydrate groups are generally not specified, but may be present nonetheless.
• a peptide or polypeptide encoded by a non-host DNA molecule is a "heterologous" peptide or polypeptide.
• an "integrated genetic element” is a segment of DNA that has been incorporated into a chromosome of a host cell after that element is introduced into the cell through human manipulation.
• integrated genetic elements are most commonly derived from linearized plasmids that are introduced into the cells by electroporation or other techniques. Integrated genetic elements are passed from the original host cell to its progeny.
• a "cloning vector” is a nucleic acid molecule, such as a plasmid, cosmid, or bacteriophage that has the capability of replicating autonomously in a host cell.
• Cloning vectors typically contain one or a small number of restriction endonuclease recognition sites that allow insertion of a nucleic acid molecule in a determinable fashion without loss of an essential biological function of the vector, as well as nucleotide sequences encoding a marker gene that is suitable for use in the identification and selection of cells transformed with the cloning vector. Marker genes typically include genes that provide tetracycline resistance or ampicillin resistance.
• An "expression vector” is a nucleic acid molecule encoding a gene that is expressed in a host cell. Typically, an expression vector comprises a transcription promoter, a gene, and a transcription terminator.
• Gene expression is usually placed under the control of a promoter, and such a gene is said to be "operably linked to” the promoter.
• a regulatory element and a core promoter are operably linked if the regulatory element modulates the activity ofthe core promoter.
• a “recombinant host” is a cell that contains a heterologous nucleic acid molecule, such as a cloning vector or expression vector.
• a recombinant host is a cell that produces Zlmda ⁇ from an expression vector.
• Zlmdao can be produced by a cell that is a "natural source" of Zlmdao, and that lacks an expression vector.
• “Integrative transformants” are recombinant host cells, in which heterologous DNA has become integrated into the genomic DNA of the cells.
• a “fusion protein” is a hybrid protein expressed by a nucleic acid molecule comprising nucleotide sequences of at least two genes.
• a fusion protein can comprise at least part of a Zlmdao polypeptide fused with a polypeptide that binds an affinity matrix.
• Such a fusion protein provides a means to isolate large quantities of Zlmda ⁇ using affinity chromatography.
• Receptor denotes a cell-associated protein that binds to a bioactive molecule termed a "ligand.” This interaction mediates the effect of the ligand on the cell.
• Receptors can be membrane bound, cytosolic or nuclear; monomeric (e.g., thyroid stimulating hormone receptor, beta-adrenergic receptor) or multimeric (e.g., PDGF receptor, growth hormone receptor, IL-3 receptor, GM-CSF receptor, G-CSF receptor, erythropoietin receptor and TL-6 receptor).
• Membrane-bound receptors are characterized by a multi-domain structure comprising an extracellular ligand-binding domain and an intracellular effector domain that is typically involved in signal transduction.
• the extracellular ligand-binding domain and the intracellular effector domain are located in separate polypeptides that comprise the complete functional receptor.
• the binding of ligand to receptor results in a conformational change in the receptor that causes an interaction between the effector domain and other molecule(s) in the cell, which in turn leads to an alteration in the metabolism of the cell.
• Metabolic events that are often linked to receptor-ligand interactions include gene transcription, phosphorylation, dephosphorylation, increases in cyclic AMP production, mobilization of cellular calcium, mobilization of membrane lipids, cell adhesion, hydrolysis of inositol lipids and hydrolysis of phospholipids.
• secretory signal sequence denotes a DNA sequence that encodes a peptide (a "secretory peptide") that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized.
• secretory peptide a DNA sequence that encodes a peptide that, as a component of a larger polypeptide, directs the larger polypeptide through a secretory pathway of a cell in which it is synthesized.
• the larger polypeptide is commonly cleaved to remove the secretory peptide during transit through the secretory pathway.
• isolated polypeptide is a polypeptide that is essentially free from contaminating cellular components, such as carbohydrate, lipid, or other proteinaceous impurities associated with the polypeptide in nature.
• a preparation of isolated polypeptide contains the polypeptide in a highly purified form, i.e., at least about 80% pure, at least about 90% pure, at least about 95% pure, greater than 95% pure, or greater than 99% pure.
• SDS sodium dodecyl sulfate
• isolated does not exclude the presence of the same polypeptide in alternative physical forms, such as dimers or alternatively glycosylated or derivatized forms.
• amino-terminal or N-terminal and “carboxyl-terminal or C- terminal” are used herein to denote positions within polypeptides. Where the context allows, these terms are used with reference to a particular sequence or portion of a polypeptide to denote proximity or relative position. For example, a certain sequence positioned carboxyl-terminal to a reference sequence within a polypeptide is located proximal to the carboxyl terminus of the reference sequence, but is not necessarily at the carboxyl terminus of the complete polypeptide.
• expression refers to the biosynthesis of a gene product.
• expression involves transcription of the structural gene into mRNA and the translation of mRNA into one or more polypeptides.
• the term "splice variant” is used herein to denote alternative forms of RNA transcribed from a gene. Splice variation arises naturally through use of alternative splicing sites within a transcribed RNA molecule, or less commonly between separately transcribed RNA molecules, and may result in several mRNAs transcribed from the same gene. Splice variants may encode polypeptides having altered amino acid sequence.
• the term splice variant is also used herein to denote a polypeptide encoded by a splice variant of an mRNA transcribed from a gene.
• the term "immunomodulator” includes cytokines, stem cell growth factors, lymphotoxins, co-stimulatory molecules, hematopoietic factors, and synthetic analogs of these molecules.
• the term "complement/anti-complement pair” denotes non-identical moieties that form a non-covalently associated, stable pair under appropriate conditions. For instance, biotin and avidin (or streptavidin) are prototypical members of a complement/anti-complement pair. Other exemplary complement/anti-complement pairs include receptor/ligand pairs, antibody/antigen (or hapten or epitope) pairs, sense/antisense polynucleotide pairs, and the like. Where subsequent dissociation of the complement/anti-complement pair is desirable, the complement/anti-complement pair preferably has a binding affinity of less than 10 9 M "1 .
• an "anti-idiotype antibody” is an antibody that binds with the variable region domain of an immunoglobulin.
• an anti-idiotype antibody binds with the variable region of an anti-Zlmda ⁇ antibody, and thus, an anti-idiotype antibody mimics an epitope of Zlmdao.
• an “antibody fragment” is a portion of an antibody such as F(ab') 2 , F(ab) , Fab', Fab, and the like. Regardless of structure, an antibody fragment binds with the same antigen that is recognized by the intact antibody. For example, an anti-Zlmda ⁇ monoclonal antibody fragment binds with an epitope of Zlmdao.
• antibody fragment also includes a synthetic or a genetically engineered polypeptide that binds to a specific antigen, such as polypeptides consisting of the light chain variable region, "Fv” fragments consisting of the variable regions of the heavy and light chains, recombinant single chain polypeptide molecules in which light and heavy variable regions are connected by a peptide linker (“scFv proteins”), and minimal recognition units consisting ofthe amino acid residues that mimic the hypervariable region.
• scFv proteins peptide linker
• a “chimeric antibody” is a recombinant protein that contains the variable domains and complementary determining regions derived from a rodent antibody, while the remainder of the antibody molecule is derived from a human antibody.
• Humanized antibodies are recombinant proteins in which murine complementarity determining regions of a monoclonal antibody have been transferred from heavy and light variable chains ofthe murine immunoglobulin into a human variable domain.
• a "therapeutic agent” is a molecule or atom that is conjugated to an antibody moiety to produce a conjugate that is useful for therapy.
• therapeutic agents include drugs, toxins, immunomodulators, chelators, boron compounds, photoactive agents or dyes, and radioisotopes.
• a "detectable label” is a molecule or atom that can be conjugated to an antibody moiety to produce a molecule useful for diagnosis. Examples of detectable labels include chelators, photoactive agents, radioisotopes, fluorescent agents, paramagnetic ions, or other marker moieties.
• affinity tag is used herein to denote a polypeptide segment that can be attached to a second polypeptide to provide for purification or detection of the second polypeptide or provide sites for attachment of the second polypeptide to a substrate.
• Affinity tags include a poly- histidine tract, protein A (Nilsson et al, EMBO J. 4:1015 (1985); Nilsson et al, Methods Enzymol. 198:3 (1991)), glutathione S transferase (Smith and Johnson, Gene 67:31 (1988)), Glu-Glu affinity tag (Grussenmeyer et al, Proc.
• naked antibody is an entire antibody, as opposed to an antibody fragment, which is not conjugated with a therapeutic agent. Naked antibodies include both polyclonal and monoclonal antibodies, as well as certain recombinant antibodies, such as chimeric and humanized antibodies. As used herein, the term "antibody component" includes both an entire antibody and an antibody fragment.
• an “immunoconjugate” is a conjugate of an antibody component with a therapeutic agent or a detectable label.
• antibody fusion protein refers to a recombinant molecule that comprises an antibody component and a therapeutic agent.
• therapeutic agents suitable for such fusion proteins include immunomodulators ("antibody-immunomodulator fusion protein”) and toxins ("antibody-toxin fusion protein”).
• tumor associated antigen is a protein normally not expressed, or expressed at lower levels, by a normal counterpart cell.
• tumor associated antigens include alpha-fetoprotein, carcinoembryonic antigen, and Her-2/neu. Many other illustrations of tumor-associated antigens are known. See, for example, Urban et al, Ann. Rev. Immunol 10:611 (1992).
• an "infectious agent” denotes both microbes and parasites.
• a “microbe” includes viruses, bacteria, rickettsia, mycoplasma, protozoa, fungi and like microorganisms.
• a “parasite” denotes infectious, generally microscopic or very small multicellular invertebrates, or ova or juvenile forms thereof, which are susceptible to immune-mediated clearance or lytic or phagocytic destruction, such as malarial parasites, spirochetes, and the like.
• infectious agent antigen is an antigen associated with an infectious agent.
• a “target polypeptide” or a “target peptide” is an amino acid sequence that comprises at least one epitope, and that is expressed on a target cell, such as a tumor cell, or a cell that carries an infectious agent antigen.
• T cells recognize peptide epitopes presented by a major histocompatibility complex molecule to a target polypeptide or target peptide and typically lyse the target cell or recruit other immune cells to the site of the target cell, thereby killing the target cell.
• antigenic peptide is a peptide that will bind a major histocompatibility complex molecule to form an MHC-peptide complex, which is recognized by a T cell, thereby inducing a cytotoxic lymphocyte response upon presentation to the T cell.
• antigenic peptides are capable of binding to an appropriate major histocompatibility complex molecule and inducing a cytotoxic T cells response, such as cell lysis or specific cytokine release against the target cell that binds or expresses the antigen.
• the antigenic peptide can be bound in the context of a class I or class II major histocompatibility complex molecule, on an antigen presenting cell or on a target cell.
• RNA polymerase II catalyzes the transcription of a structural gene to produce mRNA.
• a nucleic acid molecule can be designed to contain an RNA polymerase II template in which the RNA transcript has a sequence that is complementary to that of a specific mRNA.
• the RNA transcript is termed an "anti- sense RNA” and a nucleic acid molecule that encodes the anti-sense RNA is termed an "anti-sense gene.”
• Anti-sense RNA molecules are capable of binding to mRNA molecules, resulting in an inhibition of mRNA translation.
• an "anti-sense oligonucleotide specific for Zlmdao” or a “Zlmdao anti- sense oligonucleotide” is an oligonucleotide having a sequence (a) capable of forming a stable triplex with a portion of the Zlmda6 gene, or (b) capable of forming a stable duplex with a portion of an mRNA transcript of the Zlmdao gene.
• a "ribozyme” is a nucleic acid molecule that contains a catalytic center. The term includes RNA enzymes, self-splicing RNAs, self-cleaving RNAs, and nucleic acid molecules that perform these catalytic functions.
• a nucleic acid molecule that encodes a ribozyme is termed a "ribozyme gene.”
• An "external guide sequence” is a nucleic acid molecule that directs the endogenous ribozyme, RNase P, to a particular species of intracellular mRNA, resulting in the cleavage of the m-RNA by RNase P.
• a nucleic acid molecule that encodes an external guide sequence is termed an "external guide sequence gene.”
• variant human Zlmdao gene refers to nucleic acid molecules that encode a polypeptide having an amino acid sequence that is a modification of SEQ ID NO: 2. Such variants include naturally-occurring polymorphisms of Zlmdao genes, as well as synthetic genes that contain conservative amino acid substitutions of the amino acid sequence of SEQ ID NO: 2. Additional variant forms of Zlmdao genes are nucleic acid molecules that contain insertions or deletions of the nucleotide sequences described herein. A variant Zlmda6 gene can be identified by determining whether the gene hybridizes with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1, or its complement, under stringent conditions.
• variant Zlmda6genes can be identified by sequence comparison. Two amino acid sequences have "100% amino acid sequence identity” if the amino acid residues of the two amino acid sequences are the same when aligned for maximal correspondence. Similarly, two nucleotide sequences have "100% nucleotide sequence identity” if the nucleotide residues of the two nucleotide sequences are the same when aligned for maximal correspondence. Sequence comparisons can be performed using standard software programs such as those included in the LASERGENE bioinformatics computing suite, which is produced by DNASTAR (Madison, Wisconsin).
• a variant gene or polypeptide encoded by a variant gene is functionally characterized by its ability to bind specifically to an anti-Zlmda ⁇ antibody.
• allelic variant is used herein to denote any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in phenotypic polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequence.
• allelic variant is also used herein to denote a protein encoded by an allelic variant of a gene.
• ortholog denotes a polypeptide or protein obtained from one species that is the functional counterpart of a polypeptide or protein from a different species. Sequence differences among orthologs are the result of speciation.
• Parenters are distinct but structurally related proteins made by an organism. Paralogs are believed to arise through gene duplication. For example, - globin, ⁇ -globin, and myoglobin are paralogs of each other.
• Polynucleotides generally a cDNA sequence, of the present invention encode the described polypeptides herein.
• a cDNA sequence that encodes a polypeptide of the present invention is comprised of a series of codons, each amino acid residue of the polypeptide being encoded by a codon and each codon being comprised of three nucleotides.
• the amino acid residues are encoded by their respective codons as follows.
• Alanine (Ala) is encoded by GCA, GCC, GCG or GCT;
• Cysteine (Cys) is encoded by TGC or TGT; Aspartic acid (Asp) is encoded by GAC or GAT; Glutamic acid (Glu) is encoded by GAA or GAG; Phenylalanine (Phe) is encoded by TTC or TTT; Glycine (Gly) is encoded by GGA, GGC, GGG or GGT;
• Histidine is encoded by CAC or CAT;
• Isoleucine (He) is encoded by ATA, ATC or ATT;
• Lysine is encoded by AAA, or AAG;
• Leucine (Leu) is encoded by TTA, TTG, CTA, CTC, CTG or CTT; Methionine (Met) is encoded by ATG;
• Asparagine (Asn) is encoded by AAC or AAT; Proline (Pro) is encoded by CCA, CCC, CCG or CCT; Glutamine (Gin) is encoded by CAA or CAG; Arginine (Arg) is encoded by AGA, AGG, CGA, CGC, CGG or CGT; Serine (Ser) is encoded by AGC, AGT, TCA, TCC, TCG or TCT; Threonine (Thr) is encoded by ACA, ACC, ACG or ACT; Valine (Val) is encoded by GTA, GTC, GTG or GTT; Tryptophan (Trp) is encoded by TGG; and
• Tyrosine (Tyr) is encoded by TAG or TAT.
• mRNA messenger RNA
• T thymine nucleotide
• U uracil nucleotide
• Nucleic acid molecules encoding a human Zlmda ⁇ gene can be obtained by screening a human cDNA or genomic library using polynucleotide probes based upon SEQ ID NO: 1. These techniques are standard and well established. As an illustration, a nucleic acid molecule that encodes a human
• Zlmda ⁇ g ne can be isolated from a human cDNA library.
