Human hydrolase-like molecules

Abstract

The invention provides human hydrolase-like molecules (HHLM) and polynucleotides which identify and encode HHLM. The invention also provides expression vectors, host cells, antibodies, agonists, and antagonists. The invention also provides methods for treating or preventing disorders associated with expression of HHLM.

Description

[0001] This application is a divisional application of U.S. application Ser. No. 09/612,473, filed Jul. 7, 2000, which is a continuation-in-part application of U.S. application Ser. No. 09/013,881, filed Feb. 6, 1998, now U.S. Pat. No. 6,132,964, issued Oct. 17, 2000, all of which applications and patents are hereby incorporated herein by reference.

FIELD OF THE INVENTION

[0002] This invention relates to nucleic acid and amino acid sequences of human hydrolase-like molecules and to the use of these sequences in the diagnosis, or treatment of cell proliferation disorders, and autoimmune disorders.

BACKGROUND OF THE INVENTION

[0003] Hydrolysis is a common enzymatic mechanism. There are numerous enzymes whose catalytic mechanism involves breaking a covalent bond in a substrate by the addition of a molecule of water across the bond. The reaction involves a nucleophilic attack by the water molecule's oxygen atom on a target bond within the substrate and results in a splitting of the water molecule across the target bond, thereby breaking the bond and generating two product molecules. This general mechanism applies to a wide variety of enzymes including phosphatases, lysophospholipases, glyoxalases, and phosphodiesterases.

[0004] The protein phosphorylation/dephosphorylation cycle is one of the major regulatory mechanisms employed by eukaryotic cells to control cellular activities. During protein phosphorylation, phosphate groups are transferred from adenosine triphosphate molecules to a protein by protein kinases. During protein dephosphorylation, phosphate groups are removed from a protein by protein phosphatases using a hydrolytic mechanism. In this manner, phosphatases are involved in the control of many cellular signaling events that regulate cell growth and differentiation, cell-to-cell contact, the cell cycle, and oncogenesis. Protein phosphatases may be characterized by amino acid residue specificity, for example, serine/threonine phosphatases, tyrosine phosphatases, or dual-specificity phosphatases. Dual-specificity phosphatases contain a conserved cysteine residue essential for catalytic activity. (Ishibashi et al. (1992) Proc Natl Acad Sci 89:12170-12174.)

[0005] Lysophospholipases (LPLs) are widely distributed enzymes that regulate intracellular lipids, and occur in numerous isoforms. These isoforms vary in molecular mass, the substrate metabolized, and the optimum pH required for activity. Small isoforms, approximately 15-30 kDa, function as hydrolases; large isoforms, those exceeding 60 kDa, function both as hydrolases and transacylases. A particular substrate for LPLs, lysophosphatidylcholine, causes lysis of cell membranes when it is formed or imported into a cell. LPLs are regulated by lipid factors including acylcarnitine, arachidonic acid, and phosphatidic acid. Thus, the activity of LPLs is regulated by signaling molecules important in numerous pathways including the inflammatory response.

[0006] The glyoxylase system consists of glyoxylase I, which catalyzes the formation of S-D-lactoylglutathione from methyglyoxal, a side product of triose-phosphate energy metabolism, and glyoxylase II, which hydrolyzes S-D-lactoylglutathione to D-lactic acid and reduced glutathione. Methyglyoxal levels are elevated during hyperglycemia and are likely due to increased triosephosphate energy metabolism. Elevated levels of glyoxylase II activity have been found in human and in a rat model of non-insulin-dependent diabetes mellitus. The glyoxylase system has been implicated in the detoxification of bacterial toxins and in the control of cell proliferation and microtubule assembly. Elevated levels of S-D-lactoylglutathione, the substrate of glyoxylase II, induced growth arrest and toxicity in HL60 cells. Thus, the glyoxylase system, and glyoxylase II in particular, may be associated with cell proliferation and autoimmune disorders such as diabetes.

[0007] Sphingomyelin is a membrane phospholipid that is hydrolyzed to ceramide and phosphatidylcholine by the action of the phosphodiesterase, acid sphingomyelinase. Phosphatidylcholine is involved in numerous intracellular signaling pathways, while ceramide is an essential precursor for the generation of gangliosides, membrane lipids found in high concentration in neural tissue. Defective acid sphingomyelinase phosphodiesterase leads to a build-up of sphingomyelin molecules in lysosomes, resulting in Niemann-Pick disease.

[0008] Post-translation chemical modification of proteins, such as phosphorylation by protein kinase A, has been demonstrated to affect biochemical activity of enzymes (Krebs (1981) Curr Top Cell Regul 18:401-419). In a further example, protein kinase C a phosphorylates and activates the growth promoter Raf (Kolch et al. (1993) Nature 364: 249-252).

[0009] The discovery of new human hydrolase-like molecules and the polynucleotides encoding them satisfies a need in the art by providing new compositions which are useful in the diagnosis, or treatment of cell proliferation disorders and autoimmune disorders.

SUMMARY OF THE INVENTION

[0010] The invention features substantially purified polypeptides, human hydrolase-like molecules, referred to collectively as “HHLM” and individually as “HHLM 1-8”. In one aspect, the invention provides a substantially purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-8 or portions or fragments thereof.

[0011] The invention further provides a substantially purified variant having at least 81% amino acid identity to the amino acid sequences of SEQ ID NOs:11-8 or fragments thereof. The invention also provides an antigenic epitope selected from SEQ ID NOs:1-8, an oligopeptide selected from of SEQ ID NOs:1-8, and a biologically active portion selected from SEQ ID NOs:1-8. The invention also includes an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-8 or fragments thereof.

[0012] Additionally, the invention provides an isolated and purified polynucleotide which hybridizes under stringent conditions to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-8 or fragments thereof, as well as an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide encoding the polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NOs:1-8 or fragments thereof. The invention also provides a purified polypeptide of an amino acid sequence encoded by a polynucleotide selected from SEQ ID NOs:17-55.

[0013] The invention also provides an isolated and purified polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:9-16 or fragments thereof. The invention further provides an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucleotide sequence comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:9-16 or fragments thereof, as well as an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:9-16 or fragments thereof

[0014] The invention also provides an isolated and purified polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:17-55 or fragments thereof. The invention further provides an isolated and purified polynucleotide variant having at least 90% polynucleotide sequence identity to the polynucleotide sequence comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:17-55 or fragments thereof, as well as an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:17-55 or fragments thereof

[0015] The invention further provides an expression vector containing at least a fragment of the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs:1-8 or fragments thereof. In another aspect, the expression vector is contained within a host cell.

[0016] The invention also provides a method for producing a polypeptide comprising the amino acid sequence of SEQ ID NOs:1-8 or fragments thereof, the method comprising the steps of: (a) culturing the host cell containing an expression vector containing at least a fragment of a polynucleotide encoding the polypeptide under conditions suitable for the expression of the polypeptide; and (b) recovering the polypeptide from the host cell culture.

[0017] The invention also provides a pharmaceutical composition comprising a substantially purified HHLM having the amino acid sequence of SEQ ID NOs:1-8 or fragments thereof in conjunction with a suitable pharmaceutical carrier.

[0018] The invention further includes a purified antibody which binds to a polypeptide comprising the amino acid sequence of SEQ ID NOs:1-8 or fragments thereof, as well as a purified agonist and a purified antagonist to the polypeptide.

[0019] The invention also provides a method for treating or preventing a cell proliferation disorder, the method comprising administering to a subject in need of such treatment an effective amount of an antagonist of the polypeptide having an amino acid sequence of SEQ ID NOs:1-8 or fragments thereof.

[0020] The invention also provides a method for treating or preventing an autoimmune disorder, the method comprising administering to a subject in need of such treatment an effective amount of an antagonist of the polypeptide having an amino acid sequence of SEQ ID NOs:1-8 or fragments thereof.

[0021] The invention also provides a method for detecting a polynucleotide encoding the polypeptide comprising the amino acid sequence SEQ ID NOs:1-8 or fragments thereof in a biological sample containing nucleic acids, the method comprising the steps of: (a) hybridizing the complement of the polynucleotide sequence encoding the polypeptide comprising SEQ ID NOs:1-8 or fragments thereof to at least one of the nucleic acids of the biological sample, thereby forming a hybridization complex; and (b) detecting the hybridization complex, wherein the presence of the hybridization complex correlates with the presence of a polynucleotide encoding the polypeptide in the biological sample. In one aspect, the nucleic acids of the biological sample are amplified by the polymerase chain reaction prior to the hybridizing step.

[0022] The invention further provides a method of using a polypeptide to screen a plurality of molecules or compounds to identify a ligand which specifically binds the polypeptide. In one aspect, the molecules or compounds are selected from DNA molecules, RNA molecules, peptide nucleic acids, peptides, proteins, mimetics, agonists, antagonists, antibodies, immunoglobulins, inhibitors, and drugs.

[0023] The invention further provides a method of using a polypeptide to screen subject sample for antibodies which specifically bind the polypeptide.

[0024] The invention further provides a method of using a polypeptide to prepare and purify antibodies which specifically bind the polypeptide.

BRIEF DESCRIPTION OF THE FIGURES

[0025] FIG. 1 demonstrates the conserved chemical and structural similarities among the sequences of HHLM 1 (094168; SEQ ID NO:1) and HHLM 6 (2011230; SEQ ID NO:6), respectively. The alignment was produced using the MEGALIGN program of LASERGENE software (DNASTAR, Madison Wis.).

[0026] FIGS. 2A and 2B demonstrate the conserved chemical and structural similarities among the sequences of HHLM 3 (507537; SEQ ID NO:3) and HHLM 4 (971204; SEQ ID NO:4), respectively. The alignment was produced using the MEGALIGN program of LASERGENE software (DNASTAR).

DESCRIPTION OF THE INVENTION

[0027] Before the present proteins, nucleotide sequences, and methods are described, it is understood that this invention is not limited to the particular methodology, protocols, cell lines, vectors, and reagents described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the present invention which will be limited only by the appended claims.

[0028] It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to “a host cell” includes a plurality of such host cells, and a reference to “an antibody” is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth.

[0029] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein are cited for the purpose of describing and disclosing the cell lines, vectors, and methodologies which are reported in the publications and which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

[0030] DEFINITIONS

[0031] “HHLM” refers to the amino acid sequences of substantially purified HHLM obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and preferably the human species, from any source, whether natural, synthetic, semi-synthetic, or recombinant.

[0032] “cDNA” refers to an isolated polynucleotide, nucleic acid molecule, or any fragment or complement thereof. It may have originated recombinantly or synthetically, be double-stranded or single-stranded, represent coding and/or noncoding sequence, an exon with or without an intron from a genomic DNA molecule.

[0033] The phrase “cDNA encoding a protein” refers to a nucleic acid sequence that closely aligns with sequences which encode conserved regions, motifs or domains that were identified by employing analyses well known in the art. These analyses include BLAST (Basic Local Alignment Search Tool; Altschul (1993) J Mol Evol 36: 290-300; Altschul et al. (1990) J Mol Biol 215:403-410) which provides identity within the conserved region.

[0034] “Derivative” refers to a cDNA or a protein that has been subjected to a chemical modification. Derivatization of a cDNA can involve substitution of a nontraditional base such as queosine or of an analog such as hypoxanthine. These substitutions are well known in the art. Derivatization of a protein involves the replacement of a hydrogen by an acetyl, acyl, alkyl, amino, formyl, or morpholino group. Derivative molecules retain the biological activities of the naturally occurring molecules but may confer advantages such as longer lifespan or enhanced activity.

[0035] “Differential expression” refers to an increased, upregulated or present, or decreased, downregulated or absent, gene expression as detected by the absence, presence, or at least two-fold changes in the amount of transcribed messenger RNA or translated protein in a sample.

[0036] “Disorder” refers to conditions, diseases or syndromes in which the cDNAs and protname are differentially expressed.

[0037] “Fragment” refers to a chain of consecutive nucleotides from about 200 to about 700 base pairs in length. Fragments may be used in PCR or hybridization technologies to identify related nucleic acid molecules and in binding assays to screen for a ligand. Nucleic acids and their ligands identified in this manner are useful as therapeutics to regulate replication, transcription or translation.

