EP1313765A2 - Nouvelles proteines secretees et procedes d'utilisation de ces dernieres - Google Patents

Nouvelles proteines secretees et procedes d'utilisation de ces dernieres

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Publication number
EP1313765A2
EP1313765A2 EP01963725A EP01963725A EP1313765A2 EP 1313765 A2 EP1313765 A2 EP 1313765A2 EP 01963725 A EP01963725 A EP 01963725A EP 01963725 A EP01963725 A EP 01963725A EP 1313765 A2 EP1313765 A2 EP 1313765A2
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EP
European Patent Office
Prior art keywords
polypeptide
seq
antibody
amino acid
cells
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP01963725A
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German (de)
English (en)
Inventor
Eric Wen Su
He Wang
Yu Zhi
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Eli Lilly and Co
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Eli Lilly and Co
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Filing date
Publication date
Application filed by Eli Lilly and Co filed Critical Eli Lilly and Co
Publication of EP1313765A2 publication Critical patent/EP1313765A2/fr
Withdrawn legal-status Critical Current

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    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates to the identification and isolation of novel DNA, therapeutic and drug discovery uses, and the recombinant production of novel secreted polypeptides, designated herein as LP242, LP257, and LP259.
  • the present invention also relates to vectors, host cells, and antibodies directed to these polypeptides.
  • Extra-cellular proteins play an important role in the formation, differentiation and maintenance of multi-cellular organisms.
  • secreted polypeptides for instance, mi ogenic factors, survival factors, cytotoxic factors, differentiation factors, neuropeptides, and hormones
  • These secreted polypeptides or signaling molecules normally pass through the cellular secretory pathway to reach their site of action in the extra-cellular environment.
  • Secreted proteins have various industrial applications, including pharmaceuticals, diagnostics, biosensors, and bioreactors .
  • the present invention provides isolated LP242, LP257, and LP259 polypeptide encoding nucleic acids and the polypeptides encoded thereby, including fragments and specified variants thereof.
  • Contemplated by the present invention are LP probes, primers, recombinant vectors, host cells, transgenic animals, chimeric antibodies and constructs, LP polypeptide antibodies, as well as methods of making and using them diagnostically and therapeutically as described and enabled herein.
  • the present invention includes isolated nucleic acid molecules comprising polynucleotides that encode LP242, LP257, and LP259 polypeptides as defined herein, as well as fragments, and/or specified variants thereof, or isolated nucleic acid molecules that are complementary to polynucleotides that encode such LP polypeptides or fragments and/or specified variants thereof as defined herein.
  • a polypeptide of the present invention includes an isolated LP polypeptide comprising at least one fragment, domain, or specified variant of at least 90-100% of the contiguous amino acids of at least one portion of SEQ ID NO: 2, 4, or 6.
  • the present invention also provides an isolated LP polypeptide as described herein, wherein the polypeptide further comprises at least one specified substitution, insertion, or deletion corresponding to portions or specific residues of SEQ ID NO: 2, 4, or 6.
  • the present invention also provides an isolated nucleic acid probe, primer, or fragment, as described herein, wherein the nucleic acid comprises a polynucleotide of at least 10 nucleotides, corresponding or complementary to at least 10 nucleotides of SEQ ID NO:l, 3, or 5.
  • compositions including pharmaceutical compositions, comprising a LP polypeptide, a LP polypeptide encoding polynucleotide, a LP polynucleotide, and/or a LP polypeptide antibody, wherein the composition has a measurable effect on an activity associated with a particular LP polypeptide as disclosed herein.
  • a method of treatment or prophylaxis based on a LP polypeptide associated activity, as disclosed herein can be effected by administration of one or more of the polypeptides, nucleic acids, antibodies, vectors, host cells, transgenic cells, and/or compositions described herein to a mammal in need of such treatment or prophylactic.
  • the present invention also includes methods for the prophylaxis or treatment of a patho-physiological condition in which at least one cell type involved in said condition is sensitive or responsive to a LP polypeptide, a LP polypeptide encoding polynucleotide, a LP nucleic acid, LP polypeptide antibody, host cell, transgenic cell, and/or composition of the present invention.
  • the present invention also provides a method for identifying compounds that bind a LP polypeptide, comprising a) admixing at least one isolated LP polypeptide as described herein with a test compound or composition; and b) detecting at least one binding interaction between the polypeptide and the compound or composition, optionally further comprising detecting a change in biological activity, such as a reduction or increase.
  • the present invention also provides LP-polypeptide of SEQ IDNO: 2 for use as a medicament for the treatment of infertility, reproductive tissue disorders, endometrial cancer, pelvic inflammatory disease, fibrosis, diseases effecting the testes and prostate, and inflammatory conditions .
  • Applicants have identified cDNA clones comprising polynucleotides that encode novel polypeptides or novel variants of known polypeptides :
  • LP242 polypeptides comprising the amino acid sequence of the open reading frame encoded by the polynucleotide sequence as shown in SEQ ID NO:l are contemplated by the present invention.
  • polypeptides of the present invention comprise the amino acid sequence as shown in SEQ ID NO : 2 , as well as fragments, variants, and derivatives thereof.
  • LP242 polynucleotides encoding the LP242 polypeptides are also contemplated by the present invention.
  • LP242 polypeptide has been localized to chromosome 19 (GenBank g7022852) .
  • LP242 mRNA is mainly expressed in the digestive system (more specifically, the small intestine) and nervous system (more specifically, the brain) .
  • LP242 binds to macrophages and to tissue in the small intestine and colon, prostate, ovary, uterus, spleen, skin, heart, kidney, lymph nodes, testes.
  • the strong binding of LP242 to macrophages supports a role of this polypeptide in inflammatory conditions.
  • LP242 polypeptide as shown in SEQ ID NO: 2 shares sequence similarity' with proteoglycan link protein precursor (CRTLl; Cytogenet . Cell Genet. 87 (1-2) : 75-79 (1999); W09415627) .
  • compositions comprising LP242 polypeptides, ' polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of diseases, disorders, and/or conditions including, but not limited to, cancer, Alzheimer's disease, Parkinson's disease, Huntington's disease, Tourette syndrome, meningitis, encephalitis, demyelinationg diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, panic disorder learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, perception, and for the treatment of defects in or wounds to tissues including, but not limited to small intestine, prostate, ovary, uterus, spleen, skin, heart, kidney, lymph nodes, testes, and macrophages.
  • compositions comprising LP242 polypeptides, polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of pseudoachondroplasia (Hecht, et al., (1992)), juvenile rheumatoid arthritis (Danieli, et al . , (1992)), and aging (Mort, et al . , (1985)).
  • compositions comprising LP242 polypeptides, polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of familial hemiplegic migraine (Terwind, et al., (1996)), glioma tumor (Smith, et al .
  • LP242 polypeptides, polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of infertility, reproductive tissue disorders, endometrial cancer, pelvic inflammatory disease, fibrosis, diseases effecting the testes and prostate, and inflammatory conditions.
  • LP242 is useful for use as a medicament for the treatment of the above mentioned diseases, disorders, and/or conditions.
  • LP242 was determined to activate SMAD signaling in Ishikawa cells (endometrial cancer cells) , Example 6; Protein Kinase C in L6 cells (skeletal muscle; myoblast) and SK-N-MC cells (neuroblastoma, adenosine diphosphate-dependent) , Example 6; and the JNK/SAP kinase pathway in Saos cells (osteosarcoma cell), Example 5.
  • polypeptides comprising the amino acid sequence of the open reading frame encoded by the polynucleotide sequence as shown in SEQ ID NO: 3 are contemplated by the present invention.
  • polypeptides of the present invention comprise the amino acid sequence as shown in SEQ ID NO: 4, as well as fragments, variants, and derivatives thereof. Accordingly, polynucleotides encoding the polypeptides of the present invention are also contemplated.
  • LP257 polypeptide encoding cDNA was originally discovered as an EST in testis. Additionally, the LP257 polypeptide as shown in SEQ ID NO : 4 shares sequence similarity with tissue plasminogen activator (tPA) (Ny, et al, 1988) . tPA is widely administered as a treatment for stroke (Wang, et al . , (2000)) and heart disease (Modi, et al, (1998) . Furthermore, the LP257 polypeptide as shown in SEQ ID NO: 4 shares sequence similarity with plasma kallidrein, also known as Fletcher factor, and coagulation factor XI.
  • plasma kallidrein also known as Fletcher factor, and coagulation factor XI.
  • compositions comprising LP257 polypeptides, polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of stroke, heart disease, and for the treatment of defects in or wounds to tissues including, but not limited to, testis, and other tissues of the male reproductive system.
  • compositions comprising LP257 polypeptides, polynucleotides, and/or antibodies are also useful for the treatment of diseases related to clotting.
  • diseases include, but are not limited to, myocardial infarction, abrupt closure following angioplasty or stent placement, thrombosis as a result of peripheral vascular surgery, and sepsis.
  • polypeptides comprising the amino acid sequence of the open reading frame encoded by the polynucleotide sequence as shown in SEQ ID NO: 5 are contemplated by the present invention.
  • polypeptides of the present invention comprise the amino acid sequence as shown in SEQ ID NO: 6, as well as fragments, variants, and derivatives thereof. Accordingly, polynucleotides encoding the polypeptides of the present invention are also contemplated by the present invention.
  • LP259 polypeptide The gene encoding the LP259 polypeptide has been localized to chromosome 3 (Brown, J. , et al . , Cell. Mol. Life Sci., 54(9): 925-7, (1998)). LP259 polypeptide encoding mRNA is mainly expressed in hemic and immune system (more specifically in T-cell leukemia cell lines and eosinophils. Accordingly, compositions comprising LP259 polypeptides, polynucleotides, and/or LP polypeptide antibodies are useful for the diagnosis, treatment and prevention of diseases including, but not limited to, chromosome 3-linked frontal temporal dementia (Brown, et al .
  • compositions comprising LP259 polypeptides, polynucleotides, and/or LP polypeptide antibodies are also useful for the treatment of defects in or wounds to tissue.
  • compositions comprising LP259 polypeptides, polynucleotides, and/or antibodies are useful for diagnosis, treatment and intervention of diseases, disorders, and/or conditions including, but not limited to, brain tumors, Alzheimer's disease, Parkinson's disease, Huntington's disease, Tourette syndrome, meningitis, encephalitis, demyelinationg diseases, peripheral neuropathies, neoplasia, trauma, congenital malformations, spinal cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive compulsive disorder, panic disorder learning disabilities, ALS, psychoses, autism, and altered behaviors, including disorders in feeding, sleep patterns, balance, and/or perception.
  • polypeptides of the present invention are designated herein as "LP polynucleotides” or "LP polypeptide encoding polynucleotides” .
  • the polypeptides of the present invention are designated herein as “LP polypeptides” .
  • LP refers to a specific group of molecules as defined herein.
  • LP polypeptide encoding polynucleotides or "LP polynucleotides” and “LP polypeptides” wherein the term “LP” is followed by an actual numerical designation as used herein encompass novel polynucleotides and polypeptides, respectively, which are further defined herein.
  • the LP molecules described herein may be isolated from a variety of sources including, but not limited to human tissue types, or prepared by recombinant or synthetic methods .
  • the isolated nucleic acid comprises 1) a polynucleotide encoding a LP242, LP257, or LP259 polypeptide having an amino acid sequence as shown in SEQ ID NO:2, 4, or 6, respectively, 2) a polynucleotide complementary to such encoding nucleic acid sequences, and which remain stably bound to them under at least moderate, and optionally, high stringency conditions, or
  • LP polypeptide specifically encompasses truncated or secreted forms of a LP polypeptide, (e.g., soluble forms containing, for instance, an extra-cellular domain sequence), variant forms (e.g., alternatively spliced forms) and allelic variants of a LP polypeptide.
  • the native sequence LP polypeptide is a full-length or mature LP polypeptide comprising amino acids as shown in SEQ ID NO: 2, 4, or 6.
  • the predicted signal peptides are indicated in the sequence listing of the present application by negative integers below the amino acids disclosed for a particular polypeptide.
  • the LP polypeptides disclosed herein are shown to begin with a methionine residue designated as amino acid position 1, it is conceivable and possible that another methionine residue located either upstream or downstream from amino acid position 1 may be employed as the starting amino acid residue.
  • LP polypeptide variant is intended to refer to an "active" LP polypeptide, wherein activity is as defined herein, having at least about 90% amino acid sequence identity with a LP polypeptide having a deduced amino acid sequences as shown above.
  • Such LP polypeptide variants include, for instance, LP polypeptides, wherein one or more amino acid residues are added, substituted or deleted, at the N- or C- terminus or within the sequences shown.
  • a LP polypeptide variant will have at least about 90% amino acid sequence identity, preferably at least about 91% sequence identity, yet more preferably at least about 92% sequence identity, yet more preferably at least about 93% sequence identity, yet more preferably at least about 94% sequence identity, yet more preferably at least about 95% sequence identity, yet more preferably at least about 96% sequence identity, yet more preferably at least about 97% sequence identity, yet more preferably at least about 98% sequence identity, yet more preferably at least about 99% amino acid sequence identity with the amino acid sequence described, with or without the signal peptide.
  • Percent (%) amino acid sequence identity with respect to the LP amino acid sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a LP polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as ALIGN, ALIGN-2, Megalign (DNASTAR) or BLAST (e.g., Blast, Blast-2, WU-Blast-2) software.
  • a % amino acid sequence identity value is determined by dividing (a) the number of matching identical amino acid residues between the amino acid sequence of the LP polypeptide of interest and the comparison amino acid sequence of interest (i.e., the sequence against which the LP polypeptide of interest is being compared) as determined by WU-BLAST-2, by (b) the total number of amino acid residues of the LP polypeptide of interest, respectively.
  • LP variant polynucleotide “LP polynucleotide” variant, or “LP variant nucleic acid sequence” are intended to refer to a nucleic acid molecule as defined below having at least about 75% nucleic acid sequence identity with the polynucleotide sequence as shown in SEQ ID NO: 1, 3, or 5.
