# Patent

## Title
PTH1R receptors

## Abstract

The present invention relates to novel parathyroid hormone (PTH) and parathyroid hormone related protein (PTHrP) receptors (PTH1R and PTH3R) isolated from zebrafish. The receptors of the present invention share homology with previously identified parathyroid hormone (PTH)/parathyroid related protein (PTHrP) receptors. Isolated nucleic acid molecules are provided encoding the zebrafish PTH1R and PTH3R receptors. PTH1R and PTH3R receptor polypeptides are also provided, as are vectors, host cells and recombinant methods for producing the same. The invention further relates to screening methods for identifying agonists and antagonists of PTH1R and PTH3R receptor activity and to diagnostic and therapeutic methods.

## Background
This application is a divisional application of U.S. nonprovisional application 09/449,632 filed on Nov. 30, 1999 now U.S. Pat No. 6,541,220, which claims the benefit of the filing date of U.S. provisional application 60/110,467 filed on Nov. 30, 1998, both herein incorporated by reference.


STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY-SPONSORED RESEARCH AND DEVELOPMENT
Part of the work performed during development of this invention utilized U.S. Government funds. The U.S. Government has certain rights in this invention.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention is related to the fields of molecular biology, developmental biology, physiology, neurobiology and medicine. The invention provides polynucleotides encoding the zebrafish PTH1R receptor and polynucleotides for a novel zebrafish PTH3R receptor, as well as vectors and cells containing said polynucleotides. The invention further provides polypeptides for the PTH1R and PTH3R receptors. The polynucleotides and polypeptides of the invention are useful for the identification of agonist and antagonists of PTH1R or PTH3R receptor function and as reagents in the treatment of diseases or disorders associated with PTH1R or PTH3R function.
2. Related Art
The parathyroid hormone (PTH)/PTH-related peptide (PTHrP) receptor (PTH1R) mediates in mammals and frogs the actions of PTH and PTHrP. Both peptides, most likely evolved through a gene duplication event from a common ancestral gene, and have retained limited homology within the amino-terminal region. Because of their structural conservation, PTH and PTHrP bind with similar affinity to the PTH1R, and activate this common receptor with similar or indistinguishable efficacy. Due to this unusual ligand-specificity, the PTH1R mediates the endocrine actions of PTH, the most important peptide regulator of calcium homeostasis in mammals, and the autocrine/paracrine actions of PTHrP, which is important for normal chondrocyte proliferation and differentiation (Karaplis, et al., (1997)); Lanske, et al., (1996)), and most likely for other, still incompletely defined functions including pancreas, skin, and breast development, as well as tooth eruption (Wysolmerski, et al., (1996)).
In addition to the PTH1R, a PTH type-2 receptor (PTH2R) has been isolated from mammals and teleosts (Usdin, et al., (1995); Rubin, et al. (1999)), and at least the human PTH2R is activated by PTH and a recently isolated hypothalamus peptide (Usdin, et al., (1999)). Its biological importance remains uncertain, as does the importance of additional receptors for which there is growing biological and pharmacological evidence. For example, receptors with specificity for amino-terminal PTH and PTHrP have been described for keratinocytes, squamous carcinoma cell lines, and central nervous system cells (Orloff et al., (1995 and 1996); Fukayama, et al., (1995)), and there is evidence for a PTHrP-selective receptor in the mammalian supraoptic nucleus (Yamamoto et al., (1997) and (1998)). In addition, the midregional portion of PTHrP stimulates an increase in intracellular free calcium in some cell lines and increases placental calcium transport (Kovacs et al., (1996); Wu et al., (1996); Orloffet al., (1996)), and the carboxy-terminal portion of PTH binds to a distinct receptor on clonal cell lines (Inomata, et al., (1995); Takasu, et al., (1998)).
Research on the parathyroid hormone (PTH) has been extensive. Formulations of PTH and compounds with PTH activity have been described (see U.S. Pat. Nos. 5,496,801; 5,814,603; 5,208,041;), and methods to produce the same are also known (see U.S. Pat. Nos. 5,616,560 and 5,010,010). In addition, analogs and inhibitors of PTH may be found in the prior art (see U.S. Pat. Nos. 4,423,037; 5,693,616; 5,695,955 and 5,798,225).
Thus, the invention furthers the art by focusing on PTH receptors and providing reagents and methods that are distinct and separate from PTH.
SUMMARY OF THE INVENTION
The present invention provides isolated nucleic acid molecules comprising a polynucleotide encoding a novel PTH1R receptor having the amino acid sequence shown in FIG. 2A (SEQ ID NO:2) or the amino acid sequence encoded by the cDNA clone deposited in a bacterial host with the ATCC as patent deposit PTA-916 on Nov. 4, 1999. The present invention also relates to recombinant vectors, which include the isolated nucleic acid molecules of the present invention, and to host cells containing the recombinant vectors, as well as to methods of making such vectors and host cells and for using them for production of PTH1R polypeptides or peptides by recombinant techniques. The invention further provides an isolated PTH1R polypeptide having an amino acid sequence encoded by a polynucleotide described herein.
The present invention also provides isolated nucleic acid molecules comprising a polynucleotide encoding a novel PTH3R receptor having the amino acid sequence shown in FIG. 2B (SEQ ID NO:4) or the amino acid sequence encoded by the cDNA clone deposited in a bacterial host with the ATCC as patent deposit PTA-915 on Nov. 4, 1999. The present invention also relates to recombinant vectors, which include the isolated nucleic acid molecules of the present invention, and to host cells containing the recombinant vectors, as well as to methods of making such vectors and host cells and for using them for production of PTH3R polypeptides or peptides by recombinant techniques. The invention further provides an isolated PTH3R polypeptide having an amino acid sequence encoded by a polynucleotide described herein.
The present invention also provides a screening method for identifying compounds capable of enhancing or inhibiting a cellular response induced by the PTH1R or PTH3R receptor, which involves contacting cells which express the PTH1R or PTH3R receptor with the candidate compound, assaying a cellular response, and comparing the cellular response to a standard cellular response, the standard being assayed when contact is made in absence of the candidate compound; whereby, an increased cellular response over the standard indicates that the compound is an agonist and a decreased cellular response over the standard indicates that the compound is an antagonist.
In another aspect, a screening assay for agonists and antagonists is provided which involves determining the effect a candidate compound has on PTH or PTHrP binding to the PTH1R or PTH3R receptor. In particular, the method involves contacting the PTH1R or PTH3R receptor with a PTH or PTHrP polypeptide and a candidate compound and determining whether PTH or PTHrP polypeptide binding to the PTH1R or PTH3R receptor is increased or decreased due to the presence of the candidate compound.
An additional aspect of the invention is related to a method for treating an individual in need of an increased level of PTH1R or PTH3R activity in the body comprising administering to such an individual a composition comprising a therapeutically effective amount of an isolated PTH1R or PTH3R polypeptide of the invention or an agonist thereof.
A still further aspect of the invention is related to a method for treating an individual in need of a decreased level of PTH1R or PTH3R receptor activity in the body comprising, administering to such an individual a composition comprising a therapeutically effective amount of an PTH1R or PTH3R antagonist.
The invention further provides a diagnostic method useful during diagnosis or prognosis of diseases and disorders associated with PTH1R or PTH3R receptor expression or function.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. A) Schematic representation of exons M6/7 and M7 (A), and of the cDNA encoding the PTH1R or the PTH3R (B). Vertical boxes depict the predicted location of the membrane-spanning helices; recognition sites for restriction enzymes are shown by //. For and Rev arrows indicate the approximate location of primers used for RT-PCR, 5′ RACE, and 3′ RACE for zPTH1R and zPTH3R. C) The nucleotide sequence of the PTH1R receptor cDNA. D) The nucleotide sequence of the PTH3R receptor cDNA.
, degenerate primers; ←, zPTH1R-specific; , zPTH3R-specific; ζ, potential sites for N-linked glycosylation.
FIG. 2A) The amino acid sequence of the PTH1R receptor; B) The amino acid sequence of the PTH3R receptor.
FIG. 3 Alignment of the amino acid sequences of the zPTH1R, zPTH2R, and zPTH3R. The sequences were aligned using the GAP and pileup algorithms of the GCG package (Genetics Computer Group, Wisconsin). Conserved consensus sites for potential N-glycosyjation are identified by #; Gaps were introduced to maximize sequence homology. The seventeen residues which are lacking in one splice variant of the characterized zPTH2R (Rubin et al., (1999)) are boxed; the residues which are predicted to comprise the signal peptide are outlined with a stippled box; and those residues which are likely to be PTH3R-specific are boxed.
FIG. 4A-D. COS-7 cells transiently expressing the zPTH1R or the zPTH3R were evaluated for competitive inhibition of radioligand binding (A,B) and agonist-stimulated cAMP production (C,D). Binding studies (as described in Materials and Methods) used either 125I-[Nle8,21,Tyr34]rPTH-(1–34)amide (Panel A) or 125I-[Tyr36]hPTHrP-(1–36)amide (Panel B) as radioligand and varying amounts of unlabeled peptide. Data are expressed as % of maximal binding. Cyclic AMP accumulation is expressed as % of maximal for the zPTH1R (C) or the zPTH3R (D); basal cAMP accumulation was 3–4 pmol/well for either receptor; maximal accumulation of 106.2 pmol/well for the zPTH1R, and 285.4 pmol/well for the zPTH3R. ▪□, PTH; ●∘, PTHrP; filled symbols represent zPTH1R, open symbols represent zPTH3R. All data represent the mean±SEM of at least three independent transfections.
FIG. 5. Accumulation of total IP in COS-7 cells transiently expressing the zPTH1R, or the zPTH3R or the hPTH1R. Hydrolysis of total IPs was assessed as described in the absence or presence of PTHrP (10−6 M) or PTH (10−6 M). Data are expressed as fold above basal and represent the mean±SEM of at two independent experiments.
FIG. 6. A phylogenetic analysis, as described in Materials and Methods, indicated that the single most parsimonious tree had a length of 1549 steps, and a consistency index excluding uninformative characters of 0.863. The bootstrap confidence intervals are shown next to the branch points and indicate the percentage of trials which support a given branch in 100 branch-and-bound iterations.
FIG. 7. Southern blot analysis of wild-type (left lane) and PTH/PTHrP receptor knock out mouse genomic DNA (right lane) probed with PTH3R.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention provides novel PTH receptor nucleic acids and proteins (Rubin and Jüppner, (1999)). More specifically, the present invention provides isolated nucleic acid molecules comprising a polynucleotide encoding a novel PTH1R polypeptide having the amino acid sequence shown in FIG. 2A (SEQ ID NO:2), which was determined by sequencing a cloned cDNA. The PTH1R protein of the present invention shares sequence homology with previously identified PTH1R and PTH2R sequences. The nucleotide sequence shown in FIG. 1C (SEQ ID NO:1) was obtained by sequencing a cDNA clone (zPTH1R), which was deposited on Nov. 4, 1999 at the American Type Culture Collection, 10801 University Boulevard, Manassas, Va. 20110-2209, and given accession number PTA-916. The cDNA was inserted between the EcoRI and SphI site of plasmid pcDNAI/Amp (Invitrogen).
The present invention also provides isolated nucleic acid molecules comprising a polynucleotide encoding a novel PTH3R polypeptide having the amino acid sequence shown in FIG. 2B (SEQ ID NO:4), which was determined by sequencing a cloned cDNA. The PTH3R protein of the present invention shares sequence homology with the PTH1R protein sequence of the invention and other PTH1R and PTH2R protein sequences previously. The nucleotide sequence shown in FIG. 1C (SEQ ID NO:3) was obtained by sequencing a cDNA clone(zPTH3R), which was deposited on Nov. 4, 1999 at the American Type Culture Collection, 10801 University Boulevard, Manassas, Va. 20110-2209, and given accession number PTA-915. The cDNA was inserted between the BamHI and NotI site of plasmid pcDNAI/Amp (Invitrogen).
Nucleic Acid Molecules
Unless otherwise indicated, all nucleotide sequences determined by sequencing a DNA molecule herein were determined by manual sequencing, and all amino acid sequences of polypeptides encoded by DNA molecules determined herein were predicted by translation of a DNA sequence determined as above. Therefore, as is known in the art for any DNA sequence determined by this approach, any nucleotide sequence determined herein may contain some errors. Nucleotide sequences determined by manual sequencing are typically at least about 95% to at least about 99.9% identical to the actual nucleotide sequence of the sequenced DNA molecule. As is also known in the art, a single insertion or deletion in a determined nucleotide sequence compared to the actual sequence will cause a frame shift in translation of the nucleotide sequence such that the predicted amino acid sequence encoded by a determined nucleotide sequence will be completely different from the amino acid sequence actually encoded by the sequenced DNA molecule, beginning at the point of such an insertion or deletion.
Using the information provided herein, such as the nucleotide sequence in FIG. 1C or 1D, a nucleic acid molecule of the present invention encoding a PTH1R or PTH3R polypeptide, respectively, may be obtained using standard cloning and screening procedures, such as those for cloning cDNAs using mRNA as starting material. Illustrative of the invention, the nucleic acid molecule described in FIG. 1C (SEQ ID NO:1) was discovered using oligonucleotide primers in a polymerase chain reaction (PCR) with total RNA isolated from adult zebrafish. The determined nucleotide sequence of the PTH1R cDNA of FIG. 1C (SEQ ID NO:1) contains an open reading frame encoding a protein of about 536 amino acid residues, with a predicted leader sequence of about 24 amino acid residues, and a deduced molecular weight of about 61.4 kDa for the non-glycosylated form. The amino acid sequence of the predicted mature PTH1R receptor is shown in FIG. 2A from amino acid residue about 25 to residue about 536. The PTH1R protein shown in FIG. 2A (SEQ ID NO:2) is about 76% identical to human PTH1R sequence and about 68% identical to human PTH2R sequence.
Also illustrative of the invention is the nucleic acid molecule described in FIG. 1D (SEQ ID NO:3) was discovered in a zebrafish 1DNA library (Clontech). The determined nucleotide sequence of the FIG. 1D (SEQ ID NO:3) contains an open reading frame encoding a protein of about 542 amino acid residues, with a predicted leader sequence of about 21 amino acid residues, and a deduced molecular weight of about 59.2 kDa. The PTH3R protein shown in FIG. 2B (SEQ ID NO:4) is about 68% and 57% similar to human PTH1R and human PTH2R, respectively.
As indicated, the present invention also provides the mature form(s) of the PTH1R and PTH3R receptors of the present invention. According to the signal hypothesis, proteins secreted by mammalian cells have a signal or secretory leader sequence which is cleaved from the mature protein once export of the growing protein chain across the rough endoplasmic reticulum has been initiated. Most mammalian cells and even insect cells cleave secreted proteins with the same specificity. However, in some cases, cleavage of a secreted protein is not entirely uniform, which results in two or more mature species on the protein. Further, it has long been known that the cleavage specificity of a secreted protein is ultimately determined by the primary structure of the complete protein, that is, it is inherent in the amino acid sequence of the polypeptide. Therefore, the present invention provides a nucleotide sequence encoding the mature PTH1R polypeptides having the amino acid sequence encoded by the cDNA clone deposited in a bacterial host with the ATCC as patent deposit PTA-916 on Nov. 4, 1999 and as shown in FIG. 2A (SEQ ID NO:2). The present invention also provides a nucleotide sequence encoding the mature PTH3R polypeptides having the amino acid sequence encoded by the cDNA clone deposited in a bacterial host with the ATCC as patent deposit PTA-915 on Nov. 4, 1999 and as shown in FIG. 2B (SEQ ID NO:4). By the mature PTH1R protein having the amino acid sequence encoded by the cDNA clone contained in the bacterial host deposited with the ATCC as patent deposit PTA-916 is meant the mature form(s) of the PTH1R receptor produced by expression in a mammalian cell (e.g., COS cells, as described below) of the complete open reading frame encoded by the zebrafish DNA sequence of the clone contained in the vector in the deposited host. By the mature PTH3R protein having the amino acid sequence encoded by the cDNA clone contained in the bacterial host deposited with the ATCC as patent deposit PTA-915 is meant the mature form(s) of the PTH3R receptor produced by expression in a mammalian cell (e.g., COS cells, as described below) of the complete open reading frame encoded by the zebrafish DNA sequence of the clone contained in the vector in the deposited host. As indicated below, the mature PTH1R receptor having the amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916 may or may not differ from the predicted “mature” PTH1R protein shown in FIG. 2A (amino acids from about 25 to about 536) depending on the accuracy of the predicted cleavage. The mature PTH3R receptor having the amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-915 may or may not differ from the predicted “mature” PTH3R protein shown in FIG. 2B (amino acids from about 22 to about 542) depending on the accuracy of the predicted cleavage site.