[0038] An “allele” or an “allelic sequence” is an alternative form of the gene encoding HHLM. Alleles may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes which give rise to alleles are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

[0039] “Altered” nucleic acid sequences encoding HHLM include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polynucleotide the same HHLM or a polypeptide with at least one functional characteristic of HHLM. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding HHLM, and improper or unexpected hybridization to alleles, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding HHLM. The encoded protein may also be “altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent HHLM. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of HHLM is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, positively charged amino acids may include lysine and arginine, and amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine.

[0040] “Amino acid” or “amino acid sequence” refer to an oligopeptide, peptide, polypeptide, or protein sequence, or a portion or a fragment of any of these, and to naturally occurring or synthetic molecules. In this context, “fragments”, “immunogenic fragments”, or “antigenic fragments” refer to fragments of HHLM which are preferably about 5 to about 15 amino acids in length and which retain some biological activity or immunological activity of HHLM. Where “amino acid sequence” is recited herein to refer to an amino acid sequence of a naturally occurring protein molecule, “amino acid sequence” and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule. A “portion” of a protein refers to that length of amino acid sequence which would retain at least one biological activity, a domain identified by PFAM or PRINTS analysis or an antigenic epitope of the protein identified using Kyte-Doolittle algorithms of the PROTEAN program (DNASTAR, Madison Wis.). An “oligopeptide” is an amino acid sequence from about five residues to about 15 residues that is used as part of a fusion protein to produce an antibody.

[0041] “Amplification” relates to the production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies well known in the art. (See, e.g., Dieffenbach and Dveksler (1995) PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y., pp. 1-5.)

[0042] “Antibody” refers to intact molecules as well as to fragments thereof, such as Fa, F(ab′)2, and Fv fragments, which are capable of binding the epitopic determinant. Antibodies that bind HHLM polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or oligopeptide used to immunize an animal (e.g., a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired. Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

[0043] “Antigenic determinant” refers to that fragment of a molecule (i.e., an epitope) that makes contact with a particular antibody. When a protein or a fragment of a protein is used to immunize a host animal, numerous regions of the protein may induce the production of antibodies which bind specifically to antigenic determinants (given regions or three-dimensional structures on the protein). An antigenic determinant may compete with the intact antigen (i.e., the immunogen used to elicit the immune response) for binding to an antibody.

[0044] “Antisense” refers to any composition containing a nucleic acid sequence which is complementary to a specific nucleic acid sequence. The term “antisense strand” is used in reference to a nucleic acid strand that is complementary to the “sense” strand. Antisense molecules may be produced by any method including synthesis or transcription. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form duplexes and to block either transcription or translation. The designation “negative” can refer to the antisense strand, and the designation “positive” can refer to the sense strand.

[0045] “Biologically active” refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule. Likewise, “immunologically active” refers to the capability of the natural, recombinant, or synthetic HHLM, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

[0046] “Complementary” or “complementarity” refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base pairing. For example, the sequence 5′-A-G-T-C-3′ base pairs with 3′-T-C-A-G-5′. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands. This is of particular importance in amplification reactions, which depend upon binding between nucleic acids strands, and in the design and use of peptide nucleic acid (PNA) molecules. The complement of a cDNA of the Sequence Listing refers to a nucleic acid molecule which is completely complementary over its full length and which will hybridize to the cDNA or an mRNA under conditions of high stringency.

[0047] A “composition comprising a given polynucleotide sequence” or a “composition comprising a given amino acid sequence” refer broadly to any composition containing the given polynucleotide or amino acid sequence. The composition may comprise a dry formulation, an aqueous solution, or a sterile composition. Compositions comprising polynucleotide sequences encoding HHLM or fragments of HHLM may be employed as hybridization probes. The probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate. In hybridizations, the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., SDS), and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).

[0048] “Consensus sequence” refers to a nucleic acid sequence which has been resequenced to resolve uncalled bases, extended using XL-PCR kit (PE Biosystems, Foster City Calif.) in the 5′ and/or the 3′ direction, and resequenced, or which has been assembled from the overlapping sequences of more than one Incyte Clone using a computer program for fragment assembly, such as the GELVIEW fragment assembly system (Genetics Computer Group, Madison Wis.). Some sequences have been both extended and assembled to produce the consensus sequence.

[0049] The term “correlates with expression of a polynucleotide” indicates that the detection of the presence of nucleic acids, the same or related to a nucleic acid sequence encoding HHLM, by northern analysis is indicative of the presence of nucleic acids encoding HHLM in a sample, and thereby correlates with expression of the transcript from the polynucleotide encoding HHLM.

[0050] “Deletion” refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.

[0051] “Derivative” refers to the chemical modification of HHLM, of a polynucleotide sequence encoding HHLM, or of a polynucleotide sequence complementary to a polynucleotide sequence encoding HHLM. Chemical modifications of a polynucleotide sequence can include, for example, replacement of hydrogen by an alkyl, acyl, or amino group. A derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule. A derivative polypeptide is one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.

[0052] “Homology” refers to a degree of complementarity. There may be partial homology or complete homology. A partially complementary sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to as “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization, and the like) under conditions of reduced stringency. A substantially homologous sequence or hybridization probe will compete for and inhibit the binding of a completely homologous sequence to the target sequence under conditions of reduced stringency. This is not to say that conditions of reduced stringency are such that non-specific binding is permitted, as reduced stringency conditions require that the binding of two sequences to one another be a specific (i.e., a selective) interaction. The absence of non-specific binding may be tested by the use of a second target sequence which lacks even a partial degree of complementarity (e.g., less than about 30% homology or identity). In the absence of non-specific binding, the substantially homologous sequence or probe will not hybridize to the second non-complementary target sequence.

[0053] “Human artificial chromosomes” are linear microchromosomes which may contain DNA sequences of about 6 kbp to 10 Mbp in size, and which contain all of the elements required for stable mitotic chromosome segregation and maintenance. (See, e.g., Harrington et al. (1997) Nat Genet 15:345-355.)

[0054] “Humanized antibody” refers to antibody molecules in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.

[0055] “Hybridization” refers to any process by which a strand of nucleic acid binds with a complementary strand through base pairing. “Hybridization complex” refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary bases. A hybridization complex may be formed in solution (e.g., Cot or Rot analysis) or formed between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).

[0056] An “insertion” or “addition” refers to changes in an amino acid or nucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively, to the sequence found in the naturally occurring molecule.

[0057] “Immune response” can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.

[0058] “Microarray” refers to an arrangement of distinct polynucleotides or oligonucleotides arrayed on a substrate.

[0059] “Modulate” refers to a change in the activity of HHLM. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of HHLM.

[0060] “Polynucleotide” refers to an oligonucleotide, nucleic acid sequence, or any fragment thereof, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material. In this context, “fragments” refers to those nucleic acid sequences which are from about 60 nucleotides in length to about 10,000 nucleotides in length.

[0061] “Operably associated” or “operably linked” refer to functionally related nucleic acid sequences. A promoter is operably associated or operably linked with a coding sequence if the promoter controls the transcription of the encoded polypeptide. While operably associated or operably linked nucleic acid sequences can be contiguous and in reading frame, certain genetic elements, e.g., repressor genes, are not contiguously linked to the encoded polypeptide but still bind to operator sequences that control expression of the polypeptide.

[0062] “Oligonucleotide” refers to a nucleic acid molecule of at least about 6 nucleotides to about 60 nucleotides, which can be used in PCR amplification or in a hybridization assay or microarray and is substantially equivalent to the terms “amplimer”, “primer”, “oligomer”, and “probe”, as these terms are commonly defined in the art.

[0063] “Peptide nucleic acid” (PNA) refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA and RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell. (See, e.g., Nielsen et al. (1993) Anticancer Drug Des 8:53-63.)

[0064] “Portion” refers to any part of a protein used for any purpose; but especially, to an epitope for the screening of ligands or for the production of antibodies.

[0065] “Purified” refers to any molecule or compound that is separated from its natural environment and is from about 60% free to about 90% free from other components with which it is naturally associated.

[0066] “Sample” is used in its broadest sense as containing nucleic acids, proteins, antibodies, and the like. A sample may comprise a bodily fluid; the soluble fraction of a cell preparation, or an aliquot of media in which cells were grown; a chromosome, an organelle, or membrane isolated or extracted from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; a cell; a tissue; a tissue print; a fingerprint, buccal cells, skin, or hair; and the like.

[0067] “Similarity” as applied to sequences, refers to the quantification (usually percentage) of nucleotide or residue matches between at least two sequences aligned using a standardized algorithm such as Smith-Waterman alignment (Smith and Waterman (1981) J Mol Biol 147:195-197) or BLAST2 (Altschul et al. (1997) Nucleic Acids Res 25:3389-3402). BLAST2 may be used in a standardized and reproducible way to insert gaps in one of the sequences in order to optimize alignment and to achieve a more meaningful comparison between them.

[0068] “Specific binding” refers to a special and precise interaction between two molecules which is dependent upon their structure, particularly their molecular side groups. For example, the intercalation of a regulatory protein into the major groove of a DNA molecule, the hydrogen bonding along the backbone between two single stranded nucleic acids, or the binding between an epitope of a protein and an agonist, antagonist, or antibody.

[0069] “Stringent conditions” refers to conditions which permit hybridization between polynucleotide sequences and the claimed polynucleotide sequences. Suitably stringent conditions can be defined by, for example, the concentrations of salt or formamide in the prehybridization and hybridization solutions, or by the hybridization temperature, and are well known in the art. In particular, stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature.

[0070] The stringency of hybridization is determined by G+C content of the probe, salt concentration, and temperature. In particular, stringency can be increased by reducing the concentration of salt or raising the hybridization temperature. In solutions used for some membrane based hybridizations, addition of an organic solvent such as formamide allows the reaction to occur at a lower temperature. Hybridization can be performed at low stringency with buffers, such as 5×SSC with 1% sodium dodecyl sulfate (SDS) at 60° C., which permits the formation of a hybridization complex between nucleic acid sequences that contain some mismatches. Subsequent washes are performed at higher stringency with buffers such as 0.2×SSC with 0.1% SDS at either 45° C. (medium stringency) or 68° C. (high stringency). At high stringency, hybridization complexes will remain stable only where the nucleic acids are completely complementary. In some membrane-based hybridizations, preferably 35% or most preferably 50% formamide can be added to the hybridization solution to reduce the temperature at which hybridization is performed, and background signals can be reduced by the use of other detergents such as Sarkosyl or Triton X-100 and a blocking agent such as denatured salmon sperm DNA. Selection of components and conditions for hybridization are well known to those skilled in the art and are reviewed in Ausubel (supra) and Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y.

[0071] “Substantially purified” refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least about 60% free, preferably about 75% free, and most preferably about 90% free from other components with which they are naturally associated.

[0072] A “substitution” refers to the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively.

[0073] “Substrate” refers to any rigid or semi-rigid support to which cDNAs or proteins are bound and includes membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, capillaries or other tubing, plates, polymers, and microparticles with a variety of surface forms including wells, trenches, pins, channels and pores.

[0074] “Transformation” describes a process by which exogenous DNA enters and changes a recipient cell. Transformation may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, viral infection, electroporation, heat shock, lipofection, and particle bombardment. “Transformed” cells includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.

[0075] “Variant” refers to molecules that are recognized variations of a cDNA or a protein encoded by the cDNA. Splice variants may be determined by BLAST score, wherein the score is at least 100, and most preferably at least 400. Allelic variants have a high percent identity to the cDNAs and may differ by about three bases per hundred bases. “Single nucleotide polymorphism” (SNP) refers to a change in a single base as a result of a substitution, insertion or deletion. The change may be conservative (purine for purine) or non-conservative (purine to pyrimidine) and may or may not result in a change in an encoded amino acid. Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing biological or immunological activity may be found using computer programs well known in the art, for example, LASERGENE software (DNASTAR). The encoded protein may also contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent HHLM. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of HHLM is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, and positively charged amino acids may include lysine and arginine. Amino acids with uncharged polar side chains having similar hydrophilicity values may include: asparagine and glutamine; and serine and threonine. Amino acids with uncharged side chains having similar hydrophilicity values may include: leucine, isoleucine, and valine; glycine and alanine; and phenylalanine and tyrosine. A variant of a protein may have a biologically active region and have at least 75% amino acid similarity over at least thirty contiguous amino acid residues of the region of activity.