• the first step would be to prepare the cDNA library by isolating RNA mammary epithelial tissue.
• RNA isolation techniques must provide a method for breaking cells, a means of inhibiting RNase-directed degradation of RNA, and a method of separating RNA from DNA, protein, and polysaccharide contaminants.
• total RNA can be isolated by freezing tissue in liquid nitrogen, grinding the frozen tissue with a mortar and pestle to lyse the cells, extracting the ground tissue with a solution of phenol/chloroform to remove proteins, and separating RNA from the remaining impurities by selective precipitation with lithium chloride (see, for example, Ausubel et al. (eds.), Short Protocols in Molecular Biology, 3 rd Edition, pages 4-1 to 4-6 (John Wiley & Sons 1995) ["Ausubel
• total RNA can be isolated from mammary epithelial tissue by extracting ground tissue with guanidinium isothiocyanate, extracting with organic solvents, and separating RNA from contaminants using differential centrifugation (see, for example, Chirgwin et al, Biochemistry 18:52 (1979); Ausubel (1995) at pages 4-1 to 4-6; Wu (1997) at pages 33-41).
• poly(A) + RNA In order to construct a cDNA library, poly(A) + RNA must be isolated from a total RNA preparation. Poly(A) + RNA can be isolated from total RNA using the standard technique of oligo(dT)-cellulose chromatography (see, for example, Aviv and Leder, Proc. Nat'l Acad. Sci. USA 69: 1408 (1972); Ausubel (1995) at pages 4-11 to 4- 12).
• Double-stranded cDNA molecules are synthesized from poly(A) + RNA using techniques well-known to those in the art. (see, for example, Wu (1997) at pages 41-46). Moreover, commercially available kits can be used to synthesize double- stranded cDNA molecules. For example, such kits are available from Life Technologies, Inc. (Gaithersburg, MD), CLONTECH Laboratories, Inc. (Palo Alto, CA), Promega Corporation (Madison, WI) and STRATAGENE (La Jolla, CA). Various cloning vectors are appropriate for the construction of a cDNA library.
• a cDNA library can be prepared in a vector derived from bacteriophage, such as a ⁇ gtlO vector. See, for example, Huynh et al, "Constructing and Screening cDNA Libraries in ⁇ gtlO and ⁇ gtl 1," in DNA Cloning: A Practical Approach Vol. I, Glover (ed.), page 49 (IRL Press, 1985); Wu (1997) at pages 47-52.
• double-stranded cDNA molecules can be inserted into a plasmid vector, such as a PBLUESCRIPT vector (STRATAGENE; La Jolla, CA), a LAMDAGEM-4 (Promega Corp.) or other commercially available vectors.
• Suitable cloning vectors also can be obtained from the American Type Culture Collection (Manassas, VA).
• the cDNA library is inserted into a prokaryotic host, using standard techniques.
• a cDNA library can be introduced into competent E. coli DH5 cells, which can be obtained, for example, from Life Technologies, Inc. (Gaithersburg, MD).
• a human genomic library can be prepared by means well known in the art (see, for example, Ausubel (1995) at pages 5-1 to 5-6; Wu (1997) at pages 307-327).
• Genomic DNA can be isolated by lysing tissue with the detergent Sarkosyl, digesting the lysate with proteinase K, clearing insoluble debris from the lysate by centrifugation, precipitating nucleic acid from the lysate using isopropanol, and purifying resuspended DNA on a cesium chloride density gradient.
• DNA fragments that are suitable for the production of a genomic library can be obtained by the random shearing of genomic DNA or by the partial digestion of genomic DNA with restriction endonucleases.
• Genomic DNA fragments can be inserted into a vector, such as a bacteriophage or cosmid vector, in accordance with conventional techniques, such as the use of restriction enzyme digestion to provide appropriate termini, the use of alkaline phosphatase treatment to avoid undesirable joining of DNA molecules, and ligation with appropriate ligases. Techniques for such manipulation are well known in the art [see, for example, Ausubel (1995) at pages 5-1 to 5-6; Wu (1997) at pages 307- 327].
• Nucleic acid molecules that encode a human Zlmda6 gene can also be obtained using the polymerase chain reaction (PCR) with oligonucleotide primers having nucleotide sequences that are based upon the nucleotide sequences of the human Zlmda6 gene, as described herein.
• PCR polymerase chain reaction
• General methods for screening libraries with PCR are provided by, for example, Yu et al, "Use of the Polymerase Chain Reaction to Screen Phage Libraries," in Methods in Molecular Biology, Vol. 15: PCR Protocols: Current Methods and Applications, White (ed.), pages 211-215 (Humana Press, Inc. 1993).
• human genomic libraries can be obtained from commercial sources such as Research Genetics (Huntsville, AL) and the American Type Culture Collection (Manassas, VA).
• a library containing cDNA or genomic clones can be screened with one or more polynucleotide probes based upon SEQ ID NO: 1, using standard methods [see, for example, Ausubel (1995) at pages 6-1 to 6-11].
• Anti-Zlmda6 antibodies produced as described below, can also be used to isolate DNA sequences that encode human Z/rn ⁇ genes from cDNA libraries.
• the antibodies can be used to screen ⁇ gtl 1 expression libraries, or the antibodies can be used for immunoscreening following hybrid selection and translation (see, for example, Ausubel (1995) at pages 6-12 to 6-16; Margolis et al, "Screening ⁇ expression libraries with antibody and protein probes," in DNA Cloning 2: Expression
• a Zlmda ⁇ gene can be obtained by synthesizing nucleic acid molecules using mutually priming long oligonucleotides and the nucleotide sequences described herein (see, for example, Ausubel (1995) at pages 8-8 to 8-9).
• Established techniques using the polymerase chain reaction provide the ability to synthesize DNA molecules at least two kilobases in length (Adang et al, Plant Molec. Biol.
• nucleic acid molecules of the present invention can also be synthesized with "gene machines” using protocols such as the phosphoramidite method.
• each complementary strand is made separately.
• the production of short genes 60 to 80 base pairs) is technically straightforward and can be accomplished by synthesizing the complementary strands and then annealing them.
• longer genes >300 base pairs
• synthetic genes double-stranded are assembled in modular form from single-stranded fragments that are from 20 to 100 nucleotides in length.
• One method for building a synthetic gene requires the initial production of a set of overlapping, complementary oligonucleotides, each of which is between 20 to 60 nucleotides long.
• the sequences of the strands are planned so that, after annealing, the two end segments of the gene are aligned to give blunt ends.
• Each internal section of the gene has complementary 3' and 5' terminal extensions that are designed to base pair precisely with an adjacent section.
• synthetic genes can be designed with terminal sequences that facilitate insertion into a restriction endonuclease sites of a cloning vector and other sequences should also be added that contain signals for the proper initiation and termination of transcription and translation.
• An alternative way to prepare a full-size gene is to synthesize a specified set of overlapping oligonucleotides (40 to 100 nucleotides). After the 3' and 5' extensions (6 to 10 nucleotides) are annealed, large gaps still remain, but the base- paired regions are both long enough and stable enough to hold the structure together. The duplex is completed and the gaps filled by enzymatic DNA synthesis with E. coli DNA polymerase I. This enzyme uses the 3'-hydroxyl groups as replication initiation points and the single-stranded regions as templates. After the enzymatic synthesis is completed, the nicks are sealed with T4 DNA ligase.
• the complete gene sequence is usually assembled from double-stranded fragments that are each put together by joining four to six overlapping oligonucleotides (20 to 60 base pairs each). If there is a sufficient amount of the double-stranded fragments after each synthesis and annealing step, they are simply joined to one another. Otherwise, each fragment is cloned into a vector to amplify the amount of DNA available. In both cases, the double- stranded constructs are sequentially linked to one another to form the entire gene sequence. Each double-stranded fragment and the complete sequence should be characterized by DNA sequence analysis to verify that the chemically synthesized gene has the correct nucleotide sequence.
• the sequence of a Zb ⁇ d ⁇ tfcDNA or Zlmdao genomic fragment can be determined using standard methods. Moreover, the identification of genomic fragments containing a Zlmda6 promoter or regulatory element can be achieved using well- established techniques, such as deletion analysis (see, generally, Ausubel (1995)). Cloning of 5' flanking sequences also facilitates production of Zlmdao proteins by "gene activation," following the methods disclosed in U.S. Patent No. 5,641,670.
• an endogenous Zlmda6gcnc in a cell is altered by introducing into the Zlmda ⁇ locus a DNA construct comprising at least a targeting sequence, a regulatory sequence, an exon, and an unpaired splice donor site.
• the targeting sequence is a Zlmda65' non-coding sequence that permits homologous recombination of the construct with the endogenous Zlmda6 locus, whereby the sequences within the construct become operably linked with the endogenous Zlmdao coding sequence, hi this way, an endogenous ZZm ⁇ -/ ⁇ 5promoter can be replaced or supplemented with other regulatory sequences to provide enhanced, tissue-specific, or otherwise regulated expression.
• the present invention provides a variety of nucleic acid molecules, including DNA and RNA molecules that encode the Zlmda6 polypeptides disclosed herein.
• Table 1 sets forth the one-letter codes used within SEQ ID NOs:3, 6, and 25 to denote degenerate nucleotide positions.
• “Resolutions” are the nucleotides denoted by a code letter.
• “Complement” indicates the code for the complementary nucleotide(s). For example, the code Y denotes either C or T, and its complement R denotes A or G, A being complementary to T, and G being complementary to C.
• Table 1 sets forth the one-letter codes used within SEQ ID NOs:3, 6, and 25 to denote degenerate nucleotide positions.
• “Resolutions” are the nucleotides denoted by a code letter.
• “Complement” indicates the code for the complementary nucleotide(s). For example, the code Y denotes either C or T, and
• degenerate codons encompassing all possible codons for a given amino acid, are set forth in Table 2.
• degenerate codon representative of all possible codons encoding an amino acid.
• WSN can, in some circumstances, encode arginine
• MGN can, in some circumstances, encode serine
• some polynucleotides encompassed by the degenerate sequence may encode variant amino acid sequences, but one of ordinary skill in the art can easily identify such variant sequences by reference to the amino acid sequence of SEQ ID NO: 2. Variant sequences can be readily tested for functionality as described herein.
• preferential codon usage or “preferential codons” is a term of art referring to protein translation codons that are most frequently used in cells of a certain species, thus favoring one or a few representatives of the possible codons encoding each amino acid (See Table 2).
• the amino acid Threonine (Thr) may be encoded by ACA, ACC, ACG, or ACT, but in mammalian cells ACC is the most commonly used codon; in other species, for example, insect cells, yeast, viruses or bacteria, different Thr codons may be preferential.
• Preferential codons for a particular species can be introduced into the polynucleotides of the present invention by a variety of methods known in the art. Introduction of preferential codon sequences into recombinant DNA can, for example, enhance production of the protein by making protein translation more efficient within a particular cell type or species.
• the present invention further provides variant polypeptides and nucleic acid molecules that represent counterparts from other species (orthologs). These species include, but are not limited to mammalian, avian, amphibian, reptile, fish, insect and other vertebrate and invertebrate species. Of particular interest are Zlmda6 polypeptides from other mammalian species, including murine, porcine, ovine, bovine, canine, feline, equine, and other primate polypeptides. Orthologs of human Zlmda ⁇ can be cloned using information and compositions provided by the present invention in combination with conventional cloning techniques.
• a cDNA can be cloned using mRNA obtained from a tissue or cell type that expresses Zlmda6 ⁇ as disclosed herein. Suitable sources of mRNA can be identified by probing northern blots with probes designed from the sequences disclosed herein. A library is then prepared from mRNA of a positive tissue or cell line.
• a Zlmda6-encoding cDNA can then be isolated by a variety of methods, such as by probing with a complete or partial human cDNA or with one or more sets of degenerate probes based on the disclosed sequences.
• a cDNA can also be cloned using the polymerase chain reaction with primers designed from the representative human Zlmda6 sequences disclosed herein.
• the cDNA library can be used to transform or transfect host cells, and expression of the cDNA of interest can be detected with an antibody to Zlmdao polypeptide. Similar techniques can also be applied to the isolation of genomic clones, and to the isolation of nucleic molecules that encode murine Zlmda6.
• SEQ ID NO: 1 represents a single allele of human Zlmda6, and that allelic variation and alternative splicing are expected to occur. Allelic variants of this sequence can be cloned by probing cDNA or genomic libraries from different individuals according to standard procedures. Allelic variants of the nucleotide sequence shown in SEQ ID NO: 1, including those containing silent mutations and those in which mutations result in amino acid sequence changes, are within the scope of the present invention, as are proteins which are allelic variants of SEQ ID NO: 2.
• cDNA molecules generated from alternatively spliced mRNAs, which retain the properties of the Zlmda6 polypeptide are included within the scope of the present invention, as are polypeptides encoded by such cDNAs and mRNAs.
• Allelic variants and splice variants of these sequences can be cloned by probing cDNA or genomic libraries from different individuals or tissues according to standard procedures known in the art.
• isolated nucleic acid molecules that encode human Zlmdao can hybridize to nucleic acid molecules having the nucleotide sequence of SEQ ID NO: 1, or a sequence complementary thereto, under "stringent conditions.”
• stringent conditions are selected to be about 5°C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
• T m is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
• a nucleic acid molecule encoding a variant Zlmdao polypeptide can be hybridized with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1 (or its complement) at 42°C overnight in a solution comprising 50% formamide, 5xSSC (lxSSC: 0.15 M sodium chloride and 15 mM sodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution (lOOx Denhardt's solution: 2% (w/v) Ficoll 400, 2% (w/v) polyvinylpyrrolidone, and 2% (w/v) bovine serum albumin), 10% dextran sulfate, and 20 ⁇ g/ml denatured, sheared salmon sperm DNA.
• 5xSSC lxSSC: 0.15 M sodium chloride and 15 mM sodium citrate
• 50 mM sodium phosphate pH 7.6
• 5x Denhardt's solution l
• hybridization mixture can be incubated at a higher temperature, such as about 65°C, in a solution that does not contain formamide.
• a higher temperature such as about 65°C
• premixed hybridization solutions are available (e.g., EXPRESSHYB
• Hybridization Solution from CLONTECH Laboratories, Inc.
• hybridization can be performed according to the manufacturer's instructions.
• nucleic acid molecules can be washed to remove non-hybridized nucleic acid molecules under stringent conditions, or under highly stringent conditions.
• Typical stringent washing conditions include washing in a solution of 0.5x - 2x SSC with 0.1% sodium dodecyl sulfate (SDS) at 55 - 65°C.
• nucleic acid molecules encoding a variant Zlmda ⁇ polypeptide hybridize with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1 (or its complement) under stringent washing conditions, in which the wash stringency is equivalent to 0.5x - 2x SSC with 0.1 % SDS at 55 - 65°C, including 0.5x SSC with 0.1% SDS at 55°C, or 2xSSC with 0.1% SDS at 65°C.
• wash stringency is equivalent to 0.5x - 2x SSC with 0.1 % SDS at 55 - 65°C, including 0.5x SSC with 0.1% SDS at 55°C, or 2xSSC with 0.1% SDS at 65°C.
• SSPE for SSC in the wash solution.
• Typical highly stringent washing conditions include washing in a solution of 0. Ix - 0.2x SSC with 0.1 % sodium dodecyl sulfate (SDS) at 50 - 65°C.
• SDS sodium dodecyl sulfate
• nucleic acid molecules encoding a variant Zlmda6 polypeptide hybridize with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1 (or its complement) under highly stringent washing conditions, in which the wash stringency is equivalent to O.lx - 0.2x SSC with 0.1% SDS at 50 - 65°C, including O.lx SSC with 0.1% SDS at 50°C, or 0.2xSSC with 0.1% SDS at 65°C.
• the present invention also provides isolated Zlmda ⁇ polypeptides that have a substantially similar sequence identity to the polypeptides of SEQ ID NO: 2, or its orthologs.