Methods for predicting whether a protein has a secretory leader as well as the cleavage point for that leader sequence are available. For instance, the methods of McGeoch (Virus Res. 3:271–286 (1985)) and von Heinje (Nucleic Acids Res. 14:4683–4690 (1986)) can be used. The accuracy of predicting the cleavage points of known mammalian secretory proteins for each of these methods is in the range of 75–80%, von Heinje, supra. However, the two methods do not always produce the same predicted cleavage point(s) for a given protein. A computational method may be found in the computer program “PSORT” (K. Nakai and M. Kanehisa, Genomics 14:897–911 (1992)), which is an expert system for predicting the cellular location of a protein based on the amino acid sequence. As part of this computational prediction of localization, the methods of McGeoch and von Heinje are incorporated.
In the present case, the predicted amino acid sequence of the complete PTH1R and PTH3R polypeptides of the present invention were analyzed for structural properties by comparison to the rat PTH1R sequence. This analysis provided predicted a cleavage site between amino acids 24 and 25 in FIG. 2A (SEQ ID NO:2) and a cleavage site between amino acids 21 and 22 in FIG. 2B (SEQ ID NO:4). Thus, the leader sequence for the PTH1R receptor protein is predicted to consist of amino acid residues 1–24 in FIG. 2A (amino acids 1 to 24 in SEQ ID NO:2), while the predicted mature PTH1R protein consists of residues 25–536 (amino acids 25 to 536 in SEQ ID NO:2). The leader sequence for the PTH3R receptor protein is predicted to consist of amino acid residues 1–21 in FIG. 2B (amino acids 1–21 in SEQ ID NO:4), while the predicted mature PTH3R protein consists of residues 22–542 (amino acids 22 to 542 in SEQ ID NO:4).
As indicated, nucleic acid molecules of the present invention may be in the form of RNA, such as mRNA, or in the form of DNA, including, for instance, cDNA and genomic DNA obtained by cloning or produced synthetically. The DNA may be double-stranded or single-stranded. Single-stranded DNA or RNA may be the coding strand, also known as the sense strand, or it may be the non-coding strand, also referred to as the anti-sense strand.
As one of ordinary skill would appreciate, however, due to the possibilities of sequencing errors, the PTH I R receptor polypeptide encoded by the deposited cDNA comprises about 536 amino acids, but may be anywhere in the range of 510–561 amino acids; and the leader sequence of this protein is about 24 amino acids, but may be anywhere in the range of about 10 to about 30 amino acids. As one of ordinary skill would also appreciate, however, due to the possibilities of sequencing errors, the PTH3R receptor polypeptide encoded by the deposited cDNA comprises about 542 amino acids, but may be anywhere in the range of 500–550 amino acids; and the leader sequence of this protein is about 24 amino acids, but may be anywhere in the range of about 15 to about 35 amino acids.
As indicated, nucleic acid molecules of the present invention may be in the form of RNA, such as mRNA, or in the form of DNA, including, for instance, cDNA and genomic DNA obtained by cloning or produced synthetically. The DNA may be double-stranded or single-stranded. Single-stranded DNA or RNA may be the coding strand, also known as the sense strand, or it may be the non-coding strand, also referred to as the anti-sense strand.
By “isolated” nucleic acid molecule(s) is intended a nucleic acid molecule, DNA or RNA, which has been removed from its native environment. For example, recombinant DNA molecules contained in a vector are considered isolated for the purposes of the present invention. Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the DNA molecules of the present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
Isolated nucleic acid molecules of the present invention include DNA molecules comprising an open reading frame (ORF) shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3); DNA molecules comprising the coding sequence for the PTH1R receptor shown in FIG. 2A (SEQ ID NO:2) or the PTH3R receptor shown FIG. 2B (SEQ ID NO:4); and DNA molecules which comprise a sequence substantially different from those described above but which, due to the degeneracy of the genetic code, still encode the PTH1R or the PTH3R receptor. Of course, the genetic code is well known in the art. Thus, it would be routine for one skilled in the art to generate such degenerate variants.
In another aspect, the invention provides isolated nucleic acid molecules encoding the PTH1R polypeptide having an amino acid sequence encoded by the cDNA clone contained in the plasmid deposited with the ATCC as patent deposit PTA-916 on Nov. 4, 1999. Another aspect, the invention provides isolated nucleic acid molecules encoding the PTH3R polypeptide having an amino acid sequence encoded by the cDNA clone contained in the plasmid deposited with the ATCC as patent deposit PTA-915 on Nov. 4, 1999. Preferably, these nucleic acid molecules will encode the mature polypeptides encoded by the above-described deposited cDNA clones. In a further embodiment, nucleic acid molecules are provided encoding the PTH1R or the PTH3R polypeptide or the PTH1R or the PTH3R polypeptide lacking the N-terminal methionine. The invention also provides an isolated nucleic acid molecule having the nucleotide sequence shown in SEQ ID NO:1 or the nucleotide sequence of the PTH1R cDNA contained in the above-described deposited clone, or a nucleic acid molecule having a sequence complementary to one of the above sequences. Such isolated molecules, particularly DNA molecules, are useful as probes for gene mapping, by in situ hybridization with chromosomes, and for detecting expression of the PTH1R gene in human tissue, for instance, by Northern blot analysis. The invention also provides an isolated nucleic acid molecule having the nucleotide sequence shown in SEQ ID NO:3 or the nucleotide sequence of the cDNA contained in the above-described deposited clone, or a nucleic acid molecule having a sequence complementary to one of the above sequences. Such isolated molecules, particularly DNA molecules, are useful as probes for gene mapping, by in situ hybridization with chromosomes, and for detecting expression of the gene in human tissue, for instance, by Northern blot analysis.
The present invention is further directed to fragments of the isolated nucleic acid molecules described herein. By a fragment of an isolated nucleic acid molecule having the nucleotide sequence of the deposited cDNAs or the nucleotide sequence shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3) is intended fragments at least about 15 nt, and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt in length which are useful as diagnostic probes and primers as discussed herein. Of course, larger fragments of about 50–1550 nt in length, and more preferably at fragments least about 600 nt in length are also useful according to the present invention as are fragments corresponding to most, if not all, of the nucleotide sequence of the deposited cDNAs or as shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3). By a fragment at least 20 nt in length, for example, is intended fragments which include 20 or more contiguous bases from the nucleotide sequence of the deposited cDNAs or the nucleotide sequence as shown in FIG. 1C (SEQ ID NO: 1) or FIG. 1D (SEQ ID NO:3).
Preferred nucleic acid fragments of the present invention include nucleic acid molecules encoding: a polypeptide comprising the PTH1R receptor extracellular domain (predicted to constitute amino acid residues from about 25 to about 147 in FIG. 2A (or amino acid residues from about 25 to about 147 in SEQ ID NO:2)); a polypeptide comprising the PTH1R receptor transmembrane domain (predicted to constitute amino acid residues from about 148 to about 416 in FIG. 2A (or amino acid residues from about 148 to about 416 in SEQ ID NO:2)); and a polypeptide comprising the PTH1R receptor extracellular domain with all or part of the transmembrane domain deleted. As above with the leader sequence, the amino acid residues constituting the PTH1R receptor extracellular and transmembrane domains have been predicted. Thus, as one of ordinary skill would appreciate, the amino acid residues constituting these domains may vary slightly (e.g., by about 1 to about 15 amino acid residues) depending on the criteria used to define each domain.
Preferred nucleic acid fragments of the present invention also include nucleic acid molecules encoding: a polypeptide comprising the PTH3R receptor extracellular domain (predicted to constitute amino acid residues from about 22 to about 145 in FIG. 2B (or amino acid residues from about 22 to about 145 in SEQ ID NO:4); a polypeptide comprising the PTH3R receptor transmembrane domain (predicted to constitute amino acid residues from about 146 to about 402 in FIG. 2B (or amino acid residues from about 146 to about 402 in SEQ ID NO:4); and a polypeptide comprising the PTH3R receptor extracellular domain with all or part of the transmembrane domain deleted. As above with the leader sequence, the amino acid residues constituting the PTH3R receptor extracellular and transmembrane domains have been predicted by computer analysis. Thus, as one of ordinary skill would appreciate, the amino acid residues constituting these domains may vary slightly (e.g., by about 1 to about 15 amino acid residues) depending on the criteria used to define each domain.
Preferred nucleic acid fragments of the present invention also include nucleic acid molecules encoding epitope-bearing portions of the PTH1R or PTH3R receptor protein. As one skilled in the art would know, a nucleic acid sequence may be used to predict the polypeptide sequence encoded therein. Such information may then be used to predict antigenic determinants in the polypeptide that may be related to the corresponding polynucleotide regions encoding the antigenic determinants identified by the analysis. Methods for predicting the antigenic determinants of a polypeptide are well known in the art.
Methods for determining other such epitope-bearing portions of the PTH1R or the PTH3R protein are described in detail below.
In another aspect, the invention provides an isolated nucleic acid molecule comprising a polynucleotide which hybridizes under stringent hybridization conditions to a portion of the polynucleotide in a nucleic acid molecule of the invention described above, for instance, the cDNA clones contained in the bacterial hosts deposited with the ATCC as patent deposit PTA-915 or patent deposit PTA-916. By “stringent hybridization conditions” is intended overnight incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6),5×Denhardt's solution, 10% dextran sulfate, and 20 g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.
In another aspect, the invention provides an isolated nucleic acid molecule comprising a polynucleotide which hybridizes under low stringency hybridization conditions to a portion of the polynucleotide in a nucleic acid molecule of the invention described above, for instance, the cDNA clones contained in the bacterial hosts deposited with the ATCC as patent deposit PTA-915 or patent deposit PTA-916. By “low stringency hybridization conditions” is intended overnight incubation at 42° C. in a solution comprising: 30% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 g/ml denatured, sheared salmon sperm DNA, followed by washing the filters in a solution of 2×SSC or 1×SSC or 0.5×SSC at about 55° C. or 60° C. or 65° C.
By a polynucleotide which hybridizes to a “portion” of a polynucleotide is intended a polynucleotide (either DNA or RNA) hybridizing to at least about 15 nucleotides (nt), and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably about 30–70 nt of the reference polynucleotide. These are useful as diagnostic probes and primers as discussed above and in more detail below.
By a portion of a polynucleotide of “at least 20 nt in length,” for example, is intended 20 or more contiguous nucleotides from the nucleotide sequence of the reference polynucleotide (e.g., the deposited cDNAs or the nucleotide sequence as shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3).
Of course, a polynucleotide which hybridizes only to a poly A sequence (such as the 3′ terminal poly(A) tract of the PTH1R receptor cDNA shown in FIG. 1C (SEQ ID NO:1) or the 3′ terminal poly(A) tract of the PTH3R receptor cDNA shown in FIG. 1D (SEQ ID NO:3)), or to a complementary stretch of T (or U) resides, would not be included in a polynucleotide of the invention used to hybridize to a portion of a nucleic acid of the invention, since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone).
As indicated, nucleic acid molecules of the present invention which encode a PTH1R or PTH3R polypeptide may include, but are not limited to those encoding the amino acid sequence of the mature polypeptides, by themselves; the coding sequence for the mature polypeptides and additional sequences, such as those encoding the amino acid leader or secretory sequence, such as a pre-, or pro- or prepro-protein sequence; the coding sequence of the mature polypeptide, with or without the aforementioned additional coding sequences, together with additional, non-coding sequences, including for example, but not limited to introns and non-coding 5′ and 3′ sequences, such as the transcribed, non-translated sequences that play a role in transcription, mRNA processing, including splicing and polyadenylation signals, for example—ribosome binding and stability of mRNA; an additional coding sequence which codes for additional amino acids, such as those which provide additional functionalities. Thus, the sequence encoding the polypeptide may be fused to a marker sequence, such as a sequence encoding a peptide which facilitates purification of the fused polypeptide. In certain preferred embodiments of this aspect of the invention, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (Qiagen, Inc.), among others, many of which are commercially available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821–824 (1989), for instance, hexa-histidine provides for convenient purification of the fusion protein. The “HA” tag is another peptide useful for purification which corresponds to an epitope derived from the influenza hemagglutinin protein, which has been described by Wilson et al., Cell 37: 767 (1984). As discussed below, other such fusion proteins include the PTH1R receptor fused to Fc at the N- or C-terminus.
The present invention further relates to variants of the nucleic acid molecules of the present invention, which encode portions, analogs or derivatives of the PTH1R or PTH3R receptor. Variants may occur naturally, such as a natural allelic variant. By an “allelic variant” is intended one of several alternate forms of a gene occupying a given locus on a chromosome of an organism. Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985). Non-naturally occurring variants may be produced using art-known mutagenesis techniques.
Such variants include those produced by nucleotide substitutions, deletions or additions, which may involve one or more nucleotides. The variants may be altered in coding regions, non-coding regions, or both. Alterations in the coding regions may produce conservative or non-conservative amino acid substitutions, deletions or additions. Especially preferred among these are silent substitutions, additions and deletions, which do not alter the properties and activities of the PTH1R or PTH3R receptor or portions thereof. Also especially preferred in this regard are conservative substitutions.
Further embodiments of the invention include isolated nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 50%, 55%,60%, 65%,70%,75%,80%, 85%,90%, 91%, 92%, 93%,94%,95%,96%, 97%, 98%, or 99% identical to (a) a nucleotide sequence encoding the full-length PTH1R polypeptide having the complete amino acid sequence in SEQ ID NO:2, including the predicted leader sequence; (b) a nucleotide sequence encoding the polypeptide having the amino acid sequence in SEQ ID NO:2, but lacking the N-terminal methionine; (c) a nucleotide sequence encoding the mature PTH1R receptor (full-length polypeptide with the leader removed) having the amino acid sequence at positions from about 25 to about 536 in SEQ ID NO:2; (d) a nucleotide sequence encoding the full-length PTH1R polypeptide having the complete amino acid sequence including the leader encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916; (e) a nucleotide sequence encoding the mature PTH1R receptor having the amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916; (f) a nucleotide sequence encoding the PTH1R receptor extracellular domain; (g) a nucleotide sequence encoding the PTH1R receptor transmembrane domain; (h) a nucleotide sequence encoding the PTH1R receptor extracellular domain with all or part of the transmembrane domain deleted; and (i) a nucleotide sequence complementary to any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g) or (h).