[0076] THE INVENTION

[0077] The invention is based on the discovery of new human hydrolase-like molecules (HHLM), the polynucleotides encoding HHLM, and the use of these compositions for the diagnosis, or treatment of cell proliferation disorders and autoimmune disorders. Table 1 shows the sequence identification numbers, Incyte Clone identification number, and cDNA library for each of the human hydrolase-like molecules disclosed herein. 1 TABLE 1 Protein Nucleotide Clone ID Library SEQ ID NO:1 SEQ ID NO:9   094168 PITUNOT1 SEQ ID NO:2 SEQ ID NO:10  195647 KIDNNOT02 SEQ ID NO:3 SEQ ID NO:11  507537 TMLR3DT02 SEQ ID NO:4 SEQ ID NO:12  971204 MUSCNOT02 SEQ ID NO:5 SEQ ID NO:13 1376382 LUNGNOT10 SEQ ID NO:6 SEQ ID NO:14 2011230 TESTNOT03 SEQ ID NO:7 SEQ ID NO:15 2768301 COLANOT02 SEQ ID NO:8 SEQ ID NO:16 2886583 SINJNOT02

[0078] Nucleic acids encoding the HHLM 1 of the present invention were first identified in Incyte Clone 094168 from the human pituitary gland cDNA library (PITUNOTO01) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:9, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 094168H1 (PITUNOTO1), 2470694F6 (THP1NOT03), 3595859H1 (FIBPNOT01), 1864296F6 and 1864296T6 (PROSNOT19), 1622192F6 (BRAITUT13), 1695044F6 (COLNNOT23), and 1431642T1 (BEPINON01), SEQ ID NOs:17-24, respectively. The fragment of SEQ ID NO:9 from about nucleotide 120 to about nucleotide 180 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in neural, reproductive and cardiovascular tissue libraries, at least 61% of which are immortalized or cancerous. Of particular note is the expression of HHLM 1 in ovarian and breast cancer.

[0079] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:1. HHLM 1 is 259 amino acids in length and has a potential glycosylation site at N47, seven potential casein kinase II phosphorylation sites at T48, S52, S68, S81, T164, T192, and S231. In addition HHLM 1 has two potential protein kinase C phosphorylation sites at T48 and T225. HHLM 1 has chemical and structural homology with C. elegans 4-nitrophenylphosphatase (PPNase; g1938421). In particular, HHLM 1 and PPNase share 51% identity, as well as sharing four potential phosphorylation sites and a potential glycosylation site. The portion of SEQ ID NO:1 from about residue G217 to about residue E233 is useful as a fragment with biological activity. The portion of SEQ ID NO:1 from about residue A199 to about residue Q214 is useful as an oligopeptide. The portion of SEQ ID NO:1 from about residue Y148 to about residue A156 is useful as an antigenic epitope.

[0080] Nucleic acids encoding the HHLM 2 of the present invention were first identified in Incyte Clone 195647 from the human kidney cDNA library (KIDNNOT02) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:10, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 195647R1 (KIDNNOT02), 1795063H1 (PROSTUT05), 1813266F6 (PROSTUT12), and 728148X27 (SYNOOAT01), SEQ ID NOs:25-28, respectively. The fragment of SEQ ID NO:10 from about nucleotide 74 to about nucleotide 134 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in reproductive, neural, hematopoietic, and gastrointestinal tissue libraries, at least 43% of which are immortalized or cancerous and at least 20% of which involve inflammation and the immune response. Of particular note is the expression of HHLM 2 in brain and prostate tumors.

[0081] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:2. HHLM 2 is 392 amino acids in length, and has a protein phosphatase 2C signature sequence from Y147 through G155, as well as a potential glycosaminoglycan attachment site at S40. In addition, HHLM 2 has two potential glycosylation site at N87 and N382, two potential cAMP- and cGMP-dependent protein kinase phosphorylation sites at T81 and T82, twelve potential casein kinase II phosphorylation sites at S36, S55, T81, T82, T198, T263, S292, S305, T315, T333, S342, and S357, five potential protein kinase C phosphorylation sites atSl3, T186, T194, S208, and S248, and two potential tyrosine kinase phosphorylation sites at Y298 and Y363. HHLM 2 has chemical and structural homology with human phosphatase 2C motif (PP2C; g2114221). In particular, HHLM 2 and PP2C share 26% identity and are completely identical throughout the protein phosphatase 2C signature sequence, residues Y147 through G155 of SEQ ID NO:2. HHLM 2 and PP2C also share two potential phosphorylation sites and a potential glycosaminoglycan attachment site. The portion of SEQ ID NO:2 from about residue Y147 to about residue A163 is useful as a fragment with biological activity. The portion of SEQ ID NO:2 from about residue K185 to about residue E201 is useful as an oligopeptide. The portion of SEQ ID NO:2 from about residue K71 to about residue L92 is useful as an antigenic epitope.

[0082] Nucleic acids encoding the HHLM 3 of the present invention were first identified in Incyte Clone 507537 from the human blood mononuclear cell cDNA library (TMLR3DT02) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:11, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 507537X14 (TMLR3DT02), 868893H1 (LUNGAST01), 2272231R6 (PROSNON01), 2379239F7 (ISLTNOT01), and 1397852F1 (BRAITUT08), SEQ ID NOs:29-33, respectively. The fragment of SEQ ID NO:11 from about nucleotide 72 to about nucleotide 132 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in hematopoietic and immune, reproductive, and cardiovascular tissue libraries, at least 49% of which are immortalized or cancerous and at least 37% of which involve inflammation and the immune response. Of particular note is the expression of HHLM 3 in lymphocytes and a T-cell line.

[0083] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:3. HHLM 3 is 353 amino acids in length and has a potential cAMP- and cGMP-dependent protein kinase phosphorylation site at T265, two potential casein kinase II phosphorylation sites at S105 and S246, five potential protein kinase C phosphorylation sites at S78, T201, T272, S307, and T350, and a microbodies C-terminal targeting signal at L351. HHLM 3 has chemical and structural homology with S. cerevisiae phosphatase (ScPPase; g172168). In particular, HHLM 3 and ScPPase share 30% identity, including a potential protein kinase C phosphorylation site. The portion of SEQ ID NO:3 from about residue V124 to about residue 1138 is useful as a fragment with biological activity. The portion of SEQ ID NO:3 from about residue TIO to about residue 1114 is useful as an oligopeptide. The portion of SEQ ID NO:3 from about residue K199 to about residue Q212 is useful as an antigenic epitope.

[0084] Nucleic acids encoding the HHLM 4 of the present invention were first identified in Incyte Clone 971204 from the human muscle tissue cDNA library (MUSCNOT02) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:12, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 971204X37 (MUSCNOT02), 2822470F6 (ADRETUT06), and shotgun sequences STEQ00223R1 and STEQ02003R1, SEQ ID NOs:34-37, respectively. The fragment of SEQ ID NO:12 from about nucleotide 412 to about nucleotide 472 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in cardiovascular, neural, and reproductive tissue libraries, at least 40% of which are immortalized or cancerous. Of particular note is the expression of HHLM 4 in ovarian cancers.

[0085] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:4. HHLM 4 is 207 amino acids in length and has a tyrosine protein phosphatase active site signature sequence from V146 through L158. In addition, HHLM 4 has a potential glycosylation site at N93, three potential casein kinase II phosphorylation sites at T31, T128, and T170, and two potential protein kinase C phosphorylation sites at S21 and T54. HHLM 4 has chemical and structural homology with human dual-specificity protein phosphatase (tyrosine/serine) (HPPase; g181840). In particular, HHLM 4 and HPPase share 37% identity, including over 90% similarity in the tyrosine specific protein phosphatases active site signature sequence and the conserved cysteine residue essential for catalytic activity. The portion of SEQ ID NO:4 from about residue L145 to about residue L160 is useful as a fragment with biological activity. The portion of SEQ ID NO:4 from about residue F120 to about residue I133 is useful as an oligopeptide. The portion of SEQ ID NO:4 from about residue M76 to about residue G87 is useful as an antigenic epitope.

[0086] Nucleic acids encoding the HHLM 5 of the present invention were first identified in Incyte Clone 1376382 from the human lung tissue cDNA library (LUNGNOT10) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:13, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clone 1376382F6 (LUNGNOT10) and shotgun sequences SAEA03372R1, SAEA02307F1, SAEA02307R1, and SAEA02991R1, SEQ ID NOs:38-42, respectively. The fragment of SEQ ID NO:13 from about nucleotide 69 to about nucleotide 128 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in reproductive, gastrointestinal, and hematopoietic and immune tissue libraries, at least 55% of which are immortalized or cancerous and at least 26% of which involve inflammation and the immune response. Of particular note is the expression of HHLM 5 in tumors of the prostate, uterus, testicle, and breast.

[0087] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:5. HHLM 5 is 453 amino acids in length and has seven potential glycosylation sites at N69, N131, N222, N238, N263, N356, and N437. In addition, HHLM 5 has a potential cAMP- and cGMP-dependent protein kinase phosphorylation site at S308, six potential casein kinase II phosphorylation sites at S90, S98, T294, S324, T396 and S439, a potential glycosaminoglycan attachment site at S19, seven potential protein kinase C phosphorylation sites at S64, T164, T186, S194, T294, S303, and T423, and a potential tyrosine kinase phosphorylation site at Y353. HHLM 5 has chemical and structural homology with mouse acid sphingomyelinase-like phosphodiesterase (MASP; g1552350). In particular, HHLM 5 and MASP share 79% identity, including seven potential phosphorylation sites and five potential glycosylation sites. The portion of SEQ ID NO:5 from about residue F290 to about residue K305 is useful as a fragment with biological activity. The portion of SEQ ID NO:5 from about residue 1184 to about residue N200 is useful as an oligopeptide. The portion of SEQ ID NO:5 from about residue Q339 to about residue Q352 is useful as an antigenic epitope.

[0088] Nucleic acids encoding the HHLM 6 of the present invention were first identified in Incyte Clone 2011230 from the human testicular tissue cDNA library (TESTNOT03) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:14, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 2011230R6 (TESTNOT03), 2855308H1 (CONNNOT02), 1706605F6 (DUODNOT02), and 1482295F6 and 1481157T6 (CORPNOT02), SEQ ID NOs:43-47, respectively. The fragment of SEQ ID NO:14 from about nucleotide 19 to about nucleotide 72 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in neural, reproductive, and gastrointestinal tissue libraries, at least 47% of which are immortalized or cancerous and at least 24% of which involve inflammation and the immune response. Of particular note is the expression of HHLM 6 in tumors of the brain and ganglion.

[0089] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:6. HHLM 6 is 270 amino acids in length and has a potential amidation site at W4, a potential glycosylation site at N55, and a glycosaminoglycan attachment site at S25. In addition, HHLM 6 has three potential casein kinase II phosphorylation sites at S60, S76, and S108, and two potential protein kinase C phosphorylation sites at S57 and T235. HHLM 6 has chemical and structural homology with C. elegans 4-nitrophenylphosphatase (PPNase; g1938421). In particular, HHLM 6 and PPNase share 35% identity, including two potential phosphorylation sites and a potential glycosylation site. The portion of SEQ ID NO:6 from about residue G227 to about residue E243 is useful as a fragment with biological activity. The portion of SEQ ID NO:6 from about residue A209 to about residue Q224 is useful as an oligopeptide. The portion of SEQ ID NO:6 from about residue K155 to about residue L167 is useful as an antigenic epitope.

[0090] Nucleic acids encoding the HHLM 7 of the present invention were first identified in Incyte Clone 2768301 from the human colon tissue cDNA library (COLANOT02) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:15, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 2768301H1 (COLANOT02), 1582462F6 (DUODNOT01), 193790R6 (KIDNNOT02), 1817542F6 (PROSNOT20), and 1418115F1 (KIDNNOT09), SEQ ID NOs:48-52, respectively. The fragment of SEQ ID NO:15 from about nucleotide 113 to about nucleotide 166 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in reproductive, gastrointestinal, and developmental tissue libraries, at least 60% of which are immortalized or cancerous and at least 22% of which involve the inflammatory response. Of particular note is the expression of HHLM 7 in tumors of the breast and prostate.