• substantially similar sequence identity is used herein to denote polypeptides having at least at least 90%, at least 95% or greater sequence identity to the sequences shown in SEQ ID NO: 2, or its orthologs.
• the present invention also contemplates Zlmda6 variant nucleic acid molecules that can be identified using two criteria: a determination of the similarity between the encoded polypeptide with the amino acid sequence of SEQ ID NO: 2, and a hybridization assay, as described above.
• Such Zlmda6 variants include nucleic acid molecules (1) that hybridize with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1 (or its complement) under stringent washing conditions, in which the wash stringency is equivalent to 0.5x - 2x SSC with 0.1% SDS at 55 - 65°C, and (2) that encode a polypeptide having at least 70%, at least 80%, at least 90%, at least 95% or greater than 95% sequence identity to the amino acid sequence of SEQ ID NO: 2.
• Zlmdao variants can be characterized as nucleic acid molecules (1) that hybridize with a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1 (or its complement) under highly stringent washing conditions, in which the wash stringency is equivalent to O.lx - 0.2x SSC with 0.1% SDS at 50 - 65°C, and (2) that encode a polypeptide having at least 95% or greater than 95% sequence identity to the amino acid sequence of SEQ ID NO: 2.
• the present invention also contemplates human Zlmdao variant nucleic acid molecules identified by at least one of hybridization analysis and sequence identity determination, with reference to SEQ ID NOs: 1 and 2.
• Percent sequence identity is determined by conventional methods. See, for example, Altschul et al, Bull. Math. Bio. 48:603 (1986), and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 59:10915 (1992). Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1, and the "BLOSUM 62" scoring matrix of Henikoff and Henikoff (ibid.) as shown in Table 3 (amino acids are indicated by the standard one-letter codes). The percent identity is then calculated as: ([Total number of identical matches]/ [length of the longer sequence plus the number of gaps introduced into the longer sequence in order to align the two sequences])(100).
• the "FASTA" similarity search algorithm of Pearson and Lipm-an is a suitable protein alignment method for examining the level of identity shared by an amino acid sequence disclosed herein and the amino acid sequence of a putative Zlmda6 variant.
• the FASTA algorithm is described by Pearson and Lipman, Proc. Nat'lAcad. Sci. USA 55:2444 (1988), and by Pearson, Meth. Enzymol 183:63 (1990).
• the ten regions with the highest density of identities are then re-scored by comparing the similarity of all paired amino acids using an amino acid substitution matrix, and the ends of the regions are "trimmed" to include only those residues that contribute to the highest score.
• the trimmed initial regions are examined to determine whether the regions can be joined to form an approximate alignment with gaps.
• the highest scoring regions of the two amino acid sequences are aligned using a modification of the Needleman-Wunsch-Sellers algorithm (Needleman and Wunsch, J. Mol. Biol. 48:444 (1970); Sellers, SIAM J. Appl
• FASTA can also be used to determine the sequence identity of nucleic acid molecules using a ratio as disclosed above.
• the ktup value can range between one to six, preferably from three to six, most preferably three, with other parameters set as described above.
• the present invention includes nucleic acid molecules that encode a polypeptide having a conservative amino acid change, compared with the amino acid sequence of SEQ ID NO: 2.
• variants can be obtained that contain one or more amino acid substitutions of SEQ ID NO: 2, in which an alkyl amino acid is substituted for an alkyl amino acid in an Zlmda6 amino acid sequence, an aromatic amino acid is substituted for an aromatic amino acid in an Zlmdao amino acid sequence, a sulfur- containing amino acid is substituted for a sulfur-containing amino acid in an Zlmda ⁇ amino acid sequence, a hydroxy-containing amino acid is substituted for a hydroxy- containing amino acid in an Zlmda6 amino acid sequence, an acidic amino acid is substituted for an acidic amino acid in an Zlmdao amino acid sequence, a basic amino acid is substituted for a basic amino acid in an Zlmdao amino acid sequence, or a dibasic monocarboxylic amino acid is substituted for a dibasic monocarboxylic amino acid in an Zlmda6 amino acid sequence.
• a “conservative amino acid substitution” is illustrated by a substitution among amino acids within each of the following groups: (1) glycine, alanine, valine, leucine, and isoleucine, (2) phenylalanine, tyrosine, and tryptophan, (3) serine and threonine, (4) aspartate and glutamate, (5) glutamine and asparagine, and (6) lysine, arginine and histidine.
• the BLOSUM62 table is an amino acid substitution matrix derived from about 2,000 local multiple alignments of protein sequence segments, representing highly conserved regions of more than 500 groups of related proteins (Henikoff and Henikoff, Proc. Nat'lAcad. Sci. USA 89: 10915 (1992)). Accordingly, the BLOSUM62 substitution frequencies can be used to define conservative amino acid substitutions that may be introduced into the amino acid sequences of the present invention. Although it is possible to design amino acid substitutions based solely upon chemical properties (as discussed above), the language "conservative amino acid substitution” preferably refers to a substitution represented by a BLOSUM62 value of greater than -1. For example, an amino acid substitution is conservative if the substitution is characterized by a
• preferred conservative amino acid substitutions are characterized by a BLOSUM62 value of at least 1 (e.g., 1, 2 or 3), while more preferred conservative amino acid substitutions are characterized by a BLOSUM62 value of at least 2 (e.g., 2 or 3).
• Conservative amino acid changes in an Zlmda6 gene can be introduced by substituting nucleotides for the nucleotides recited in SEQ ID NO: 1.
• Such “conservative amino acid” variants can be obtained, for example, by oligonucleotide- directed mutagenesis, linker-scanning mutagenesis, mutagenesis using the polymerase chain reaction, and the like (see Ausubel (1995) at pages 8-10 to 8-22; and McPherson (ed.), Directed Mutagenesis: A Practical Approach (IRL Press 1991)).
• the ability of such variants to promote anti-viral or anti-proliferative activity can be determined using a standard method, such as the assay described herein.
• a variant Zlmdao polypeptide can be identified by the ability to specifically bind anti-Zlmda6 antibodies.
• the proteins of the present invention can also comprise non-naturally occurring amino acid residues.
• Non-naturally occurring amino acids include, without limitation, tr ⁇ n-s-3-methylproline, 2,4-methanoproline, m-4-hydroxy ⁇ roline, trans-4- hydroxyproline, N-methylglycine, // ⁇ -threonine, methylthreonine, hydroxyethylcysteine, hydroxyethylhomocysteine, nitroglutamine, homoglutamine, pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline, tert-leucine, norvaline, 2-azaphenylalanine, 3-azaphenylalanine, 4- azaphenylalanine, and 4-fluorophenylalanine.
• coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, or 4- fluorophenylalanine).
• a natural amino acid that is to be replaced e.g., phenylalanine
• the desired non-naturally occurring amino acid(s) e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, or 4- fluorophenylalanine.
• the non-naturally occurring amino acid is incorporated into the protein in place of its natural counterpart. See, Koide et al, Biochem. 33:1410 (1994).
• Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the
• Non-conservative amino acids, amino acids that are not encoded by the genetic code, non-naturally occurring amino acids, and unnatural amino acids may be substituted for Zlmda6 amino acid residues.
• Essential amino acids in the polypeptides of the present invention can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244:1081 (1989), Bass et al, Proc. Nat'lAcad. Sci. USA 5S:4498 (1991), Coombs and Corey, "Site- Directed Mutagenesis and Protein Engineering," in Proteins: Analysis and Design, Angeletti (ed.), pages 259-311 (Academic Press, Inc.
• variants of the disclosed Zlmda ⁇ nucleotide and polypeptide sequences can also be generated through DNA shuffling as disclosed by Stemmer, Nature 370:389 (1994), Stemmer, Proc. Nat'lAcad. Sci. USA 91:10141 (1994), and international publication No. WO 97/20078. Briefly, variant DNAs are generated by in vitro homologous recombination by random fragmentation of a parent DNA followed by reassembly using PCR, resulting in randomly introduced point mutations. This technique can be modified by using a family of parent DNAs, such as allelic variants or DNAs from different species, to introduce additional variability into the process.
• Mutagenesis methods as disclosed herein can be combined with high- throughput, automated screening methods to detect activity of cloned, mutagenized polypeptides in host cells.
• Mutagenized DNA molecules that encode biologically active polypeptides, or polypeptides that bind with anti-Zlmda ⁇ antibodies can be recovered from the host cells and rapidly sequenced using modern equipment. These methods allow the rapid determination of the importance of individual amino acid residues in a polypeptide of interest, and can be applied to polypeptides of unknown structure.
• the present invention also includes "functional fragments" of Zlmda6 polypeptides and nucleic acid molecules encoding such functional fragments. Routine deletion analyses of nucleic acid molecules can be performed to obtain functional fragments of a nucleic acid molecule that encodes a Zlmdao polypeptide.
• the present invention also provides polypeptide fragments or peptides comprising an epitope-bearing portion of a Zlmda ⁇ polypeptide described herein.
• Such fragments or peptides may comprise an "immunogenic epitope," which is a part of a protein that elicits an antibody response when the entire protein is used as an immunogen.
• Immunogenic epitope-bearing peptides can be identified using standard methods (see, for example, Geysen et al, Proc. Nat'lAcad. Sci. USA 81:3998 (1983)).
• polypeptide fragments or peptides may comprise an immunogen.
• antigenic epitope which is a region of a protein molecule to which an antibody can specifically bind. Certain epitopes consist of a linear or contiguous stretch of amino acids, and the antigenicity of such an epitope is not disrupted by denaturing agents. It is known in the art that relatively short synthetic peptides that can mimic epitopes of a protein can be used to stimulate the production of antibodies against the protein (see, for example, Sutcliffe et al, Science 219:660 (1983)). Accordingly, antigenic epitope- bearing peptides and polypeptides of the present invention are useful to raise antibodies that bind with the polypeptides described herein.
• Antigenic epitope-bearing peptides and polypeptides preferably contain at least four to ten amino acids, at least ten to fifteen amino acids, or about 15 to about 30 amino acids of SEQ ID NO: 2.
• Such epitope-bearing peptides and polypeptides can be produced by fragmenting a Zlmdao polypeptide, or by chemical peptide synthesis, as described herein.
• epitopes can be selected by phage display of random peptide libraries (see, for example, Lane and Stephen, Curr. Opin. Immunol 5:268 (1993), and Cortese et al, Curr. Opin. Biotechnol 7:616 (1996)).
• epitope-bearing polypeptides are polypeptides comprised of SEQ ID NOs: 3-40.
• Zlmda6 polypeptide including variants and fusion proteins, one of ordinary skill in the art can readily generate a fully degenerate polynucleotide sequence encoding that variant using the information set forth in Tables 1 and 2 above.
• the present invention includes a computer-readable medium encoded with a data structure that provides at least one of the following sequences: SEQ ID NOs: 1-40.
• Suitable forms of computer-readable media include magnetic media and optically- readable media. Examples of magnetic media include a hard or fixed drive, a random access memory (RAM) chip, a floppy disk, digital linear tape (DLT), a disk cache, and a ZIP disk.
• Optically readable media are exemplified by compact discs (e.g., CD-read only memory (ROM), CD-rewritable (RW), and CD-recordable), and digital versatile/video discs (DVD) (e.g., DVD-ROM, DVD-RAM, and DVD+RW).
• compact discs e.g., CD-read only memory (ROM), CD-rewritable (RW), and CD-recordable
• DVD digital versatile/video discs
• Fusion proteins of Zlmda6 can be used to express Zlmdao in a recombinant host, and to isolate expressed Zlmda6. As described below, particular Zlmda6 fusion proteins also have uses in diagnosis and therapy.
• One type of fusion protein comprises a peptide that guides a Zlmda6 polypeptide from a recombinant host cell.
• a secretory signal sequence also known as a signal peptide, a leader sequence, prepro sequence or pre sequence
• the secretory signal sequence may be derived from
• a suitable signal sequence may also be derived from another secreted protein or synthesized de novo.
• the secretory signal sequence is operably linked to a Zlmda6- encoding sequence such that the two sequences are joined in the correct reading frame and positioned to direct the newly synthesized polypeptide into the secretory pathway of the host cell.
• Secretory signal sequences are commonly positioned 5' to the nucleotide sequence encoding the polypeptide of interest, although certain secretory signal sequences may be positioned elsewhere in the nucleotide sequence of interest (see, e.g., Welch et al, U.S. Patent No. 5,037,743; Holland et al, U.S. Patent No.
• yeast signal sequence is preferred for expression in yeast cells.
• suitable yeast signal sequences are those derived from yeast mating phermone -factor (encoded by the MFal gene), invertase (encoded by the SUC2 gene), or acid phosphatase (encoded by the PH05 gene).
• Zlmda6 can be expressed as a fusion protein comprising a glutathione S-transferase polypeptide.
• Glutathione S-transferease fusion proteins are typically soluble, and easily purifiable from E. coli lysates on immobilized glutathione columns.
• a Zlmda6 fusion protein comprising a maltose binding protein polypeptide can be isolated with an amylose resin column, while a fusion protein comprising the C-terminal end of a truncated Protein A gene can be purified using IgG-Sepharose.
• Established techniques for expressing a heterologous polypeptide as a fusion protein in a bacterial cell are described, for example, by Williams et al. , "Expression of Foreign Proteins in E. coli Using Plasmid Vectors and Purification of Specific Polyclonal Antibodies," in DNA Cloning 2: A Practical Approach, 2 nd Edition, Glover and Hames (Eds.), pages 15-58 (Oxford University Press 1995).
• the PINPOINT Xa protein purification system provides a method for isolating a fusion protein comprising a polypeptide that becomes biotinylated during expression with a resin that comprises avidin.
• Peptide tags that are useful for isolating heterologous polypeptides expressed by either prokaryotic or eukaryotic cells include polyHistidine tags (which have an affinity for nickel-chelating resin), c-myc tags, calmodulin binding protein (isolated with calmodulin affinity chromatography), substance P, the RYIRS tag (which binds with anti-RYIRS antibodies), the Glu-Glu tag, and the FLAG tag (which binds with anti-FLAG antibodies). See, for example, Luo et al, Arch. Biochem. Biophys.
• fusion protein comprises a Zlmda6 polypeptide and an immunoglobulin heavy chain constant region, typically an F c fragment, which contains two or three constant region domains and a hinge region but lacks the variable region.
• an immunoglobulin heavy chain constant region typically an F c fragment
• F c fragment an immunoglobulin heavy chain constant region
• Chang et al, U.S. Patent No. 5,723,125 describe a fusion protein comprising a human interferon and a human immunoglobulin Fc fragment.
• the C- terminal of the interferon is linked to the N-terminal of the Fc fragment by a peptide linker moiety.
• An example of a peptide linker is a peptide comprising primarily a T cell inert sequence, which is immunologically inert.
• An exemplary peptide linker has the amino acid sequence: GGSGG SGGGG SGGGG S (SEQ ID NO: 41).
• a preferred Fc moiety is a human ⁇ 4 chain, which is stable in solution and has little or no complement activating activity.
• the present invention contemplates an Zlmda ⁇ fusion protein that comprises an Zlmdao moiety and a human Fc fragment, wherein the C-terminus of the Zlmda6 ⁇ moiety is attached to the N- terminus of the Fc fragment via a peptide linker.
• the Zlmdao moiety can be a Zlmda6 molecule or a fragment thereof.
• an Zlmdao fusion protein comprises an IgG sequence, an Zlmdao moiety covalently joined to the aminoterminal end of the IgG sequence, and a signal peptide that is covalently joined to the aminoterminal of the Zlmda6 moiety, wherein the IgG sequence consists of the following elements in the following order: a hinge region, a CH 2 domain, and a CH 3 domain. Accordingly, the IgG sequence lacks a domain.
• Fusion proteins comprising a Zlmda6 moiety and an Fc moiety can be used, for example, as an in vitro assay tool.