Embodiments of the invention also include isolated nucleic acid molecules comprising a polynucleotide having a nucleotide sequence at least 50%, 55%, 60%, 65%,70%,75%,80%,85%, 90%,91%,92%,93%, 94%,95%, 96%, 97%, 98%, or 99% identical to (a) a nucleotide sequence encoding the full-length PTH3R polypeptide having the complete amino acid sequence in FIG. 2B (SEQ ID NO:4), including the predicted leader sequence; (b) a nucleotide sequence encoding the polypeptide having the amino acid sequence in SEQ ID NO:4, but lacking the N-terminal methionine; (c) a nucleotide sequence encoding the mature PTH3R receptor (full-length polypeptide with the leader removed) having the amino acid sequence at positions from about 22 to about 542 in SEQ ID NO:4; (d) a nucleotide sequence encoding the full-length PTH3R polypeptide having the complete amino acid sequence including the leader encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-915; (e) a nucleotide sequence encoding the mature PTH3R receptor having the amino acid sequence encoded by the cDNA deposited with the ATCC as patent deposit PTA-915; (f) a nucleotide sequence encoding the PTH3R receptor extracellular domain; (g) a nucleotide sequence encoding the PTH3R receptor transmembrane domain; (h) a nucleotide sequence encoding the PTH3R receptor extracellular domain with all or part of the transmembrane domain deleted; and (i) a nucleotide sequence complementary to any of the nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), or (h).
By a polynucleotide having a nucleotide sequence at least, for example, 95% “identical” to a reference nucleotide sequence encoding a PTH1R or PTH3R polypeptide is intended that the nucleotide sequence of the polynucleotide is identical to the reference sequence except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the reference nucleotide sequence encoding the PTH1R or PTH3R receptor. In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence may be deleted or substituted with another nucleotide, or a number of nucleotides up to 5% of the total nucleotides in the reference sequence may be inserted into the reference sequence. These mutations of the reference sequence may occur at the 5′ or 3′ terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular nucleic acid molecule is at least 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%,90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to, for instance, the nucleotide sequence shown in FIG. 1C or 1D or to the nucleotides sequence of the deposited cDNA clones can be determined conventionally using known computer programs such as the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711. Bestfit uses the local homology algorithm of Smith and Waterman, Advances in Applied Mathematics 2: 482–489 (1981), to find the best segment of homology between two sequences. When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence according to the present invention, the parameters are set, of course, such that the percentage of identity is calculated over the full length of the reference nucleotide sequence and that gaps in homology of up to 5% of the total number of nucleotides in the reference sequence are allowed.
The present application is directed to nucleic acid molecules at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the nucleic acid sequence shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3) or to the nucleic acid sequence of the deposited cDNAs, irrespective of whether they encode a polypeptide having PTH1R or PTH3R receptor activity. This is because even where a particular nucleic acid molecule does not encode a polypeptide having PTH1R or PTH3R receptor activity, one of skill in the art would still know how to use the nucleic acid molecule, for instance, as a hybridization probe or a polymerase chain reaction (PCR) primer. Uses of the nucleic acid molecules of the present invention that do not encode a polypeptide having PTH1R or PTH3R receptor activity include, inter alia, (1) isolating the PTH1R or PTH3R receptor gene or allelic variants thereof in a cDNA library; (2) in situ hybridization (e.g., “FISH”) to metaphase chromosomal spreads to provide precise chromosomal location of the PTH1R or PTH3R receptor gene, as described in Verma et al., Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New York (1988); and (3) Northern Blot analysis for detecting PTH1R or PTH3R receptor mRNA expression in specific tissues.
Preferred, however, are nucleic acid molecules having sequences at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the nucleic acid sequence shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3) or to the nucleic acid sequence of the deposited cDNA which do, in fact, encode a polypeptide having PTH1R or PTH3R receptor activity. By “a polypeptide having PTH1R or PTH3R receptor activity” is intended polypeptides exhibiting activity similar, but not necessarily identical, to an activity of the PTH1R or PTH3R receptor of the invention, as measured in a particular biological assay. For example, PTH1R or PTH3R receptor activity can be measured using competition binding experiments of labeled PTH or PTHrP to cells expressing the candidate PTH1R or PTH3R polypeptide as described in Treanor et al., Nature 382:80–83 (1996) or Jing et al., Cell 85: 1113–1124 (1996).
As demonstrated in Examples 3 and 4 herein, assays to address PTH1R and PTH3R function are well known in the art. Any cell line expressing the PTH1R or PTH3R receptor, or variants thereof, may be used to assay ligand binding and second messenger activation as described in Examples 3 and 4. Of course, due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the nucleic acid molecules having a sequence at least 95%, 96%, 97%, 98%, or 99% identical to the nucleic acid sequence of the deposited cDNAs or the nucleic acid sequence shown in FIG. 1C (SEQ ID NO:1) or FIG. 1D (SEQ ID NO:3) will encode a polypeptide “having PTH1R or PTH3R receptor activity.” In fact, since degenerate variants of these nucleotide sequences all encode the same polypeptide, this will be clear to the skilled artisan even without performing the above described comparison assay. It will be further recognized in the art that, for such nucleic acid molecules that are not degenerate variants, a reasonable number will also encode a polypeptide having PTH1R or PTH3R protein activity. This is because the skilled artisan is fully aware of amino acid substitutions that are either less likely or not likely to significantly effect protein function (e.g., replacing one aliphatic amino acid with a second aliphatic amino acid).
For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie, J. U. et al., “Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions,” Science 247:1306–1310 (1990), wherein the authors indicate that proteins are surprisingly tolerant of amino acid substitutions.
The invention also provides a method for the isolation of a nucleic acid molecule comprising: (a) selecting a fragment of SEQ ID NO:3 as a nucleic acid probe; (b) hybridizing said probe overnight to at least one test sequence by incubation at 42° C. in a solution of 30% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 g/ml denatured, sheared salmon sperm DNA; (c) removing nonhydridized probe by washing with a solution of 2×SSC or 1×SSC or 0.5×SSC at about 55° C. or 60° C. or 65° C.; and (d) identifying a target sequence bound by said probe; wherein said identified target sequence is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from the group consisting of: (e) a nucleotide sequence encoding the PTH3R receptor having the complete amino acid sequence at positions from about 1 to about 542 in (SEQ ID NO:4); (f) a nucleotide sequence encoding the PTH3R receptor having the amino acid sequence at positions from about 2 to about 542 in (SEQ ID NO:4); (g) a nucleotide sequence encoding the mature PTH3R receptor having the amino acid sequence at positions from about 22 to about 542 in (SEQ ID NO:4); (h) a nucleotide sequence encoding the PTH3R receptor having the complete amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-915; (i) a nucleotide sequence encoding the mature PTH3R receptor having the amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-915; (j) a nucleotide sequence encoding the PTH3R extracellular domain; (k) a nucleotide sequence encoding the PTH3R transmembrane domain; and (1) a nucleotide sequence complementary to any of the nucleotide sequences in (e), (f), (g), (h), (i), (j) or (k).
The invention also provides a method for the isolation of a nucleic acid molecule comprising: (a) selecting a fragment of SEQ ID NO:1 as a nucleic acid probe; (b) hybridizing said probe overnight to at least one test sequence by incubation at 42° C. in a solution of 30% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 g/ml denatured, sheared salmon sperm DNA; (c) removing nonhydridized probe by washing with a solution of 2×SSC or 1×SSC or 0.5×SSC at about 55° C. or 60° C. or 65° C.; and (d) identifying a target sequence bound by said probe; wherein said identified target sequence is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to a sequence selected from the group consisting of: (e) a nucleotide sequence encoding the PTH1R receptor having the complete amino acid sequence at positions from about 1 to about 536 in SEQ ID NO:2; (f) a nucleotide sequence encoding the PTH1R receptor having the amino acid sequence at positions from about 2 to about 536 in SEQ ID NO:2; (g) a nucleotide sequence encoding the mature PTH1R receptor having the amino acid sequence at positions from about 25 to about 536 in SEQ ID NO:2; (h) a nucleotide sequence encoding the PTH1R receptor having the complete amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916; (i) a nucleotide sequence encoding the mature PTH1R receptor having the amino acid sequence encoded by the cDNA deposited with the ATCC as patent deposit PTA-916; (j) a nucleotide sequence encoding the PTH1R extracellular domain; (k) a nucleotide sequence encoding the PTH1R transmembrane domain; and (1) a nucleotide sequence complementary to any of the nucleotide sequences in (e), (f), (g), (h), (i), (j) or (k).
Vectors and Host Cells
The present invention also relates to vectors which include the isolated DNA molecules of the present invention, host cells which are genetically engineered with the recombinant vectors, and the production of PTH1R or PTH3R polypeptides or fragments thereof by recombinant techniques.
The polynucleotides may be joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.
The DNA insert should be operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp and tac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination and, in the transcribed region, a ribosome binding site for translation. The coding portion of the mature transcripts expressed by the constructs will preferably include a translation initiating at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.
As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase or neomycin resistance for eukaryotic cell culture and tetracycline or ampicillin resistance genes for culturing in E. coli and other bacteria. Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS and Bowes melanoma cells; and plant cells. Appropriate culture mediums and conditions for the above-described host cells are known in the art.
Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from Qiagen; pBS vectors, Phagescript vectors, Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available from Stratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Other suitable vectors will be readily apparent to the skilled artisan.
Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986).
The polypeptide may be expressed in a modified form, such as a fusion protein, and may include not only secretion signals, but also additional heterologous functional regions. For instance, a region of additional amino acids, particularly charged amino acids, may be added to the N-terminus of the polypeptide to improve stability and persistence in the host cell, during purification, or during subsequent handling and storage. Also, peptide moieties may be added to the polypeptide to facilitate purification. Such regions may be removed prior to final preparation of the polypeptide. The addition of peptide moieties to polypeptides to engender secretion or excretion, to improve stability and to facilitate purification, among others, are familiar and routine techniques in the art. A preferred fusion protein comprises a heterologous region from immunoglobulin that is useful to solubilize proteins. For example, EP-A-O 464 533 (Canadian counterpart 2045869) discloses fusion proteins comprising various portions of constant region of immunoglobin molecules together with another human protein or part thereof. In many cases, the Fc part in a fusion protein is thoroughly advantageous for use in therapy and diagnosis and thus results, for example, in improved pharmacokinetic properties (EP-A 0232 262). On the other hand, for some uses it would be desirable to be able to delete the Fc part after the fusion protein has been expressed, detected and purified in the advantageous manner described. This is the case when Fe portion proves to be a hindrance to use in therapy and diagnosis, for example when the fusion protein is to be used as antigen for immunizations. In drug discovery, for example, human proteins, such as, hIL5-receptor has been fused with Fe portions for the purpose of high-throughput screening assays to identify antagonists of hIL-5. See, D. Bennett et al., Journal of Molecular Recognition, Vol. 8:52–58 (1995) and K. Johanson et al., The Journal of Biological Chemistry, Vol. 270, No. 16:9459–9471 (1995).
The PTH1R or PTH3R receptor can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography (“HPLC”) is employed for purification. Polypeptides of the present invention include naturally purified products, products of chemical synthetic procedures, and products produced by recombinant techniques from a prokaryotic or eukaryotic host, including, for example, bacterial, yeast, higher plant, insect and mammalian cells. Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. In addition, polypeptides of the invention may also include an initial modified methionine residue, in some cases as a result of host-mediated processes.
PTH1R and PTH3R Polypeptides and Fragments
The invention further provides an isolated PTH1R or PTH3R polypeptide having the amino acid sequence encoded by the deposited cDNAs, or the amino acid sequence in FIG. 2A (SEQ ID NO:2) or FIG. 2B (SEQ ID NO:4), or a peptide or polypeptide comprising a portion of the above polypeptides.
It will be recognized in the art that some amino acid sequences of the PTH1R or PTH3R receptor can be varied without significant effect of the structure or function of the protein. If such differences in sequence are contemplated, it should be remembered that there will be critical areas on the protein which determine activity. Thus, the invention further includes variations of the PTH1R or PTH3R receptor which show substantial PTH1R or PTH3R receptor activity or which include regions of PTH1R or PTH3R protein such as the protein portions discussed below. Such mutants include deletions, insertions, inversions, repeats, and type substitutions. As indicated above, guidance concerning which amino acid changes are likely to be phenotypically silent can be found in Bowie, J. U., et al., “Deciphering the Message in Protein Sequences: Tolerance to Amino Acid Substitutions,” Science 247:1306–1310 (1990).
Thus, the fragment, derivative or analog of the polypeptide of FIG. 2A (SEQ ID NO:2) or FIG. 2B (SEQ ID NO:4), or that encoded by the deposited cDNAs, may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues includes a substituent group, or (iii) one in which the mature polypeptide is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or (iv) one in which the additional amino acids are fused to the mature polypeptide, such as an IgG Fc fusion region peptide or leader or secretory sequence or a sequence which is employed for purification of the mature polypeptide or a proprotein sequence. Such fragments, derivatives and analogs are deemed to be within the scope of those skilled in the art from the teachings herein.
Of particular interest are substitutions of charged amino acids with another charged amino acid and with neutral or negatively charged amino acids. The latter results in proteins with reduced positive charge to improve the characteristics of the PTH1R or PTH3R protein. The prevention of aggregation is highly desirable. Aggregation of proteins not only results in a loss of activity but can also be problematic when preparing pharmaceutical formulations, because they can be immunogenic. (Pinckard et al., Clin Exp. Immunol. 2:331–340(1967); Robbins et al., Diabetes 36:838–845 (1987); Cleland et al. Crit. Rev. Therapeutic Drug Carrier Systems 10:307–377 (1993)).
The replacement of amino acids can also change the selectivity of binding to cell surface receptors. Ostade et al., Nature 361:266–268 (1993) describes certain mutations resulting in selective binding of TNF-α to only one of the two known types of TNF receptors. Thus, the PTH1R or PTH3R receptor of the present invention may include one or more amino acid substitutions, deletions or additions, either from natural mutations or human manipulation.
As indicated, changes are preferably of a minor nature, such as conservative amino acid substitutions that do not significantly affect the folding or activity of the protein (see Table 1).







