WO2001090321A2 - 55158, a novel human carbonic anhydrase and uses thereof - Google Patents

Abstract

The invention provides isolated nucleic acid molecules, designated CAH nucleic acid molecules, which encode novel CAH-related carbonic anhydrase molecules. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing CAH nucleic acid molecules, host cells into which the expression vectors have been introduced, and nonhuman transgenic animals in which a CAH gene has been introduced or disrupted. The invention still further provides isolated CAH proteins, fusion proteins, antigenic peptides and anti-CAH antibodies. Diagnostic methods utilizing compositions of the invention are also provided.

Description

55158, A NOVEL HUMAN CARBONIC ANHYDRASE AND USES THEREOF

Related Applications

This application claims the benefit of prior-filed provisional patent application Serial No. 60/205,449, filed May 19, 2000, entitled "55158, A NOVEL HUMAN CARBONIC ANHYDRASE AND USES THEREOF." The entire content ofthe above-referenced application is incorporated herein by this reference.

Background of the Invention Regulation ofthe availability of carbon dioxide is of critical importance in most metabolic and catabolic pathways in cells. A large family of enzymes that facilitates the interconversion of carbon dioxide to carbonic acid, termed the carbonic anhydrase family, has been identified. In the forward reaction, these enzymes catalyze the reversible hydration of carbon dioxide, thereby forming a carbonyl group on the substrate. These enzymes are also able to participate in the reverse reaction, wherein a carbonyl group on the target molecule, carbonic acid, is reduced by the transfer of a hydride group to the enzyme. In both reaction mechanisms, a coordinated zinc ion mediates the activity ofthe enzyme. Members ofthe carbonic anhydrase family are ubiquitous, and have been isolated from nearly all organisms. Family members can be grouped into three different classes: the α-CA, β-CA, and γ-CA, which share little structural similarity, but which all use zinc as a cofactor (Hewett-Emmett and Tashian (1996) Molec. Phylogenet. Evol. 5:50-77). The α-CA are exclusively found in animals, while the β-CA and γ-CA have been identified in plants and bacteria, and archaebacteria, respectively (Burnell et al. (1990) Plant Physiol. 92: 37-40; Alber and Ferry (1994) Proc. Natl Acad. Sci. USA 91 : 6909-6913). In animals, members of the α-CA family have been further classified into seven categories (CA I-CA VII) according to localization and regulation ofthe enzyme. Subgroups CA I, II, III and VII are localized to the cytosol, CA IV is membrane-bound, CA V enzymes are found in the mitochondria, and CA VI enzymes are most commonly found in the saliva (Lindskog (1997) Pharmacol. Ther. 74(1): 1-20). The carbon dioxide hydration turnover rates of these enzymes also differ, with CA II having a high turnover rate (about 10⁶ sec^"1 at pH 9 and 25 °C) (Khalifah (1971) J. Biol Chem. 246: 2561-2573; Steiner et al (1975) Eur. J. Biochem. 59: 253-259), and CA III having a much lower turnover rate (about 8 x 10 sec^" at 25 °C (Jewell et al. (1991) Biochemistry 30:1484-1490). Carbonic anhydrases have been well-characterized in terms of function and structure. The crystal structures of many ofthe α-CA family members are known (Liljas et al. (1972)

Nature New Biol. 235: 131-137; Kannan et al (1975) Proc. Natl Acad. Sci. USA 72: 51-55; Eriksson et al. (1988a) Proteins Structure Funct. Genet. 4: 274-282; Hakansson et al. (1992) J. Mol Biol. 227: 1192-1204; Eriksson and Liljas (1993) Proteins Struc. Funct. Genet. 16: 29-42; Boriack-Sjodin et al (1995) Proc. Natl Acad. Sci. USA 92: 10949-10953; Stams et al. (1996) Proc. Natl Acad. Sci. USA 93: 13589-13594). Structural similarities between family members are most frequently found in the active site, where the zinc ion is coordinated to the enzyme. Structural studies have found that the zinc ion is physically found near the bottom ofthe active site cavity, and is coordinated to three nitrogen atoms from three nearby histidines in a tetrahedral geometry, with a hydroxide ion or a water molecule as the fourth ligand (Lidskog (1997), supra). Residues which are conserved among α-CA family members include these three histidine molecules and ten other residues (including Gln-28, Ser-29, Pro-30, Asn-61, Ser-105, Glu-117, Gly-196, Thr-199, Trp-209, and Arg-246), many of which are thought to participate in indirect coordination ofthe substrate or the zinc ion (Lindskog (1997), supra).

Carbonic anhydrases play an important role in the production and breakdown of carbon dioxide and carbonic acid. Both of these compounds are of vital importance in the normal metabolic pathways and homeostatic regulatory mechanisms ofthe cell. For example, carbon dioxide is required for metabolic functions as diverse as gluconeogenesis and purine base biosynthesis. Similarly, fatty acid synthesis cannot proceed without carbonic acid (Stryer (1988) Biochemistry, 3^rd ed.). Biologic processes including the formation of various fluids (e.g., cerebrospinal fluid, gastric acid, vitreous humor, and saliva), calcification, bone resorption, respiration, and overall acid-base balance are also closely associated with the activity of carbonic anhydrases (Dodgson et al (1991) The Carbonic Anhydrases: Cellular Physiology and Molecular Genetics. New York: Plenum). Furthermore, carbonic acid synthesis has been linked to the transport of sodium ions across cellular membranes (Friedland and Maren (1984) Pharmacology ofthe Eye. Berlin: Springer- Verlag), and is linked to maintenance of cellular pH. As such, their activity contributes to the ability ofthe cell to grow and differentiate, to proliferate, to communicate and interact with other cells, and to regulate homeostasis. Underscoring the importance of this family of enzymes, modulation ofthe activity of one or more carbonic anhydrases have been linked to a number of human diseases, including glaucoma (Hoyng and van Beek (2000) Drugs 59(3): 411-434), osteoporosis (Hu et al. (1997) Hum. Mutat. 9: 383-387); Fathallah et al (1997) Hum. Genet. 99: 634-647), and Sjogren's disease (in which antibodies to carbonic anhydrase have been isolated) (Fox et al (1998) Curr. Opin. Rheumatol 10(5): 446-456).

Summary of the Invention The present invention is based, at least in part, on the discovery of novel members of the family of carbonic anhydrase molecules, referred to herein as CAH nucleic acid and protein molecules. The CAH nucleic acid and protein molecules ofthe present invention are useful as modulating agents in regulating a variety of cellular processes, e.g., cellular proliferation, growth, differentiation, or migration. Accordingly, in one aspect, this invention provides isolated nucleic acid molecules encoding CAH proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection of CAH-encoding nucleic acids. In one embodiment, a CAH nucleic acid molecule ofthe invention is at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the nucleotide sequence (e.g., to the entire length ofthe nucleotide sequence) shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , or a complement thereof. In a preferred embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown in SEQ ID NO:l or 3, or a complement thereof. In another embodiment, the nucleic acid molecule includes SEQ ID NO:3 and nucleotides 1-59 of SEQ ID NO: 1. In yet a further embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 1047- 1855 of SEQ ID NO: 1. In another preferred embodiment, the nucleic acid molecule consists ofthe nucleotide sequence shown in SEQ ID NO:l or 3.

In another embodiment, a CAH nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence sufficiently identical to the amino acid sequence of SEQ ID NO:2, or an amino acid sequence encoded by the DNA insert ofthe plasmid deposited with ATCC as Accession Number . In a preferred embodiment, a CAH nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the entire length ofthe amino acid sequence of SEQ ID NO:2, or the amino acid sequence encoded by the DNA insert ofthe plasmid deposited with ATCC as Accession Number

In another preferred embodiment, an isolated nucleic acid molecule encodes the amino acid sequence of human CAH. In yet another preferred embodiment, the nucleic acid molecule includes a nucleotide sequence encoding a protein having the amino acid sequence of SEQ ID NO:2, or the amino acid sequence encoded by the DNA insert ofthe plasmid deposited with ATCC as Accession Number . In yet another preferred embodiment, the nucleic acid molecule is at least 20, 30, 40, 50, 53, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 878, 900, 950, 1000, 1050, 1 100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850 or more nucleotides in length. In a further preferred embodiment, the nucleic acid molecule is at least 20, 30, 40, 50, 53, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 878, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850 or more nucleotides in length and encodes a protein having a CAH activity (as described herein). Another embodiment ofthe invention features nucleic acid molecules, preferably CAH nucleic acid molecules, which specifically detect CAH nucleic acid molecules relative to nucleic acid molecules encoding non-CAH proteins. For example, in one embodiment, such a nucleic acid molecule is at least 20, 30, 40, 50, 53, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 878, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850 or more nucleotides in length and hybridizes under stringent conditions to a complement of a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NO:l, the nucleotide sequence shown in SEQ ID NO:3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , or a complement thereof.

In preferred embodiments, the nucleic acid molecules are at least 15 (e.g., 15 contiguous) nucleotides in length and hybridize under stringent conditions to a complement ofthe nucleotide molecule set forth in SEQ ID NO: 1.

In other preferred embodiments, the nucleic acid molecule encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, or an amino acid sequence encoded by the DNA insert ofthe plasmid deposited with

ATCC as Accession Number , wherein the nucleic acid molecule hybridizes to a complement of a nucleic acid molecule comprising SEQ ID NO:l or 3, respectively, under stringent conditions. Another embodiment ofthe invention provides an isolated nucleic acid molecule which is antisense to a CAH nucleic acid molecule, e.g., the coding strand of a CAH nucleic acid molecule.

Another aspect ofthe invention provides a vector comprising a CAH nucleic acid molecule. In certain embodiments, the vector is a recombinant expression vector. In another embodiment, the invention provides a host cell containing a vector ofthe invention. In yet another embodiment, the invention provides a host cell containing a nucleic acid molecule ofthe invention. The invention also provides a method for producing a protein, preferably a CAH protein, by culturing in a suitable medium, a host cell, e.g., a mammalian host cell such as a non-human mammalian cell, ofthe invention containing a recombinant expression vector, such that the protein is produced.

Another aspect of this invention features isolated or recombinant CAH proteins and polypeptides. In one embodiment, an isolated CAH protein includes at least one or more of the following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain. In a preferred embodiment, a CAH protein includes at least one or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain, and has an amino acid sequence at least about 50%, 55%, 60%, 65%, 67%, 68%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the amino acid sequence of SEQ ID NO:2, or the amino acid sequence encoded by the DNA insert ofthe plasmid deposited with ATCC as Accession Number

In another preferred embodiment, a CAH protein includes at least one or more of the following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain, and has a CAH activity (as described herein).

In yet another preferred embodiment, a CAH protein includes at least one or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain, and is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a complement of a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l or 3.

In another embodiment, the invention features fragments ofthe protein having the amino acid sequence of SEQ ID NO:2, wherein the fragment comprises at least 12 amino acids (e.g., contiguous amino acids) ofthe amino acid sequence of SEQ ID NO:2, or an amino acid sequence encoded by the DNA insert ofthe plasmid deposited with the ATCC as

Accession Number . In another embodiment, a CAH protein has the amino acid sequence of SEQ ID NO:2.

In another embodiment, the invention features a CAH protein which is encoded by a nucleic acid molecule consisting of a nucleotide sequence at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to a nucleotide sequence of SEQ ID NO:l or 3, or a complement thereof. This invention further features a CAH protein which is encoded by a nucleic acid molecule consisting of a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l or 3, or a complement thereof.

The proteins ofthe present invention or portions thereof, e.g., biologically active portions thereof, can be operatively linked to a non-CAH polypeptide (e.g., heterologous amino acid sequences) to form fusion proteins. The invention further features antibodies, such as monoclonal or polyclonal antibodies, that specifically bind proteins ofthe invention, preferably CAH proteins. In addition, the CAH proteins or biologically active portions thereof can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.

In another aspect, the present invention provides a method for detecting the presence of a CAH nucleic acid molecule, protein, or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting a CAH nucleic acid molecule, protein, or polypeptide such that the presence of a CAH nucleic acid molecule, protein or polypeptide is detected in the biological sample. In another aspect, the present invention provides a method for detecting the presence of CAH activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of CAH activity such that the presence of CAH activity is detected in the biological sample. In another aspect, the invention provides a method for modulating CAH activity comprising contacting a cell capable of expressing CAH with an agent that modulates CAH activity such that CAH activity in the cell is modulated. In one embodiment, the agent inhibits CAH activity. In another embodiment, the agent stimulates CAH activity. In one embodiment, the agent is an antibody that specifically binds to a CAH protein. In another embodiment, the agent modulates expression of CAH by modulating transcription of a CAH gene or translation of a CAH mRNA. In yet another embodiment, the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of a CAH mRNA or a CAH gene.

In one embodiment, the methods ofthe present invention are used to treat a subject having a disorder characterized by aberrant or unwanted CAH protein or nucleic acid expression or activity by administering an agent which is a CAH modulator to the subject. In one embodiment, the CAH modulator is a CAH protein. In another embodiment the CAH modulator is a CAH nucleic acid molecule. In yet another embodiment, the CAH modulator is a peptide, peptidomimetic, or other small molecule. In a preferred embodiment, the disorder characterized by aberrant or unwanted CAH protein or nucleic acid expression is a carbonic anhydrase-associated disorder, e.g. , a CNS disorder, a cardiovascular disorder, a muscular disorder, a cell proliferation, growth, differentiation, or migration disorder (e.g., cancer), an ocular disorder, or a disorder of bone resorption, or calcification/bone formation. The present invention also provides diagnostic assays for identifying the presence or absence of a genetic alteration characterized by at least one of (i) aberrant modification or mutation of a gene encoding a CAH protein; (ii) mis-regulation ofthe gene; and (iii) aberrant post-translational modification of a CAH protein, wherein a wild-type form ofthe gene encodes a protein with a CAH activity. In another aspect the invention provides methods for identifying a compound that binds to or modulates the activity of a CAH protein, by providing an indicator composition comprising a CAH protein having CAH activity, contacting the indicator composition with a test compound, and determining the effect ofthe test compound on CAH activity in the indicator composition to identify a compound that modulates the activity of a CAH protein.

Other features and advantages ofthe invention will be apparent from the following detailed description and claims. Brief Description of the Drawings

Figures 1A-B depicts the cDNA sequence and predicted amino acid sequence of human CAH (clone Fbb.55158). The nucleotide sequence corresponds to nucleic acids 1 to 1855 of SEQ ID NO:l. The amino acid sequence corresponds to amino acids 1 to 328 of SEQ ID NO:2. The coding region without the 3' untranslated region ofthe human CAH gene is shown in SEQ ID NO:3.

Figure 2 depicts a hydrophobicity analysis ofthe human CAH protein.

Figures 3 A and B depict the results of a search which was performed against the HMM database using the amino acid sequence of human CAH (SEQ ID NO:2) and which resulted in the identification of a "eukary otic-type carbonic anhydrase domain" in the human CAH protein.

Figure 4 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a human tissue panel, as determined using Taqman™ analysis (l=normal artery, 2=normal vein, 3=early aortic smooth muscle cells, 4=coronary smooth muscle cells, 5=static HUVEC, 6=shear HUVEC, 7=normal heart tissue, 8=congestive heart failure

(CHF) heart tissue, 9=kidney tissue, 10=skeletal muscle, 1 l=normal adipose, 12=pancreas, 13 =primary osteoblasts, 14 =differentiated osteoclasts, 15=normal skin tissue , 16=normal spinal cord, 17=normal brain cortex, 18=brain hypothalamus, 19=nerve tissue, 20 =dorsal root ganglia (DRG), 21=glial cells, 22 =glioblastoma tissue, 23= normal breast tissue, 24= berate tumor tissue, 25=normal ovary tissue, 26=ovary tumor tissue, 27= normal prostate tissue, 28=prostate tumor tissue, 29=prostate epithelial cells, 30=normal colon tissue, 3 l=colon tumor tissue, 32=normal lung, 33=lung tumor tissue, 34=chronic obstructive pulmonary disease (COPD) lung tissue, 35=infiammatory bowel disease (IBD) colon tissue, 36= normal liver tissue, 37=liver fibrosis tissue, 38=dermal cells-fibroblasts, 39= normal spleen tissue, 40=normal tonsil tissue, 41=lymph node tissue, 42=small intestine tissue, 43=skin-decubitus, 44=synovium, 45=bone marrow, 46=activated PBMC).

Figure 5 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a panel containing human normal (N) and tumor (T) lung tissue, as determined using Taqman™ analysis. Figure 6 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a panel containing human normal (N) and tumor (T) ovary tissue, as determined using Taqman™ analysis.

Figure 7 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a panel containing human normal (N) and tumor (T) breast tissue, as determined using Taqman™ analysis.

Figure 8 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a panel containing human normal (N) and tumor (T) brain tissue, as determined using Taqman™ analysis. Figure 9 is a graphic depiction ofthe relative levels of human CAH mRNA expression in a human normal (N) and tumor (T) colon tissue panel, including colon tumor metastases to the liver, (liver met), as determined using Taqman™ analysis.

Detailed Description of the Invention

The present invention is based, at least in part, on the discovery of novel molecules, referred to herein as "carbonic anhydrase" or "CAH" or "CAH55158" nucleic acid and protein molecules, which are novel members of a family of enzymes possessing carbonic anhydrase activity. As used herein, the term "carbonic anhydrase" includes a molecule which is involved in the interconversion of carbon dioxide and carbonic acid by the reversible transfer of a hydride to carbon dioxide. Carbonic anhydrase molecules are involved in numerous metabolic and catabolic processes in a cell (including respiration, fatty acid biosynthesis, and purine biosynthesis), including those required for energy production or storage, and for metabolism or catabolism of metabolically important biomolecules. Carbonic anhydrase molecules are also involved in regulating homeostasis, (e.g., intracellular pH), in permitting cellular transport and signaling (e.g., sodium ion import), and in systemic processes such as fluid production (e.g., saliva, gastric fluid, intraocular fluid, and cerebrospinal fluid), calcification, and bone resorption. Thus, the CAH molecules ofthe present invention provide novel diagnostic targets and therapeutic agents to control carbonic anhydrase-associated disorders.