• the presence of a Zlmda6 receptor in a biological sample can be detected using a Zlmda ⁇ -immunoglobulin fusion protein, in which the Zlmda6 moiety is used to target the cognate receptor, and a macromolecule, such as Protein A or anti-Fc antibody, is used to detect the bound fusion protein-receptor complex.
• fusion proteins can be used to identify agonists and antagonists that interfere with the binding of Zlmdao to its receptor.
• antibody-Zlmda ⁇ fusion proteins comprising antibody variable domains, are useful as therapeutic proteins, in which the antibody moiety binds with a target antigen, such as a tumor associated antigen.
• a target antigen such as a tumor associated antigen.
• Methods of making antibody- cytokine fusion proteins are known to those of skill in the art.
• antibody fusion proteins comprising an interleukin-2 moiety are described by Boleti et al, Ann. Oncol. 6:945 (1995), Nicolet et al, Cancer Gene Ther. 2:161 (1995), Becker et al, Proc. Nat'lAcad. Sci. USA 93:7826 (1996), Hank etal, Clin. Cancer Res. 2:1951 (1996), and Hu etal, Cancer Res.
• cytokine-antibody fusion proteins include IL-8, IL-12, or Zlmda ⁇ as the cytokine moiety (Holzer et al, Cytokine 8:214 (1996); Gillies et al, J. Immunol.
• hybrid Zlmdao proteins can be constructed using regions or domains of the inventive (see, for example, Picard, Cur. Opin. Biology 5:511 (1994)). These methods allow the determination of the biological importance of larger domains or regions in a polypeptide of interest. Such hybrids may alter reaction kinetics, binding, constrict or expand the substrate specificity, or alter tissue and cellular localization of a polypeptide, and can be applied to polypeptides of unknown structure. Fusion proteins can be prepared by methods known to those skilled in the art by preparing each component of the fusion protein and chemically conjugating them.
• a polynucleotide encoding both components of the fusion protein in the proper reading frame can be generated using known techniques and expressed by the methods described herein.
• fusion proteins may exhibit other properties as disclosed herein.
• General methods for enzymatic and chemical cleavage of fusion proteins are described, for example, by Ausubel (1995) at pages 16-19 to 16-25.
• the present invention also contemplates chemically modified Zlmdao compositions, in which a Zlmda6 polypeptide is linked with a polymer.
• the polymer is water-soluble so that the Zlmdao conjugate does not precipitate in an aqueous environment, such as a physiological environment.
• An example of a suitable polymer is one that has been modified to have a single reactive group, such as an active ester for acylation, or an aldehyde for alkylation. In this way, the degree of polymerization can be controlled.
• An example of a reactive aldehyde is polyethylene glycol propionaldehyde, or mono-(Cl-ClO) alkoxy, or aryloxy derivatives thereof (see, for example, Harris, et al, U.S. Patent No. 5,252,714).
• the polymer may be branched or unbranched.
• a mixture of polymers can be used to produce Zlmda6 conjugates.
• Zlmda6 conjugates used for therapy should preferably comprise pharmaceutically acceptable water-soluble polymer moieties. Conjugation of interferons with water-soluble polymers has been shown to enhance the circulating half- life of the interferon, and to reduce the immunogenicity of the polypeptide [see, for example, Nieforth et al, Clin. Pharmacol. Ther. 59:636 (1996), and Monkarsh et al, Anal Biochem. 247:434 (1997)].
• Suitable water-soluble polymers include polyethylene glycol (PEG), monomethoxy-PEG, mono-(Cl-C10)alkoxy-PEG, aryloxy-PEG, poly-(N- vinyl pyrrolidone)PEG, tresyl monomethoxy PEG, PEG propionaldehyde, bw-succinimidyl carbonate PEG, propylene glycol homopolymers, a polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, dextran, cellulose, or other carbohydrate-based polymers.
• Suitable PEG may have a molecular weight from about 600 to about 60,000, including, for example, 5,000, 12,000, 20,000 and 25,000.
• a Zlmda6 conjugate can also comprise a mixture of such water-soluble polymers.
• Zlmdao conjugate comprises a Zlmdao moiety and a polyalkyl oxide moiety attached to the N-terminus of the Zlmdao moiety.
• PEG is one suitable polyalkyl oxide.
• Zlmda6 can be modified with PEG, a process known as "PEGylation.” PEGylation of Zlmda6 can be carried out by any of the PEGylation reactions known in the art [see, for example, EP 0 154 316, Delgado et al, Critical Reviews in Therapeutic Drug Carrier Systems 9:249 (1992), Duncan and Spreafico, Clin. Pharmacokinet.
• PEGylation can be performed by an acylation reaction or by an alkylation reaction with a reactive polyethylene glycol molecule.
• Zlmda6 conjugates are formed by condensing activated PEG, in which a terminal hydroxy or amino group of PEG has been replaced by an activated linker (see, for example, Karasiewicz et al, U.S. Patent No. 5,382,657).
• PEGylation by acylation typically requires reacting an active ester derivative of PEG with a Zlmdao polypeptide.
• An example of an activated PEG ester is PEG esterified to N-hydroxysuccinimide.
• acylation includes the following types of linkages between Zlmdao and a water-soluble polymer: amide, carbamate, urethane, and the like.
• Methods for preparing PEGylated Zlmda6 by acylation will typically comprise the steps of (a) reacting an Zlmda6 polypeptide with PEG (such as a reactive ester of an aldehyde derivative of PEG) under conditions whereby one or more PEG groups attach to Zlmdao, and (b) obtaining the reaction product(s).
• PEG such as a reactive ester of an aldehyde derivative of PEG
• the optimal reaction conditions for acylation reactions will be determined based upon known parameters and desired results. For example, the larger the ratio of PEG: Zlmda ⁇ , the greater the percentage of polyPEGylated Zlmdao product.
• the product of PEGylation by acylation is typically a polyPEGylated Zlmdao product, wherein the lysine ⁇ -amino groups are PEGylated via an acyl linking group.
• An example of a connecting linkage is an amide.
• the resulting Zlmda6 will be at least 95% mono-, di-, or tri-pegylated, although some species with higher degrees of PEGylation may be formed depending upon the reaction conditions.
• PEGylated species can be separated from unconjugated Zlmda6 polypeptides using standard purification methods, such as dialysis, ultrafiltration, ion exchange chromatography, affinity chromatography, and the like.
• PEGylation by alkylation generally involves reacting a terminal aldehyde derivative of PEG with Zlmdao in the presence of a reducing agent.
• PEG groups are preferably attached to the polypeptide via a -CH - ⁇ H group.
• Derivatization via reductive alkylation to produce a monoPEGylated product takes advantage of the differential reactivity of different types of primary amino groups available for derivatization.
• the reaction is performed at a pH that allows one to take advantage of the pKa differences between the ⁇ -amino groups of the lysine residues and the ⁇ -amino group of the N-terminal residue of the protein.
• a water-soluble polymer that contains a reactive group such as an aldehyde
• the conjugation with the polymer occurs predominantly at the N-terminus of the protein without significant modification of other reactive groups such as the lysine side chain amino groups.
• the present invention provides a substantially homogenous preparation of Zlmdao monopolymer conjugates.
• Reductive alkylation to produce a substantially homogenous population of monopolymer Zlmdao conjugate molecule can comprise the steps of: (a) reacting an Zlmda6 polypeptide with a reactive PEG under reductive alkylation conditions at a pH suitable to permit selective modification of the ⁇ -amino group at the amino terminus of the Zlmda6, and (b) obtaining the reaction product(s).
• the reducing agent used for reductive alkylation should be stable in aqueous solution and preferably be able to reduce only the Schiff base formed in the initial process of reductive alkylation.
• Preferred reducing agents include sodium borohydride, sodium cyanoborohydri.de, dimethylamine borane, trimethylamine borane, and pyridine borane.
• the reductive alkylation reaction conditions are those that permit the selective attachment of the water-soluble polymer moiety to the N-terminus of Zlmda6.
• Such reaction conditions generally provide for pKa differences between the lysine amino groups and the ⁇ -amino group at the N-terminus.
• the pH also affects the ratio of polymer to protein to be used. In general, if the pH is lower, a larger excess of polymer to protein will be desired because the less reactive the N-terminal ⁇ -group, the more polymer is needed to achieve optimal conditions. If the pH is higher, the polymer:Zlmda6 need not be as large because more reactive groups are available. Typically, the pH will fall within the range of 3 - 9, or 3 - 6.
• the molecular weight of the water-soluble polymer is the higher the molecular weight of the polymer, the fewer number of polymer molecules which may be attached to the protein.
• the typical molecular weight is about 2 kDa to about 100 kDa, about 5 kDa to about 50 kDa, or about 12 kDa to about 25 kDa.
• Zlmdao will generally be in the range of 1 : 1 to 100: 1.
• the molar ratio of water-soluble polymer to Zlmda6 will be 1:1 to 20:1 for polyPEGylation, and 1:1 to 5:1 for monoPEGylation.
• polypeptides of the present invention can be produced in recombinant host cells following conventional techniques.
• a nucleic acid molecule encoding the polypeptide must be operably linked to regulatory sequences that control transcriptional expression in an expression vector and then, introduced into a host cell.
• expression vectors can include translational regulatory sequences and a marker gene suitable for selection of cells that carry the expression vector.
• Expression vectors that are suitable for production of a foreign protein in eukaryotic cells typically contain (1) prokaryotic DNA elements coding for a bacterial replication origin and an antibiotic resistance marker to provide for the growth and selection of the expression vector in a bacterial host; (2) eukaryotic DNA elements that control initiation of transcription, such as a promoter; and (3) DNA elements that control the processing of transcripts, such as a transcription termination/polyadenylation sequence.
• expression vectors can also include nucleotide sequences encoding a secretory sequence that directs the heterologous polypeptide into the secretory pathway of a host cell.
• a Zlmda6 expression vector may comprise a Zlmda6 gene and a secretory sequence derived from a Zlmda6 gene or another secreted gene.
• Zlmdao proteins of the present invention may be expressed in mammalian cells.
• suitable mammalian host cells include African green monkey kidney cells (Vero; ATCC CRL 1587), human embryonic kidney cells (293- HEK; ATCC CRL 1573), baby hamster kidney cells (BHK-21, BHK-570; ATCC CRL 8544, ATCC CRL 10314), canine kidney cells (MDCK; ATCC CCL 34), Chinese hamster ovary cells (CHO-K1; ATCC CCL61; CHO DG44 [Chasin et al, Som. Cell Molec. Genet. 12:555 (1986)]], rat pituitary cells (GH1 ; ATCC CCL82), HeLa S3 cells
• H-4-H-E rat hepatoma cells
• COS-1 SV40-transformed monkey kidney cells
• NIH- 3T3 murine embryonic cells
• the transcriptional and translational regulatory signals may be derived from viral sources, such as adenovirus, bovine papilloma virus, simian virus, or the like, in which the regulatory signals are associated with a particular gene which has a high level of expression.
• viral sources such as adenovirus, bovine papilloma virus, simian virus, or the like, in which the regulatory signals are associated with a particular gene which has a high level of expression.
• Suitable transcriptional and translational regulatory sequences also can be obtained from mammalian genes, such as actin, collagen, myosin, and metallothionein genes.
• Transcriptional regulatory sequences include a promoter region sufficient to direct the initiation of RNA synthesis.
• Suitable eukaryotic promoters include the promoter of the mouse metallothionein I gene [Hamer et al, J. Molec. Appl Genet. 1:213 (1982)], the TK promoter of Herpes virus [McKnight, Cell 31:355 (1982)], the SV40 early promoter [Benoist et al, Nature 290:304 (1981)], the Rous sarcoma virus promoter (Gorman et al, Proc. Nat'lAcad. Sci.
• a prokaryotic promoter such as the bacteriophage T3 RNA polymerase promoter, can be used to control Zhnda6 gene expression in mammalian cells if the prokaryotic promoter is regulated by a eukaryotic promoter [Zhou et al, Mol Cell Biol 10:4529 (1990), and Kaufman et al, Nucl Acids Res. 19:4485 (1991)].
• An expression vector can be introduced into host cells using a variety of standard techniques including calcium phosphate transfection, liposome-mediated transfection, microprojectile-mediated delivery, electroporation, and the like.
• the transfected cells are selected and propagated to provide recombinant host cells that comprise the expression vector stably integrated in the host cell genome.
• Techniques for introducing vectors into eukaryotic cells and techniques for selecting such stable transformants using a dominant selectable marker are described, for example, by Ausubel
• one suitable selectable marker is a gene that provides resistance to the antibiotic neomycin.
• selection is carried out in the presence of a neomycin-type drug, such as G-418 or the like.
• Selection systems can also be used to increase the expression level of the gene of interest, a process referred to as "amplification.” Amplification is carried out by culturing transfectants in the presence of a low level of the selective agent and then increasing the amount of selective agent to select for cells that produce high levels of the products of the introduced genes.
• a preferred amplifiable selectable marker is dihydrofolate reductase, which confers resistance to methotrexate.
• markers that introduce an altered phenotype such as green fluorescent protein, or cell surface proteins such as CD4, CD8, Class I MHC, placental alkaline phosphatase may be used to sort transfected cells from untransfected cells by such means as FACS sorting or magnetic bead separation technology.
• Zlmda6 polypeptides can also be produced by cultured mammalian cells using a viral delivery system. Exemplary viruses for this purpose include adenovirus, herpesvirus, vaccinia virus and adeno-associated virus (AAV).
• Adenovirus a double- stranded DNA virus
• Advantages of the adenovirus system include the accommodation of relatively large DNA inserts, the ability to grow to high-titer, the ability to infect a broad range of mammalian cell types, and flexibility that allows use with a large number of available vectors containing different promoters. By deleting portions of the adenovirus genome, larger inserts (up to 7 kb) of heterologous DNA can be accommodated.
• inserts can be incorporated into the viral DNA by direct ligation or by homologous recombination with a co- transfected plasmid.
• An option is to delete the essential El gene from the viral vector, which results in the inability to replicate unless the El gene is provided by the host cell.
• Adenovirus vector-infected human 293 cells ATCC Nos. CRL- 1573, 45504, 45505
• Zlmdao genes may also be expressed in other higher eukaryotic cells, such as avian, fungal, insect, yeast, or plant cells.
• the baculovirus system provides an efficient means to introduce cloned Zlmdao genes into insect cells.
• Suitable expression vectors are based upon the Autographa calif ornica multiple nuclear polyhedrosis virus (AcMNPV), and contain well-known promoters such as Drosophila heat shock protein (hsp) 70 promoter, Autographa calif ornica nuclear polyhedrosis virus immediate-early gene promoter (ie-1) and the delayed early 39K promoter, baculovirus plO promoter, and the Drosophila metallothionein promoter.
• hsp Drosophila heat shock protein
• ie-1 Autographa calif ornica nuclear polyhedrosis virus immediate-early gene promoter
• baculovirus plO promoter the Drosophila metallothionein
• a second method of making recombinant baculovirus utilizes a transposon-based system described by Luckow (Luckow, et al, J. Virol. 67:4566 (1993)).
• This system which utilizes transfer vectors, is sold in the BAC-to-BAC kit (Life Technologies, Rockville, MD).
• This system utilizes a transfer vector, PFASTB AC (Life Technologies) containing a Tn7 transposon to move the DNA encoding the Zlmda ⁇ polypeptide into a baculovirus genome maintained in E. coli as a large plasmid called a "bacmid.” See, Hill-Perkins and Possee, J. Gen. Virol. 71:911 (1990), Bonning, et al, J.
• transfer vectors can include an in-frame fusion with DNA encoding an epitope tag at the C- or N-terminus of the expressed Zlmda6 polypeptide, for example, a Glu-Glu epitope tag (Grussenmeyer et al, Proc. N t'Z Acad. Sci. 82:1952 (1985)).
• a transfer vector containing a Zlmda6 gene is transformed into E. coli, and screened for bacmids that contain an interrupted lacZ gene indicative of recombinant baculovirus.