TABLE 1





Conservative Amino Acid Substitutions.


















Aromatic
Phenylalanine




Tryptophan




Tyrosine



Hydrophobic
Leucine




Isoleucine




Valine



Polar
Glutamine




Asparagine



Basic
Arginine




Lysine




Histidine



Acidic
Aspartic Acid




Glutamic Acid



Small
Alanine




Serine




Threonine




Methionine




Glycine










Amino acids in the PTH1R or PTH3R protein of the present invention that are essential for function can be identified by methods known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, Science 244:1081–1085 (1989)). The latter procedure introduces single alanine mutations at every residue in the molecule. The resulting mutant molecules are then tested for biological activity such as receptor binding or in vitro proliferative activity. Sites that are critical for ligand-receptor binding can also be determined by structural analysis such as crystallization, nuclear magnetic resonance or photoaffinity labeling (Smith et al., J. Mol. Biol. 224:899–904 (1992) and de Vos et al. Science 255:306–312 (1992)).
The polypeptides of the present invention are preferably provided in an isolated form. By “isolated polypeptide” is intended a polypeptide removed from its native environment. Thus, a polypeptide produced and/or contained within a recombinant host cell is considered isolated for purposes of the present invention. Also intended as an “isolated polypeptide” are polypeptides that have been purified, partially or substantially, from a recombinant host cell. For example, a recombinantly produced version of the antimicrobial peptide polypeptide can be substantially purified by the one-step method described in Smith and Johnson, Gene 67:31–40 (1988).
The polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified. A recombinantly produced version of the PTH1R or PTH3R receptor can be substantially purified by the one-step method described in Smith and Johnson, Gene 67:31–40 (1988).
The polypeptides of the present invention also include the polypeptide encoded by the deposited PTH1R cDNA including the leader, the polypeptide encoded by the deposited the cDNA minus the leader (i.e., the mature protein), the polypeptide of FIG. 2A (SEQ ID NO:2) including the leader, the polypeptide of FIG. 2A (SEQ ID NO:2) minus the leader, the extracellular domain, the transmembrane domain, a polypeptide comprising amino acids about 1 to about 536 in SEQ ID NO:2, and a polypeptide comprising amino acids about 2 to about 536 in SEQ ID NO:2, as well as polypeptides which are at least 95% identical, still more preferably at least 96%, 97%, 98% or 99% identical to the polypeptides described above, and also include portions of such polypeptides with at least 30 amino acids and more preferably at least 50 amino acids.
The polypeptides of the present invention also include the polypeptide encoded by the deposited PTH3R cDNA including the leader, the polypeptide encoded by the deposited the cDNA minus the leader (i.e., the mature protein), the polypeptide of FIG. 2 (SEQ ID NO:4) including the leader, the polypeptide of FIG. 4 (SEQ ID NO:4) minus the leader, the extracellular domain, the transmembrane domain, a polypeptide comprising amino acids about 1 to about 542 in SEQ ID NO:4, and a polypeptide comprising amino acids about 2 to about 542 in SEQ ID NO:4, as well as polypeptides which are at least 95% identical, still more preferably at least 96%, 97%, 98% or 99% identical to the polypeptides described above, and also include portions of such polypeptides with at least 30 amino acids and more preferably at least 50 amino acids.
By a polypeptide having an amino acid sequence at least, for example, 95% “identical” to a reference amino acid sequence of a PTH1R or PTH3R polypeptide is intended that the amino acid sequence of the polypeptide is identical to the reference sequence except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the reference amino acid of the PTH1R or PTH3R receptor. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular polypeptide is at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to, for instance, the amino acid sequence shown in FIG. 2A (SEQ ID NO:2) or FIG. 2B (SEQ ID NO:4) or to the amino acid sequence encoded by deposited cDNA clones can be determined conventionally using known computer programs such the Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711). When using Bestfit or any other sequence alignment program to determine whether a particular sequence is, for instance, 95% identical to a reference sequence according to the present invention, the parameters are set, of course, such that the percentage of identity is calculated over the full length of the reference amino acid sequence and that gaps in homology of up to 5% of the total number of amino acid residues in the reference sequence are allowed.
The polypeptide of the present invention could be used as a molecular weight marker on SDS-PAGE gels or on molecular sieve gel filtration columns using methods well known to those of skill in the art.
As described in detail below, the polypeptides of the present invention can also be used to raise polyclonal and monoclonal antibodies, which are useful in assays for detecting PTH1R or PTH3R expression as described below or as agonists and antagonists capable of enhancing or inhibiting PTH1R or PTH3R receptor function. Further, such polypeptides can be used in the yeast two-hybrid system to “capture” PTH1R or PTH3R receptor binding proteins which are also candidate agonist and antagonist according to the present invention. The yeast two hybrid system is described in Fields and Song, Nature 340:245–246 (1989).
In another aspect, the invention provides a peptide or polypeptide comprising an epitope-bearing portion of a polypeptide of the invention. The epitope of this polypeptide portion is an immunogenic or antigenic epitope of a polypeptide described herein. An “immunogenic epitope” is defined as a part of a protein that elicits an antibody response when the whole protein is the immunogen. On the other hand, a region of a protein molecule to which an antibody can bind is defined as an “antigenic epitope.” The number of immunogenic epitopes of a protein generally is less than the number of antigenic epitopes. See, for instance, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998–4002 (1983).
As to the selection of peptides or polypeptides bearing an antigenic epitope (i.e., that contain a region of a protein molecule to which an antibody can bind), it is well known in that art that relatively short synthetic peptides that mimic part of a protein sequence are routinely capable of eliciting an antiserum that reacts with the partially mimicked protein. See, for instance, Sutcliffe, J. G., Shinnick, T. M., Green, N. and Learner, R. A. (1983) Antibodies that react with predetermined sites on proteins. Science 219:660–666. Peptides capable of eliciting protein-reactive sera are frequently represented in the primary sequence of a protein, can be characterized by a set of simple chemical rules, and are confined neither to immunodominant regions of intact proteins (i.e., immunogenic epitopes) nor to the amino or carboxyl terminals.
Antigenic epitope-bearing peptides and polypeptides of the invention are therefore useful to raise antibodies, including monoclonal antibodies, that bind specifically to a polypeptide of the invention. See, for instance, Wilson et al., Cell 37:767–778 (1984) at 777. Antigenic epitope-bearing peptides and polypeptides of the invention preferably contain a sequence of at least seven, more preferably at least nine and most preferably between at least about 15 to about 30 amino acids contained within the amino acid sequence of a polypeptide of the invention.
Thus, one skilled in the art will have the requisite knowledge to select antigenic epitope bearing regions from the polypeptides in FIG. 2A (SEQ ID NO:2) and FIG. 2B (SEQ ID NO:4).
The epitope-bearing peptides and polypeptides of the invention may be produced by any conventional means. For example, Houghten provides a general method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids Houghten, R. A., Proc. Natl. Acad. Sci. USA 82:5131–5135 (1985)). This “Simultaneous Multiple Peptide Synthesis (SMPS)” process is further described in U.S. Pat. No. 4,631,211 to Houghten et al. (1986).
As one of skill in the art will appreciate, PTH1R or PTH3R polypeptides of the present invention and the epitope-bearing fragments thereof described above can be combined with parts of the constant domain of immunoglobulins (IgG), resulting in chimeric polypeptides. These fusion proteins facilitate purification and show an increased half-life in vivo. This has been shown, e.g., for chimeric proteins consisting of the first two domains of the human CD4-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins (EPA 394,827; Traunecker et al., Nature 331:84–86 (1988)). Fusion proteins that have a disulfide-linked dimeric structure due to the IgG part can also be more efficient in binding and neutralizing other molecules than the monomeric PTH1R or PTH3R protein or protein fragment alone (Fountoulakis et al., J. Biochem 270:3958–3964 (1995)).
Diagnosis and Prognosis
It is believed that certain tissues in mammals with certain diseases and disorders express significantly decreased levels of the PTH1R or PTH3R receptor and mRNA encoding the PTH1R or PTH3R receptor when compared to a corresponding “standard” mammal, i.e., a mammal of the same species not having the disorder. Further, it is believed that enhanced levels of the PTH1R or PTH3R receptor can be detected in certain body fluids (e.g., sera, plasma, urine, and spinal fluid) from mammals with cancer when compared to sera from mammals of the same species not having the disorder. Thus, the invention provides a diagnostic method useful during diagnosis of diseases and disorders, for example, which involves assaying the expression level of the gene encoding the PTH1R or PTH3R receptor in mammalian cells or body fluid and comparing the gene expression level with a standard PTH1R or PTH3R receptor gene expression level, whereby an decrease in the gene expression level over the standard is indicative of certain disorders.
Where a diagnosis of a disorder has already been made according to conventional methods, the present invention is useful as a prognostic indicator, whereby patients exhibiting decreased PTH1R or PTH3R gene expression will experience a worse clinical outcome relative to patients expressing the gene at a higher level.
By “assaying the expression level of the gene encoding the PTH1R or PTH3R protein” is intended qualitatively or quantitatively measuring or estimating the level of the PTH1R or PTH3R protein or the level of the mRNA encoding the PTH1R or PTH3R receptor in a first biological sample either directly (e.g., by determining or estimating absolute protein level or mRNA level) or relatively (e.g., by comparing to the PTH1R or PTH3R protein level or mRNA level in a second biological sample).
Preferably, the PTH1R or PTH3R protein level or mRNA level in the first biological sample is measured or estimated and compared to a standard PTH1R or PTH3R protein level or mRNA level, the standard being taken from a second biological sample obtained from an individual not having the cancer. As will be appreciated in the art, once a standard PTH1R or PTH3R protein level or mRNA level is known, it can be used repeatedly as a standard for comparison.
By “biological sample” is intended any biological sample obtained from an individual, cell line, tissue culture, or other source which contains PTH1R or PTH3R protein or mRNA. Biological samples include mammalian body fluids (such as sera, plasma, urine, synovial fluid and spinal fluid) which contain PTH1R or PTH3R protein, and ovarian, prostate, heart, placenta, pancreas liver, spleen, lung, breast, neural, and umbilical tissue.
The present invention is useful for detecting disorders in mammals. In particular the invention is useful during diagnosis of diseases and disorders in mammals involving PTH1R or PTH3R receptor expression or function. Mutations that affect PTH1R or PTH3R sequence and/or expression levels of PTH1R or PTH3R could be diagnostic for patients with diseases or disorders of a developmental, physiological or neurological nature. Preferred mammals include monkeys, apes, cats, dogs, cows, pigs, horses, rabbits and humans. Particularly preferred are humans.
Total cellular RNA can be isolated from a biological sample using the single-step guanidinium-thiocyanate-phenol-chloroform method described in Chomczynski and Sacchi, Anal. Biochem. 162:156–159(1987). Levels ofmRNA encoding the PTH1R or PTH3R receptor are then assayed using any appropriate method. These include Northern blot analysis (Harada et al., Cell 63:303–312 (1990)), S1 nuclease mapping (Fujita et al., Cell 49:357–367 (1987)), the polymerase chain reaction (PCR), reverse transcription in combination with the polymerase chain reaction (RT-PCR) (Fujita et al., Cell 49:357–367(1987)), and reverse transcription in combination with the ligase chain reaction (RT-LCR).