  • a LP polynucleotide variant will have at least about 75% nucleic acid sequence identity, more preferably at least about 80% nucleic acid sequence identity, yet more preferably at least about 81% nucleic acid sequence identity, ⁇ yet more preferably at least about 82% nucleic acid sequence identity, yet more preferably at least about 83% nucleic acid sequence identity, yet more preferably at least about 84% nucleic acid sequence identity, yet more preferably at least about 85% nucleic acid sequence identity, yet more preferably at least about 86% nucleic acid sequence identity, yet more preferably at least about 87% nucleic acid sequence identity, yet more preferably at least about 88% nucleic acid sequence identity, yet more preferably at least about 89% nucleic acid sequence identity, yet more preferably at least about 90% nucleic acid sequence identity, yet more preferably at least about 91% nucleic acid sequence identity, yet more preferably at least about 92% nucleic acid sequence identity, yet more preferably at least about 93% nucleic acid sequence identity, yet
  • Percent (%) nucleic acid sequence identity with respect to the LP polynucleotide sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in the LP sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as ALIGN, Align-2, Megalign (DNASTAR), or BLAST (e.g., Blast, Blast-2) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • a % nucleic acid sequence identity value is determined by dividing (a) the number of matching identical nucleotides between the nucleic acid sequence of the LP polypeptide-encoding nucleic acid molecule of interest and the comparison nucleic acid molecule of interest (i.e., the sequence against which the LP polypeptide-encoding nucleic acid molecule of interest is being compared) as determined byWU-BLAST-2 , by (b) the total number of nucleotides of the LP polypeptide-encoding nucleic acid molecule of interest.
  • the LP variant polypeptides are encoded by nucleic acid molecules which are capable of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding the full-length LP polypeptide as shown in SEQ ID NO: 2, 4, or 6.
  • This scope of variant polynucleotides specifically excludes those sequences that are known as of the filing and/or priority dates of the present application.
  • mature protein or "mature polypeptide” as used herein refers to the form(s) of the protein produced by expression in a mammalian cell. It is generally hypothesized that once export of a growing protein chain across the rough endoplasmic reticulum has been initiated, proteins secreted by mammalian cells have a signal peptide (SP) sequence which is cleaved from the complete polypeptide to produce a "mature" form of the protein. Oftentimes, cleavage of a secreted protein is not uniform and may result in more than one species of mature protein. The cleavage site of a secreted protein is determined by the primary amino acid sequence of the complete protein and generally cannot be predicted with complete accuracy.
  • SP signal peptide
  • a cleavage point may exist within the N-terminal domain between amino acid 10 and amino acid 35. More specifically the cleavage point is likely to exist after amino acid 15 but before amino acid 30, more likely after amino acid 27. As one of ordinary skill would appreciate, however, cleavage sites sometimes vary from organism to organism and cannot be predicted with absolute certainty. Optimally, cleavage sites for a secreted protein are determined experimentally by amino-terminal sequencing of the one or more species of mature proteins found within a purified preparation of the protein.
  • the % identity value of positives is determined by the fraction of residues scoring a positive value in the BLOSUM 62 matrix. This value is determined by dividing (a) the number of amino acid residues scoring a positive value in the BLOSUM62 matrix of WU-BLAST-2 between the LP polypeptide amino acid sequence of interest and the comparison amino acid sequence (i.e., the amino acid sequence against which the LP polypeptide sequence is being compared) as determined by WU- BLAST-2, by (b) the total number of amino acid residues of the LP polypeptide of interest.
  • isolated when used to describe the various polypeptides disclosed herein, means a polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Preferably, the isolated polypeptide is free of association with all components with which it is naturally associated. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
  • the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non- reducing or reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the LP polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • isolated LP polypeptide-encoding nucleic acid or "isolated LP nucleic acid” is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the nucleic acid. Such an isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecule as it exists in natural cells.
  • an isolated LP polypeptide- encoding nucleic acid molecule includes LP polypeptide- encoding nucleic acid molecules contained in cells that ordinarily express LP polypeptide where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells .
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice .
  • amino acid is used herein in its broadest sense, and includes naturally occurring amino acids as well as non-naturally occurring amino acids, including amino acid analogs and derivatives .
  • the latter includes molecules containing an amino acid moiety.
  • reference herein to an amino acid includes, for example, naturally occurring proteogenic L-amino acids; D-amino acids; chemically modified amino acids such as amino acid analogs and derivatives; naturally occurring non-proteogenic amino acids such as norleucine, ⁇ -alanine, ornithine, etc . ,- and chemically synthesized compounds having properties known in the art to be characteristic of amino acids.
  • proteogenic indicates that the amino acid can be incorporated into a peptide, polypeptide, or protein in a cell through a metabolic pathway.
  • D- LP polypeptides The incorporation of non-natural amino acids, including synthetic non-native amino acids, substituted amino acids, or one or more D-amino acids into the LP peptides, polypeptides, or proteins of the present invention.
  • D-amino acid-containing peptides, etc. exhibit increased stability in vi tro or in vivo compared to L-amino acid-containing counterparts.
  • the construction of peptides, etc., incorporating D-amino acids can be particularly useful when greater intracellular stability is desired or required.
  • D-peptides, etc. are resistant to endogenous peptidases and proteases, thereby providing improved bioavailability of the molecule, and prolonged lifetimes in vivo when such properties are desirable.
  • the use of L-amino acids therein will permit endogenous peptidases, proteases, etc., in a cell to digest the molecule in vivo, thereby limiting the cell's exposure to the molecule.
  • D-peptides, etc. cannot be processed efficienty for major histocompatibility complex class II- restricted presentation to T helper cells, and are therefore less likely to induce humoral immune responses in the whole organism.
  • modifications in the amino acid sequence of a peptide, polypeptide, or protein can result in equivalent, or possibly improved, second generation peptides, etc., that display equivalent or superior functional characteristics when compared to the original amino acid sequences.
  • Alterations in the LP peptides, polypeptides, or proteins of the present invention can include one or more amino acid insertions, deletions, substitutions, truncations, fusions, shuffling of subunit sequences, and the like, either from natural mutations or human manipulation, provided that the sequences produced by such modifications have substantially the same (or improved or reduced, as may be desirable) activity (ies) as the naturally occurring counterpart sequences disclosed herein.
  • hydropathic index of amino acids One factor that can be considered in making such changes is the hydropathic index of amino acids.
  • the importance of the hydropathic amino acid index in conferring interactive biological function on a protein has been discussed by Kyte and Doolittle (1982, J. Mol . Biol . , 157: 105-132) . It is accepted that the relative hydropathic character of amino acids contributes to the secondary structure of the resultant protein. This, in turn, affects the interaction of the protein with molecules such as enzymes, substrates, receptors, ligands, DNA, antibodies, antigens, etc.
  • each amino acid has been assigned a hydropathic index as follows: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4) ; threonine (-0.7) ; serine (-0.8) ; tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate/glutamine/aspartate/asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • amino acids in a peptide, polypeptide, or protein can be substituted for other amino acids having a similar hydropathic index or score and produce a resultant peptide, etc., having similar biological activity, i.e., which still retains biological functionality.
  • amino acids having hydropathic indices within ⁇ 2 are substituted for one another. More preferred substitutions are those wherein the amino acids have hydropathic indices within ⁇ 1. Most preferred substitutions are those wherein the amino acids have hydropathic indices within ⁇ 0.5.
  • hydrophilicity values have been assigned to amino acids: arginine/lysine (+3.0); aspartate/glutamate (+3.0+1); serine (+0.3); asparagine/glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine/histidine (- 0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine/isoleucine (-1.8); tyrosine (-2.3); phenylalanine (- 2.5); and tryptophan (-3.4) .
  • one amino acid in a peptide, polypeptide, or protein can be substituted by another amino acid having a similar hydrophilicity score and still produce a resultant peptide, etc., having similar biological activity, i.e., still retaining correct biological function.
  • amino acids having hydropathic indices within +2 are preferably substituted for one another, those within +1 are more preferred, and those within ⁇ 0.5 are most preferred.
  • amino acid substitutions in the LP polypeptides of the present invention can be based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, etc.
  • Exemplary substitutions that take various of the foregoing characteristics into consideration in order to produce conservative amino acid changes resulting in silent changes within the present peptides , etc . can be selected from other members of the class to which the naturally occurring amino acid belongs .
  • Amino acids can be divided into the following four groups: (1) acidic amino acids; (2) basic amino acids; (3) neutral polar amino acids; and (4) neutral non-polar amino acids.
  • amino acids within these various groups include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, cystine, tyrosine, asparagine, and glutamine; and (4) neutral non- polar amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
  • the present invention includes peptides, etc., such as those discussed herein, containing the amino acid modifications discussed above, alone or in various combinations. To the extent that such modifications can be made while substantially retaining the activity of the peptide, etc., they are included within the scope of the present invention.
  • the utility of such modified peptides, etc. can be determined without undue experimentation by, for example, the methods described herein.
  • biologically functional equivalents of the present LP polypeptides can " have any number of conservative or non-conservative amino acid changes that do not significantly affect their activity (ies) , or that increase or decrease activity as desired, 40, 30, 20, 10, 5, or 3 changes, such as 1-30 changes or any range or value therein, may be preferred. In particular, 10 or fewer amino acid changes may be preferred. More preferably, seven or fewer amino acid changes may be preferred; most preferably, five or fewer amino acid changes may be preferred.
  • the encoding nucleotide sequences (gene, plasmid DNA, cDNA, synthetic DNA, or mRNA, for example) will thus have corresponding base substitutions, permitting them to code on expression for the biologically functional equivalent forms of the LP polypeptides.
  • the LP peptides, polypeptides, or proteins exhibit the same or similar biological or immunological activity (ies) as that (those) of the LP polypeptides specifically disclosed herein, or increased or reduced activity, if desired.
  • the activity (ies) of the variant LP polypeptides can be determined by the methods described herein.
  • Variant LP polypeptides biologically functionally equivalent to those specifically disclosed herein have activity (ies) differing from those of the presently disclosed molecules by about ⁇ 50% or less, preferably by about ⁇ 40% or less, more preferably by about ⁇ 30% or less, more preferably by about ⁇ 20% or less, and even more preferably by about ⁇ 10% or less, when assayed by the methods disclosed herein.
  • Amino acids in a LP molecule of the present invention that are essential for activity can be identified by methods known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, 1989, Science 244:1081-1085). The latter procedure introduces single alanine mutations at every residue in the molecule. The resulting mutant molecules are then tested for biological activity. Sites that are critical for ligand- protein binding can also be identified by structural analysis such as crystallization, nuclear magnetic resonance, or photoaffinity labeling (Smith, et al . , 1992, J. Mol . Biol . 224:899-904 (1992) and de Vos, et al . , Science 255:306-312 (1992)).
  • “Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes required higher temperatures for proper annealing, while short probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reactions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel et al . , Current Protocols in Molecular Biology, Wiley Interscience Publishers, 1995.
  • “Stringent conditions” or “high stringency conditions”, as defined herein, may be identified by those that (1) employ low ionic strength and high temperature for washing, for example, 15 mM sodium chloride/1.5 mM sodium citrate/0.1% sodium dodecyl sulfate at 50°C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride/75 mM sodium citrate at 42°C; or (3) employ 50% formamide, 5X SSC (750 mM sodium chloride, 75 mM sodium citrate) , 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5X Denhardt's solution, sonicated salmon sperm DNA (50 ⁇ g/ml), 0.1% SDS, and 10% dextran
  • Modely stringent conditions may be identified as described by Sambrook et al . [Molecular Cloning: A Laboratory Manual , New York: Cold Spring Harbor Press, (1989)], and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and %SDS) less stringent than those described above.
  • moderately stringent conditions is overnight incubation at 37°C in a solution comprising: 20% formamide, 5X SSC (750 mM sodium chloride, 75 mM sodium citrate) , 50 mM sodium phosphate at pH 7.6, 5X Denhardt's solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in IX SSC at about 37-50°C.
  • 5X SSC 750 mM sodium chloride, 75 mM sodium citrate
  • 50 mM sodium phosphate at pH 7.6
  • 5X Denhardt's solution 10% dextran sulfate
  • 20 mg/mL denatured sheared salmon sperm DNA followed by washing the filters in IX SSC at about 37-50°C.
  • the skilled artisan will recognize how to adjust the temperature, ionic strength, etc., as necessary to accommodate factors such as probe length and the like.
  • epitope tagged refers to a chimeric polypeptide comprising a LP polypeptide, or domain sequence thereof, fused to a "tag polypeptide".
  • the tag polypeptide has enough residues to provide an epitope against which an antibody may be made, or which can be identified by some other agent, yet is short enough such that it does not interfere with the activity of the LP polypeptide.
  • the tag polypeptide preferably is also fairly unique so that the antibody does not substantially cross-react with other epitopes .
  • Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 to about 50 amino acid residues (preferably, between about 10 to about 20 residues) .
  • immunoadhesin designates antibody-like molecules that combine the binding specificity of a heterologous protein (an “adhesion") with the effector functions of immunoglobulin constant domains.
  • the immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is "heterologous"), and an immunoglobulin constant domain sequence.
  • the adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand.
  • the immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG-1, IgG-2, IgG-3 or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM.
  • immunoglobulin such as IgG-1, IgG-2, IgG-3 or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, IgD or IgM.
  • Activity refers to form(s) of LP which retain the biologic and/or immunologic activities of native or naturally-occurring LP polypeptide.
  • biological activity refers to a biological function (either inhibitory or stimulatory) caused by a native or naturally-occurring LP polypeptide other than the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring LP polypeptide.
  • immunological activity refers only to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring LP polypeptide.
  • a preferred biological activity includes, for example, the ability to treat Parkinson's disease, chronic lymphocytic leukemia, Papillon-Lefevre syndrome, prepubertal peridontis, salivary gland muceopidermoid carcinoma, multiple sclerosis, or T cell lymphoblastic leukemia.