[0091] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:7. HHLM 7 is 231 amino acids in length. HHLM 7 has a potential glycosylation site at N160, four potential casein kinase II phosphorylation sites at S18, S39, S74, and S162, and two potential protein kinase C phosphorylation sites at T46 and S162. HHLM 7 has chemical and structural homology with mouse lysophospholipase I (MLP; g1864159). In particular, HHLM 7 and MLP share 65% identity. The portion of SEQ ID NO:7 from about residue H137 to about residue R153 is useful as a fragment with biological activity. The portion of SEQ ID NO:7 from about residue A158 to about residue H172 is useful as an oligopeptide. The portion of SEQ ID NO:7 from about residue P84 to about residue N98 is useful as an antigenic epitope.

[0092] Nucleic acids encoding the HHLM 8 of the present invention were first identified in Incyte Clone 2886583 from the human jejunum tissue cDNA library (SINJNOT02) using a computer search for amino acid sequence alignments. A consensus sequence, SEQ ID NO:16, was derived from the following overlapping and/or extended nucleic acid sequences: Incyte Clones 2886583H1 (SINJNOT02), 1666224F6 (BRSTNOT09), and 1223154R1 (COLNTUT02), SEQ ID NOs:53-55, respectively. The fragment of SEQ ID NO:16 from about nucleotide 66 to about nucleotide 123 is useful as a hybridization probe. Northern analysis shows the expression of this sequence in gastrointestinal and reproductive tissue libraries, at least 69% of which are immortalized or cancerous and at least 26% of which involve inflammation and the immune response. Of particular note is the expression of HHLM in tumors of the prostate and colon.

[0093] In one embodiment, the invention encompasses a polypeptide comprising the amino acid sequence of SEQ ID NO:8. HHLM is 254 amino acids in length and has four potential casein kinase II phosphorylation sites at S177, S203, T204, and S218, and two potential protein kinase C phosphorylation sites at S14 and S1 19. HHLM 8 has chemical and structural homology with A. thaliana glyoxylase II (AGLX; g1644427). In particular, HHLM and AGLX share 57% identity, including a potential phosphorylation site. The portion of SEQ ID NO:8 from about residue D188 to about residue T201 is useful as a fragment with biological activity. The portion of SEQ ID NO:8 from about residue G169 to about residue 1182 is useful as an oligopeptide. The portion of SEQ ID NO:8 from about residue G41 to about residue I51 is useful as an antigenic epitope.

[0094] As shown in FIG. 1, HHLM 1 has chemical and structural homology with HHLM 6. In particular, HHLM 1 and HHLM 6 share 41% identity, including two potential phosphorylation sites, and a potential glycosylation site. In addition, HHLM 1 and HHLM 6 share a conserved region between A199-E233 and A209-E243, respectively. The conserved regions of HHLM 1 and HHLM 6 share 66% identity (77% similarity with conservative residue substitutions) and include a potential protein kinase C phosphorylation site at T225 and T235, respectively.

[0095] As shown in FIGS. 2A and 2B, HHLM 3 has chemical and structural homology with HHLM 4. In particular, HHLM 3 and HHLM 4 share 18% identity, including a conserved region between L125-1138 and L145-L158, respectively, and a potential casein kinase II phosphorylation site. The conserved regions of HHLM 3 and HHLM 4 share 64% identity (79% similarity with conservative residue substitutions) and includes a cysteine residue potentially essential for catalytic activity.

[0096] The invention also encompasses HHLM variants. A preferred HHLM variant is one which has at least about 80%, more preferably at least about 90%, and most preferably at least about 95% amino acid sequence identity to the HHLM amino acid sequence, and which contains at least one functional or structural characteristic of HHLM.

[0097] The invention also encompasses polynucleotides which encode HHLM. In a particular embodiment, the invention encompasses a polynucleotide sequence comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:9-16, which encode HHLM.

[0098] The invention also encompasses polynucleotides which encode a portion of HHLM. In a particular embodiment, the invention encompasses a polynucleotide sequence comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOs:17-55, which encode a portion of HHLM.

[0099] The invention also encompasses a variant of a polynucleotide sequence encoding HHLM. In particular, such a variant polynucleotide sequence will have at least about 80%, more preferably at least about 90%, and most preferably at least about 95% polynucleotide sequence identity to the polynucleotide sequence encoding HHLM. Any one of the polynucleotide variants can encode an amino acid sequence which contains at least one functional or structural characteristic of HHLM.

[0100] It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of polynucleotide sequences encoding HHLM, some bearing minimal homology to the polynucleotide sequences of any known and naturally occurring gene, may be produced. Thus, the invention contemplates each and every possible variation of polynucleotide sequence that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code as applied to the polynucleotide sequence of naturally occurring HHLM, and all such variations are to be considered as being specifically disclosed.

[0101] Although nucleotide sequences which encode HHLM and its variants are preferably capable of hybridizing to the nucleotide sequence of the naturally occurring HHLM under appropriately selected conditions of stringency, it may be advantageous to produce nucleotide sequences encoding HHLM or its derivatives possessing a substantially different codon usage. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host. Other reasons for substantially altering the nucleotide sequence encoding HHLM and its derivatives without altering the encoded amino acid sequences include the production of RNA transcripts having more desirable properties, such as a greater half-life, than transcripts produced from the naturally occurring sequence.

[0102] The invention also encompasses production of DNA sequences which encode HHLM and HHLM derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents that are well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a sequence encoding HHLM or any fragment thereof.

[0103] Also encompassed by the invention are polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NOs:9-16 or fragments thereof under various conditions of stringency. The invention also encompasses polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NOs:17-55 or fragments thereof under various conditions of stringency. (See, e.g., Wahl and Berger (1987) Methods Enzymol. 152:399-407; and Kimmel (1987) Methods Enzymol. 152:507-511.)

[0104] Methods for DNA sequencing are well known and generally available in the art and may be used to practice any of the embodiments of the invention. The methods may employ such enzymes as the Klenow fragment of DNA polymerase I, T7 SEQUENASE DNA polymerase, Taq DNA polymerase, THERMOSEQUENASE DNA polymerase (Amersham Pharmacia Biotech (APB), Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies, Gaithersburg Md.). Preferably, the process is automated with machines such as the MICROLAB 2200 system (Hamilton, Reno Nev.), DNA ENGINE thermal cycler (MJ Research, Watertown Mass.) and ABI CATALYST thermal cycler and the ABI PRISM 373 and 377 sequencing systems (PE Biosystems).

[0105] The nucleic acid sequences encoding HHLM may be extended utilizing a partial nucleotide sequence and employing various methods known in the art to detect upstream sequences, such as promoters and regulatory elements. For example, one method which may be employed, restriction-site PCR, uses universal primers to retrieve unknown sequence adjacent to a known locus. (See, e.g., Sarkar (1993) PCR Methods Applic 2:318-322.) In particular, genomic DNA is first amplified in the presence of a primer which is complementary to a linker sequence within the vector and a primer specific to a region of the nucleotide sequence. The amplified sequences are then subjected to a second round of PCR with the same linker primer and another specific primer internal to the first one. Products of each round of PCR are transcribed with an appropriate RNA polymerase and sequenced using reverse transcriptase.

[0106] Inverse PCR may also be used to amplify or extend sequences using divergent primers based on a known region. (See, e.g., Triglia et al. (1988) Nucleic Acids Res 16:8186.) The primers may be designed using commercially available software such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth, Minn.) or another appropriate program to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to 72° C. The method uses several restriction enzymes to generate a suitable fragment in the known region of a gene. The fragment is then circularized by intramolecular ligation and used as a PCR template.

[0107] Another method which may be used is capture PCR, which involves PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA. (See, e.g., Lagerstrom et al. (1991) PCR Methods Applic 1:111-119.) In this method, multiple restriction enzyme digestions and ligations may be used to place an engineered double-stranded sequence into an unknown fragment of the DNA molecule before performing PCR. Other methods which may be used to retrieve unknown sequences are known in the art. (See, e.g., Parker et al. (1991) Nucleic Acids Res 19:3055-3060.) Additionally, one may use PCR and nested primers to walk genomic DNA. This process avoids the need to screen libraries and is useful in finding intron/exon junctions.

[0108] When screening for full-length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. Also, random-primed libraries are preferable in that they will include more sequences which contain the 5′ regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into 5′ non-transcribed regulatory regions.

[0109] Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products. In particular, capillary sequencing may employ flowable polymers for electrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and a charge coupled device camera for detection of the emitted wavelengths. Output/light intensity may be converted to electrical signal using appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR analysis software, PE Biosystems), and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled. Capillary electrophoresis is especially preferable for the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample.

[0110] In another embodiment of the invention, polynucleotide sequences or fragments thereof which encode HHLM may be used in recombinant DNA molecules to direct expression of HHLM, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced, and these sequences may be used to clone and express HHLM.

[0111] As will be understood by those of skill in the art, it may be advantageous to produce HHLM-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce an RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.

[0112] The nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter HHLM-encoding sequences for a variety of reasons including, but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations, and so forth.

[0113] In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences encoding HHLM may be ligated to a heterologous sequence to encode a fusion protein. For example, to screen peptide libraries for inhibitors of HHLM activity, it may be useful to encode a chimeric HHLM protein that can be recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the HHLM-encoding sequence and the heterologous protein sequence, so that HHLM may be cleaved and purified away from the heterologous moiety.

[0114] In another embodiment, sequences encoding HHLM may be synthesized, in whole or in part, using chemical methods well known in the art. (See, e.g., Caruthers et al. (1980) Nucleic Acids Symp Ser (7) 215-223; and Horn et al. (1980) Nucleic Acids Symp Ser (7) 225-232.) Alternatively, the protein itself may be produced using chemical methods to synthesize the amino acid sequence of HHLM, or a fragment thereof. For example, peptide synthesis can be performed using various solid-phase techniques. (See, e.g., Roberge et al. (1995) Science 269:202-204.) Automated synthesis may be achieved using the ABI 431A peptide synthesizer (PE Biosystems). Additionally, the amino acid sequence of HHLM, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide.

[0115] The peptide may be substantially purified by preparative high performance liquid chromatography. (See, e.g, Chiez and Regnier (1990) Methods Enzymol 182:392-421.) The composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing. (See, e.g., Creighton (1983) Proteins, Structures and Molecular Properties, W H Freeman and Co., New York N.Y.)

[0116] In order to express a biologically active HHLM, the nucleotide sequences encoding HHLM or derivatives thereof may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.

[0117] Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding HHLM and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y., ch. 4, 8, and 16-17; and Ausubel et al. (1995, and periodic supplements) Current Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., ch. 9, 13, and 16.)

[0118] A variety of expression vector/host systems may be utilized to contain and express sequences encoding HHLM. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus (CaMV) or tobacco mosaic virus (TMV)) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems. The invention is not limited by the host cell employed.

[0119] The “control elements” or “regulatory sequences” are those non-translated regions, e.g., enhancers, promoters, and 5′ and 3′ untranslated regions, of the vector and polynucleotide sequences encoding HHLM which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters, e.g., hybrid lacZ promoter of the BLUESCRIPT phagemid (Stratagene, La Jolla Calif.) or PSPORT1 plasmid (Life Technologies), may be used. The baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO, and storage protein genes) or from plant viruses (e.g., viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding HHLM, vectors based on SV40 or EBV may be used with an appropriate selectable marker.

[0120] In bacterial systems, a number of expression vectors may be selected depending upon the use intended for HHLM. For example, when large quantities of HHLM are needed for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be used. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the sequence encoding HHLM may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of &bgr;-galactosidase so that a hybrid protein is produced, and pIN vectors. (See, e.g., Van Heeke and Schuster (1989) J Biol Chem 264:5503-5509.) PGEX vectors (APB) may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.

[0121] In the yeast Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH, may be used. (See, e.g., Ausubel, supra; and Grant et al. (1987) Methods Enzymol 153:516-544.)

[0122] In cases where plant expression vectors are used, the expression of sequences encoding HHLM may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu (1987) EMBO J 6:307-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used. (See, e.g., Coruzzi et al. (1984) EMBO J 3:1671-1680; Broglie et al. (1984) Science 224:838-843; and Winter et al. (1991) Results Probl Cell Differ 17:85-105.) These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews. (See, McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York N.Y.; pp. 191-196.)

[0123] An insect system may also be used to express HIIHLM. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequences encoding HHLM may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of sequences encoding HHLM will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which HHLM may be expressed. (See, e.g., Engelhard et al. (1994) Proc Natl Acad Sci 91:3224-3227.)