As used herein, a "carbonic anhydrase-mediated activity" includes an activity which involves the catalysis of reversible hydration of carbon dioxide to form carbonic acid (e.g., catalysis ofthe hydration of carbon dioxide to form carbonic acid and/or catalysis ofthe reverse reaction). Carbonic anhydrase-mediated activities include those cellular or systemic activities which require carbon dioxide and/or carbonic acid. Such activities include cellular metabolism, intra- or intercellular signaling, maintenance of cellular homeostasis (e.g., cellular pH), and systemic activities, such as calcification, bone resorption, and formation of various biological fluids, including saliva, cerebrospinal fluid, intraocular fluid, and gastric fluid. Such activities also include modulation or regulation of cellular proliferation, growth, differentiation, migration, and inter-or intra-cellular communication.

The term "family" when referring to the protein and nucleic acid molecules ofthe invention (e.g., the CAH family of proteins and/or nucleic acids) is intended to mean two or more proteins or nucleic acid molecules having a common structural domain or motif and having sufficient amino acid or nucleotide sequence homology as defined herein. Such family members can be naturally or non-naturally occurring and can be from either the same or different species. For example, a family can contain a first protein of human origin, as well as other, distinct proteins of human origin or alternatively, can contain homologues of non-human origin, e.g., mouse or monkey proteins. Members of a family may also have common functional characteristics.

For example, the family of CAH proteins comprises at least one signal sequence or signal peptide. The prediction of such a signal peptide can be made, for example, utilizing the computer algorithm SignalP (Henrik, et al (1997) Protein Engineering 10:1-6). As used herein, a "signal sequence" or "signal peptide" includes a peptide containing about 15 or more amino acids which occurs at the N-terminus of secretory and membrane bound proteins and which contains a large number of hydrophobic amino acid residues. For example, a signal sequence contains at least about 10-30 amino acid residues, preferably about 15-25 amino acid residues, more preferably about 18-20 amino acid residues, and more preferably about 19 amino acid residues, and has at least about 35-65%, preferably about 38-50%, and more preferably about 40-45% hydrophobic amino acid residues (e.g., Valine, Leucine, Isoleucine or Phenylalanine). Such a "signal sequence", also referred to in the art as a "signal peptide", serves to direct a protein containing such a sequence to a lipid bilayer, and is cleaved in secreted and membrane bound proteins. A signal sequence was identified in the amino acid sequence of human CAH at about amino acids 1-21 of SEQ ID NO:2.

In another embodiment, a CAH molecule ofthe present invention is identified based on the presence of a "carbonic anhydrase domain" in the protein or corresponding nucleic acid molecule. As used herein, the term "carbonic anhydrase domain" includes a protein domain having an amino acid sequence of about 150-300 amino acid residues, and a bit score of at least 70 when compared against a carbonic anhydrase Hidden Markov Model (HMM), e.g., PFAM accession number PF00194. In a preferred embodiment, a carbonic anhydrase domain includes a protein domain having an amino acid sequence of about 200- 250 amino acid residues and a bit score of at least 100. In another preferred embodiment, a carbonic anhydrase domain includes a protein domain having an amino acid sequence of about 235-240 amino acid residues and a bit score of at least 125 (e.g., at least 130, 140, 150, 160, 170). To identify the presence of a carbonic anhydrase domain in a CAH protein, the amino acid sequence ofthe protein is used to search a database of known Hidden Markov Models (HMMs) e.g., the PFAM HMM database. The carbonic anhydrase domain (HMM) has been assigned the PFAM Accession PF00194

(http://genome.wustl.edu/Pfam/html). For example, a search was performed against the HMM database using the amino acid sequence (SEQ ID NO:2) of human CAH, resulting in the identification of a carbonic anhydrase domain in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 63-301 of SEQ ID NO:2, having a score of 170. In another embodiment ofthe invention, a CAH protein is identified based on the presence of at least one "CAH signature motif in the protein or corresponding nucleic acid molecule. As used herein, the term "CAH signature motif includes an amino acid sequence that contains at least about 7-27 amino acid residues that are conserved among CAH family members. In one embodiment, a CAH signature motif includes an amino acid sequence at least about 10-24 amino acid residues, more preferably about 12-22 amino acid residues, even more preferably 15-19 amino acid residues and most preferably 17 amino acid residues in length and having the following amino acid sequence: S-E-[HN]-X-[LIVM]-X(4)-[FYH]- X(2)-E-[LIVMGA]-X-[LIVMFA](2), (SEQ ID NO:4), where X indicates any amino acid (see, for example, Edwards, Y. (1990) Biochem. Soc. Trans. 18:171-175). Accordingly, preferred proteins include the conserved amino acid residues ofthe above-recited CAH signature motif. Proteins including at least 10, 11, 12, 13, 14, 15, or 16 or more conserved amino acid residues ofthe above-recited CAH signature motif are also considered to be within the scope ofthe present invention.

In a preferred embodiment, the CAH molecules ofthe invention include at least one, preferably two or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain. Isolated proteins ofthe present invention, preferably CAH proteins, have an amino acid sequence sufficiently identical to the amino acid sequence of SEQ ID NO:2, or are encoded by a nucleotide sequence sufficiently identical to SEQ ID NO:l or 3. As used herein, the term "sufficiently identical" refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences share common structural domains or motifs and/or a common functional activity. For example, amino acid or nucleotide sequences which share common structural domains have at least 30%, 40%, or 50% homology, preferably 60% homology, more preferably 70%-80%, and even more preferably 90-95% homology across the amino acid sequences of the domains and contain at least one and preferably two structural domains or motifs, are defined herein as sufficiently identical. Furthermore, amino acid or nucleotide sequences which share at least 30%, 40%, or 50%, preferably 60%, more preferably 70-80%, or 90- 95% homology and share a common functional activity are defined herein as sufficiently identical.

As used interchangeably herein, an "CAH activity", "biological activity of CAH" or "functional activity of CAH", refers to an activity exerted by a CAH protein, polypeptide or nucleic acid molecule on a CAH responsive cell or tissue, or on a CAH protein substrate, as determined in vivo, or in vitro, according to standard techniques. In one embodiment, a CAH activity is a direct activity, such as an association with a CAH-target molecule. As used herein, a "target molecule" or "binding partner" is a molecule with which a CAH protein binds or interacts in nature, such that CAH-mediated function is achieved. A CAH target molecule can be a non-CAH molecule or a CAH protein or polypeptide ofthe present invention (e.g. , a zinc ion, or other cofactor). In an exemplary embodiment, a CAH target molecule is a CAH substrate (e.g., carbon dioxide or carbonic acid). Alternatively, a CAH activity is an indirect activity, such as a metabolic activity mediated by interaction ofthe CAH protein with a CAH substrate. The biological activities of CAH are described herein. In an exemplary embodiment, the CAH proteins ofthe present invention have at least one of the following activities: i) interaction with a CAH substrate; ii) interaction with a cofactor; and iii) conversion of a CAH substrate to product (e.g., catalysis ofthe conversion of substrate to product). In yet another embodiment, the CAH proteins ofthe present invention have one or more ofthe following activities: 1) modulate metabolism and catabolism of biochemical molecules necessary for energy production or storage, or of metabolically important molecules, 2) modulate intra- or intercellular signaling, 3) regulate cellular homeostasis; 4) modulate calcification; 5) modulate bone resorption; 6) modulate fluid production; and 7) modulate cellular proliferation, growth, and/or differentiation.

Accordingly, another embodiment ofthe invention features isolated CAH proteins and polypeptides having a CAH activity. Other preferred proteins are CAH proteins having one or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain and, preferably, a CAH activity.

Additional preferred proteins have at least one or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain, and are, preferably, encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a complement of a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l or 3.

The nucleotide sequence ofthe isolated human CAH cDNA and the predicted amino acid sequence ofthe human CAH polypeptide are shown in Figure 1 and in SEQ ID NOs:l and 2, respectively. Plasmids containing the nucleotide sequence encoding human CAH were deposited with the American Type Culture Collection (ATCC), 10801 University

Boulevard, Manassas, VA 20110-2209, on and assigned Accession Numbers .

These deposits will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. These deposits were made merely as a convenience for those of skill in the art and are not an admission that deposits are required under 35 U.S.C. §112.

The human CAH gene, which is approximately 1855 nucleotides in length, encodes a protein having a molecular weight of approximately 36.1 kD and which is approximately 328 amino acid residues in length.

Various aspects ofthe invention are described in further detail in the following subsections: Isolated Nucleic Acid Molecules

One aspect ofthe invention pertains to isolated nucleic acid molecules that encode CAH proteins or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes to identify CAH-encoding nucleic acid molecules (e.g. , CAH mRNA) and fragments for use as PCR primers for the amplification or mutation of CAH nucleic acid molecules. As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs ofthe DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double- stranded DNA.

The term "isolated nucleic acid molecule" includes nucleic acid molecules which are separated from other nucleic acid molecules which are present in the natural source ofthe nucleic acid. For example, with regards to genomic DNA, the term "isolated" includes nucleic acid molecules which are separated from the chromosome with which the genomic DNA is naturally associated. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends ofthe nucleic acid) in the genomic DNA ofthe organism from which the nucleic acid is derived. For example, in various embodiments, the isolated CAH nucleic acid molecule can contain less than about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA ofthe cell from which the nucleic acid is derived. Moreover, an "isolated" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. A nucleic acid molecule ofthe present invention, e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:l or 3, or the nucleotide sequence ofthe

DNA insert ofthe plasmid deposited with ATCC as Accession Number , or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or portion ofthe nucleic acid sequence of SEQ ID NO: 1 or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with

ATCC as Accession Number as a hybridization probe, CAH nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).

Moreover, a nucleic acid molecule encompassing all or a portion of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number can be isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as

Accession Number .

A nucleic acid ofthe invention can be amplified using cDNA, mRNA or, alternatively, genomic DNA as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to CAH nucleotide sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer. In a preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises the nucleotide sequence shown in SEQ ID NO:l or 3. This cDNA may comprise sequences encoding the human CAH protein (i.e., "the coding region", from nucleotides 60- 1046), as well as 5' untranslated sequences (nucleotides 1-59) and 3' untranslated sequences (nucleotides 1047-1855) of SEQ ID NO:l. Alternatively, the nucleic acid molecule can comprise only the coding region of SEQ ID NO:l (e.g., nucleotides 60-1046, corresponding to SEQ ID NO:3).

In another preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises a nucleic acid molecule which is a complement ofthe nucleotide sequence shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert of the plasmid deposited with ATCC as Accession Number , or a portion of any of these nucleotide sequences. A nucleic acid molecule which is complementary to the nucleotide sequence shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , is one which is sufficiently complementary to the nucleotide sequence shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number such that it can hybridize to the nucleotide sequence shown in SEQ ID NO: 1 or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as

Accession Number , respectively, thereby forming a stable duplex.

In still another preferred embodiment, an isolated nucleic acid molecule ofthe present invention comprises a nucleotide sequence which is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the entire length ofthe nucleotide sequence shown in SEQ ID NO:l or 3, or the entire length ofthe nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , or a portion of any of these nucleotide sequences. Moreover, the nucleic acid molecule ofthe invention can comprise only a portion of the nucleic acid sequence of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , for example, a fragment which can be used as a probe or primer or a fragment encoding a portion of a CAH protein, e.g., a biologically active portion of a CAH protein. The nucleotide sequence determined from the cloning ofthe CAH gene allows for the generation of probes and primers designed for use in identifying and/or cloning other CAH family members, as well as CAH homologues from other species. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12 or 15, preferably about 20 or 25, more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 consecutive nucleotides of a sense sequence of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number of an anti- sense sequence of SEQ ID NO: 1 or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number or of a naturally occurring allelic variant or mutant of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number . In one embodiment, a nucleic acid molecule ofthe present invention comprises a nucleotide sequence which is greater than 20, 30, 40, 50, 53, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 878, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850 or more nucleotides in length and hybridizes under stringent hybridization conditions to a complement of a nucleic acid molecule of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number .

Probes based on the CAH nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In preferred embodiments, the probe further comprises a label group attached thereto, e.g., the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells or tissue which misexpress a CAH protein, such as by measuring a level of a CAH-encoding nucleic acid in a sample of cells from a subject e.g., detecting CAH mRNA levels or determining whether a genomic CAH gene has been mutated or deleted.

A nucleic acid fragment encoding a "biologically active portion of a CAH protein" can be prepared by isolating a portion ofthe nucleotide sequence of SEQ ID NO: 1 or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as

Accession Number which encodes a polypeptide having a CAH biological activity

(the biological activities ofthe CAH proteins are described herein), expressing the encoded portion ofthe CAH protein (e.g., by recombinant expression in vitro) and assessing the activity ofthe encoded portion ofthe CAH protein.

The invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number due to degeneracy ofthe genetic code and thus encode the same CAH proteins as those encoded by the nucleotide sequence shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number . In another embodiment, an isolated nucleic acid molecule ofthe invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ID NO:2.

In addition to the CAH nucleotide sequences shown in SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession

Number , it will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences ofthe CAH proteins may exist within a population (e.g., the human population). Such genetic polymoφhism in the CAH genes may exist among individuals within a population due to natural allelic variation. As used herein, the terms "gene" and "recombinant gene" refer to nucleic acid molecules which include an open reading frame encoding a CAH protein, preferably a mammalian CAH protein, and can further include non-coding regulatory sequences, and introns. Allelic variants of human CAH include both functional and non-functional CAH proteins. Functional allelic variants are naturally occurring amino acid sequence variants of the human CAH protein that maintain the ability to bind a CAH ligand or substrate and/or modulate cell proliferation and/or migration mechanisms. Functional allelic variants will typically contain only conservative substitution of one or more amino acids of SEQ ID NO:2, or substitution, deletion or insertion of non-critical residues in non-critical regions of the protein.

Non-functional allelic variants are naturally occurring amino acid sequence variants ofthe human CAH protein that do not have the ability to either bind a CAH ligand and/or modulate any ofthe CAH activities described herein. Non-functional allelic variants will typically contain a non-conservative substitution, a deletion, or insertion or premature truncation ofthe amino acid sequence of SEQ ID NO:2, or a substitution, insertion or deletion in critical residues or critical regions ofthe protein.

The present invention further provides non-human orthologues ofthe human CAH protein. Orthologues ofthe human CAH protein are proteins that are isolated from non- human organisms and possess the same CAH ligand binding and/or modulation of membrane excitability activities ofthe human CAH protein. Orthologues ofthe human CAH protein can readily be identified as comprising an amino acid sequence that is substantially identical to SEQ ID NO:2.

Moreover, nucleic acid molecules encoding other CAH family members and, thus, which have a nucleotide sequence which differs from the CAH sequences of SEQ ID NO: 1 or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as

Accession Number are intended to be within the scope ofthe invention. For example, another CAH cDNA can be identified based on the nucleotide sequence of human CAH. Moreover, nucleic acid molecules encoding CAH proteins from different species, and which, thus, have a nucleotide sequence which differs from the CAH sequences of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with

ATCC as Accession Number are intended to be within the scope ofthe invention. For example, a mouse CAH cDNA can be identified based on the nucleotide sequence of a human CAH.

Nucleic acid molecules corresponding to natural allelic variants and homologues of the CAH cDNAs ofthe invention can be isolated based on their homology to the CAH nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Nucleic acid molecules corresponding to natural allelic variants and homologues ofthe CAH cDNAs ofthe invention can further be isolated by mapping to the same chromosome or locus as the CAH gene.

Accordingly, in another embodiment, an isolated nucleic acid molecule ofthe invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to a complement ofthe nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number . In other embodiment, the nucleic acid is at least 20, 30, 40, 50, 53, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 878, 900, 950, 1000, 1050, 1100, 1 150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850 or more nucleotides in length. As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences that are significantly identical or homologous to each other remain hybridized to each other. Preferably, the conditions are such that sequences at least about 70%, more preferably at least about 80%, even more preferably at least about 85% or 90% identical to each other remain hybridized to each other. Such stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, Ausubel et al, eds., John Wiley & Sons, Inc. (1995), sections 2, 4 and 6. Additional stringent conditions can be found in Molecular Cloning: A Laboratory Manual, Sambrook et al , Cold Spring Harbor Press, Cold Spring Harbor, NY (1989), chapters 7, 9 and 11. A preferred, non-limiting example of stringent hybridization conditions includes hybridization in 4X sodium chloride/sodium citrate (SSC), at about 65-70°C (or hybridization in 4X SSC plus 50% formamide at about 42-50°C) followed by one or more washes in IX SSC, at about 65-70° C. A preferred, non-limiting example of highly stringent hybridization conditions includes hybridization in IX SSC, at about 65-70°C (or hybridization in IX SSC plus 50% formamide at about 42-50°C) followed by one or more washes in 0.3X SSC, at about 65-70° C. A preferred, non-limiting example of reduced stringency hybridization conditions includes hybridization in 4X SSC, at about 50-60°C (or alternatively hybridization in 6X SSC plus 50% formamide at about 40-45°C) followed by one or more washes in 2X SSC, at about 50-60°C. Ranges intermediate to the above-recited values, e.g., at 65-70°C or at 42- 50°C are also intended to be encompassed by the present invention. SSPE (lxSSPE is 0.15M NaCl, 1 OmM NaH₂PO₄, and 1.25mM EDTA, pH 7.4) can be substituted for SSC (lxSSC is 0.15M NaCl and 15mM sodium citrate) in the hybridization and wash buffers; washes are performed for 15 minutes each after hybridization is complete. The hybridization temperature for hybrids anticipated to be less than 50 base pairs in length should be 5-10°C less than the melting temperature (T_m) ofthe hybrid, where T_m is determined according to the following equations. For hybrids less than 18 base pairs in length, T_m(°C) = 2(# of A + T bases) + 4(# of G + C bases). For hybrids between 18 and 49 base pairs in length, T_m(°C) = 81.5 + 16.6(logιo[Na⁺]) + 0.41 (%G+C) - (600/N), where N is the number of bases in the hybrid, and [Na⁺] is the concentration of sodium ions in the hybridization buffer ([Na⁺] for lxSSC = 0.165 M). It will also be recognized by the skilled practitioner that additional reagents may be added to hybridization and/or wash buffers to decrease non-specific hybridization of nucleic acid molecules to membranes, for example, nitrocellulose or nylon membranes, including but not limited to blocking agents (e.g., BSA or salmon or herring sperm carrier DNA), detergents (e.g., SDS), chelating agents (e.g., EDTA), Ficoll, PVP and the like. When using nylon membranes, in particular, an additional preferred, non-limiting example of stringent hybridization conditions is hybridization in 0.25-0.5M NaH₂PO₄, 7% SDS at about 65°C, followed by one or more washes at 0.02M NaH₂PO₄, 1% SDS at 65°C, see e.g., Church and Gilbert (1984) Proc. Natl Acad. Sci. USA 81 :1991-1995, (or alternatively 0.2X SSC, 1% SDS).