  • antagonist is used in the broadest sense and includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native LP polypeptide disclosed herein.
  • agonist is used in the broadest sense and includes any molecule that mimics a biological activity of a native LP polypeptide disclosed herein.
  • Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments or amino acid sequence variants of native LP polypeptides, peptides, ribozymes, anti-sense nucleic acids, small organic molecules, etc.
  • Methods for identifying agonists or antagonists of a LP polypeptide may comprise contacting a LP polypeptide with a candidate agonist or antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the LP polypeptide.
  • Antibodies are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules that lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
  • antibody is used in the broadest sense and specifically covers, without limitation, intact monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies) formed from at least two intact antibodies, and antibody fragments so long as they exhibit the desired biological activity.
  • treating refers to curative therapy, prophylactic therapy, and preventive therapy.
  • An example of “preventive therapy” is the prevention or lessened targeted pathological condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
  • Chronic administration refers to administration of the agent (s) in a continuous mode as opposed to an acute mode, so as to maintain the initial therapeutic effect (activity) for an extended period of time.
  • Intermittent administration is treatment that is not consecutively done without interruption but, rather, is cyclic in nature.
  • Administration "in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
  • a “therapeutically-effective amount” is the minimal amount of active agent (e.g., a LP polypeptide, antagonist or agonist thereof) which is necessary to impart therapeutic benefit to a mammal.
  • a "therapeutically- effective amount" to a mammal suffering or prone to suffering or to prevent it from suffering from a schizophrenia, chronic lymphocytic leukemia, Papillon-Lefevre syndrome, prepubertal peridontis, salivary gland muceopidermoid carcinoma, tuberous sclerosis, and T cell lymphoblastic leukemia disorder is such an amount which induces, ameliorates or otherwise causes an improvement in the pathological symptoms, disease progression, physiological conditions associated with or resistance to succumbing to the aforedescribed disorder.
  • Carriers as used herein include pharmaceutically- acceptable carriers, excipients, or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically-acceptable carrier is an aqueous pH buffered solution.
  • physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecule weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvmylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt- forming counterions such as sodium; and/or nonionic surfactants such as TWEENTM, polyethylene glycol (PEG) , and PLURONICTM.
  • buffers such as phosphate, citrate, and other organic acids
  • antioxidants including ascorbic acid
  • low molecule weight (less than about 10 residues) polypeptides proteins, such as serum
  • Antibody fragments comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody.
  • antibody fragments include Fab, Fab', F(ab')l and Fv fragments; diabodies; linear antibodies (Zapata et al . , Protein Engin . 8 (10): 1057-1062 (1995)); single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
  • Fv is the minimum antibody fragment which contains a complete antigen-recognition and binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VHVL dimer. Collectively, the six CDRs confer antigen- binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDR specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
  • Single-chain Fv or “sFv” antibody fragments comprise the V H and V L domains of antibody, wherein these domains are present in a single polypeptide chain.
  • the Fv polypeptide further comprises a polypeptide linker between the V H and V L domain, which enables the sFv to form the desired structure for antigen binding.
  • diabodies refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (V H ) connected to a light-chain variable domain (V L ) in the same polypeptide chain (V H -VT .
  • V H heavy-chain variable domain
  • V L light-chain variable domain
  • V H -VT light-chain variable domain
  • linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites.
  • Diabodies are described more fully in, for example, EP 404.097, WO 93/11161; and Hollinger et al . , Proc. Natl . Acad. Sci . USA 90 : 6444-6448 (1993).
  • an “isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or non- proteinaceous solutes.
  • the antibody will be purified (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid fc.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • LP polypeptide antibody refers to an antibody as defined herein that recognizes and binds at least one epitope of a LP polypeptide of the present invention.
  • the term “LP polypeptide antibody” or “LP antibody” wherein the term “LP” is followed by a numerical designation refers to an antibody that recognizes and binds to at least one epitope of that particular LP polypeptide as disclosed herein.
  • a “liposome” is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug (such as a LP polypeptide or antibody thereto) to a mammal.
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes .
  • a "small molecule” is defined herein to have a molecule weight below about 500 daltons.
  • modulate means to affect (e.g., either upregulate, downregulate or otherwise control) the level of a signaling pathway.
  • Cellular processes under the control of signal transduction include, but are not limited to, transcription of specific genes, normal cellular functions, such as metabolism, proliferation, differentiation, adhesion, apoptosis and survival, as well as abnormal processes, such as transformation, blocking of differentiation and metastasis.
  • a LP polypeptide encoding polynucleotide or similarly a LP polynucleotide can be composed of any polyribonucleotide or polydeoxyribo-nucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • LP polynucleotides can be composed of single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
  • LP polynucleotides can be composed of triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • LP polynucleotides may also contain one or more modified bases or DNA or RNA backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • polynucleotide embraces chemically, enzymatically, or etabolically modified forms.
  • LP polypeptides can be composed of amino acids joined to each other by peptide bonds or modified peptide bonds, i.e., peptide isosteres, and may contain amino acids other than the gene-encoded amino acids.
  • the LP polypeptides may be modified by either natural processes, such as post- translational processing, or by chemical modification techniques which are well known in the art. Such modifications are well-described in basic texts and in more detailed monographs, as well as in a voluminous research literature. Modifications can occur anywhere in the LP polypeptides, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini.
  • LP polypeptides may be branched, for example, as a result of ubiquitination, and they may be cyclic, with or without branching. Cyclic, branched, and branched cyclic LP polypeptides may result from posttranslation natural processes or may be made by synthetic methods.
  • Modifications include acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyrogluta ate, formylation, gamma- carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
  • Variations in the full-length sequence LP or in various domains of the LP polypeptide described herein can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Patent NO. 5,364,934.
  • Variations may be a substitution, deletion or insertion of one or more codons encoding LP polypeptide that results in a change in the amino acid sequence of the LP polypeptide as compared with the native sequence LP polypeptide or a LP polypeptide as disclosed herein.
  • the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of the LP polypeptide.
  • Guidance in determining which amino acid residue may be inserted, substituted, or deleted without adversely affecting the desired activity may be found by comparing the sequence of the LP polypeptide with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements .
  • Insertions or deletions may optionally be in the range of 1 to 5 amino acids.
  • the variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity (such as in any of the in vi tro assays described herein) for activity exhibited by the full-length or mature polypeptide sequence.
  • LP polypeptide fragments are also provided herein. Such fragments may be truncated at the N-terminus or C-terminus, or may lack internal residues, for example, when compared with a full length or native protein. Certain fragments contemplated by the present invention may lack amino acid residues that are not essential for a desired biological activity of the LP polypeptide . LP polypeptide fragments may be prepared by any of a number of conventional techniques . Desired peptide frag ents may be chemically synthesized.
  • An alternative approach involves generating LP fragments by enzymatic digestion, e.g., by treating the protein with an enzyme known to cleave proteins at sites defined by particular amino acid residues, or by digesting the DNA with suitable restriction enzymes and isolating the desired fragment.
  • Yet another suitable technique involves isolating and amplifying a DNA fragment encoding a desired polypeptide fragment bypolymerase chain reaction (PCR) . Oligonucleotides that define the desired termini of the DNA fragment are employed at the 5' and 3' primers in the PCR.
  • LP polypeptide fragments share at least one biological and/or immunological activity with at least one of the LP polypeptides as shown in SEQ ID NO: 2, 4, or 6.
  • Covalent modifications of LP polypeptides are included within the scope of this invention.
  • One type of covalent modification includes reacting targeted amino acid residues of a LP polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues of a LP polypeptide.
  • Derivatization with bifunctional agents is useful, for instance, for crosslinking LP to a water-insoluble support matrix or surface for use in the method for purifying anti-LP polypeptide antibodies, and vice-versa.
  • crosslinking agents include, e.g., 1, 1-bis (diazo-acetyl) -2-phenylethane, glutaraldehyde, N-hydroxy-succinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccini idyl esters such as 3 , 3'-dithiobis- (succini idylproprionate) , bifunctional maleimides such as bis-N-maleimido-1, 8-octane and agents such as methyl-3- [ (p- azidophenyl) -dithiolproprioimidate .
  • 1, 1-bis (diazo-acetyl) -2-phenylethane glutaraldehyde
  • N-hydroxy-succinimide esters for example, esters with 4-azidosalicylic acid
  • homobifunctional imidoesters including disuccini i
  • Another type of covalent modification of the LP polypeptides included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide.
  • "Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence LP polypeptide and/or adding one or more glycosylation sites that are not present in the native sequences of LP. Additionally, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present .
  • Addition of glycosylation sites to LP polypeptides may be accomplished by altering the amino acid sequence thereof.
  • the alteration may be made, for example, by the addition of, or substitution by, one or more serine or threonine residues to the native sequences of LP (for O-linked glycosylation sites).
  • the LP amino acid sequences may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the LP polypeptides at preselected bases such that codons are generated that will translate into the desired amino acids .
  • Another means of increasing the number of carbohydrate moieties on the LP polypeptides is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330, published 11 September 1987, and in Aplin and Wriston, CRC Cri t . Rev. Biochem. , pp. 259-306 (1981).
  • Removal of carbohydrate moieties present on the LP polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation.
  • Chemical deglycosylation techniques are known in the art and described, for instance, by Sojar et al . , Arch . Biochem. Biophys . 259: 52-7 (1987) and by Edge et al . , Anal . Biochem. 118: 131-7 (1981) .
  • Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of. endo- and exo-glycosidases as described by Thotakura et al . , Meth . Enzymol . 138: 350-9 (1987).
  • Another type of covalent modification of LP comprises linking any one of the LP polypeptides to one of a variety of nonproteinaceous 20 polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos . 4640,835; 4,496,689; 4,301,144; 4.670,417; 4.791,192 or 4,179,337.
  • nonproteinaceous 20 polymers e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes
  • LP polypeptides of the present invention may also be modified in a way to form chimeric molecules comprising a LP polypeptide fused to another heterologous polypeptide or amino acid sequence.
  • a chimeric molecule comprises a fusion of a LP polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind.
  • the epitope tag is generally placed at the amino- or carboxyl- terminus of LP242, LP257, or LP259 polypeptide. The presence of such epitope-tagged forms of LP can be detected using an antibody against the tag polypeptide.
  • provision of the epitope tag enables a LP polypeptide to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
  • the chimeric molecule may comprise a fusion of a LP polypeptide with an immunoglobulin or a particular region of an immunoglobulin.
  • a fusion could be to the Fc region of an IgG molecule.
  • the Ig fusions preferably include the substitution of a soluble transmembrane domain deleted or inactivated form of a LP polypeptide in place of at least one variable region within an Ig molecule.
  • the immunoglobulin fusion includes the hinge, CH2 and CH3 or the hinge, CHI, CH2 and CH3 regions of an IgGl molecule.
  • the LP polypeptides of the present invention may also be modified in a way to form a chimeric molecule comprising a LP polypeptide fused to a leucine zipper.
  • leucine zipper polypeptides have been described in the art. See, e.g., Landschulz et al . , Science 240(4860): 1759-64 (1988); WO 94/10308; Hoppe et al . , FEBS Letters 344(2-3): 191-5 (1994); Abel et al . , Nature 341(6237): 24-5 (1989) .
  • a leucine zipper fused to a LP polypeptide may be desirable to assist in dimerizing or trimerizing soluble LP polypeptide in solution.
  • zipper may be fused at either the N- or C-terminal end of LP.
  • LP polypeptides by culturing cells transformed or transfected with a vector containing a LP polypeptide-encoding nucleic acid. It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare LP polypeptides.
  • the LP polypeptide sequence, or portions thereof may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al . , Solid-Phase Peptide Synthesis, W.H. Freeman Co., San Francisco, CA (1969); Merrifield, J " . Am. Chem . Soc . 85: 2149-2154 (1963)].
  • LP polypeptide may be chemically synthesized separately and combined using chemical or enzymatic methods to produce a full-length LP polypeptide.
  • DNA encoding a LP polypeptide may be obtained from a cDNA library prepared from tissue believed to possess the LP polypeptide-encoding mRNA and to express it at a detectable level.
  • Libraries can be screened with probes (such as antibodies to a LP polypeptide or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al . , Molecular Cloning: A Laboratory Manual , Cold Spring Harbor Laboratory Press, NY (1989) .
  • Nucleic acids LP polypeptides may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time and, if necessary, using conventional primer extension procedures as described in Sambrook et al . , supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA.
  • Host cells are transfected or transformed with expression or cloning vectors described herein for LP polypeptide production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the culture conditions such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: A Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook et al . , supra. Methods of transfection are known to the ordinarily skilled artisan, for example, CaP0 4 and electroporation.
  • Suitable host cells for cloning or expressing the nucleic acid (e.g., DNA) in the vectors herein include prokaryote, yeast, or higher eukaryote cells.
  • Suitable prokaryotes include but are not limited to eubacteria, such as Gram- negative or Gram-positive organisms, for example, Enterobacteriacea such as E. coli.
  • Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 3 1.446); E.
  • E. coli Xl 776 ATCC 3 1.537
  • E. coli strain W3 110 ATCC 27.325)
  • K5 772 ATCC 53.635
  • Other suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g.. E. coli, Enterobacter, Erwinia, Klebisella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and Shigeila, as well as Bacilli such as B. subtilis and B. lichentformis (e.g., B.
  • Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes.
  • strain W3 110 may be modified to effect a genetic mutation in a gene encoding a protein endogenous to the host, with examples of such hosts including E. coli W3110 strain 1A2, which has the complete genotype ronA; E.
  • E. coli W3 110 strain 9E4 which has the complete genotype ton4 ptr3
  • E. coli W3110 strain 27C7 (ATCC 55,244), which has the complete genotype tonA, ptr3 phoA E15 (argF-lac) 169 degP ompT /can'
  • E. coli W3110 strain 40B4 which is strain 37D6 with a non-kanamycin resistant degP deletion mutation
  • in vivo methods of cloning e.g., PCR or other nucleic acid polymerase reactions, are suitable.