• the bacmid D ⁇ A containing the recombinant baculovirus genome is then isolated using common techniques.
• the illustrative PFASTBAC vector can be modified to a considerable degree.
• the polyhedrin promoter can be removed and substituted with the baculovirus basic protein promoter (also known as Pcor, p6.9 or MP promoter) which is expressed earlier in the baculovirus infection, and has been shown to be advantageous for expressing secreted proteins (see, for example, Hill-Perkins and Possee, J. Gen. Virol. 71:911 (1990), Bonning, et al, J. Gen. Virol. 75:1551 (1994), and Chazenbalk and Rapoport, J. Biol Chem.
• transfer vector constructs a short or long version of the basic protein promoter can be used.
• transfer vectors can be constructed that replace the native Zlmdao secretory signal sequences with secretory signal sequences derived from insect proteins. For example, a secretory signal sequence from ⁇ cdysteroid Glucosyltransferase ( ⁇ GT), honey bee Melittin
• baculovirus gp67 (PharMingen: San Diego, CA) can be used in constructs to replace the native Zlmdao secretory signal sequence.
• Suitable insect host cells include cell lines derived from IPLB-S/-21, a Spodopter a frugiperda pupal ovarian cell line, such as S ⁇ (ATCC CRL 1711), S 21 A ⁇ , and S 21 (Invitrogen
• Suitable media are Sf900 flTM (Life Technologies) or ⁇ SF 921TM (Expression Systems) for the Sf9 cells; and Ex-cellO405TM (JRH Biosciences, Lenexa, KS) or
• the cells are typically grown up from an inoculation density of approximately 2-5 x 10 cells to a density of 1-2 x 10 cells at which time a recombinant viral stock is added at a multiplicity of infection (MOI) of 0.1 to 10, more typically near 3.
• MOI multiplicity of infection
• Established techniques for producing recombinant proteins in baculovirus systems are provided by Bailey et al, "Manipulation of Baculovirus Vectors," in Methods in Molecular Biology, Volume 7: Gene Transfer and Expression Protocols, Murray (ed.), pages 147-168 (The Humana Press, Inc.
• yeast cells can also be used to express the genes described herein.
• Yeast species of particular interest in this regard include Saccharomyces cerevisiae, Pichia pastoris, and Pichia methanolica.
• Suitable promoters for expression in yeast include promoters from GAL1 (galactose), PGK (phosphoglycerate kinase), ADH (alcohol dehydrogenase), AOX1 (alcohol oxidase), HIS4 (histidinol dehydrogenase), and the like.
• GAL1 galactose
• PGK phosphoglycerate kinase
• ADH alcohol dehydrogenase
• AOX1 alcohol oxidase
• HIS4 histidinol dehydrogenase
• These vectors include Yip-based vectors, such as YIp5, YRp vectors, such as YRpl7, YEp vectors such as YEpl3 and YCp vectors, such as YCpl9.
• Methods for transforming S. cerevisiae cells with exogenous DNA and producing recombinant polypeptides therefrom are disclosed by, for example, Kawasaki, U.S. Patent No. 4,599,311, Kawasaki et al, U.S. Patent No. 4,931,373, Brake, U.S. Patent No. 4,870,008, Welch et al, U.S. Patent No. 5,037,743, and Murray et al, U.S. Patent No.
• Transformed cells are selected by phenotype determined by the selectable marker, commonly drug resistance or the ability to grow in the absence of a particular nutrient (e.g., leucine).
• a preferred vector system for use in Saccharomyces cerevisiae is the POT1 vector system disclosed by Kawasaki et al (U.S. Patent No. 4,931,373), which allows transformed cells to be selected by growth in glucose-containing media. Additional suitable promoters and terminators for use in yeast include those from glycolytic enzyme genes (see, e.g., Kawasaki, U.S. Patent No. 4,599,311, Kingsman et al, U.S. Patent No. 4,615,974, and Bitter, U.S. Patent No.
• Pichia methanolica as host for the production of recombinant proteins is disclosed by Raymond, U.S. Patent No. 5,716,808, Raymond, U.S. Patent No. 5,736,383, Raymond et al, Yeast 14: 11-23 (1998), and in international publication Nos. WO 97/17450, WO 97/17451, WO 98/02536, and WO 98/02565.
• DNA molecules for use in transforming R. methanolica will commonly be prepared as double-stranded, circular plasmids, which are preferably linearized prior to transformation.
• the promoter and terminator in the plasmid be that of a R.
• methanolica gene such as a R. methanolica alcohol utilization gene (AUGl or AUG2).
• Other useful promoters include those of the dihydroxyacetone synthase (DHAS), formate dehydrogenase (FMD), and catalase (CAT) genes.
• DHAS dihydroxyacetone synthase
• FMD formate dehydrogenase
• CAT catalase
• a preferred selectable marker for use in Pichia methanolica is a R. methanolica ADE2 gene, which encodes phosphoribosyl-5-aminoimidazole carboxylase (AIRC; EC 4.1.1.21), and which allows ade2 host cells to grow in the absence of adenine.
• methanolica cells can be transformed by electroporation using an exponentially decaying, pulsed electric field having a field strength of from 2.5 to 4.5 kV/cm, preferably about 3.75 kV/cm, and a time constant (t) of from 1 to 40 milliseconds, most preferably about 20 milliseconds.
• Expression vectors can also be introduced into plant protoplasts, intact plant tissues, or isolated plant cells.
• Methods for introducing expression vectors into plant tissue include the direct infection or co-cultivation of plant tissue with Agrobacterium tumefaciens, microprojectile-mediated delivery, DNA injection, electroporation, and the like. See, for example, Horsch et al, Science 227:1229 (1985), Klein et al, Biotechnology 10:268 (1992), and Miki et al, "Procedures for Introducing Foreign DNA into Plants," in Methods in Plant Molecular Biology and Biotechnology, Glick etal. (eds.), pages 67-88 (CRC Press, 1993).
• Zlmdao genes can be expressed in prokaryotic host cells.
• Suitable promoters that can be used to express Zlmda6 polypeptides in a prokaryotic host are well-known to those of skill in the art and include promoters capable of recognizing the T4, T3, Sp6 and T7 polymerases, the P R and P L promoters of bacteriophage lambda, the trp, recA, heat shock, lacUV5, tac, Ipp-lacSpr, phoA, and lacZ promoters of E. coli, promoters of R.
• subtilis subtilis, the promoters of the bacteriophages of Bacillus, Streptomyces promoters, the int promoter of bacteriophage lambda, the bla promoter of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene.
• Prokaryotic promoters have been reviewed by Glick, J. bid. Microbiol 1:211 (1987), Watson et al, Molecular Biology ofthe Gene, 4th Ed. (Benjamin Cummins 1987), and by Ausubel et al (1995).
• Preferred prokaryotic hosts include E. coli and Bacillus subtilus.
• Suitable strains of E. coli include BL21(D ⁇ 3), BL21(DE3) ⁇ LysS, BL21(DE3)pLysE, DH1, DH4I, DH5, DH5I, DH5IF', DH51MCR, DH10B, DH10B/p3, DH11S, C600, HB101, JM101, JM105, JM109, JM110, K38, RR1, Y1088, Y1089, CSH18, ER1451, and ER1647 (see, for example, Brown (ed.), Molecular Biology Labfax [Academic Press 1991)).
• Suitable strains of Bacillus subtilus include BR151, YB886, Mil 19, MI120, and B170 (see, for example, Hardy, "Bacillus Cloning Methods,” in DNA Cloning: A Practical Approach, Glover (ed.) (IRL Press 1985)].
• the polypeptide When expressing a Zlmdao polypeptide in bacteria such as E. coli, the polypeptide may be retained in the cytoplasm, typically as insoluble granules, or may be directed to the periplasmic space by a bacterial secretion sequence. In the former case, the cells are lysed, and the granules are recovered and denatured using, for example, guanidine isothiocyanate or urea. The denatured polypeptide can then be refolded and dimerized by diluting the denaturant, such as by dialysis against a solution of urea and a combination of reduced and oxidized glutathione, followed by dialysis against a buffered saline solution.
• the denaturant such as by dialysis against a solution of urea and a combination of reduced and oxidized glutathione
• the polypeptide can be recovered from the periplasmic space in a soluble and functional form by disrupting the cells (by, for example, sonication or osmotic shock) to release the contents of the periplasmic space and recovering the protein, thereby obviating the need for denaturation and refolding.
• polypeptides of the present invention It is preferred to purify the polypeptides of the present invention to at least about 80% purity, more preferably to at least about 90% purity, even more preferably to at least about 95% purity, or even greater than 95% purity with respect to contaminating macromolecules, particularly other proteins and nucleic acids, and free of infectious and pyrogenic agents.
• the polypeptides of the present invention may also be purified to a pharmaceutically pure state, which is greater than 99.9% pure.
• a purified polypeptide is substantially free of other polypeptides, particularly other polypeptides of animal origin.
• Fractionation and/or conventional purification methods can be used to obtain preparations of Zlmda6 purified from natural sources (e.g., coronary artery smooth muscle tissue, placental tissue, uterine tissue, or tracheal tissue), and recombinant Zlmda6 polypeptides and fusion Zlmda6 polypeptides purified from recombinant host cells.
• natural sources e.g., coronary artery smooth muscle tissue, placental tissue, uterine tissue, or tracheal tissue
• ammonium sulfate precipitation and acid or chaotrope extraction may be used for fractionation of samples.
• Exemplary purification steps may include hydroxyapatite, size exclusion, FPLC and reverse-phase high performance liquid chromatography.
• Suitable chromatographic media include derivatized dextrans, agarose, cellulose, polyacrylamide, specialty silicas, and the like. PEI, DEAE, QAE and Q derivatives are preferred.
• Exemplary chromatographic media include those media derivatized with phenyl, butyl, or octyl groups, such as Phenyl- Sepharose FF (Pharmacia), Toyopearl butyl 650 (Toso Haas, Montgomeryville, PA), Octyl-Sepharose (Pharmacia) and the like; or polyacrylic resins, such as Amberchrom CG 71 (Toso Haas) and the like.
• Suitable solid supports include glass beads, silica- based resins, cellulosic resins, agarose beads, cross-linked agarose beads, polystyrene beads, cross-linked polyacrylamide resins and the like that are insoluble under the conditions in which they are to be used. These supports may be modified with reactive groups that allow attachment of proteins by amino groups, carboxyl groups, sulfhydryl groups, hydroxyl groups and/or carbohydrate moieties.
• Examples of coupling chemistries include cyanogen bromide activation, N-hydroxysuccinimide activation, epoxide activation, sulfhydryl activation, hydrazide activation, and carboxyl and amino derivatives for carbodiimide coupling chemistries. These and other solid media are well known and widely used in the art, and are available from commercial suppliers. Selection of a particular method for polypeptide isolation and purification is a matter of routine design and is determined in part by the properties of the chosen support. See, for example, Affinity Chromatography: Principles & Methods (Pharmacia LKB Biotechnology 1988), and Doonan, Protein Purification Protocols (The Humana Press 1996).
• Zlmda6 isolation and purification can be devised by those of skill in the art.
• anti-Zlmda6 antibodies obtained as described below, can be used to isolate large quantities of protein by immunoaffinity purification.
• monoclonal antibody columns to purify interferons from recombinant cells and from natural sources has been described, for example, by Staehelin et al, J. Biol. Chem. 256:9150 (1981), and by Adolf et al, J. Biol Chem.
• polypeptides of the present invention can also be isolated by exploitation of particular properties.
• immobilized metal ion adsorption ( AC) chromatography can be used to purify histidine-rich proteins, including those comprising polyhistidine tags. Briefly, a gel is first charged with divalent metal ions to form a chelate [Sulkowski, Trends in Biochem. 3:1 (1985)]. Histidine-rich proteins will be adsorbed to this matrix with differing affinities, depending upon the metal ion used, and will be eluted by competitive elution, lowering the pH, or use of strong chelating agents.
• Zlmda6 polypeptides or fragments thereof may also be prepared through chemical synthesis, as described below. Zlmda6 polypeptides may be monomers or multimers; glycosylated or non-glycosylated; PEGylated or non- PEGylated; and may or may not include an initial methionine amino acid residue. 8. Chemical Synthesis of Zlmdao Polypeptides
• Zlmdao polypeptides of the present invention can also be synthesized by exclusive solid phase synthesis, partial solid phase methods, fragment condensation or classical solution synthesis.
• the polypeptides are preferably prepared by solid phase peptide synthesis, for example as described by Merrifield, J. Am. Chem. Soc. &5:2149 (1963).
• the synthesis is carried out with amino acids that are protected at the alpha- amino terminus.
• Trifunctional amino acids with labile side-chains are also protected with suitable groups to prevent undesired chemical reactions from occurring during the assembly of the polypeptides.
• the alpha-amino protecting group is selectively removed to allow subsequent reaction to take place at the amino-terminus. The conditions for the- removal of the alpha-amino protecting group do not remove the side-chain protecting groups.
• the "expressed protein ligation” method is a semi-synthesis variation of the ligation approach (see, for example, Muir et al, Proc. Nat'lAcad. Sci. USA 95:6105 (1998); Severinov and Muir, /. Biol. Chem. 273:16205 (1998)).
• synthetic peptides and protein cleavage fragments are linked to form the desired protein product.
• This method is particularly useful for the site-specific incorporation of unnatural amino acids (e.g., amino acids comprising biophysical or biochemical probes) into proteins.
• Affinity chromatography with a chitin resin is used to purify the expressed fusion protein, and the chemical ligation step is initiated by incubating the resin-bound protein with thiophenol and synthetic peptide in buffer. This mixture produces the in situ generation of a highly reactive phenyl ⁇ thioester derivative of the protein that rapidly ligates with the synthetic peptide to produce the desired semi-synthetic protein.
• a Zlmda6 variant will possess a Zlmdao biological activity, as determined by the in vitro assays described below.
• a polypeptide produced by a Zlmdao variant gene is considered to be a Zlmda6 agonist if the polypeptide exhibits a biological activity
• a Zlmda6 variant gene product that lacks biological activity may be a Zlmda ⁇ antagonist.
• These biologically inactive Zlmda6 variants can be initially identified on the basis of hybridization analysis, sequence identity determination, or by the ability to specifically bind anti-Zlmda6 antibody.
• a Zlmda6 antagonist can be further characterized by its ability to inhibit the biological response induced by Zlmdao or by a Zlmda6 agonist. This inhibitory effect may result, for example, from the competitive or non-competitive binding of the antagonist to the Zlmda6 receptor.
• Zlmda6 its agonists and antagonists are valuable in both in vivo and in vitro uses.
• cytokines can be used as components of defined cell culture media, alone or in combination with other cytokines and hormones, to replace serum that is commonly used in cell culture.
• Antagonists are also useful as research reagents for characterizing sites of interaction between Zlmda6 and its receptor.
• pharmaceutical compositions comprising Zlmdao antagonists can be used to inhibit Zlmdao activity.
• Zlmda6 analogs are agonists or antagonists having an amino acid sequence that is a mutation of the amino acid sequences disclosed herein.
• Zlmda6 analogs Another general class of Zlmda6 analogs is provided by anti-idiotype antibodies, and fragments thereof, as described below. Moreover, recombinant antibodies comprising anti-idiotype variable domains can be used as analogs (see, for example, Monfardini et al, Proc. Assoc. Am. Physicians 108:420 (1996)). Since the variable domains of anti- idiotype Zlmda ⁇ antibodies mimic Zlmdao, these domains can provide either Zlmda6 agonist or antagonist activity. A third approach to identifying Zlmdao analogs is provided by the use of combinatorial libraries.
• Zlmda6, its analogs, and anti-iodiotype Zlmda6 antibodies can be used to identify and to isolate Zlmdao receptors.