[0124] In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, sequences encoding HHLM may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing HHLM in infected host cells. (See, e.g., Logan and Shenk (1984) Proc Natl Acad Sci 81:3655-3659.) In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.

[0125] Human artificial chromosomes (HACs) may also be employed to deliver larger fragments of DNA than can be contained and expressed in a plasmid. HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes.

[0126] Specific initiation signals may also be used to achieve more efficient translation of sequences encoding HHLM. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding HHLM and its initiation codon and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular cell system used. (See, e.g., Scharf et at. (1994) Results Probl Cell Differ 20:125-162.)

[0127] In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding, and/or function. Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and W138), are available from the American Type Culture Collection (ATCC, Manssas Va.) and may be chosen to ensure the correct modification and processing of the foreign protein.

[0128] For long term, high yield production of recombinant proteins, stable expression is preferred. For example, cell lines capable of stably expressing HHLM can be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched media before being switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.

[0129] Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase genes and adenine phosphoribosyltransferase genes, which can be employed in tk- or apr- cells, respectively. (See, e.g., Wigler et al. (1977) Cell 11:223-232; and Lowy et al. (1980) Cell 22:817-823.) Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate; npt confers resistance to the aminoglycosides neomycin and G-418; and als or pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. (See, e.g., Wigler et al. (1980) Proc Nati Acad Sci 77:3567-3570; and Colbere-Garapin et al. (1981) J Mol Biol 150:1-14) Additional selectable genes have been described, e.g., trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine. (See, e.g., Hartman and Mulligan (1988) Proc Natl Acad Sci 85:8047-8051.) Visible markers, e.g., anthocyanins, &bgr; glucuronidase and its substrate GUS, luciferase and its substrate luciferin may be used. Green fluorescent proteins (GFP; Clontech, Palo Alto Calif.) can also be used. These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system. (See, e.g., Rhodes et al. (1995) Methods Mol Biol 55:121-131.)

[0130] Although the presence/absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding HHLM is inserted within a marker gene sequence, transformed cells containing sequences encoding HHLM can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding HHLM under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

[0131] Alternatively, host cells which contain the nucleic acid sequence encoding HHLM and express HHLM may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.

[0132] The presence of polynucleotide sequences encoding HHLM can be detected by DNA-DNA or DNA-RNA hybridization or amplification using probes or fragments or fragments of polynucleotides encoding HHLM. Nucleic acid amplification based assays involve the use of oligonucleotides or oligomers based on the sequences encoding HHLM to detect transfonnants containing DNA or RNA encoding HHLM.

[0133] A variety of protocols for detecting and measuring the expression of HHLM, using either polyclonal or monoclonal antibodies specific for the protein, are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on HHLM is preferred, but a competitive binding assay may be employed. These and other assays are well described in the art. (See, e.g., Hampton et al. (1990) Serological Methods, a Laboratory Manual, APS Press, St Paul Minn., Section IV; and Maddox et al. (1983) J Exp Med 158:1211-1216).

[0134] A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding HHLM include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide. Alternatively, the sequences encoding HHLM, or any fragments thereof, may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits, such as those provided by APB and Promega (Madison Wis.). Suitable reporter molecules or labels which may be used for ease of detection include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

[0135] Host cells transformed with nucleotide sequences encoding HHLM may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode HHLM may be designed to contain signal sequences which direct secretion of HHLM through a prokaryotic or eukaryotic cell membrane. Other constructions may be used to join sequences encoding HHLM to nucleotide sequences encoding a polypeptide domain which will facilitate purification of soluble proteins. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex, Seattle Wash.). The inclusion of cleavable linker sequences, such as those specific for Factor XA or enterokinase (Invitrogen, San Diego Calif.), between the purification domain and the HHLM-encoding sequence may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing HHLM and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on immobilized metal ion affinity chromatography. (See, e.g., Porath et al. (1992) Prot Exp Purif 3:263-281.) The enterokinase cleavage site provides a means for purifying HHLM from the fusion protein. (See, e.g., Kroll et al. (1993) DNA Cell Biol 12:441-453.)

[0136] Fragments of HHLM may be produced not only by recombinant production, but also by direct peptide synthesis using solid-phase techniques. (See, e.g., Creighton (1984) Protein: Structures and Molecular Properties, pp. 55-60, W. H. Freeman, New York N.Y.) Protein synthesis may be performed by manual techniques or by automation. Automated synthesis may be achieved, for example, using the ABI 431A peptide synthesizer (PE Biosystems). Various fragments of HHLM may be synthesized separately and then combined to produce the full length molecule.

[0137] THERAPEUTICS

[0138] Chemical and structural homology exists among the human hydrolase-like molecules of the invention. In addition, HHLM is expressed in cancerous or immortalized tissues and tissues associated with inflammation and the autoimmune response. There fore, HHLM appears to play a role in cell proliferation disorders, and autoimmune disorders.

[0139] Therefore, in one embodiment, an antagonist of HHLM may be administered to a subject to treat or prevent a cell proliferation disorder. Such a disorder may include, but is not limited to, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease, myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, nerves, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus. In one aspect, an antibody which specifically binds HHLM may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express HHLM.

[0140] In an additional embodiment, a vector expressing the complement of the polynucleotide encoding HHLM may be administered to a subject to treat or prevent a cell proliferation disorder including, but not limited to, those described above.

[0141] In a further embodiment, an antagonist of HHLM may be administered to a subject to treat or prevent an autoimmune disorder. Such a disorder may include, but is not limited to, AIDS, Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis ,bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, rheumatoid arthritis, scleroderma, Sjogren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, Werner syndrome, and complications of cancer, hemodialysis, and extracorporeal circulation; viral, bacterial, fungal, parasitic, protozoal, and helminthic infections; and trauma.

[0142] In an additional embodiment, a vector expressing the complement of the polynucleotide encoding HHLM may be administered to a subject to treat or prevent an autoimmune disorder including, but not limited to, those described above.

[0143] In other embodiments, any of the proteins, antagonists, antibodies, agonists, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.

[0144] An antagonist of HHLM may be produced using methods which are generally known in the art. In particular, purified HHLM may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind HHLM. Antibodies to HHLM may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are especially preferred for therapeutic use.

[0145] For the production of antibodies, various hosts including goats, rabbits, rats, mice, humans, and others may be immunized by injection with HHLM or with any fragment or oligopeptide thereof which has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are especially preferable.

[0146] It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to HHLM have an amino acid sequence consisting of at least about 5 amino acids, and, more preferably, of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein and contain the entire amino acid sequence of a small, naturally occurring molecule. Short stretches of HHLM amino acids may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.

[0147] Monoclonal antibodies to HHLM may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. (See, e.g., Kohler et al. (1975) Nature 256:495-497; Kozbor et al. (1985) J Immunol Methods 81:31-42; Cote et al. (1983) Proc Natl Acad Sci 80:2026-2030; and Cole et al. (1984) Mol Cell Biol 62:109-120.)

[0148] In addition, techniques developed for the production of “chimeric antibodies,” such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used. (See, e.g., Morrison et al. (1984) Proc Natl Acad Sci 81:6851-6855; Neuberger et al. (1984) Nature 312:604-608; and Takeda et al. (1985) Nature 314:452-454.) Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce HHLM-specific single chain antibodies. Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries. (See, e.g., Burton (1991) Proc Natl Acad Sci 88:10134-10137.)

[0149] Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature. (See, e.g., Orlandi et al. (1989) Proc Natl Acad Sci 86: 3833-3837; Winter et al. (1991) Nature 349:293-299.)

[0150] Antibody fragments which contain specific binding sites for HHLM may also be generated. For example, such fragments include, but are not limited to, F(ab′)2 fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. (See, e.g., Huse et al. (1989) Science 246:1275-1281.)

[0151] Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between HHLM and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering HHLM epitopes is preferred, but a competitive binding assay may also be employed. (Maddox, supra.)

[0152] In another embodiment of the invention, the polynucleotides encoding HHLM, or any fragment or complement thereof, may be used for therapeutic purposes. In one aspect, the complement of the polynucleotide encoding HHLM may be used in situations in which it would be desirable to block the transcription of the mRNA. In particular, cells may be transformed with sequences complementary to polynucleotides encoding HHLM. Thus, complementary molecules or fragments may be used to modulate HHLM activity, or to achieve regulation of gene function. Such technology is now well known in the art, and sense or antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding HHLM.

[0153] Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. Methods which are well known to those skilled in the art can be used to construct vectors which will express nucleic acid sequences complementary to the polynucleotides of the gene encoding HHLM. (See, e.g., Sambrook, supra; and Ausubel, supra.)

[0154] Genes encoding HHLM can be turned off by transforming a cell or tissue with expression vectors which express high levels of a polynucleotide, or fragment thereof, encoding HHLM. Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell. Even in the absence of integration into the DNA, such vectors may continue to transcribe RNA molecules until they are disabled by endogenous nucleases. Transient expression may last for a month or more with a non-replicating vector, and may last even longer if appropriate replication elements are part of the vector system.

[0155] As mentioned above, modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA, or PNA) to the control, 5′, or regulatory regions of the gene encoding HHLM. Oligonucleotides derived from the transcription initiation site, e.g., between about positions −10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature. (See, e.g., Gee et al. (1994) in Huber and Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco N.Y., pp. 163-177.) A complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

[0156] Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. For example, engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding HHLM.

[0157] Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites, including the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, may be evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.

[0158] Complementary ribonucleic acid molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding HHLM. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as T7 or SP6. Alternatively, these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.

[0159] RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends of the molecule, or the use of pliosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.

[0160] Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient. Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art. (See, e.g., Goldman et al. (1997) Nat Biotech 15:462-466.)

[0161] Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.

[0162] An additional embodiment of the invention relates to the administration of a pharmaceutical or sterile composition, in conjunction with a pharmaceutically acceptable carrier, for any of the therapeutic effects discussed above. Such pharmaceutical compositions may consist of HHLM, antibodies to HHLM, and mimetics, agonists, antagonists, or inhibitors of HHLM. The compositions may be administered alone or in combination with at least one other agent, such as a stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier including, but not limited to, saline, buffered saline, dextrose, and water. The compositions may be administered to a patient alone, or in combination with other agents, drugs, or hormones.

[0163] The pharmaceutical compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.

[0164] In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing, Easton Pa.).

[0165] Pharmaceutical compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.

[0166] Pharmaceutical preparations for oral use can be obtained through combining active compounds with solid excipient and processing the resultant mixture of granules (optionally, after grinding) to obtain tablets or dragee cores. Suitable auxiliaries can be added, if desired. Suitable excipients include carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, and sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; gums, including arabic and tragacanth; and proteins, such as gelatin and collagen. If desired, disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, and alginic acid or a salt thereof, such as sodium alginate.

[0167] Dragee cores may be used in conjunction with suitable coatings, such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.

[0168] Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol. Push-fit capsules can contain active ingredients mixed with fillers or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.

[0169] Pharmaceutical formulations suitable for parenteral administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils, such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate, triglycerides, or liposomes. Non-lipid polycationic amino polymers may also be used for delivery. Optionally, the suspension may also contain suitable stabilizers or agents to increase the solubility of the compounds and allow for the preparation of highly concentrated solutions.

[0170] For topical or nasal administration, penetrants appropriate to the particular barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[0171] The pharmaceutical compositions of the present invention may be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.

[0172] The pharmaceutical composition may be provided as a salt and can be formed with many acids, including but not limited to, hydrochloric, sulfuric, acetic, lactic, tartaric, malic, and succinic acid. Salts tend to be more soluble in aqueous or other protonic solvents than are the corresponding free base forms. In other cases, the preferred preparation may be a lyophilized powder which may contain any or all of the following: 1 mM to 50 mM histidine, 0.1% to 2% sucrose, and 2% to 7% mannitol, at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.

[0173] After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. For administration of HHLM, such labeling would include amount, frequency, and method of administration.

[0174] Pharmaceutical compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose. The determination of an effective dose is well within the capability of those skilled in the art.

[0175] For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, e.g., of neoplastic cells or in animal models such as mice, rats, rabbits, dogs, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

[0176] A therapeutically effective dose refers to that amount of active ingredient, for example HHLM or fragments thereof, antibodies of HHLM, and agonists, antagonists or inhibitors of HHLM, which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED50 (the dose therapeutically effective in 50% of the population) or LD50 (the dose lethal to 50% of the population) statistics. The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the LD50/ED50 ratio. Pharmaceutical compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that includes the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration.