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for LP vectors.
  • Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.
  • Others include Schizosaccharomyces pombe [Beach and Nurse, Nature 290: 140-3 (1981); EP 139,383 published 2 May 1995]; Muyveromyces hosts [U.S. Patent No. 4,943,529; Fleer et al .
  • K lactis (MW98-8C, CBS683, CBS4574) [de Louvencourt et al . , J. Bacteriol . 154(2): 737-42 (1983)]; K. fiagilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K wickeramii (ATCC 24,178), K waltii (ATCC 56,500), K. drosophilarum (ATCC 36.906) [Van den Berg et al . , Bio / 'Technology 8 (2) : 135-9 (1990)]; K. thermotoierans, and K.
  • Schwanniomyces such as Schwanniomyces occidentulis (EP 394,538 published 31 October 1990); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 January 1991) , and Aspergillus hosts such as A. nidulans [Ballance et al . , Biochem. Biophys . Res . Comm. 112(1): 284-9 (1983)]; Tilburn et al . , Gene 26(2-3): 205-21 (1983); Yelton et al . , Proc . Natl . Acad. Sci .
  • Methylotropic yeasts are selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotoruia. A list of specific species that are exemplary of this class of yeast may be found in C. Antony, The Biochemistry of Methylotrophs 269 (1982) .
  • Suitable host cells for the expression of glycosylated LP polypeptides are derived from multicellular organisms.
  • invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sp, Spodoptera high.5 as well as plant cells.
  • useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line [293 or 293 cells subcloned for growth in suspension culture, Graham et al . , J " . Gen Virol .
  • LP polypeptides may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • the signal sequence may be a component of the vector, or it may be a part of the LP polypeptide-encoding DNA that is inserted into the vector.
  • the signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders.
  • the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces cc-factor leaders, the latter described in U.S. Patent No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179), or the signal described in WO 90/13646.
  • yeast invertase leader alpha factor leader (including Saccharomyces and Kluyveromyces cc-factor leaders, the latter described in U.S. Patent No. 5,010,182)
  • acid phosphatase leader the C. albicans glucoamylase leader
  • mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species as well as viral secretory leaders.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram- negative bacteria, the 2u plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • Selection genes will typically contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement autotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the LP polypeptide-encoding nucleic acid, such as DHFR or thymidine kinase.
  • An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described Urlaub and Chasin, Proc . Natl . Acad. Sci . USA, 77(7): 4216-20 (1980).
  • a suitable selection gene for use in yeast is the trpl gene present in the yeast plasmid YRp7 [Stinchcomb et al . , Nature 282(5734): 39-43 (1979); Kings an et al . , Gene 7(2): 141-52
  • the trpl gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEPC1 [Jones, Genetics 85: 23-33 (1977)].
  • Expression and cloning vectors usually contain a promoter operably linked to the LP polypeptide-encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the ⁇ - lactamase and lactose promoter systems [Chang et al . , Nature 275(5681): 617-24 (1978); Goeddel et al . , Nature 281(5732): 544-8 (1979)], alkaline phosphatase, a tryptophan (up) promoter system [Goeddel, Nucleic Acids Res . 8(18): 4057-74
  • Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding LP .
  • S.D. Shine-Dalgarno
  • Suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman et al . , J " . Biol . Chem. 255(24): 12073-80
  • enolase such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
  • Transcription of LP polypeptide-encoding mRNA from vectors in mammalian host cells may be controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis- B virus and Simian Virus 40 (SV40) , from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems .
  • viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis- B
  • Enhancers are cis- acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription.
  • Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a-ketoprotein, and insulin) . Typically, however, one will use an enhancer from a eukaryotic cell virus.
  • Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270) , the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the LP polypeptide coding sequence but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms
  • sequences are commonly available from the 5' and occasionally 3' untranslated regions of eukaryotic or viral DNAs or cDNAs . These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding LP.
  • Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc . Natl . Acad. Sci.. USA 77(9): 5201-5 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein.
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes .
  • the antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • Gene expression may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product.
  • Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence provided herein or against exogenous sequence fused to a LP polypeptide-encoding DNA and encoding a specific antibody epitope.
  • LP polypeptide may be recovered from culture medium or from host cell lysates . If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g., Triton-X 100) or by enzymatic cleavage.
  • a suitable detergent solution e.g., Triton-X 100
  • Cells employed in expression of a LP polypeptide can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.
  • LP polypeptides may be desireable to purify LP polypeptides from recombinant cell proteins or polypeptides .
  • the following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reversed-phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forms of a LP polypeptide.
  • Nucleotide sequences (or their complement) encoding LP polypeptides have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA.
  • LP polypeptide-encoding nucleic acids will also be useful for the preparation of LP polypeptides by the recombinant techniques described herein.
  • the full-length LP polypeptide-encoding nucleotide sequence may be useful as hybridization probes for probing a cDNA or genomic library to isolate the full-length LP polypeptide-encoding cDNA or genomic sequences including promoters, enhancer elements and introns of native sequence LP polypeptide-encoding DNA or to isolate still other genes (for instance, those encoding naturally-occurring variants of LP polypeptides or the same from other species) which have a desired sequence identity to the LP polypeptide-encoding nucleotide sequence disclosed in SEQ ID N0:1, 3, or 5.
  • Hybridization techniques are well known in the art, some of which are described in further detail in the Examples below.
  • LP polypeptide-encoding nucleic acids include anti-sense or sense oligonucleotides comprising a single-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target LP polypeptide- encoding mRNA (sense) of LP polypeptide-encoding DNA (anti- sense) sequences.
  • Anti-sense or sense oligonucleotides comprise a fragment of the coding region of LP polypeptide-encoding DNA. Such a fragment generally comprises at least about 14 nucleotides, preferably from about 14 to 30 nucleotides.
  • binding of anti-sense or sense oligonucleotides to target nucleic acid sequences results in the formation of duplexes that block transcription or translation of the target sequence by one of several means, including enhanced degradation of the duplexes, premature termination of transcription or translation, or by other means.
  • the anti-sense oligonucleotides thus may be used to block expression of LP mRNA and therefore any LP polypeptide encoded thereby.
  • Anti- sense or sense oligonucleotides further comprise oligonucleotides having modified sugar-phosphodiester backbones (or other sugar linkages, such as those described in WO 91/06629) and wherein such sugar linkages are resistant to endogenous nucleases.
  • Such oligonucleotides with resistant sugar linkages are stable in vivo (i.e., capable of resisting enzymatic degradation) but retain sequence specificity to be able to bind to target nucleotide sequences.
  • sense or anti-sense oligonucleotides include those oligonucleotides which are covalently linked to organic moieties, such as those described in WO 90/10448, and other moieties that increase affinity of the oligonucleotide for a target nucleic acid sequence, such poly-L-lysine.
  • intercalating agents such as ellipticine, and alkylating agents or metal complexes may be attached to sense or anti-sense oligonucleotides to modify binding specificities of the anti-sense or sense oligonucleotide for the target nucleotide sequence.
  • Anti-sense or sense oligonucleotides may be introduced into a cell containing the target nucleic acid sequence by any gene transfer method, including, for example, CaP0-mediated DNA transfection, electroporation, or by using gene transfer vectors such as Epstein-Barr virus.
  • an anti-sense or sense oligonucleotide is inserted into a suitable retroviral vector.
  • a cell containing the target nucleic acid sequence is contacted with the recombinant retroviral vector, either in vivo or ex vivo .
  • Suitable retroviral vectors include, but are not limited to, those derived from the urine retrovirus M-MSV, N2 (a retrovirus derived from M-MuLV) , or the double copy vectors designated CDTSA, CTSB and DCTSC (see WO 90/13641) .
  • a sense or an anti-sense oligonucleotide may be introduced into a cell containing the target nucleic acid sequence by formation of an oligonucleotide-lipid complex, as described inWO 90/10448.
  • the sense or anti-sense oligonucleotide-lipid complex is preferably dissociated within the cell by an endogenous lipase.
  • the LP polypeptide can be used in assays to identify the other proteins or molecules involved in the binding interaction. By such methods, inhibitors of the receptor/ligand binding interaction can be identified. Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction. Also, a receptor LP polypeptide can be used to isolate correlative ligand (s) .
  • Screening assays can be designed to find lead compounds that mimic the biological activity of the LP polypeptides disclosed herein or a receptor for such LP polypeptides .
  • Typical screening assays will include assays amenable to high- throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates .
  • Small molecules contemplated include synthetic organic or inorganic compounds.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art.
  • Nucleic acids which encode a LP polypeptide of the present invention or any of its modified forms can also be used to generate either transgenic animals or "knock out" animals which, in turn, are useful in the development and screening of therapeutically useful reagents.
  • Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009.
  • particular cells would be targeted for a LP transgene incorporation with tissue-specific enhancers.
  • Transgenic animals that include a copy of a transgene introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding a LP polypeptide.
  • Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression.
  • an animal is treated with the reagent and a reduced incidence of the pathological condition, compared to untreated animals bearing the transgene, would indicate a potential therapeutic intervention for the pathological condition.
  • non-human homologues of LP can be used to construct a "knock out" animal which has a defective or altered gene encoding a particular LP polypeptide as a result of homologous recombination between the endogenous gene encoding the LP polypeptide and the altered genomic DNA introduced into an embryonic cell of the animal.
  • cDNA encoding a LP polypeptide can be used to clone genomic DNA encoding that LP polypeptide in accordance with established techniques.
  • a portion of the genomic DNA encoding a LP polypeptide can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration.
  • flanking DNA typically, several kilobases of unaltered flanking DNA (both at the 5' and 3' ends) are included in the vector [see, e.g., Thomas and Capecchi, Cell 51(3): 503-12 (1987) for a description of homologous recombination vectors] .
  • the vector is introduced into an embryonic stem cell line (e.g., by electroporation), and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected [see, e.g., Li et al . , Cell 69(6): 915-26 (1992)].
  • the selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see, e.g., Bradley, Teratocarcinomas and Embryonic Stem Cells : A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987) , pp. 113-152] .
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a "knock out" animal.
  • Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knockout animals can be characterized, for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the native LP polypeptide.
  • Transgenic non-human mammals are useful as an animal models in both basic research and drug development endeavors .
  • Transgenic animals expressing at least one LP polypeptide or nucleic acid can be used to test compounds or other treatment modalities which may prevent, suppress, or cure a pathology or disease associated with at least one of the above mentioned activities .
  • Such transgenic animals can also serve as a model for the testing of diagnostic methods for those same diseases.
  • tissues derived from such transgenic non-human mammals are useful as a source of cells for cell culture in efforts to develop in vi tro bioassays to identify compounds that modulate LP polypeptide activity or LP polypeptide dependent signaling.
  • another aspect of the present invention contemplates a method of identifying compounds efficacious in the treatment of at least one previously described disease or pathology associated with a LP polypeptide associated activity.
  • a non-limiting example of such a method comprises: a) generating a transgenic non-human animal which expresses a LP polypeptide of the present invention and which is, as compared to a wild-type animal, pathologically distinct in some detectable or measurable manner from wild- type version of said non-human mammal; b) exposing said transgenic animal to a compound, and; c) determining the progression of the pathology in the treated transgenic animal, wherein an arrest, delay, or reversal in disease progression in transgenic animal treated with said compound as compared to the progression of the pathology in an untreated control animals is indicative that the compound is useful for the treatment of said pathology.
  • Another embodiment of the present invention provides a method of identifying compounds capable of inhibiting LP polypeptide activity in vivo and/or in vi tro wherein said method comprises: a) administering an experimental compound to a LP polypeptide expressing transgenic non-human animal, or tissues derived therefrom, exhibiting one or more physiological or pathological conditions attributable to the expression of a LP transgene; and b) observing or assaying said animal and/or animal tissues to detect changes in said physiological or pathological condition or conditions.
  • Another embodiment of the invention provides a method for identifying compounds capable of overcoming deficiencies in LP polypeptide activity in vivo or in vi tro wherein said method comprises: a) administering an experimental compound to a LP polypeptide expressing transgenic non-human animal, or tissues derived therefrom, exhibiting one or more physiological or pathological conditions attributable to the disruption of the endogenous LP polypeptide-encoding gene; and b) observing or assaying said animal and/or animal tissues to detect changes in said physiological or pathological condition or conditions.
  • Various means for determining a compound's ability to modulate the activity of a LP polypeptide in the body of the transgenic animal are consistent with the invention. Observing the reversal of a pathological condition in the LP polypeptide expressing transgenic animal after administering a compound is one such means. Another more preferred means is to assay for markers of LP activity in the blood of a transgenic animal before and after administering an experimental compound to the animal. The level of skill of an artisan in the relevant arts readily provides the practitioner with numerous methods for assaying physiological changes related to therapeutic modulation of LP activity.
  • Gene therapy includes both conventional gene therapy, where a lasting effect is achieved by a single treatment, and the administration of gene therapeutic agents, which involves the one time or repeated administration of a therapeutically effective DNA or mRNA.
  • Anti-sense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo . It has already been shown that short anti- sense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by their restricted uptake by the cell membrane [Zamecnik et al . , Proc . Natl . Acad Sci . USA 83(12): 4143-6 (1986)].
  • the oligonucleotides can be modified to enhance their uptake, e.g., by substituting their negatively charged phosphodiester groups with uncharged groups.
  • the currently preferred in vivo gene transfer techniques include transfection with viral (typically, retroviral) vectors and viral coat protein-liposome mediated transfection [Dzau et al., Trends in Biotechnology 11(5): 205-10 (1993)].
  • viral typically, retroviral
  • viral coat protein-liposome mediated transfection [Dzau et al., Trends in Biotechnology 11(5): 205-10 (1993)].
  • agent that targets the target cells, such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cells, etc.
  • proteins which bind to a cell surface membrane protein associated with endocytosis may by used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof trophic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half-life.