• proteins and peptides of the present invention can be immobilized on a column and used to bind receptor proteins from membrane preparations that are run over the column (Hermanson et al. (eds.), Immobilized Affinity Ligand Techniques, pages 195-202 (Academic Press 1992)).
• Radiolabeled or affinity labeled Zlmda6 polypeptides can also be used to identify or to localize Zlmda6 receptors in a biological sample (see, for example, Deutscher (ed.), Methods in Enzymol, vol. 182, pages 721-37 (Academic Press 1990); Branner et al, Ann. Rev. Biochem. 62:483 (1993); Fedan et al, Biochem.. Pharmacol 33:1167 (1984)). Also see, Narthakavi and Minocha, J. Gen. Virol 77:1875 (1996), who describe the use of anti-idiotype antibodies for receptor identification.
• a solid phase system can be used to identify a Zlmdao receptor, or an agonist or antagonist of a Zlmda6 receptor.
• a Zlmda6 polypeptide or Zlmdao fusion protein can be immobilized onto the surface of a receptor chip of a commercially available biosensor instrument (BIACORE, Biacore AB;
• a Zlmdao polypeptide or fusion protein is covalently attached, using amine or sulfhydryl chemistry, to dextran fibers that are attached to gold film within a flow cell.
• a test sample is then passed through the cell. If a receptor is present in the sample, it will bind to the immobilized polypeptide or fusion protein, causing a change in the refractive index of the medium, which is detected as a change in surface plasmon resonance of the gold film.
• This system allows the determination of on- and off-rates, from which binding affinity can be calculated, and assessment of stoichiometry of binding. This system can also be used to examine antibody-antigen interactions, and the interactions of other complement/anti-complement pairs.
• Antibodies to Zlmda ⁇ can be obtained, for example, using the product of a Zlmda6 expression vector or Zlmda6 isolated from a natural source as an antigen.
• Particularly useful anti-Zlmda6 antibodies "bind specifically" with Zlmdao.
• Antibodies are considered to be specifically binding if the antibodies exhibit at least one of the following two properties: (1) antibodies bind to Zlmdao with a threshold level of binding activity, and (2) antibodies do not significantly cross-react with polypeptides related to Zlmdao.
• antibodies specifically bind if they bind to a Zlmda6 polypeptide, peptide or epitope with a binding affinity (K a ) of 10 6 M “1 or greater, preferably 10 7 M “1 or greater, more preferably 10 8 M “1 or greater, and most preferably 10 9 M “1 or greater.
• K a binding affinity
• the binding affinity of an antibody can be readily determined by one of ordinary skill in the art, for example, by Scatchard analysis (Scatchard, Ann. NY Acad. Sci. 51:660 (1949)).
• antibodies do not significantly cross-react with related polypeptide molecules, for example, if they detect Zlmdao, but not known related polypeptides using a standard Western blot analysis. Examples of known related polypeptides are orthologs and proteins from the same species that are members of a protein family.
• Anti-Zlmda6 antibodies can be produced using antigenic Zlmda ⁇ epitope-bearing peptides and polypeptides.
• Antigenic epitope-bearing peptides and polypeptides of the present invention contain a sequence of at least nine, preferably between 15 to about 30 amino acids contained within SEQ ID NO: 2.
• peptides or polypeptides comprising a larger portion of an amino acid sequence of the invention, containing from 30 to 50 amino acids, or any length up to and including the entire amino acid sequence of a polypeptide of the invention, also are useful for inducing antibodies that bind with Zlmda6.
• amino acid sequence of the epitope-bearing peptide is selected to provide substantial solubility in aqueous solvents (i.e. , the sequence includes relatively hydrophilic residues, while hydrophobic residues are preferably avoided). Moreover, amino acid sequences containing proline residues may be also be desirable for antibody production.
• the Jameson- Wolf method predicts potential antigenic determinants by combining six major subroutines for protein structural prediction. Briefly, the Hopp- Woods method, Hopp et al, Proc. Nat'lAcad. Sci. USA 78:3824 (1981), was first used to identify amino acid sequences representing areas of greatest local hydrophilicity
• a surface contour value designated as the "antigenic index.”
• a peak broadening function was applied to the antigenic index, which broadens major surface peaks by adding 20, 40, 60, or 80% of the respective peak value to account for additional free energy derived from the mobility of surface regions relative to interior regions. This calculation was not applied, however, to any major peak that resides in a helical region, since helical regions tend to be less flexible.
• amino acids 14 to 45 of SEQ ID NO: 2 amino acids 37 to 69 (SEQ ID NO: 4), 63 to 87 (SEQ ID NO: 5), amino acids 80 to 103 (SEQ ID NO: 6), amino acids 80 to 119 (SEQ ID NO: 7), amino acids 93 to 125 (SEQ ID NO: 8), amino acids 115 to 151 (SEQ ID NO: 9), amino acids 135 to 168 (SEQ ID NO: 10), amino acids 165 to 217 (SEQ ID NO: 11), amino acids 214 to 251 (SEQ ID NO: 12), amino acids 249 to 279 (SEQ ID NO: 13), amino acids 249 to 289 (SEQ ID NO: 14), amino acids 272 to 304 (SEQ ID NO: 3), amino acids 37 to 69 (SEQ ID NO: 4), 63 to 87 (SEQ ID NO: 5), amino acids 80 to 103 (SEQ ID NO: 6), amino acids 80 to 119 (SEQ ID NO: 7), amino acids 93 to 125 (SEQ ID NO
• Polyclonal antibodies to recombinant Zlmda ⁇ protein or to Zlmdao isolated from natural sources can be prepared using methods well known to those of skill in the art. See, for example, Green et al, "Production of Polyclonal Antisera,” in Immunochemical Protocols (Manson, ed.), pages 1-5 (Humana Press 1992), and Williams et al., "Expression of foreign proteins in E. coli using plasmid vectors and purification of specific polyclonal antibodies," in DNA Cloning 2: Expression Systems, 2nd Edition, Glover et al. (eds.), page 15 (Oxford University Press 1995).
• the immunogenicity of a Zlmda6 polypeptide can be increased through the use of an adjuvant, such as alum (aluminum hydroxide) or Freund's complete or incomplete adjuvant.
• an adjuvant such as alum (aluminum hydroxide) or Freund's complete or incomplete adjuvant.
• Polypeptides useful for immunization also include fusion polypeptides, such as fusions of Zlmda6 or a portion thereof with an immunoglobulin polypeptide or with maltose binding protein.
• the polypeptide immunogen may be a full-length molecule or a portion thereof.
• polypeptide portion is "hapten-like,” such portion may be advantageously joined or linked to a macromolecular carrier (such as keyhole limpet hemocyanin (KLH), bovine serum albumin (BS A) or tetanus toxoid) for immunization.
• a macromolecular carrier such as keyhole limpet hemocyanin (KLH), bovine serum albumin (BS A) or tetanus toxoid
• an anti- Zlmda6 antibody of the present invention may also be derived from a subhuman primate antibody.
• General techniques for raising diagnostically and therapeutically useful antibodies in baboons may be found, for example, in Goldenberg et al., international patent publication No. WO 91/11465, and in Losman et al, Int. J. Cancer 46:310 (1990).
• monoclonal anti-Zlmda ⁇ antibodies can be generated.
• Rodent monoclonal antibodies to specific antigens may be obtained by methods known to those skilled in the art [see, for example, Kohler et al, Nature 256:495 (1975), Coligan et al (eds.), Current Protocols in Immunology, Vol. 1, pages 2.5.1-2.6.7 (John Wiley & Sons 1991) ("Coligan”)], Picksley et al, "Production of monoclonal antibodies against proteins expressed in E. coli," in DNA Cloning 2: Expression
• monoclonal antibodies can be obtained by injecting mice with a composition comprising an Zlmda6 gene product, verifying the presence of antibody production by removing a serum sample, removing the spleen to obtain B-lymphocytes, fusing the B-lymphocytes with myeloma cells to produce hybridomas, cloning the hybridomas, selecting positive clones which produce antibodies to the antigen, culturing the clones that produce antibodies to the antigen, and isolating the antibodies from the hybridoma cultures.
• an anti-Zlmda6 antibody ofthe present invention maybe derived from a human monoclonal antibody.
• Human monoclonal antibodies are obtained from transgenic mice that have been engineered to produce specific human antibodies in response to antigenic challenge. L this technique, elements of the human heavy and light chain locus are introduced into strains of mice derived from embiyonic stem cell lines that contain targeted disruptions ofthe endogenous heavy chain and light chain loci.
• the transgenic mice can synthesize human antibodies specific for human antigens, and the mice can be used to produce human antibody-secreting hybridomas. Methods for obtaining human antibodies from transgenic mice are described, for example, by Green et al, Nature Genet. 7:13 (1994), Lonberg et al, Nature 368:856 (1994), and Taylor et al, Int. Immun. 6:519 (1994).
• Monoclonal antibodies can be isolated and purified from hybridoma cultures by a variety of well-established techniques. Such isolation techniques include affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography [see, for example, Coligan at pages 2.7.1-2.7.12 and pages 2.9.1-2.9.3; Baines et al, "Purification of Immunoglobulin G (IgG),” in Methods in Molecular Biology, Vol. 10, pages 79-104 (The Humana Press, Inc. 1992)]. For particular uses, it may be desirable to prepare fragments of anti-
• antibody fragments can be obtained, for example, by proteolytic hydrolysis of the antibody.
• Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods.
• antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab') .
• This fragment can be further cleaved using a thiol reducing agent to produce 3.5S Fab' monovalent fragments.
• the cleavage reaction can be performed using a blocking group for the sulfhydryl groups that result from cleavage of disulfide linkages.
• an enzymatic cleavage using pepsin produces two monovalent Fab fragments and an Fc fragment directly.
• Fv fragments comprise an association of V H and V L chains. This association can be noncovalent, as described by Inbar et al, Proc. Nat'l Acad. Sci. USA 69:2659 (1972).
• the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde (see, for example, Sandhu, Crit. Rev. Biotech. 12:431 (1992)).
• the Fv fragments may comprise V H and V L chains which are connected by a peptide linker.
• These single-chain antigen binding proteins are prepared by constructing a structural gene comprising DNA sequences encoding the V H and V domains which are connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell, such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains.
• a scFV can be obtained by exposing lymphocytes to Zlmda ⁇ polypeptide in vitro, and selecting antibody display libraries in phage or similar vectors (for instance, through use of immobilized or labeled Zlmdao protein or peptide).
• Genes encoding polypeptides having potential Zlmdao polypeptide-binding domains can be obtained by screening random peptide libraries displayed on phage (phage display) or on bacteria, such as E. coli.
• Nucleotide sequences encoding the polypeptides can be obtained in a number of ways, such as through random mutagenesis and random polynucleotide synthesis.
• random peptide display libraries can be used to screen for peptides that interact with a known target which can be a protein or polypeptide, such as a ligand or receptor, a biological or synthetic macromolecule, or organic or inorganic substances.
• a known target can be a protein or polypeptide, such as a ligand or receptor, a biological or synthetic macromolecule, or organic or inorganic substances.
• Techniques for creating and screening such random peptide display libraries are known in the art [(Ladner et al, U.S. Patent No. 5,223,409, Ladner et al, U.S. Patent No. 4,946,778, Ladner et al, U.S. Patent No. 5,403,484, Ladner et al, U.S. Patent No. 5,571,698, and Kay et al, Phage Display of Peptides and Proteins (Academic Press, Inc.
• Random peptide display libraries can be screened using the Zlmdao sequences disclosed herein to identify proteins that bind to Zlmdao.
• CDR peptides (“minimal recognition units") can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells [see, for example, Larrick et al, Methods: A Companion to Methods in Enzymology 2:106 (1991), Courtenay-Luck, "Genetic Manipulation of Monoclonal Antibodies," in
• an anti-Zlmda ⁇ antibody may be derived from a
• humanized monoclonal antibody Humanized monoclonal antibodies are produced by transferring mouse complementary determining regions from heavy and light variable chains of the mouse immunoglobulin into a human variable domain. Typical residues of human antibodies are then substituted in the framework regions of the murine counterparts. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the immunogenicity of murine constant regions. General techniques for cloning murine immunoglobulin variable domains are described, for example, by Orlandi et al, Proc. Nat'l Acad. Sci. USA 86:3833 (1989).
• Polyclonal anti-idiotype antibodies can be prepared by immunizing animals with anti-Zlmda ⁇ antibodies or antibody fragments, using standard techniques. See, for example, Green et al, "Production of Polyclonal Antisera,” in Methods In Molecular Biology: Immunochemical Protocols, Manson (ed.), pages 1-12 (Humana Press 1992). Also, see Coligan at pages 2.4.1-2.4.7.
• monoclonal anti- idiotype antibodies can be prepared using anti-Zlmda ⁇ antibodies or antibody fragments as immunogens with the techniques, described above.
• humanized anti-idiotype antibodies or subhuman primate anti-idiotype antibodies can be prepared using the above-described techniques.
• Nucleic acid molecules can be used to detect the expression of an Zlmda6 gene in a biological sample.
• probe molecules can include murine Zlmdao encoding sequences
• preferred probe molecules include double-stranded nucleic acid molecules comprising the nucleotide sequence of SEQ ID NO: 1, or a fragment thereof, as well as single-stranded nucleic acid molecules having the complement of the nucleotide sequence of SEQ ID NO: 1 or a fragment thereof.
• Probe molecules may be DNA, RNA, oligonucleotides, and the like. In a basic assay, a single-stranded probe molecule is incubated with
• RNA isolated from a biological sample, under conditions of temperature and ionic strength that promote base pairing between the probe and target Zlmdao RNA species. After separating unbound probe from hybridized molecules, the amount of hybrids is detected.
• Illustrative biological samples include blood, urine, saliva, tissue biopsy, and autopsy material.
• RNA detection include northern analysis and dot/slot blot hybridization (see, for example, Ausubel (1995) at pages 4-1 to 4-27, and Wu et al (eds.), "Analysis of Gene Expression at the RNA Level,” in Methods in Gene Biotechnology, pages 225-239 (CRC Press, hie. 1997)).
• Nucleic acid probes can be detectably labeled with radioisotopes such as 32 P or 35 S.
• Zlmda6 RNA can be detected with a nonradioactive hybridization method (see, for example, Isaac (ed.), Protocols for Nucleic Acid Analysis by Nonradioactive Probes (Humana Press, Inc. 1993)).
• nonradioactive detection is achieved by enzymatic conversion of chromogenic or chemiluminescent substrates.
• Illustrative nonradioactive moieties include biotin, fluorescein, and digoxigenin.
• Z/ d ⁇ oligonucleotide probes are also useful for in vivo diagnosis.
• 18 F-labeled oligonucleotides can be administered to a subject and visualized by positron emission tomography [Tavitian et al, Nature Medicine 4:461 (1998)].
• PCR polymerase chain reaction
• Standard techniques for performing PCR are well-known [see, generally, Mathew (ed.), Protocols in Human Molecular Genetics (Humana Press, Inc. 1991), White (ed.), PCR Protocols: Current Methods and Applications (Humana Press, Inc. 1993), Cotter (ed.), Molecular Diagnosis of Cancer (Humana Press, Inc. 1996), Hanausek and Walaszek (eds.), Tumor Marker Protocols (Humana Press, Inc. 1998), Lo (ed.), Clinical Applications of PCR (Humana Press, Inc. 1998), and Meltzer (ed.), PCR in Bioanalysis (Humana Press, Inc. 1998)].
• RNA is isolated from a biological sample, reverse transcribed to cDNA, and the cDNA is incubated with Zlmdao primers [see, for example, Wu et al. (eds.), "Rapid Isolation of Specific cDNAs or Genes by PCR,” in Methods in Gene Biotechnology, pages 15-28 (CRC Press, Inc. 1997)].
• Zlmdao primers see, for example, Wu et al. (eds.), "Rapid Isolation of Specific cDNAs or Genes by PCR," in Methods in Gene Biotechnology, pages 15-28 (CRC Press, Inc. 1997).