[0177] The exact dosage will be determined by the practitioner, in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.

[0178] Normal dosage amounts may vary from about 0.1 &mgr;g to 100,000 &mgr;g, up to a total dose of about 1 gram, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

[0179] DIAGNOSTICS

[0180] In another embodiment, antibodies which specifically bind HHLM may be used for the diagnosis of disorders characterized by expression of HHLM, or in assays to monitor patients being treated with HHLM or agonists, antagonists, or inhibitors of HHLM. Antibodies useful for diagnostic purposes may be prepared in the same manner as described above for therapeutics. Diagnostic assays for HHLM include methods which utilize the antibody and a label to detect HHLM in human body fluids or in extracts of cells or tissues. The antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule. A wide variety of reporter molecules, several of which are described above, are known in the art and may be used.

[0181] A variety of protocols for measuring HHLM, including ELISAs, RIAs, and FACS, are known in the art and provide a basis for diagnosing altered or abnormal levels of HHLM expression. Normal or standard values for HHLM expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably human, with antibody to HHLM under conditions suitable for complex formation The amount of standard complex formation may be quantitated by various methods, preferably by photometric means. Quantities of HHLM expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease.

[0182] In another embodiment of the invention, the polynucleotides encoding HHLM may be used for diagnostic purposes. The polynucleotides which may be used include oligonucleotide sequences, complementary RNA and DNA molecules, and PNAs. The polynucleotides may be used to detect and quantitate gene expression in biopsied tissues in which expression of HHLM may be correlated with disease. The diagnostic assay may be used to determine absence, presence, and excess expression of HHLM, and to monitor regulation of HHLM levels during therapeutic intervention.

[0183] In one aspect, hybridization with PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding HHLM or closely related molecules may be used to identify nucleic acid sequences which encode HHLM. The specificity of the probe, whether it is made from a highly specific region, e.g., the 5′ regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification (maximal, high, intermediate, or low), will determine whether the probe identifies only naturally occurring sequences encoding HHLM, alleles, or related sequences.

[0184] Probes may also be used for the detection of related sequences, and should preferably have at least 50% sequence identity to any of the HHLM-encoding sequences. The hybridization probes of the subject invention may be DNA or RNA and may be derived from the sequence SEQ ID NOs:9-16 and 17-55, or from genomic sequences including promoters, enhancers, and introns of the HHLM gene.

[0185] Means for producing specific hybridization probes for DNAs encoding HHLM include the cloning of polynucleotide sequences encoding HHLM or HHLM derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides. Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as 32P or 35S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.

[0186] Polynucleotide sequences encoding HHLM may be used for the diagnosis of a disorder associated with expression of HHLM. Examples of such a disorder include, but are not limited to, cell proliferation disorders such as arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease, myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, nerves, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; and autoimmune disorders such as AIDS, Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, ulcerative colitis, Werner syndrome, and complications of cancer, hemodialysis, and extracorporeal circulation; viral, bacterial, fungal, parasitic, protozoal, and helminthic infections; and trauma. The polynucleotide sequences encoding HHLM may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies; in dipstick, pin, and multiwell assays; and in microarrays utilizing fluids or tissues from patients to detect altered HHLM expression. Such qualitative or quantitative methods are well known in the art.

[0187] In a particular aspect, the nucleotide sequences encoding HHLM may be useful in assays that detect the presence of associated disorders, particularly those mentioned above. The nucleotide sequences encoding HHLM may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantitated and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of nucleotide sequences encoding HHLM in the sample indicates the presence of the associated disorder. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.

[0188] In order to provide a basis for the diagnosis of a disorder associated with expression of HHLM, a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding HHLM, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.

[0189] Once the presence of a disorder is established and a treatment protocol is initiated, hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.

[0190] Additional diagnostic uses for oligonucleotides designed from the sequences encoding HHLM may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced in vitro. Oligomers will preferably contain a fragment of a polynucleotide encoding HHLM, or a fragment of a polynucleotide complementary to the polynucleotide encoding HHLM, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantitation of closely related DNA or RNA sequences.

[0191] Methods which may also be used to quantitate the expression of HHLM include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves. (See, e.g., Melby et al. (1993) J Immunol Methods 159:235-244; and Duplaa et al. (1993) Anal Biochem 212:229-236.) The speed of quantitation of multiple samples may be accelerated by running the assay in a multiwell format where the oligomer of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.

[0192] Transcript images which profile the expression of the polynucleotides of the present invention may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir et al. (1999) Mol Carcinog 24:153-159; Steiner and Anderson (2000) Toxicol Lett 112-113:467-471, expressly incorporated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity. (See, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released Feb. 29, 2000, available at http://www.niehs.nih.gov/oc/news/toxchip.htm.) Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

[0193] Another particular embodiment relates to the use of the polypeptide sequences of the present invention to analyze a protein expression image of a tissue or cell type. A protein expression image represents the global pattern of expression at the protein level. Patterns of expression at the protein level are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. Thus a protein expression image may be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is performed using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized, typically by staining with an agent, including but not limited to Coomassie Blue, silver, or fluorescent stains. The optical densities of the protein spots are proportional to the levels of those proteins in the sample, and the proteins in the spots are sequenced using standard methods. The optical densities of protein spots from treated and untreated samples are compared to identify any changes related to the treatment. Protein spots are identified by comparing partial sequences from the spots, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, identification is uncertain with a partial sequence of 5 amino acid residues, and further sequence information is collected for definitive identification.

[0194] A protein expression image may also be generated using antibodies specific for HHLM to quantify the levels of expression at the protein level. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking et al. (1999) Anal Biochem 270:103-111; Mendoze et al. (1999) Biotechniques 27:778-788). Detection may be performed by a variety of methods known in the art, for example by reacting the proteins in the sample with a thiol- or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.

[0195] Toxicant signatures at the protein level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson and Seilheimer (1997) Electrophoresis 18:533-537), so protein level toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so the protein expression image may be more reliable and informative in such cases.

[0196] In one embodiment, the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.

[0197] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amounts of the proteins are compared to the amounts of corresponding proteins in an untreated biological sample. Differences in the amounts of proteins between the two samples are indicative of a toxic response to the test compound in the treated sample. Individual proteins from the separated proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the polypeptides of the present invention.

[0198] In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies, so that the amounts of the proteins recognized by the antibodies may be quantified. The amounts of the proteins in the treated biological sample are compared with the amounts in an untreated biological sample. Differences in the amounts of proteins between the two samples are indicative of a toxic response to the test compound in the treated sample.

[0199] In further embodiments, oligonucleotides or longer fragments derived from any of the polynucleotide sequences described herein may be used as targets in a microarray. The microarray can be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and polymorphisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, and to develop and monitor the activities of therapeutic agents.

[0200] Microarrays may be prepared, used, and analyzed using methods known in the art. (See, e.g., Chee et al. (1995) PCT application WO95/11995; Fodor et al. (1995) U.S. Pat. No. 5,424,186; Brennan et al. (1995) U.S. Pat. No. 5,474,796; Schena et al. (1996) Proc Natl Acad Sci 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon etal. (1995) PCT application WO95/35505; Lockhart et al. (1996) Nat Biotech 14:1675-1680; Heller et al. (1997) Proc Natl Acad Sci 94:2150-2155; and Heller et al. (1997) U.S. Pat. No. 5,605,662.)

[0201] In another embodiment of the invention, nucleic acid sequences encoding HHLM may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence. The sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial P1 constructions, or single chromosome cDNA libraries. (See, e.g., Price (1993) Blood Rev 7:127-134; and Trask (1991) Trends Genet 7:149-154.)

[0202] Fluorescent in situ hybridization (FISH) may be correlated with other physical chromosome mapping techniques and genetic map data. (See, e.g., Heinz-Ulrich, et al. (1995) in Meyers (ed.) Molecular Biology and Biotechnology, VCH Publishers New York N.Y., pp. 965-968.) Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) site. Correlation between the location of the gene encoding HHLM on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder. The nucleotide sequences of the invention may be used to detect differences in gene sequences among normal, carrier, and affected individuals.

[0203] In situ hybridization of chromosomal preparations and physical mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of a particular human chromosome is not known. New sequences can be assigned to chromosomal arms by physical mapping. This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the disease or syndrome has been crudely localized by genetic linkage to a particular genomic region, e.g., AT to 11q22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation. (See, e.g., Gatti et al. (1988) Nature 336:577-580.) The nucleotide sequence of the subject invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.

[0204] In another embodiment of the invention, HHLM, its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques. The fragment employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes between HHLM and the agent being tested may be measured.

[0205] Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest. (See, e.g., Geysen, et al. (1984) PCT application WO84/03564.) In this method, large numbers of different small test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. The test compounds are reacted with HHLM, or fragments thereof, and washed. Bound HHLM is then detected by methods well known in the art. Purified HHLM can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.

[0206] In another embodiment, one may use competitive drug screening assays in which neutralizing antibodies capable of binding HHLM specifically compete with a test compound for binding HHLM. In this manner, antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with HHLM.

[0207] In additional embodiments, the nucleotide sequences which encode HHLM may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.

[0208] The examples below are provided to illustrate the subject invention and are not included for the purpose of limiting the invention.

EXAMPLES

[0209] For purposes of example, the preparation and sequencing of the LUNGNOT10 cDNA library, from which Incyte Clone 1376382 was isolated, is described. Preparation and sequencing of cDNAs in libraries in the LIFESEQ database (Incyte Genomics, Inc., Palo Alto Calif.) have varied over time, and the gradual changes involved use of kits, plasmids, and machinery available at the particular time the library was made and analyzed.

[0210] I LUNGNOT10 cDNA Library Construction

[0211] The LUNGNOT10 cDNA library was constructed from normal lung tissue obtained from a 23-week-old Caucasian male fetus. The frozen tissue was homogenized and lysed using a POLYTRON homogenizer (PT-3000; Brinkmann Instruments, Westbury N.J.) in guanidinium isothiocyanate solution. The lysate was centrifuged over a 5.7 M CsCl cushion using an SW28 rotor in an L8-70M ultracentrifuge (Beckman Coulter, Fullerton Calif.) for 18 hours at 25,000 rpm at ambient temperature. The RNA was extracted with acid phenol, pH 4.0, precipitated using 0.3 M sodium acetate and 2.5 volumes of ethanol, resuspended in RNAse-free water, and treated with DNase at 37° C. RNA extraction and precipitation were repeated as before. The mRNA was isolated with the OLIGOTEX kit (Qiagen, Chatsworth Calif.) and used to construct the cDNA library.

[0212] The mRNA was handled according to the recommended protocols in the SUPERSCRIPT plasmid system(Life Technologies). cDNAs were fractionated on a SEPHAROSE CL4B column (APB), and those cDNAs exceeding 400 bp were ligated into pINCY I plasmid (Incyte Genomics). The plasmid pINCY was subsequently transformed into DH5&agr; competent cells (Life Technologies).

[0213] II Isolation and Sequencing of cDNA Clones

[0214] Plasmid DNA was released from the cells and purified using the REAL PREP 96 plasmid kit (Qiagen). This kit enabled the simultaneous purification of 96 samples in a 96-well block using multi-channel reagent dispensers. The recommended protocol was employed except for the following changes: 1) the bacteria were cultured in 1 ml of sterile Terrific Broth (Life Technologies) with carbenicillin (Carb) at 25 mg/l and glycerol at 0.4%; 2) after inoculation, the cultures were incubated for 19 hours and at the end of incubation, the cells were lysed with 0.3 ml of lysis buffer; and 3) following isopropanol precipitation, the plasmid DNA pellet was resuspended in 0.1 ml of distilled water. After the last step in the protocol, samples were transferred to a 96-well block for storage at 4° C.

[0215] The cDNAs were prepared using a MICROLAB 2200 system (Hamilton) in combination with DNA ENGINE thermal cyclers (MJ Research) and sequenced by the method of Sanger and Coulson (1975; J Mol Biol 94:441-448) using ABI PRISM 373 or 377 sequencing systems (PE Biosystems); and the reading frame was determined.