  • the technique of receptor- mediated endocytosis is described, for example by Wu et al . , J. Biol . Chem . 262(10): 4429-32 (1987); and Wagner et al . , Proc . Natl . Acad. Sci . USA 87(9): 3410-4 (1990).
  • Wu et al . J. Biol . Chem . 262(10): 4429-32 (1987); and Wagner et al . , Proc . Natl . Acad. Sci . USA 87(9): 3410-4 (1990).
  • nucleic acid molecules encoding LP polypeptides or fragments thereof described herein are useful for chromosome identification.
  • Each LP polypeptide-encoding nucleic acid molecule of the present invention can be used as a chromosome marker.
  • a LP polypeptide-encoding nucleic acid or fragments thereof can also be used for chromosomal localization of the gene encoding that LP polypeptide.
  • the present invention further provides anti-LP polypeptide antibodies.
  • exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heterocon ugate antibodies.
  • the anti-LP polypeptide antibodies of the present invention may comprise polyclonal antibodies. Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections.
  • the immunizing agent may include the LP polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized.
  • immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.
  • adjuvants which may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate) .
  • the immunization protocol may be selected by one skilled in the art without undue experimentation.
  • Anti-LP polypeptide antibodies may, alternatively, be monoclonal antibodies.
  • Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature 256(5517): 495-7 (1975).
  • a hybridoma method a mouse, hamster, or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
  • the lymphocytes may be immunized in vi tro .
  • the immunizing agent will typically include a LP polypeptide or a fusion protein thereof.
  • a LP polypeptide or a fusion protein thereof Generally, either peripheral blood lymphocytes ("PBLs") are used, if cells of human origin are desired, or spleen cells or lymph node cells are used, if non-human mammalian sources are desired.
  • PBLs peripheral blood lymphocytes
  • the lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, Monoclonal Antibodies : Principles and Practice, Academic Press, (1986) pp. 59-103] .
  • Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin.
  • rat or mouse myeloma cell lines are employed.
  • the hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells.
  • a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells.
  • the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ( "HAT medium” ) , which prevents the growth of HGPRT- deficient cells.
  • Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, California, and the American Type Culture Collection, Rockville, Maryland. Human myeloma and mouse- human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, J " . Immunol . 133(6): 3001-5 (1984); Brodeur et al . , Monoclonal Antibody Production Techniques and Applications , Marcel Dekker, Inc., NY, (1987) pp. 51-63].
  • the culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against a LP polypeptide.
  • the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vi tro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA) .
  • RIA radioimmunoassay
  • ELISA enzyme-linked immunoabsorbent assay
  • the binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Rodbard, Anal. Biochem. 107(1) : 220-39 ( 1980) .
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods [Goding, Monoclonal Antibodies : Principles and Practice, Academic Press, (1986) pp. 59-103] .
  • Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium.
  • the hybridoma cells may be grown in vivo as ascites in a mammal .
  • the monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S. Patent No. 4,816,567.
  • DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies) .
  • the hybridoma cells of the invention serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • the DNA also may be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences [U.S. Patent No. 4,816,567; Morrison et al . , Proc. Natl . Acad. Sci .
  • non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.
  • Anti-LP polypeptide antibodies may be monovalent antibodies .
  • Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.
  • the anti-LP polypeptide antibodies of the invention may further comprise humanized antibodies or human antibodies.
  • Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab') 2 or other antigen- binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary-determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • CDR complementary-determining region
  • Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin, and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc) , typically that of a human immunoglobulin [Jones et al .
  • a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import” variable domain. Humanization can be essentially performed following the method of Winter and co- workers [Jones et al . , Nature 321(6069): 522-5 (1986); Riechmann et al .
  • humanized antibodies are chimeric antibodies (U.S. Patent No. 4,816,567) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non- human species.
  • humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • Hu an anti-LP polypeptide antibodies can also be produced using various techniques known in the art, including phage display libraries [Hoogenboo and Winter, J " . Mol . Biol . 227(2): 381-8 (1992); Marks et al . , J. Mol . Biol . 222(3): 581- 97 (1991)].
  • the techniques of Cole et al . and Boerner et al . are also available for the preparation of human monoclonal antibodies (Cole et al . , Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al . , J “ . Immunol . 147(1): 86-95 (1991)].
  • human anti-LP polypeptide antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or complete inactivated. Upon challenge, human LP polypeptide antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly and antibody repertoire. This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in the following scientific publications: Marks et al . , Biotechnology 10(7): 779-83 (1992); Lonberg et al .
  • Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens.
  • one of the binding specificities is for a LP polypeptide, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit .
  • Methods for making bispecific antibodies are known in the art.
  • Antibodies with more than two valencies are contemplated.
  • trispecific antibodies can be prepared [Tutt et al . , J " Immunol . 147(1): 60-9 (1991)].
  • Heteroconjugate antibodies are also within the scope of the present invention.
  • Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Patent No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/20373] .
  • the antibodies may be prepared in vi tro using known methods in synthetic protein chemistry, including those involving crosslinking agents.
  • immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4- mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980.
  • the invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant or animal origin, or fragments thereof, or a small molecule toxin) , or a radioactive isotope (i.e., a radioconjugate) .
  • a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant or animal origin, or fragments thereof, or a small molecule toxin)
  • toxin e.g., an enzymatically active toxin of bacterial, fungal, plant or animal origin, or fragments thereof, or a small molecule toxin
  • radioactive isotope i.e., a radioconjugate
  • Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3- (2-pyridyldithiol) propionate (SPDP) , iminothiolane (IT) , bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL) , active esters (such as disuccinimidyl suberate) , aldehydes (such as glutaraldehyde) , bis-azido compounds, bis-diazonium derivatives (such as bis-2- diazoniumbenzoyl) -ethylenediamine) ⁇ diisocyanates (such as tolyene 2 , 6-diisocyanate) , and bioactive fluorine compounds.
  • SPDP N-succinimidyl-3- (2-pyridyldithiol) propionate
  • IT iminothiolane
  • imidoesters
  • a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238(4830): 1098-104 (1987).
  • Carbon-14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody.
  • the antibody may be conjugated to a "receptor” (such as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent, and then administration of a "ligand” (e.g., avidin) which is conjugated to a cytotoxic agent (e.g., a radionucleotide).
  • a receptor such as streptavidin
  • a ligand e.g., avidin
  • cytotoxic agent e.g., a radionucleotide
  • the antibodies disclosed herein may also be formulated as immunoliposomes .
  • Liposomes containing the antibody are prepared by methods known in the art, such as described in Eppstein et al . , Proc . Natl . Acad. Sci . USA 82: 3688-92 (1985); Hwang et al . , Proc. Natl . Acad. Sci . USA 77(7): 4030-4 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Patent No. 5,013,556.
  • Particularly useful liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG- derivatized phosphatidylethanolamine (PEG-PE) .
  • Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter.
  • Fab' fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al . , J. Biol . Chem. 257(1): 286-8 (1982) via a disulfide interchange reaction.
  • a chemotherapeutic agent such as Doxorubicin is optionally contained within the liposome. See Gabizon et al .
  • Antibodies specifically binding a LP polypeptide identified herein, as well as other molecules identified by the screening assays disclosed hereinbefore, can be administered for the treatment of various disorders in the form of pharmaceutical compositions .
  • a LP polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred.
  • lipofections or liposomes can also be used to deliver the antibody, or an antibody fragment into cells.
  • the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred.
  • peptide molecules can be designed that retain the ability to bind the target protein sequence.
  • Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al . , Proc . Natl . Acad. Sci . USA 90(16): 7889-93 (1993) .
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • the composition may comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokines, chemotherapeutic agent, or growth-inhibitory agent.
  • cytotoxic agent such as, for example, a cytotoxic agent, cytokines, chemotherapeutic agent, or growth-inhibitory agent.
  • Such molecules are suitable present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsules prepared, for example, by coascervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or felatin-microcapsules and poly- (methylmethactylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules) or in macroe ulsions .
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules
  • the formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly (2-hydroxyethyl-methacrylate) , or poly(vinylalcohol) ) , polylactides (U.S. Pat. No.
  • encapsulated antibodies When encapsulated antibodies remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanisms involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thiosuifide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions .
  • the anti-LP polypeptide antibodies of the present invention have various utilities.
  • such antibodies may be used in diagnostic assays for LP polypeptide expression, e.g., detecting expression in specific cells, tissues, or serum.
  • diagnostic assay techniques known in the art may be used, such as competitive binding assays, direct or indirect sandwich assays and immunoprecipitation assays conducted in either heterogeneous or homogeneous phases [Zola, Monoclonal Antibodies : A Manual of Techniques, CRC Press, Inc. (1987) pp. 147-158] .
  • the antibodies used in the assays can be labeled with a detectable moiety.
  • the detectable moiety should be capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as 3 H, 14 C, 32 P, 35 S, or 125 I, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • a radioisotope such as 3 H, 14 C, 32 P, 35 S, or 125 I
  • a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine, or luciferin
  • an enzyme such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • Any method known in the art for conjugating the antibody to the detectable moiety may be employed, including those methods described by Hunter et al . , Nature 144: 945 (1962); David e
  • Anti-LP polypeptide antibodies also are useful for affinity purification from recombinant cell culture or natural sources.
  • the antibodies are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art.
  • the immobilized antibody is then contacted with a sample containing the LP polypeptide to be purified, and thereafter the support is washed with a suitable solvent that will remove substantially all the material in the sample except the LP polypeptide, which is bound to the immobilized antibody. Finally, the support is washed with another suitable solvent that will release the desired polypeptide from the antibody.
  • This invention encompasses methods of screening compounds to identify those that mimic the activity of the LP polypeptide (agonists) disclosed herein or prevent the effects of the LP polypeptide (antagonists) .
  • Screening assays for antagonist drug candidates are designed to identity compounds that bind or complex with a LP polypeptide encoded by the genes identified herein or otherwise interfere with the interaction of LP polypeptides with other cellular proteins.
  • Such screening assays will include assays amenable to high- throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates .
  • the assays can be performed in a variety of formats .
  • binding assays the interaction is binding, and the complex formed can be isolated or detected in the reaction mixture.
  • a LP polypeptide encoded by a gene identified herein or the drug candidate is immobilized on a solid phase, e.g., on a microtiter plate, by covalent or non- covalent attachments.
  • Non-covalent attachment generally is accomplished by coating the solid surface with a solution comprising LP polypeptide and drying.
  • an immobilized antibody e.g., a monoclonal antibody, specific for the polypeptide to be immobilized can be used to anchor it to a solid surface .
  • the assay is performed by adding the non- immobilized component, which may be labeled by a detectable label, to the immobilized component, e.g., the coated surface containing the anchored component.
  • the non-reacted components are removed, e.g., by washing, and complexes anchored on the solid surface are detected.
  • the detection of label immobilized on the surface indicates that complexing occurred.
  • complexing can be detected, for example, by using a labeled antibody specifically binding the immobilized complex.
  • the candidate compound interacts with but does not bind to a LP polypeptide
  • its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions.
  • assays include traditional approaches, such as, e.g., cross-linking, co- immunoprecipitation, and co-purification through gradients or chromatographic columns.
  • protein-protein interactions can be monitored through gradients or chromatographic columns.
  • protein-protein interactions can be monitored by using a yeast-based genetic system described by Fields and co-workers [Fields and Song, Nature 340(6230): 245-6 (1989); Chien et al . , Proc. Natl . Acad. Sci .
  • yeast GAL4 consist of two physically discrete modular domains, one acting as the DNA- binding domain, while the other functions as the transcription- activation domain.
  • the yeast expression system described in the foregoing publications (generally referred to as the "two- hybrid system") takes advantage of this property, and employs two hybrid proteins, one in which the target protein is fused to the DNA-binding domain of GAL4, and another in which candidate activating proteins are fused to the activation domain.
  • GALl-lacZ reporter gene under control of a GAL4-activated promoter depends on reconstitution of GAL4 activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with chromogenic substrate for ⁇ -galactosidase.
  • a complete kit (MATCHMAKERTM) for identifying protein-protein interactions between two specific proteins using the two-hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions .
  • a reaction mixture is prepared containing the product of the gene and the intra- or extra-cellular component under conditions and for a time allowing for the interaction and binding of the two products.
  • a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound.
  • a placebo may be added to a third reaction mixture to serve as a positive control.
  • the binding (complex formation) between the test compound and the intra- or extra-cellular component present in the mixture is monitored as described hereinabove.
  • the formation of a complex in the control reaction (s) but not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.
  • Antagonists may be detected by combining at least one LP polypeptide and a potential antagonist with a membrane-bound or recombinant receptor for that LP polypeptide under appropriate conditions for a competitive inhibition assay.
  • the LP polypeptide can be labeled, such as by radioactivity, such that the number of LP polypeptide molecules bound to the. receptor can be used to determine the effectiveness of the potential antagonist.
  • the gene encoding the receptor for a LP polypeptide can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. See Coligan et al . , Current Protocols in Immunology 1(2): Ch. 5 (1991).
  • expression cloning is employed such that polyadenylated mRNA is prepared from a cell responsive to the secreted form of a particular LP polypeptide, and a cDNA library created from this mRNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the secreted LP polypeptide.
  • Transfected cells that are grown on glass slides are exposed to the labeled LP polypeptide.
  • the LP polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protei kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an interactive sub-pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.
  • a labeled LP polypeptide can be photoaffinity-linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro-sequencing. The amino acid sequence obtained from micro-sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.
  • mammalian cells or a membrane preparation expressing the receptor would be incubated with a labeled LP polypeptide in the presence of the candidate compound. The ability of the compound to enhance or block this interaction could then be removed.
  • a potential antagonist may be a closely related protein, for example, a mutated form of the LP polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the polypeptide.
  • Another potential LP antagonist is an anti-sense RNA or DNA construct prepared using anti-sense technology, where, e.g., an anti-sense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and prevent its translation into protein.
  • Anti-sense technology can be used to control gene expression through triple-helix formation or anti-sense DNA or RNA, both of which methods are based on binding of a polynucleotide to DNA or RNA.