Assaying PTH1R or PTH3R protein levels in a biological sample can occur using antibody-based techniques. For example, PTH1R or PTH3R protein expression in tissues can be studied with classical immunohistological methods (Jalkanen, M., et al., J. Cell. Biol. 101:976–985 (1985); Jalkanen, M., et al., J. Cell. Biol. 105:3087–3096 (1987)). Other antibody-based methods useful for detecting PTH1R or PTH3R receptor gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA).
Suitable labels are known in the art and include enzyme labels, such as glucose oxidase, and radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium (99mTc), and fluorescent labels, such as fluorescein and rhodamine, and biotin.
Agonists and Antagonists of the PTH1R or PTH3R
The present invention also provides a screening method for identifying compounds capable of enhancing or inhibiting a cellular response induced by the PTH1R or PTH3R receptor, which involves contacting cells which express the PTH1R or PTH3R receptor with the candidate compound, assaying a cellular response, and comparing the cellular response to a standard cellular response, the standard being assayed when contact is made in absence of the candidate compound; whereby, an increased cellular response over the standard indicates that the compound is an agonist and a decreased cellular response over the standard indicates that the compound is an antagonist.
In another aspect, a screening assay for agonists and antagonists is provided which involves determining the effect a candidate compound has on PTH or PTHrP binding to the PTH1R or PTH3R receptor. In particular, the method involves contacting the PTH1R or PTH3R receptor with a PTH or a PTHrP polypeptide and a candidate compound and determining whether PTH or PTHrP polypeptide binding to the PTH1R or PTH3R receptor is increased or decreased due to the presence of the candidate compound.
By “agonist” is intended naturally occurring and synthetic compounds capable of enhancing or potentiating PTH1R or PTH3R receptor response (e.g., signaling through the cAMP or inositol phosphate pathway). By “antagonist” is intended naturally occurring and synthetic compounds capable of inhibiting PTH1R or PTH3R receptor response (e.g., signaling through the cAMP or inositol phosphate pathway). Whether any candidate “agonist” or “antagonist” of the present invention can enhance or inhibit PTH1R or PTH3R receptor activity can be determined using art-known competition binding assays, including those described in more detail below.
One such screening procedure involves the use of melanophores which are transfected to express a receptor of the present invention. Such a screening technique is described in PCT WO 92/01810, published Feb. 6, 1992. Such an assay may be employed, for example, for screening for a compound which inhibits (or enhances) activation of the PTH1R or PTH3R receptor polypeptide of the present invention by contacting the melanophore cells which encode the receptor with both PTH or PTHrP as a ligand and the candidate antagonist (or agonist). Inhibition or enhancement of the signal generated by the ligand indicates that the compound is an antagonist or agonist of the ligand/receptor signaling pathway.
Other screening techniques include the use of cells which express the receptor (for example, transfected CHO cells) in a system which measures extracellular pH changes caused by receptor activation, for example, as described in Science 246:181–296 (October 1989). For example, compounds may be contacted with a cell which expresses the PTH1R or PTH3R receptor polypeptide of the present invention and a second messenger response, e.g., signal transduction or pH changes, may be measured to determine whether the potential compound activates or inhibits the receptor.
Another such screening technique involves introducing RNA encoding the PTH1R or PTH3R receptor into Xenopus oocytes to transiently express the receptor. The receptor oocytes may then be contacted with the receptor ligand and a compound to be screened, followed by detection of inhibition or activation of a calcium signal in the case of screening for compounds which are thought to inhibit activation of the receptor.
Another screening technique involves expressing in cells a construct wherein the receptor is linked to a phospholipase C or D. Such cells include endothelial cells, smooth muscle cells, embryonic kidney cells, etc. The screening 110 may be accomplished as hereinabove described by detecting activation of the PTH1R or PTH3R receptor or inhibition of activation of the PTH1R or PTH3R receptor from the phospholipase signal.
Another method involves screening for compounds which inhibit activation of the receptor polypeptide of the present invention antagonists by determining inhibition of binding of labeled ligand to cells which have the receptor on the surface thereof. Such a method involves transfecting a eukaryotic cell with DNA encoding the PTH1R or PTH3R receptor such that the cell expresses the receptor on its surface and contacting the cell with a compound in the presence of a labeled form of a known ligand. The ligand can be labeled, e.g., by radioactivity. The amount of labeled ligand bound to the receptors is measured, e.g., by measuring radioactivity of the receptors. If the compound binds to the receptor as determined by a reduction of labeled ligand which binds to the receptors, the binding of labeled ligand to the receptor is inhibited.
Further screening assays for agonist and antagonist of the present invention are described in Tartaglia, L. A., and Goeddel, D. V., J. Biol. Chem. 267(7):4304–4307(1992).
Thus, in a further aspect, a screening method is provided for determining whether a candidate agonist or antagonist is capable of enhancing or inhibiting a cellular response to PTH or PTHrP. The method involves contacting cells which express the PTH1R or PTH3R polypeptide with a candidate compound and the PTH or PTHrP ligand, assaying a cellular response, and comparing the cellular response to a standard cellular response, the standard being assayed when contact is made with the ligand in absence of the candidate compound, whereby an increased cellular response over the standard indicates that the candidate compound is an agonist of the ligand/receptor signaling pathway and a decreased cellular response compared to the standard indicates that the candidate compound is an antagonist of the ligand/receptor signaling pathway. By “assaying a cellular response” is intended qualitatively or quantitatively measuring a cellular response to a candidate compound and/or PTH or PTHrP (e.g., determining or estimating an increase or decrease in cell proliferation or tritiated thymidine labeling). By the invention, a cell expressing the PTH1R or PTH3R polypeptide can be contacted with either an endogenous or exogenously administered PTH or PTHrP.
Agonist according to the present invention include naturally occurring and synthetic compounds such as, for example, PTH or PTHrP peptide fragments, or other known compounds that behave as PTH or PTHrP agonist. Preferred agonist include chemotherapeutic drugs such as, for example, cisplatin, doxorubicin, bleomycin, cytosine arabinoside, nitrogen mustard, methotrexate and vincristine. Others include ethanol and β-amyloid peptide. (Science 267:1457–1458 (1995)). Further preferred agonist include polyclonal and monoclonal antibodies raised against the PTH1R or PTH3R polypeptide, or a fragment thereof.
Antagonist according to the present invention include naturally occurring and synthetic compounds such as, for example, the CD40 ligand, neutral amino acids, zinc, estrogen, androgens, viral genes (such as Adenovirus E1B, Baculovirus p35 and JAP, Cowpox virus crmA, Epstein-Barr virus BHRF1, LMP-1, African swine fever virus LMW5-HL, and Herpesvirus yl 34.5), calpain inhibitors, cysteine protease inhibitors, and tumor promoters (such as PMA, Phenobarbital, and α-Hexachlorocyclohexane).
Other potential antagonists include antisense molecules. Antisense technology can be used to control gene expression through antisense DNA or RNA or through triple-helix formation. Antisense techniques are discussed, for example, in Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988). Triple helix formation is discussed in, for instance Lee et al., Nucleic Acids Research 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251:1360 (1991). The methods are based on binding of a polynucleotide to a complementary DNA or RNA.
For example, the 5′ coding portion of a polynucleotide that encodes the mature polypeptide of the present invention may be used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription thereby preventing transcription and the production of the receptor. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into receptor polypeptide. The oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the receptor.
Further antagonist according to the present invention include soluble forms of PTH1R or PTH3R fragments that include the ligand binding domain from the extracellular region of the full length receptor. Such soluble forms of the receptor, which may be naturally occurring or synthetic, antagonize PTH1R or PTH3R mediated signaling by competing with the cell surface PTH1R or PTH3R for binding to PTH or PTHrP. These are preferably expressed as dimers or trimers, since these have been shown to be superior to monomeric forms of soluble receptor as antagonists, e.g., IgGFc-PTH1R or IgGFc-PTH3R receptor family fusions.
Modes of Administration
It will be appreciated that conditions caused by a decrease in the standard or normal level of PTH1R or PTH3R receptor activity in an individual, can be treated by administration of PTH1R or PTH3R protein. Thus, the invention further provides a method of treating an individual in need of an increased level of PTH1R or PTH3R receptor activity comprising administering to such an individual a pharmaceutical composition comprising an effective amount of an isolated PTH1R or PTH3R polypeptide of the invention, effective to increase the PTH1R or PTH3R receptor activity level in such an individual.
The invention also relates to a method of treating an individual in need of an increased level of PTH 1R or PTH3R receptor activity comprising administering to such an individual a pharmaceutical composition comprising an effective amount of an agonist for PTH1R or PTH3R. The invention further relates to a method of treating an individual in need of a decreased level of PTH1R or PTH3R receptor activity comprising administering to such an individual a pharmaceutical composition comprising an effective amount of an antagonist for PTH1R or PTH3R.
As a general proposition, the total pharmaceutically effective amount of PTH1R or PTH3R polypeptide or its agonists or antagonists administered parenterally per dose will be in the range of about 1 μg/kg/day to 10 mg/kg/day of patient body weight, although, as noted above, this will be subject to therapeutic discretion. More preferably, this dose is at least 0.01 mg/kg/day, and most preferably for humans between about 0.01 and 1 mg/kg/day for the hormone. If given continuously, the PTH1R or PTH3R polypeptide is typically administered at a dose rate of about 1 μg/kg/hour to about 50 μg/kg/hour, either by 1–4 injections per day or by continuous subcutaneous infusions, for example, using a mini-pump. An intravenous bag solution may also be employed.
Pharmaceutical compositions containing the PTH1R or PTH3R polypeptide(s)of the invention or its agonists or antagonsits may be administered orally, rectally, parenterally, intracistemally, intravaginally, intraperitoneally, topically (as by powders, ointments, drops or transdermal patch), bucally, or as an oral or nasal spray. By “pharmaceutically acceptable carrier” is meant a non-toxic solid, semisolid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. The term “parenteral” as used herein refers to modes of administration which include intravenous, intramuscular, intraperitoneal, intrasternal, subcutaneous and intraarticular injection and infusion.
Chromosome Assays
The nucleic acid molecules of the present invention are also valuable for chromosome identification. The sequence is specifically targeted to and can hybridize with a particular location on an individual human chromosome. The mapping of DNAs to chromosomes according to the present invention is an important first step in correlating those sequences with genes associated with disease.