Preferably, an isolated nucleic acid molecule ofthe invention that hybridizes under stringent conditions to the sequence of SEQ ID NO:l or 3, and corresponds to a naturally- occurring nucleic acid molecule. As used herein, a "naturally-occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).

In addition to naturally-occurring allelic variants ofthe CAH sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number , thereby leading to changes in the amino acid sequence ofthe encoded CAH proteins, without altering the functional ability ofthe CAH proteins. For example, nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ID NO:l or 3, or the nucleotide sequence of the DNA insert ofthe plasmid deposited with ATCC as Accession Number . A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequence of CAH (e.g., the sequence of SEQ ID NO: 2) without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity. For example, amino acid residues that are conserved among the CAH proteins ofthe present invention, e.g., those present in a carbonic anhydrase consensus sequence, are predicted to be particularly unamenable to alteration. Furthermore, additional amino acid residues that are conserved between the CAH proteins ofthe present invention and other members ofthe CAH family are not likely to be amenable to alteration.

Accordingly, another aspect ofthe invention pertains to nucleic acid molecules encoding CAH proteins that contain changes in amino acid residues that are not essential for activity. Such CAH proteins differ in amino acid sequence from SEQ ID NO:2, yet retain biological activity. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to SEQ ID NO:2. An isolated nucleic acid molecule encoding a CAH protein identical to the protein of

SEQ ID NO:2 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO:l or 3, or the nucleotide sequence of the DNA insert ofthe plasmid deposited with ATCC as Accession Number such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ID NO:l or 3, or the nucleotide sequence of the DNA insert ofthe plasmid deposited with ATCC as Accession Number by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non- essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g. , lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a CAH protein is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a CAH coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for CAH biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ID NO:l or 3, or the nucleotide sequence of the DNA insert ofthe plasmid deposited with ATCC as Accession Number , the encoded protein can be expressed recombinantly and the activity ofthe protein can be determined.

In a preferred embodiment, a mutant CAH protein can be assayed for the ability to metabolize or catabolize important biochemical molecules (e.g., those necessary for energy production or storage, or which are themselves metabolically important), to permit intra- or intercellular signaling, to regulate homeostasis (e.g., cellular pH), to modulate calcification or bone resorption, or to modulate fluid production (e.g., saliva, cerebrospinal fluid, gastric fluid, or intraocular fluid).

In addition to the nucleic acid molecules encoding CAH proteins described above, another aspect ofthe invention pertains to isolated nucleic acid molecules which are antisense thereto. An "antisense" nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire CAH coding strand, or to only a portion thereof. In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" ofthe coding strand of a nucleotide sequence encoding a CAH. The term "coding region" refers to the region ofthe nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the coding region of human CAH corresponds to SEQ ID NO:3). In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" ofthe coding strand of a nucleotide sequence encoding CAH. The term "noncoding region" refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).

Given the coding strand sequences encoding CAH disclosed herein (e.g., SEQ ID NO: 3), antisense nucleic acids ofthe invention can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of CAH mRNA, but more preferably is an oligonucleotide which is antisense to only a portion ofthe coding or noncoding region of CAH mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of CAH mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleic acid ofthe invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability ofthe molecules or to increase the physical stability ofthe duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl- 2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1 -methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2- methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7- methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D- mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6- isopentenyladenine, uracil-5 -oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5- oxyacetic acid methylester, uracil-5 -oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3- N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).

The antisense nucleic acid molecules ofthe invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a CAH protein to thereby inhibit expression ofthe protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove ofthe double helix. An example of a route of administration of antisense nucleic acid molecules ofthe invention include direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations ofthe antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

In yet another embodiment, the antisense nucleic acid molecule ofthe invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625- 6641). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al (1987) FEBS Lett. 215:327-330).

In still another embodiment, an antisense nucleic acid ofthe invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave CAH mRNA transcripts to thereby inhibit translation of CAH mRNA. A ribozyme having specificity for a CAH-encoding nucleic acid can be designed based upon the nucleotide sequence of a CAH cDNA disclosed herein (i.e., SEQ ID NO:l or 3, or the nucleotide sequence ofthe DNA insert ofthe plasmid deposited with ATCC as Accession Number ). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence ofthe active site is complementary to the nucleotide sequence to be cleaved in a CAH-encoding mRNA. See, e.g., Cech et al. U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742. Alternatively, CAH mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261 :1411-1418.

Alternatively, CAH gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region ofthe CAH (e.g., the CAH promoter and/or enhancers; e.g. , nucleotides 1-59 of SEQ ID NO: 1) to form triple helical structures that prevent transcription ofthe CAH gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6): 569-84; Helene, C. et al. (1992) Ann. N Y. Acad. Sci. 660:27-36; and Maher, L.J. (1992) Bioassays 14(12):807-15.

In yet another embodiment, the CAH nucleic acid molecules ofthe present invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility ofthe molecule. For example, the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic & Medicinal Chemistry 4 (1): 5-23). As used herein, the terms "peptide nucleic acids" or "PNAs" refer to nucleic acid mimics, e.g. , DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra; Perry-O'Keefe et al. Proc. Natl Acad. Sci. 93: 14670-675.

PNAs of CAH nucleic acid molecules can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence- specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication. PNAs of CAH nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, (e.g., by PNA-directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, (e.g., SI nucleases (Hyrup B. (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al. (1996) supra; Perry-O'Keefe supra).

In another embodiment, PNAs of CAH can be modified, (e.g., to enhance their stability or cellular uptake), by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras of CAH nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, (e.g., RNAse H and DNA polymerases), to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup B. (1996) supra). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup B. (1996) supra and Finn P.J. et al (1996) Nucleic Acids Res. 24 (17): 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used as a between the PNA and the 5' end of DNA (Mag, M. et al. ( 1989) Nucleic Acid Res. 17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. (1996) supra). Alternatively, chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser, K.H. et al. (1975) Bioorganic Med. Chem. Lett. 5: 1 119-11 124). In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et al (1987) Proc. Natl Acad. Sci. USA 84:648-652; PCT Publication No. W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No. W089/10134). In addition, oligonucleotides can be modified with hybridization-triggered cleavage agents (See, e.g., Krol et al (1988) Bio-Techniques 6:958-976) or intercalating agents. (See, e.g., Zon (1988) Pharm. Res. 5:539-549). To this end, the oligonucleotide may be conjugated to another molecule, (e.g., a peptide, hybridization triggered cross- linking agent, transport agent, or hybridization-triggered cleavage agent). Alternatively, the expression characteristics of an endogenous CAH gene within a cell line or microorganism may be modified by inserting a heterologous DNA regulatory element into the genome of a stable cell line or cloned microorganism such that the inserted regulatory element is operatively linked with the endogenous CAH gene. For example, an endogenous CAH gene which is normally "transcriptionally silent", i.e., a CAH gene which is normally not expressed, or is expressed only at very low levels in a cell line or microorganism, may be activated by inserting a regulatory element which is capable of promoting the expression of a normally expressed gene product in that cell line or microorganism. Alternatively, a transcriptionally silent, endogenous CAH gene may be activated by insertion of a promiscuous regulatory element that works across cell types.

A heterologous regulatory element may be inserted into a stable cell line or cloned microorganism, such that it is operatively linked with an endogenous CAH gene, using techniques, such as targeted homologous recombination, which are well known to those of skill in the art, and described, e.g., in Chappel, U.S. Patent No. 5,272,071; PCT publication No. WO 91/06667, published May 16, 1991.

II. Isolated CAH Proteins and Anti-CAH Antibodies

One aspect ofthe invention pertains to isolated CAH proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti-CAH antibodies. In one embodiment, native CAH proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, CAH proteins are produced by recombinant DNA techniques. Alternative to recombinant expression, a CAH protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques. An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the CAH protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of CAH protein in which the protein is separated from cellular components ofthe cells from which it is isolated or recombinantly produced. In one embodiment, the language "substantially free of cellular material" includes preparations of CAH protein having less than about 30% (by dry weight) of non- CAH protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-CAH protein, still more preferably less than about 10% of non-CAH protein, and most preferably less than about 5% non-CAH protein. When the CAH protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% ofthe volume ofthe protein preparation.

The language "substantially free of chemical precursors or other chemicals" includes preparations of CAH protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis ofthe protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals" includes preparations of CAH protein having less than about 30% (by dry weight) of chemical precursors or non-CAH chemicals, more preferably less than about 20% chemical precursors or non-CAH chemicals, still more preferably less than about 10% chemical precursors or non-CAH chemicals, and most preferably less than about 5% chemical precursors or non-CAH chemicals.

As used herein, a "biologically active portion" of a CAH protein includes a fragment of a CAH protein which participates in an interaction between a CAH molecule and a non- CAH molecule. Biologically active portions of a CAH protein include peptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence of the CAH protein, e.g., the amino acid sequence shown in SEQ ID NO:2, which include less amino acids than the full length CAH proteins, and exhibit at least one activity of a CAH protein. Typically, biologically active portions comprise a domain or motif with at least one activity ofthe CAH protein, e.g., modulating membrane excitability. A biologically active portion of a CAH protein can be a polypeptide which is, for example, 12, 25, 50, 75, 100, 125, 150, 175, 200, 250, 300 or more amino acids in length. Biologically active portions of a CAH protein can be used as targets for developing agents which modulate a CAH mediated activity, e.g., a proliferative response.

It is to be understood that a preferred biologically active portion of a CAH protein of the present invention may contain at least one or more ofthe following motifs or domains: a signal peptide, a CAH signature motif, and/or a carbonic anhydrase domain. Moreover, other biologically active portions, in which other regions ofthe protein are deleted, can be prepared by recombinant techniques and evaluated for one or more ofthe functional activities of a native CAH protein. In a preferred embodiment, the CAH protein has an amino acid sequence shown in

SEQ ID NO:2. In other embodiments, the CAH protein is substantially identical to SEQ ID NO:2, and retains the functional activity ofthe protein of SEQ ID NO:2, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail in subsection I above. Accordingly, in another embodiment, the CAH protein is a protein which comprises an amino acid sequence at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to SEQ ID NO:2.

To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison puφoses (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-identical sequences can be disregarded for comparison puφoses). In a preferred embodiment, the length of a reference sequence aligned for comparison puφoses is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, and even more preferably at least 70%, 80%, or 90% of the length ofthe reference sequence (e.g., when aligning a second sequence to the CAH amino acid sequence of SEQ ID NO:2 having 328 amino acid residues, at least 50, preferably at least 100, more preferably at least 150, even more preferably at least 200, and even more preferably at least 300 or more amino acid residues are aligned). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid "identity" is equivalent to amino acid or nucleic acid "homology"). The percent identity between the two sequences is a function ofthe number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment ofthe two sequences.

The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J. Mol Biol. (48):444-453 (1970)) algorithm which has been incoφorated into the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (Comput. Appl Biosci., 4: 11-17 (1988)) which has been incoφorated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.

The nucleic acid and protein sequences ofthe present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to CAH nucleic acid molecules ofthe invention. BLAST protein searches can be performed with the XBLAST program, score = 100, wordlength = 3 to obtain amino acid sequences homologous to CAH protein molecules ofthe invention. To obtain gapped alignments for comparison puφoses, Gapped BLAST can be utilized as described in Altschul et al, (1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, the default parameters ofthe respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.

The invention also provides CAH chimeric or fusion proteins. As used herein, a CAH "chimeric protein" or "fusion protein" comprises a CAH polypeptide operatively linked to a non-CAH polypeptide. An "CAH polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a CAH molecule, whereas a "non-CAH polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the CAH protein, e.g., a protein which is different from the CAH protein and which is derived from the same or a different organism. Within a CAH fusion protein the CAH polypeptide can correspond to all or a portion of a CAH protein. In a preferred embodiment, a CAH fusion protein comprises at least one biologically active portion of a CAH protein. In another preferred embodiment, a CAH fusion protein comprises at least two biologically active portions of a CAH protein. Within the fusion protein, the term "operatively linked" is intended to indicate that the CAH polypeptide and the non-CAH polypeptide are fused in-frame to each other. The non-CAH polypeptide can be fused to the N-terminus or C-terminus ofthe CAH polypeptide.

For example, in one embodiment, the fusion protein is a GST-CAH fusion protein in which the CAH sequences are fused to the C-terminus ofthe GST sequences. Such fusion proteins can facilitate the purification of recombinant CAH.

In another embodiment, the fusion protein is a CAH protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g. , mammalian host cells), expression and/or secretion of CAH can be increased through use of a heterologous signal sequence. The CAH fusion proteins ofthe invention can be incoφorated into pharmaceutical compositions and administered to a subject in vivo. The CAH fusion proteins can be used to affect the bioavailability of a CAH substrate. Use of CAH fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, (i) aberrant modification or mutation of a gene encoding a CAH protein; (ii) mis-regulation ofthe CAH gene; and (iii) aberrant post-translational modification of a CAH protein.

Moreover, the CAH-fusion proteins ofthe invention can be used as immunogens to produce anti-CAH antibodies in a subject, to purify CAH ligands and in screening assays to identify molecules which inhibit the interaction of CAH with a CAH substrate.

Preferably, a CAH chimeric or fusion protein ofthe invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). A CAH-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the CAH protein.

The present invention also pertains to variants ofthe CAH proteins which function as either CAH agonists (mimetics) or as CAH antagonists. Variants ofthe CAH proteins can be generated by mutagenesis, e.g., discrete point mutation or truncation of a CAH protein. An agonist ofthe CAH proteins can retain substantially the same, or a subset, of the biological activities ofthe naturally occurring form of a CAH protein. An antagonist of a CAH protein can inhibit one or more ofthe activities ofthe naturally occurring form ofthe CAH protein by, for example, competitively modulating a CAH-mediated activity of a CAH protein. Thus, specific biological effects can be elicited by treatment with a variant of limited function. In one embodiment, treatment of a subject with a variant having a subset ofthe biological activities ofthe naturally occurring form ofthe protein has fewer side effects in a subject relative to treatment with the naturally occurring form ofthe CAH protein.

In one embodiment, variants of a CAH protein which function as either CAH agonists (mimetics) or as CAH antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of a CAH protein for CAH protein agonist or antagonist activity. In one embodiment, a variegated library of CAH variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of CAH variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential CAH sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of CAH sequences therein. There are a variety of methods which can be used to produce libraries of potential CAH variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all ofthe sequences encoding the desired set of potential CAH sequences. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3; Itakura et /. (1984) Annu. Rev. Biochem. 53:323; I akura et a/. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11 All.

In addition, libraries of fragments of a CAH protein coding sequence can be used to generate a variegated population of CAH fragments for screening and subsequent selection of variants of a CAH protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a CAH coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with SI nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes ofthe CAH protein.

Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of CAH proteins. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation ofthe vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify CAH variants (Arkin and Yourvan (1992) Proc. Natl Acad. Sci. USA 89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3): 327-331).

In one embodiment, cell based assays can be exploited to analyze a variegated CAH library. For example, a library of expression vectors can be transfected into a cell line, e.g., a neuronal cell line, which ordinarily responds to a CAH ligand in a particular CAH ligand- dependent manner. The transfected cells are then contacted with a CAH ligand and the effect of expression ofthe mutant on, e.g., membrane excitability of CAH can be detected. Plasmid DNA can then be recovered from the cells which score for inhibition, or alternatively, potentiation of signaling by the CAH ligand, and the individual clones further characterized. An isolated CAH protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind CAH using standard techniques for polyclonal and monoclonal antibody preparation. A full-length CAH protein can be used or, alternatively, the invention provides antigenic peptide fragments of CAH for use as immunogens. The antigenic peptide of CAH comprises at least 8 amino acid residues ofthe amino acid sequence shown in SEQ ID NO:2 and encompasses an epitope of CAH such that an antibody raised against the peptide forms a specific immune complex with the CAH protein. Preferably, the antigenic peptide comprises at least 10 amino acid residues, more preferably at least 15 amino acid residues, even more preferably at least 20 amino acid residues, and most preferably at least 30 amino acid residues.

Preferred epitopes encompassed by the antigenic peptide are regions of CAH that are located on the surface ofthe protein, e.g., hydrophilic regions, as well as regions with high antigenicity (see, for example, Appendix A). A CAH immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen. An appropriate immunogenic preparation can contain, for example, recombinantly expressed CAH protein or a chemically synthesized CAH polypeptide. The preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic CAH preparation induces a polyclonal anti-CAH antibody response.

Accordingly, another aspect ofthe invention pertains to anti-CAH antibodies. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as a CAH. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')₂ fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind CAH molecules. The term "monoclonal antibody" or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of CAH. A monoclonal antibody composition thus typically displays a single binding affinity for a particular CAH protein with which it immunoreacts.