[0216] III. Homology Searching of cDNA Clones and Their Deduced Proteins

[0217] The cDNAs of the Sequence Listing or their deduced amino acid sequences were used to query databases such as GenBank, SwissProt, BLOCKS, and the like. These databases that contain previously identified and annotated sequences or domains were searched using BLAST or BLAST 2 (Altschul et al. supra; Altschul, supra) to produce alignments and to determine which sequences were exact matches or homologs. The alignments were to sequences of prokaryotic (bacterial) or eukaryotic (animal, fungal, or plant) origin. Alternatively, algorithms such as the one described in Smith and Smith (1992; Protein Engineering 5:35-51) could have been used to deal with primary sequence patterns and secondary structure gap penalties. All of the sequences disclosed in this application have lengths of at least 49 nucleotides, and no more than 12% uncalled bases (where N is recorded rather than A, C, G, or T).

[0218] As detailed in Karlin (supra), BLAST matches between a query sequence and a database sequence were evaluated statistically and only reported when they satisfied the threshold of 10−25 for nucleotides and 10−14 for peptides. Homology was also evaluated by product score calculated as follows: the % nucleotide or amino acid identity [between the query and reference sequences] in BLAST is multiplied by the % maximum possible BLAST score [based on the lengths of query and reference sequences] and then divided by 100. In comparison with hybridization procedures used in the laboratory, the electronic stringency for an exact match was set at 70, and the conservative lower limit for an exact match was set at approximately 40 (with 1-2% error due to uncalled bases).

[0219] The BLAST software suite, freely available sequence comparison algorithms (NCBI, Bethesda Md.; http://www.ncbi.nlm.nih.gov/gorf/b12.htm1), includes various sequence analysis programs including “blastn” that is used to align nucleic acid molecules and BLAST 2 that is used for direct pairwise comparison of either nucleic or amino acid molecules. BLAST programs are commonly used with gap and other parameters set to default settings, e.g.: Matrix: BLOSUM62; Reward for match: 1; Penalty for mismatch: −2; Open Gap: 5 and Extension Gap: 2 penalties; Gap×drop-off: 50; Expect: 10; Word Size: 11; and Filter: on. Identity is measured over the entire length of a sequence or some smaller portion thereof. Brenner et al. (1998; Proc NatI Acad Sci 95:6073-6078, incorporated herein by reference) analyzed the BLAST for its ability to identify structural homologs by sequence identity and found 30% identity is a reliable threshold for sequence alignments of at least 150 residues and 40%, for alignments of at least 70 residues.

[0220] The cDNA was further analyzed using MAcDNASIS PRO software (Hitachi Software Engineering), and LASERGENE software (DNASTAR) and queried against public databases such as the GenBank rodent, mammalian, vertebrate, prokaryote, and eukaryote databases, SwissProt, BLOCKS, PRINTS, PFAM, and Prosite.

[0221] IV. Northern Analysis

[0222] Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook, supra, ch. 7; and Ausubel et al. supra, ch. 4 and 16.)

[0223] Analogous computer techniques applying BLAST are used to search for identical or related molecules in nucleotide databases such as GenBank or LIFESEQ database (Incyte Genomics). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or homologous.

[0224] The basis of the search is the product score, which is defined as: 1 % ⁢   ⁢ sequence ⁢   ⁢ identity × % ⁢   ⁢ maximum ⁢   ⁢ BLAST ⁢   ⁢ score ⁢   100

[0225] The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. For example, with a product score of 40, the match will be exact within a 1% to 2% error, and, with a product score of 70, the match will be exact. Homologous molecules are usually identified by selecting those which show product scores between 15 and 40, although lower scores may identify related molecules.

[0226] The results of northern analysis are reported as a list of libraries in which the transcript encoding HHLM occurs. Abundance and percent abundance are also reported. Abundance directly reflects the number of times a particular transcript is represented in a cDNA library, and percent abundance is abundance divided by the total number of sequences examined in the cDNA library.

[0227] V. Extension of HHLM Encoding Polynucleotides

[0228] The nucleic acid sequences of Incyte Clones 094168, 195647, 507537, 971204, 1376382, 2011230, 2768301, and 2886583 were used to design oligonucleotide primers for extending partial nucleotide sequences to full length. For each nucleic acid sequence, one primer was synthesized to initiate extension of an antisense polynucleotide, and the other was synthesized to initiate extension of a sense polynucleotide. Primers were used to facilitate the extension of the known sequence “outward” generating amplicons containing new unknown nucleotide sequence for the region of interest. The initial primers were designed from the cDNA using OLIGO 4.06 primer analysis software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations was avoided.

[0229] Selected human cDNA libraries (Life Technologies) were used to extend the sequence. If more than one extension is necessary or desired, additional sets of primers are designed to further extend the known region.

[0230] High fidelity amplification was obtained by following the instructions for the XL-PCR kit (PE Biosystems) and thoroughly mixing the enzyme and reaction mix. PCR was performed using the DNA ENGINE thermal cycler (M.J. Research), beginning with 40 pmol of each primer and the recommended concentrations of all other components of the kit, with the following parameters: 2 Step 1 94° C. for 1 min (initial denaturation) Step 2 65° C. for 1 min Step 3 68° C. for 6 min Step 4 94° C. for 15 sec Step 5 65° C. for 1 min Step 6 68° C. for 7 min Step 7 Repeat steps 4 through 6 for an additional 15 cycles Step 8 94° C. for 15 sec Step 9 65° C. for 1 min Step 10 68° C. for 7:15 min Step 11 Repeat steps 8 through 10 for an additional 12 cycles Step 12 72° C. for 8 min Step 13 4° C. (and holding)

[0231] A 5 &mgr;l to 10 &mgr;l aliquot of the reaction mixture was analyzed by electrophoresis on a low concentration (about 0.6% to 0.8%) agarose mini-gel to determine which reactions were successful in extending the sequence. Bands thought to contain the largest products were excised from the gel, purified using QIAQUICK kit (Qiagen), and trimmed of overhangs using Klenow enzyme to facilitate religation and cloning.

[0232] After ethanol precipitation, the products were redissolved in 13 &mgr;l of ligation buffer, 1 &mgr;l T4-DNA ligase (15 units) and 1 &mgr;l T4 polynucleotide kinase were added, and the mixture was incubated at room temperature for 2 to 3 hours, or overnight at 16° C. Competent E. coli cells (in 40,&mgr;l of appropriate media) were transformed with 3 &mgr;l of ligation mixture and cultured in 80 &mgr;l of SOC medium. (See, e.g., Sambrook, supra, Appendix A, p. 2.) After incubation for one hour at 37° C., the E. coli mixture was plated on Luria Bertani (LB) agar (See, e.g., Sambrook, supra, Appendix A, p. 1) containing 2× Carb. The following day, several colonies were randomly picked from each plate and cultured in 150 &mgr;l of liquid LB/2× Carb medium placed in an individual well of an appropriate commercially-available sterile 96-well microtiter plate. The following day, 5 &mgr;l of each overnight culture was transferred into a non-sterile 96-well plate and, after dilution 1:10 with water, 5 &mgr;l from each sample was transferred into a PCR array.

[0233] For PCR amplification, 18 &mgr;l of concentrated PCR reaction mix (3.3×) containing 4 units of rTth DNA polymerase, a vector primer, and one or both of the gene specific primers used for the extension reaction were added to each well. Amplification was performed using the following conditions: 3 Step 1 94° C. for 60 sec Step 2 94° C. for 20 sec Step 3 55° C. for 30 sec Step 4 72° C. for 90 sec Step 5 Repeat steps 2 through 4 for an additional 29 cycles Step 6 72° C. for 180 sec Step 7 4° C. (and holding)

[0234] Aliquots of the PCR reactions were run on agarose gels together with molecular weight markers. The sizes of the PCR products were compared to the original partial cDNAs, and appropriate clones were selected, ligated into plasmid, and sequenced.

[0235] In like manner, the nucleotide sequences of SEQ ID NOs:916 and 17-55 are used to obtain 5′ regulatory sequences using the procedure above, oligonucleotides designed for 5′ extension, and an appropriate genomic library.

[0236] VI. Labeling and Use of Individual Hybridization Probes

[0237] Hybridization probes derived from SEQ ID NOs:9-16 and 17-55 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 primer analysis software (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250 &mgr;Ci of [&ggr;-32 P] adenosine triphosphate (APB), and T4 polynucleotide kinase (NEN Life Science Products, Boston Mass.). The labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine resin column (APB). An aliquot containing 107 counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba 1, or Pvu II (NEN Life Science Products).

[0238] The DNA from each digest is fractionated on a 0.7 percent agarose gel and transferred to NYTRAN PLUS membranes (Schleicher & Schuell, Durham N.H.). Hybridization is carried out for 16 hours at 40° C. To remove nonspecific signals, blots are sequentially washed at room temperature under increasingly stringent conditions up to 0.1×saline sodium citrate and 0.5% sodium dodecyl sulfate. After XOMAT AR film (Eastman Kodak, Rochester N.Y.) is exposed to the blots for several hours, hybridization patterns are compared visually.

[0239] VII. Microarrays

[0240] To produce oligonucleotides for a microarray, one of the nucleotide sequences of the present invention is examined using a computer algorithm which starts at the 3′ end of the nucleotide sequence. For each, the algorithm identifies oligomers of defined length that are unique to the nucleic acid sequence, have a GC content within a range suitable for hybridization, and lack secondary structure that would interfere with hybridization. The algorithm identifies approximately 20 oligonucleotides corresponding to each nucleic acid sequence. For each sequence-specific oligonucleotide, a pair of oligonucleotides is synthesized in which the first oligonucleotides differs from the second oligonucleotide by one nucleotide in the center of the sequence. The oligonucleotide pairs can be arranged on a substrate, e.g. a silicon chip, using a light-directed chemical process. (See, e.g., Chee, supra.)

[0241] Probe sequences may be selected by screening a large number of clones from a variety of cDNA libraries in order to find sequences with conserved protein motifs common to genes coding for signal sequence containing polypeptides. In one embodiment, sequences identified from cDNA libraries, are analyzed to identify those gene sequences with conserved protein motifs using an appropriate analysis program, e.g., the Block 2 bioanalysis program (Incyte Genomics). This motif analysis program, based on sequence information contained in the Swiss-Prot Database and PROSITE, is a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences. (See, e.g., Bairoch et al. (1997) Nucleic Acids Res 25:217-221; and Attwood et al. (1997) J Chem Inf Comput Sci 37:417-424.) PROSITE may be used to identify functional or structural domains that cannot be detected using conserved motifs due to extreme sequence divergence. The method is based on weight matrices. Motifs identified by this method are then calibrated against the SWISS-PROT database in order to obtain a measure of the chance distribution of the matches.

[0242] In another embodiment, Hidden Markov models (HMMs) may be used to find shared motifs, specifically consensus sequences. (See, e.g., Pearson and Lipman (1988) Proc Natl Acad Sci 85:2444-2448; and Smith and Waterman (1981) J Mol Biol 147:195-197.) HMMs were initially developed to examine speech recognition patterns, but are now being used in a biological context to analyze protein and nucleic acid sequences as well as to model protein structure. (See, e.g., Krogh et al. (1994) J Mol Biol 235:1501-1531; and Collin et al. (1993) Protein Sci 2:305-314.) HMMs have a formal probabilistic basis and use position-specific scores for amino acids or nucleotides. The algorithm continues to incorporate information from newly identified sequences to increase its motif analysis capabilities.

[0243] In the alternative, a chemical coupling procedure and an ink jet device can be used to synthesize oligomers on the surface of a substrate. (See, e.g., Baldeschweiler, supra.) An array analogous to a dot or slot blot may also be used to arrange and link fragments or oligonucleotides to the surface of a substrate using or thermal, UV, mechanical, or chemical bonding procedures, or a vacuum system. A typical array may be produced by hand or using available methods and machines and contain any appropriate number of elements. After hybridization, nonhybridized probes are removed and a scanner used to determine the levels and patterns of fluorescence. The degree of complementarity and the relative abundance of each oligonucleotide sequence on the microarray may be assessed through analysis of the scanned images.

[0244] In another alternative, full-length cDNAs or Expressed Sequence Tags (ESTs) comprise the elements of the microarray. Full-length cDNAs or ESTs corresponding to one of the nucleotide sequences of the present invention, or selected at random from a cDNA library relevant to the present invention, are arranged on an appropriate substrate, e.g., a glass slide. The cDNA is fixed to the slide using, e.g., UV cross-linking followed, by thermal and chemical and subsequent drying. (See, e.g., Schena et al. (1995) Science 270:467-470; and Shalon et al. (1996) Genome Res 6:639-645.) Fluorescent probes are prepared and used for hybridization to the elements on the substrate. The substrate is analyzed by procedures described above.