• RNA is isolated from biological sample using, for example, the gunadinium-thiocyanate cell lysis procedure described above.
• a solid-phase technique can be used to isolate mRNA from a cell lysate.
• a reverse transcription reaction can be primed with the isolated RNA using random oligonucleotides, short homopolymers of dT, or Z/md ⁇ tfanti-sense oligomers.
• Oligo-dT primers offer the advantage that various mRNA nucleotide sequences are amplified that can provide control target sequences.
• Zlmdao sequences are amplified by the polymerase chain reaction using two flanking oligonucleotide primers that are typically 20 bases in length.
• PCR amplification products can be detected using a variety of approaches.
• PCR products can be fractionated by gel electrophoresis, and visualized by ethidium bromide staining.
• fractionated PCR products can be transferred to a membrane, hybridized with a detectably-labeled Zlmdao probe, and examined by autoradiography.
• Additional alternative approaches include the use of digoxigenin-labeled deoxyribonucleic acid triphosphates to provide chemiluminescence detection, and the C-TRAK colorimetric assay.
• CPT cycling probe technology
• NASBA nucleic acid sequence-based amplification
• CATCH cooperative amplification of templates by cross-hybridization
• LCR ligase chain reaction
• Zlmda6 probes and primers can also be used to detect and to localize Zlmda6 gene expression in tissue samples.
• Methods for such in situ hybridization are well-known to those of skill in the art (see, for example, Choo (ed.), In Situ Hybridization Protocols (Humana Press, Inc. 1994), Wu et al (eds.), "Analysis of Cellular DNA or Abundance of mRNA by Radioactive In Situ Hybridization (RISH),” in Methods in Gene Biotechnology, pages 259-278 (CRC Press, Inc. 1997), and Wu et al.
• Nucleic acid molecules comprising Zlmda6 nucleotide sequences can also be used to determine whether a subject's chromosomes contain a mutation in the Zlmda6 gene.
• Detectable chromosomal aberrations at the Zlmdao gene locus include, but are not limited to, aneuploidy, gene copy number changes, insertions, deletions, restriction site changes and rearrangements. Of particular interest are genetic alterations that inactivate the Zlmda6 gene.
• Aberrations associated with the Zlmda6 locus can be detected using nucleic acid molecules of the present invention by employing molecular genetic techniques, such as restriction fragment length polymorphism (RFLP) analysis, short tandem repeat (STR) analysis employing PCR techniques, amplification-refractory mutation system analysis (ARMS), single-strand conformation polymorphism (SSCP) detection, RNase cleavage methods, denaturing gradient gel electrophoresis, fluorescence-assisted mismatch analysis (FAMA), and other genetic analysis techniques known in the art [see, for example, Mathew (ed.), Protocols in Human Molecular Genetics (Humana Press, Inc.
• RNA is isolated from a biological sample, and used to synthesize cDNA. PCR is then used to amplify the Zlmdao target sequence and to introduce an RNA polymerase promoter, a translation initiation sequence, and an in-frame ATG triplet. PCR products are transcribed using an RNA polymerase, and the transcripts are translated in vitro with a T7-coupled reticulocyte lysate system.
• the translation products are then fractionated by SDS-PAGE to determine the lengths ofthe translation products.
• the protein truncation test is described, for example, by Dracopoli et al. (eds.), Current Protocols in Human Genetics, pages 9.11.1 - 9.11.18 (John Wiley & Sons 1998).
• Zlmdao protein is isolated from a subject, the molecular weight of the isolated Zlmdao protein is determined, and then compared with the molecular weight a normal Zlmdao protein, such as a protein having the amino acid sequence of SEQ ID NO: 2.
• a substantially lower molecular weight for the isolated Zlmdao protein is indicative that the protein is truncated.
• substantially lower molecular weight refers to at least about 10 percent lower, and preferably, at least about 25 percent lower.
• the Zlmdao protein may be isolated by various procedures known in the art including immunoprecipitation, solid phase radioimmunoassay, enzyme-linked immunosorbent assay, or Western blotting.
• the molecular weight of the isolated Zlmdao protein can be determined using standard techniques, such as SDS-polyacrylamide gel electrophoresis.
• kits for performing a diagnostic assay for Zlmda6 gene expression or to detect mutations in the Zlmda6gea comprise nucleic acid probes, such as double-stranded nucleic acid molecules comprising the nucleotide sequence of SEQ ID NO: 1, or a fragment thereof, as well as single-stranded nucleic acid molecules having the complement of the nucleotide sequence of SEQ ID NO: 1, or a fragment thereof.
• Probe molecules may be DNA, RNA, oligonucleotides, and the like.
• Kits may comprise nucleic acid primers for performing PCR. Preferably, such a kit contains all the necessary elements to perform a nucleic acid diagnostic assay described above.
• a kit will comprise at least one container comprising a Zlmda6 probe or primer.
• the kit may also comprise a second container comprising one or more reagents capable of indicating the presence of Zlmda6 sequences.
• indicator reagents include detectable labels such as radioactive labels, fluorochromes, chemiluminescent agents, and the like.
• a kit may also comprise a means for conveying to the user that the Zlmdao probes and primers are used to detect Zlmdao gene expression.
• written instructions may state that the enclosed nucleic acid molecules can be used to detect either a nucleic acid molecule that encodes Zlmdao, or a nucleic acid molecule having a nucleotide sequence that is complementary to a Zlmda ⁇ -encoding nucleotide sequence.
• the written material can be applied directly to a container, or the written material can be provided in the form of a packaging insert.
• the present invention contemplates the use of anti-Zlmda ⁇ antibodies to screen biological samples in vitro for the presence of Zlmdao.
• anti-Zlmda ⁇ antibodies are used in liquid phase. For example, the presence of
• Zlmdao in a biological sample can be tested by mixing the biological sample with a trace amount of labeled Zlmdao and an anti-Zlmda ⁇ antibody under conditions that promote binding between Zlmdao and its antibody.
• Complexes of Zlmdao and anti-Zlmda ⁇ in the sample can be separated from the reaction mixture by contacting the complex with an immobilized protein which binds with the antibody, such as an Fc antibody or
• Staphylococcus protein A The concentration of Zlmdao in the biological sample will be inversely proportional to the amount of labeled Zlmdao bound to the antibody and directly related to the amount of free-labeled Zlmdao.
• Illustrative biological samples include blood, urine, saliva, tissue biopsy, and autopsy material.
• in vitro assays can be performed in which anti-Zlmda ⁇ antibody is bound to a solid-phase carrier.
• antibody can be attached to a polymer, such as aminodextran, in order to link the antibody to an insoluble support such as a polymer-coated bead, a plate or a tube.
• an insoluble support such as a polymer-coated bead, a plate or a tube.
• anti-Zlmda ⁇ antibodies can be used to detect
• Immunochemical detection can be performed by contacting a biological sample with an anti-Zlmda ⁇ antibody, and then contacting the biological sample with a detectably labeled molecule that binds to the antibody.
• the detectably labeled molecule can comprise an antibody moiety that binds to anti-Zlmda ⁇ antibody.
• the anti-Zlmda ⁇ antibody can be conjugated with avidin streptavidin (or biotin) and the detectably labeled molecule can comprise biotin (or avidin/streptavidin).
• an anti-Zlmda ⁇ antibody can be conjugated with a detectable label to form an anti-Zlmda ⁇ immunoconjugate.
• detectable labels include, for example, a radioisotope, a fluorescent label, a chemiluminescent label, an enzyme label, a bioluminescent label or colloidal gold. Methods of making and detecting such detectably labeled immunoconjugates are described in more detail below.
• the detectable label can be a radioisotope that is detected by autoradiography.
• Isotopes that are particularly useful for the purpose of the present invention are 3 H, 125 1, 131 1, 35 S and 14 C.
• Anti-Zlmda ⁇ immunoconjugates can also be labeled with a fluorescent compound.
• the presence of a fluorescently labeled antibody is determined by exposing the immunoconjugate to light ofthe proper wavelength and detecting fhe resultant fluorescence.
• Fluorescent labeling compounds include fluorescein isothiocyanate, rhoda- mine, phycoerytherin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.
• anti-Zlmda ⁇ immunoconjugates can be detectably labeled by coupling an antibody component to a chemiluminescent compound.
• the presence of the chemiluminescent-tagged immunoconjugate is determined by detecting the presence of luminescence that arises during the course of a chemical reaction.
• chemiluminescent labeling compounds include luminol, isoluminol, an aromatic acridinium ester, an imidazole, an acridinium salt and an oxalate ester.
• Bioluminescent compound can be used to label anti-Zlmda ⁇ immunoconjugates of the present invention.
• Bioluminescence is a type of chemiluminescence found in biological systems in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence.
• Bioluminescent compounds that are useful for labeling include luciferin, luciferase and aequorin.
• anti-Zlmda ⁇ immunoconjugates can be detectably labeled by linking an anti-Zlmda ⁇ antibody component to an enzyme.
• the enzyme moiety reacts with the substrate to produce a chemical moiety that can be detected, for example, by spectrophotometric, fluorometric or visual means.
• enzymes that can be used to detectably label polyspecific immunoconjugates include ⁇ -galactosidase, glucose oxidase, peroxidase and alkaline phosphatase.
• marker moieties to anti-Zlmda ⁇ antibodies can be accomplished using standard techniques. Typical methodology in this regard is described by Kennedy etal, Clin. Chim. Acta 70:1 (1976), Schurs etal, Clin. Chim. Ada 81:1 (1977), Shih et al, Int'U. Cancer 46:1101 (1990), Stein etal, Cancer Res. 50:1330 (1990), and Coligan, supra.
• biotin- or FITC-labeled Zlmdao can be used to identify cells that bind Zlmdao. Such can binding can be detected, for example, using flow cytometry.
• kits for performing an immunological diagnostic assay for Zlmdao gene expression comprise at least one container comprising an anti-Zlmda ⁇ antibody, or antibody fragment.
• a kit may also comprise a second container comprising one or more reagents capable of indicating the presence of Zlmdao antibody or antibody fragments. Examples of such indicator reagents include detectable labels such as a radioactive label, a fluorescent label, a chemiluminescent label, an enzyme label, a bioluminescent label, colloidal gold, and the like.
• a kit may also comprise a means for conveying to the user that Zlmdao antibodies or antibody fragments are used to detect Zlmdao protein. For example, written instructions may state that the enclosed antibody or antibody fragment can be used to detect Zlmdao. The written material can be applied directly to a container, or the written material can be provided in the form of a packaging insert.
• the dosage of administered Zlmdao will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition and previous medical history. Typically, it is desirable to provide the recipient with a dosage of Zlmdao that is in the range of from about 1 pg/kg to 10 mg/kg (amount of agent/body weight of patient), although a lower or higher dosage also may be administered as circumstances dictate.
• Administration of a molecule having Zlmdao activity to a subject can be intravenous, intraarterial, intraperitoneal, intramuscular, subcutaneous, intrapleural, intrathecal, by perfusion through a regional catheter, or by direct intralesional injection.
• the administration may be by continuous infusion or by single or multiple boluses.
• Zlmdao can be administered as a controlled release formulation. Additional routes of administration include oral, dermal, mucosal-membrane, pulmonary, and transcutaneous.
• Oral delivery is suitable for polyester microspheres, zein microspheres, proteinoid microspheres, polycyanoacrylate microspheres, and lipid-based systems [see, for example, DiBase and Morrel, "Oral Delivery of Microencapsulated Proteins," in Protein Delivery: Physical Systems, Sanders and Hendren (eds.), pages 255-288
• a pharmaceutical composition comprising a protein, polypeptide, or peptide having Zlmdao activity can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby the therapeutic proteins are combined in a mixture with a pharmaceutically acceptable carrier.
• a composition is said to be a "pharmaceutically acceptable carrier" if its administration can be tolerated by a recipient patient.
• Sterile phosphate-buffered saline is one example of a pharmaceutically acceptable carrier.
• Other suitable carriers are well known to those in the art. See, for example, Gennaro (ed.), Remington's Pharmaceutical Sciences, 19th Edition (Mack Publishing Company 1995).
• molecules having Zlmdao activity and a pharmaceutically acceptable carrier are administered to a patient in a therapeutically effective amount.
• a combination of a protein, polypeptide, or peptide having Zlmdao activity and a pharmaceutically acceptable carrier is said to be administered in a "therapeutically effective amount" if the amount administered is physiologically significant.
• An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient.
• a pharmaceutical composition comprising molecules having Zlmda ⁇ activity can be furnished in liquid form, in an aerosol, or in solid form. Proteins having Zlmdao activity, such as human or murine Zlmdao, can be administered as a conjugate with a pharmaceutically acceptable water- soluble polymer moiety, as described above. Liquid forms, including liposome- encapsulated formulations, are illustrated by injectable solutions and oral suspensions.
• Exemplary solid forms include capsules, tablets, and controlled-release forms, such as a miniosmotic pump or an implant.
• Other dosage forms can be devised by those skilled in the art, as shown, for example, by Ansel and Popovich, Pharmaceutical Dosage Forms and Drug Delivery Systems, 5 th Edition (Lea & Febiger 1990), Gennaro (ed.), Remington's Pharmaceutical Sciences, 19 th Edition (Mack Publishing Company 1995), and by Ranade and Hollinger, Drug Delivery Systems (CRC Press 1996).
• Zlmdao pharmaceutical compositions may be supplied as a kit comprising a container that comprises Zlmdao, a Zlmdao agonist, or a Zlmdao antagonist (e.g., an anti-Zlmda ⁇ antibody or antibody fragment).
• Zlmdao can be provided in the form of an injectable solution for single or multiple doses, or as a sterile powder that will be reconstituted before injection.
• a kit can include a dry-powder disperser, liquid aerosol generator, or nebulizer for administration of a therapeutic polypeptide.
• Such a kit may further comprise written information on indications and usage of the pharmaceutical composition. Moreover, such information may include a statement that the Zlmdao composition is contraindicated in patients with known hypersensitivity to Zlmdao.
• Immunomodulator genes can be introduced into a subject to enhance immunological responses.
• immunomodulator gene therapy has been examined in model systems using vectors that express IL-2, IL-3, IL-4, IL-6, IL- 10, IL-12, IL-15, tumor necrosis factor- ⁇ , or granulocyte-macrophage colony- stimulating factor (see, for example, Cao et al, J. Gastroenterol Hepatol. 11:1053
• a therapeutic expression vector can be provided that inhibits Zlmdao gene expression, such as an anti-sense molecule, a ribozyme, or an external guide sequence molecule.
• cells are isolated from a subject, transfected with a vector that expresses a Zlmdao gene, and then transplanted into the subject.
• a Zlmda6 gene an expression vector is constructed in which a nucleotide sequence encoding a Zlmda6 gene is operably linked to a core promoter, and optionally a regulatory element, to control gene transcription.
• a core promoter a promoter that controls the expression of a Zlmda6 gene transcription.
• a Zlmda6geo& can be delivered using recombinant viral vectors, including for example, adenoviral vectors [e.g., Kass-Eisler et al, Proc. Nat'l
• herpes viral vectors e.g., U.S. Patent ⁇ os. 4,769,331, 4,859,587, 5,288,641 and 5,328,688
• parvo virus vectors Kelpes viral vectors
• pox virus vectors [Ozaki et al, Biochem. Biophys. Res. Comm. 193:653 (1993), Panicali and Paoletti, Proc. Nat'l Acad. Sci.
• pox viruses such as canary pox virus or vaccinia virus [Fisher-Hoch et al, Proc. Nat'lAcad. Sci. USA 86:311 (1989), and Flexner etal, Ann. N.Y. Acad. Sci. 569:86 (1989)]
• retroviruses e.g., Baba etal, J. Neurosurg 79:129 (1993), Ram et al, Cancer Res. 53:83 (1993), Takamiya et al, J. Neurosci. Res 33:493 (1992), Vile and Hart, Cancer Res. 53:962 (1993), Vile and Hart, Cancer Res.