Polyclonal anti-CAH antibodies can be prepared as described above by immunizing a suitable subject with a CAH immunogen. The anti-CAH antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized CAH. If desired, the antibody molecules directed against CAH can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as protein A chromatography to obtain the IgG fraction. At an appropriate time after immunization, e.g., when the anti-CAH antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol 127:539-46; Brown et al. (1980) J. Biol. Chem .255:4980-83; Yeh et α/. (1976) Proc. Natl Acad. Sci. USA 76:2927-31; and Yeh et al (1982) Int. J._. Cancer 29:269-75), the more recent human B cell hybridoma technique (Kozbor et al. (1983) Immunol Today 4:72), the EBV-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing monoclonal antibody hybridomas is well known (see generally R. H. Kenneth, in Monoclonal Antibodies: A New Dimension In Biological Analyses, Plenum Publishing Coφ., New York, New York (1980); E. A. Lerner (1981) Yale J. Biol Med, 54:387-402; M. L. Gefter et al. (1977) Somatic Cell Genet. 3:231-36). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with a CAH immunogen as described above, and the culture supernatants ofthe resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds CAH.

Any ofthe many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the puφose of generating an anti-CAH monoclonal antibody (see, e.g., G. Galfre et al. (1977) Nature 266:55052; Gefter et al. Somatic Cell Genet. , cited supra; Lerner, Yale J. Biol. Med. , cited supra; Kenneth, Monoclonal Antibodies, cited supra). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods which also would be useful. Typically, the immortal cell line (e.g., a myeloma cell line) is derived from the same mammalian species as the lymphocytes. For example, murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation ofthe present invention with an immortalized mouse cell line. Preferred immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium"). Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e.g., the P3-NSl/l-Ag4-l, P3- x63-Ag8.653 or Sp2/O-Agl4 myeloma lines. These myeloma lines are available from ATCC. Typically, HAT- sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG"). Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed). Hybridoma cells producing a monoclonal antibody ofthe invention are detected by screening the hybridoma culture supernatants for antibodies that bind CAH, e.g. , using a standard ELISA assay. Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal anti-CAH antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with CAH to thereby isolate immunoglobulin library members that bind CAH. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAP™ Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S. Patent No. 5,223,409; Kang et al. PCT International Publication No. WO 92/18619; Dower et al PCT International Publication No. WO 91/17271; Winter et al. PCT International Publication WO 92/20791; Markland et al PCT International Publication No. WO 92/15679; Breitling et al PCT International Publication WO 93/01288; McCafferty et al. PCT International Publication No. WO 92/01047; Garrard et al. PCT International Publication No. WO 92/09690; Ladner et al. PCT International Publication No. WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246: 1275-1281; Griffiths et al. (1993) EMBOJ 12:725-734; Hawkins et al. (1992) J. Mol. Biol. 226:889-896; Clarkson et al. (1991) Nature 352:624-628; Gram et al. (1992) Proc. Natl Acad. Sci. USA 89:3576- 3580; Garrad et al. (1991) Bio/Technology 9:1373-1377; Hoogenboom et al. (1991) Nuc. Acid Res. 19:4133-4137; Barbas et al. (1991) Proc. Natl. Acad. Sci. USA 88:7978-7982; and McCafferty et al. Nature (1990) 348:552-554.

Additionally, recombinant anti-CAH antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope ofthe invention. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US86/02269; Akira, et al European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al. European Patent Application 173,494; Neuberger et al. PCT International Publication No. WO 86/01533; Cabilly et al. U.S. Patent No. 4,816,567; Cabilly et al. European Patent Application 125,023; Better et al (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol 139:3521-3526; Sun et al. (1987) Proc. Natl Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Cane. Res. 47:999- 1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl Cancer Inst. 80:1553-1559); Morrison, S. L. (1985) Science 229:1202-1207; Oi et al (1986) BioTechniques 4:214; Winter U.S. Patent 5,225,539; Jones et al. (1986) Nature 321:552- 525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al (1988) J. Immunol. 141 :4053-4060. An anti-CAH antibody (e.g. , monoclonal antibody) can be used to isolate CAH by standard techniques, such as affinity chromatography or immunoprecipitation. An anti- CAH antibody can facilitate the purification of natural CAH from cells and of recombinantly produced CAH expressed in host cells. Moreover, an anti-CAH antibody can be used to detect CAH protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression ofthe CAH protein. Anti-CAH antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or H.

III. Recombinant Expression Vectors and Host Cells

Another aspect ofthe invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding a CAH protein (or a portion thereof). As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

The recombinant expression vectors ofthe invention comprise a nucleic acid ofthe invention in a form suitable for expression ofthe nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis ofthe host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression ofthe nucleotide sequence (e.g. , in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cells and those which direct expression ofthe nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice ofthe host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors ofthe invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., CAH proteins, mutant forms of CAH proteins, fusion proteins, and the like).

The recombinant expression vectors ofthe invention can be designed for expression of CAH proteins in prokaryotic or eukaryotic cells. For example, CAH proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase. Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus ofthe recombinant protein. Such fusion vectors typically serve three puφoses: 1) to increase expression of recombinant protein; 2) to increase the solubility ofthe recombinant protein; and 3) to aid in the purification ofthe recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction ofthe fusion moiety and the recombinant protein to enable separation ofthe recombinant protein from the fusion moiety subsequent to purification ofthe fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

Purified fusion proteins can be utilized in CAH activity assays, (e.g., direct assays or competitive assays described in detail below), or to generate antibodies specific for CAH proteins, for example. In a preferred embodiment, a CAH fusion protein expressed in a retroviral expression vector of the present invention can be utilized to infect bone marrow cells which are subsequently transplanted into irradiated recipients. The pathology ofthe subject recipient is then examined after sufficient time has passed (e.g. , six (6) weeks).

Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al, (1988) Gene 69:301-315) and pET 1 Id (Studier et al, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid tφ-lac fusion promoter. Target gene expression from the pET l id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control ofthe lacUV 5 promoter.

One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185,

Academic Press, San Diego, California (1990) 1 19-128). Another strategy is to alter the nucleic acid sequence ofthe nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al, (1992) Nucleic Acids Res. 20:21 1 1-21 18). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

In another embodiment, the CAH expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et al , (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al, (1987) Gene 54: 113-123), pYES2 (Invitrogen Coφoration, San Diego, CA), and picZ (InVitrogen Coφ, San Diego, CA).

Alternatively, CAH proteins can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39). In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nαtwre 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adeno virus 2, cytomegalovirus and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.

In another embodiment, the recombinant mammalian expression vector is capable of directing expression ofthe nucleic acid preferentially in a particular cell type (e.g., tissue- specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1 :268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBOJ. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g. , the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Patent No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).

The invention further provides a recombinant expression vector comprising a DNA molecule ofthe invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to CAH mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression ofthe antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion ofthe regulation of gene expression using antisense genes see Weintraub, H. et al, Antisense RNA as a molecular tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) 1986.

Another aspect ofthe invention pertains to host cells into which a CAH nucleic acid molecule ofthe invention is introduced, e.g., a CAH nucleic acid molecule within a recombinant expression vector or a CAH nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site ofthe host cell's genome. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope ofthe term as used herein.

A host cell can be any prokaryotic or eukaryotic cell. For example, a CAH protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.

Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DΕAΕ-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.

For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding a CAH protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incoφorated the selectable marker gene will survive, while the other cells die).

A host cell ofthe invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) a CAH protein. Accordingly, the invention further provides methods for producing a CAH protein using the host cells ofthe invention. In one embodiment, the method comprises culturing the host cell ofthe invention (into which a recombinant expression vector encoding a CAH protein has been introduced) in a suitable medium such that a CAH protein is produced. In another embodiment, the method further comprises isolating a CAH protein from the medium or the host cell. The host cells ofthe invention can also be used to produce non-human transgenic animals. For example, in one embodiment, a host cell ofthe invention is a fertilized oocyte or an embryonic stem cell into which CAH-coding sequences have been introduced. Such host cells can then be used to create non-human transgenic animals in which exogenous CAH sequences have been introduced into their genome or homologous recombinant animals in which endogenous CAH sequences have been altered. Such animals are useful for studying the function and/or activity of a CAH and for identifying and/or evaluating modulators of CAH activity. As used herein, a "transgenic animal" is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more ofthe cells ofthe animal includes a transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. A transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome ofthe mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a "homologous recombinant animal" is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous CAH gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell ofthe animal, e.g., an embryonic cell ofthe animal, prior to development ofthe animal. A transgenic animal ofthe invention can be created by introducing a CAH-encoding nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal. The CAH cDNA sequence of SEQ ID NO:l can be introduced as a transgene into the genome of a non-human animal. Alternatively, a nonhuman homologue of a human CAH gene, such as a mouse or rat CAH gene, can be used as a transgene. Alternatively, a CAH gene homologue, such as another CAH family member, can be isolated based on hybridization to the CAH cDNA sequences of SEQ ID NO:l or 3, or the DNA insert ofthe plasmid deposited with ATCC as Accession Number (described further in subsection

I above) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression ofthe transgene. A tissue-specific regulatory sequence(s) can be operably linked to a CAH transgene to direct expression of a CAH protein to particular cells. Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009, both by Leder et al, U.S. Patent No. 4,873,191 by Wagner et al. and in Hogan, B., Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986). Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of a CAH transgene in its genome and/or expression of CAH mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding a CAH protein can further be bred to other transgenic animals carrying other transgenes. To create a homologous recombinant animal, a vector is prepared which contains at least a portion of a CAH gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the CAH gene. The CAH gene can be a human gene (e.g., the cDNA of SEQ ID NO:3), but more preferably, is a non-human homologue of a human CAH gene (e.g., a cDNA isolated by stringent hybridization with the nucleotide sequence of SEQ ID NO: 1). For example, a mouse CAH gene can be used to construct a homologous recombination nucleic acid molecule, e.g. , a vector, suitable for altering an endogenous CAH gene in the mouse genome. In a preferred embodiment, the homologous recombination nucleic acid molecule is designed such that, upon homologous recombination, the endogenous CAH gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector). Alternatively, the homologous recombination nucleic acid molecule can be designed such that, upon homologous recombination, the endogenous CAH gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression ofthe endogenous CAH protein). In the homologous recombination nucleic acid molecule, the altered portion ofthe CAH gene is flanked at its 5' and 3' ends by additional nucleic acid sequence ofthe CAH gene to allow for homologous recombination to occur between the exogenous CAH gene carried by the homologous recombination nucleic acid molecule and an endogenous CAH gene in a cell, e.g., an embryonic stem cell. The additional flanking CAH nucleic acid sequence is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both at the 5' and 3' ends) are included in the homologous recombination nucleic acid molecule (see, e.g., Thomas, K.R. and Capecchi, M. R. (1987) Cell 51 :503 for a description of homologous recombination vectors). The homologous recombination nucleic acid molecule is introduced into a cell, e.g., an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced CAH gene has homologously recombined with the endogenous CAH gene are selected (see e.g. , Li, E. et αl (1992) Cell 69:915). The selected cells can then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A. in Terαtocαrcinomαs and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells ofthe animal contain the homologously recombined DNA by germline transmission ofthe transgene. Methods for constructing homologous recombination nucleic acid molecules, e.g., vectors, or homologous recombinant animals are described further in Bradley, A. (1991) Current Opinion in Biotechnology 2:823-829 and in PCT International Publication Nos.: WO 90/11354 by Le Mouellec et al; WO 91/01140 by Smithies et al; WO 92/0968 by Zijlstra et al ; and WO 93/04169 by Berns et al

In another embodiment, transgenic non-human animals can be produced which contain selected systems which allow for regulated expression ofthe transgene. One example of such a system is the cre/loxP recombinase system of bacteriophage PI . For a description ofthe cre/loxP recombinase system, see, e.g., Lakso et al (1992) Proc. Natl Acad. Sci. USA 89:6232-6236. Another example of a recombinase system is the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251 :1351-1355. If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required. Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.

Clones ofthe non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al. (1997) Nature 385:810-813 and PCT International Publication Nos. WO 97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic cell, from the transgenic animal can be isolated and induced to exit the growth cycle and enter Go phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal ofthe same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal. The offspring borne of this female foster animal will be a clone ofthe animal from which the cell, e.g. , the somatic cell, is isolated.

IV. Pharmaceutical Compositions

The CAH nucleic acid molecules, fragments of CAH proteins, and anti-CAH antibodies (also referred to herein as "active compounds") ofthe invention can be incoφorated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absoφtion delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incoφorated into the compositions.

A pharmaceutical composition ofthe invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance ofthe required particle size in the case of dispersion and by the use of surfactants. Prevention ofthe action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absoφtion ofthe injectable compositions can be brought about by including in the composition an agent which delays absoφtion, for example, aluminum monostearate and gelatin. Sterile injectable solutions can be prepared by incoφorating the active compound

(e.g., a fragment of a CAH protein or an anti-CAH antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incoφorating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder ofthe active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the puφose of oral therapeutic administration, the active compound can be incoφorated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouth wash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part ofthe composition. The tablets, pills, capsules, troches and the like can contain any ofthe following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Coφoration and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811. It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms ofthe invention are dictated by and directly dependent on the unique characteristics ofthe active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.

Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% ofthe population) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration ofthe test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

As defined herein, a therapeutically effective amount of protein or polypeptide (i.e., an effective dosage) ranges from about 0.001 to 30 mg/kg body weight, preferably about 0.01 to 25 mg/kg body weight, more preferably about 0.1 to 20 mg/kg body weight, and even more preferably about 1 to 10 mg/kg, 2 to 9 mg/kg, 3 to 8 mg/kg, 4 to 7 mg/kg, or 5 to 6 mg/kg body weight. The skilled artisan will appreciate that certain factors may influence the dosage required to effectively treat a subject, including but not limited to the severity of the disease or disorder, previous treatments, the general health and/or age ofthe subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of a protein, polypeptide, or antibody can include a single treatment or, preferably, can include a series of treatments.

In a preferred example, a subject is treated with antibody, protein, or polypeptide in the range of between about 0.1 to 20 mg/kg body weight, one time per week for between about 1 to 10 weeks, preferably between 2 to 8 weeks, more preferably between about 3 to 7 weeks, and even more preferably for about 4, 5, or 6 weeks. It will also be appreciated that the effective dosage of antibody, protein, or polypeptide used for treatment may increase or decrease over the course of a particular treatment. Changes in dosage may result and become apparent from the results of diagnostic assays as described herein.

The present invention encompasses agents which modulate expression or activity. An agent may, for example, be a small molecule. For example, such small molecules include, but are not limited to, peptides, peptidomimetics, amino acids, amino acid analogs, polynucleotides, polynucleotide analogs, nucleotides, nucleotide analogs, organic or inorganic compounds (i.e.,. including heteroorganic and organometallic compounds) having a molecular weight less than about 10,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 5,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 1 ,000 grams per mole, organic or inorganic compounds having a molecular weight less than about 500 grams per mole, and salts, esters, and other pharmaceutically acceptable forms of such compounds. It is understood that appropriate doses of small molecule agents depends upon a number of factors within the ken ofthe ordinarily skilled physician, veterinarian, or researcher. The dose(s) ofthe small molecule will vary, for example, depending upon the identity, size, and condition ofthe subject or sample being treated, further depending upon the route by which the composition is to be administered, if applicable, and the effect which the practitioner desires the small molecule to have upon the nucleic acid or polypeptide ofthe invention.

Exemplary doses include milligram or microgram amounts ofthe small molecule per kilogram of subject or sample weight (e.g. , about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram. It is furthermore understood that appropriate doses of a small molecule depend upon the potency ofthe small molecule with respect to the expression or activity to be modulated. Such appropriate doses may be determined using the assays described herein. When one or more of these small molecules is to be administered to an animal (e.g., a human) in order to modulate expression or activity of a polypeptide or nucleic acid ofthe invention, a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained. In addition, it is understood that the specific dose level for any particular animal subject will depend upon a variety of factors including the activity ofthe specific compound employed, the age, body weight, general health, gender, and diet ofthe subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.

Further, an antibody (or fragment thereof) may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent or a radioactive metal ion. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1 -dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6- thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and vinblastine).

The conjugates ofthe invention can be used for modifying a given biological response; the drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, alpha- interferon, beta-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator; or, biological response modifiers such as, for example, lymphokines, interleukin-1 ("ιL-1 "), interleukin-2 ("IL-2"), interleukin-6 ("IL-6"), granulocyte macrophase colony stimulating factor ("GM-CSF"), granulocyte colony stimulating factor ("G-CSF"), or other growth factors.

Techniques for conjugating such therapeutic moiety to antibodies are well known, see, e.g., Arnon et al, "Monoclonal Antibodies For Immunotargeting Of Drugs In Cancer Therapy", in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et al, "Antibodies For Drug Delivery", in Controlled Drug Delivery (2nd Ed.), Robinson et al (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thoφe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", in Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); "Analysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapy", in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp. 303-16 (Academic Press 1985), and Thoφe et al, "The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates", Immunol. Rev., 62: 119-58 (1982). Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No. 4,676,980.

The nucleic acid molecules ofthe invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, , intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al (1994) Proc. Natl Acad. Sci. USA 91 :3054-3057). The pharmaceutical preparation ofthe gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.

The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

V. Uses and Methods of the Invention

The nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more ofthe following methods: a) screening assays; b) predictive medicine (e.g., diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics); and c) methods of treatment (e.g., therapeutic and prophylactic). As described herein, a CAH protein ofthe invention has one or more ofthe following activities: 1) it modulates metabolism and catabolism of biochemical molecules necessary for energy production or storage, or of metabolically important molecules, 2) it modulates intra- or intercellular signaling, 3) it regulates cellular homeostasis; 4) it modulates calcification; 5) it modulates bone resoφtion; and 6) it modulates fluid production. The isolated nucleic acid molecules ofthe invention can be used, for example, to express CAH protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect CAH mRNA (e.g., in a biological sample) or a genetic alteration in a CAH gene, and to modulate CAH activity, as described further below. The CAH proteins can be used to treat disorders characterized by insufficient or excessive production of a CAH substrate or production of CAH inhibitors. In addition, the CAH proteins can be used to screen for naturally occurring CAH substrates, to screen for drugs or compounds which modulate CAH activity, as well as to treat disorders characterized by insufficient or excessive production of CAH protein or production of CAH protein forms which have decreased, aberrant or unwanted activity compared to CAH wild type protein (e.g., carbonic anhydrase-associated disorders).