[0245] VIII. Complementary Polynucleotides

[0246] Sequences complementary to the HHLM-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring HHLM. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using OLIGO 4.06 primer analysis software (National Biosciences) and the coding sequence of HBLM. To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5′ sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the HHLM-encoding transcript.

[0247] IX. Expression of HHLM

[0248] Expression of HHLM is accomplished by subcloning the cDNA into an appropriate vector and transforming the vector into host cells. This vector contains an appropriate promoter, e.g., &bgr;-galactosidase upstream of the cloning site, operably associated with the cDNA of interest. (See, e.g., Sambrook, supra, pp. 404-433; and Rosenberg et al. (1983) Methods Enzymol 101:123-138.)

[0249] Induction of an isolated, transformed bacterial strain with isopropyl beta-D-thiogalactopyranoside using standard methods produces a fusion protein which consists of the first 8 residues of &bgr;-galactosidase, about 5 to 15 residues of linker, and the full length protein. The signal residues direct the secretion of HHLM into bacterial growth media which can be used directly in the following assay for activity.

[0250] X. Demonstration of HHLM Activity

[0251] For purposes of example, an assay measuring the phosphatase activity of an HHLM molecule is described. Varying amounts of HHLM are incubated with a fixed amount of [32P]-labeled myelin basic protein (MBP). After incubation under appropriate conditions of time, temperature, pH, and ionic strength described by Li et al. (1995, Biochemistry 34:1988-1996), the proteins are precipitated with cold trichloroacetic acid and collected on nitrocellulose filters with a 0.45 &mgr;m pore size (Millipore, Bedford Mass.). The filters are dried and immersed in a commercially available scintillation fluid prior to counting in a scintillation counter (Beckman Coulter). The amount of [32P]phosphate released from MBP by HHLM is proportional to the activity of HHLM in the sample.

[0252] XI. Production of HHLM Specific Antibodies

[0253] HHLM substantially purified using PAGE electrophoresis (see, e.g., Harrington (1990) Methods Enzymol 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols. The HHLM amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel et al. supra, ch. 11.)

[0254] Typically, the oligopeptides are 15 residues in length, and are synthesized using an ABI 431A peptide synthesizer (PE Biosystems) using Fmoc-chemistry and coupled to KLH (Sigma Aldrich, St. Louis Mo.) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester to increase immunogenicity. (See, e.g., Ausubel et al. supra.) Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide activity, for example, by binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG.

[0255] XII. Purification of Naturally Occurring HHLM Using Specific Antibodies

[0256] Naturally occurring or recombinant HHLM is substantially purified by immunoaffinity chromatography using antibodies specific for HHLM. An immunoaffinity column is constructed by covalently coupling anti-HHLM antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (APB). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

[0257] Media containing HHLM are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of HHLM (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/HHLM binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and HHLM is collected.

[0258] XIII. Identification of Molecules which Interact with HHLM

[0259] HHLM, or biologically active fragments thereof, are labeled with 125I Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973) Biochem J 133:529-539.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled HHLM, washed, and any wells with labeled HHLM complex are assayed. Data obtained using different concentrations of HHLM are used to calculate values for the number, affinity, and association of HHLM with the candidate molecules.

[0260] Various modifications and variations of the described methods and systems of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims.

Claims

1. An isolated polypeptide selected from the group consisting of:

a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8,

b) a polypeptide comprising a naturally occurring amino acid sequence at least 81% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:1-8,

c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-8, and

d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

2. An isolated polypeptide of claim 1 comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

3. An isolated polynucleotide encoding a polypeptide of claim 1.

4. An isolated polynucleotide encoding a polypeptide of claim 2.

5. An isolated polynucleotide of claim 4 comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:9-16.

6. A recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide of claim 3.

7. A cell transformed with a recombinant polynucleotide of claim 6.

8. A transgenic organism comprising a recombinant polynucleotide of claim 6.

9. A method of producing a polypeptide of claim 1, the method comprising:

a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide, and said recombinant polynucleotide comprises a promoter sequence operably linked to a polynucleotide encoding the polypeptide of claim 1, and

b) recovering the polypeptide so expressed.

10. A method of claim 9, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

11. An isolated antibody which specifically binds to an isolated polypeptide comprising an amino acid sequence, wherein said polypeptide is selected from the group consisting of:

a) a polypeptide comprising the amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8,

b) a naturally occurring polypeptide comprising an amino acid sequence at least 81% identical to the full length of an amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8 and which has hydrolase activity,

c) a biologically active fragment of a polypeptide having the amino acid sequence of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8 and which has hydrolase activity, and

d) an immunogenic fragment comprising at least 5 contiguous amino acid residues of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:7 or SEQ ID NO:8.

12. An isolated polynucleotide selected from the group consisting of:

a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:9-16,

b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO:9-16,

c) a polynucleotide complementary to a polynucleotide of a),

d) a polynucleotide complementary to a polynucleotide of b), and

e) an RNA equivalent of a)-d).

13. An isolated polynucleotide comprising at least 60 contiguous nucleotides of a polynucleotide of claim 12.

14. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising:

a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and

b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.

15. A method of claim 14, wherein the probe comprises at least 60 contiguous nucleotides.

16. A method of detecting a target polynucleotide in a sample, said target polynucleotide having a sequence of a polynucleotide of claim 12, the method comprising:

a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and

b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.

17. A composition comprising a polypeptide of claim 1 and a pharmaceutically acceptable excipient.

18. A composition of claim 17, wherein the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

19. A method for treating a disease or condition associated with decreased expression of functional HHLM, comprising administering to a patient in need of such treatment the composition of claim 17.

20. A method of screening a compound for effectiveness as an agonist of a polypeptide of claim 1, the method comprising:

a) exposing a sample comprising a polypeptide of claim 1 to a compound, and

b) detecting agonist activity in the sample.

21. A composition comprising an agonist compound identified by a method of claim 20 and a pharmaceutically acceptable excipient.

22. A method for treating a disease or condition associated with decreased expression of functional HHLM, comprising administering to a patient in need of such treatment a composition of claim 21.

23. A method of screening a compound for effectiveness as an antagonist of a polypeptide of claim 1, the method comprising:

a) exposing a sample comprising a polypeptide of claim 1 to a compound, and

b) detecting antagonist activity in the sample.

24. A composition comprising an antagonist compound identified by a method of claim 23 and a pharmaceutically acceptable excipient.

25. A method for treating a disease or condition associated with overexpression of functional HHLM, comprising administering to a patient in need of such treatment a composition of claim 24.

26. A method of screening for a compound that specifically binds to the polypeptide of claim 1, the method comprising:

a) combining the polypeptide of claim 1 with at least one test compound under suitable conditions, and

b) detecting binding of the polypeptide of claim 1 to the test compound, thereby identifying a compound that specifically binds to the polypeptide of claim 1.

27. A method of screening for a compound that modulates the activity of the polypeptide of claim 1, the method comprising:

a) combining the polypeptide of claim 1 with at least one test compound under conditions permissive for the activity of the polypeptide of claim 1,

b) assessing the activity of the polypeptide of claim 1 in the presence of the test compound, and

c) comparing the activity of the polypeptide of claim 1 in the presence of the test compound with the activity of the polypeptide of claim 1 in the absence of the test compound, wherein a change in the activity of the polypeptide of claim 1 in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide of claim 1.

28. A method of screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a sequence of claim 5, the method comprising:

a) exposing a sample comprising the target polynucleotide to a compound, under conditions suitable for the expression of the target polynucleotide,

b) detecting altered expression of the target polynucleotide, and

c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

29. A method of assessing toxicity of a test compound, the method comprising:

a) treating a biological sample containing nucleic acids with the test compound,

b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide of claim 12 under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide of claim 12 or fragment thereof,

c) quantifying the amount of hybridization complex, and

d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

30. A method for a diagnostic test for a condition or disease associated with the expression of HHLM in a biological sample, the method comprising:

a) combining the biological sample with an antibody of claim 11, under conditions suitable for the antibody to bind the polypeptide and form an antibody:polypeptide complex, and

b) detecting the complex, wherein the presence of the complex correlates with the presence of the polypeptide in the biological sample.

31. The antibody of claim 11, wherein the antibody is:

a) a chimeric antibody,

b) a single chain antibody,

c) a Fab fragment,

d) a F(ab′)2 fragment, or

e) a humanized antibody.

32. A composition comprising an antibody of claim 11 and an acceptable excipient.

33. A method of diagnosing a condition or disease associated with the expression of HHLM in a subject, comprising administering to said subject an effective amount of the composition of claim 32.

34. A composition of claim 32, further comprising a label.

35. A method of diagnosing a condition or disease associated with the expression of HHLM in a subject, comprising administering to said subject an effective amount of the composition of claim 34.

36. A method of preparing a polyclonal antibody with the specificity of the antibody of claim 11, the method comprising:

a) immunizing an animal with a polypeptide consisting of an amino acid sequence selected from the group consisting of SEQ ID NO:1-8, or an immunogenic fragment thereof, under conditions to elicit an antibody response,

b) isolating antibodies from the animal, and

c) screening the isolated antibodies with the polypeptide, thereby identifying a polyclonal antibody which specifically binds to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

37. A polyclonal antibody produced by a method of claim 36.

38. A composition comprising the polyclonal antibody of claim 37 and a suitable carrier.

39. A method of making a monoclonal antibody with the specificity of the antibody of claim 11, the method comprising:

a) immunizing an animal with a polypeptide consisting of an amino acid sequence selected from the group consisting of SEQ ID NO:1-8, or an immunogenic fragment thereof, under conditions to elicit an antibody response,

b) isolating antibody producing cells from the animal,

c) fusing the antibody producing cells with immortalized cells to form monoclonal antibody-producing hybridoma cells,

d) culturing the hybridoma cells, and

e) isolating from the culture monoclonal antibody which specifically binds to a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

40. A monoclonal antibody produced by a method of claim 39.

41. A composition comprising the monoclonal antibody of claim 40 and a suitable carrier.

42. The antibody of claim 11, wherein the antibody is produced by screening a Fab expression library.

43. The antibody of claim 11, wherein the antibody is produced by screening a recombinant immunoglobulin library.

44. A method of detecting a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8 in a sample, the method comprising:

a) incubating the antibody of claim 11 with the sample under conditions to allow specific binding of the antibody and the polypeptide, and

b) detecting specific binding, wherein specific binding indicates the presence of a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8 in the sample.

45. A method of purifying a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8 from a sample, the method comprising:

a) incubating the antibody of claim 11 with the sample under conditions to allow specific binding of the antibody and the polypeptide, and

b) separating the antibody from the sample and obtaining the purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:1-8.

46. A microarray wherein at least one element of the microarray is a polynucleotide of claim 13.

47. A method of generating an expression profile of a sample which contains polynucleotides, the method comprising:

a) labeling the polynucleotides of the sample,

b) contacting the elements of the microarray of claim 46 with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and

c) quantifying the expression of the polynucleotides in the sample.

48. An array comprising different nucleotide molecules affixed in distinct physical locations on a solid substrate, wherein at least one of said nucleotide molecules comprises a first oligonucleotide or polynucleotide sequence specifically hybridizable with at least 30 contiguous nucleotides of a target polynucleotide, and wherein said target polynucleotide is a polynucleotide of claim 12.

49. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 30 contiguous nucleotides of said target polynucleotide.

50. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to at least 60 contiguous nucleotides of said target polynucleotide.

51. An array of claim 48, wherein said first oligonucleotide or polynucleotide sequence is completely complementary to said target polynucleotide.

52. An array of claim 48, which is a microarray.

53. An array of claim 48, further comprising said target polynucleotide hybridized to a nucleotide molecule comprising said first oligonucleotide or polynucleotide sequence.

54. An array of claim 48, wherein a linker joins at least one of said nucleotide molecules to said solid substrate.

55. An array of claim 48, wherein each distinct physical location on the substrate contains multiple nucleotide molecules, and the multiple nucleotide molecules at any single distinct physical location have the same sequence, and each distinct physical location on the substrate contains nucleotide molecules having a sequence which differs from the sequence of nucleotide molecules at another distinct physical location on the substrate.