In certain preferred embodiments in this regard, the cDNA herein disclosed is used to clone genomic DNA of a PTH1R or PTH3R receptor gene. This can be accomplished using a variety of well known techniques and libraries, which generally are available commercially. The genomic DNA then is used for in situ chromosome mapping using well known techniques for this purpose. In addition, in some cases, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15–25 bp) from the cDNA. Computer analysis of the 3′ untranslated region of the gene is used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers are then used for PCR screening of somatic cell hybrids containing individual human chromosomes.
Fluorescence in situ hybridization (“FISH”) of a cDNA clone to a metaphase chromosomal spread can be used to provide a precise chromosomal location in one step. This technique can be used with probes from the cDNA as short as 50 or 60 bp. For a review of this technique, see Verma et al., Human Chromosomes: A Manual Of Basic Techniques, Pergamon Press, New York (1988).
Once a sequence has been mapped to a precise chromosomal location, the physical position of the 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 on-line through Johns Hopkins University, Welch Medical Library. The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes).
Next, it is necessary to determine the differences in the cDNA or genomic sequence between affected and unaffected individuals. If a mutation is observed in some or all of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease.
Having generally described the invention, the same will be more readily understood by reference to the following examples, which are provided by way of illustration and are not intended as limiting.
EXAMPLES
Example 1
Isolation of Genomic DNA Clones Encoding the Zebrafish PTH1R and a novel type-3 receptor, PTH3R
Using zebrafish genomic DNA and several degenerate forward and reverse primers (FIG. 1), two distinct products of approximately 200 and 840 bp, respectively were obtained under stringent conditions. Forward (For) and reverse (Rev) degenerate primers (synthesized by the MGH Polymer core facility) for nested PCR (nPCR) were based on previously isolated mammalian and frog PTH1R sequences. Primers were located in exon M6/7 which encodes in mammals the third extracellular loop and the amino-terminal portion of transmembrane (TM) helix 7, and exon M7 which encodes the carboxy-terminal portion of TM7 and the beginning of the intracellular tail (Kong, et al., (1994); Schipani, et al., (1995)) (FIG. 1).
The primers for the first PCR reaction were the following: For M6a (5′TTYGGIGTSCAYTAYATHGTVTT; (SEQ ID NO:26) 576-fold degenerate), or For M6b (5′GTSYTBRTGCCICTHYTYGG; (SEQ ID NO:6) 1152-fold degenerate), and Rev M7 (CTCDCCATTRCAGWARCAGTADAT; (SEQ ID NO:7) 72-fold degenerate) (FIG. 1). PCR was performed using 1 mg of zebrafish (Danio rerio) genomic DNA, Gibco Taq (5 units), and the following PCR profile [initial denaturation at 95° for 3 min, (denature at 94° for 1 min, anneal at 50° for 1 min, and polymerize at 72° for 4 or 6 min) for 35 cycles] on an MJ research thermal cycler (Watertown, Mass.). nPCR was performed using 2 μl of a 1:100 dilution of the initial PCR product with a degenerate nested primer Rev M7#2 (5′GTADATRATDGMMACAAARAADCC; (SEQ ID NO:8) 432-fold degenerate), and either For M6a or For M6b using the same PCR profile as before (FIG. 1). nPCR products were identified on a 1.5% agarose gel with ethidium bromide, and DNA species of approximately 210 bp and 850 bp were excised, spun through a spin column (Bio 101, La Jolla, Calif.), ethanol precipitated overnight [( 1/10 vol of 3M sodium acetate was added, 2 vol of ethanol, 1 μl of glycogen (Pharmacia, Uppsala, Sweden)], and ligated into pGEM-T (Promega, Madison, Wis.). After transformation of competent DH5a E. coli cells (Gibco, Grand Island, N. Y.), plasmid DNA from single colonies was purified using standard protocols, and sequenced by 33P cycle sequencing (Amersham, Arlington Heights, Ill.) on an 8M urea 6% polyacrylamide field gradient gel (Rubin et al, 1998). The DNA sequences, from the nested PCRs using For M6a or For M6b, were analyzed by the GCG package program (GCG, Univ. WI) and subsequently refered to as zPTH1R(TM6/7)/GEM-T and zPTH3R(TM6/7)/GEM-T, respectively.
Nucleotide sequence analysis revealed that both clones showed significant homology at their 5′ and 3′ ends with the hPTH1R (78% and 73% identity, respectively). While clone #1, zPTH1R(TM6/7), contained 84 bp of intronic sequence (compared to 81 bp of the hPTH1R) (Schipani, et al., (1995)), clone #2, zPTH3R(TM6/7), contained an intron of more than 700 bp. These findings indicated that portions of two distinct genes had been isolated which both share higher homology with PTH1R than with PTH2R (64% and 70% identity, respectively).
Example 2
Isolation of Partial cDNA Clones Encoding zPTH1R and zPTH3R
Total RNA from adult zebrafish was isolated as previously described (Rubin et al., (1999)) and used as a template for RT-PCR (Gibco). For and Rev primers for RT-PCR were based on either zPTH1R or zPTH3R genomic DNA sequences corresponding to the mammalian exons M6/7 and M7, zPTH1R(TM6/7)/GEM-T and zPTH3R(TM6/7)/GEM-T, respectively (FIG. 1). Reverse transcription (RT) was performed using Superscript II RNAase H− reverse transcriptase and 5 μg total RNA at 42° C. with zPTH1R/Rev 6(1) (5′GCATTTCATAATGCATCTGGATTTG) (SEQ ID NO:9), or zPTH3R/Rev 6(1) (5′CTGTGAAGAATTGAAGAGCATCTC) (SEQ ID NO: 10), respectively. PCR, using the For 313 (5′ACMAACTACTAYTGGATYCTGGTG (SEQ ID NO:11); 8-fold degenerate) and either of the two Rev 6(1) primers was performed using Gibco Taq (5 units) and the following PCR profile [initial denaturation at 95° for 3 min, (denature at 94° for 1 min, anneal at 56° for 1 min, and polymerize at 72° for 2 min) for 35 cycles]. nPCR was performed using 2 μl of a 1:100 dilution from the initial zPTH1R or zPTH3R RT-PCR product, and either zPTH1R/Rev 6(2) (5′AGAAACTTCTGTGTAAGGCATCGC) (SEQ ID NO: 12) or zPTH3R/Rev 6(2) (5′ AAGAGCCATGAACAGCATGTAATG) (SEQ ID NO:13), and the For 313 primer using the previous PCR profile except for 35 cycles.
zPTH1R and zPTH3R PCR products were identified on a 1.5% agarose gel with ethidium bromide, cDNA species of approximately 450 bp were cloned, as described above, into pGEM-T to yield zPTH1R(TM3/6)/pGEMT and zPTH3R(TM3/6)/pGEMT, respectively.
Example 3
Isolation of Full-Length cDNAs Encoding the zPTH1R
RT-PCR using For313 and primers specific for zPTH1R(TM6/7) produced a 450 bp cDNA, zPTH1R(TM3/6), corresponding to TM3 through TM6 of the mammalian PTH1R. Subsequently, 5 ′ and 3 ′ RACE reactions were performed to generate overlapping sequences, and a full-length zPTH1R clone was constructed using a unique MfeI endonuclease restriction site (FIG. 1).
5′ and 3′ RACE reactions (Gibco) were performed using total RNA, and primers based on zPTH1R(TM3/6)/pGEMT nucleotide sequence. RT for 5′ RACE was performed, as described above, except that Rev 6(2) was used. The first 5 ′RACE PCR was performed using Rev 6(3) (5′GAAGACTATGTAGTGAACACCGAA) (SEQ ID NO:14), Gibco Taq (2.5 units) and the following PCR profile [initial denaturation at 95° for 3 min, (denature at 94° for 1 min, anneal at 55° for 1 min, and polymerize at 720 for 2 min) for 7 cycles, followed by 28 cycles with annealing at 64°. The first nPCR was performed using 5 μl of a 1:100 dilution from the previous PCR, Rev TM5 primer (5′ATATTGTTGTCTGGTGTCACATCT) (SEQ ID NO: 15), (KlenTaq, 5.0 units) (Clontech, Calif.), and the following PCR profile [initial denaturation at 95° for 3 min, [(denature at 94° for 1 min, anneal at 62° for 1 min, and polymerize at 72° for 2 min) for 35 cycles} with a final extension of 10 min at 72°]. A second nPCR was performed using 5 μl of a 1:100 dilution from the first nPCR, Rev 4×primer (5′CGCATTTGTTTCTCGAAGTTTTGTTGC) (SEQ ID NO:16), Gibco Taq (5.0 units) and the same PCR profile as the first NPCR. The second nPCR products were purified as described above and ligated into pGEM-T EASY (Promega) to yield zPTH1R(5′)/pGEMTeasy, for transformation of TOP 10 E. coli cells (Invitrogen).
For 3′ RACE, RT was performed as before but with an oligo-dT anchor primer (Gibco). PCR was performed using the For TM3 primer (5′ATCTTCATGACCTTCTTCTCAGAC) (SEQ ID NO:17), Gibco Taq (2.5 units) and the following profile [initial denaturation at 95° for 3 min, [(denature at 94° for 1 min, anneal at 64° for 1 min, and polymerize at 72° for 3 min) for 35 cycles} with a final extension of 10 min at 72°]. nPCR was performed using the previous PCR profile with 5 μl of a 1:100 dilution from the previous PCR, and For 4(1) (5′AGGAAGTACCTCTGGGGCTTCA) (SEQ ID NO:18). The 3′ RACE nPCR products were purified and cloned to yield zPTH1R(3′)/pGEMTeasy.
Midiprep DNA of zPTH1R(5′)/pGEMTeasy and zPTH1R(3′)/pGEMTeasy were digested with Mfe I and Nde I (New England Biolabs, Beverly, Mass.), and a 1.0 Kb fragment from zPTH1R(3′) was ligated into an approximately 4.5 Kb fragment from ZPTH1R(5 ′)/pGEMTeasy to yield the full length zPTH1R clone, zPTH1R(FL)/pGEMTeasy. The zPTH1R(FL)/pGEMTeasy plasmid DNA was digested with EcoRI and SacI, and cloned into the corresponding sites in pGEM-3 (Promega) to yield zPTH1R(FL)/pGEM3. Subsequently, an EcoRI/SphI fragment, from the insert of zPTH1R(FL)/pGEM3 which comprises the entire coding region, of the zPTH1R was cloned into the corresponding sites of pcDNAI/Amp (Invitrogen) to yield zPTH1R(FL)/pcDNAI/Amp (zPTH1R).
The 5′ RACE reactions generated two PCR products which contained an identical Kozak sequence and coding region (including the putative signal sequence) but varied in the length of the 5′ UT; 5′RACE#29 was 149 bp and 5′RACE#25 was 391 bp. Both clones, zPTH1R#25 and zPTH1R#29, were characterized by radioligand assay, total IP generation, and cAMP accumulation.
The amino acid sequence encoded by zPTH1R cDNA (536 residues, FIG. 2A) showed highest sequence homology to the frog and mammalian PTH1Rs (Bergwitz, et al., (1998); Kong, et al., (1994)). The overall amino acid sequence homology with the hPTH1R was 76% but only 68% when compared to the hPTH2R. Similar to the mammalian PTH1Rs, the 3′ non-coding region of zPTH1R did not contain a typical polyadenylation signal sequence, however, an imperfect sequence was found (TATAAA) 49 bp upstream of the poly A(n) tail.
Example 4
Isolation of Full-Length cDNAs Encoding the zPTH3R
The genomic clone, zPTH3R(TM6/7), contained, at the 5′ and 3′ end, nucleotide sequences which were similar to but distinct from zPTH1R and zPTH2R, and contained approximately 700 bp, rather than 84 bp, of intronic sequence. This information indicated that portions of a novel gene had been isolated, subsequently refered to as zPTH3R. RT-PCR using For313 and primers specific for zPTH3R(TM6/7) produced a 450 bp cDNA clone, zPTH3R(TM3/6), which encodes TM3 through TM6 of the zPTH3R.
A zebrafish 1 gtl 1 cDNA library (Clontech) was screened by plaque hybridization using a 450 bp 32P-radiolabeled cDNA probe which was generated by PCR from zPTH3R(TM3/6)/pGEMT. Filters containing 1.5×106 pfu were hybridized (42° for 18 hrs) in 50% formamide (Rubin et al., 1999), and washes were performed for 30 min each at RT, 50°, and at 55°, respectively, with 1×SSC/0.1% SDS. Autoradiography was performed for 5 days at −70° with a DuPont Cronex intensifying screen and Kodak XAR film. A single phage was plaque-purified and subcloned into the EcoRI site of pcDNAI/Amp using the λ TRAP phage kit (Clontech) to yield zeb3-3′/pcDNAI/Amp.
5′ RACE reactions (Gibco) were performed as above using three successive reverse zPTH3R primers [TM1 (5′ GAAGAGGTGGATGTGGATGTAGTT) (SEQ ID NO:19), G (5′ GCAGTGGAGACGTTTGAAATA) (SEQ ID NO:20), and E3 (5′ CCAGTTACCTGATGCATCACAGTG) (SEQ ID NO:21)]. The cDNA products were ligated to pGEMT-EASY (yielding zeb3-5′/pGEMT), minipreped, and their sequences analysed for homology to the known PTH receptors using GCG. Inserts which were determined to contain a nucleotide sequence with homology to the signal sequence of the mammalian PTH1Rs were ligated into zeb3-3′/pcDNAI/Amp using sites for BamHI, ApaLI, and NotI to yield zPTH3R(FL)/pcDNAI/Amp (zPTH3R).
From 1.5×106 screened PFUs, a single phage clone was identified and the 2.5 Kb insert was subcloned to yield zeb3-3′/pcDNAI/Amp. Sequence analysis showed that the clone was closely related to the known PTH1Rs from the region corresponding to the mammalian exon E1 through the carboxy-terminal region encoded by exon T (Kong, et al., (1994)). However, the cDNA portion encoding the amino-terminal, extracellular domain and most of the 3′ untranslated region immediately following the termination codon were missing. 5′RACE on total zebrafish RNA revealed the presence of several putative splice variants which is similar to the findings with the zPTH2R (Rubin et al., (1999)). Seven of the ten zeb3-5′ clones were identified as containing cDNA sequences similar to the mammalian exons E3 and E1, which encode portions of the amino-terminal extracellular domain of the PTH1Rs. These clones also contained a Kozak sequence and a nucleotide sequence with homology to the signal peptide sequence found in the mammalian PTH1Rs (Kong, et al., (1994); Schipani, et al., (1995)). Three other zeb3-5′ clones, which also contained the E3 and E1 equivalent, had different 5′ ends and could therefore represent putative splice variants. Similar to the zPTH2R (Rubin et al., (1999)) and the human PTH1R (Joun et al. (1997), Bettoun et al., (1997)), one of these zPTH3R putative splice variants lacked a signal peptide sequence but did contain an initiator AUG two codons upstream of the exon E1 equivalent. The second putative splice variant lacked a Kozak sequence, an initiator AUG, and contained a highly charged sequence upstream of the equivalent of E1 which is unlikely to represent a signal peptide. Only those clones which contained a Kozak sequence, an inframe AUG, and a 5′ coding region with homology to the zPTH1R, were ligated into the ApaLI site of zeb3-3′/pcDNAI/Amp to yield the full-length zPTH3R (FIG. 1).