In a preferred embodiment, the CAH molecules ofthe invention are useful for catalyzing the reversible hydration of carbon dioxide to carbonic acid. As such, these molecules may be employed in small or large-scale synthesis of either carbon dioxide or carbonic acid, or in chemical processes that require the production or interconversion of these compounds. Such processes are known in the art (see, e.g., Ullmann et al. (1999) Ullmann's Encyclopedia of Industrial Chemistry, 6^th ed. VCH: Weinheim; Gutcho (1983) Chemicals by Fermentation. Park ridge, NJ: Noyes Data Coφoration (ISBN 0818805086); Rehm et al. (eds.) (1993) Biotechnology, 2^nd ed. VCH: Weinheim; and Michal, G. (1999) Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology. New York: John Wiley & Sons, and references contained therein.)

As used herein, a "carbonic anhydrase-associated disorder" includes a disorder, disease or condition which is caused or characterized by a misregulation (e.g., downregulation or upregulation) of carbonic anhydrase activity. Carbonic anhydrase- associated disorders can detrimentally affect cellular functions such as cellular proliferation, growth, differentiation, or migration, inter- or intra-cellular communication; tissue function, such as cardiac function or musculoskeletal function; systemic responses in an organism, such as nervous system responses, ocular function, or bone formation/resoφtion. Examples of carbonic anhydrase-associated disorders include CNS disorders such as cognitive and neurodegenerative disorders, examples of which include, but are not limited to, Alzheimer's disease, dementias related to Alzheimer's disease (such as Pick's disease), Parkinson's and other Lewy diffuse body diseases, senile dementia, Huntington's disease, Gilles de la Tourette's syndrome, multiple sclerosis, amyotrophic lateral sclerosis, progressive supranuclear palsy, epilepsy, and Jakob-Creutzfieldt disease; autonomic function disorders such as hypertension and sleep disorders, and neuropsychiatric disorders, such as depression, schizophrenia, schizoaffective disorder, korsakoff s psychosis, mania, anxiety disorders, or phobic disorders; learning or memory disorders, e.g., amnesia or age-related memory loss, attention deficit disorder, dysthymic disorder, major depressive disorder, mania, obsessive-compulsive disorder, psychoactive substance use disorders, anxiety, phobias, panic disorder, as well as bipolar affective disorder, e.g., severe bipolar affective (mood) disorder (BP-1), and bipolar affective neurological disorders, e.g., migraine and obesity. Further CNS-related disorders include, for example, those listed in the American Psychiatric Association's Diagnostic and Statistical manual of Mental Disorders (DSM), the most current version of which is incoφorated herein by reference in its entirety.

Further examples of carbonic anhydrase-associated disorders include cardiac-related disorders. Cardiovascular system disorders in which the CAH molecules ofthe invention may be directly or indirectly involved include arteriosclerosis, ischemia reperfusion injury, restenosis, arterial inflammation, vascular wall remodeling, ventricular remodeling, rapid ventricular pacing, coronary microembolism, tachycardia, bradycardia, pressure overload, aortic bending, coronary artery ligation, vascular heart disease, atrial fibrilation, Jervell syndrome, Lange-Nielsen syndrome, long-QT syndrome, congestive heart failure, sinus node dysfunction, angina, heart failure, hypertension, atrial fibrillation, atrial flutter, dilated cardiomyopathy, idiopathic cardiomyopathy, myocardial infarction, coronary artery disease, coronary artery spasm, and arrhythmia. CAH-mediated or related disorders also include disorders ofthe musculoskeletal system such as paralysis and muscle weakness, e.g., ataxia, myotonia, and myokymia. Carbonic anhydrase disorders also include cellular proliferation, growth, differentiation, or migration disorders. Cellular proliferation, growth, differentiation, or migration disorders include those disorders that affect cell proliferation, growth, differentiation, or migration processes. As used herein, a "cellular proliferation, growth, differentiation, or migration process" is a process by which a cell increases in number, size or content, by which a cell develops a specialized set of characteristics which differ from that of other cells, or by which a cell moves closer to or further from a particular location or stimulus. The CAH molecules ofthe present invention are involved in signal transduction mechanisms, which are known to be involved in cellular growth, differentiation, and migration processes. Thus, the CAH molecules may modulate cellular growth, differentiation, or migration, and may play a role in disorders characterized by aberrantly regulated growth, differentiation, or migration. Such disorders include cancer, e.g., carcinoma, sarcoma, or leukemia; tumor angiogenesis and metastasis; skeletal dysplasia; hepatic disorders; and hematopoietic and/or myeloproliferative disorders.

CAH-associated or related disorders also include ocular disorders, particularly disorders in which intraocular fluid or intraocular pressure is aberrant. Examples of such disorders and diseases include glaucoma and vitreous opacities.

CAH-associated or related disorders also include disorders of bone formation and resoφtion, including osteoporosis, and osteopetrosis, as well as calcification disorders, such as kidney stone or bone spur formation. CAH-associated or related disorders also include disorders affecting tissues in which

CAH protein is expressed, e.g., cancer, such as lung cancer, ovarian cancer, breast cancer, brain cancer, or colon cancer, or CNS disorders affecting, for example, the brain, hypothalamus, DGR, or the spinal cord.

Moreover, the anti-CAH antibodies ofthe invention can be used to detect and isolate CAH proteins, regulate the bioavailability of CAH proteins, and modulate CAH activity. A. Screening Assays:

The invention provides a method (also referred to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g. , peptides, peptidomimetics, small molecules or other drugs) which interact with or bind to CAH proteins, have a stimulatory or inhibitory effect on, for example, CAH expression or CAH activity, or have a stimulatory or inhibitory effect on, for example, the availability of CAH substrate.

In one embodiment, the invention provides assays for screening candidate or test compounds which are substrates of a CAH protein or polypeptide or biologically active portion thereof (e.g., carbon dioxide or carbonic acid, or compounds which are structurally related thereto). In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of a CAH protein or polypeptide or biologically active portion thereof (e.g., zinc ions or other cofactors, or inhibitory molecules). The test compounds of the present invention can be obtained using any ofthe numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12: 145).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl Acad. Sci. U.S.A. 90:6909; Erb et al (1994) Proc. Natl Acad. Sci. USA 91 : 1 1422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261 : 1303; Carrell et al. (1994) Angew. Chem. Int. Ed. Engl 33:2059; Carell et al (1994) Angew. Chem. Int. Ed. Engl 33:2061 ; and in Gallop et al. (1994) J Med. Chem. 37:1233.

Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner USP 5,223,409), spores (Ladner USP '409), plasmids (Cull et al (1992) Proc Natl Acad Sci USA 89: 1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al. (1990) Proc. Natl Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310); (Ladner supra.). In one embodiment, an assay is a cell-based assay in which a cell which expresses a

CAH protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate CAH activity is determined. Determining the ability of the test compound to modulate CAH activity can be accomplished by monitoring, for example, the production of one or more specific CAH substrates or products in a cell which expresses CAH (see, e.g., Saada et al (2000) Biochem Biophys. Res.Commun. 269: 382-386). The cell, for example, can be of mammalian origin. The ability ofthe test compound to modulate CAH binding to a substrate (e.g. , carbon dioxide or carbonic acid) or to bind to CAH can also be determined. Determining the ability ofthe test compound to modulate CAH binding to a substrate can be accomplished, for example, by coupling the CAH substrate with a radioisotope or paramagnetic label such that binding ofthe CAH substrate to CAH can be determined by detecting the labeled CAH substrate in a complex. Alternatively, CAH could be coupled with a radioisotope or enzymatic label to monitor the ability of a test compound to modulate CAH binding to a CAH substrate in a complex. Determining the ability ofthe test compound to bind CAH can be accomplished, for example, by coupling the compound with a radioisotope or enzymatic label such that binding ofthe compound to CAH can be determined by detecting the labeled CAH compound in a complex. For example, compounds (e.g., CAH substrates) can be labeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting. Similarly, compounds (e.g., CAH substrates) can be labeled with a paramagnetic label, and the label detected by electroparamagnetic resonance. Alternatively, compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.

It is also within the scope of this invention to determine the ability of a compound (e.g., a CAH substrate) to interact with CAH without the labeling of any ofthe interactants. For example, a microphysiometer can be used to detect the interaction of a compound with CAH without the labeling of either the compound or the CAH. McConnell, H. M. et al. (1992) Science 257:1906-1912. As used herein, a "microphysiometer" (e.g., Cytosensor) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator ofthe interaction between a compound and CAH. In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a CAH target molecule (e.g., a CAH substrate) with a test compound and determining the ability ofthe test compound to modulate (e.g., stimulate or inhibit) the activity ofthe CAH target molecule. Determining the ability ofthe test compound to modulate the activity of a CAH target molecule can be accomplished, for example, by determining the ability ofthe CAH protein to bind to or interact with the CAH target molecule.

Determining the ability ofthe CAH protein, or a biologically active fragment thereof, to bind to or interact with a CAH target molecule (e.g., a substrate or inhibitor) can be accomplished by one ofthe methods described above for determining direct binding. In a preferred embodiment, determining the ability ofthe CAH protein to bind to or interact with a CAH target molecule can be accomplished by determining the activity or availability ofthe target molecule. For example, a target-regulated cellular activity, such as a biosynthetic pathway which requires the participation ofthe target molecule (e.g., fatty acid synthesis or purine biosynthesis), may be monitored.

In yet another embodiment, an assay ofthe present invention is a cell-free assay in which a CAH protein or biologically active portion thereof is contacted with a test compound and the ability ofthe test compound to associate with, to bind to, or to serve as a substrate for the CAH protein or biologically active portion thereof is determined. Preferred biologically active portions ofthe CAH proteins to be used in assays ofthe present invention include fragments which participate in interactions with non-CAH molecules, e.g., fragments with high surface probability scores (see, for example, Appendix A). Binding of the test compound to the CAH protein can be determined either directly or indirectly as described above. In a preferred embodiment, the assay includes contacting the CAH protein or biologically active portion thereof with a known compound which interacts with CAH to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability ofthe test compound to interact with a CAH protein, wherein determining the ability ofthe test compound to interact with a CAH protein comprises determining the ability ofthe test compound to preferentially bind to or interact with CAH or a biologically active portion thereof as compared to the known compound.

In another embodiment, the assay is a cell-free assay in which a CAH protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity ofthe CAH protein or biologically active portion thereof is determined. Determining the ability ofthe test compound to modulate the activity of a CAH protein can be accomplished, for example, by determining the ability ofthe CAH protein to bind to or associate with a CAH target molecule by one ofthe methods described above for determining direct binding. Determining the ability ofthe CAH protein to bind to a CAH target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis

(BIA). Sjolander, S. and Urbaniczky, C. (1991) Anal. Chem. 63:2338-2345 and Szabo et al. (1995) Curr. Opin. Struct. Biol 5:699-705. As used herein, "BIA" is a technology for studying biospecific interactions in real time, without labeling any ofthe interactants (e.g., BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.

In an alternative embodiment, determining the ability ofthe test compound to modulate the activity of a CAH protein can be accomplished by determining the ability of the CAH protein to further modulate the activity of a downstream effector of a CAH target molecule. For example, the activity ofthe effector molecule on an appropriate target can be determined or the binding ofthe effector to an appropriate target can be determined as previously described.

In yet another embodiment, the cell-free assay involves contacting a CAH protein or biologically active portion thereof with a known compound which binds the CAH protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability ofthe test compound to interact with the CAH protein, wherein determining the ability ofthe test compound to interact with the CAH protein comprises determining the ability ofthe CAH protein to preferentially bind to or catalyze the transfer of a hydride moiety to or from the target substrate (e.g., carbon dioxide or carbonic acid).

In more than one embodiment ofthe above assay methods ofthe present invention, it may be desirable to immobilize either CAH or its target molecule to facilitate separation of complexed from uncomplexed forms of either ofthe interactants, as well as to accommodate automation ofthe assay. Binding of a test compound to a CAH protein, or interaction of a CAH protein with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtitre plates, test tubes, and micro- centrifuge tubes. In one embodiment, a fusion protein can be provided which adds a domain that allows the CAH protein to be bound to a matrix. For example, glutathione-S- transferase/CAH fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or CAH protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtitre plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of CAH binding or activity determined using standard techniques. Other techniques for immobilizing proteins on matrices can also be used in the screening assays ofthe invention. For example, a CAH protein can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated CAH protein can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with CAH protein but which do not interfere with binding ofthe CAH protein to its target molecule can be derivatized to the wells ofthe plate, and unbound target or CAH protein trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the CAH protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the CAH protein.

In another embodiment, modulators of CAH expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of CAH mRNA or protein in the cell is determined. The level of expression of CAH mRNA or protein in the presence ofthe candidate compound is compared to the level of expression of CAH mRNA or protein in the absence ofthe candidate compound. The candidate compound can then be identified as a modulator of CAH expression based on this comparison. For example, when expression of CAH mRNA or protein is greater (statistically significantly greater) in the presence ofthe candidate compound than in its absence, the candidate compound is identified as a stimulator of CAH mRNA or protein expression. Alternatively, when expression of CAH mRNA or protein is less (statistically significantly less) in the presence ofthe candidate compound than in its absence, the candidate compound is identified as an inhibitor of CAH mRNA or protein expression. The level of CAH mRNA or protein expression in the cells can be determined by methods described herein for detecting CAH mRNA or protein.

In yet another aspect ofthe invention, the CAH proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g. , U.S. Patent No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268: 12046-12054; Barrel et al (1993) Biotechniques 14:920-924; Iwabuchi et al (1993) Oncogene 8: 1693- 1696; and Brent WO94/10300), to identify other proteins, which bind to or interact with CAH ("CAH-binding proteins" or "CAH-6-bp") and are involved in CAH activity. Such CAH-binding proteins are also likely to be involved in the propagation of signals by the CAH proteins or CAH targets as, for example, downstream elements of a CAH-mediated signaling pathway. Alternatively, such CAH-binding proteins are likely to be CAH inhibitors.

The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for a CAH protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein ("prey" or "sample") is fused to a gene that codes for the activation domain ofthe known transcription factor. If the "bait" and the "prey" proteins are able to interact, in vivo, forming a CAH-dependent complex, the DNA-binding and activation domains ofthe transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene that encodes the protein which interacts with the CAH protein.

In another aspect, the invention pertains to a combination of two or more ofthe assays described herein. For example, a modulating agent can be identified using a cell- based or a cell free assay, and the ability ofthe agent to modulate the activity of a CAH protein can be confirmed in vivo, e.g., in an animal such as an animal model for cellular transformation and/or tumorigenesis.

Animal based models for studying tumorigenesis in vivo are well known in the art (reviewed in Animal Models of Cancer Predisposition Syndromes, Hiai, H and Hino, O

(eds.) 1999, Progress in Experimental Tumor Research, Vol. 35; Clarke AR Carcinogenesis (2000) 21 :435-41) and include, for example, carcinogen-induced tumors (Rithidech, K et al. Mutat Res (1999) 428:33-39; Miller, ML et al. Environ Mol Mutagen (2000) 35:319-327), injection and/or transplantation of tumor cells into an animal, as well as animals bearing mutations in growth regulatory genes, for example, oncogenes (e.g., ras) (Arbeit, JM et al. Am JPathol (1993) 142:1187-1197; Sinn, E et al. Cell (1987) 49:465-475; Thorgeirsson, SS et al Toxicol Lett (2000) 112-113:553-555) and tumor suppressor genes (e.g., p53) (Vooijs, M et al. Oncogene (1999) 18:5293-5303; Clark AR Cancer Metast Rev (1995) 14:125-148; Kumar, TR et al. J Intern Med (1995) 238:233-238; Donehower, LA et al. (1992) Nature 356215-221). Furthermore, experimental model systems are available for the study of, for example, colon cancer (Heyer J, et al. (1999) Oncogene 18(38):5325-33), ovarian cancer (Hamilton, TC et al Semin Oncol (1984) 11 :285-298; Rahman, NA et al. Mol Cell Endocrinol (1998) 145:167-174; Beamer, WG et al. Toxicol Pathol (1998) 26:704-710), gastric cancer (Thompson, J et al. Int J Cancer (2000) 86:863-869; Fodde, R et al Cytogenet Cell Genet (1999) 86:105-111), breast cancer (Li, M et al Oncogene (2000)

19:1010-1019; Green, JE et al. Oncogene (2000) 19:1020-1027), melanoma (Satyamoorthy, K et al. Cancer Metast Rev (1999) 18:401-405), and prostate cancer (Shirai, T et al Mutat Res (2000) 462:219-226; Bostwick, DG et al Prostate (2000) 43:286-294).

This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., a CAH modulating agent, an antisense CAH nucleic acid molecule, a CAH-specific antibody, a CAH substrate or a CAH-binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein. In one embodiment, the invention features a method of treating a subject having a cellular growth or proliferation disorder that involves administering to the subject a CAH modulator such that treatment occurs. In another embodiment, the invention features a method of treating a subject having cancer that involves treating a subject with a CAH modulator, such that treatment occurs. Preferred CAH modulators include, but are not limited to, CAH proteins or biologically active fragments, CAH nucleic acid molecules, CAH antibodies, ribozymes, and CAH antisense oligonucleotides designed based on the CAH nucleotide sequences disclosed herein, as well as peptides, organic and non-organic small molecules identified as being capable of modulating CAH expression and/or activity, for example, according to at least one ofthe screening assays described herein.

Any ofthe compounds, including but not limited to compounds such as those identified in the foregoing assay systems, may be tested for the ability to ameliorate cellular growth or proliferation disorder symptoms. Cell-based and animal model-based assays for the identification of compounds exhibiting such an ability to ameliorate cellular growth or proliferation disorder systems are described herein.