  • the 5' coding portion of the polynucleotide sequence, which encodes the mature form of a LP polypeptide can be used to design an anti-sense RNA oligonucleotide sequence of about 10 to 40 base pairs in length.
  • a DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription [triple helix; see Lee et al . , Nucl . Acids Res 6(9): 3073-91 (1979); Cooney et al . , Science 241(4864): 456-9 (1988); Beal and Dervan, Science 251(4999): 1360-3 (1991)], thereby preventing transcription and production of the LP polypeptide.
  • the anti-sense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecules [anti-sense; see Okano, J " . Neurochem.
  • oligonucleotides as Anti-sense Inhibitors of Gene Expression (CRC Press: Boca Raton, FL 1988)].
  • the oligonucleotides described above can also be delivered to cells such that the anti-sense RNA or DNA may be expressed in vivo to inhibit production of the LP polypeptide.
  • anti- sense DNA oligodeoxyribonucleotides derived from the translation-initiation site, e.g., between about -10 and +10 positions of the target gene nucleotide sequence, are preferred.
  • Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the LP polypeptide, thereby blocking the normal biological activity of the LP polypeptide.
  • small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non-peptidyl organic or inorganic compounds .
  • Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details, see, e.g., Rossi, Current Biology 4(5): 469-71 (1994) and PCT publication No. WO 97/33551 (published September 18, 1997).
  • Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single-stranded and composed of deoxynucleotides.
  • the base composition of these oligonucleotides is designed such that, it promotes triple- helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex.
  • Hoogsteen base-pairing rules which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex.
  • Another use of the compounds of the invention is to help diagnose whether a disorder is driven to some extent by the modulation of signaling by a LP polypeptide
  • a diagnostic assay to determine whether a particular disorder is driven by LP polypeptide dependent signaling can be carried out using the following steps: a) culturing test cells or tissues expressing a LP polypeptide; b) administering a compound which can inhibit LP polypeptide dependent signaling; and c) measuring LP polypeptide mediated phenotypic effects in the test cells.
  • the steps can be carried out using standard techniques in light of the present disclosure.
  • Appropriate controls take into account the possible cytotoxic effect of a compound, such as treating cells not associated with a cell proliferative disorder (e.g., control cells) with a test compound and can also be used as part of the diagnostic assay.
  • the diagnostic methods of the invention involve the screening for agents that modulate the effects of LP-polypeptide associated disorders.
  • LP polypeptides or antibodies thereto as well as LP polypeptide antagonists or agonists can be employed as .therapeutic agents .
  • Such therapeutic agents are formulated according to known methods to prepare pharmaceutically useful compositions, whereby the LP polypeptide or antagonist or agonist thereof is combined in a mixture with a pharmaceutically acceptable carrier.
  • LP polypeptide antagonistic or agonistic antibodies if the LP polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred.
  • lipofections or liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment which specifically binds to the binding domain of the target protein is preferred.
  • peptide molecules can be designed which retain the ability to bind the target protein sequence.
  • Such peptides can be synthesized chemically and/or produced by recombinant DNA technology [see, e.g., Marasco et al . , Proc . Natl . Acad. Sci . USA 90(16): 7889- 93 (1993) ] .
  • Therapeutic formulations are prepared for storage by mixing the active ingredient having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers [Remington 's Pharmaceutical Sciences 16th edition (1980)], in the form of lyophilized formulations or aqueous solutions .
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly- (methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microe ulsions, nano-particles and nanocapsules) or in macroemulsions .
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microe ulsions, nano-particles and nanocapsules
  • the formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
  • compositions herein generally are placed into a container having a sterile access port, for example, and intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable. matrices of solid hydrophobic polymers containing the therapeutic agent (s), which matrices are in the form of shaped articles, e.g., films, or microcapsules.
  • sustained-release matrices include polyesters, hydrogels [for example, poly (2-hydroxyethyl-methacrylate) , or poly (vinylalcohol) ] , polylactides, copolymers of L-glutamic acid and gamma-ethyl-L-glutamate, non-degradable ethylene- vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate) , and poly-D- (-) -3-hydroxybutyric acid.
  • polyesters for example, poly (2-hydroxyethyl-methacrylate) , or poly (vinylalcohol)
  • polylactides copolymers of L-glutamic acid and gamma-ethyl-L-glutamate
  • non-degradable ethylene- vinyl acetate non-degrad
  • the sustained-release formulations of these proteins may be developed using polylactic-coglycolic acid (PLGA) polymer due to its biocompatibility and wide range of biodegradable properties.
  • PLGA polylactic-coglycolic acid
  • the degradation products of PLGA, lactic and glycolic acids, can be cleared quickly within the human body.
  • the degradability of this polymer can be adjusted from months to years depending on its molecular weight and composition. See Lewis, "Controlled release of bioactive agents from lactide/glycolide polymer" in Biodegradable Polymers as Drug Delivery Systems (Marcel Dekker; New York,
  • the compounds including, but not limited to, antibodies, small organic and inorganic molecules, peptides, anti-sense molecules, ribozymes, etc., of the present invention may be used to treat various conditions including those characterized by overexpression and/or activation of the disease-associated genes identified herein.
  • the active agents of the present invention are administered to a mammal, preferably a human, in accord with known methods, such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerebral, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, intraoccular, intralesional, oral, topical, inhalation, pulmonary, and/or through sustained release.
  • a mammal preferably a human
  • known methods such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerebral, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, intraoccular, intralesional, oral, topical, inhalation, pulmonary, and/or through sustained release.
  • LP polypeptide antagonists or antagonists may be combined with the administration of LP polypeptide antagonists or antagonists, anti-cancer agents, e.g., antibodies of the instant invention.
  • an active agent e.g., an antibody, polypeptide, nucleic acid, ribozyme, or small organic or inorganic molecule
  • an active agent e.g., an antibody, polypeptide, nucleic acid, ribozyme, or small organic or inorganic molecule
  • the agent is suitably administered to the patient at one time or over a series of treatments.
  • Dosages and desired drug concentration of pharmaceutical compositions of the present invention may vary depending on the particular use envisioned. The determination of the appropriate dosage or route of administration is well within the skill of an ordinary artisan. Animal experiments provide reliable guidance for the determination of effective does for human therapy. Interspecies scaling of effective doses can be performed following the principles laid down by Mordenti and Chappell, "The Use of Interspecies Scaling in Toxicokinetics, " in Toxicokinetics and New Drug Development, Yacobi et al . , Eds., Pergamon Press, NY 1989, pp.4246.
  • a composition comprising a LP polypeptide, a LP-polypeptide epitope recognizing antibody, nucleic acid, ribozyme, or small organic or inorganic molecule
  • normal dosage amounts may vary from about 1 ng/kg up to 100 mg/kg of mammal body weight or more per day, preferably about 1 pg/kg/day up to 100 mg/kg of mammal body weight or more per day, depending upon the route of administration.
  • Guidance as to particular dosages and methods of delivery is provided in the literature; see, for example, U.S. Pat. Nos. 4,657,760, 5,206,344 or 5,225,212.
  • dosages may be administered by one or more separate administrations or by continuous infusion. For repeated administrations over several days or longer, depending on the condition, the treatment is sustained until a desired suppression of disease symptoms occurs. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.
  • therapeutic utility of the LP polypeptide is determined by measuring phosphorylation of tyrosine residues on specific cell lines, Example 5.
  • the early cellular response of cells stimulated with the majority of proteins is protein phosphorylation of the tyrosine residues.
  • This response includes autophosphor- ylation of corresponding receptors, which thereby leads to the activation of catalytic properties and the initiation of intracellular pathways specific to the cell type.
  • signaling downstream of receptors requires phosphorylation of specific kinases inside the cell and other intracellular enzymes of different origin as well as the phosphorylation of multiple adapter/scaffold, structural proteins and transcriptional factors. Therefore, diverse protein-induced cell responses can be visualized by monitoring the state of protein phosphorylation after cell stimulation.
  • Immunodetection is used to detect the protein phosphorylation of the stimulated cell.
  • Several antibodies that are directed against specific phosphorylated epitopes in signaling molecules are. readily available. Two specific antibodies are used: phosphospecific anti-MAPK and anti-AKT antibodies. Additionally, non-specific anti-phosphotyrosine antibodies, which recognize tyrosine-phosphorylated proteins, are used. While anti-phosphotyrosine antibodies allow detection of diverse tyrosine phosphorylated proteins without directly addressing the nature of their identity, the phosphospecific anti-MAPK and anti-AKT antibodies recognize only the corresponding proteins in their phosphorylated form.
  • LP polypeptides Another embodiment to determine utility of LP polypeptides involves transfection of cell lines with reporter plasmids followed by cell stimulation with an LP polypeptide, Example 6.
  • Each reporter consists of a defined element, responsive to specific intracellular signaling pathways, upstream of a sequence involving a reporter protein such as luciferase.
  • reporter transcription and translation ensues, and the resulting protein levels can be detected using an assay such as a luminescence assay.
  • the cell stimulation period depends on the reporter plasmid used.
  • positive controls are designed in the form of agonist cocktails which include approximately maximal stimulatory doses of several ligands known to stimulate the represented signaling pathway. Using this design, the chances of finding a positive stimulus for each cell line is maximized.
  • some cell line/reporter combinations will not be stimulated by the specific agonist cocktail, due to lack of an appropriate ligand in the cocktail.
  • the lack of signal induction by an agonist cocktail may be the lack of all signaling components within a particular cell line to activate the transcriptional element. Cell line/reporter combinations with no exogenous stimulus added make up the negative controls .
  • utility of LP proteins is determined by proliferation of cells, Example 7.
  • gross changes in the number of cells remaining in a culture are monitored after exposure to an LP polypeptide for three days.
  • the cells are incubated in an appropriate assay medium to produce a sub-optimal growth rate .
  • an appropriate assay medium usually a 1:10 or 1:20 dilution of normal culture medium results in a 40 to 60% reduction in cell number compared to the undiluted culture medium.
  • This broad growth zone is chosen so that if an LP polypeptide is a stimulator of growth, the cells have room to expand, and conversely, if the LP polypeptide is deleterious, a reduction in cell density can be detected.
  • the assay media is replaced with media containing a detection agent such as Calcein AM, a membrane-permeant fluorescent dye, allowing quantification of the cell number.
  • a FLAG-HIS (FLIS) -tagged version of the LP polypeptide is expressed using mammalian cells such as HEK-293EBNA, COS-7, or HEK293T.
  • the coding region of the cDNA is amplified by PCR of a vector containing a fragment encoding the LP polypeptide.
  • the PCR-generated fragment is cleaved with restriction enzymes and gel- purified.
  • the fragment is then ligated into a mammalian expression vector containing the FLIS epitope tag fused to the C-terminus.
  • Protein expressed by this plasmid construct includes both the FLAG tag (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys) and the 6X His tag at the COOH -terminus of the protein. This tag provides epitopes for commercially available tag- specific antibodies, enabling detection of the protein.
  • a protein-binding assay is performed.
  • the fixed tissue sample is exposed to the FLIS-tagged LP polypeptide, followed by exposure to a primary antibody and a secondary antibody containing a fluorescent dye.
  • Tagged LP polypeptide which binds to the antigens in the tissue will fluoresce. Binding of the protein to an antigen in the tissue suggests that the protein is expressed in that tissue, Example 8. Thus, protein expression can be determined by measuring which tissues fluoresce.
  • the bacterial expression vector pQE60 is used for bacterial expression in this example. (QIAGEN, Inc.,
  • pQE60 encodes ampicillin antibiotic resistance (“Ampr”) and contains a bacterial origin of replication (“ori”), an IPTG inducible promoter, a ribosome binding site (“RBS”), six codons encoding histidine residues that allow affinity purification using nickel-nitrilo-tri- acetic acid ( "Ni-NTA” ) affinity resin sold by QIAGEN, Inc., and suitable single restriction enzyme cleavage sites.
  • a DNA fragment encoding a polypeptide can be inserted in such a way as to produce that polypeptide with the six His residues (i.e., a "6 X His tag") covalently linked to the carboxyl terminus of that polypeptide.
  • a polypeptide coding sequence can optionally be inserted such that translation of the six His codons is prevented and, therefore, a polypeptide is produced with no 6 X His tag.
  • the nucleic acid sequence encoding the desired portion of a LP polypeptide lacking the hydrophobic leader sequence is amplified from a cDNA clone using PCR oligonucleotide primers (based on the sequences presented, e.g., in SEQ ID NO:l, 3, or 5), which anneal to the amino terminal encoding DNA sequences of the desired portion of the LP polypeptide- encoding nucleic acid and to sequences in the construct 3 ' to the cDNA coding sequence. Additional nucleotides containing restriction sites to facilitate cloning in the pQE60 vector are added to the 5' and 3' sequences, respectively.
  • the 5' and 3' primers have nucleotides corresponding or complementary to a portion of the coding sequence of the LP polypeptide-encoding nucleic acid, e.g., as presented in SEQ ID NO: 1, 3, or 5, according to known method steps.
  • the point in a polynucleotide sequence where the 5 ' primer begins can be varied to amplify a desired portion of the complete polypeptide enoding polynucleotide shorter or longer than the polynucleotide which encodes the mature form of the polypeptide.
  • the amplified nucleic acid fragments and the vector pQE60 are digested with appropriate restriction enzymes and the digested DNAs are then ligated together. Insertion of the LP polypeptide-encoding DNA into the restricted pQE60 vector places the LP242, LP257, or LP259 polypeptide coding region including its associated stop codon downstream from the IPTG-inducible promoter and in-frame with an initiating AUG codon. The associated stop codon prevents translation of the six histidine codons downstream of the insertion point.
  • E. coli strain Ml5/rep4 containing multiple copies of the plasmid pREP4, which expresses the lac repressor and confers kanamycin resistance ("Kanr"), is used in carrying out the illustrative example described herein.