Overall, the sequence encoded by this novel receptor (542 residues, FIG. 2B) shared 66% AA similarity and 59% AA identity with zPTH1R, but only 55% similarity with the zPTH2R. Similar to the frog PTH1Rs, zPTH1R and zPTH3R lacked the equivalent of the cDNA encoded by exon E2, suggesting that the appearance of this non-essential exon represents a mammalian evolutionary innovation (Lee, et al., (1994)).
In contrast to this mammalian E2 apomorphy, zPTH1R and zPTH3R contain the same eight extracellular cysteines as all known mammalian and non-mammalian members of this family of G protein-coupled receptors as well as several other “signature residues”. However, there are differences in the number of consensus sequences (N-X-S or N-X-T) for potential N-glycosylation between zPTH1R and zPTH3R; only two are conserved for all zebrafish PTH receptors (FIG. 2C). Furthermore, analysis of the intracellular tail residues indicates that this region has a higher rate of sequence variation between PTH receptor subtypes and was therefore used for further comparison (Table 2). For example, the homology between zPTH1R and hPTHlR in this region is 56%, which is similar to the 58% AA similarity for zPTH2R and hPTH2R. In contrast, the homology between the tail regions of zPTH3R and hiPTH1R is 38%, and 28% when compared to hPTH2R (Table 2). The zPTH3R was therefore identified as a novel member within the PTH/PTHrP receptor family.
Example 5
Functional characterization of zPTH1R and zPTH3R in COS-7 cells
Plasmid DNAs encoding the two full length ZPTH1Rs (#25 and #29) and the zPTH3R were transiently expressed in COS-7 cells. COS-7 African green monkey kidney cells (approximately 200,000 cells/well in a 24-well plate) were cultured and transfected with plasmid DNA (200 ng/well) as described (Rubin et al., (1998)). After transfection, cells were cultured for 72 hrs at 37° with daily exchanges of medium, followed by an additional 24 hrs at 33° (Gardella et al., (1997)) until they were functionally evaluated after 96 hrs.
Radioligand studies with COS-7 cells expressing either zPTH1R or zPTH3R were performed as described using either 125I-labeled [Nle8,21,Tyr34]rPTH-(1–34)amide (rPTH) (SEQ ID NO:22) or 125I-labeled [Tyr36]hPTHrP-(1–36)amide (PTHrP) (SEQ ID NO:23), and increasing concentrations of either [Tyr34]hPTH(1–34)amide (PTH) (SEQ ID NO:24), or [Tyr36]hPTHrP(1–36)amide (PTHrP) (SEQ ID NO:25) (Bergwitz et al., (1997)). Peptides were synthesized by the MGH polymer core facility as described (Gardella et al., (1996)). Specific binding was calculated by subtracting radioligand binding in the presence of excess unlabeled peptide from the total binding. All points represent mean±S.E.M. of two to three replicates from two or more independent experiments. IC50 values (dose of a competing ligand which resulted in 50% inhibition of radioligand binding) were calculated as previously described (Gardella et al., (1996)).
In order to assess agonist-dependent cAMP accumulation of COS-7 cells expressing zPTH1R and zPTH3R, experiments were done in 24-well plates with COS-7 cells stimulated in the presence of increasing concentrations of either PTH or PTHrP, and intracellular cAMP was determined as described (Bergiwtz et al.,(1998)). EC50 values were determined as previously described (Gardella et al., (1996)).
In order to determine total inositol phosphate turnover for COS-7 cells expressing zPTH1R, zPTH3R, and hPTH1R, cells were grown in 6-well plates with COS-7 cells (approximately 200,00 cells/well transfected with either 1 μg/well of zPTH1R, zPTH3R, or hPTH 1R (stina)). Cells were cultured for 3 days inDMEM/7% fetal bovine serum (FBS) at 37° C. with daily exchanges of medium. The cells were then preloaded with 3 μCi/ml myo-[3H]inositol (New England Nuclear, Boston, Mass.) in inositol-free DMEM (Gibco)/7% FBS (33° C. for 18 hr). The following day, plates were rinsed and then incubated with 10−6 M of either PTH, PTHrP in DMEM/0.1% BSA, or with DMEM/0.1% BSA alone (40 min at 37° C.), in the presence of 30 mM LiCl. Total inositol phosphate (IPs) were isolated by anion exchange column chromatography as previously described (Iida-Klein et al., (1994 and 1995)), and 1 ml of the eluate (1⁄8th of total) was counted in a liquid scintillation counter (model LS 60001C, Beckman, Fullerton, Calif.). All points represent mean±S.E.M. of two to three replicates from two or more independent experiments.
Both zPTH1R clones showed high affinity binding of radiolabeled rPTH and PTHrP (Table 2, FIG. 4). Apparently, due to the shorter 5′ UT, zPTH1R#29 showed in comparison to #25 slightly higher expression levels and higher maximal cAMP accumulation (101.6 pmole/well for hPT1rP and 106.2 pmole/well for hPTH versus 92.4 pmole/well for hPTHrP and 90.4 pmole/well for hPTH; see Table 2), but otherwise both clones were indistinguishable. Only the functional data for zPTH1R#29 are therefore presented (FIG. 3, Table 3). Interestingly, zPTH3R showed a higher specific binding for radiolabeled PTHrP than rPTH. Furthermore, the zPTH3R showed a higher apparent Kd for PTHrP than PTH (approximately 3 nM versus approximately 100 nM, respectively). These results indicate that zPTH3R preferentially interacts with PTHrP.
Similar to these binding data, COS-7 cells expressing the zPTH1R showed very similar EC50s for cAMP accumulation in response to either PTH or PTHrP which is similar to the findings with mammalian PTH1Rs (EC50: 0.8±0.03 nM for PTH and 0.3±0.04 nM for PTHrP, Table 2). The zPTH3R showed a higher maximal cAMP accumulation (285.4 nM for PTH and 227.4 for PTHrP nM), but in contrast to the zPTH1R, zPTH3R showed a reduced efficacy for PTH (EC50s: 5.98±0.24 nM for PTH and 0.49±0.17 nM for PTHrP, Table 2, FIG. 4). Furthermore, in addition to being more efficiently activated by PTHrP, the zPTH3R showed a significant activation at 10−11 M (FIG. 4). These results confirmed the radioreceptor studies which had indicated that the zPTH3R interacts preferentially with PTHrP.
Similar to the mammalian PTH1Rs, COS-7 cells expressing the zPTH1R showed an equivalent increase of IP accumulation (2-fold) when stimulated with either PTH or PTHrP. In contrast, despite higher expression levels, no IP accumulation was detectable when challenged with either ligand (FIG. 5). The lack of signaling through this second messenger may be related to significant structural alterations in the second intracellular loop of zPTH3R (FIG. 4). Previous studies with the rat PTH1R have shown that this portion of the receptor is important for IP signaling, since replacement of some residues in this “EKKY” cassette either impaired or abolished phospholipase C activation. While the ZPTH1R contains a conserved DRKY sequence instead of the mammalian EKKY, the corresponding AA residues of the zPTH3R are DKNC (FIG. 3). The two most important residues are therefore altered in the novel receptor which could explain the signaling selectivity of the zPTH3R. The zPTH3R is therefore a naturally occurring PTH/PTHrP receptor which appears to be incapable of signaling through IP.
Example 6
Southern Blot Analysis of Zebrafish Genomic DNA
To confirm that zPTH1R and zPTH3 Rare encoded by distinct genes, three infrequently cutting restriction endonucleases were utilized to digest zebrafish genomic DNA to completion (data not shown). Approximately 16 μg of zebrafish genomic DNA was digested to completion with either BamHI, EcoRI, or HindIII, split into two equal aliquots for electrophoresis through a 0.8% agarose gel containing ethidium bromide, and transferred onto a nitrocellulose membrane (MSI, Westborough, Mass.). After baking in vacuo for 2 hr at 80° C., the blots were hybridized in 50% formamide (42° for 18 hrs) with PCR-generated 32p-labeled probes (Schowalter and Sommer, 1989) encoding either the carboxy-terminal tail of zPTH1R or zPTH3R (240 and 335 bp, respectively). Washes were performed for 30 min each at RT and 42° in 1×SSC/0.1% SDS, and at 50° in 0.5×SSC/0.1% SDS followed by autoradiography at −70° for 7 days with a DuPont Cronex intensifying screen and Kodak XAR film.
Initial Southern blot data using probes corresponding to TM3 through TM6 of either receptor showed multiple hybridizing DNA species, indicating that these probes cross hybridized with each others gene or with closely related genes (data not shown). To increase the specificity for either subtype, hybridizations were performed with radiolabeled probes comprising only the tail region of each receptor, zPTH1R/tail or zPTH3R/tail, which showed the highest rates of sequence variation between PTH receptor subtypes. For each digest the tail probes hybridized, under stringent conditions, to a single but different genomic DNA fragment indicating that distinct genes encode zPTH1R and zPTH3R (data not shown).
Example 7
Phylogenetic and Structural Analyses of All Known PTHRs
Alignment of all known PTH1Rs, PTH2Rs, the goldfish VIP receptor (#U56391), and the human CRF receptor (#P34998) sequences was performed as previously described (Rubin et al., (1999)). Sequences were subsequently aligned within MacClade 3.0 (Maddison and Maddison, 1992) and gaps were entered to maximize the homology of the native proteins. Each AA was treated as an unweighted character when analyzed using the branch-and-bound search option of PAUP 3.1 (Swofford, 1993). A bootstrapping analysis using the branch-and-bound option on 100 replicates (Hedges, (1992)) was performed and only groups which were compatible with the 50% majority-rule consensus were retained (Swofford and Olsen, (1990); Swofford, (1993)).
GCG was used for comparing the tail regions of zPTH1R, zPTH2R, zPTH3R, hPTH1R, and hPTH2R. A further analysis was performed within MacClade to determine unambiguous residues which may be character-dependent for each PTH/PTHrP receptor subtype (Madison and Maddison, 1992; Swofford, 1993; Rubin et al., 1999).
The single most parsimonious Bootstrap consensus tree revealed two statistically significant PTH/PTHrP receptor clades; the PTH1R/PTH3R clade and the PTH2R clade (FIG. 7). Furthermore, within the PTH1R/PTH3R lade, the PTH1R groups significantly different from PTH3R and, at least for the PTH1R, the terminal branches contained within are congruent with morphologically based phylogenies (Pough, et al., (1989)).
Whereas the overall amino acid conservation between zPTH1R and zPTH3R is relatively high, particularly within the transmembrane region, multivariate analysis led to the identification of amino acid residues that may be specific for PTH3Rs (FIG. 3). Although additional PTH3R sequences from other species are required to confirm the receptor specificity of these residues, the limited number of amino acid changes may already allow mutational studies to explore their functional importance, particularly with regard to phospholipase C activation.
Example 7
Southern Blot Analysis of Mouse Genomic DNA
In order to establish the occurrence of PTH3R in mammals, Southern blot analysis was done with genomic DNA from a wild-type mouse (FIG. 7, left lane, 10 μg) and from a mouse lacking both copies of the PTH/PTHrP receptor gene (FIG. 7, right lane 2 μg).
Briefly, genomic DNAs were digested to completion with the restriction enzyme BamHI, subjected to agarose gel electrophoresis and transferred to a membrane for probing with radiolabeled PTH3R DNA (approximately 300 bp encoding the tail portion of the zPTH3R). Hybridization was performed under conditions of 30% formamide at 42 degrees Celsius overnight. The blot was subjected to a final wash of 1×SSC at 60 degrees Celsius. Radiography was performed by exposing the blot to film for 3 days at −80 C with an intensifying screen. The detection of a band in the PTH/PTHrP receptor knockout (KO) DNA indicates the presence of PTH3R in mouse genomic DNA.
Table 2. Comparisons of the Amino Acid sequences of the Intracellular, Carboxy-Terminal Tail of Different PTH Receptors
Residues comprising the tail region of the zPTH1R and zPTH3R were compared to corresponding regions of the zPTH2R, and the human PTH1R or PTH2R. Percent similarity and percent identity are indicated.