In one aspect, cell-based systems, as described herein, may be used to identify compounds which may act to ameliorate cellular growth or proliferation disorder symptoms, for example, reduction in tumor burden, tumor size, tumor cell growth, differentiation, and/or proliferation, and invasive and/or metastatic potential before and after treatment. For example, such cell systems may be exposed to a compound, suspected of exhibiting an ability to ameliorate cellular growth or proliferation disorder symptoms, at a sufficient concentration an for a time sufficient to elicit such an amelioration of cellular growth or proliferation disorder symptoms in the exposed cells. After exposure, the cells are examined to determine whether one or more ofthe cellular growth or proliferation disorder cellular phenotypes has been altered to resemble a more normal or more wild type, non- cellular growth or proliferation disorder phenotype. Cellular phenotypes that are associated with cellular growth and/or proliferation disorders include aberrant proliferation, growth, and migration, anchorage independent growth, and loss of contact inhibition.

In addition, animal-based cellular growth or proliferation disorder systems, such as those described herein, may be used to identify compounds capable of ameliorating cellular growth or proliferation disorder symptoms. Such animal models may be used as test substrates for the identification of drugs, pharmaceuticals, therapies, and interventions which may be effective in treating cellular growth or proliferation disorders. For example, animal models may be exposed to a compound, suspected of exhibiting an ability to ameliorate cellular growth or proliferation disorder symptoms, at a sufficient concentration and for a time sufficient to elicit such an amelioration of cellular growth or proliferation disorder symptoms in the exposed animals. The response ofthe animals to the exposure may be monitored by assessing the reversal of cellular growth or proliferation disorders, or symptoms associated therewith, for example, reduction in tumor burden, tumor size, and invasive and/or metastatic potential before and after treatment.

With regard to intervention, any treatments which reverse any aspect of cellular growth or proliferation disorder symptoms should be considered as candidates for human cellular growth or proliferation disorder therapeutic intervention. Dosages of test compounds may be determined by deriving dose-response curves.

Additionally, gene expression patterns may be utilized to assess the ability of a compound to ameliorate cellular growth and/or proliferation disorder symptoms. For example, the expression pattern of one or more genes may form part of a "gene expression profile" or "transcriptional profile" which may be then be used in such an assessment. "Gene expression profile" or "transcriptional profile", as used herein, includes the pattern of mRNA expression obtained for a given tissue or cell type under a given set of conditions. Such conditions may include, but are not limited to, cell growth, proliferation, differentiation, transformation, tumorigenesis, metastasis, and carcinogen exposure. Gene expression profiles may be generated, for example, by utilizing a differential display procedure, Northern analysis and/or RT-PCR. In one embodiment, CAH gene sequences may be used as probes and/or PCR primers for the generation and corroboration of such gene expression profiles.

Gene expression profiles may be characterized for known states within the cell- and/or animal-based model systems. Subsequently, these known gene expression profiles may be compared to ascertain the effect a test compound has to modify such gene expression profiles, and to cause the profile to more closely resemble that of a more desirable profile.

For example, administration of a compound may cause the gene expression profile of a cellular growth or proliferation disorder model system to more closely resemble the control system. Administration of a compound may, alternatively, cause the gene expression profile of a control system to begin to mimic a cellular growth and/or proliferation disorder state. Such a compound may, for example, be used in further characterizing the compound of interest, or may be used in the generation of additional animal models.

B. Detection Assays

Portions or fragments ofthe cDNA sequences identified herein (and the corresponding complete gene sequences) can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.

1. Chromosome Mapping Once the sequence (or a portion ofthe sequence) of a gene has been isolated, this sequence can be used to map the location ofthe gene on a chromosome. This process is called chromosome mapping. Accordingly, portions or fragments ofthe CAH nucleotide sequences, described herein, can be used to map the location ofthe CAH genes on a chromosome. The mapping ofthe CAH sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease.

Briefly, CAH genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the CAH nucleotide sequences. Computer analysis of the CAH sequences can be used to predict primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the CAH sequences will yield an amplified fragment.

Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes. By using media in which mouse cells cannot grow, because they lack a particular enzyme, but human cells can, the one human chromosome that contains the gene encoding the needed enzyme, will be retained. By using various media, panels of hybrid cell lines can be established. Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. (D'Eustachio P. et al. (1983) Science 220:919-924). Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions. PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the CAH nucleotide sequences to design oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map a CAH sequence to its chromosome include in situ hybridization (described in Fan, Y. et al. (1990) Proc. Natl. Acad. Sci. USA, 87:6223-27), pre-screening with labeled flow-sorted chromosomes, and pre-selection by hybridization to chromosome specific cDNA libraries. Fluorescence in situ hybridization (FISH) of a DNA sequence to a metaphase chromosomal spread can further be used to provide a precise chromosomal location in one step. Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical such as colcemid that disrupts the mitotic spindle. The chromosomes can be treated briefly with trypsin, and then stained with Giemsa. A pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually. The FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. Preferably 1,000 bases, and more preferably 2,000 bases will suffice to get good results at a reasonable amount of time. For a review of this technique, see Verma et al. , Human Chromosomes: A Manual of Basic Techniques (Pergamon Press, New York 1988).

Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions ofthe genes actually are preferred for mapping puφoses. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.

Once a sequence has been mapped to a precise chromosomal location, the physical position ofthe sequence on the chromosome can be correlated with genetic map data. (Such data are found, for example, in V. McKusick, Mendelian Inheritance in Man, available online through Johns Hopkins University Welch Medical Library). The relationship between a gene and a disease, mapped to the same chromosomal region, can then be identified through linkage analysis (co-inheritance of physically adjacent genes), described in, for example, Egeland, J. et al. (1987) Nature, 325:783-787.

Moreover, differences in the DNA sequences between individuals affected and unaffected with a disease associated with the CAH gene can be determined. If a mutation is observed in some or all ofthe affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent ofthe particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymoφhisms.

2. Tissue Typing

The CAH sequences ofthe present invention can also be used to identify individuals from minute biological samples. The United States military, for example, is considering the use of restriction fragment length polymoφhism (RFLP) for identification of its personnel. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification. This method does not suffer from the current limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult. The sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).

Furthermore, the sequences ofthe present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome. Thus, the CAH nucleotide sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.

Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences. The sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue. The CAH nucleotide sequences of the invention uniquely represent portions ofthe human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases. Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification puφoses. Because greater numbers of polymoφhisms occur in the noncoding regions, fewer sequences are necessary to differentiate individuals. The noncoding sequences of SEQ ID NO:l can comfortably provide positive individual identification with a panel of perhaps 10 to 1 ,000 primers which each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as that in SEQ ID NO:3, are used, a more appropriate number of primers for positive individual identification would be 500-2,000.

If a panel of reagents from CAH nucleotide sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual. Using the unique identification database, positive identification of the individual, living or dead, can be made from extremely small tissue samples.

3. Use of CAH Sequences in Forensic Biology

DNA-based identification techniques can also be used in forensic biology. Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a peφetrator of a crime. To make such an identification, PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification ofthe origin ofthe biological sample. The sequences ofthe present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual). As mentioned above, actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments. Sequences targeted to noncoding regions of SEQ ID NO: 1 are particularly appropriate for this use as greater numbers of polymoφhisms occur in the noncoding regions, making it easier to differentiate individuals using this technique. Examples of polynucleotide reagents include the CAH nucleotide sequences or portions thereof, e.g., fragments derived from the noncoding regions of SEQ ID NO:l having a length of at least 20 bases, preferably at least 30 bases.

The CAH nucleotide sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., thymus or brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such CAH probes can be used to identify tissue by species and/or by organ type.

In a similar fashion, these reagents, e.g., CAH primers or probes can be used to screen tissue culture for contamination (i.e. screen for the presence of a mixture of different types of cells in a culture).

C. Predictive Medicine:

The present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, and monitoring clinical trials are used for prognostic (predictive) puφoses to thereby treat an individual prophylactically. Accordingly, one aspect ofthe present invention relates to diagnostic assays for determining CAH protein and/or nucleic acid expression as well as CAH activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant or unwanted CAH expression or activity. The invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with CAH protein, nucleic acid expression or activity. For example, mutations in a CAH gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive puφose to thereby phophylactically treat an individual prior to the onset of a disorder characterized by or associated with CAH protein, nucleic acid expression or activity.

Another aspect ofthe invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of CAH in clinical trials.

These and other agents are described in further detail in the following sections.

1. Diagnostic Assays

An exemplary method for detecting the presence or absence of CAH protein or nucleic acid in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting CAH protein or nucleic acid (e.g., mRNA, or genomic DNA) that encodes CAH protein such that the presence of CAH protein or nucleic acid is detected in the biological sample. A preferred agent for detecting CAH mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to CAH mRNA or genomic DNA. The nucleic acid probe can be, for example, the CAH nucleic acid set forth in SEQ ID NO: 1 or 3, or the DNA insert ofthe plasmid deposited with ATCC as Accession Number , or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to CAH mRNA or genomic DNA. Other suitable probes for use in the diagnostic assays of the invention are described herein.

A preferred agent for detecting CAH protein is an antibody capable of binding to CAH protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab')2) can be used. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling ofthe probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling ofthe probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin. The term "biological sample" is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method ofthe invention can be used to detect CAH mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of CAH mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detection of CAH protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence. In vitro techniques for detection of CAH genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of CAH protein include introducing into a subject a labeled anti-CAH antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques. In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a serum sample isolated by conventional means from a subject.

In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting CAH protein, mRNA, or genomic DNA, such that the presence of CAH protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of CAH protein, mRNA or genomic DNA in the control sample with the presence of CAH protein, mRNA or genomic DNA in the test sample. The invention also encompasses kits for detecting the presence of CAH in a biological sample. For example, the kit can comprise a labeled compound or agent capable of detecting CAH protein or mRNA in a biological sample; means for determining the amount of CAH in the sample; and means for comparing the amount of CAH in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect CAH protein or nucleic acid.

2. Prognostic Assays

The diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant or unwanted CAH expression or activity. As used herein, the term "aberrant" includes a CAH expression or activity which deviates from the wild type CAH expression or activity. Aberrant expression or activity includes increased or decreased expression or activity, as well as expression or activity which does not follow the wild type developmental pattern of expression or the subcellular pattern of expression. For example, aberrant CAH expression or activity is intended to include the cases in which a mutation in the CAH gene causes the CAH gene to be under-expressed or over-expressed and situations in which such mutations result in a non-functional CAH protein or a protein which does not function in a wild-type fashion, e.g., a protein which does not interact with a CAH substrate, or one which interacts with a non-CAH substrate. As used herein, the term "unwanted" includes an unwanted phenomenon involved in a biological response such as cellular proliferation. For example, the term unwanted includes a CAH expression or activity which is undesirable in a subject.

The assays described herein, such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with a misregulation in CAH protein activity or nucleic acid expression, such as a CNS disorder (e.g., a cognitive or neurodegenerative disorder), a cellular proliferation, growth, differentiation, or migration disorder (e.g., cancer), a cardiovascular disorder, musculoskeletal disorder, an ocular disorder, or a disorder of bone resoφtion, or calcification/bone formation. Alternatively, the prognostic assays can be utilized to identify a subject having or at risk for developing a disorder associated with a misregulation in CAH protein activity or nucleic acid expression, such as a CNS disorder, a cellular proliferation, growth, differentiation, or migration disorder (e.g., cancer), a musculoskeletal disorder, a cardiovascular disorder, an ocular disorder, or a disorder of bone resoφtion, or calcification bone formation. Thus, the present invention provides a method for identifying a disease or disorder associated with aberrant or unwanted CAH expression or activity in which a test sample is obtained from a subject and CAH protein or nucleic acid (e.g., mRNA or genomic DNA) is detected, wherein the presence of CAH protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant or unwanted CAH expression or activity. As used herein, a "test sample" refers to a biological sample obtained from a subject of interest. For example, a test sample can be a biological fluid (e.g., cerebrospinal fluid or serum), cell sample, or tissue.

Furthermore, the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant or unwanted CAH expression or activity. For example, such methods can be used to determine whether a subject can be effectively treated with an agent for a CNS disorder, a muscular disorder, a cellular proliferation, growth, differentiation, or migration disorder (e.g., cancer), an ocular disorder, or a disorder of bone resoφtion, or calcification/bone formation. Thus, the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant or unwanted CAH expression or activity in which a test sample is obtained and CAH protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of CAH protein or nucleic acid expression or activity is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant or unwanted CAH expression or activity).

The methods ofthe invention can also be used to detect genetic alterations in a CAH gene, thereby determining if a subject with the altered gene is at risk for a disorder characterized by misregulation in CAH protein activity or nucleic acid expression, such as a CNS disorder, a musculoskeletal disorder, a cellular proliferation, growth, differentiation, or migration disorder (e.g., cancer), a cardiovascular disorder, an ocular disorder, or a disorder of bone resoφtion, or calcification/bone formation. In preferred embodiments, the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characterized by at least one of an alteration affecting the integrity of a gene encoding a CAH-protein, or the mis-expression ofthe CAH gene. For example, such genetic alterations can be detected by ascertaining the existence of at least one of 1) a deletion of one or more nucleotides from a CAH gene; 2) an addition of one or more nucleotides to a CAH gene; 3) a substitution of one or more nucleotides of a CAH gene, 4) a chromosomal rearrangement of a CAH gene; 5) an alteration in the level of a messenger RNA transcript of a CAH gene, 6) aberrant modification of a CAH gene, such as ofthe methylation pattern ofthe genomic DNA, 7) the presence of a non- wild type splicing pattern of a messenger RNA transcript of a CAH gene, 8) a non- wild type level of a CAH-protein, 9) allelic loss of a CAH gene, and 10) inappropriate post-translational modification of a CAH-protein. As described herein, there are a large number of assays known in the art which can be used for detecting alterations in a CAH gene. A preferred biological sample is a tissue or serum sample isolated by conventional means from a subject.

In certain embodiments, detection ofthe alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241 :1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91 :360-364), the latter of which can be particularly useful for detecting point mutations in a CAH gene (see Abravaya et al. (1995) Nucleic Acids Res .23:675-682). This method can include the steps of collecting a sample of cells from a subject, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells ofthe sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a CAH gene under conditions such that hybridization and amplification ofthe CAH gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size ofthe amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any ofthe techniques used for detecting mutations described herein.

Alternative amplification methods include: self sustained sequence replication (Guatelli, J.C. et al, (1990) Proc. Natl Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh, D.Y. et al, (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi, P.M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection ofthe amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.

In an alternative embodiment, mutations in a CAH gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA. Moreover, the use of sequence specific ribozymes (see, for example, U.S. Patent No. 5,498,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.

In other embodiments, genetic mutations in CAH can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin, M.T. et al (1996) Human Mutation 1: 244-255; Kozal, M.J. et al (1996) Nature Medicine 2: 753-759). For example, genetic mutations in CAH can be identified in two-dimensional arrays containing light- generated DNA probes as described in Cronin, M.T. et al. supra. Briefly, a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.

In yet another embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence the CAH gene and detect mutations by comparing the sequence ofthe sample CAH with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Biotechniques 19:448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993) Appl Biochem. Biotechnol 38:147-159).

Other methods for detecting mutations in the CAH gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al (1985) Science 230:1242). In general, the art technique of "mismatch cleavage" starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type CAH sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes are treated with an agent which cleaves single-stranded regions ofthe duplex such as which will exist due to basepair mismatches between the control and sample strands. For instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with S 1 nuclease to enzymatically digesting the mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion ofthe mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton et al (1988) Proc. Natl Acad Sci USA 85:4397; Saleeba et al. (1992) Methods Enzymol 217:286- 295. In a preferred embodiment, the control DNA or RNA can be labeled for detection.

In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in CAH cDNAs obtained from samples of cells. For example, the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662). According to an exemplary embodiment, a probe based on a CAH sequence, e.g., a wild-type CAH sequence, is hybridized to a cDNA or other DNA product from a test cell(s). The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, for example, U.S. Patent No. 5,459,039.

In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in CAH genes. For example, single strand conformation polymoφhism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sci USA: 86:2766, see also Cotton (1993) Mutat. Res. 285:125-144; and Hayashi (1992) Genet. Anal. Tech. Appl 9:73-79). Single- stranded DNA fragments of sample and control CAH nucleic acids will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change. The DNA fragments may be labeled or detected with labeled probes. The sensitivity ofthe assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In a preferred embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al (1991) Trends Genet 7:5).

In yet another embodiment the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGΕ) (Myers et al (1985) Nαtwre 313:495). When DGGΕ is used as the method of analysis, DΝA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DΝA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem 265:12753).

Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki et al. (1989) Proc. Natl Acad. Sci USA 86:6230). Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.

Alternatively, allele specific amplification technology which depends on selective PCR amplification may be used in conjunction with the instant invention. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11 :238). In addition it may be desirable to introduce a novel restriction site in the region ofthe mutation to create cleavage-based detection (Gasparini et al. (1992) Mol. Cell Probes 6: 1). It is anticipated that in certain embodiments amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3' end ofthe 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification. The methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a CAH gene. Furthermore, any cell type or tissue in which CAH is expressed may be utilized in the prognostic assays described herein.

3. Monitoring of Effects During Clinical Trials

Monitoring the influence of agents (e.g., drugs) on the expression or activity of a CAH protein (e.g., the modulation of cell proliferation and/or migration) can be applied not only in basic drug screening, but also in clinical trials. For example, the effectiveness of an agent determined by a screening assay as described herein to increase CAH gene expression, protein levels, or upregulate CAH activity, can be monitored in clinical trials of subjects exhibiting decreased CAH gene expression, protein levels, or downregulated CAH activity. Alternatively, the effectiveness of an agent determined by a screening assay to decrease CAH gene expression, protein levels, or downregulate CAH activity, can be monitored in clinical trials of subjects exhibiting increased CAH gene expression, protein levels, or upregulated CAH activity. In such clinical trials, the expression or activity of a CAH gene, and preferably, other genes that have been implicated in, for example, a CAH-associated disorder can be used as a "read out" or markers ofthe phenotype of a particular cell.