  • This strain which is only one of many that are suitable for expressing LP polypeptides, is available commercially from QIAGEN, Inc. Transformants are identified by their ability to grow on LB plates in the presence of ampicillin and kanamycin. Plasmid DNA is isolated from resistant colonies and the identity of the cloned DNA confirmed by restriction analysis, PCR and DNA sequencing.
  • Clones containing the desired constructs are grown overnight ("O/N") in liquid culture in LB media supplemented with both ampicillin (100 ⁇ g/ml) and kanamycin (25 ⁇ g/ml) .
  • the O/N culture is used to inoculate a large culture, at a dilution of approximately 1:25 to 1:250.
  • the cells are grown to an optical density at 600 nm ("OD600") of between 0.4 and 0.6.
  • Isopropyl-b-D-thiogalactopyranoside (“IPTG”) is then added to a final concentration of 1 mM to induce transcription from the lac repressor sensitive promoter, by inactivating the lacl repressor.
  • Cells subsequently are incubated further for 3 to 4 hours. Cells then are harvested by centrifugation.
  • the cells are then stirred for 3-4 hours at 4°C in 6M guanidine-HCl, pH8.
  • the cell debris is removed by centrifugation, and the supernatant containing the LP polypeptide is dialyzed against 50 mM Na-acetate buffer pH6, supplemented with 200 mM NaCI.
  • a LP polypeptide can be successfully refolded by dialyzing it against 500 mM NaCI, 20% glycerol, 25 mM Tris/HCl pH7.4, containing protease inhibitors .
  • the protein is made soluble according to known method steps. After re- naturation, the LP polypeptide is purified by ion exchange, hydrophobic interaction, and size exclusion chromatography. Alternatively, an affinity chromatography step such as an antibody column is used to obtain a purified form of the LP polypeptide.
  • the purified polypeptide is stored at 4°C or frozen at -40°C to -120°C.
  • the plasmid shuttle vector pA2 GP is used to insert the cloned DNA encoding the mature LP polypeptide into a baculovirus, using a baculovirus leader and standard methods as described in Summers, et al . , A Manual of Methods for Baculovirus Vectors and Insect Cell Cul ture Procedures, Texas Agricultural Experimental Station Bulletin No. 1555 (1987).
  • This expression vector contains the strong polyhedrin promoter of the Autographa californica nuclear polyhedrosis virus (AcMNPV) followed by the secretory signal peptide (leader) of the baculovirus gp67 polypeptide and convenient restriction sites such as BamHI, Xba I, and Asp718.
  • the polyadenylation site of the simian virus 40 ("SV40") is used for efficient polyadenylation.
  • the plasmid contains the beta-galactosidase gene from E. coli under control of a weak Drosophila promoter in the same orientation, followed by the polyadenylation signal of the polyhedrin gene.
  • the inserted genes are flanked on both sides by viral sequences for cell-mediated homologous recombination with wild-type viral DNA to generate viable virus that expresses the cloned polynucleotide.
  • baculovirus vectors are used in place of the vector above, such as pAc373, pVL941 and pAcIMl, as one skilled in the art would readily appreciate, as long as the construct provides appropriately located signals for transcription, translation, secretion and the like, including a signal peptide and an in-frame AUG as required.
  • Such vectors are described, for instance, in Luckow, et al . , Virology 170:31-39.
  • the cDNA sequence lacking the AUG initiation codon and the naturally associated nucleotide binding site but encoding a mature LP polypeptide is amplified using PCR oligonucleotide primers corresponding to the 5 ' and 3 ' sequences of the gene.
  • Non-limiting examples include 5' and 3 ' primers having nucleotides corresponding or complementary to a portion of the coding sequence of a LP polypeptide- encoding polynucleotide, e.g., as presented in SEQ ID N0:1, 3, or 5, according to known method steps.
  • the amplified fragment is isolated from a 1% agarose gel using a commercially available kit (e.g., "Geneclean, " BIO 101 Inc., La Jolla, CA) .
  • the fragment then is then digested with the appropriate restriction enzyme and again is purified on a 1% agarose gel. This fragment is designated herein "Fl” .
  • the plasmid is digested with the corresponding restriction enzymes and optionally, can be dephosphorylated using calf intestinal phosphatase, using routine procedures known in the art.
  • the DNA is then isolated from a 1% agarose gel using a commercially available kit ("Geneclean” BIO 101 Inc., La Jolla, CA) . This vector DNA is designated herein "VI” .
  • E. coli HB101 or other suitable E. coli hosts such as XL-1 Blue (Stratagene Cloning Systems, La Jolla, CA) cells are transformed with the ligation mixture and spread on culture plates.
  • Bacteria are identified that contain the plasmid bearing a huma LP polypeptide encoding polynucleotide using the PCR method, in which one of the primers that is used to amplify the gene and the second primer is from well within the vector so that only those bacterial colonies containing a LP polypeptide encoding polynucleotide fragment will show amplification of the DNA.
  • the sequence of the cloned fragment is confirmed by DNA sequencing.
  • the resulting plasmid is designated herein as pBacLP .
  • a pBacLP plasmid construct Five ⁇ g of a pBacLP plasmid construct is co-transfected with 1.0 ⁇ g of a commercially available linearized baculovirus DNA ( "BaculoGoldTM baculovirus DNA", Pharmingen, San Diego, CA) , using the lipofection method described by Feigner, et al . , Proc. Natl . Acad. Sci . USA 84:7413-7417 (1987). 1 ⁇ g of BaculoGoldTM virus DNA and 5 ⁇ g of the plasmid pBacLP are mixed in a sterile well of a microtiter plate containing 50 ⁇ l of serum-free Grace's medium (Life Technologies, Inc., Rockville, MD) .
  • plaque assay After four days the supernatant is collected and a plaque assay is performed.
  • An agarose gel with "Blue Gal” (Life Technologies, Inc., Rockville, MD) is used to allow easy identification and isolation of gal-expressing clones, which produce blue-stained plaques.
  • a detailed description of a "plaque assay” of this type can also be found in the user's guide for insect cell culture and baculovirology distributed by Life Technologies, Inc., Rockville, MD, page 9-10) . After appropriate incubation, blue stained plaques are picked with a micropipettor tip (e.g., Eppendorf) .
  • the agar containing the recombinant viruses is then resuspended in a microcentrifuge tube containing 200 ⁇ l of Grace's medium and the suspension containing the recombinant baculovirus is used to infect Sf9 cells seeded in 35mm dishes. Four days later the supernatants of these culture dishes are harvested and then they are stored at 4°C.
  • Sf9 cells are grown in Grace's medium supplemented with 10% heat-inactivated FBS.
  • the cells are infected with the recombinant baculovirus at a multiplicity of infection ("MOI") of about 2.
  • MOI multiplicity of infection
  • the medium is removed and is replaced with SF900 II medium minus methionine and cysteine (available, e.g., from Life Technologies, Inc., Rockville, MD) .
  • SF900 II medium minus methionine and cysteine available, e.g., from Life Technologies, Inc., Rockville, MD
  • radiolabeled polypeptides 42 hours later, 5 mCi of 35 S-methionine and 5 mCi 35 S- cysteine (available from Amersham) are added.
  • the cells are further incubated for 16 hours and then they are harvested by centrifugation.
  • polypeptides in the supernatant as well as the intracellular polypeptides are analyzed by SDS- PAGE followed by autoradiography (if radiolabeled) . Microsequencing of the amino acid sequence of the amino terminus of purified polypeptide can be used to determine the amino terminal sequence of the mature polypeptide and thus the cleavage point and length of the secretory signal peptide.
  • a typical mammalian expression vector contains at least one promoter element, which mediates the initiation of transcription of mRNA, the polypeptide coding sequence, and signals required for the termination of transcription and polyadenylation of the transcript . Additional elements include enhancers, Kozak sequences and intervening sequences flanked by donor and acceptor sites for RNA splicing. Highly efficient transcription can be achieved with the early and late promoters from SV40, the long terminal repeats (LTRS) from Retroviruses, e.g., RSV, HTLVI, HIVI and the early promoter of the cytomegalovirus (CMV) . However, cellular elements can also be used (e.g., the human actin promoter) .
  • Suitable expression vectors for use in practicing the present invention include, for example, vectors such as pIRESlneo, pRetro-Off, pRetro-On, PLXSN, or pLNCX (Clonetech Labs, Palo Alto, CA) , pcDNA3.1 (+/-), pcDNA/Zeo (+/-) or pcDNA3.1/Hygro (+/-) (Invitrogen), PSVL and PMSG (Pharmacia, Uppsala, Sweden), pRSVcat (ATCC 37152), pSV2dhfr (ATCC 37146) and pBCl2MI (ATCC 67109).
  • vectors such as pIRESlneo, pRetro-Off, pRetro-On, PLXSN, or pLNCX (Clonetech Labs, Palo Alto, CA) , pcDNA3.1 (+/-), pcDNA/Zeo (+/-) or pc
  • mammalian host cells include human Hela 293, H9 , Jurkat cells, mouse NIH3T3, C127 cells, Cos 1, Cos 7 and CV 1, quail QC1-3 cells, mouse L cells and Chinese hamster ovary (CHO) cells.
  • the gene is expressed in stable cell lines that contain the gene integrated into a chromosome.
  • a selectable marker such as DHRF (dihydrofolate reductase) , GPT neomycin, or hygromycin allows the identification and isolation of the transfected cells .
  • the transfected gene can also be amplified to express large amounts of the encoded polypeptide.
  • the DHFR marker is useful to develop cell lines that carry several hundred or even several thousand copies of the gene of interest.
  • Another useful selection marker is the enzyme glutamine synthase (GS) (Murphy, et al . , Biochem. J. 227:277-279 (1991); Bebbington, et al . , Bio/Technology 10 : 169-175 (1992)) .
  • GS glutamine synthase
  • the mammalian cells are grown in selective medium and the cells with the highest resistance are selected.
  • These cell lines contain the amplified gene(s) integrated into a chromosome. Chinese hamster ovary (CHO) and NSO cells are often used for the production of polypeptides.
  • the expression vectors pCl and pC4 contain the strong promoter (LTR) of the Rous Sarcoma Virus (Cullen, et al . , Molec. Cell . Biol . 5:438-447 (1985)) plus a fragment of the CMV-enhancer (Boshart, et al . , Cell 41:521-530 (1985)). Multiple cloning sites, e.g., with the restriction enzyme cleavage sites BamHI, Xbal and Asp718, facilitate the cloning of the gene of interest.
  • the vectors contain in addition the 3 ' intron, the polyadenylation and termination signal of the rat preproinsulin gene .
  • the expression plasmid, pLP HA is made by cloning a cDNA encoding a LP 1 polypeptide into the expression vector pcDNAI/Amp or pcDNAIII (which can be obtained from Invitrogen, Inc.) .
  • the expression vector pcDNAI/amp contains: (1) an E. coli origin of replication effective for propagation in E. coli and other prokaryotic cells; (2) an ampicillin resistance gene for selection of plasmid-containing prokaryotic cells; (3) an SV40 origin of replication for propagation in eukaryotic cells; (4) a CMV promoter, a polylinker, an SV40 intron; (5) several codons encoding a hemagglutinin fragment (i.e., an "HA" tag to facilitate purification) or HIS tag (see, e.g, Ausubel, supra) followed by a termination codon and polyadenylation signal arranged so that a cDNA can be conveniently placed under expression control of the CMV promoter and operably linked to the SV40 intron and the polyadenylation signal by means of restriction sites in the polylinker.
  • an E. coli origin of replication effective for propagation in E. coli and other prokaryotic cells
  • an ampicillin resistance gene for selection
  • the HA tag corresponds to an epitope derived from the influenza hemagglutinin polypeptide described by Wilson, et al . , Cell 37:767-778 (1984) .
  • the fusion of the HA tag to the target polypeptide allows easy detection and recovery of the recombinant polypeptide with an antibody that recognizes the HA epitope.
  • pcDNAIII contains, in addition, the selectable neomycin marker .
  • a DNA fragment encoding the LP polypeptide is cloned into the polylinker region of the vector so that recombinant polypeptide expression is directed by the CMV promoter.
  • the plasmid construction strategy is as follows.
  • the LP- polypeptide encoding cDNA of a clone is amplified using primers that contain convenient restriction sites, much as described above for construction of vectors for expression of LP polypeptides in E. coli .
  • suitable primers include those based on the coding sequences presented in SEQ ID 110:1, 3, or 5.
  • the PCR amplified DNA fragment and the vector, pcDNAI/Amp, are digested with suitable restriction enzyme (s) and then ligated.
  • the ligation mixture is transformed into E. coli strain SURE (available from Stratagene Cloning Systems, 11099 North Torrey Pines Road, La Jolla, CA 92037), and the transformed culture is plated on ampicillin media plates which then are incubated to allow growth of ampicillin resistant colonies. Plasmid DNA is isolated from resistant colonies and examined by restriction analysis or other means for the presence of the LP polypeptide-encoding fragme t .
  • COS cells are transfected with an expression vector, as described above, using DEAE-DEXTRAN, as described, for instance, in Sambrook, et al . , Molecular Cloning: a Laboratory Manual , Cold Spring Laboratory Press, Cold Spring Harbor, New York (1989) . Cells are incubated under conditions suitable for expression of the LP-polypeptide encoding polynucleotide by the vector.
  • LP polypeptide-HA fusion polypeptide is detected by radiolabeling and immunoprecipitation, using methods described in, for example Harlow, et al . , Antibodies : A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1988) .
  • the cells are labeled by incubation in media containing 35 S-cysteine for 8 hours.
  • the cells and the media are collected, and the cells are washed and lysed with detergent-containing RIPA buffer: 150 mM NaCI, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM TRIS, pH 7.5, as described by Wilson, et al . cited above.
  • Proteins are precipitated from the cell lysate and from the culture media using an HA-specific monoclonal antibody.
  • the precipitated polypeptides then are analyzed by SDS-PAGE and autoradiography. An expression product of the expected size is seen in the cell lysate, which is not seen in negative controls .
  • Plasmid pC4 is used for the expression of The LP polypeptide.