TABLE 2







zPTH1R
zPTH2R
zPTH3R
hPTH1R




















zPTH2R
38/31





zPTH3R
36/33
26/23


hPTH1R
56/50
35/28
38/33


hPTH2R
38/29
58/53
28/25
38/31









Table 3. Binding and cAMP Signaling Properties of PTH and PTHrP Analogs on the zPTH1R and the zPTH3R
Competitive binding and cAMP stimulation assays were performed at room temperature with intact COS-7 cells that expressed either the zPTH1R or the zPTH3R, as described in Materials and Methods. Homologous binding reactions utilized 125I-rPTH with unlabeled rPTH, and 125I-hPTHrP with unlabeled hPTHrP, heterologous binding reactions utilized 125I-hPTH with unlabeled rPTH. EC50 and IC50 values were determined as previously described (Gardella et al., 1996). Values are the mean±SEM of at least three independent transfections. ND, not determined.











TABLE 3









zPPR3
zPPR1#29
zPPR1#25

















Binding
cAMP
AMP
Binding
cAMP
cAMP
Binding
cAMP
cAMP



IC50
EC50
Maximum
IC50
EC50
Maximum
IC50
EC50
Maximum


Ligand
(nM)
(nM)
(pmol/well)
(nM)
(nM)
(pmol/well)
(nM)
(nM)
(pmol/well)



















hPTHrP
~3.0
0.49 ± 0.17
285.4 ± 3.4 
~3.0
0.3 ± 0.04
101.6 ± 3.6
~3.0
0.90 ± 0.09
92.4 ± 8.00


hPTH
~100
5.98 ± 0.24
227.4 ± 41.6
~3.0
0.8 ± 0.03
106.2 ± 4.8
~3.0
~3.0
90.4 ± 11.4









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## Claims

1. An isolated PTH1R polypeptide selected from the group consisting of:
(a) the amino acid sequence of the PTH1R polypeptide having the complete amino acid sequence from positions 1 to 536 in SEQ ID NO:2;
(b) the amino acid sequence of the PTH1R polypeptide having the amino acid sequence from positions 2 to 536 in SEQ ID NO:2;
(c) the amino acid sequence of the mature PTH1R polypeptide having the amino acid sequence from positions 25 to 536 in SEQ ID NO:2;
(d) the amino acid sequence of the PTH1R polypeptide having the complete amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916;
(e) the amino acid sequence of the mature PTH1R polypeptide having the amino acid sequence encoded by the eDNA clone deposited with the ATCC as patent deposit PTA-916;
(f) the amino acid sequence of the PTH1R receptor extracellular domain, said extracellular domain having the amino acid sequence from position 25 to position 147 in SEQ ID NO:2;
(g) the amino acid sequence of the PTH1R receptor transmembrane domain, said transmembrane domain consisting of the amino acid sequence from position 148 to position 416 in SEQ ID NO:2.

2. The polypeptide of claim 1, wherein said polypeptide has the amino acid sequence of position 1 to 536 of SEQ ID NO:2.

3. The polypeptide of claim 1, wherein said polypeptide has the amino acid sequence of position 2 to 536 of SEQ ID NO:2.

4. The polypeptide of claim 1, wherein said polypeptide has the amino acid sequence of position 25 to 536 of SEQ ID NO:2.

5. The polypeptide of claim 1, wherein said polypeptide has the complete amino acid sequence encoded by the cDNA clone deposited with the ATCC as patent deposit PTA-916.

6. The polypeptide of claim 1, wherein said polypeptide has the amino acid sequence of position 25 to 147 of SEQ ID NO:2.

7. The polypeptide of claim 1, wherein said polypeptide has the amino acid sequence of position 148 to 416 of SEQ ID NO:2.