For example, and not by way of limitation, genes, including CAH, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates CAH activity (e.g., identified in a screening assay as described herein) can be identified. Thus, to study the effect of agents on CAH-associated disorders (e.g., disorders characterized by deregulated cell proliferation and/or migration), for example, in a clinical trial, cells can be isolated and RNA prepared and analyzed for the levels of expression of CAH and other genes implicated in the CAH-associated disorder, respectively. The levels of gene expression (e.g., a gene expression pattern) can be quantified by northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one ofthe methods as described herein, or by measuring the levels of activity of CAH or other genes. In this way, the gene expression pattern can serve as a marker, indicative ofthe physiological response ofthe cells to the agent. Accordingly, this . response state may be determined before, and at various points during treatment ofthe individual with the agent.

In a preferred embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) including the steps of (i) obtaining a pre-administration sample from a subject prior to administration ofthe agent; (ii) detecting the level of expression of a CAH protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity ofthe CAH protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity ofthe CAH protein, mRNA, or genomic DNA in the pre-administration sample with the CAH protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration ofthe agent to the subject accordingly. For example, increased administration ofthe agent may be desirable to increase the expression or activity of CAH to higher levels than detected, i.e., to increase the effectiveness ofthe agent. Alternatively, decreased administration ofthe agent may be desirable to decrease expression or activity of CAH to lower levels than detected, i.e. to decrease the effectiveness ofthe agent. According to such an embodiment, CAH expression or activity may be used as an indicator ofthe effectiveness of an agent, even in the absence of an observable phenotypic response. D. Methods of Treatment:

The present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant or unwanted CAH expression or activity, e.g., a carbonic anhydrase-associated disorder such as a CNS disorder; a cellular proliferation, growth, differentiation, or migration disorder (e.g., cancer); a, musculoskeletal disorder; a cardiovascular disorder; an ocular disorder, or a disorder of bone resoφtion, or calcification/bone formation.

"Treatment", as used herein, is defined as the application or administration of a therapeutic agent to a patient, or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has a disease or disorder, a symptom of disease or disorder or a predisposition toward a disease or disorder, with the puφose of curing, healing, alleviating, relieving, altering, remedying, ameliorating, improving or affecting the disease or disorder, the symptoms of disease or disorder or the predisposition toward a disease or disorder. A therapeutic agent includes, but is not limited to, small molecules, peptides, antibodies, ribozymes and antisense oligonucleotides. With regard to both prophylactic and therapeutic methods of treatment, such treatments may be specifically tailored or modified, based on knowledge obtained from the field of pharmacogenomics. "Pharmacogenomics", as used herein, refers to the application of genomics technologies such as gene sequencing, statistical genetics, and gene expression analysis to drugs in clinical development and on the market. More specifically, the term refers the study of how a patient's genes determine his or her response to a drug (e.g., a patient's "drug response phenotype", or "drug response genotype"). Thus, another aspect ofthe invention provides methods for tailoring an individual's prophylactic or therapeutic treatment with either the CAH molecules ofthe present invention or CAH modulators according to that individual's drug response genotype. Pharmacogenomics allows a clinician or physician to target prophylactic or therapeutic treatments to patients who will most benefit from the treatment and to avoid treatment of patients who will experience toxic drug-related side effects.

1. Prophylactic Methods

In one aspect, the invention provides a method for preventing in a subject, a disease or condition associated with an aberrant or unwanted CAH expression or activity, by administering to the subject a CAH or an agent which modulates CAH expression or at least one CAH activity. Subjects at risk for a disease which is caused or contributed to by aberrant or unwanted CAH expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the CAH aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending on the type of CAH aberrancy, for example, a CAH, CAH agonist or CAH antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein.

2. Therapeutic Methods

Another aspect ofthe invention pertains to methods of modulating CAH expression or activity for therapeutic puφoses. Accordingly, in an exemplary embodiment, the modulatory method ofthe invention involves contacting a cell with a CAH or agent that modulates one or more ofthe activities of CAH protein activity associated with the cell. An agent that modulates CAH protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring target molecule of a CAH protein (e.g., a CAH substrate), a CAH antibody, a CAH agonist or antagonist, a peptidomimetic of a CAH agonist or antagonist, or other small molecule. In one embodiment, the agent stimulates one or more CAH activities. Examples of such stimulatory agents include active CAH protein and a nucleic acid molecule encoding CAH that has been introduced into the cell. In another embodiment, the agent inhibits one or more CAH activities. Examples of such inhibitory agents include antisense CAH nucleic acid molecules, anti-CAH antibodies, and CAH inhibitors. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). As such, the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant or unwanted expression or activity of a CAH protein or nucleic acid molecule. In one embodiment, the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., upregulates or downregulates) CAH expression or activity. In another embodiment, the method involves administering a CAH protein or nucleic acid molecule as therapy to compensate for reduced, aberrant, or unwanted CAH expression or activity.

Stimulation of CAH activity is desirable in situations in which CAH is abnormally downregulated and/or in which increased CAH activity is likely to have a beneficial effect. Likewise, inhibition of CAH activity is desirable in situations in which CAH is abnormally upregulated and/or in which decreased CAH activity is likely to have a beneficial effect.

3. Pharmacogenomics

The CAH molecules ofthe present invention, as well as agents, or modulators which have a stimulatory or inhibitory effect on CAH activity (e.g. , CAH gene expression) as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) CAH-associated disorders (e.g., proliferative disorders (e.g., cancer), CNS disorders, cardiac disorders, metabolic disorders, muscular disorders, ocular disorders, or disorders of bone resoφtion, or calcification/bone formation) associated with aberrant or unwanted CAH activity. In conjunction with such treatment, pharmacogenomics (i.e., the study ofthe relationship between an individual's genotype and that individual's response to a foreign compound or drug) may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration ofthe pharmacologically active drug. Thus, a physician or clinician may consider applying knowledge obtained in relevant pharmacogenomics studies in determining whether to administer a CAH molecule or CAH modulator as well as tailoring the dosage and/or therapeutic regimen of treatment with a CAH molecule or CAH modulator.

Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, for example, Eichelbaum, M. et al. (1996) Clin. Exp. Pharmacol. Physiol 23(10-11): 983-985 and Linder, M.W. et al. (1997) Clin. Chem. 43(2):254-266. In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). These pharmacogenetic conditions can occur either as rare genetic defects or as naturally-occurring polymoφhisms. For example, glucose-6-ρhosphate dehydrogenase deficiency (G6PD) is a common inherited enzymopathy in which the main clinical complication is haemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and consumption of fava beans.

One pharmacogenomics approach to identifying genes that predict drug response, known as "a genome-wide association", relies primarily on a high-resolution map ofthe human genome consisting of already known gene-related markers (e.g., a "bi-allelic" gene marker map which consists of 60,000-100,000 polymoφhic or variable sites on the human genome, each of which has two variants.) Such a high-resolution genetic map can be compared to a map ofthe genome of each of a statistically significant number of patients taking part in a Phase II/III drug trial to identify markers associated with a particular observed drug response or side effect. Alternatively, such a high resolution map can be generated from a combination of some ten-million known single nucleotide polymoφhisms (SNPs) in the human genome. As used herein, a "SNP" is a common alteration that occurs in a single nucleotide base in a stretch of DNA. For example, a SNP may occur once per every 1000 bases of DNA. A SNP may be involved in a disease process, however, the vast majority may not be disease-associated. Given a genetic map based on the occurrence of such SNPs, individuals can be grouped into genetic categories depending on a particular pattern of SNPs in their individual genome. In such a manner, treatment regimens can be tailored to groups of genetically similar individuals, taking into account traits that may be common among such genetically similar individuals.

Alternatively, a method termed the "candidate gene approach", can be utilized to identify genes that predict drug response. According to this method, if a gene that encodes a drug target is known (e.g., a CAH protein ofthe present invention), all common variants of that gene can be fairly easily identified in the population and it can be determined if having one version ofthe gene versus another is associated with a particular drug response.

As an illustrative embodiment, the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action. The discovery of genetic polymoφhisms of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19) has provided an explanation as to why some patients do not obtain the expected drug effects or show exaggerated drug response and serious toxicity after taking the standard and safe dose of a drug. These polymoφhisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations. For example, the gene coding for CYP2D6 is highly polymoφhic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite moφhine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification. Alternatively, a method termed the "gene expression profiling", can be utilized to identify genes that predict drug response. For example, the gene expression of an animal dosed with a drug (e.g., a CAH molecule or CAH modulator ofthe present invention) can give an indication whether gene pathways related to toxicity have been turned on. Information generated from more than one ofthe above pharmacogenomics approaches can be used to determine appropriate dosage and treatment regimens for prophylactic or therapeutic treatment of an individual. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with a CAH molecule or CAH modulator, such as a modulator identified by one ofthe exemplary screening assays described herein. VI. Electronic Apparatus Readable Media and Arrays

Electronic apparatus readable media comprising CAH sequence information is also provided. As used herein, "CAH sequence information" refers to any nucleotide and/or amino acid sequence information particular to the CAH molecules ofthe present invention, including but not limited to full-length nucleotide and/or amino acid sequences, partial nucleotide and/or amino acid sequences, polymoφhic sequences including single nucleotide polymoφhisms (SNPs), epitope sequences, and the like. Moreover, information "related to" said CAH sequence information includes detection ofthe presence or absence of a sequence (e.g., detection of expression of a sequence, fragment, polymoφhism, etc.), determination of the level of a sequence (e.g., detection of a level of expression, for example, a quantative detection), detection of a reactivity to a sequence (e.g., detection of protein expression and/or levels, for example, using a sequence-specific antibody), and the like. As used herein, "electronic apparatus readable media" refers to any suitable medium for storing, holding or containing data or information that can be read and accessed directly by an electronic apparatus. Such media can include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as compact disc; electronic storage media such as RAM, ROM, EPROM, EEPROM and the like; general hard disks and hybrids of these categories such as magnetic/optical storage media. The medium is adapted or configured for having recorded thereon CAH sequence information ofthe present invention.

As used herein, the term "electronic apparatus" is intended to include any suitable computing or processing apparatus or other device configured or adapted for storing data or information. Examples of electronic apparatus suitable for use with the present invention include stand-alone computing apparatus; networks, including a local area network (LAN), a wide area network (WAN) Internet, Intranet, and Extranet; electronic appliances such as a personal digital assistants (PDAs), cellular phone, pager and the like; and local and distributed processing systems.

As used herein, "recorded" refers to a process for storing or encoding information on the electronic apparatus readable medium. Those skilled in the art can readily adopt any of the presently known methods for recording information on known media to generate manufactures comprising the CAH sequence information.

A variety of software programs and formats can be used to store the sequence information on the electronic apparatus readable medium. For example, the sequence information can be represented in a word processing text file, formatted in commercially- available software such as WordPerfect and MicroSoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like, as well as in other forms. Any number of data processor structuring formats (e.g., text file or database) may be employed in order to obtain or create a medium having recorded thereon the CAH sequence information.

By providing CAH sequence information in readable form, one can routinely access the sequence information for a variety of puφoses. For example, one skilled in the art can use the sequence information in readable form to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions ofthe sequences ofthe invention which match a particular target sequence or target motif.

The present invention therefore provides a medium for holding instructions for performing a method for determining whether a subject has a CAH- associated disease or disorder or a pre-disposition to a CAH-associated disease or disorder, wherein the method comprises the steps of determining CAH sequence information associated with the subject and based on the CAH sequence information, determining whether the subject has a CAH - associated disease or disorder or a pre-disposition to a CAH-associated disease or disorder and/or recommending a particular treatment for the disease, disorder or pre-disease condition.

The present invention further provides in an electronic system and/or in a network, a method for determining whether a subject has a CAH-associated disease or disorder or a pre-disposition to a disease associated with a CAH wherein the method comprises the steps of determining CAH sequence information associated with the subject, and based on the CAH sequence information, determining whether the subject has a CAH -associated disease or disorder or a pre-disposition to a CAH-associated disease or disorder, and/or recommending a particular treatment for the disease, disorder or pre-disease condition. The method may further comprise the step of receiving phenotypic information associated with the subject and/or acquiring from a network phenotypic information associated with the subject.

The present invention also provides in a network, a method for determining whether a subject has a CAH-associated disease or disorder or a pre-disposition to a CAH associated disease or disorder associated with CAH, said method comprising the steps of receiving CAH sequence information from the subject and/or information related thereto, receiving phenotypic information associated with the subject, acquiring information from the network corresponding to CAH and/or a CAH-associated disease or disorder, and based on one or more ofthe phenotypic information, the CAH information (e.g., sequence information and/or information related thereto), and the acquired information, determining whether the subject has a CAH-associated disease or disorder or a pre-disposition to a CAH-associated disease or disorder (e.g., a carbonic anhydrase-associated disorder such as a CNS disorder; a cellular proliferation, growth, differentiation, or migration disorder; a, musculoskeletal disorder; a cardiovascular disorder; an ocular disorder, or a disorder of bone resoφtion, or calcification/bone formation). The method may further comprise the step of recommending a particular treatment for the disease, disorder or pre-disease condition.

The present invention also provides a business method for determining whether a subject has a CAH-associated disease or disorder or a pre-disposition to a CAH-associated disease or disorder, said method comprising the steps of receiving information related to CAH (e.g., sequence information and/or information related thereto), receiving phenotypic information associated with the subject, acquiring information from the network related to CAH and/or related to a CAH-associated disease or disorder, and based on one or more of the phenotypic information, the CAH information, and the acquired information, determining whether the subject has a CAH-associated disease or disorder or a predisposition to a CAH-associated disease or disorder. The method may further comprise the step of recommending a particular treatment for the disease, disorder or pre-disease condition.

The invention also includes an array comprising a CAH sequence ofthe present invention. The array can be used to assay expression of one or more genes in the array. In one embodiment, the array can be used to assay gene expression in a tissue to ascertain tissue specificity of genes in the array. In this manner, up to about 7600 genes can be simultaneously assayed for expression, one of which can be CAH. This allows a profile to be developed showing a battery of genes specifically expressed in one or more tissues. In addition to such qualitative determination, the invention allows the quantitation of gene expression. Thus, not only tissue specificity, but also the level of expression of a battery of genes in the tissue is ascertainable. Thus, genes can be grouped on the basis of their tissue expression er se and level of expression in that tissue. This is useful, for example, in ascertaining the relationship of gene expression between or among tissues. Thus, one tissue can be perturbed and the effect on gene expression in a second tissue can be determined. In this context, the effect of one cell type on another cell type in response to a biological stimulus can be determined. Such a determination is useful, for example, to know the effect of cell-cell interaction at the level of gene expression. If an agent is administered therapeutically to treat one cell type but has an undesirable effect on another cell type, the invention provides an assay to determine the molecular basis of the undesirable effect and thus provides the opportunity to co-administer a counteracting agent or otherwise treat the undesired effect. Similarly, even within a single cell type, undesirable biological effects can be determined at the molecular level. Thus, the effects of an agent on expression of other than the target gene can be ascertained and counteracted. In another embodiment, the array can be used to monitor the time course of expression of one or more genes in the array. This can occur in various biological contexts, as disclosed herein, for example development of a CAH-associated disease or disorder, progression of CAH-associated disease or disorder, and processes, such a cellular transformation associated with the CAH-associated disease or disorder.

The array is also useful for ascertaining the effect ofthe expression of a gene on the expression of other genes in the same cell or in different cells (e.g., ascertaining the effect of CAH expression on the expression of other genes). This provides, for example, for a selection of alternate molecular targets for therapeutic intervention if the ultimate or downstream target cannot be regulated.

The array is also useful for ascertaining differential expression patterns of one or more genes in normal and abnormal cells. This provides a battery of genes (e.g., including CAH) that could serve as a molecular target for diagnosis or therapeutic intervention.

This invention is further illustrated by the following examples which should not be construed as limiting. The contents of all references, patents and published patent applications cited throughout this application, as well as the Figures, are incoφorated herein by reference.

EXAMPLES

EXAMPLE 1: IDENTIFICATION AND CHARACTERIZATION OF HUMAN CAH cDNA

In this example, the identification and characterization ofthe gene encoding human CAH (clone Fbh.55158) is described.

Isolation ofthe CAH cDNA The invention is based, at least in part, on the discovery of a human gene encoding a novel protein, referred to herein as CAH. The entire sequence of human clone Fbh.55158, was determined and found to contain an open reading frame termed human "CAH", set forth in Figure 1. The amino acid sequence of this human CAH expression product is set forth in Figure 1. The CAH protein sequence set forth in SEQ ID NO:2 comprises about 328 amino acids and is shown in Figure 1. The coding region (open reading frame) of SEQ ID NO: 1 is set forth as SEQ ID NO:3. Clone Fbh.55158, comprising the coding region of human CAH, was deposited with the American Type Culture Collection (ATCC®), 10801 University Boulevard, Manassas, VA 20110-2209, on , and assigned Accession No. .

Analysis ofthe Human CAH Molecules

The amino acid sequence of human CAH was analyzed using the program PSORT (http://www. psort.nibb.ac.jp) to predict the localization ofthe protein within the cell. This program assesses the presence of different targeting and localization amino acid sequences within the query sequence. The results ofthe analyses show that the human CAH (SEQ ID NO:2) may be localized, for example, to the nucleus, to the mitochondrion, to the cytoplasm, to the plasma membrane, or to secretory vesicles. Results also show the presence of several dileucine motifs in the tail ofthe amino acid sequence ofthe human CAH (SEQ ID NO:2) at amino acids 10-11, 146-147, 216-217, 269-270, and 326-327.

An analysis ofthe amino acid sequence of human CAH using the Signal P program (Henrik, et al (1997) Protein Engineering 10:1-6), identified the presence of a signal peptide from amino acids 1-21.

A search ofthe amino acid sequence of CAH was also performed against the HMM database (Figure 3). This search resulted in the identification of a "eukaryotic-type carbonic anhydrase domain" in the amino acid sequence of CAH (SEQ ID NO:2) at about residues 63-301 (score = 170.6) (Figure 3).