  • Plasmid pC4 is a derivative of the plasmid pSV2-dh.fr (ATCC Accession No. 37146) .
  • the plasmid contains the mouse DHFR gene under control of the SV40 early promoter.
  • Chinese hamster ovary cells or other cells lacking dihydrofolate activity that are transfected with these plasmids can be selected by growing the cells in a selective medium (alpha minus MEM, Life Technologies) supplemented with methotrexate.
  • MTX methotrexate
  • Plasmid pC4 contains for expressing the gene of interest the strong promoter of the long terminal repeat (LTR) of the Rous Sarcoma Virus (Cullen, et al . , Molec . Cell . Biol . 5:438-447 (1985)) plus a fragment isolated from the enhancer of the immediate early gene of human cytomegalovirus (CMV) (Boshart, et al . , Cell 41:521-530 (1985)) . Downstream of the promoter are BamHI, Xbal, and Asp718 restriction enzyme cleavage sites that allow integration of the genes.
  • LTR long terminal repeat
  • CMV cytomegalovirus
  • the plasmid contains the 3 ' intron and polyadenylation site of the rat preproinsulin gene.
  • Other high efficiency promoters can also be used for the expression, e.g., the human b-actin promoter, the SV40 early or late promoters or the long terminal repeats from other retroviruses, e.g., HIV and HTLVI .
  • Clontech's Tet-Off and Tet-On gene expression systems and similar systems can be used to express the LP in a regulated way in mammalian cells (M. Gossen, and H. Bujard, Proc . Natl . Acad. Sci . USA 89: 5547-5551 (1992)).
  • Stable cell lines carrying a gene of interest integrated into the chromosomes can also be selected upon co-transfection with a selectable marker such as gpt, G418 or hygromycin. It is advantageous to use more than one selectable marker in the beginning, e.g., G418 plus methotrexate .
  • the plasmid pC4 is digested with restriction enzymes and then dephosphorylated using calf intestinal phosphatase by procedures known in the art.
  • the vector is then isolated from a 1% agarose gel.
  • the DNA sequence encoding the complete LP polypeptide is amplified using PCR oligonucleotide primers corresponding to the 5' and 3' sequences of the gene.
  • Non-limiting examples include 5 ' and 3 ' primers having nucleotides corresponding or complementary to a portion of the coding sequences of a LP polypeptide-encoding polynucleotide, e.g., as presented in SEQ ID NO: 1, 3, or 5, according to known method steps .
  • the amplified fragment is digested with suitable endonucleases and then purified again on a 1% agarose gel.
  • the isolated fragment and the dephosphorylated vector are then ligated with T4 DNA ligase.
  • E. coli HB101 or XL-1 Blue cells are then transformed and bacteria are identified that contain the fragment inserted into plasmid pC4 using, for instance, restriction enzyme analysis.
  • Chinese hamster ovary (CHO) cells lacking an active DHFR gene are used for transfection.
  • 5 ⁇ g of the expression plasmid pC4 is cotransfected with 0.5 ⁇ g of the plasmid pSV2-neo using lipofectin.
  • the plasmid pSV2neo contains a dominant selectable marker, the neo gene from Tn5 encoding an enzyme that confers resistance to a group of antibiotics including G418.
  • the cells are seeded in alpha minus MEM supplemented with 1 ⁇ g/ml G418.
  • the cells are trypsinized and seeded in hybridoma cloning plates (Greiner, Germany) in alpha minus MEM supplemented with 10, 25, or 50 ng/ml of methotrexate plus 1 ⁇ g/ml G418. After about 10-14 days single clones are trypsinized and then seeded in 6-well petri dishes or 10 ml flasks using different concentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM) .
  • Clones growing at the highest concentrations of methotrexate are then transferred to new 6-well plates containing even higher concentrations of methotrexate (1 mM, 2 mM, 5 mM, 10 mM, 20 mM) . The same procedure is repeated until clones are obtained which grow at a concentration of 100 - 200 mM. Expression of the desired gene product is analyzed, for instance, by SDS-PAGE and Western blot or by reverse phase HPLC analysis.
  • Northern blot analysis is carried out to examine expression of LP-polypeptide encoding mRNA in human tissues, using methods described by, among others, Sambrook, et al . , cited above.
  • a cDNA probe preferably encoding the entire LP polypeptide is labeled with 32 using the RediprimeTM DNA labeling system (Amersham Life Science) , according to the manufacturer's instructions. After labeling, the probe is purified using a CHROMA SPIN-100TM column (Clontech Laboratories, Inc.), according to the manufacturer's protocol number PT1200-1. The purified and labeled probe is used to examine various human tissues for LP polypeptide mRNA.
  • MTN Multiple Tissue Northern
  • H human tissues
  • IM human immune system tissues
  • Protein-induced cell responses are determined by monitoring tyrosine phosphorylation upon stimulation of cells by addition of LP proteins. This is accomplished in two steps: cell manipulation and immunodetection .
  • Protein phosphorylation of LP242 is measured using the Saos (osteosarcoma) cell line.
  • the cells are plated into poly-D-lysine- coated, 96 well plates containing cell propagation medium [DMEM:F12 (3:1), 20 mM Hepes at pH 7.5 , 5% FBS, and 50 ⁇ g/mL Gentamicin] .
  • the cells are seeded at a concentration of 20,000 cells per well in 100 ⁇ L medium.
  • the propagation medium in each well is replaced with 100 ⁇ L starvation medium containing DMEM.-F12 (3:1), 20mM Hepes at pH 7.5, 0.5% FBS, and 50 ⁇ g/mL Gentamicin.
  • the cells are incubated overnight .
  • pervanadate solution is made 10 minutes before cell lysis; pervanadate is prepared by mixing 100 ⁇ L of sodium orthovanadate (100 mM) and 3.4 ⁇ L of H0 2 (producing 100X stock pervanadate solution) .
  • the lysis buffer is then prepared: 50mM Hepes at pH 7.5, 150 mM NaCl, 10% glycerol, 1% TRITON X-100, 1 mM EDTA, 1 mM pervanadate, and BM protease inhibitors.
  • the cells are stimulated by adding 10 ⁇ L of an LP protein solution to the cells, and incubating for 10 minutes. Next, the medium is aspirated, and 75 ⁇ L lysis buffer are added to each well.
  • the cells are lysed at 4°C for 15 minutes, then 25 ⁇ L of 4X loading buffer are added to the cell lysates .
  • the resultant solution is mixed then heated to 95°C.
  • Detection of tyrosine phosphorylation is accomplished by Western immunoblotting. Twenty microliters of each cell sample are loaded onto SDS-PAGE 8-16% AA ready gels from Bio-Rad, and the gels are run. The proteins are electrotransferred in transfer buffer (25 mM Tris base at pH 8.3, 0.2 M glycine, 20% methanol) from the gel to a nitrocellulose membrane using 250 mA per gel over a one hour period. The membrane is incubated for one hour at ambient conditions in blocking buffer consisting of TBST (20 mM TrisHCl at pH 7.5, 150 mM NaCl, 0.1% TWEEN-20) with 1% BSA.
  • transfer buffer 25 mM Tris base at pH 8.3, 0.2 M glycine, 20% methanol
  • the antibodies are added to the membrane.
  • the membrane is incubated overnight at 4°C with gentle rocking in primary antibody solution consisting of the antibody, TBST, and 1% BSA.
  • the next day the membrane is washed three times, five minutes per wash, with TBST.
  • the membrane is then incubated in the secondary antibody solution consisting of the antibody, TBST, and 1% BSA for 1 hour at ambient conditions with gentle rocking. After the incubation, the membrane is washed four times with TBST, ten minutes per wash.
  • Detection is accomplished by incubating the membrane with 10 to 30 mL of SuperSignal Solution for 1 minute at ambient conditions. After 1 minute, excess developing solution is removed, and the membrane is wrapped in plastic wrap. The membrane is exposed to X-ray film for 20 second, 1 minute, and 2 minute exposures (or longer if needed) . The number and intensity of immunostained protein bands are compared to bands for the negative control-stimulated cells (basal level of phosphorylation) by visual comparison. LP242 was detected to activate the JNK/SAP kinase pathway in Saos cells.
  • Example 6 LP242 Cell Stimulation with Detection Utilizing Reporters Protein-induced cell responses are measured using reporters. The following cell line/reporter combinations are used:
  • positive controls are designed in the form of agonist cocktails . These cocktails included approximate maximal stimulatory doses of several ligands known to stimulate the regulated signal pathway. The following agonist cocktails are used as positive controls:
  • the cells are transiently transfected with the reporter plasmids in tissue culture flasks using a standard optimized protocol for all cell lines (see Example 1) .
  • the cells are trypsinized and seeded into 96-well poly-D-lysine coated assay plates at a rate of 20,000 cells per well in growth medium.
  • the medium is replaced with serum-free growth medium.
  • stimulants for those reporters which required a 24-hour stimulation period are added.
  • stimulants for the reporters which required a 5-hour stimulation period are added. Five hours later, all conditions are lysed using a lysis/luciferin cocktail, and the fluorescence of the samples is determined using a Micro Beta reader.
  • Each assay plate is plated to contain 4 positive control wells, 16 negative control wells, and 64 test sample wells (2 replicates of 32 test samples) .
  • the threshold value for a positive "hit” is a fluorescence signal equal to the mean plus two standard deviations of the negative control wells. Any test sample that, in both replicates, generates a signal above that threshold is defined as a "hit.”
  • LP242 was determined to activate SMAD signaling in Ishikawa cells and Protein Kinase C in L6 and SK-N-MC cells.
  • Example 7 Cell Proliferation and Cytotoxicity Determination of LP242 Utilizing Fluorescence Detection This assay is designed to monitor gross changes in the number of cells remaining in culture after exposure to LP proteins for a period of three days. The following cells are used in this assay:
  • GTl-7 hypothalamic SV40 transformed cell line
  • HEP-G2 (ATCC HB-8065)
  • ECV304 endothelial cell line
  • GLUTag SV40 Tag transformed enteroendocrine cell line
  • HUVEC (Clonetics # CC2517T150)
  • balb/c 3T3 (ATCC CCL-163)
  • HDF skin fibroblasts
  • M07E leukemia cell line
  • THP-1 (ATCC TIB-202)
  • T1165 B cell line
  • an appropriate assay medium Prior to assay, cells are incubated in an appropriate assay medium to produce a sub-optimal growth rate, e.g., a 1:10 or 1:20 dilution of normal culture medium.
  • Cells are grown in T-150 flasks, then harvested by trypsin digestion and replated at 40 to 50% confluence into poly-D-lysine- treated 96-well plates. Cells are only plated into the inner 32 wells to prevent edge artifacts due to medium evaporation; the outer wells are filled with buffer alone.
  • LP proteins are added to the appropriate wells . Each protein is assayed in triplicate at two different concentrations, IX and 0. IX dilution in assay medium. Two controls are also included on each assay plate: assay medium and normal growth medium.
  • the plates are processed to determine the number of viable cells. Plates are spun to increase the attachment of cells to the plate. The medium is then discarded, and 50 ⁇ L of detection buffer is added to each well.
  • the detection buffer consisted on MEM medium containing no phenol red (Gibco) with calcein AM (Molecular Probes) and PLURONICTM F-127 (Molecular Probes), each at a 1:2000 dilution. After incubating the plates in the dark at room temperature for thirty minutes, the fluorescence intensity of each well is measured using a Cytofluor 4000-plate reader (PerSeptive Biosysterns) . For a given cell type, the larger the fluorescence intensity, the greater the number of cells in the well.
  • Binding of LP242 protein to human tissues is determined by protein staining with fluorescent dye.
  • the following human tissues are used in this assay:
  • Staining intensity Key +++ Strong staining; ++ Moderate Staining; + Weak Staining; - No detectable Staining All tissues are fixed with 3% paraformaldehyde and embedded in paraffin.
  • Tissues are prepared for analysis by removing the paraffin with xylene then gradually rehydrating the tissue with graded solutions of ethanol and water.
  • Antigen retrieval is performed to unmask antigenic sites so that antibodies can recognize the antigen. This is accomplished by soaking the tissue in citrate buffer (Dako, Carpinteria, CA) for twenty minutes at 80 to 90°C followed 10 minutes at ambient temperature. The tissue is then washed in tris- buffered saline (TBS) containing 0.05% TWEENTM 20 and 0.01% thimerosol. To minimize non-specific background staining, the tissue is soaked in non-serum protein block (Dako) for 45 minutes, after which the protein block is removed by blowing air over the tissue.
  • TBS tris- buffered saline
  • the tissue is exposed for 2 hours to the FLAG-HIS tagged LP protein at 10 ⁇ g/mL. Following exposure, the tissue is washed twice with tris-buffered saline (TBS) containing 0.05% TWEENTM 20 and 0.01% thimerosol. The tissue sample is then incubated for one hour with mouse anti-FLAG antibody at 10 ⁇ g/mL. Subsequently, the tissue is washed twice with tris-buffered saline (TBS) containing 0.05% TWEENTM 20 and 0.01% thimerosol.
  • TBS tris-buffered saline
  • the tissue is exposed to rabbit anti-mouse Ig with Alexa 568, a fluorescent dye, at 10 ⁇ g/mL for one hour, followed again by two washes with tris-buffered saline (TBS) containing 0.05% TWEENTM 20 and 0.01% thimerosol. Finally, the tissue is coverslipped with fluorescence mounting media, and the fluorescence is measured. A positive fluorescence, reading indicates that the protein binds with antigens on the tissue, suggesting that the protein is expressed in that tissue.
  • TBS tris-buffered saline

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Abstract

La présente invention concerne des séquences d'acide nucléique codant de nouvelles protéines humaines. Ces nouveaux acides nucléiques sont utiles pour construire les vecteurs d'ADN et les cellules hôtes selon l'invention et pour préparer les acides nucléiques, les protéines de recombinaison et les anticorps selon l'invention qui sont utiles dans les procédés et les utilisations en médecine selon l'invention.
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