• adenovirus a double-stranded DNA virus
• a viral particle which contains the viral vector may be utilized in the methods and compositions described below.
• adenovirus a double-stranded DNA virus
• Douglas and Curiel Science & Medicine 4:44 (1997).
• the adenovirus system offers several advantages including: (i) the ability to accommodate relatively large DNA inserts, (ii) the ability to be grown to high-titer, (iii) the ability to infect a broad range of mammalian cell types, and (iv) the ability to be used with many different promoters including ubiquitous, tissue specific, and regulatable promoters.
• adeno viruses can be administered by intravenous injection, because the viruses are stable in the bloodstream.
• adenovirus vectors where portions of the adenovirus genome are deleted, inserts are incorporated into the viral DNA by direct ligation or by homologous recombination with a co-transfected plasmid.
• the essential El gene is deleted from the viral vector, and the virus will not replicate unless the El gene is provided by the host cell.
• adenovirus When intravenously administered to intact animals, adenovirus primarily targets the liver. Although an adenoviral delivery system with an El gene deletion cannot replicate in the host cells, the host's tissue will express and process an encoded heterologous protein. Host cells will also secrete the heterologous protein if the corresponding gene includes a secretory signal sequence. Secreted proteins will enter the circulation from tissue that expresses the heterologous gene (e.g., the highly vascularized liver).
• adenoviral vectors containing various deletions of viral genes can be used to reduce or eliminate immune responses to the vector.
• Such adenoviruses are El -deleted, and in addition, contain deletions of E2A or E4 [Lusky et al, J. Virol. 72:2022 (1998); Raper et al, Human Gene Therapy 9:671 (1998)].
• the deletion of E2b has also been reported to reduce immune responses [Amalfitano et al, J. Virol. 72:926 (1998)].
• By deleting the entire adenovirus genome very large inserts of heterologous DNA can be accommodated.
• High titer stocks of recombinant viruses capable of expressing a therapeutic gene can be obtained from infected mammalian cells using standard methods.
• recombinant HSV can be prepared in Vero cells, as described by Brandt et al, J. Gen. Virol 72:2043 (1991), Herold et Z., J. Gen. Virol. 75:1211 (1994), Visalli and Brandt, Virology 185:419 (1991), Grau et al, Invest. Ophthalmol
• an expression vector comprising a Zlmda6 gene can be introduced into a subject's cells by lipofection in vivo using liposomes.
• Synthetic cationic lipids can be used to prepare liposomes for in vivo transfection of a gene encoding a marker [Feigner et al, Proc. Nat'lAcad. Sci. USA 84:1413 (1987); Mackey et al, Proc. Nat'l Acad. Sci.
• Liposomes can be used to direct transfection to particular cell types, which is particularly advantageous in a tissue with cellular heterogeneity, such as the pancreas, liver, kidney, and brain.
• Lipids may be chemically coupled to other molecules for the purpose of targeting.
• Targeted peptides e.g., hormones or neurotransmitters
• proteins such as antibodies, or non-peptide molecules can be coupled to liposomes chemically.
• Electroporation is another alternative mode of administration.
• Aihara and Miyazaki Nature Biotechnology 16:861 (1998), have demonstrated the use of in vivo electroporation for gene transfer into muscle.
• a therapeutic gene may encode a Zlmdao anti-sense RNA that inhibits the expression of Zlmdao.
• Suitable sequences for anti-sense molecules can be derived from the nucleotide sequences of Zlmda ⁇ disclosed herein.
• an expression vector can be constructed in which a regulatory element is operably linked to a nucleotide sequence that encodes a ribozyme.
• Ribozymes can be designed to express endonuclease activity that is directed to a certain target sequence in a mRNA molecule (see, for example, Draper and Macejak, U.S. Patent No. 5,496,698, McSwiggen, U.S. Patent No. 5,525,468, Chowrira and McSwiggen, U.S. Patent No. 5,631,359, and Robertson and Goldberg, U.S. Patent No. 5,225,337).
• ribozymes include nucleotide sequences that bind with ZImda ⁇ mRNA.
• expression vectors can be constructed in which a regulatory element directs the production of RNA transcripts capable of promoting RNase P-mediated cleavage of mRNA molecules that encode an Zlmdao gene.
• an external guide sequence can be constructed for directing the endogenous ribozyme, RNase P, to a particular species of intracellular mRNA, which is subsequently cleaved by the cellular ribozyme (see, for example, Altaian et al, U.S. Patent No. 5,168,053, Yuan etal, Science 263:1269 (1994), Pace et al, international publication No. WO 96/18733, George et al, international publication No.
• the external guide sequence comprises a ten to fifteen nucleotide sequence complementary to Zlmda6 mRNA, and a 3'-NCCA nucleotide sequence, wherein N is preferably a purine.
• the external guide sequence transcripts bind to the targeted mRNA species by the formation of base pairs between the mRNA and the complementary external guide sequences, thus promoting cleavage of mRNA by RNase P at the nucleotide located at the 5'-side of the base-paired region.
• the dosage of a composition comprising a therapeutic vector having a Zlmda6 nucleotide acid sequence, such as a recombinant virus will vary depending upon such factors as the subject's age, weight, height, sex, general medical condition and previous medical history.
• Suitable routes of administration of therapeutic vectors include intravenous injection, intraarterial injection, intraperitoneal injection, and intramuscular injection.
• a composition comprising viral vectors, non-viral vectors, or a combination of viral and non- viral vectors of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby vectors or viruses are combined in a mixture with a pharmaceutically acceptable carrier.
• a composition such as phosphate-buffered saline is said to be a "pharmaceutically acceptable carrier” if its administration can be tolerated by a recipient subject.
• suitable carriers are well-known to those in the art [see, for example, Remington's Pharmaceutical Sciences, 19th Ed. (Mack Publishing Co. 1995), and Gilman's the Pharmacological Basis of Therapeutics, 7th Ed. (MacMillan Publishing Co. 1985)] .
• a therapeutic gene expression vector, or a recombinant virus comprising such a vector, and a pharmaceutically acceptable carrier are administered to a subject in a therapeutically effective amount.
• a combination of an expression vector (or virus) and a pharmaceutically acceptable carrier is said to be administered in a "therapeutically effective amount" if the amount administered is physiologically significant.
• An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient subject
• the therapy is preferably somatic cell gene therapy. That is, the preferred treatment of a human with a therapeutic gene expression vector or a recombinant virus does not entail introducing into cells a nucleic acid molecule that can form part of a human germ line and be passed onto successive generations (i.e., human germ line gene therapy). 15. Production of Transgenic Mice
• Transgenic mice can be engineered to over-express the human or murine Zlmda6genc in all tissues or under the control of a tissue-specific or tissue-preferred regulatory element. These over-producers of Zlmdao can be used to characterize the phenotype that results from over-expression, and the transgenic animals can serve as models for human disease caused by excess Zlmdao. Transgenic mice that over-express Zlmdao also provide model bioreactors for production of Zlmdao in the milk or blood of larger animals.
• a method for producing a transgenic mouse that expresses a Zlmda6 gene can begin with adult, fertile males (studs) [B6C3f 1, 2-8 months of age (Taconic Farms, Germantown, NY)], vasectomized males (duds) [B6D2fl, 2-8 months, (Taconic Farms)], prepubescent fertile females (donors) [B6C3fl, 4-5 weeks, (Taconic Farms)] and adult fertile females (recipients) [B6D2fl, 2-4 months, (Taconic Farms)].
• the donors are acclimated for one week and then injected with approximately 8 IU/mouse of Pregnant Mare's Serum gonadotrophin (Sigma Chemical Company; St. Louis, MO) IP., and 46-47 hours later, 8 IU/mouse of human Chorionic Gonadotropin (hCG (Sigma)) LP. to induce superovulation.
• Donors are mated with studs subsequent to hormone injections. Ovulation generally occurs within 13 hours of hCG injection. Copulation is confirmed by the presence of a vaginal plug the morning following mating.
• Fertilized eggs are collected under a surgical scope.
• the oviducts are collected and eggs are released into urinanalysis slides containing hyaluronidase (Sigma). Eggs are washed once in hyaluronidase, and twice in Whitten's W640 medium
• Plasmid DNA is microinjected into harvested eggs contained in a drop of W640 medium overlaid by warm, CO 2 -equilibrated mineral oil.
• the DNA is drawn into an injection needle (pulled from a 0.75mm ID, 1mm OD borosilicate glass capillary), and injected into individual eggs. Each egg is penetrated with the injection needle, into one or both of the haploid pronuclei. Picoliters of DNA are injected into the pronuclei, and the injection needle withdrawn without coming into contact with the nucleoli. The procedure is repeated until all the eggs are injected.
• Successfully microinjected eggs are transferred into an organ tissue-culture dish with pre-gassed W640 medium for storage overnight in a 37°C/5% CO 2 incubator.
• two-cell embryos are transferred into pseudopregnant recipients.
• the recipients are identified by the presence of copulation plugs, after copulating with vasectomized duds.
• Recipients are anesthetized and shaved on the dorsal left side and transferred to a surgical microscope.
• a small incision is made in the skin and through the muscle wall in the middle of the abdominal area outlined by the ribcage, the saddle, and the hind leg, midway between knee and spleen.
• the reproductive organs are exteriorized onto a small surgical drape.
• the fat pad is stretched out over the surgical drape, and a baby serrefine (Roboz, Rockville, MD) is attached to the fat pad and left hanging over the back of the mouse, preventing the organs from sliding back in.
• a baby serrefine Robot, Rockville, MD
• 12-17 healthy two-cell embryos from the previous day's injection are transferred into the recipient.
• the swollen ampulla is located and holding the oviduct between the ampulla and the bursa, a nick in the oviduct is made with a 28 g needle close to the bursa, making sure not to tear the ampulla or the bursa.
• the pipette is transferred into the nick in the oviduct, and the embryos are blown in, allowing the first air bubble to escape the pipette.
• the fat pad is gently pushed into the peritoneum, and the reproductive organs allowed to slide in.
• the peritoneal wall is closed with one suture and the skin closed with a wound clip.
• the mice recuperate on a 37°C slide warmer for a minimum of four hours.
• the recipients are returned to cages in pairs, and allowed 19-21 days gestation. After birth, 19-21 days postpartum is allowed before weaning.
• the weanlings are sexed and placed into separate sex cages, and a 0.5 cm biopsy (used for genotyping) is snipped off the tail with clean scissors.
• Genomic DNA is prepared from the tail snips using, for example, a QIAGEN DNEASY kit following the manufacturer's instructions. Genomic DNA is analyzed by PCR using primers designed to amplify a Zlmdao gene or a selectable marker gene that was introduced in the same plasmid. After animals are confirmed to be transgenic, they are back-crossed into an inbred strain by placing a transgenic female with a wild-type male, or a transgenic male with one or two wild-type female(s). As pups are born and weaned, the sexes are separated, and their tails snipped for genotyping. To check for expression of a transgene in a live animal, a partial hepatectomy is performed.
• a surgical prep is made of the upper abdomen directly below the zyphoid process. Using sterile technique, a small 1.5-2 cm incision is made below the sternum and the left lateral lobe of the liver exteriorized. Using 4-0 silk, a tie is made around the lower lobe securing it outside the body cavity. An atraumatic clamp is used to hold the tie while a second loop of absorbable Dexon (American Cyanamid; Wayne, N. J.) is placed proximal to the first tie. A distal cut is made from the Dexon tie and approximately 100 mg of the excised liver tissue is placed in a sterile petri dish.
• the excised liver section is transferred to a 14 ml polypropylene round bottom tube and snap frozen in liquid nitrogen and then stored on dry ice.
• the surgical site is closed with suture and wound clips, and the animal's cage placed on a 37°C heating pad for 24 hours post operatively.
• the animal is checked daily post operatively and the wound clips removed 7-10 days after surgery.
• the expression level of Zlmdao mRNA is examined for each transgenic mouse using an RNA solution hybridization assay or polymerase chain reaction.
• transgenic mice that over-express Zlmdao
• Such transgenic mice provide useful models for diseases associated with a lack of Zlmdao.
• Zlmdao gene expression can be inhibited using anti- sense genes, ribozyme genes, or external guide sequence genes.
• inhibitory sequences are targeted to murine Zlmda6 mRNA.
• An alternative approach to producing transgenic mice that have little or no Zlmdao gene expression is to generate mice having at least one normal Zlmdao allele replaced by a nonfunctional Zlmdao gene.
• One method of designing a nonfunctional Zlmdao gene is to insert another gene, such as a selectable marker gene, within a nucleic acid molecule that encodes murine Zlmdao.
• Standard methods for producing these so-called “knockout mice” are known to those skilled in the art [see, for example, Jacob, "Expression and Knockout of Interfer ns in Transgenic Mice," in Overexpression and Knockout of Cytokines in Transgenic Mice, Jacob (ed.), pages 111- 124 (Academic Press, Ltd. 1994), and Wu et al, "New Strategies for Gene Knockout,” in Methods in Gene Biotechnology, pages 339-365 (CRC Press 1997)].
• Polynucleotides and polypeptides of the present invention will additionally find use as educational tools as a laboratory practicum kits for courses related to genetics and molecular biology, protein chemistry and antibody production and analysis. Due to its unique polynucleotide and polypeptide sequence molecules of Zlmdao can be used as standards or as "unknowns" for testing purposes.
• Zlmdao polynucleotides can be used as an aid, such as, for example, to teach a student how to prepare expression constructs for bacterial, viral, and/or mammalian expression, including fusion constructs, wherein Zlmdao is the gene to be expressed; for determining the restriction endonuclease cleavage sites of the polynucleotides; determining mRNA and DNA localization of Zlmdao polynucleotides in tissues (i.e., by Northern and Southern blotting as well as polymerase chain reaction); and for identifying related polynucleotides and polypeptides by nucleic acid hybridization.
• Zlmdao polypeptides can be used educationally as an aid to teach preparation of antibodies; identifying proteins by Western blotting; protein purification; determining the weight of expressed Zlmdao polypeptides as a ratio to total protein expressed; identifying peptide cleavage sites; coupling amino and carboxyl terminal tags; amino acid sequence analysis, as well as, but not limited to monitoring biological activities of both the native and tagged protein (i.e., receptor binding, signal transduction, proliferation, and differentiation) in vitro and in vivo.
• native and tagged protein i.e., receptor binding, signal transduction, proliferation, and differentiation
• Zlmdao polypeptides can also be used to teach analytical skills such as mass spectrometry, circular dichroism to determine conformation, especially of the four alpha helices, x-ray crystallography to determine the three-dimensional structure in atomic detail, nuclear magnetic resonance spectroscopy to reveal the structure of proteins in solution.
• analytical skills such as mass spectrometry, circular dichroism to determine conformation, especially of the four alpha helices, x-ray crystallography to determine the three-dimensional structure in atomic detail, nuclear magnetic resonance spectroscopy to reveal the structure of proteins in solution.
• a kit containing the Zlmdao can be given to the student to analyze. Since the amino acid sequence would be known by the professor, the protein can be given to the student as a test to determine the skills or develop the skills of the student, the teacher would then know whether or not the student has correctly analyzed the polypeptide. Since every polypeptide is unique, the educational utility of Zlmdao would be unique unto itself.
• the antibodies that bind specifically to Zlmdao can be used as a teaching aid to instruct students how to prepare affinity chromatography columns to purify Zlmdao, cloning and sequencing the polynucleotide that encodes an antibody and thus as a practicum for teaching a student how to design humanized antibodies.
• the Zlmdao gene, polypeptide or antibody would then be packaged by reagent companies and sold to universities so that the students gain skill in art of molecular biology. Because each gene and protein is unique, each gene and protein creates unique challenges and learning experiences for students in a lab practicum.
• Such educational kits, containing the Zlmda6 gene, polypeptide or antibody are considered within the scope of the present invention.

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