A search ofthe amino acid sequence of CAH was also performed against the ProDom database. This search resulted in the identification of a domain "similar to carbonic anhydrase I" in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 15-85 (score=l 14), a "carbonic anhydrase dehydratase lyase carbonate zinc precursor signal protein glycoprotein domain" in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 47-300, a "carbonic anhydrase lyase carbonate dehydratase zinc precursor signal II domain" in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 33-300 (score=476), an "anhydrase-related carbonic caφ CA-XI II CA-RP precursor signal unnamed product domain" in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 1-62 (score=293), and a "carbonic anhydrase domain" in the amino acid sequence of human CAH (SEQ ID NO:2) at about residues 11-72 (score=71). A search ofthe amino acid sequence of CAH was also performed against the ProSite database. This search resulted in the identification of several "N-glycosylation sites" in the amino acid sequence of CAH (SEQ ID NO:2) at about residues 1 16-1 19, 168-171, and 302- 305, two "cAMP- and cGMP-dependent protein kinase phosphorylation sites" at residues 64-67 and 92-95, several "protein kinase C phosphorylation sites" at amino acids 25-27, 101-103, 106-108, 125-127, 209-211, and 266-268, a "casein kinase II phosphorylation site" at residues 281-284, several "N-myristoylation sites" at residues 51-56, 96-101, 119-124, 136-141, and 149-154, and two "amidation sites" at residues 62-65 and 90-93.

The CAH proteins ofthe present invention include many features indicative ofthe carbonic anhydrase family of proteins. For instance, the CAH proteins ofthe present invention contain conserved residues known to be located in the active site and/or to coordinate the zinc ion in most carbonic anhydrases ofthe α class. These residues include Gln66, Ser67, and Pro68, Serl43 and Glul55. Additionally, a number ofthe other conserved residues are present, but shifted by one (AsnlOO) or three (Gly234, Thr237, Tφ247, or Arg 284) residues from their location in the typical α-CAH molecule. As such, the CAH family of proteins are referred to herein as carbonic anhydrase proteins.

Tissue Distribution of CAH mRNA by Taqman™ analysis This example describes the tissue distribution of human CAH mRNA in a variety of cells and tissues, as determined using the TaqMan™ procedure. The Taqman™ procedure is a quantitative, reverse transcription PCR-based approach for detecting mRNA. The RT- PCR reaction exploits the 5' nuclease activity of AmpliTaq Gold™ DNA Polymerase to cleave a TaqMan™ probe during PCR. Briefly, cDNA was generated from the samples of interest, e.g., various human normal and tumor tissues, and used as the starting material for PCR amplification. In addition to the 5' and 3' gene-specific primers, a gene-specific oligonucleotide probe (complementary to the region being amplified) was included in the reaction (i.e., the Taqman™ probe). The TaqMan™ probe includes the oligonucleotide with a fluorescent reporter dye covalently linked to the 5' end ofthe probe (such as FAM (6- carboxyfluorescein), TET (6-carboxy-4,7,2', 7 '-tetrachlorofluorescein), JOE (6-carboxy-4,5- dichloro-2,7-dimethoxyfluorescein), or VIC) and a quencher dye (TAMRA (6-carboxy- N,N,N',N'-tetramethylrhodamine) at the 3' end ofthe probe.

During the PCR reaction, cleavage ofthe probe separates the reporter dye and the quencher dye, resulting in increased fluorescence ofthe reporter. Accumulation of PCR products is detected directly by monitoring the increase in fluorescence ofthe reporter dye. When the probe is intact, the proximity ofthe reporter dye to the quencher dye results in suppression ofthe reporter fluorescence. During PCR, if the target of interest is present, the probe specifically anneals between the forward and reverse primer sites. The 5 '-3' nucleolytic activity ofthe AmpliTaq™ Gold DNA Polymerase cleaves the probe between the reporter and the quencher only if the probe hybridizes to the target. The probe fragments are then displaced from the target, and polymerization ofthe strand continues. The 3' end ofthe probe is blocked to prevent extension ofthe probe during PCR. This process occurs in every cycle and does not interfere with the exponential accumulation of product. RNA was prepared using the trizol method and treated with DNase to remove contaminating genomic DNA. cDNA was synthesized using standard techniques. Mock cDNA synthesis in the absence of reverse transcriptase resulted in samples with no detectable PCR amplification ofthe control gene confirms efficient removal of genomic DNA contamination.

A human tissue panel was tested revealing highest expression of human CAH mRNA in the brain, hypothalamus, dorsal root ganglia (DRG), kidney tissue, and spinal cord (see Figure 4).

A panel containing various human lung, ovary, and breast normal and tumor tissue samples indicated highest expression of human CAH mRNA in lung tumor tissue, with weak expression in normal lung tissue (see Figure 5). High expression was also detected in normal ovary tissue, with weak expression detected in ovary tumor tissue (see Figure 6). Weak expression was also detected in normal breast tissue with higher expression detected in breast tumor tissue (see Figure 7). A panel containing various human colon, liver, and brain normal and tumor tissue samples indicated highest expression of human CAH mRNA in normal brain tissue, with weak expression in brain tumor tissue. Weak expression was also detected in astrocytes, HMVEC, placental tissue, fetal adrenal gland, and fetal liver tissue (see Figure 8). Expression was also detected in normal colon tissue, with weaker expression detected in colon tumor tissue. Expression was also detected in colon tumor metastases to the liver, with weaker expression detected in a normal liver tissue sample (see Figure 9).

Various normal and cancer cell lines were also tested for CAH mRNA expression, including human breast carcinoma cell lines, human colon carcinoma cell lines, and human lung carcinoma cell lines. Relative expression of human CAH mRNA is shown in Table 1, below.

Table 1.

Average Average Relative

Cell lines 55158.2 B-2 55158.2 Beta-2 ΔCt Expression

(CAH) (CAH)

MCF-7 39.02 18.75 38.96 18.545 20.415 0.00 38.9 18.34

ZR75 34.71 18.33 34.73 18.31 16.42 0.01 34.75 18.29

T47D 36.03 17.28 36.03 17.28 18.75 0.00

MDA 231 38.98 16.83 38.495 17 21.495 0.00 38.01 17.17

MDA 435 33.47 15.44 33.505 15.47 18.035 0.00 33.54 15.5

DLD-1 34.86 18.91 34.735 18.84 15.895 0.02 34.61 18.77

SW 480 38.01 16.4 38.01 16.4 21.61 0.00

SW 620

HCT 116

HT 29 39.04 15.26 39.52 15.315 24.205 0.00 40 15.37

Colo 205 37.1 14.55 37.345 14.535 22.81 0.00 37.59 14.52

NCIH 125 40 17.28 38.605 17.31 21.295 0.00 37.21 17.34

NCIH 67 36.7 18.38 36.665 18.375 18.29 0.00 36.63 18.37

NCIH 322

NCIH 460 37.34 17.22 20.12. 0.00

37.34 17.22

A549 38.67 18.24 38.625 18.155 20.47 0.00 38.58 18.07

NHBE 34.75 18.17 34.82 18.315 16.505 0.01 34.89 18.46

NTC 40 39.98 39.14 39.99 38.28 40

Tissue Distribution of CAH mRNA by Northern Analysis This example describes the tissue distribution of CAH mRNA, as determined by

Northern analysis.

Northern blot hybridizations with the various RNA samples are performed under standard conditions and washed under stringent conditions, i.e., 0.2xSSC at 65°C. The

DNA probe is radioactively labeled with 32p_dCTP using the Prime-It kit (Stratagene, La Jolla, CA) according to the instructions ofthe supplier. Filters containing human mRNA

(MuItiTissue Northern I and MuItiTissue Northern II from Clontech, Palo Alto, CA) are probed in ExpressHyb hybridization solution (Clontech) and washed at high stringency according to manufacturer's recommendations.

Tissue Distribution of CAH mRNA by in situ Analysis For in situ analysis, various tissues, e.g. tissues obtained from brain, are first frozen on dry ice. Ten-micrometer-thick sections ofthe tissues are postfixed with 4% formaldehyde in DEPC treated IX phosphate- buffered saline at room temperature for 10 minutes before being rinsed twice in DEPC IX phosphate-buffered saline and once in 0.1 M triethanolamine-HCl (pH 8.0). Following incubation in 0.25% acetic anhydride-0.1 M triethanolamine-HCl for 10 minutes, sections are rinsed in DEPC 2X SSC (IX SSC is

0.15M NaCl plus 0.015M sodium citrate). Tissue is then dehydrated through a series of ethanol washes, incubated in 100% chloroform for 5 minutes, and then rinsed in 100% ethanol for 1 minute and 95% ethanol for 1 minute and allowed to air dry. Hybridizations are performed with 35s-radiolabeled (5 X 10 cpm/ml) cRNA probes. Probes are incubated in the presence of a solution containing 600 mM NaCl, 10 mM Tris (pH 7.5), 1 mM EDTA, 0.01% sheared salmon sperm DNA, 0.01% yeast tRNA, 0.05% yeast total RNA type XI, IX Denhardt's solution, 50% formamide, 10% dextran sulfate, 100 mM dithiothreitol, 0.1% sodium dodecyl sulfate (SDS), and 0.1% sodium thiosulfate for 18 hours at 55°C. After hybridization, slides are washed with 2X SSC. Sections are then sequentially incubated at 37°C in TNE (a solution containing 10 mM Tris-HCl (pH 7.6), 500 mM NaCl, and 1 mM EDTA), for 10 minutes, in TNE with lOμg of RNase A per ml for 30 minutes, and finally in TNE for 10 minutes. Slides are then rinsed with 2X SSC at room temperature, washed with 2X SSC at 50°C for 1 hour, washed with 0.2X SSC at 55°C for 1 hour, and 0.2X SSC at 60°C for 1 hour. Sections are then dehydrated rapidly through serial ethanol-

0.3 M sodium acetate concentrations before being air dried and exposed to Kodak Biomax

MR scientific imaging film for 24 hours and subsequently dipped in NB-2 photoemulsion and exposed at 4°C for 7 days before being developed and counter stained.

EXAMPLE 2: EXPRESSION OF RECOMBINANT CAH PROTEIN IN

BACTERIAL CELLS

In this example, CAH is expressed as a recombinant glutathione-S-transferase (GST) fusion polypeptide in E. coli and the fusion polypeptide is isolated and characterized. Specifically, CAH is fused to GST and this fusion polypeptide is expressed in E. coli, e.g., strain PEB 199. Expression ofthe GST-CAH fusion protein in PEB 199 is induced with

IPTG. The recombinant fusion polypeptide is purified from crude bacterial lysates ofthe induced PEB 199 strain by affinity chromatography on glutathione beads. Using polyacrylamide gel electrophoretic analysis ofthe polypeptide purified from the bacterial lysates, the molecular weight ofthe resultant fusion polypeptide is determined.

EXAMPLE 3: EXPRESSION OF RECOMBINANT CAH PROTEIN

IN COS CELLS To express the CAH gene in COS cells, the pcDNA/Amp vector by Invitrogen

Coφoration (San Diego, CA) is used. This vector contains an SV40 origin of replication, an ampicillin resistance gene, an E. coli replication origin, a CMV promoter followed by a polylinker region, and an SV40 intron and polyadenylation site. A DNA fragment encoding the entire CAH protein and an HA tag (Wilson et al (1984) Cell 37:767) or a FLAG tag fused in-frame to its 3' end ofthe fragment is cloned into the polylinker region ofthe vector, thereby placing the expression ofthe recombinant protein under the control ofthe CMV promoter. To construct the plasmid, the CAH DNA sequence is amplified by PCR using two primers. The 5' primer contains the restriction site of interest followed by approximately twenty nucleotides ofthe CAH coding sequence starting from the initiation codon; the 3' end sequence contains complementary sequences to the other restriction site of interest, a translation stop codon, the HA tag or FLAG tag and the last 20 nucleotides of the CAH coding sequence. The PCR amplified fragment and the pCDNA/Amp vector are digested with the appropriate restriction enzymes and the vector is dephosphorylated using the CIAP enzyme (New England Biolabs, Beverly, MA). Preferably the two restriction sites chosen are different so that the CAH gene is inserted in the correct orientation. The ligation mixture is transformed into E. coli cells (strains HB101, DH5α, SURE, available from Stratagene Cloning Systems, La Jolla, CA, can be used), the transformed culture is plated on ampicillin media plates, and resistant colonies are selected. Plasmid DNA is isolated from transformants and examined by restriction analysis for the presence ofthe correct fragment. COS cells are subsequently transfected with the CAH-pcDNA/Amp plasmid DNA using the calcium phosphate or calcium chloride co-precipitation methods, DEAE-dextran- mediated transfection, lipofection, or electroporation. Other suitable methods for transfecting host cells can be found in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989. The expression ofthe CAH polypeptide is detected by radiolabelling (³⁵S-methionine or ³⁵S-cysteine available from NEN, Boston, MA, can be used) and immunoprecipitation (Harlow, E. and Lane, D. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988) using an HA specific monoclonal antibody. Briefly, the cells are labeled for 8 hours with ³⁵S-methionine (or ³⁵S-cysteine). The culture media are then collected and the cells are lysed using detergents (RIPA buffer, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM Tris, pH 7.5). Both the cell lysate and the culture media are precipitated with an HA-specific monoclonal antibody. Precipitated polypeptides are then analyzed by SDS-PAGE.

Alternatively, DNA containing the CAH coding sequence is cloned directly into the polylinker ofthe pCDNA/Amp vector using the appropriate restriction sites. The resulting plasmid is transfected into COS cells in the manner described above, and the expression of the CAH polypeptide is detected by radiolabelling and immunoprecipitation using a CAH- specific monoclonal antibody.

Equivalents Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments ofthe invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

What is claimed:

1. An isolated nucleic acid molecule selected from the group consisting of:

(a) a nucleic acid molecule comprising the nucleotide sequence set forth in

SEQ ID NO: 1; and

(b) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ID NO:3.

2. An isolated nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 2.

3. An isolated nucleic acid molecule comprising the nucleotide sequence contained in the plasmid deposited with ATCC® as Accession Number .

4. An isolated nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2.

5. An isolated nucleic acid molecule selected from the group consisting of:

a) a nucleic acid molecule comprising a nucleotide sequence which is at least 60% identical to the nucleotide sequence of SEQ ID NO: 1 or 3, or a complement thereof; b) a nucleic acid molecule comprising nucleotides 1-53 ofthe nucleotide sequence of SEQ ID NO: 1 , or a complement thereof; c) a nucleic acid molecule comprising a fragment of at least 878 nucleotides of a nucleic acid comprising the nucleotide sequence of SEQ ID NO:l or 3, or a complement thereof; d) a nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence at least about 60% identical to the amino acid sequence of SEQ ID

NO:2; and e) a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, wherein the fragment comprises at least 12 contiguous amino acid residues ofthe amino acid sequence of SEQ ID NO:2.

6. An isolated nucleic acid molecule which hybridizes to the nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5 under stringent conditions.

7. An isolated nucleic acid molecule comprising a nucleotide sequence which is complementary to the nucleotide sequence ofthe nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5.

8. An isolated nucleic acid molecule comprising the nucleic acid molecule of any one of claims 1 , 2, 3, 4, or 5, and a nucleotide sequence encoding a heterologous polypeptide.

9. A vector comprising the nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5.

10. The vector of claim 9, which is an expression vector.

11. A host cell transfected with the expression vector of claim 10.

12. A method of producing a polypeptide comprising culturing the host cell of claim 1 1 in an appropriate culture medium to, thereby, produce the polypeptide.

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

a) a fragment of a polypeptide comprising the amino acid sequence of

SEQ ID NO:2, wherein the fragment comprises at least 12 contiguous amino acids of SEQ ID NO:2; b) a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO:2, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule consisting of SEQ ID NO: l or 3 under stringent conditions; c) a polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 60% identical to a nucleic acid comprising the nucleotide sequence of SEQ ID NO: 1 or 3; d) a polypeptide comprising an amino acid sequence which is at least 60% identical to the amino acid sequence of SEQ ID NO:2.

14. The isolated polypeptide of claim 13 comprising the amino acid sequence of

SEQ ID NO:2.

15. The polypeptide of claim 13, further comprising heterologous amino acid sequences.

16. An antibody which selectively binds to a polypeptide of claim 13.

17. A method for detecting the presence of a polypeptide of claim 13 in a sample comprising: a) contacting the sample with a compound which selectively binds to the polypeptide; and b) determining whether the compound binds to the polypeptide in the sample to thereby detect the presence of a polypeptide of claim 13 in the sample.

18. The method of claim 17, wherein the compound which binds to the polypeptide is an antibody.

19. A kit comprising a compound which selectively binds to a polypeptide of claim 13 and instructions for use.

20. A method for detecting the presence of a nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5 in a sample comprising: a) contacting the sample with a nucleic acid probe or primer which selectively hybridizes to the nucleic acid molecule; and b) determining whether the nucleic acid probe or primer binds to a nucleic acid molecule in the sample to thereby detect the presence of a nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5 in the sample.

21. The method of claim 20, wherein the sample comprises mRNA molecules and is contacted with a nucleic acid probe.

22. A kit comprising a compound which selectively hybridizes to a nucleic acid molecule of any one of claims 1, 2, 3, 4, or 5 and instructions for use.

23. A method for identifying a compound which binds to a polypeptide of claim 13 comprising: a) contacting the polypeptide, or a cell expressing the polypeptide with a test compound; and b) determining whether the polypeptide binds to the test compound.

24. The method of claim 23, wherein the binding ofthe test compound to the polypeptide is detected by a method selected from the group consisting of: a) detection of binding by direct detection of test compound/polypeptide binding; b) detection of binding using a competition binding assay; and c) detection of binding using an assay for CAH activity.

25. A method for modulating the activity of a polypeptide of claim 13 comprising contacting the polypeptide or a cell expressing the polypeptide with a compound which binds to the polypeptide in a sufficient concentration to modulate the activity ofthe polypeptide.

26. A method for identifying a compound which modulates the activity of a polypeptide of claim 13 comprising: a) contacting a polypeptide of claim 13 with a test compound; and b) determining the effect ofthe test compound on the activity ofthe polypeptide to thereby identify a compound which modulates the activity ofthe polypeptide.